@article {pmid39897492,
year = {2025},
author = {Keleher, JG and Strope, TA and Estrada, NE and Griggs Mathis, AM and Easson, CG and Fiore, C},
title = {Freshwater sponges in the southeastern U.S. harbor unique microbiomes that are influenced by host and environmental factors.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e18807},
pmid = {39897492},
issn = {2167-8359},
mesh = {*Porifera/microbiology ; *Microbiota ; Animals ; *Fresh Water/microbiology ; North Carolina ; *Symbiosis ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Marine, and more recently, freshwater sponges are known to harbor unique microbial symbiotic communities relative to the surrounding water; however, our understanding of the microbial ecology and diversity of freshwater sponges is vastly limited compared to those of marine sponges. Here we analyzed the microbiomes of three freshwater sponge species: Radiospongilla crateriformis, Eunapius fragilis, and Trochospongilla horrida, across four sites in western North Carolina, U.S.A. Our results support recent work indicating that freshwater sponges indeed harbor a distinct microbiome composition compared to the surrounding water and that these varied across sampling site indicating both environmental and host factors in shaping this distinct community. We also sampled sponges at one site over 3 months and observed that divergence in the microbial community between sponge and water occurs at least several weeks after sponges emerge for the growing season and that sponges maintain a distinct community from the water as the sponge tissue degrades. Bacterial taxa within the Gammproteobacteria, Alphproteobacteria, Bacteroidota (Flavobacteriia in particular), and Verrucomicrobia, were notable as enriched in the sponge relative to the surrounding water across sponge individuals with diverging microbial communities from the water. These results add novel information on the assembly and maintenance of microbial communities in an ancient metazoan host and is one of few published studies on freshwater sponge microbial symbiont communities.},
}

*Porifera/microbiology
*Microbiota
Animals
*Fresh Water/microbiology
North Carolina
*Symbiosis
Bacteria/classification/genetics/isolation & purification

@article {pmid39890664,
year = {2025},
author = {Zhou, Y and Jiang, P and Ding, Y and Zhang, Y and Yang, S and Liu, X and Cao, C and Luo, G and Ou, L},
title = {Deciphering the Distinct Associations of Rhizospheric and Endospheric Microbiomes with Capsicum Plant Pathological Status.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {1},
pmid = {39890664},
issn = {1432-184X},
support = {2023YFD1201502//National Key Research and Development Program of China/ ; 42107262//National Natural Science Foundation of China/ ; CARS-24-A05//China Agriculture Research System of MOF and MARA/ ; },
mesh = {*Capsicum/microbiology/growth & development ; *Rhizosphere ; *Microbiota ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; Endophytes/isolation & purification/classification/physiology/genetics ; Plant Diseases/microbiology ; Plant Roots/microbiology ; Fungi/classification/genetics/isolation & purification/physiology ; },
abstract = {Exploring endospheric and rhizospheric microbiomes and their associations can help us to understand the pathological status of capsicum (Capsicum annuum L.) for implementing appropriate management strategies. To elucidate the differences among plants with distinct pathological status in the communities and functions of the endospheric and rhizospheric microbiomes, the samples of healthy and diseased capsicum plants, along with their rhizosphere soils, were collected from a long-term cultivation field. The results indicated a higher bacterial richness in the healthy rhizosphere than in the diseased rhizosphere (P < 0.05), with rhizospheric bacterial diversity surpassing endospheric bacterial diversity. The community assemblies of both the endospheric and rhizospheric microbiomes were driven by a combination of stochastic and deterministic processes, with the stochastic processes playing a primary role. The majority of co-enriched taxa in the healthy endophyte and rhizosphere mainly belonged to bacterial Proteobacteria, Actinobacteria, and Firmicutes, as well as fungal Ascomycota. Most of the bacterial indicators, primarily Alphaproteobacteria and Actinobacteria, were enriched in the healthy rhizosphere, but not in the diseased rhizosphere. In addition, most of the fungal indicators were enriched in both the healthy and diseased endosphere. The diseased endophyte constituted a less complex and stable microbial community than the healthy endophyte, and meanwhile, the diseased rhizosphere exhibited a higher complexity but lower stability than the healthy rhizosphere. Notably, only a microbial function, namely biosynthesis of other secondary metabolites, was higher in the healthy endophytes than in the diseased endophyte. These findings indicated the distinct responses of rhizospheric and endospheric microbiomes to capsicum pathological status, and in particular, provided a new insight into leveraging soil and plant microbial resources to enhance agriculture production.},
}

*Capsicum/microbiology/growth & development
*Rhizosphere
*Microbiota
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification
Endophytes/isolation & purification/classification/physiology/genetics
Plant Diseases/microbiology
Plant Roots/microbiology
Fungi/classification/genetics/isolation & purification/physiology

@article {pmid39890294,
year = {2025},
author = {Baker, JM and Dickson, RP},
title = {The Microbiome and Pulmonary Immune Function.},
journal = {Clinics in chest medicine},
volume = {46},
number = {1},
pages = {77-91},
doi = {10.1016/j.ccm.2024.10.006},
pmid = {39890294},
issn = {1557-8216},
mesh = {Humans ; *Microbiota/immunology/physiology ; *Lung/microbiology/immunology ; Lung Diseases/immunology/microbiology ; },
abstract = {In the last decade, the lung microbiome field has matured into a promising area of translational and clinical research due to emerging evidence indicating a role for respiratory microbiota in lung immunity and pathogenesis. Here, we review recent insights pertaining to the lung microbiome's relationship with pulmonary immune function. We discuss areas of future investigation that will be essential to the development of immunomodulatory therapies targeting the respiratory microbiome.},
}

Humans
*Microbiota/immunology/physiology
*Lung/microbiology/immunology
Lung Diseases/immunology/microbiology

@article {pmid39889603,
year = {2025},
author = {Fu, P and Zhai, J and Yang, X and Gao, J and Ren, Z and Guo, B and Qi, P},
title = {Distribution and influencing factors of antibiotic resistance genes in two mussel species along the coasts of the East China Sea and the Yellow Sea.},
journal = {Journal of hazardous materials},
volume = {488},
number = {},
pages = {137399},
doi = {10.1016/j.jhazmat.2025.137399},
pmid = {39889603},
issn = {1873-3336},
abstract = {Antibiotic resistance genes (ARGs) raise a global public health concern. The ARGs profile in marine aquaculture environments was well reported, yet it is poorly revealed in marine bivalves. This study investigated the microbiota, resistome, and environmental factors within the digestive glands of two mussel species (Mytilus coruscus and Mytilus galloprovincialis) cultivated in the East China Sea and Yellow Sea. The microbial communities in the digestive glands of mussels exhibit significant variations across different sampling sites and between the two seas. The three bacterial phyla that predominated in all samples were Firmicutes, Bacteroidota, and Proteobacteria. A total of 88 ARGs were detected, with aminoglycoside resistance genes and multidrug resistance genes being the dominant categories. Analysis revealed that the quinolone resistance gene qnrB, associated with clinically relevant human pathogens, was ubiquitous in all samples. Members of the Enterobacteriaceae family may serve as a reservoir for qnrB within the investigated environment. The distribution of ARGs shows potential associations with the composition of microbial communities in the digestive glands, environmental factors, and mobile genetic elements (MGEs). These findings enhance the elucidation of microbial ecology and antibiotic resistance in marine aquaculture.},
}

@article {pmid39587684,
year = {2025},
author = {DuBose, JG and Crook, TB and Matzkin, LM and Haselkorn, TS},
title = {The relative importance of host phylogeny and dietary convergence in shaping the bacterial communities hosted by several Sonoran Desert Drosophila species.},
journal = {Journal of evolutionary biology},
volume = {38},
number = {2},
pages = {180-189},
doi = {10.1093/jeb/voae143},
pmid = {39587684},
issn = {1420-9101},
support = {//University of Central Arkansas Southwest Energy Research Fellowship program/ ; },
mesh = {Animals ; *Drosophila/microbiology/genetics ; *Phylogeny ; *Diet ; *Desert Climate ; *Microbiota ; Bacteria/genetics/classification ; Symbiosis ; Arizona ; },
abstract = {Complex eukaryotes vary greatly in the mode and extent that their evolutionary histories have been shaped by the microbial communities that they host. A general understanding of the evolutionary consequences of host-microbe symbioses requires that we understand the relative importance of host phylogenetic divergence and other ecological processes in shaping variation in host-associated microbial communities. To contribute to this understanding, we described the bacterial communities hosted by several Drosophila species native to the Sonoran Desert of North America. Our sampling consisted of four species that span multiple dietary shifts to cactophily, as well as the dietary generalist D. melanogaster, allowing us to partition the influences of host phylogeny and extant ecology. We found that bacterial communities were compositionally indistinguishable when considering incidence only but varied when considering the relative abundances of bacterial taxa. Variation in community composition was not explained by host phylogenetic divergence but could be partially explained by dietary variation. In support of the important role of diet as a source of ecological selection, we found that specialist cactophilic Drosophila deviated more from neutral predictions than dietary generalists. Overall, our findings provide insight into the evolutionary and ecological factors that shape host-associated microbial communities in a natural context.},
}

Animals
*Drosophila/microbiology/genetics
*Phylogeny
*Diet
*Desert Climate
*Microbiota
Bacteria/genetics/classification
Symbiosis
Arizona

@article {pmid39885242,
year = {2025},
author = {Grafmüller, J and Möllmer, J and Muehe, EM and Kammann, CI and Kray, D and Schmidt, HP and Hagemann, N},
title = {Publisher Correction: Granulation compared to co-application of biochar plus mineral fertilizer and its impacts on crop growth and nutrient leaching.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {3796},
doi = {10.1038/s41598-025-87051-2},
pmid = {39885242},
issn = {2045-2322},
}

@article {pmid39884152,
year = {2025},
author = {Maphosa, S and Steyn, M and Lebre, PH and Gokul, JK and Convey, P and Marais, E and Maggs-Kölling, G and Cowan, DA},
title = {Rhizosphere bacterial communities of Namib Desert plant species: Evidence of specialised plant-microbe associations.},
journal = {Microbiological research},
volume = {293},
number = {},
pages = {128076},
doi = {10.1016/j.micres.2025.128076},
pmid = {39884152},
issn = {1618-0623},
abstract = {Rhizosphere microbial communities are intimately associated with plant root surfaces. The rhizosphere microbiome is recruited from the surrounding soil and is known to impact positively on the plant host via enhanced resistance to pathogens, increased nutrient availability, growth stimulation and increased resistance to desiccation. Desert ecosystems harbour a diversity of perennial and annual plant species, generally exhibiting considerable physiological adaptation to the low-water environment. In this study, we explored the rhizosphere bacterial microbiomes associated with selected desert plant species. The rhizosphere bacterial communities of 11 plant species from the central Namib Desert were assessed using 16S rRNA gene-dependent phylogenetic analyses. The rhizosphere microbial community of each host plant species was compared with control soils collected from their immediate vicinity, and with those of all other host plants. Rhizosphere and control soil bacterial communities differed significantly and were influenced by both location and plant species. Rhizosphere-associated genera included 67 known plant growth-promoting taxa, including Rhizobium, Bacillus, Microvirga, Kocuria and Paenibacillus. Other than Kocuria, these genera constituted the 'core' rhizosphere bacterial microbiome, defined as being present in > 90 % of the rhizosphere communities. Nine of the 11 desert plant species harboured varying numbers and proportions of species-specific microbial taxa. Predictive analyses of functional pathways linked to rhizosphere microbial taxa showed that these were significantly enriched in the biosynthesis or degradation of a variety of substances such as sugars, secondary metabolites, phenolic compounds and antimicrobials. Overall, our data suggest that plant species in the Namib Desert recruit unique taxa to their rhizosphere bacterial microbiomes that may contribute to their resilience in this extreme environment.},
}

@article {pmid39883228,
year = {2024},
author = {Han, JR and Li, S and Li, WJ and Dong, L},
title = {Mining microbial and metabolic dark matter in extreme environments: a roadmap for harnessing the power of multi-omics data.},
journal = {Advanced biotechnology},
volume = {2},
number = {3},
pages = {26},
pmid = {39883228},
issn = {2948-2801},
support = {32270076//National Natural Science Foundation of China/ ; 2022xjkk1200//The Third Xinjiang Scientific Expedition Program/ ; 2022B0202110001//The Key-Area Research and Development Program of Guangdong Province/ ; },
abstract = {Extreme environments such as hyperarid, hypersaline, hyperthermal environments, and the deep sea harbor diverse microbial communities, which are specially adapted to extreme conditions and are known as extremophiles. These extremophilic organisms have developed unique survival strategies, making them ideal models for studying microbial diversity, evolution, and adaptation to adversity. They also play critical roles in biogeochemical cycles. Additionally, extremophiles often produce novel bioactive compounds in response to corresponding challenging environments. Recent advances in technologies, including genomic sequencing and untargeted metabolomic analysis, have significantly enhanced our understanding of microbial diversity, ecology, evolution, and the genetic and physiological characteristics in extremophiles. The integration of advanced multi-omics technologies into culture-dependent research has notably improved the efficiency, providing valuable insights into the physiological functions and biosynthetic capacities of extremophiles. The vast untapped microbial resources in extreme environments present substantial opportunities for discovering novel natural products and advancing our knowledge of microbial ecology and evolution. This review highlights the current research status on extremophilic microbiomes, focusing on microbial diversity, ecological roles, isolation and cultivation strategies, and the exploration of their biosynthetic potential. Moreover, we emphasize the importance and potential of discovering more strain resources and metabolites, which would be boosted greatly by harnessing the power of multi-omics data.},
}

@article {pmid39882875,
year = {2025},
author = {Cross, K and Beckman, N and Jahnes, B and Sabree, ZL},
title = {Microbiome metabolic capacity is buffered against phylotype losses by functional redundancy.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0236824},
doi = {10.1128/aem.02368-24},
pmid = {39882875},
issn = {1098-5336},
abstract = {UNLABELLED: Many animals contain a species-rich and diverse gut microbiota that likely contributes to several host-supportive services that include diet processing and nutrient provisioning. Loss of microbiome taxa and their associated metabolic functions as result of perturbations may result in loss of microbiome-level services and reduction of metabolic capacity. If metabolic functions are shared by multiple taxa (i.e., functional redundancy), including deeply divergent lineages, then the impact of taxon/function losses may be dampened. We examined to what degree alterations in phylotype diversity impact microbiome-level metabolic capacity. Feeding two nutritionally imbalanced diets to omnivorous Periplaneta americana over 8 weeks reduced the diversity of their phylotype-rich gut microbiomes by ~25% based on 16S rRNA gene amplicon sequencing, yet PICRUSt2-inferred metabolic pathway richness was largely unaffected due to their being polyphyletic. We concluded that the nonlinearity between taxon and metabolic functional losses is due to microbiome members sharing many well-characterized metabolic functions, with lineages remaining after perturbation potentially being capable of preventing microbiome "service outages" due to functional redundancy.

IMPORTANCE: Diet can affect gut microbiome taxonomic composition and diversity, but its impacts on community-level functional capabilities are less clear. Host health and fitness are increasingly being linked to microbiome composition and further modeling of the relationship between microbiome taxonomic and metabolic functional capability is needed to inform these linkages. Invertebrate animal models like the omnivorous American cockroach are ideal for this inquiry because they are amenable to various diets and provide high replicates per treatment at low costs and thus enabling rigorous statistical analyses and hypothesis testing. Microbiome taxonomic composition is diet-labile and diversity was reduced after feeding on unbalanced diets (i.e., post-treatment), but the predicted functional capacities of the post-treatment microbiomes were less affected likely due to the resilience of several abundant taxa surviving the perturbation as well as many metabolic functions being shared by several taxa. These results suggest that both taxonomic and functional profiles should be considered when attempting to infer how perturbations are altering gut microbiome services and possible host outcomes.},
}

@article {pmid39882867,
year = {2025},
author = {Asmus, AE and Gaire, TN and Schweisthal, KJ and Staben, SM and Noyes, NR},
title = {Microbiome characterization of two fresh pork cuts during production in a pork fabrication facility.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0220924},
doi = {10.1128/spectrum.02209-24},
pmid = {39882867},
issn = {2165-0497},
abstract = {The goal of this study was to characterize the microbial profile of two different fresh pork cuts, bootjack (BJ) trim and tenderloin (TL), through a 16S rRNA sequencing workflow developed specifically for investigating low-biomass fresh meat within a commercial production schedule. Additionally, this study aimed to determine a baseline Salmonella prevalence and enumeration profile across these two fresh pork cuts. Results showed that microbiome diversity was different between the BJ and TL, and also differed significantly by processing date. The relative abundance of key bacterial genera associated with food safety and spoilage was also different between the two meat types. However, over the course of the production shift, changes in the meat microbiome were limited in both the BJ and TL. The crude prevalence and enumerated burden of Salmonella were lower than what has been previously reported in similar fresh pork cuts, and all of the Salmonella-positive samples occurred on just two processing windows of 1-2 days each. Taken together, the results of this study suggest that the microbial profile of two fresh pork cuts is significantly different even within the same plant at the same time points, and that day-to-day variability within the production process likely influences both the fresh pork microbiome and Salmonella profile of these two meat types.IMPORTANCEModern pork processing involves a series of processes that begin with the handling and transport of the live animals, proceed through harvest and fabrication, and end with the packaging and distribution of fresh pork to the consumer. Each step in this process can alter the microbial community of fresh pork and influence the meat's safety and shelf life. However, little is known about the microbial ecology of individual, unprocessed pork cuts and if the diversity of the meat microbiome remains consistent throughout a production schedule. Additionally, the crude prevalence and enumeration of Salmonella have not been well established for individual fresh pork cuts throughout a production schedule. A more thorough understanding of the microbial profile at different stages of pork production will help processors determine processing steps that impact the microbial characteristics of fresh pork. This insight will help processors implement targeted intervention strategies to enhance food safety and quality.},
}

@article {pmid39880965,
year = {2025},
author = {Contreras-Negrete, G and Valiente-Banuet, A and Molina-Freaner, F and Partida-Martínez, LP and Hernández-López, A},
title = {Agricultural Practices and Environmental Factors Drive Microbial Communities in the Mezcal-Producing Agave angustifolia Haw.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {181},
pmid = {39880965},
issn = {1432-184X},
support = {CV549242//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; 319061//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; 319061//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; 319061//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; },
mesh = {*Agave/microbiology ; *Soil Microbiology ; *Microbiota ; *Bacteria/genetics/classification/isolation & purification ; *Fungi/genetics/classification/isolation & purification ; *Agriculture ; *RNA, Ribosomal, 16S/genetics ; Mexico ; Alcoholic Beverages/microbiology ; Biodiversity ; Rhizosphere ; },
abstract = {Mezcal, a traditional Mexican alcoholic beverage, has been a vital source of livelihood for indigenous and rural communities for centuries. However, increasing international demand is exerting pressure on natural resources and encouraging intensive agricultural practices. This study investigates the impact of management practices (wild, traditional, and conventional) and environmental factors on the microbial communities associated with Agave angustifolia, a key species in mezcal production. High-throughput sequencing of the 16S rRNA and ITS2 gene regions revealed distinct prokaryotic and fungal community structures across different plant compartments (endosphere, episphere, and soil), identifying 8214 prokaryotic and 7459 fungal ASVs. Core microbial communities were dominated by Proteobacteria, Actinobacteria, Ascomycota, and Basidiomycota. Alpha diversity analyses showed significant increases in prokaryotic diversity from the endosphere to soil, while fungal diversity remained stable. Notably, conventional management practices were associated with reductions in beneficial microbial taxa. Environmental factors such as precipitation and temperature significantly influenced microbial diversity and composition, especially in the rhizosphere. Beta diversity patterns underscored the strong impact of plant compartment, with management practices and aridity further shaping microbial communities. These results reveal the intricate interactions between management practices, environmental conditions, and microbial diversity, providing valuable insights for the sustainable cultivation of A. angustifolia.},
}

*Agave/microbiology
*Soil Microbiology
*Microbiota
*Bacteria/genetics/classification/isolation & purification
*Fungi/genetics/classification/isolation & purification
*Agriculture
*RNA, Ribosomal, 16S/genetics
Mexico
Alcoholic Beverages/microbiology
Biodiversity
Rhizosphere

@article {pmid39880083,
year = {2025},
author = {Moortele, TV and Verschaffelt, P and Huang, Q and Doncheva, NT and Holstein, T and Jachmann, C and Dawyndt, P and Martens, L and Mesuere, B and Van Den Bossche, T},
title = {PathwayPilot: A User-Friendly Tool for Visualizing and Navigating Metabolic Pathways.},
journal = {Molecular & cellular proteomics : MCP},
volume = {},
number = {},
pages = {100918},
doi = {10.1016/j.mcpro.2025.100918},
pmid = {39880083},
issn = {1535-9484},
abstract = {Metaproteomics, the study of collective proteomes in environmental communities, plays a crucial role in understanding microbial functionalities affecting ecosystems and human health. Pathway analysis offers structured insights into the biochemical processes within these communities. However, no existing tool effectively combines pathway analysis with peptide- or protein-level data. We here introduce PathwayPilot, a web-based application designed to improve metaproteomic data analysis by integrating pathway analysis with peptide- and protein-level data, filling a critical gap in current metaproteomics bioinformatics tools. By allowing users to compare functional annotations across different samples or multiple organisms within a sample, PathwayPilot provides valuable insights into microbial functions. In the re-analysis of a case study examining the effects of caloric restriction on gut microbiota, the tool successfully identified shifts in enzyme expressions linked to short-chain fatty acid biosynthesis, aligning with its original findings. PathwayPilot's user-friendly interface and robust capabilities make it a significant advancement in metaproteomics, with potential for widespread application in microbial ecology and health sciences. All code is open source under the Apache2 license and is available at https://pathwaypilot.ugent.be.},
}

@article {pmid39878512,
year = {2025},
author = {Flanagan, K and Gassner, K and Lang, M and Ozelyte, J and Hausmann, B and Crepaz, D and Pjevac, P and Gasche, C and Berry, D and Vesely, C and Pereira, FC},
title = {Human-derived microRNA 21 regulates indole and L-tryptophan biosynthesis transcripts in the gut commensal Bacteroides thetaiotaomicron.},
journal = {mBio},
volume = {},
number = {},
pages = {e0392824},
doi = {10.1128/mbio.03928-24},
pmid = {39878512},
issn = {2150-7511},
abstract = {UNLABELLED: In the gut, microRNAs (miRNAs) produced by intestinal epithelial cells are secreted into the lumen and can shape the composition and function of the gut microbiome. Crosstalk between gut microbes and the host plays a key role in irritable bowel syndrome (IBS) and inflammatory bowel diseases, yet little is known about how the miRNA-gut microbiome axis contributes to the pathogenesis of these conditions. Here, we investigate the ability of miR-21, a miRNA that we found decreased in fecal samples from IBS patients, to associate with and regulate gut microbiome function. When incubated with the human fecal microbiota, miR-21 revealed a rapid internalization or binding to microbial cells, which varied in extent across different donor samples. Fluorescence-activated cell sorting and sequencing of microbial cells incubated with fluorescently labeled miR-21 identified organisms belonging to the genera Bacteroides, Limosilactobacillus, Ruminococcus, or Coprococcus, which predominantly interacted with miR-21. Surprisingly, these and other genera also interacted with a miRNA scramble control, suggesting that physical interaction and/or uptake of these miRNAs by gut microbiota is not sequence-dependent. Nevertheless, transcriptomic analysis of the gut commensal Bacteroides thetaiotaomicron revealed a miRNA sequence-specific effect on bacterial transcript levels. Supplementation of miR-21, but not of small RNA controls, resulted in significantly altered levels of many cellular transcripts and increased transcription of a biosynthetic operon for indole and L-tryptophan, metabolites known to regulate host inflammation and colonic motility. Our study identifies a novel putative miR-21-dependent pathway of regulation of intestinal function through the gut microbiome with implications for gastrointestinal conditions.

IMPORTANCE: The mammalian gut represents one of the largest and most dynamic host-microbe interfaces. Host-derived microRNAs (miRNAs), released from the gut epithelium into the lumen, have emerged as important contributors to host-microbe crosstalk. Levels of several miRNAs are altered in the stool of patients with irritable bowel syndrome or inflammatory bowel disease. Understanding how miRNAs interact with and shape gut microbiota function is crucial as it may enable the development of new targeted treatments for intestinal diseases. This study provides evidence that the miRNA miR-21 can rapidly associate with diverse microbial cells form the gut and increase levels of transcripts involved in tryptophan synthesis in a ubiquitous gut microbe. Tryptophan catabolites regulate key functions, such as gut immune response or permeability. Therefore, this mechanism represents an unexpected host-microbe interaction and suggests that host-derived miR-21 may help regulate gut function via the gut microbiota.},
}

@article {pmid39878482,
year = {2025},
author = {Rodriguez-Garcia, C and Wall, H and Ottesen, E and Grainy, J},
title = {Characterization of extended-spectrum beta-lactamase-producing Enterobacteriaceae from recreational water in Athens, GA, using an undergraduate laboratory module.},
journal = {Journal of microbiology & biology education},
volume = {},
number = {},
pages = {e0005624},
doi = {10.1128/jmbe.00056-24},
pmid = {39878482},
issn = {1935-7877},
abstract = {We present a laboratory module that uses isolation of antibiotic-resistant bacteria from locally collected stream water samples to introduce undergraduate students to basic microbiological culture-based and molecular techniques. This module also educates them on the global public health threat of antibiotic-resistant organisms. Through eight laboratory sessions, students are involved in quality testing of water sources from their neighborhoods, followed by isolation of extended-spectrum beta-lactamase-producing Enterobacteriaceae. By the end of the module, students should be able to isolate Enterobacteriaceae from the environment using selective and differential media, identify isolates using biochemical tests, characterize antibiotic resistance phenotypes using Kirby Bauer and MIC tests, and evaluate the presence of select beta-lactamase genes of interest using PCR. To complement laboratory sessions, students participated in a weekly flipped classroom session with collaborative peer discussions and activities to reinforce concepts applied in the laboratory. Learning outcomes were measured over four semesters with concept checks, in-lecture activities, exams, and laboratory reports. We hypothesized that more than 50% of the student population would achieve each learning objective through the implementation of this authentic research laboratory module. Here, we highlight specific questions used to assess learning objective comprehension and demonstrate that each learning objective was achieved by 65%-100% of the student population. We present a ready-to-adapt module with flexible resources that can be implemented in courses across disciplines in biology, microbiology, environmental sciences, and public health.},
}

@article {pmid39876091,
year = {2025},
author = {Tocarruncho, OI and Neuta, Y and Lesmes, Y and Castillo, DM and Leal, S and Chambrone, L and Lafaurie, GI},
title = {Submucosal Microbiome Profiles in Paired and Unpaired Samples From Healthy and Peri-Implantitis Dental Implants.},
journal = {Clinical implant dentistry and related research},
volume = {27},
number = {1},
pages = {e13423},
doi = {10.1111/cid.13423},
pmid = {39876091},
issn = {1708-8208},
support = {490-21//Research Vice Rectory of Universidad El Bosque/ ; },
mesh = {Humans ; *Peri-Implantitis/microbiology ; *Microbiota ; Cross-Sectional Studies ; Female ; Male ; *Dental Implants/microbiology/adverse effects ; Middle Aged ; RNA, Ribosomal, 16S/analysis ; Adult ; Aged ; },
abstract = {BACKGROUND: This cross-sectional study aimed to compare the composition of the submucosal microbiome of peri-implantitis with paired and unpaired healthy implant samples.

METHODS: We evaluated submucosal plaque samples obtained in 39 cases, including 13 cases of peri-implantitis, 13 cases involving healthy implants from the same patient (paired samples), and 13 cases involving healthy implants from different individuals (unpaired samples). The patients were evaluated using next-generation genomic sequencing (Illumina) based on 16S rRNA gene amplification. The sequences were grouped according to the amplicon sequence variant (ASV) to define the taxonomic categories. Alpha diversity was analyzed using Shannon's and Simpson's indices, while beta diversity was evaluated using principal coordinate analysis, analysis of similarities, and permutational multivariate variance analysis. Additionally, UniFrac distances were evaluated using Quantitative Insights into Microbial Ecology 2. Finally, we evaluated between-group differences in the taxonomic components.

RESULTS: There were no significant between-group differences in alpha diversity. The average bacterial ratios of Filifactor alocis, Porphyromona endodontalis, Tannerella forsythia, Treponema denticola, Peptostreptococcaceae [Eubacterium nodatum], Desulfobulbus sp. HTM 041, and Mogibacterium timidum significantly differed between peri-implantitis samples and unpaired samples from the healthy implants (p < 0.05). However, there were few differences in the microbiota between peri-implantitis samples and those paired with healthy implants in the same patient.

CONCLUSIONS: Future studies comparing the microbiome compositions using sequencing techniques between healthy implants and implants with peri-implantitis should focus on retrieving samples from the same patient, especially in individuals with a history of periodontitis.},
}

Humans
*Peri-Implantitis/microbiology
*Microbiota
Cross-Sectional Studies
Female
Male
*Dental Implants/microbiology/adverse effects
Middle Aged
RNA, Ribosomal, 16S/analysis
Adult
Aged

@article {pmid39874167,
year = {2025},
author = {Zhang, F and Zhang, S and Wu, Y and Liu, J and Zhao, S and Qiu, Z and Zhu 朱, M墨},
title = {Powdery Mildew of Echinacea purpurea Caused by Podosphaera xanthii in China.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-12-24-2632-PDN},
pmid = {39874167},
issn = {0191-2917},
abstract = {Echinacea purpurea (Eastern Purple Coneflower) is a perennial herbaceous plant belonging to the Asteraceae. It originated from North America and is cultivated all over the world. Extracts of E. purpurea are widely used for the treatments of colds and sore throats (Jiao et al. 2020). In October 2024, powdery mildew-like signs and symptoms were observed on leaves of E. purpurea plants (n=100) cultivated in a garden (20 m2) in Xinxiang city, Henan Province, China (35.32° N, 113.92° E). A specimen (PX-ZM20241024) was stored in Xinxiang Key Laboratory of Plant Stress Biology. The infected leaves were covered with white and thin masses and showed senescence symptoms. More than 80% of plants (n=100) exhibited these signs and symptoms. White colonies were on both sides surfaces of the leaves, covering about 80% of the leaf area. The slightly curved or straight Conidia chain (n = 50) were 70 to 156 × 8 to 12 μm in size and consisted of foot cells, shorter cells, and conidia. Foot cells were straight, 30 to 60 μm long. Conidia were ellipsoid to oval, 20 to 35 × 12 to 17 μm (n = 50), with a length/width ratio of 1.8 to 2.2, containing fibrosin bodies. These morphological characteristics were similar to Podosphaera xanthii (Braun and Cook 2012). Following a previously reported method (Zhu et al. 2022), the internal transcribed spacer (ITS) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) regions of a selected specimen of the fungus were amplified and sequenced with primers ITS1/ITS4 (White et al. 1990) and GAPDH1/GAPDH3R (Bradshaw et al. 2022). The resulting sequences were deposited in GenBank (Accession No. PQ508348 and PQ734986). BLASTn analysis indicated that the ITS and GAPDH sequences had 99.82 % (564/565 bp) and 100% (238/238 bp) identity with reported P. xanthii (MW300956 and ON075660) on Xanthium strumarium and Cucurbita moschata, respectively (Zhu et al. 2024; Bradshaw et al. 2022). By phylogenetic analysis, the isolated fungus clustered with previously reported P. xanthii (Zhu et al. 2024; Bradshaw et al. 2022). Therefore, the morphology and phylogenetic analysis indicated that the pathogen was P. xanthii. To complete Koch's postulates, mature leaves of three healthy E. purpurea (30 cm high) were inoculated with fungal conidia by gently pressing surfaces of infested leaves onto leaves of healthy plants. Three untreated plants served as controls. Both the control and inoculated plants were separately placed in greenhouses (humidity, 60%; light/dark, 16 h/8 h; temperature, 18°C). 10 to 12 days post inoculation, the leaves of the inoculated plants exhibited signs of powdery mildew, whereas the control group remained unaffected. The experiments were repeated three times and the same results were obtained. Therefore, the pathogenicity of this fungal pathogen was confirmed. Previously, P. xanthii was reported on E. purpurea in Korea (Choi et al. 2020). To the best of our knowledge, this is the first report of P. xanthii on E. purpurea in China. The sudden presence of powdery mildew caused by P. xanthii may adversely affect plant health and thus reduce the medicinal value of E. purpurea. Therefore, the identification and confirmation of P. xanthii infecting E. purpurea enhances our comprehension of hosts of this pathogen and provides fundamental information for forthcoming disease control studies.},
}

@article {pmid39873755,
year = {2025},
author = {Mwaheb, MA and El-Aziz, BMA and Abd-Elhalim, BT and El-Kassim, NA and Radwan, TEE},
title = {Correction to: Study of Different Cultivated Plants Rhizosphere Soil Fungi-Mediated Pectinase: Insights into Production, Optimization, Purification, Biocompatibility, and Application.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {180},
doi = {10.1007/s00248-025-02498-0},
pmid = {39873755},
issn = {1432-184X},
}

@article {pmid39871445,
year = {2025},
author = {Zahir, Z and Khan, F and Hall, BD},
title = {Sulfate and Dissolved Organic Carbon Concentrations Drive Distinct Microbial Community Patterns in Prairie Wetland Ponds.},
journal = {Environmental microbiology reports},
volume = {17},
number = {1},
pages = {e70069},
doi = {10.1111/1758-2229.70069},
pmid = {39871445},
issn = {1758-2229},
support = {//Agricultural Development Fund/ ; //Natural Sciences and Engineering Research Council of Canada/ ; //Faculty of Graduate Studies and Research, University of Regina/ ; //Government of Canada/ ; },
mesh = {*Wetlands ; *Carbon/metabolism/analysis ; *Sulfates/metabolism ; *Ponds/microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbiota ; Phylogeny ; Geologic Sediments/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; },
abstract = {Prairie wetland ponds on the Great Plains of North America offer a diverse array of geochemical scenarios that can be informative about their impact on microbial communities. These ecosystems offer invaluable ecological services while experiencing significant stressors, primarily through drainage and climate change. In this first study systematically combining environmental conditions with microbial community composition to identify various niches in prairie wetland ponds, sediments had higher microbial abundance but lower phylogenetic diversity in ponds with lower concentrations of dissolved organic carbon ([DOC]; 10-18 mg/L) and sulfate ([SO4 [2-]]; 37-58 mg/L) in water. As [DOC] and [SO4 [2-]] increased, there was an initial decline in abundance but not phylogenetic diversity. Maximum values of both abundance and phylogenetic diversity occurred between 56 and 115 mg/L [DOC] and 5,000-6,000 mg/L [SO4 [2-]] and decreased thereafter in ponds with 150-180 mg/L and 8,000-14,000 mg/L [DOC] and [SO4 [2-]], respectively. These findings confirm that environmental variables shape the microbial communities and that key microbial taxa involved in sulfur and carbon cycling dominated these ponds potentially impacting vital biogeochemical processes such as bioavailability of heavy metals, carbon sequestration, and methane emissions.},
}

*Wetlands
*Carbon/metabolism/analysis
*Sulfates/metabolism
*Ponds/microbiology
*Bacteria/classification/genetics/metabolism/isolation & purification
*Microbiota
Phylogeny
Geologic Sediments/microbiology/chemistry
RNA, Ribosomal, 16S/genetics
Biodiversity

@article {pmid39871406,
year = {2025},
author = {Noell, SE and Abbaszadeh, J and Richards, H and Labat Saint Vincent, M and Lee, CK and Herbold, CW and Stott, MB and Cary, SC and McDonald, IR},
title = {Antarctic Geothermal Soils Exhibit an Absence of Regional Habitat Generalist Microorganisms.},
journal = {Environmental microbiology},
volume = {27},
number = {1},
pages = {e70032},
doi = {10.1111/1462-2920.70032},
pmid = {39871406},
issn = {1462-2920},
support = {18-UOW-028//Marsden Fund/ ; },
mesh = {Antarctic Regions ; *Soil Microbiology ; *Archaea/classification/genetics ; *Bacteria/classification/isolation & purification/genetics ; *Ecosystem ; Microbiota ; Phylogeny ; Hot Springs/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Active geothermal systems are relatively rare in Antarctica and represent metaphorical islands ideal to study microbial dispersal. In this study, we tested the macro-ecological concept that high dispersal rates result in communities being dominated by either habitat generalists or specialists by investigating the microbial communities on four geographically separated geothermal sites on three Antarctic volcanoes (Mts. Erebus, Melbourne, and Rittman). We found that the microbial communities at higher temperature (max 65°C) sites (Tramway Ridge on Erebus and Rittmann) were unique from each other and were dominated by a variety of novel Archaea from class Nitrososphaeria, while lower temperature (max 50°C) sites (Western Crater on Erebus and Melbourne) had characteristically mesophilic communities (Planctomycetes, Acidobacteriota, etc.) that were highly similar. We found that 97% of the detected microbial taxa were regional habitat specialists, with no generalists, with community assembly driven by high dispersal rates and drift (25% and 30% of community assembly, respectively), not environmental selection. Our results indicate that for microbial communities experiencing high dispersal rates between isolated communities, habitat specialists may tend to out-compete habitat generalists.},
}

Antarctic Regions
*Soil Microbiology
*Archaea/classification/genetics
*Bacteria/classification/isolation & purification/genetics
*Ecosystem
Microbiota
Phylogeny
Hot Springs/microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid39871020,
year = {2025},
author = {Zhang, Z and Zhang, Q and Guo, X and Zeng, Z and Wang, Y and Zhang, P and Gao, D and Deng, G and Sun, G and Yang, Y and Wang, J},
title = {Forest Soil pH and Dissolved Organic Matter Aromaticity Are Distinct Drivers for Soil Microbial Community and Carbon Metabolism Potential.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {177},
pmid = {39871020},
issn = {1432-184X},
support = {2023A1515110368//Guangdong Basic and Applied Basic Research Foundation/ ; 2023B1212060002//Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control/ ; },
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Forests ; *Carbon/metabolism ; Hydrogen-Ion Concentration ; China ; *Microbiota ; Carbon Cycle ; Bacteria/metabolism/classification/genetics/isolation & purification ; Ecosystem ; Organic Chemicals/metabolism ; Microbial Interactions ; },
abstract = {The ecological niche separation of microbial interactions in forest ecosystems is critical to maintaining ecological balance and biodiversity and has yet to be comprehensively explored in microbial ecology. This study investigated the impacts of soil properties on microbial interactions and carbon metabolism potential in forest soils across 67 sites in China. Using redundancy analysis and random forest models, we identified soil pH and dissolved organic matter (DOM) aromaticity as the primary drivers of microbial interactions, representing abiotic conditions and resource niches, respectively. Our network comparison results highlighted significant differences in microbial interactions between acidic and non-acidic soils, suggesting the critical influences of abiotic conditions on microbial interactions. Conversely, abiotic resource niches played a more pivotal role in shaping the carbon metabolism of soil microbes, supporting the concept that resource niche-based processes drive microbial carbon cycling. Additionally, we demonstrated that microbial interactions contributed significantly to ecosystem function stability and served as potential ecological indicators of microbial functional resilience under environmental stress. These insights emphasize the critical need to preserve microbial interactions for effective forest ecosystem management and projection of ecological outcomes in response to future environmental changes.},
}

*Soil Microbiology
*Soil/chemistry
*Forests
*Carbon/metabolism
Hydrogen-Ion Concentration
China
*Microbiota
Carbon Cycle
Bacteria/metabolism/classification/genetics/isolation & purification
Ecosystem
Organic Chemicals/metabolism
Microbial Interactions

@article {pmid39870904,
year = {2025},
author = {Stenger, PL and Tribollet, A and Guilhaumon, F and Cuet, P and Pennober, G and Jourand, P},
title = {A Multimarker Approach to Identify Microbial Bioindicators for Coral Reef Health Monitoring-Case Study in La Réunion Island.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {179},
pmid = {39870904},
issn = {1432-184X},
mesh = {*Coral Reefs ; *Microbiota ; *Anthozoa/microbiology ; Animals ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Reunion ; *Fungi/classification/genetics/isolation & purification/metabolism ; Seawater/microbiology ; Indian Ocean ; Seasons ; Biodiversity ; Environmental Monitoring/methods ; Islands ; Microalgae/classification/metabolism ; Geologic Sediments/microbiology ; },
abstract = {The marine microbiome arouses an increasing interest, aimed at better understanding coral reef biodiversity, coral resilience, and identifying bioindicators of ecosystem health. The present study is a microbiome mining of three environmentally contrasted sites along the Hermitage fringing reef of La Réunion Island (Western Indian Ocean). This mining aims to identify bioindicators of reef health to assist managers in preserving the fringing reefs of La Réunion. The watersheds of the fringing reefs are small, steeply sloped, and are impacted by human activities with significant land use changes and hydrological modifications along the coast and up to mid-altitudes. Sediment, seawater, and coral rubble were sampled in austral summer and winter at each site. For each compartment, bacterial, fungal, microalgal, and protist communities were characterized by high throughput DNA sequencing methodology. Results show that the reef microbiome composition varied greatly with seasons and reef compartments, but variations were different among targeted markers. No significant variation among sites was observed. Relevant bioindicators were highlighted per taxonomic groups such as the Firmicutes:Bacteroidota ratio (8.4%:7.0%), the genera Vibrio (25.2%) and Photobacterium (12.5%) dominating bacteria; the Ascomycota:Basidiomycota ratio (63.1%:36.1%), the genera Aspergillus (40.9%) and Cladosporium (16.2%) dominating fungi; the genus Ostreobium (81.5%) in Chlorophyta taxon for microalgae; and the groups of Dinoflagellata (63.3%) and Diatomea (22.6%) within the protista comprising two dominant genera: Symbiodinium (41.7%) and Pelagodinium (27.8%). This study highlights that the identified bioindicators, mainly in seawater and sediment reef compartments, could be targeted by reef conservation stakeholders to better monitor La Réunion Island's reef state of health and to improve management plans.},
}

*Coral Reefs
*Microbiota
*Anthozoa/microbiology
Animals
*Bacteria/classification/genetics/isolation & purification/metabolism
Reunion
*Fungi/classification/genetics/isolation & purification/metabolism
Seawater/microbiology
Indian Ocean
Seasons
Biodiversity
Environmental Monitoring/methods
Islands
Microalgae/classification/metabolism
Geologic Sediments/microbiology

@article {pmid39870843,
year = {2025},
author = {Li, Q and Shao, H},
title = {The Role of Pathogens in Plant Invasion: Accumulation of Local Pathogens Hypothesis.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {178},
pmid = {39870843},
issn = {1432-184X},
support = {No.2023E01012//Ministry of Science and Technology of the People's Republic of China/ ; 2022D01D02//Science and Technology Department of Xinjiang Uygur Autonomous Region/ ; },
mesh = {*Introduced Species ; *Plants/microbiology ; *Plant Diseases/microbiology ; *Soil Microbiology ; Host-Pathogen Interactions ; Bacteria/genetics/metabolism ; },
abstract = {In the past decades, dozens of invasion hypotheses have been proposed to elucidate the invasion mechanisms of exotic species. Among them, the accumulation of local pathogens hypothesis (ALPH) posits that invasive plants can accumulate local generalist pathogens that have more negative effect on native species than on themselves; as a result, invasive plants might gain competitive advantages that eventually lead to their invasion success. However, research on this topic is still quite insufficient. In this context, we performed a comprehensive literature survey in order to provide a detailed description of the origin and theoretical framework of ALPH; in addition, challenges in contemporary research such as limitations in technical methods and the complexity of interactions between plants and soil microorganisms, as well as future directions of ALPH research, are also discussed in this review. So far, there are less than ten case studies supporting ALPH; therefore, more work is needed to demonstrate whether ALPH is a suitable hypothesis to elucidate the invasion success of certain plant species.},
}

*Introduced Species
*Plants/microbiology
*Plant Diseases/microbiology
*Soil Microbiology
Host-Pathogen Interactions
Bacteria/genetics/metabolism

@article {pmid39868213,
year = {2025},
author = {Schechter, MS and Trigodet, F and Veseli, IA and Miller, SE and Klein, ML and Sever, M and Maignien, L and Delmont, TO and Light, SH and Eren, AM},
title = {Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.15.633187},
pmid = {39868213},
issn = {2692-8205},
abstract = {The increasing availability of microbial genomes is essential to gain insights into microbial ecology and evolution that can propel biotechnological and biomedical advances. Recent advances in genome recovery have significantly expanded the catalogue of microbial genomes from diverse habitats. However, the ability to explain how well a set of genomes account for the diversity in a given environment remains challenging for individual studies or biome-specific databases. Here we present EcoPhylo, a computational workflow to characterize the phylogeography of any gene family through integrated analyses of genomes and metagenomes, and our application of this approach to ribosomal proteins to quantify phylogeny-aware genome recovery rates across three biomes. Our findings show that genome recovery rates vary widely across taxa and biomes, and that single amplified genomes, metagenome-assembled genomes, and isolate genomes have non-uniform yet quantifiable representation of environmental microbes. EcoPhylo reveals highly resolved, reference-free, multi-domain phylogenies in conjunction with distribution patterns of individual clades across environments, providing a means to assess genome recovery in individual studies and benchmark biome-level genome collections.},
}

@article {pmid39868180,
year = {2025},
author = {Peters, DI and Shin, IJ and Deever, AN and Kaspar, JR},
title = {Design, Development and Validation of New Fluorescent Strains for Studying Oral Streptococci.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.14.632972},
pmid = {39868180},
issn = {2692-8205},
abstract = {Bacterial strains that are genetically engineered to constitutively produce fluorescent proteins have aided our study of bacterial physiology, biofilm formation, and interspecies interactions. Here, we report on the construction and utilization of new strains that produce the blue fluorescent protein mTagBFP2, the green fluorescent protein sfGFP, and the red fluorescent protein mScarlet-I3 in species Streptococcus gordonii, Streptococcus mutans , and Streptococcus sanguinis . Gene fragments, developed to contain the constitutive promoter P veg , the fluorescent gene of interest as well as aad9 , providing resistance to the antibiotic spectinomycin, were inserted into selected open reading frames on the chromosome that were both transcriptionally silent and whose loss caused no measurable changes in fitness. All strains, except for sfGFP in S. sanguinis , were validated to produce a detectable and specific fluorescent signal. Individual stains, along with extracellular polymeric substances (EPS) within biofilms, were visualized and quantified through either widefield or super-resolution confocal microscopy approaches. Finally, to validate the ability to perform single cell-level analysis using the strains, we imaged and analyzed a triculture mixed-species biofilm of S. gordonii, S. mutans , and S. sanguinis grown with and without addition of human saliva. Quantification of the loss in membrane integrity using a SYTOX dye revealed that all strains had increased loss of membrane integrity with water or human saliva added to the growth media, but the proportion of the population stained by the SYTOX dye varied by species. In all, these fluorescent strains will be a valuable resource for the continued study of oral microbial ecology.},
}

@article {pmid39862387,
year = {2025},
author = {Almeida-Silva, F and Van de Peer, Y},
title = {doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf043},
pmid = {39862387},
issn = {1367-4811},
abstract = {SUMMARY: Gene and genome duplications are major evolutionary forces that shape the diversity and complexity of life. However, different duplication modes have distinct impacts on gene function, expression, and regulation. Existing tools for identifying and classifying duplicated genes are either outdated or not user-friendly. Here, we present doubletrouble, an R/Bioconductor package that provides a comprehensive and robust framework for analyzing duplicated genes from genomic data. doubletrouble can detect and classify gene pairs as derived from six duplication modes (segmental, tandem, proximal, retrotransposon-derived, DNA transposon-derived, and dispersed duplications), calculate substitution rates, detect signatures of putative whole-genome duplication events, and visualize results as publication-ready figures. We applied doubletrouble to classify the duplicated gene repertoire in 822 eukaryotic genomes, and results were made available through a user-friendly web interface.

doubletrouble is available on Bioconductor (https://bioconductor.org/packages/doubletrouble), and the source code is available in a GitHub repository (https://github.com/almeidasilvaf/doubletrouble). doubletroubledb is available online at https://almeidasilvaf.github.io/doubletroubledb/.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online and at https://github.com/almeidasilvaf/doubletrouble_paper.},
}

@article {pmid39861970,
year = {2025},
author = {Saati-Santamaría, Z and Navarro-Gómez, P and Martínez-Mancebo, JA and Juárez-Mugarza, M and Flores, A and Canosa, I},
title = {Genetic and species rearrangements in microbial consortia impact biodegradation potential.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf014},
pmid = {39861970},
issn = {1751-7370},
abstract = {Genomic reorganisation between species and horizontal gene transfer have been considered the most important mechanism of biological adaptation under selective pressure. Still, the impact of mobile genes in microbial ecology is far from being completely understood. Here we present the collection and characterisation of microbial consortia enriched from environments contaminated with emerging pollutants, such as non-steroidal anti-inflammatory drugs. We have obtained and further enriched two ibuprofen-degrading microbial consortia from two unrelated wastewater treatment plants. We have also studied their ability to degrade the drug and the dynamics of the reorganisations of the genetic information responsible for its biodegradation among the species within the consortium. Our results show that genomic reorganisation within microorganisms and species rearrangements occur rapidly and efficiently during the selection process, which may be facilitated by plasmids and/or transposable elements located within the sequences. We show the evolution of at least two different plasmid backbones on samples from different locations, showing rearrangements of genomic information, including genes encoding activities for IBU degradation. As a result, we found variations in the expression pattern of the consortia after evolution under selective pressure, as an adaptation process to the new conditions. This work provides evidence for changes in the metagenomes of microbial communities that allow adaptation under a selective constraint -ibuprofen as a sole carbon source- and represents a step forward in knowledge that can inspire future biotechnological developments for drug bioremediation.},
}

@article {pmid39857259,
year = {2025},
author = {Chung, CC and Gong, GC and Tseng, HC and Chou, WC and Ho, CH},
title = {Dominance of Sulfur-Oxidizing Bacteria, Thiomicrorhabdus, in the Waters Affected by a Shallow-Sea Hydrothermal Plume.},
journal = {Biology},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/biology14010028},
pmid = {39857259},
issn = {2079-7737},
support = {NSTC 113-2611-M-019-006//National Science and Technology Council of Taiwan/ ; },
abstract = {The shallow-sea hydrothermal vent at Guishan Islet, located off the coast of Taiwan, serves as a remarkable natural site for studying microbial ecology in extreme environments. In April 2019, we investigated the composition of prokaryotic picoplankton communities, their gene expression profiles, and the dissolved inorganic carbon uptake efficiency. Our results revealed that the chemolithotrophs Thiomicrorhabdus spp. contributed to the majority of primary production in the waters affected by the hydrothermal vent plume. The metatranscriptomic analysis aligned with the primary productivity measurements, indicating the significant gene upregulations associated with carboxysome-mediated carbon fixation in Thiomicrorhabdus. Synechococcus and Prochlorococcus served as the prokaryotic photoautotrophs for primary productivity in the waters with lower influence from hydrothermal vent emissions. Thiomicrorhabdus and picocyanobacteria jointly provided organic carbon for sustaining the shallow-sea hydrothermal vent ecosystem. In addition to the carbon fixation, the upregulation of genes involved in the SOX (sulfur-oxidizing) pathway, and the dissimilatory sulfate reduction indicated that energy generation and detoxification co-occurred in Thiomicrorhabdus. This study improved our understanding of the impacts of shallow-sea hydrothermal vents on the operation of marine ecosystems and biogeochemical cycles.},
}

@article {pmid39856188,
year = {2025},
author = {Tokodi, N and Łobodzińska, A and Klimczak, B and Antosiak, A and Młynarska, S and Šulčius, S and Avrani, S and Yoshida, T and Dziga, D},
title = {Proliferative and viability effects of two cyanophages on freshwater bloom-forming species Microcystis aeruginosa and Raphidiopsis raciborskii vary between strains.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {3152},
pmid = {39856188},
issn = {2045-2322},
support = {PPN/ULM/2019/1/00219//Narodowa Agencja Wymiany Akademickiej/ ; 2021/41/N/NZ9/02957//Narodowym Centrum Nauki/ ; 2021/41/N/NZ9/02957//Narodowym Centrum Nauki/ ; 2020/38/L/NZ9/00135//Narodowym Centrum Nauki/ ; S-LL-21-10//Research Council of Lithuania/ ; 1386/20//Israel Science Foundation/ ; },
mesh = {*Microcystis/virology/physiology ; *Bacteriophages/physiology ; *Fresh Water/virology ; Eutrophication ; Ecosystem ; Cyanobacteria/virology/physiology ; Photosynthesis ; Host Specificity ; },
abstract = {Viruses that infect cyanobacteria are an integral part of aquatic food webs, influencing nutrient cycling and ecosystem health. However, the significance of virus host range, replication efficiency, and host compatibility on cyanobacterial dynamics, growth, and toxicity remains poorly understood. In this study, we examined the effects of cyanophage additions on the dynamics and activity of optimal, sub-optimal, and non-permissive cyanobacterial hosts in cultures of Microcystis aeruginosa and Raphidiopsis raciborskii. Our findings reveal that cross-infectivity can substantially reduce the proliferative success of the cyanophage under conditions of high-density of sub-optimal hosts which suggests phage dispersal limitation as a result of shared infections, in turn impairing their top-down control over the host community. Furthermore, we found that cyanophage addition triggers host strain-specific responses in photosynthetic performance, population size and toxin production, even among non-permissive hosts. These non-lytic effects suggest indirect impacts on co-existing cyanobacteria, increasing the overall complexity and variance in many ecologically relevant cyanobacterial traits. The high variability in responses observed with a limited subset of cyanophage-cyanobacteria combinations not only highlights the intricate role of viral infections in microbial ecosystems but also underscores the significant challenges in predicting the composition, toxicity, and dynamics of cyanobacterial blooms.},
}

*Microcystis/virology/physiology
*Bacteriophages/physiology
*Fresh Water/virology
Eutrophication
Ecosystem
Cyanobacteria/virology/physiology
Photosynthesis
Host Specificity

@article {pmid39855017,
year = {2025},
author = {Savadova-Ratkus, K and Grendaitė, D and Karosienė, J and Stonevičius, E and Kasperovičienė, J and Koreivienė, J},
title = {Modelling harmful algal blooms in a mono- and a polydominant eutrophic lake under temperature and nutrient changes.},
journal = {Water research},
volume = {275},
number = {},
pages = {123138},
doi = {10.1016/j.watres.2025.123138},
pmid = {39855017},
issn = {1879-2448},
abstract = {Cyanobacterial blooms, driven by nutrient loading and temperature, pose significant ecological and economic challenges. This study employs a combined data-driven and trait-based modelling approach to predict changes in cyanobacterial communities in a mono- and a polydominant shallow temperate lakes under varying temperature and nutrient scenarios. Results of the AQUATOX simulation model for two aquatic systems suggest that a 2 °C temperature increase, consistent with Intergovernmental Panel on Climate Change's predictions, may influence cyanobacteria species composition and dominance, with trends indicating a possible shift favouring Nostocales over Oscillatoriales and Chroococcales. Temperature increases by 4 °C clearly promoted the dominance of Nostocales. Nutrient dynamics appear to influence community structure. In a nutrient-rich monodominant lake, temperature was the primary driver, while in a nutrient-limited polydominant lake, phosphorus availability influenced cyanobacteria species dominance. Combined warming and phosphorus alterations significantly affected cyanobacteria bloom intensity and duration, particularly enhancing Nostocales growth. The study highlights the complexity of cyanobacterial responses to climate change, emphasizing the need for more analysis and comprehensive models to predict harmful algal blooms (HABs) in freshwater ecosystems. While the findings suggest that temperature and nutrient availability may be critical drivers of cyanobacterial dominance, additional research across a broader range of systems is necessary.},
}

@article {pmid39854900,
year = {2025},
author = {Reid, CJ and Farrell, M and Kirby, JK},
title = {Microbial communities in biosolids-amended soils: A critical review of high-throughput sequencing approaches.},
journal = {Journal of environmental management},
volume = {375},
number = {},
pages = {124203},
doi = {10.1016/j.jenvman.2025.124203},
pmid = {39854900},
issn = {1095-8630},
abstract = {Sustainable reuse of treated wastewater sludge or biosolids in agricultural production requires comprehensive understanding of their risks and benefits. Microbes are central mediators of many biosolids-associated risks and benefits, however understanding of their responses to biosolids remains minimal. Application of biosolids to soils amounts to a coalescence of two distinct microbial communities adapted to vastly different matrices. High-throughput DNA and RNA sequencing (HTS) approaches are required to accurately describe the compositional and functional outcomes of this process as they currently provide the highest possible resolution to deal with complex community-scale phenomena. Furthermore, linkage of HTS data to physicochemical and functional data can reveal biotic and abiotic drivers of coalescence, impacts of biosolids-borne contaminants and the collective downstream implications for soil and plant health. Here we review the current body of literature examining microbial communities in biosolids-amended soils using HTS of total community DNA and RNA. We provide a critical synthesis of soil microbial community composition and functional responses, the physical, chemical and biological drivers of these responses, and the influence of three major biosolids-borne anthropogenic contaminants of concern; antimicrobials and antimicrobial resistance genes, plastics, and per- and polyfluoroalkyl substances (PFAS). Finally, we identify methodological limitations and outstanding research questions precluding a holistic understanding of microbial responses in biosolids-amended soils and envision future research whereby sequence-based microbial ecology is integrated with soil, plant, and contaminant data to preserve soil health, support plant productivity, and remediate contaminants.},
}

@article {pmid39853499,
year = {2025},
author = {Lucia, Z and Giulio, G and Matteo, G and Stefano, C and Irene, LP and Paolo, P and Giorgio, B and Hauffe, HC},
title = {More Than Meets the Eye: Unraveling the Interactions Between Skin Microbiota and Habitat in an Opportunistic Amphibian.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {176},
pmid = {39853499},
issn = {1432-184X},
mesh = {Animals ; *Skin/microbiology ; *Microbiota ; *Ecosystem ; *Anura/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Italy ; Fungi/classification/isolation & purification/genetics ; Hydrogen-Ion Concentration ; Batrachochytrium ; Wetlands ; Temperature ; },
abstract = {With amphibians still holding the record as the most threatened class of terrestrial vertebrates, their skin microbiota has been shown to play a relevant role in their survival in a fast-changing world. Yet little is known about how abiotic factors associated with different aquatic habitats impact these skin microorganisms. Here we chose the yellow-bellied toad (Bombina variegata), a small anuran that colonizes a wide range of wetland habitats, to investigate how the diversity and composition of both its bacterial and fungal skin communities vary across different habitats and with water characteristics (temperature, pH, and dissolved oxygen) of these habitats. Skin microbiota was sampled from 14 sites in the Province of Trento (Italy), including natural pools, ephemeral ponds, irrigation tanks, and farm ponds. Interestingly, the diversity of the two microbial components was also highly correlated. Close associations between both the diversity and composition of water and skin communities were noted for each habitat and sampling site, suggesting that water bodies actively contribute to the skin microbiota assemblage. In addition, water pH, temperature, and dissolved oxygen affected both bacterial and fungal diversity of skin. We confirmed the presence of Batrachochytrium dendrobatidis in skin samples of animals collected from eight waterbodies, as well as more than 60 microbial taxa previously associated with resistance to this pathogen. We concluded that both skin bacterial and fungal communities appear to be influenced by each other as well as by environmental communities and conditions, and these relationships connecting the whole ecosystem should be considered in future research concerning amphibian conservation.},
}

Animals
*Skin/microbiology
*Microbiota
*Ecosystem
*Anura/microbiology
*Bacteria/classification/genetics/isolation & purification
Italy
Fungi/classification/isolation & purification/genetics
Hydrogen-Ion Concentration
Batrachochytrium
Wetlands
Temperature

@article {pmid39849986,
year = {2025},
author = {Liu, Y and Geng, Y and Jiang, Y and Li, P and Li, YZ and Zhang, Z},
title = {Global microbial community biodiversity increases with antimicrobial toxin abundance of rare taxa.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf012},
pmid = {39849986},
issn = {1751-7370},
abstract = {One of the central questions in microbial ecology is how to explain the high biodiversity of communities. A large number of rare taxa in the community have not been excluded by abundant taxa with competitive advantages, a contradiction known as the biodiversity paradox. Recently, increasing evidence has revealed the central importance of antimicrobial toxins as crucial weapons of antagonism in microbial survival. The powerful effects of antimicrobial toxins result in simple combinations of microorganisms failing to coexist under laboratory conditions, but it is unclear whether they also have a negative impact on the biodiversity of natural communities. Here, we revealed that microbial communities worldwide universally possess functional potential for antimicrobial toxin production. Counterintuitively, the biodiversity of global microbial communities increases, rather than decreases, as the abundance of antimicrobial toxins in rare taxa rises. Rare taxa may encode more antimicrobial toxins than abundant taxa, which is associated with the maintenance of the high biodiversity of microbial communities amid complex interactions. Our findings suggest that the antagonistic interaction caused by antimicrobial toxins may play a positive role in microbial community biodiversity at the global scale.},
}

@article {pmid39849009,
year = {2025},
author = {Calderón-Osorno, M and Rojas-Villalta, D and Lejzerowicz, F and Cortés, J and Arias-Andres, M and Rojas-Jimenez, K},
title = {The influence of depth on the global deep-sea plasmidome.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {2959},
pmid = {39849009},
issn = {2045-2322},
support = {SIA 0483-21//Universidad Nacional de Costa Rica/ ; C1455//Vicerrectoría de Investigacion de la Universidad Costa Rica/ ; C2650//Vicerrectoría de Investigacion de la Universidad Costa Rica/ ; C3509//Vicerrectoría de Investigacion de la Universidad Costa Rica/ ; },
mesh = {*Plasmids/genetics ; Metagenome ; Seawater/microbiology ; Ecosystem ; Oceans and Seas ; Gammaproteobacteria/genetics/classification ; Alphaproteobacteria/genetics ; },
abstract = {Plasmids play a crucial role in facilitating genetic exchange and enhancing the adaptability of microbial communities. Despite their importance, environmental plasmids remain understudied, particularly those in fragile and underexplored ecosystems such as the deep-sea. In this paper we implemented a bioinformatics pipeline to study the composition, diversity, and functional attributes of plasmid communities (plasmidome) in 81 deep-sea metagenomes from the Tara and Malaspina expeditions, sampled from the Pacific, Atlantic, and Indian Oceans at depths ranging from 270 to 4005 m. We observed an association between depth and plasmid traits, with the 270-1000 m range (mesopelagic samples) exhibiting the highest number of plasmids and the largest plasmid sizes. Plasmids of Alphaproteobacteria and Gammaproteobacteria were predominant across the oceans, particularly in this depth range, which also showed the highest species diversity and abundance of metabolic pathways, including aromatic compound degradation. Surprisingly, relatively few antibiotic resistance genes were found in the deep-sea ecosystem, with most being found in the mesopelagic layer. These included classes such as beta-lactamase, biocide resistance, and aminoglycosides. Our study also identified the MOBP and MOBQ relaxase families as prevalent across various taxonomic classes. This research underscores the importance of studying the plasmidome independently from the chromosomal context. Our limited understanding of the deep-sea's microbial ecology, especially its plasmidome, necessitates caution in human activities like mining. Such activities could have unforeseen impacts on this largely unexplored ecosystem.},
}

*Plasmids/genetics
Metagenome
Seawater/microbiology
Ecosystem
Oceans and Seas
Gammaproteobacteria/genetics/classification
Alphaproteobacteria/genetics

@article {pmid39848193,
year = {2025},
author = {Odales-Bernal, L and González, LML and Ghysels, S and Lobanov, V and De Vrieze, J and Barrera, EL and Ronsse, F},
title = {Optimized hydrothermal carbonization of chicken manure and anaerobic digestion of its process water for better energy management.},
journal = {Journal of environmental management},
volume = {375},
number = {},
pages = {124191},
doi = {10.1016/j.jenvman.2025.124191},
pmid = {39848193},
issn = {1095-8630},
abstract = {Modern poultry production is faced with the challenge of properly managing its associated wastes, in particular chicken manure (CM). There is a need to improve the management of CM through conversion processes that allow the production of value-added products, particularly for energy purposes, such as hydrothermal carbonization (HTC) and anaerobic digestion (AD). The objectives of this study were: i) to optimize the CM-HTC, using response surface methodology with simultaneous optimization of mass yield and higher heating value (HHV), and ii) to evaluate the biomethane potential of the process water generated from hydrochar production under the optimized condition. An analysis of the overall energy potential was also performed. The optimal condition for HTC was 234 °C for 30 min, resulting in hydrochar with an HHV of 14.88 ± 0.22 MJ/kg and a mass yield of 50.00 ± 3.13 wt%. The cumulative methane yield was 179.2 ± 13.1 NmL CH4/g VSadded and 255.5 ± 14.5 NmL CH4/g VSadded for process water at 180 °C and 234 °C, respectively. The addition of hydrochar improved the methane yield by 49.6 ± 10.8%, indicating that this is a valuable option for energy recovery from CM. Overall, the HTC-AD integration approach achieved an energy recovery potential of more than 79%, offering an efficient strategy for CM valorization.},
}

@article {pmid39847340,
year = {2025},
author = {Ganley, JG and Seyedsayamdost, MR},
title = {Iron limitation triggers roseoceramide biosynthesis and membrane remodeling in marine roseobacter.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {4},
pages = {e2414434122},
doi = {10.1073/pnas.2414434122},
pmid = {39847340},
issn = {1091-6490},
support = {Postdoctoral Fellowship in Marine Microbial Ecology//Simons Foundation (SF)/ ; R35 GM152049/GM/NIGMS NIH HHS/United States ; },
mesh = {*Roseobacter/metabolism ; *Iron/metabolism ; Cell Membrane/metabolism ; Seaweed/metabolism ; Symbiosis/physiology ; },
abstract = {Chemical communication between marine bacteria and their algal hosts drives population dynamics and ultimately determines the fate of major biogeochemical cycles in the ocean. To gain deeper insights into this small molecule exchange, we screened niche-specific metabolites as potential modulators of the secondary metabolome of the roseobacter, Roseovarius tolerans. Metabolomic analysis led to the identification of a group of cryptic lipids that we have termed roseoceramides. The roseoceramides are elicited by iron-binding algal flavonoids, which are produced by macroalgae that Roseovarius species associate with. Investigations into the mechanism of elicitation show that iron limitation in R. tolerans initiates a stress response that results in lowered oxidative phosphorylation, increased import and catabolism of algal exudates, and reconfiguration of lipid ynthesis to prioritize production of roseoceramides over phospholipids, likely to fortify membrane integrity as well as promote a sessile and symbiotic lifestyle. Our findings add new small molecule words and their "meanings" to the algal-bacterial lexicon and have implications for the initiation of these interactions.},
}

*Roseobacter/metabolism
*Iron/metabolism
Cell Membrane/metabolism
Seaweed/metabolism
Symbiosis/physiology

@article {pmid39845484,
year = {2024},
author = {Tóth, VR},
title = {Photosynthetic traits of Phragmites australis along an ecological gradient and developmental stages.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1476142},
pmid = {39845484},
issn = {1664-462X},
abstract = {Common reed (Phragmites australis) is a cosmopolitan species, though its dieback is a worldwide phenomenon. In order to assess the evolutionary role of phenotypic plasticity in a successful plant, the values and plasticity of photophysiological traits of Phragmites australis were investigated in the Lake Fertő wetlands at 5 sites with different degrees of reed degradation and along a seasonal sequence. On the one hand, along the established ecological degradation gradient, photophysiological traits of Phragmites changed significantly, affecting plant productivity, although no consistent gradient-type trends were observed. Gradual changes within a season in the values of photosynthetic traits were observed that were recorded in both degraded and stable stands, suggesting a universal response to seasonally changing environmental conditions that could not be overridden by the ecological gradient. On the other hand, reed plants exposed to different levels of degradation showed comparable physiological plasticity; there was no difference in trait variability between stable and degraded stands. This relatively uniform plasticity is likely to contribute to the resilience of reed plants by providing a wider range of adaptive traits under different conditions. In contrast, the 150-200% gradual change in photophysiological trait plasticity with senescence in Phragmites was also demonstrated, reflecting a more dynamic response of the photosynthetic apparatus to seasonal changes. Senescence affected the plasticity of plant traits independently of their degradation status, suggesting a more universal nature of seasonal changes. This research shows that under conditions of conservative resource use determined by stressful habitats, trait values respond to conditions, while trait plasticity shows minimal changes. Furthermore, phenological sequence significantly influenced both the values and the plasticity of the photosynthetic traits studied. Our results underline the impact of ecological degradation on reed physiology and highlight the importance of understanding both trait values and plasticity in plant responses to environmental and seasonal change.},
}

@article {pmid39844349,
year = {2025},
author = {de Souza, LF and Oliveira, HG and Pellegrinetti, TA and Mendes, LW and Bonatelli, ML and Romão Dumaresq, AS and Sinatti, VVC and Pinheiro, JB and Azevedo, JL and Quecine, MC},
title = {Co-inoculation with Bacillus thuringiensis RZ2MS9 and rhizobia improves the soybean development and modulates soil functional diversity.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf013},
pmid = {39844349},
issn = {1574-6941},
abstract = {Despite the beneficial effects of Plant Growth-Promoting Rhizobacteria (PGPR) on agriculture, understanding the consequences of introducing foreign microbes into soil taxonomic and functional diversity is necessary. This study evaluated the effects co-inoculation of soybean with Bacillus thuringiensis (Bt) RZ2MS9 and commercial rhizobia on the natural microbial community structure and functional potential. Our results indicated that soybean development was positively influenced by co-inoculation, plants exhibited greater height and a higher number of pods, and no reductions in productivity estimates. Soil prokaryotic diversity and community structure remained unchanged by Bt RZMS9 inoculation or co-inoculation with rhizobia 147 Days After Sowing (DAS). However, functional diversity was influenced by sole Bt inoculation, potentially due to community quorum sensing disruption by N-acyl homoserine lactone hydrolases. The genes enriched by co-inoculation were mostly related to soil phosphorus cycling, with gcd showing the most pronounced increase. The nifA genes increased when rhizobia alone were inoculated, suggesting that this pathway could be affected by Bt RZ2MS9 inoculation. This study demonstrates the synergistic activity of rhizobia and Bt RZ2MS9 on soybean development, without significantly interfering with natural microbial community, presenting a promising approach for sustainable crop management.},
}

@article {pmid39844346,
year = {2025},
author = {Melville, DW and Meyer, M and Kümmerle, C and Alvarado-Barrantes, KA and Wilhelm, K and Sommer, S and Tschapka, M and Risely, A},
title = {Delayed feeding disrupts diurnal oscillations in the gut microbiome of a neotropical bat in captivity.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf012},
pmid = {39844346},
issn = {1574-6941},
abstract = {Diurnal rhythms of the gut microbiota are emerging as an important yet often overlooked facet of microbial ecology. Feeding is thought to stimulate gut microbial rhythmicity, but this has not been explicitly tested. Moreover, the role of the gut environment is entirely unexplored, with rhythmic changes to gut pH rather than feeding per se possibly affecting gut microbial fluctuations. In this study, we experimentally manipulated the feeding schedule of captive lesser long-nosed bats, Leptonycteris yerbabuenae, to dissociate photic and feeding cues, and measured the fecal microbiota and gut pH every two hours. We detected strong diurnal rhythms in both microbial alpha- and beta diversity as well as in pH within the control group. However, a delay in feeding disrupted oscillations of gut microbial diversity and composition, but did not affect rhythms in gut pH. The oscillations of some genera, such as Streptococcus, which aid in metabolizing nutrients, shifted in accordance with the delayed feeding cue and were correlated with pH. For other bacterial genera, oscillations were disturbed and no connection to pH was found. Our findings suggest that the rhythmic proliferation of bacteria matches peak feeding times, providing evidence that diurnal rhythms of the gut microbiota likely evolved to optimize their metabolic support to the host's circadian phenotype.},
}

@article {pmid39843903,
year = {2025},
author = {Tóth, AB and Terauds, A and Chown, SL and Hughes, KA and Convey, P and Hodgson, DA and Cowan, DA and Gibson, J and Leihy, RI and Murray, NJ and Robinson, SA and Shaw, JD and Stark, JS and Stevens, MI and van den Hoff, J and Wasley, J and Keith, DA},
title = {A dataset of Antarctic ecosystems in ice-free lands: classification, descriptions, and maps.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {133},
pmid = {39843903},
issn = {2052-4463},
support = {LP170101143//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; LP170101143//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; LP170101143//Department of Education and Training | Australian Research Council (ARC)/ ; },
abstract = {Antarctica, Earth's least understood and most remote continent, is threatened by human disturbances and climate-related changes, underscoring the imperative for biodiversity inventories to inform conservation. Antarctic ecosystems support unique species and genetic diversity, deliver essential ecosystem services and contribute to planetary stability. We present Antarctica's first comprehensive ecosystem classification and map of ice-free lands, which host most of the continent's biodiversity. We used latent variables in factor analyses to partition continental-scale abiotic variation, then biotic variation represented in spatial models, and finally recognised regional-scale variation among biogeographic units. This produced a spatially explicit hierarchical classification with nine Major Environment Units (Tier 1), 33 Habitat Complexes (Tier 2) and 269 Bioregional Ecosystem Types (Tier 3) mapped at 100 m resolution and aligned with 'level 4' of the IUCN Global Ecosystem Typology. This comprehensive ecosystem inventory provides foundational data to inform protected area designation under the Antarctic Treaty's Environmental Protocol and track risks to Antarctic ecosystems. Its tiered structure and workflow accommodate data scarcity and facilitate updates, promoting robustness as knowledge builds.},
}

@article {pmid39840338,
year = {2024},
author = {Salerno, B and Cornaggia, M and Sabatino, R and Di Cesare, A and Mantovani, C and Barco, L and Cordioli, B and Bano, L and Losasso, C},
title = {The "best practices for farming" successfully contributed to decrease the antibiotic resistance gene abundances within dairy farms.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1420282},
pmid = {39840338},
issn = {2297-1769},
abstract = {INTRODUCTION: Farms are significant hotspots for the dissemination of antibiotic-resistant bacteria and genes (ARGs) into the environment and directly to humans. The prevalence of ARGs on farms underscores the need for effective strategies to reduce their spread. This study aimed to evaluate the impact of a guideline on "best practices for farming" aimed at reducing the dissemination of antibiotic resistance.

METHODS: A guideline focused on prudent antibiotic use, selective therapy, and hygienic and immune-prophylactic practices was developed and provided to the owners of 10 selected dairy farms and their veterinarians. Fecal samples were collected from lactating cows, dry cows, and calves both before and after the implementation of the guideline. ARGs (bla TEM, ermB, sul2, and tetA) were initially screened by end-point PCR, followed by quantification using digital droplet PCR. ARG abundance was expressed in relative terms by dividing the copy number of ARGs by the copy number of the 16S rRNA gene.

RESULTS: The ARG abundances were higher in lactating cows compared to other categories. Despite similar levels of antibiotic administration (based on veterinary prescription data from the sampled farms) in both sampling campaigns, the total abundance of selected ARGs, particularly bla TEM and tetA, significantly decreased after the adoption of the farming guidelines.

DISCUSSION: This study highlights the positive impact of prudent antibiotic use and the implementation of farming best practices in reducing the abundance of ARGs. The lactating cow category emerged as a crucial point of intervention for reducing the spread of antibiotic resistance. These findings contribute to ongoing efforts to address antibiotic resistance in farm environments and strengthen the evidence supporting the adoption of good farming practices.},
}

@article {pmid39838963,
year = {2024},
author = {Guan, J and Ji, Y and Peng, C and Zou, W and Tang, X and Shang, J and Sun, Y},
title = {GOPhage: protein function annotation for bacteriophages by integrating the genomic context.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {1},
pages = {},
doi = {10.1093/bib/bbaf014},
pmid = {39838963},
issn = {1477-4054},
support = {11209823//City University of Hong Kong/ ; },
mesh = {*Bacteriophages/genetics ; *Genome, Viral ; *Molecular Sequence Annotation ; *Viral Proteins/genetics/metabolism ; Genomics/methods ; Computational Biology/methods ; Software ; },
abstract = {Bacteriophages are viruses that target bacteria, playing a crucial role in microbial ecology. Phage proteins are important in understanding phage biology, such as virus infection, replication, and evolution. Although a large number of new phages have been identified via metagenomic sequencing, many of them have limited protein function annotation. Accurate function annotation of phage proteins presents several challenges, including their inherent diversity and the scarcity of annotated ones. Existing tools have yet to fully leverage the unique properties of phages in annotating protein functions. In this work, we propose a new protein function annotation tool for phages by leveraging the modular genomic structure of phage genomes. By employing embeddings from the latest protein foundation models and Transformer to capture contextual information between proteins in phage genomes, GOPhage surpasses state-of-the-art methods in annotating diverged proteins and proteins with uncommon functions by 6.78% and 13.05% improvement, respectively. GOPhage can annotate proteins lacking homology search results, which is critical for characterizing the rapidly accumulating phage genomes. We demonstrate the utility of GOPhage by identifying 688 potential holins in phages, which exhibit high structural conservation with known holins. The results show the potential of GOPhage to extend our understanding of newly discovered phages.},
}

*Bacteriophages/genetics
*Genome, Viral
*Molecular Sequence Annotation
*Viral Proteins/genetics/metabolism
Genomics/methods
Computational Biology/methods
Software

@article {pmid39838210,
year = {2025},
author = {Ouyang, XM and Lin, JH and Lin, Y and Zhao, XL and Huo, YN and Liang, LY and Huang, YD and Xie, GJ and Mi, P and Ye, ZY and Guleng, B},
title = {The SERPINB4 gene mutation identified in twin patients with Crohn's disease impaires the intestinal epithelial cell functions.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {2638},
pmid = {39838210},
issn = {2045-2322},
support = {81970460//National Natural Science Foundation of China/ ; 2023J011598//Natural Science Foundation Program, Fujian Province, China/ ; },
mesh = {Humans ; *Crohn Disease/genetics/pathology ; *Mutation ; Female ; Male ; Serpins/genetics/metabolism ; Apoptosis/genetics ; Exome Sequencing ; Epithelial Cells/metabolism/pathology ; Intestinal Mucosa/metabolism/pathology ; Genetic Predisposition to Disease ; Cell Proliferation ; Adult ; Cell Movement/genetics ; Twins/genetics ; },
abstract = {Crohn's disease (CD) is a chronic inflammatory autoimmune disease of unknown etiology. To identify new targets related to the initiation of CD, we screened a pair of twins with CD, which is a rare phenomenon in the Chinese population, for genetic susceptibility factors. Whole-exome sequencing (WES) of these patients revealed a mutation in their SERPINB4 gene. Therefore, we studied a wider clinical cohort of patients with CD or ulcerous colitis (UC), healthy individuals, and those with a family history of CD for this mutation by Sanger sequencing. The single-nucleotide difference in the SERPINB4 gene, which was unique to the twin patients with CD, led to the substitution of lysine by a glutamic acid residue. Functional analysis indicated that this mutation of SERPINB4 inhibited the proliferation, colony formation, wound healing, and migration of intestinal epithelial cells (IECs). Furthermore, mutation of SERPINB4 induced apoptosis and activated apoptosis-related proteins in IECs, and a caspase inhibitor significantly reduced these effects. Transcriptome sequencing revealed that the expression of genes encoding proinflammatory proteins (IL1B, IL6, IL17, IL24, CCL2, and CXCR2) and key proteins in the immune response (S100A9, MMP3, and MYC) was significantly upregulated during SERPINB4 mutant-induced apoptosis. Thus, the heterozygous SERPINB4 gene mutation causes the dysfunction of IECs, which would disrupt the intestinal epithelial barrier and contribute to the development of intestinal inflammation. The activation of SERPINB4 might represent a novel therapeutic target for inflammatory bowel disease.},
}

Humans
*Crohn Disease/genetics/pathology
*Mutation
Female
Male
Serpins/genetics/metabolism
Apoptosis/genetics
Exome Sequencing
Epithelial Cells/metabolism/pathology
Intestinal Mucosa/metabolism/pathology
Genetic Predisposition to Disease
Cell Proliferation
Adult
Cell Movement/genetics
Twins/genetics

@article {pmid39838107,
year = {2025},
author = {Teso-Pérez, C and López-Gazcón, A and Peralta-Sánchez, JM and Martínez-Bueno, M and Valdivia, E and Fárez-Vidal, ME and Martín-Platero, AM},
title = {Bacteriocin-Producing Enterococci Modulate Cheese Microbial Diversity.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {175},
pmid = {39838107},
issn = {1432-184X},
support = {PEJ2018-003019-A//Plan Estatal de Garantía Juvenil (Fondo Social Europeo, Gobierno de España/ ; Group BIO 309//PAIDI Program/ ; A-BIO-083-UGR18//Programa Operativo FEDER Andalucía 2014-2020/ ; },
mesh = {*Cheese/microbiology ; *Bacteriocins/metabolism/biosynthesis ; *Enterococcus/metabolism/genetics ; *Microbiota ; Biodiversity ; Food Microbiology ; RNA, Ribosomal, 16S/genetics ; Milk/microbiology ; Animals ; },
abstract = {Cheese production involves various lactic acid bacteria (LAB) that break down lactose, milk proteins, and fats, producing key nutrients and influencing the cheese's flavor. They form communities that play a crucial role in determining the cheese's organoleptic properties. The composition of cheeses' microbial communities is shaped by physicochemical factors (e.g., temperature, pH, and salinity) and biological factors (i.e. microbial interactions). While starter cultures are introduced to control these communities, non-starter LAB represent a significant portion of the final microbial assemblage, but their interactions remain unclear. LAB often produce bacteriocins, antimicrobial peptides that antagonize other bacteria, but their role within LAB communities is not fully understood. This study aimed to assess the impact of bacteriocin production on LAB diversity in cheese, using Enterococcus as a model organism, a common bacteriocin producer. We analyzed enterocin production of enterococcal isolates by antimicrobial assays and microbial diversity differences in raw milk cheeses by two approaches: 16S RNA gene amplicon metagenomic sequencing for the whole microbial community and multi-locus sequence analysis (MLSA) for the enterococcal diversity. Our results revealed that LAB communities were dominated by lactococci, lactobacilli, and streptococci, with enterococci present in lower numbers. However, cheeses containing bacteriocin-producing enterococci exhibited higher microbial diversity. Interestingly, the highest diversity occurred at low levels of bacteriocin producers, but this effect was not observed within enterococcal populations. These findings suggest that bacteriocin production plays a key role in shaping LAB communities during cheese ripening, although further research is needed to understand its broader implications in other microbial ecosystems.},
}

*Cheese/microbiology
*Bacteriocins/metabolism/biosynthesis
*Enterococcus/metabolism/genetics
*Microbiota
Biodiversity
Food Microbiology
RNA, Ribosomal, 16S/genetics
Milk/microbiology
Animals

@article {pmid39716385,
year = {2025},
author = {Lu, Z and Entwistle, E and Kuhl, MD and Durrant, AR and Barreto Filho, MM and Goswami, A and Morris, JJ},
title = {Coevolution of marine phytoplankton and Alteromonas bacteria in response to pCO2 and coculture.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {39716385},
issn = {1751-7370},
mesh = {*Phytoplankton/genetics/metabolism/growth & development ; *Carbon Dioxide/metabolism ; *Alteromonas/genetics/metabolism ; *Prochlorococcus/genetics/metabolism/growth & development ; Seawater/microbiology ; Coculture Techniques ; Biological Coevolution ; Diatoms/genetics/growth & development/metabolism ; Microbial Interactions ; },
abstract = {As a result of human activity, Earth's atmosphere and climate are changing at an unprecedented pace. Models based on short-term experiments predict major changes will occur in marine phytoplankton communities in the future ocean, but rarely consider how evolution or interactions with other microbes may influence these changes. Here, we experimentally evolved several phytoplankton in coculture with a heterotrophic bacterium, Alteromonas sp. EZ55, under either present-day or predicted future pCO2 conditions. Growth rates of phytoplankton generally increased over time under both conditions, but only Thalassiosira oceanica had evidence of a growth rate tradeoff in the ancestral environment after evolution at elevated pCO2. The growth defects observed in ancestral Prochlorococcus cultures at elevated pCO2 and in axenic culture were diminished after evolution, possibly due to regulatory mutations in antioxidant genes. Except for Prochlorococcus, mutational profiles suggested phytoplankton experienced primarily purifying selection, but most Alteromonas lineages showed evidence of directional selection, where evolution appeared to favor a metabolic switch between growth on small organic acids with cyanobacteria versus catabolism of more complex carbon substrates with eukaryotic phytoplankton. Evolved Alteromonas were also poorer "helpers" for Prochlorococcus, consistent with that interaction being a competitive Black Queen process rather than a true mutualism. This work provides new insights on how phytoplankton will respond to increased pCO2 and on the evolutionary mechanisms governing phytoplankton:bacteria interactions. It also clearly demonstrates that both evolution and interspecies interactions must be considered to predict future marine biogeochemistry.},
}

*Phytoplankton/genetics/metabolism/growth & development
*Carbon Dioxide/metabolism
*Alteromonas/genetics/metabolism
*Prochlorococcus/genetics/metabolism/growth & development
Seawater/microbiology
Coculture Techniques
Biological Coevolution
Diatoms/genetics/growth & development/metabolism
Microbial Interactions

@article {pmid39836327,
year = {2025},
author = {Flores Clavo, R and Suclupe-Campos, DO and Castillo Rivadeneira, L and Velez Chicoma, RLJ and Sánchez-Purihuamán, M and Quispe Choque, KG and Casado Peña, FL and Binatti Ferreira, M and Fantinatti Garboggini, F and Carreño-Farfan, C},
title = {Harnessing PGPRs from Asparagus officinalis to Increase the Growth and Yield of Zea mays L.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {174},
pmid = {39836327},
issn = {1432-184X},
mesh = {*Asparagus Plant/microbiology/growth & development ; *Zea mays/microbiology/growth & development ; *Soil Microbiology ; *Rhizosphere ; *Plant Roots/microbiology/growth & development ; *Bacteria/genetics/classification/isolation & purification/metabolism/growth & development ; *RNA, Ribosomal, 16S/genetics ; Indoleacetic Acids/metabolism ; Peru ; Phosphates/metabolism ; Salt Tolerance ; Soil/chemistry ; },
abstract = {Microbial biotechnology employs techniques that rely on the natural interactions that occur in ecosystems. Bacteria, including rhizobacteria, play an important role in plant growth, providing crops with an alternative that can mitigate the negative effects of abiotic stress, such as those caused by saline environments, and increase the excessive use of chemical fertilizers. The present study examined the promoting potential of bacterial isolates obtained from the rhizospheric soil and roots of the Asparagus officinalis cultivar UF-157 F2 in Viru, la Libertad, Peru. This region has high soil salinity levels. Seventeen strains were isolated, four of which are major potential plant growth-promoting traits, and were characterized based on their morphological and molecular characteristics. These salt-tolerant bacteria were screened for phosphate solubilization, indole acetic acid, deaminase activity, and molecular characterization by 16S rDNA sequencing. Fifteen samples were from saline soils of A. officinalis plants in the northern coastal desert of San Jose, Lambayeque, Peru. The bacterial isolates were screened in a range of salt tolerances from 3 to 6%. Isolates 05, 08, 09, and 11 presented maximum salt tolerance, ammonium quantification, phosphate solubilization, and IAA production. The four isolates were identified by sequencing the amplified 16S rRNA gene and were found to be Enterobacter sp. 05 (OQ885483), Enterobacter sp. 08 (OQ885484), Pseudomonas sp. 09 (OR398704) and Klebsiella sp. 11 (OR398705). These microorganisms promoted the germination of Zea mays L. plants, increased the germination rates in the treatments with chemical fertilizers at 100% and 50%, and the PGPRs increased the height and length of the roots 40 days after planting. The beneficial effects of salt-tolerant PGPR isolates isolated from saline environments may lead to new species that can be used to overcome the detrimental effects of salt stress on plants. The biochemical response and inoculation of the three isolates prove the potential of these strains as sources of products to develop new compounds, confirming their potential as biofertilizers for saline environments.},
}

*Asparagus Plant/microbiology/growth & development
*Zea mays/microbiology/growth & development
*Soil Microbiology
*Rhizosphere
*Plant Roots/microbiology/growth & development
*Bacteria/genetics/classification/isolation & purification/metabolism/growth & development
*RNA, Ribosomal, 16S/genetics
Indoleacetic Acids/metabolism
Peru
Phosphates/metabolism
Salt Tolerance
Soil/chemistry

@article {pmid39833680,
year = {2025},
author = {Sbissi, I and Chouikhi, F and Ghodhbane-Gtari, F and Gtari, M},
title = {Ecogenomic insights into the resilience of keystone Blastococcus Species in extreme environments: a comprehensive analysis.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {51},
pmid = {39833680},
issn = {1471-2164},
mesh = {*Extreme Environments ; Genome, Bacterial ; Phylogeny ; Genomics/methods ; Ecosystem ; Adaptation, Physiological/genetics ; Metals, Heavy/toxicity ; Biodegradation, Environmental ; Soil Microbiology ; },
abstract = {BACKGROUND: The stone-dwelling genus Blastococcus plays a key role in ecosystems facing extreme conditions such as drought, salinity, alkalinity, and heavy metal contamination. Despite its ecological significance, little is known about the genomic factors underpinning its adaptability and resilience in such harsh environments. This study investigates the genomic basis of Blastococcus's adaptability within its specific microniches, offering insights into its potential for biotechnological applications.

RESULTS: Comprehensive pangenome analysis revealed that Blastococcus possesses a highly dynamic genetic composition, characterized by a small core genome and a large accessory genome, indicating significant genomic plasticity. Ecogenomic assessments highlighted the genus's capabilities in substrate degradation, nutrient transport, and stress tolerance, particularly on stone surfaces and archaeological sites. The strains also exhibited plant growth-promoting traits, enhanced heavy metal resistance, and the ability to degrade environmental pollutants, positioning Blastococcus as a candidate for sustainable agriculture and bioremediation. Interestingly, no correlation was found between the ecological or plant growth-promoting traits (PGPR) of the strains and their isolation source, suggesting that these traits are not linked to their specific environments.

CONCLUSIONS: This research highlights the ecological and biotechnological potential of Blastococcus species in ecosystem health, soil fertility improvement, and stress mitigation strategies. It calls for further studies on the adaptation mechanisms of the genus, emphasizing the need to validate these findings through wet lab experiments. This study enhances our understanding of microbial ecology in extreme environments and supports the use of Blastococcus in environmental management, particularly in soil remediation and sustainable agricultural practices.},
}

*Extreme Environments
Genome, Bacterial
Phylogeny
Genomics/methods
Ecosystem
Adaptation, Physiological/genetics
Metals, Heavy/toxicity
Biodegradation, Environmental
Soil Microbiology

@article {pmid39830292,
year = {2024},
author = {Crous, PW and Wingfield, MJ and Jurjević, Ž and Balashov, S and Osieck, ER and Marin-Felix, Y and Luangsa-Ard, JJ and Mejía, LC and Cappelli, A and Parra, LA and Lucchini, G and Chen, J and Moreno, G and Faraoni, M and Zhao, RL and Weholt, Ø and Borovička, J and Jansen, GM and Shivas, RG and Tan, YP and Akulov, A and Alfenas, AC and Alfenas, RF and Altés, A and Avchar, R and Barreto, RW and Catcheside, DEA and Chi, TY and Esteve-Raventós, F and Fryar, SC and Hanh, LTM and Larsbrink, J and Oberlies, NH and Olsson, L and Pancorbo, F and Raja, HA and Thanh, VN and Thuy, NT and Ajithkumar, K and Akram, W and Alvarado, P and Angeletti, B and Arumugam, E and Khalilabad, AA and Bandini, D and Baroni, TJ and Barreto, GG and Boertmann, D and Bose, T and Castañeda Ruiz, RF and Couceiro, A and Cykowska-Marzencka, B and Dai, YC and Darmostuk, V and da Silva, SBG and Dearnaley, JDW and de Azevedo Santiago, ALCM and Declercq, B and de Freitas, LWS and De la Peña-Lastra, S and Delgado, G and de Lima, CLF and Dhotre, D and Dirks, AC and Eisvand, P and Erhard, A and Ferro, LO and García, D and García-Martín, A and Garrido-Benavent, I and Gené, J and Ghobad-Nejhad, M and Gore, G and Gunaseelan, S and Gusmão, LFP and Hammerbacher, A and Hernández-Perez, AT and Hernández-Restrepo, M and Hofmann, TA and Hubka, V and Jiya, N and Kaliyaperumal, M and Keerthana, KS and Ketabchi, M and Kezo, K and Knoppersen, R and Kolarczyková, D and Kumar, TKA and Læssøe, T and Langer, E and Larsson, E and Lodge, DJ and Lynch, MJ and Maciá-Vicente, JG and Mahadevakumar, S and Mateos, A and Mehrabi-Koushki, M and Miglio, BV and Noor, A and Oliveira, JA and Pereira, OL and Piątek, M and Pinto, A and Ramírez, GH and Raphael, B and Rawat, G and Renuka, M and Reschke, K and Mateo, AR and Saar, I and Saba, M and Safi, A and Sánchez, RM and Sandoval-Denis, M and Savitha, AS and Sharma, A and Shelke, D and Sonawane, H and Souza, MGAP and Stryjak-Bogacka, M and Thines, M and Thomas, A and Torres-Garcia, D and Traba, JM and Vauras, J and Vermaas, M and Villarreal, M and Vu, D and Whiteside, EJ and Zafari, D and Starink-Willemse, M and Groenewald, JZ},
title = {Fungal Planet description sheets: 1697-1780.},
journal = {Fungal systematics and evolution},
volume = {14},
number = {},
pages = {325-577},
doi = {10.3114/fuse.2024.14.19},
pmid = {39830292},
issn = {2589-3831},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Antarctica, Leuconeurospora bharatiensis from accumulated snow sediment sample. Argentina, Pseudocercospora quetri on leaf spots of Luma apiculata. Australia, Polychaetomyces verrucosus on submerged decaying wood in sea water, Ustilaginoidea cookiorum on Scleria levis, Xylaria guardiae as endophyte from healthy leaves of Macaranga tanarius. Belgium, Iodophanus taxi on leaf of Taxus baccata. Belize, Hygrocybe mirabilis on soil. Brazil, Gongronella irregularis from soil, Linodochium splendidum on decaying sheath of Euterpe oleracea, Nothophysalospora agapanthi (incl. Nothophysalospora gen. nov.) on flower stalks of Agapanthus praecox, Phaeosphaeria tabebuiae on leaf of Tabebuia sp., Verrucohypha endophytica (incl. Verrucohypha gen. nov.) from healthy roots of Acrocomia aculeata. Estonia, Inosperma apricum on soil under Quercus robur. Greece, Monosporascus solitarius isolated from surface-sterilised, asymptomatic roots of Microthlaspi perfoliatum. India, Diaporthe neocapsici on young seedling stems of Capsicum annuum, Fuscoporia naditirana on dead wood, Sebacina spongicarpa on soil, Torula kanvae from the gut of a Copris signatus beetle. Iran, Sarcinomyces pruni from twig and petiole tissues of Prunus persica and Prunus armeniaca, Xenodidymella quercicola from leaf spots of Quercus brantii. Italy, Agaricus aereiceps on grass, Agaricus bellui in meadows, Agaricus fabrianensis in urban grasslands, Beaucarneamyces muscorum on moss growing in forest, Xenoanthostomella quercus on leaf litter of Quercus ilex. Netherlands, Alfaria neerlandica on stem lesions of Cortaderia selloana, Neodictyosporium juncicola on culms of Juncus maritimus, Penicillium geertdesnooi from soil under Papaver rhoeas, Russula abscondita on rich calcareous soil with Quercus, Russula multiseptata on rich clay soil with Quercus, Russula purpureopallescens on soil with Populus, Sarocladium caricicola on leaves of Carex riparia. Pakistan, Circinaria shimlaensis on limestone rocks. Panama, Acrocalymma philodendri on leaf spots of Philodendron sp., Caligospora panamaensis on leaf litter, Chlamydocillium simulans associated with a Xylaria sp., Corynesporina panamaensis on leaf litter, Cylindromonium panamaense on twig litter of angiosperm, Cyphellophora panamaensis on twig litter of angiosperm, Microcera panamensis on leaf litter of fern, Pseudotricholoma pusillum in tropical montane forest dominated by Quercus spp., Striaticonidium panamaense on leaf litter, Yunnanomyces panamaensis on leaf litter. Poland, Albocremella abscondita (incl. Albocremella gen. nov.) from rhizoids of liverwort Conocephalum salebrosum. Portugal, Agaricus occidualis in meadows. South Africa, Alternaria elsarustiae on culms of unidentified Poaceae, Capronia capensis on dead twig of unidentified angiosperm, Codinaeella bulbinicola on dead leaves of Bulbine frutescens, Cytospora carpobroticola on leaf of Carpobrotus quadrifidus, Neophaeomoniella watsoniae on leaf of Watsonia sp., Neoplatysporoides aloigena on leaf of Aloe khamiesensis, Nothodactylaria comitabilis on living leaf of Itea rhamnoides, Nothopenidiella beaucarneae (incl. Nothopenidiella gen. nov.) on dead leaves of Beaucarnea stricta, Orbilia kirstenboschensis on dead flower stalks of Agapanthus praecox, Phragmocephala agapanthi on dead flower stalks of Agapanthus praecox, Podocarpigena hagahagaensis (incl. Podocarpigena gen. nov.) on leaf spots of Podocarpus falcatus, Sporisorium enterogonipteri from the gut of Gonipterus sp., Synnemapestaloides searsiae on leaf of Searsia populifolia, Xenophragmocapnias diospyri (incl. Xenophragmocapnias gen. nov.) on leaf spots of Diospyros sp., Yunnanomyces hagahagaensis on leaf spots of Sideroxylon inerme. Spain, Agaricus basicinctus in meadows, Agaricus quercetorum among leaf litter in oak forests, Coprinopsis palaciosii on degraded woody debris, Inocybe complutensis in calcareous loamy soil, Inocybe tanitiae in calcareous sandy soil, Mycena subfragosa on dead leaves of Salix atrocinerea, Pseudobaeospora cortegadensis in laurel forests, Trichoderma sedimenticola from fluvial sediments. Sweden, Inocybe badjelanndana on calcareous soil. Ukraine, Beaucarneamyces lupini on overwintered stems of Lupinus polyphyllus, Protocreopsis globulosa on thallus and apothecia of Lecania cyrtella on bark of Populus sp., Thyridium tiliae on dead twigs of Tilia sp. USA, Cladosporium louisianense, Cyphellophora americana from a bedroom vent, Extremus massachusettsianus from lyse buffer, Myxotrichum tapetae on carpet in basement, Neospissiomyces floridanus (incl. Neospissiomyces gen. nov.) on swab from hospital, Polychaetomyces marinus (incl. Polychaetomyces gen. nov.) on submerged driftwood in sea water, Steccherinum fragrans on hardwood fallen on the beach, Steinbeckomyces carnegieae (incl. Steinbeckomyces gen. nov.) on Carnegiea gigantea, Tolypocladium pennsylvanicum from air sampled in basement. Vietnam, Acidomyces ducanhii from Aglaia flowers, Acidomyces paludis from dead bark of Acacia sp., Phakopsora sageretiae on Sageretia theezans, Puccinia stixis on Stixis scandens. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Wingfield MJ, Jurjević Ž, et al. (2024). Fungal Planet description sheets: 1697-1780. Fungal Systematics and Evolution 14: 325-577. doi: 10.3114/fuse.2024.14.19.},
}

@article {pmid39828718,
year = {2025},
author = {Wang, Z and Fuad, MTI and Liu, J and Lin, K and Liu, L and Gao, C and Wang, W and Liu, X},
title = {Spatial Patterns of Microbial Communities in Intertidal Sediments of the Yellow River Estuary, China.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {173},
pmid = {39828718},
issn = {1432-184X},
support = {41976131//National Natural Science Foundation of China/ ; },
mesh = {*Geologic Sediments/microbiology ; *Archaea/classification/genetics/isolation & purification ; China ; *Bacteria/classification/genetics/isolation & purification ; *Estuaries ; *Rivers/microbiology ; *Microbiota ; Biodiversity ; Ecosystem ; Metals, Heavy/analysis ; },
abstract = {Estuarine ecosystems are among the most important natural ecosystems on Earth and contribute substantially to human survival and development. The Yellow River Estuary (YRE) is the second largest estuary in China. Microbial communities play an essential role in the material cycle and energy flow in estuarine ecosystems. To date, our knowledge of the spatial patterns of bacterial and archaeal communities is limited. In this study, we investigated the spatial profile of bacterial and archaeal communities and their co-occurrence patterns, functional roles, and environmental driving factors in the intertidal sediments of the YRE from June to July, 2019. The results showed that Proteobacteria, Bacteroidetes, Chloroflexi, and Planctomycetes were the dominant bacterial phyla, whereas Nanoarchaeaeota, Euryarchaeota and Thaumarchaeota were the dominant archaeal phyla in the intertidal sediments of the YRE. Diversity indices and differential abundance analyses revealed significant (p < 0.05) differences in the bacterial and archaeal communities in the intertidal sediments of the YRE. Bacterial communities demonstrated distinct correlations with heavy metals and pollutants. Six archaeal genera exhibited co-occurrence patterns with bacterial genera. Functions associated with sulfur cycles, disease, and pollution were specific to bacterial communities. This study presents a detailed outline of the spatial patterns of microbial communities in the YRE, enriching our understanding of microbial ecology, especially of bacteria and archaea.},
}

*Geologic Sediments/microbiology
*Archaea/classification/genetics/isolation & purification
China
*Bacteria/classification/genetics/isolation & purification
*Estuaries
*Rivers/microbiology
*Microbiota
Biodiversity
Ecosystem
Metals, Heavy/analysis

@article {pmid39826456,
year = {2025},
author = {Wang, Y and Zhang, F and Yang, L and Zhang, G and Wang, H and Zhu, S and Zhang, H and Guo, T},
title = {Synergy of plastics and heavy metals weakened soil bacterial diversity by regulating microbial functions in the Qinghai-Tibet Plateau.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137241},
doi = {10.1016/j.jhazmat.2025.137241},
pmid = {39826456},
issn = {1873-3336},
abstract = {How plastics coupled with metals regulate microbial functions-diversity relationships remain unknown in plateau soil environment. Three representative catchments in the Qinghai-Tibet Plateau, focusing on microplastics, their plasticisers, and metals in soils, were investigated. This research explores responses of bacterial diversity and functions to the co-existence of target pollutants, and pathways by which target pollutants regulate the diversity. Soil bacterial beta diversity and functional genes exhibited negative correlations with phthalate esters across three catchments (p < 0.05). Dibutyl phthalate emerged as a primary factor affecting beta diversity, rather than the quantity of microplastics. Additionally, the synergy of cadmium and fiber-shaped microplastics exacerbated the impact on diversity. Structural equation modeling further elucidated that plastics, copper, and iron influenced nirK/nirS genes and phoD gene, subsequently affected cbbL/cbbM genes, and ultimately the diversity. In this context, microplastics, phthalate esters and copper, iron exerted antagonistic effects on one another. Consequently, the co-existence of plastics and cadmium weakened soil bacterial diversity in the Qinghai-Tibet Plateau by disrupting microbial functions, but micronutrients alleviated these negative impacts. This research reveals that the co-existence of plastics and metals regulates soil bacterial diversity in the Qinghai-Tibet Plateau, providing a valuable reference for the protection of microbial ecology in plateau regions.},
}

@article {pmid39826104,
year = {2025},
author = {Lin, A and Jiang, A and Huang, L and Li, Y and Zhang, C and Zhu, L and Mou, W and Liu, Z and Zhang, J and Cheng, Q and Wei, T and Luo, P},
title = {From chaos to order: optimizing fecal microbiota transplantation for enhanced immune checkpoint inhibitors efficacy.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2452277},
doi = {10.1080/19490976.2025.2452277},
pmid = {39826104},
issn = {1949-0984},
mesh = {Humans ; *Fecal Microbiota Transplantation ; *Immune Checkpoint Inhibitors/therapeutic use ; *Gastrointestinal Microbiome ; *Neoplasms/therapy/microbiology ; Animals ; Immunotherapy/methods ; Tumor Microenvironment/drug effects ; Treatment Outcome ; Combined Modality Therapy ; },
abstract = {The integration of fecal microbiota transplantation (FMT) with immune checkpoint inhibitors (ICIs) presents a promising approach for enhancing cancer treatment efficacy and overcoming therapeutic resistance. This review critically examines the controversial effects of FMT on ICIs outcomes and elucidates the underlying mechanisms. We investigate how FMT modulates gut microbiota composition, microbial metabolite profiles, and the tumor microenvironment, thereby influencing ICIs effectiveness. Key factors influencing FMT efficacy, including donor selection criteria, recipient characteristics, and administration protocols, are comprehensively discussed. The review delineates strategies for optimizing FMT formulations and systematically monitoring post-transplant microbiome dynamics. Through a comprehensive synthesis of evidence from clinical trials and preclinical studies, we elucidate the potential benefits and challenges of combining FMT with ICIs across diverse cancer types. While some studies report improved outcomes, others indicate no benefit or potential adverse effects, emphasizing the complexity of host-microbiome interactions in cancer immunotherapy. We outline critical research directions, encompassing the need for large-scale, multi-center randomized controlled trials, in-depth microbial ecology studies, and the integration of multi-omics approaches with artificial intelligence. Regulatory and ethical challenges are critically addressed, underscoring the imperative for standardized protocols and rigorous long-term safety assessments. This comprehensive review seeks to guide future research endeavors and clinical applications of FMT-ICIs combination therapy, with the potential to improve cancer patient outcomes while ensuring both safety and efficacy. As this rapidly evolving field advances, maintaining a judicious balance between openness to innovation and cautious scrutiny is crucial for realizing the full potential of microbiome modulation in cancer immunotherapy.},
}

Humans
*Fecal Microbiota Transplantation
*Immune Checkpoint Inhibitors/therapeutic use
*Gastrointestinal Microbiome
*Neoplasms/therapy/microbiology
Animals
Immunotherapy/methods
Tumor Microenvironment/drug effects
Treatment Outcome
Combined Modality Therapy

@article {pmid39825576,
year = {2025},
author = {Fouché, J and Lebre, PH and Melville, HA and Cowan, DA},
title = {The Functional and Structural Succession of Mesic-Grassland Soil Microbiomes Beneath Decomposing Large Herbivore Carcasses.},
journal = {Environmental microbiology},
volume = {27},
number = {1},
pages = {e70022},
doi = {10.1111/1462-2920.70022},
pmid = {39825576},
issn = {1462-2920},
mesh = {*Soil Microbiology ; Animals ; *Microbiota ; *Herbivory ; *Grassland ; *Bacteria/classification/genetics/metabolism ; *RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Carbon/metabolism ; },
abstract = {Plant detritus is abundant in grasslands but decomposes slowly and is relatively nutrient-poor, whereas animal carcasses are labile and nutrient-rich. Recent studies have demonstrated that labile nutrients from carcasses can significantly alter the long-term soil microbial function at an ecosystem scale. However, there is a paucity of knowledge on the functional and structural response and temporal scale of soil microbiomes beneath large herbivore carcasses. This study compared microbiome functions and structures of soil beneath Connochaetes taurinus (hereafter 'wildebeest') carcasses at various postmortem intervals of decomposition to matched control samples over 18 months. Microbial functions were compared by their community-level physiological profiles determined by sole-carbon substrate utilisation and structures by metagenomic sequences using 16S rRNA gene markers. Overall metabolism and metabolic diversity remained increased and functionally dissimilar to control soils throughout the experimental period, with successive sole-carbon substrate utilisation observed. Conversely, diversity was initially reduced and structurally dissimilar from the control soil but recovered within the experimental period. The study contributes to the knowledge of carcass decomposition by investigating the long-term soil microbiome dynamics resulting from large herbivore carcasses decomposing in a mesic grassland. Microbial functional succession and ecologically relevant bacterial biomarkers of soil beneath the decomposing carcasses were identified for various postmortem intervals.},
}

*Soil Microbiology
Animals
*Microbiota
*Herbivory
*Grassland
*Bacteria/classification/genetics/metabolism
*RNA, Ribosomal, 16S/genetics
Soil/chemistry
Carbon/metabolism

@article {pmid39825218,
year = {2025},
author = {de Freitas, AS and Zagatto, LFG and Rocha, GS and Muchalak, F and Martins, GL and Silva-Zagatto, SDS and Hanada, RE and Muniz, AW and Tsai, SM},
title = {Harnessing the synergy of Urochloa brizantha and Amazonian Dark Earth microbiomes for enhanced pasture recovery.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {27},
pmid = {39825218},
issn = {1471-2180},
support = {2021/10626-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2022/05561-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 01.02.016301.00293/2021//Fundação de Amparo à Pesquisa do Estado do Amazonas/ ; },
mesh = {*Soil Microbiology ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Plant Roots/microbiology ; Brazil ; *Poaceae/microbiology ; Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; Rainforest ; Biodiversity ; },
abstract = {Amazonian Dark Earths (ADEs) are fertile soils from the Amazon rainforest that harbor microorganisms with biotechnological potential. This study aimed to investigate the individual and potential synergistic effects of a 2% portion of ADEs and Urochloa brizantha cv. Marandu roots (Brazil's most common grass species used for pastures) on soil prokaryotic communities and overall soil attributes in degraded soil. We conducted a comprehensive plant succession experiment in the greenhouse, utilizing vase soil samples for next-generation sequencing of 16 S rDNA, enzymatic activity assays, and soil chemical properties analysis. Univariate and multivariate analyses were performed to understand better the prokaryotic interactions within soil environments influenced by ADEs and U. brizantha roots, including differential abundance, diversity, and network analyses. Our findings reveal a complementary relationship between U. brizantha and ADEs, each contributing to distinct positive aspects of soil bacterial communities and quality. The combined influence of U. brizantha roots and ADEs exhibited synergies that enhanced prokaryotic diversity and enzyme activity. This balance supported plant growth and increased the general availability of beneficial bacteria in the soil, such as Chujaibacter and Curtobacterium while reducing the presence of potentially pathogenic taxa. This research provided valuable insights into the intricate dynamics of plant-soil feedback, emphasizing the potential for complementary interactions between specific plant species and unique soil environments like ADEs. The findings highlight the potential for pasture ecological rehabilitation and underscore the benefits of integrating plant and soil management strategies to optimize soil characteristics.},
}

*Soil Microbiology
*Microbiota/genetics
*Bacteria/genetics/classification/isolation & purification/metabolism
*Plant Roots/microbiology
Brazil
*Poaceae/microbiology
Soil/chemistry
RNA, Ribosomal, 16S/genetics
Rainforest
Biodiversity

@article {pmid39821365,
year = {2025},
author = {Zhang, D and Cai, Y and Sun, Y and Zeng, P and Wang, W and Wang, W and Jiang, X and Lian, Y},
title = {A Real-World Disproportionality Analysis of Histamine H2-Receptors Antagonists (Famotidine): A Pharmacovigilance Study Based on Spontaneous Reports in the FDA Adverse Event Reporting System.},
journal = {Drug development research},
volume = {86},
number = {1},
pages = {e70045},
doi = {10.1002/ddr.70045},
pmid = {39821365},
issn = {1098-2299},
support = {//This study was funded by the National Natural Science Foundation of China (Grant No: 82303109), the Natural Science Foundation of Fujian Province, China (Grant No: 2022J05299), Cross-Strait Postdoctoral Exchange Funding Program of Fujian Province, China (Grant No: 2021B002)./ ; },
mesh = {Humans ; *Famotidine/adverse effects ; *Adverse Drug Reaction Reporting Systems/statistics & numerical data ; United States/epidemiology ; *Histamine H2 Antagonists/adverse effects ; *Pharmacovigilance ; *United States Food and Drug Administration ; Female ; Male ; Adult ; Middle Aged ; Aged ; Adolescent ; Young Adult ; Child ; Child, Preschool ; Drug-Related Side Effects and Adverse Reactions/epidemiology ; Databases, Factual ; Infant ; },
abstract = {Famotidine is an H2 receptor antagonist and is currently used on a large scale in gastroenterology. However, Famotidine may also cause severe toxicity to organ systems, including the blood system, digestive system, and urinary system. The objective of this study was to scientifically and systematically investigate the adverse events (AEs) of Famotidine in the real world through the FDA Adverse Event Reporting System (FAERS) database. A disproportionality analysis was used to quantify the signals of AEs associated with Famotidine in FAERS data from the first quarter of 2004 to the first quarter of 2023. The clinical features, onset time, oral and intravenous administration and severe consequences of Famotidine induced AEs were further analyzed. Among the four tests, we found several AEs that were not mentioned in the drug label. For example, abdominal pain upper, abdominal discomfort, dyspepsia, liver disorder, gastrooesophageal reflux disease, and rhabdomyolysis. These AEs are consistent with the drug instructions. Interestingly, we found several unreported AEs, such as: cerebral infarction, hypocalcaemia, hallucination, visual, hypomagnesaemia, hypoparathyroidism, diabetes insipidus, vulvovaginal candidiasis, retro-orbital neoplasm, neuroblastoma recurrent, and malignant cranial nerve neoplasm. Most of our findings are consistent with clinical observations and drug labels, and we also found possible new and unexpected AEs signals, which suggest the need for prospective clinical studies to confirm these results and explain their relationships. Our findings provide valuable evidence for further safety studies.},
}

Humans
*Famotidine/adverse effects
*Adverse Drug Reaction Reporting Systems/statistics & numerical data
United States/epidemiology
*Histamine H2 Antagonists/adverse effects
*Pharmacovigilance
*United States Food and Drug Administration
Female
Male
Adult
Middle Aged
Aged
Adolescent
Young Adult
Child
Child, Preschool
Drug-Related Side Effects and Adverse Reactions/epidemiology
Databases, Factual
Infant

@article {pmid39820572,
year = {2025},
author = {Azpiazu-Muniozguren, M and García-Martínez, M and Zabaleta, A and Antiguedad, I and Garaizar, J and Laorden, L and Martinez-Malaxetxebarria, I and Martinez-Ballesteros, I},
title = {Prokaryotic Diversity and Community Distribution in the Complex Hydrogeological System of the Añana Continental Saltern.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {171},
pmid = {39820572},
issn = {1432-184X},
support = {US19/01//Euskal Herriko Unibertsitatea/ ; US19/01//Euskal Herriko Unibertsitatea/ ; US19/01//Euskal Herriko Unibertsitatea/ ; US19/01//Euskal Herriko Unibertsitatea/ ; GIU21/021//Euskal Herriko Unibertsitatea/ ; US19/01//Euskal Herriko Unibertsitatea/ ; IT1678-22//Eusko Jaurlaritza/ ; IT1678-22//Eusko Jaurlaritza/ ; },
mesh = {*Bacteria/genetics/classification/isolation & purification ; *Archaea/genetics/classification/isolation & purification ; Spain ; *RNA, Ribosomal, 16S/genetics ; *Salinity ; *Microbiota ; *Biodiversity ; Phylogeny ; Natural Springs/microbiology ; Water Microbiology ; },
abstract = {The Añana Salt Valley (northern Spain) is a continental saltern consisting of a series of natural springs that have been used for salt production for at least 7000 years. This habitat has been relatively understudied; therefore, prokaryotic diversity was investigated through Illumina-based 16S rRNA gene sequencing to determine if the waters within the valley exhibit distinctive microbiological characteristics. Two main types of water were found in the valley: salty (approximately 200 g/L salinity) from the diapiric structure and brackish (≤ 20 g/L salinity) from shallow streams. The beta diversity indices showed that salinity was the primary factor influencing the prokaryotic distribution. However, a niche-specific influence was observed between waters of the same origin, with significant differences in the relative abundance of the ASVs. The microbiome of the saltern revealed that the archaeal domain was mainly restricted to salty waters, while the bacterial domain was ubiquitous throughout the saltern, with a notable prevalence in brackish waters. The main bacterial and archaeal phyla identified were Pseudomonadota and Halobacterota, respectively. The genus Halorubrum was abundant and widespread in salty waters, while Pseudomonas was a significant part of the prokaryote community, mainly in brackish waters. The relative abundance of the genera Haloplanus and Salinibacter increased in the salt ponds used for salt production. The taxa involved in chemoheterotrophy and fermentation were widespread, sharing the same niche. Overall, the location of this saltern on a diapiric structure favors the occurrence of waters with different origins that affect the prokaryotic distribution beyond the niche location in the valley.},
}

*Bacteria/genetics/classification/isolation & purification
*Archaea/genetics/classification/isolation & purification
Spain
*RNA, Ribosomal, 16S/genetics
*Salinity
*Microbiota
*Biodiversity
Phylogeny
Natural Springs/microbiology
Water Microbiology

@article {pmid39820498,
year = {2025},
author = {Luo, H and Xie, K and Dong, P and Zhang, Y and Ren, T and Sui, C and Ma, C and Zhao, C and Dewangan, NK and Gong, Z},
title = {Assessing the Risks of Potential Pathogens and Antibiotic Resistance Genes Among Heterogeneous Habitats in a Temperate Estuary Wetland: a Meta-analysis.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {172},
pmid = {39820498},
issn = {1432-184X},
support = {H2022011//Horizontal scientific research project (microbial-enhanced treatment of petroleum hydrocarbon pollutants: technical and engineering demonstration)/ ; H2022011//Horizontal scientific research project (microbial-enhanced treatment of petroleum hydrocarbon pollutants: technical and engineering demonstration)/ ; H2022011//Horizontal scientific research project (microbial-enhanced treatment of petroleum hydrocarbon pollutants: technical and engineering demonstration)/ ; H2022011//Horizontal scientific research project (microbial-enhanced treatment of petroleum hydrocarbon pollutants: technical and engineering demonstration)/ ; H2022011//Horizontal scientific research project (microbial-enhanced treatment of petroleum hydrocarbon pollutants: technical and engineering demonstration)/ ; H2022011//Horizontal scientific research project (microbial-enhanced treatment of petroleum hydrocarbon pollutants: technical and engineering demonstration)/ ; H2022011//Horizontal scientific research project (microbial-enhanced treatment of petroleum hydrocarbon pollutants: technical and engineering demonstration)/ ; H2022011//Horizontal scientific research project (microbial-enhanced treatment of petroleum hydrocarbon pollutants: technical and engineering demonstration)/ ; 32303039//National Natural Science Foundation of China/ ; 32303039//National Natural Science Foundation of China/ ; 32303039//National Natural Science Foundation of China/ ; 32303039//National Natural Science Foundation of China/ ; 32303039//National Natural Science Foundation of China/ ; 32303039//National Natural Science Foundation of China/ ; 32303039//National Natural Science Foundation of China/ ; 32303039//National Natural Science Foundation of China/ ; 32303039//National Natural Science Foundation of China/ ; 32303039//National Natural Science Foundation of China/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; },
mesh = {*Wetlands ; *Estuaries ; *Bacteria/genetics/classification/drug effects/isolation & purification ; Soil Microbiology ; Ecosystem ; Drug Resistance, Microbial/genetics ; Geologic Sediments/microbiology ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Water Microbiology ; Drug Resistance, Bacterial/genetics ; },
abstract = {Temperate estuary wetlands act as natural filters for microbiological contamination and have a profound impact on "One Health." However, knowledge of microbiological ecology security across the different habitats in temperate estuarine wetlands remains limited. This study employed meta-analysis to explore the characteristics of bacterial communities, potential pathogens, and antibiotic resistance genes (ARGs) across three heterogeneous habitats (water, soil, and sediment) within the Liaohe Estuary landscape. The diversity and composition of the three bacterial communities differed with biogeography, temperature, and pH, with the highest α-diversity showing a significantly negative correlation along latitude in soil. Furthermore, aminoglycosides were significantly enriched in water and soil, while dihydrofolate was more likely to be enriched in soil. The potential pathogens, Pseudoalteromonas and Planococcus, were dominant in water and sediment, while Stenotrophomonas was the dominant bacterium in soil. The network topology parameter revealed interspecific interactions within the community. PLS-PM highlights the main direct factors affecting the abundance of potential pathogens and the spread of ARGs, while temperature and pH indirectly influence these potential pathogens. This study advances our understanding of bacterial communities in estuarine wetlands, while highlighting the need for effective monitoring to mitigate the risks associated with potential pathogens and ARGs in these ecosystems.},
}

*Wetlands
*Estuaries
*Bacteria/genetics/classification/drug effects/isolation & purification
Soil Microbiology
Ecosystem
Drug Resistance, Microbial/genetics
Geologic Sediments/microbiology
Genes, Bacterial
Anti-Bacterial Agents/pharmacology
Water Microbiology
Drug Resistance, Bacterial/genetics

@article {pmid39820407,
year = {2025},
author = {Hahn, MW and Kisand, V},
title = {Editorial FEMS EC Thematic Issue Aquatic Microbial Ecology.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf005},
pmid = {39820407},
issn = {1574-6941},
}

@article {pmid39817738,
year = {2025},
author = {Wittlinger, J-P and Castejón, N and Hausmann, B and Berry, D and Schnorr, SL},
title = {Shewanella is a putative producer of polyunsaturated fatty acids in the gut soil of the composting earthworm Eisenia fetida.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0206924},
doi = {10.1128/aem.02069-24},
pmid = {39817738},
issn = {1098-5336},
abstract = {Polyunsaturated fatty acids (PUFAs) play a crucial role in aiding bacteria to adapt to extreme and stressful environments. While there is a well-established understanding of their production, accrual, and transfer within marine ecosystems, knowledge about terrestrial environments remains limited. Investigation of the intestinal microbiome of earthworms has illuminated the presence of PUFAs presumably of microbial origin, which contrasts with the surrounding soil. To comprehensively study this phenomenon, a multi-faceted approach was employed, combining fatty acid analysis with amplicon sequencing of the PfaA-KS domain of the anaerobic fatty acid synthase gene (pfa), as well as the 16S rRNA and 18S rRNA genes. This methodology was applied to scrutinize the gut microbiome of Eisenia fetida, its compost-based dietary source, and the resultant castings. This study unveiled a distinct gut soil ecosystem from input compost and output castings in fatty acid profile as well as type and abundance of organisms. 16S sequencing provided insights into the microbial composition, showing increased relative abundance of certain Pseudomonadota, including Shewanellaceae, and Planctomycetota, including Gemmataceae within the gut microbiome compared to input bulk soil compost, while Actinomycetota and Bacillota were relatively enriched compared to the casted feces. Sequencing of the PfaA-KS domain revealed amplicon sequence variants (ASVs) belonging primarily to Shewanella. Intriguingly, the 20C PUFAs were identified only in gut soil samples, though PfaA-KS sequence abundance was highest in output castings, indicating a unique metabolism occurring only in the gut. Overall, the results indicate that Shewanella can explain PUFA enrichment in the gut environment because of the pfa gene presence detected via PfaA-KS sequence data.IMPORTANCEPrior research has demonstrated that earthworm microbiomes can potentially harbor polyunsaturated fatty acids (PUFAs) that are not found within their residing soil environment. Moreover, distinct indicator species have been pinpointed for various microbial genera in earthworm microbiomes. Nevertheless, none of these studies have integrated metataxonomic and fatty acid analyses to explore the origin of PUFA synthesis in any earthworm species, with the objective of identifying the specific organisms and locations responsible for this production. This study suggests that earthworms accumulate PUFAs produced from bacteria, especially Shewanella, activated through the gut ecosystem.},
}

@article {pmid39813101,
year = {2025},
author = {Shan, Y and Hao, H and He, J and Hu, N and Liu, P and Zhan, M and Jiao, W and Yin, Y},
title = {Thermal Enhanced Electrokinetic Bacterial Transport in Porous Media.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c07954},
pmid = {39813101},
issn = {1520-5851},
abstract = {Soil bacterial communities are crucial to various ecosystem services, with significant implications for environmental processes and human health. Delivering functional bacterial strains to target locations enhances the preferred ecological features. However, the delivery process is often constrained by limited bacterial transport through low-permeability soil. Although electrokinetics breaks the bottleneck of bacterial transport in thin porous media, its efficiency remains limited. Here, we tested the hypothesis that thermal effects enhance electrokinetic transport by shifting the net force acting on the bacterium. We found that heating significantly increased electrokinetic transport by 2.75-fold at 1 V cm[-1] through porous media. Thermal enhancement mechanisms were interpreted by the heating shift of net force integrating matrix attractive and electrokinetic forces and verified by the Quartz Crystal Microbalance with Dissipation Monitoring (QCMD) observed adhesion rigidity shift. Thermal-dependent parameters liquid viscosity and dielectric constant were the primary contributors to the net force shift. Their variations reduce the attractive force and augment the electrokinetic forces, resulting in lower adhesion rigidity and enhanced bacterial transport. A mechanism-based approach interlinking electric field strength, thermal effect, and collision efficiency was established to facilitate the application of thermally enhanced electrokinetic bacterial transport. These findings provide new prospects for improving bacterial transport, hence optimizing soil ecosystem functions.},
}

@article {pmid39811355,
year = {2025},
author = {Paredes Contreras, BV and Vermelho, AB and Casanova, L and de Alencar Santos Lage, C and Spindola Vilela, CL and da Silva Cardoso, V and Pacheco Arge, LW and Cardoso-Rurr, JS and Correa, SS and Passos De Mansoldo, FR and Pinheiro Pereira Reis-Mansur, MC and Alves da Silva, E and Schultz, J and Rosado, AS},
title = {Enhanced UV-B photoprotection activity of carotenoids from the novel Arthrobacter sp. strain LAPM80 isolated from King George Island, Antarctica.},
journal = {Heliyon},
volume = {11},
number = {1},
pages = {e41400},
pmid = {39811355},
issn = {2405-8440},
abstract = {Antarctica's harsh environmental conditions, characterized by high levels of ultraviolet (UV) radiation, pose challenges for microorganisms. To survive in these extreme cold regions with heightened UV exposure, microorganisms employ various adaptive strategies, including photoprotective carotenoid synthesis. Carotenoids are garnering attention in the skin health industry because of their UV photoprotection potential, given the direct relationship between UV exposure and skin burns, and cancer. Also, there is a growing demand for natural and environmentally friendly photoprotectors, such as microbial-based products, in opposition to synthetic photoprotective agents with known adverse effects. In this study, we assessed the carotenoid-producing abilities of Actinomycetota strains from Antarctic Peninsula soils and the photoprotective carotenoid action on UV irradiation resistance. Among 20 evaluated strains, one exhibited significant carotenoid production and it was identified through genomic analysis as a likely novel Arthrobacter sp. strain, LAPM80. This strain's genome revealed the presence of genes coding for the biosynthesis of decaprenoxanthin C50 carotenoid. The LAPM80 strain exhibited enhanced resistance against UV-B irradiation, correlating with increased total carotenoid production in its stationary growth phase. Chemical characterization of the carotenoid extract identified major components as C50 carotenoids, probably decaprenoxanthin and/or sarcinaxanthin. Scanning electron microscopy revealed minimal surface changes in bacteria during carotenoid-rich phase after UV-B irradiation exposure. These findings highlight the likely ability of LAPM80 strain's C50 carotenoids to improve UV-B iiradiation resistance, indicating their potential for developing natural photoprotective compounds for the dermo-cosmetic industry.},
}

@article {pmid39808188,
year = {2025},
author = {Nguyen, MP and Lehosmaa, K and Martz, F and Koskimäki, JJ and Toth, K and Ahonen, SHK and Häggman, H and Pirttilä, AM},
title = {Dynamics of fungal endophytic communities in bilberry (Vaccinium myrtillus L.) fruits through development is shaped by host phenolic compounds.},
journal = {FEMS microbiology ecology},
volume = {101},
number = {1},
pages = {},
doi = {10.1093/femsec/fiae168},
pmid = {39808188},
issn = {1574-6941},
support = {//Finnish Cultural Foundation/ ; //European Regional Development Fund/ ; 240208//Alfred Kordelin Foundation/ ; },
mesh = {*Fruit/microbiology ; *Vaccinium myrtillus/microbiology ; *Endophytes/genetics/isolation & purification/classification/metabolism ; *Fungi/genetics/classification/isolation & purification/growth & development ; *Phenols/metabolism ; *Mycobiome ; },
abstract = {The physical and chemical properties of wild berry fruits change dramatically during development, and the ripe berries host species-specific endophytic communities. However, the development of fungal endophytic communities during berry ripening is unknown. We studied bilberries (Vaccinium myrtillus L.), valuable natural resources in northern Europe and richest sources of phenolic compounds, to characterize dynamics of the fungal communities over fruit developmental stages (raw, veraison, and ripe). Our focus was to examine the changes in the fruit phenolic compounds associated with the fungal community structure using liquid chromatography-mass spectrometry for phenolic compounds and high-throughput sequencing technology targeting the internal transcribed spacer 2 ribosomal DNA region for endophytic fungi. We found that the fungal diversity increased with the ripening stages. The fungal profile changed dramatically through fruit development, and the veraison stage was a transition stage, where the core mycobiome of fruits changed. The fungal community structure and abundance of the most dominant genera in raw and ripe stages, Monilinia and Cladosporium, respectively, were driven by the bilberry phenolic profile. We conclude that sampling time, tissue age, and phenolic compounds play important roles in the development of fruit fungal community. Moreover, phenolic compounds could be the host's strategy to recruit beneficial microbes.},
}

*Fruit/microbiology
*Vaccinium myrtillus/microbiology
*Endophytes/genetics/isolation & purification/classification/metabolism
*Fungi/genetics/classification/isolation & purification/growth & development
*Phenols/metabolism
*Mycobiome

@article {pmid39807875,
year = {2025},
author = {Schloss, PD},
title = {phylotypr: an R package for classifying DNA sequences.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0114424},
doi = {10.1128/mra.01144-24},
pmid = {39807875},
issn = {2576-098X},
abstract = {The phylotypr R package implements the popular naive Bayesian classification algorithm that is frequently used to classify 16S rRNA and other gene sequences to taxonomic lineages. A companion data package, phylotyprrefdata, also provides numerous versions of taxonomic databases from the Ribosomal Database Project, SILVA, and greengenes.},
}

@article {pmid39806487,
year = {2025},
author = {Dieppa-Colón, E and Martin, C and Kosmopoulos, JC and Anantharaman, K},
title = {Prophage-DB: a comprehensive database to explore diversity, distribution, and ecology of prophages.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {5},
pmid = {39806487},
issn = {2524-6372},
support = {T32GM135066/GM/NIGMS NIH HHS/United States ; R35GM143024/GM/NIGMS NIH HHS/United States ; R35GM143024/GM/NIGMS NIH HHS/United States ; },
abstract = {BACKGROUND: Viruses that infect prokaryotes (phages) constitute the most abundant group of biological agents, playing pivotal roles in microbial systems. They are known to impact microbial community dynamics, microbial ecology, and evolution. Efforts to document the diversity, host range, infection dynamics, and effects of bacteriophage infection on host cell metabolism are extremely underexplored. Phages are classified as virulent or temperate based on their life cycles. Temperate phages adopt the lysogenic mode of infection, where the genome integrates into the host cell genome forming a prophage. Prophages enable viral genome replication without host cell lysis, and often contribute novel and beneficial traits to the host genome. Current phage research predominantly focuses on lytic phages, leaving a significant gap in knowledge regarding prophages, including their biology, diversity, and ecological roles.

RESULTS: Here we develop and describe Prophage-DB, a database of prophages, their proteins, and associated metadata that will serve as a resource for viral genomics and microbial ecology. To create the database, we identified and characterized prophages from genomes in three of the largest publicly available databases. We applied several state-of-the-art tools in our pipeline to annotate these viruses, cluster them, taxonomically classify them, and detect their respective auxiliary metabolic genes. In total, we identify and characterize over 350,000 prophages and 35,000 auxiliary metabolic genes. Our prophage database is highly representative based on statistical results and contains prophages from a diverse set of archaeal and bacterial hosts which show a wide environmental distribution.

CONCLUSION: Given that prophages are particularly overlooked and merit increased attention due to their vital implications for microbiomes and their hosts, we created Prophage-DB to advance our understanding of prophages in microbiomes through a comprehensive characterization of prophages in publicly available genomes. We propose that Prophage-DB will serve as a valuable resource for advancing phage research, offering insights into viral taxonomy, host relationships, auxiliary metabolic genes, and environmental distribution.},
}

@article {pmid39805038,
year = {2025},
author = {Wei, L and Van Beeck, W and Hanlon, M and DiCaprio, E and Marco, ML},
title = {Lacto-Fermented Fruits and Vegetables: Bioactive Components and Effects on Human Health.},
journal = {Annual review of food science and technology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-food-052924-070656},
pmid = {39805038},
issn = {1941-1421},
abstract = {Lacto-fermented fruits and vegetables (FVs) such as kimchi, sauerkraut, and fermented olives and nonalcoholic juices have a long history as dietary staples. Herein, the production steps and microbial ecology of lacto-fermented FVs are discussed alongside findings from human and laboratory studies investigating the health benefits of these foods. Lacto-fermented FVs are enriched in bioactive compounds, including lactic and acetic acids, phenolic compounds, amino acid derivatives such as indole-3-lactic acid, phenyl-lactic acid, γ-aminobutyric acid, and bacteriocins, and beneficial live microbes. At least 11 human studies have been performed on kimchi, whereas others have been investigated in only one or two trials. Besides exploring the health benefits, it is imperative to ensure that these foods made either commercially or at home have minimal risk for foodborne illness and exposure to undesired compounds like biogenic amines. Development of starter-culture strains and production protocols can lead to lacto-fermented FVs designed for specific health benefits.},
}

@article {pmid39804671,
year = {2025},
author = {Broderick, CM and Benucci, GMN and Bachega, LR and Miller, GD and Evans, SE and Hawkes, CV},
title = {Long-term climate establishes functional legacies by altering microbial traits.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf005},
pmid = {39804671},
issn = {1751-7370},
abstract = {Long-term climate history can influence rates of soil carbon cycling but the microbial traits underlying these legacy effects are not well understood. Legacies may result if historical climate differences alter the traits of soil microbial communities, particularly those associated with carbon cycling and stress tolerance. However, it is also possible that contemporary conditions can overcome the influence of historical climate, particularly under extreme conditions. Using shotgun metagenomics, we assessed the composition of soil microbial functional genes across a mean annual precipitation gradient that previously showed evidence of strong climate legacies in soil carbon flux and extracellular enzyme activity. Sampling coincided with recovery from a regional, multi-year severe drought, allowing us to document how the strength of climate legacies varied with contemporary conditions. We found increased investment in genes associated with resource cycling with historically higher precipitation across the gradient, particularly in traits related to resource transport and complex carbon degradation. This legacy effect was strongest in seasons with the lowest soil moisture, suggesting that contemporary conditions-particularly, resource stress under water limitation-influences the strength of legacy effects. In contrast, investment in stress tolerance did not vary with historical precipitation, likely due to frequent periodic drought throughout the gradient. Differences in the relative abundance of functional genes explained over half of variation in microbial functional capacity-potential enzyme activity-more so than historical precipitation or current moisture conditions. Together, these results suggest that long-term climate can alter the functional potential of soil microbial communities, leading to legacies in carbon cycling.},
}

@article {pmid39799671,
year = {2025},
author = {Mo, Y and Abdolahpur Monikh, F and Jaffer, YD and Mugani, R and Ionescu, D and Chen, G and Yang, J and Grossart, HP},
title = {Effects of tire wear particles on freshwater bacterial-fungal community dynamics and subsequent elemental cycles using microcosms.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137062},
doi = {10.1016/j.jhazmat.2024.137062},
pmid = {39799671},
issn = {1873-3336},
abstract = {Ecological impacts of tire wear particles (TWPs) on microbial communities and biogeochemical cycles in freshwater remain largely unknown. Here, we conducted a microcosm experiment to investigate interactions between the overlying water and sediment without and with TWPs addition in a rural vs. urban lake system. Our results revealed the degree of change in microbial community diversity in water is higher than that in sediment following TWPs addition. For bacterial communities, TWPs addition changed their composition in the water, but only little in the sediment. For fungal communities, TWPs addition changed their composition both in water and sediments. Furthermore, in water, TWPs addition increased network complexity between bacteria-bacteria, fungi-fungi and bacteria-fungi in the urban system but reduced it in the rural one. In contrast, TWPs presence did not significantly change network complexity among microbial communities in the sediment of both lakes. Isotope labeling analysis uncovered that based on a short-term (6 hours) incubation experiment, TWPs addition did not significantly change carbon nor nitrogen cycling in the water. Yet, certain changes could be observed, especially in the long-term experiment (1 month), indicating that TWPs pollution has the potential to impact elemental cycling and thus ecosystem functions by altering microbial communities. Our results provide new insights into TWPs-induced ecological effects on microorganisms and potential biogeochemical consequences in a rural vs. urban lakes.},
}

@article {pmid39798462,
year = {2025},
author = {Kovarova, A and Prole, G and Farrell, ML and Maguire, M and Murphy, LC and Chueiri, A and O'Connor, L and Miliotis, G and Morris, D and Burke, LP},
title = {Antimicrobial resistant Enterobacterales of clinical importance in mute swans.},
journal = {The Science of the total environment},
volume = {961},
number = {},
pages = {178400},
doi = {10.1016/j.scitotenv.2025.178400},
pmid = {39798462},
issn = {1879-1026},
abstract = {Urban water environments, including canals, harbours and estuaries are susceptible to contamination with antimicrobials and drug-resistant bacteria through domestic and industrial wastewater discharges and storm water overflows. There is potential for wildlife using these waters to acquire and transmit drug-resistant bacteria and antimicrobial resistance genes (ARGs) of clinical importance. This study aimed to assess clinically important drug-resistant bacteria in urban waterfowl, particularly mute swans. Faecal samples were collected from 17 mute swans in the Greater Dublin Area, Ireland during July, August, October, and November of 2022. Samples were swabbed directly onto agars to select for carbapenem resistant, Extended-spectrum Beta-lactamase (ESBL)-producing, ciprofloxacin resistant and colistin resistant bacteria. Isolates identified by MALDI-TOF as Enterobacterales were tested for susceptibility to a panel of 16 antimicrobials and real-time PCR was employed to detect cefotaximase and carbapenemase genes (CRGs). Drug-resistant isolates were characterised by Whole Genome Sequencing (WGS), including long read sequencing for carbapenemase and mobile colistin resistance (mcr) gene-producing Enterobacterales isolates. Eleven of seventeen (65 %) swan samples were positive for the resistant organism(s) (n = 35), comprising Escherichia coli (n = 32; 82 %) and other Enterobacterales (n = 3). Twenty E. coli (63 %) produced ESBL, with 16/20 (80 %) identified as positive for blaCTX-M-group 1 enzymes, comprising CTX-M-15 (n = 13), CTX-M-55 (n = 2) and CTX-M-1 (n = 1) and 4/20 (20 %) positive for blaCTX-M-group 9 enzymes CTX-M-27 (n = 2) and CTX-M-9 (n = 2). Three E. coli isolates were phenotypically ertapenem resistant, one of which was an ST4450 isolate which carried plasmid encoded blaOXA-181 and blaCMY-141 with blaCTX-M-15 identified chromosomally. One colistin resistant E. coli bore the mcr-1 gene chromosomally. Bioinformatic analysis revealed high-risk pathogenic ESBL E. coli clones including ST38 (n = 3), ST69 (n = 3), and ST131 (n = 2). The study indicates mute swans are a reservoir for drug-resistant Enterobacterales and ARGs of clinical importance and may be a useful sentinel species for antimicrobial resistance (AMR) surveillance in wildlife.},
}

@article {pmid39798088,
year = {2025},
author = {Stefanic, P and Stare, E and Floccari, VA and Kovac, J and Hertel, R and Rocha, U and Kovács, ÁT and Mandić-Mulec, I and Strube, ML and Dragoš, A},
title = {Ecology of prophage-like elements in Bacillus subtilis at global and local geographical scales.},
journal = {Cell reports},
volume = {44},
number = {1},
pages = {115197},
doi = {10.1016/j.celrep.2024.115197},
pmid = {39798088},
issn = {2211-1247},
abstract = {Prophages constitute a substantial portion of bacterial genomes, yet their effects on hosts remain poorly understood. We examine the abundance, distribution, and activity of prophages in Bacillus subtilis using computational and laboratory analyses. Genome sequences from the NCBI database and riverbank soil isolates reveal prophages primarily related to mobile genetic elements in laboratory strains. Distinct and previously unknown prophages in local isolates prompt an investigation into factors shaping prophage presence, with phylogenetic relatedness predicting the prophage repertoire slightly better than geographical origin. Data also show that prophages exhibit strong co-occurrence and exclusion patterns within genomes. Laboratory experiments indicate that most predicted prophages are cryptic, as they are not induced under DNA-damaging conditions. Importantly, stress responses increase with the number of predicted prophages, suggesting their influence on host physiology. This study highlights the diversity, integration patterns, and potential roles of prophages in B. subtilis, shedding light on bacterial genome evolution and phage-host dynamics.},
}

@article {pmid39797436,
year = {2025},
author = {Shopen Gochev, C and Demory, D and Lopes Dos Santos, A and Carlson, MCG and Gutiérrez-Rodríguez, A and Weitz, JS and Lindell, D},
title = {Cold Surface Waters of the Sub-Antarctic Pacific Ocean Support High Cyanophage Abundances and Infection Levels.},
journal = {Environmental microbiology},
volume = {27},
number = {1},
pages = {e70031},
doi = {10.1111/1462-2920.70031},
pmid = {39797436},
issn = {1462-2920},
support = {2679/20//Israel Science Foundation/ ; 639682//Simons Foundation/ ; 721231//Simons Foundation/ ; 721254//Simons Foundation/ ; },
mesh = {Pacific Ocean ; *Seawater/virology/microbiology ; *Bacteriophages/isolation & purification ; *Cold Temperature ; Cyanobacteria/virology ; Synechococcus/virology ; Prochlorococcus/virology ; Antarctic Regions ; },
abstract = {Cyanobacterial distributions are shaped by abiotic factors including temperature, light and nutrient availability as well as biotic factors such as grazing and viral infection. In this study, we investigated the abundances of T4-like and T7-like cyanophages and the extent of picocyanobacterial infection in the cold, high-nutrient-low-chlorophyll, sub-Antarctic waters of the southwest Pacific Ocean during austral spring. Synechococcus was the dominant picocyanobacterium, ranging from 4.7 × 10[3] to 1.2 × 10[5] cells∙mL[-1], while Prochlorococcus abundances were relatively low overall, ranging from 1.0 × 10[3] to 3.9 × 10[4] cells∙mL[-1]. Using taxon-specific, single-virus and single-cell polony methods, we found that cyanophages were on average 15-fold, and up to 50-fold, more abundant than cyanobacteria in these waters. T4-like cyanophages (ranging from 1.7 × 10[5] to 6.5 × 10[5] phage·mL[-1]) were 2.7-fold more abundant than T7-like cyanophages (ranging from 3.1 × 10[4] to 2.8 × 10[5] phage·mL[-1]). Picocyanobacteria were primarily infected by T4-like cyanophages with more Synechococcus (4.8%-12.1%) infected than Prochlorococcus (2.5%-6.2%), whereas T7-like cyanophages infected less than 1% of both genera. These infection levels translated to daily mortality in the range of 5.7%-26.2% and 2.9%-14.3% of the standing stock of Synechococcus and Prochlorococcus, respectively. Our findings suggest that T4-like cyanophages are significant agents of cyanobacterial mortality in the cold, low-iron, sub-Antarctic waters of the South Pacific Ocean.},
}

Pacific Ocean
*Seawater/virology/microbiology
*Bacteriophages/isolation & purification
*Cold Temperature
Cyanobacteria/virology
Synechococcus/virology
Prochlorococcus/virology
Antarctic Regions

@article {pmid39794865,
year = {2025},
author = {Passarelli-Araujo, H and Venancio, TM and Hanage, WP},
title = {Relating ecological diversity to genetic discontinuity across bacterial species.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {8},
pmid = {39794865},
issn = {1474-760X},
mesh = {*Genome, Bacterial ; *Bacteria/genetics/classification ; Genetic Variation ; Phylogeny ; Mycobacterium tuberculosis/genetics ; Machine Learning ; Evolution, Molecular ; Biodiversity ; },
abstract = {BACKGROUND: Genetic discontinuity represents abrupt breaks in genomic identity among species. Advances in genome sequencing have enhanced our ability to track and characterize genetic discontinuity in bacterial populations. However, exploring the degree to which bacterial diversity exists as a continuum or sorted into discrete and readily defined species remains a challenge in microbial ecology. Here, we aim to quantify the genetic discontinuity (δ) and investigate how this metric is related to ecology.

RESULTS: We harness a dataset comprising 210,129 genomes to systematically explore genetic discontinuity patterns across several distantly related species, finding clear breakpoints which vary depending on the taxa in question. By delving into pangenome characteristics, we uncover a significant association between pangenome saturation and genetic discontinuity. Closed pangenomes are associated with more pronounced breaks, exemplified by Mycobacterium tuberculosis. Additionally, through a machine learning approach, we detect key features such as gene conservation patterns and functional annotations that significantly impact genetic discontinuity prediction.

CONCLUSIONS: Our study clarifies bacterial genetic patterns and their ecological impacts, enhancing the delineation of species boundaries and deepening our understanding of microbial diversity.},
}

*Genome, Bacterial
*Bacteria/genetics/classification
Genetic Variation
Phylogeny
Mycobacterium tuberculosis/genetics
Machine Learning
Evolution, Molecular
Biodiversity

@article {pmid39794276,
year = {2025},
author = {Tang, L and Manefield, M},
title = {Aeration promotes Proteobacteria over Firmicutes in macerated food waste resulting in superior anaerobic digestion efficiency.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf001},
pmid = {39794276},
issn = {1574-6968},
abstract = {Aeration is a common pretreatment method to enhance biogas production via anaerobic digestion of waste organic feedstocks such as unused food. While impacts on downstream anaerobic digestion have been intensively investigated, the consequence of aeration on the microbial community in food waste has not been characterised. Food waste has a low pH resulting from the dominance of lactic acid bacteria within the Firmicutes phylum. This excludes other phylotypes with a higher potential to hydrolyse complex biopolymers in food waste. In this study we reveal that aeration of macerated food waste results in a dramatic shift away from Firmicutes towards dominance of Proteobacteria that are better known for extracellular enzyme production. Given that hydrolysis is the rate limiting step in anaerobic digestion, this explains why aeration improves the efficiency of biogas production from food waste. The discovery that Proteobacteria dominate microbial communities in aerated food waste opens up opportunities to manipulate extracellular enzyme production through gene expression mechanisms common among Proteobacteria such as quorum sensing.},
}

@article {pmid39792461,
year = {2025},
author = {Tan, G and LeCates, CN and Simpson, A and Holtzen, S and Parris, DJ and Stewart, FJ and Stockton, A and , },
title = {Amplicon Sequencing Reveals Diversity in Spatially Separated Microbial Communities in the Icelandic Mars Analog Environment Mælifellssandur.},
journal = {Astrobiology},
volume = {},
number = {},
pages = {},
doi = {10.1089/ast.2023.0124},
pmid = {39792461},
issn = {1557-8070},
abstract = {Exploration missions to Mars rely on landers or rovers to perform multiple analyses over geographically small sampling regions, while landing site selection is done using large-scale but low-resolution remote-sensing data. Utilizing Earth analog environments to estimate small-scale spatial and temporal variation in key geochemical signatures and biosignatures will help mission designers ensure future sampling strategies meet mission science goals. Icelandic lava fields can serve as Mars analog sites due to conditions that include low nutrient availability, temperature extremes, desiccation, and isolation from anthropogenic contamination. This work reports analysis of samples collected using methods analogous to those of planetary missions to characterize microbial communities at different spatial scales in Mælifellssandur, Iceland, an environment with homogeneity at "remote imaging" resolution (overall temperature, apparent moisture content, and regolith grain size). Although microbial richness did not vary significantly among samples, the phylogenetic composition of the sediment microbiome differed significantly among sites separated by 100 m, which suggests distinct microbial signatures despite apparent homogeneity from remote observations. This work highlights the importance of considering microenvironments in future life-detection missions to extraterrestrial planetary bodies.},
}

@article {pmid39792290,
year = {2025},
author = {Foffi, R and Brumley, DR and Peaudecerf, FJ and Stocker, R and Słomka, J},
title = {Slower swimming promotes chemotactic encounters between bacteria and small phytoplankton.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {2},
pages = {e2411074122},
doi = {10.1073/pnas.2411074122},
pmid = {39792290},
issn = {1091-6490},
support = {PZ00P2_202188//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; ANR-22-CPJ2-0015-01//Agence Nationale de la Recherche (ANR)/ ; GBMF9197//Gordon and Betty Moore Foundation (GBMF)/ ; 542395FY22//Simons Foundation (SF)/ ; 205321_207488//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; CRSII5-186422//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; 51NF40_180575//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; 955910//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; },
mesh = {*Phytoplankton/physiology ; *Chemotaxis/physiology ; Bacteria/metabolism ; Bacterial Physiological Phenomena ; Models, Biological ; },
abstract = {Chemotaxis enables marine bacteria to increase encounters with phytoplankton cells by reducing their search times, provided that bacteria detect noisy chemical gradients around phytoplankton. Gradient detection depends on bacterial phenotypes and phytoplankton size: large phytoplankton produce spatially extended but shallow gradients, whereas small phytoplankton produce steeper but spatially more confined gradients. To date, it has remained unclear how phytoplankton size and bacterial swimming speed affect bacteria's gradient detection ability and search times for phytoplankton. Here, we compute an upper bound on the increase in bacterial encounter rate with phytoplankton due to chemotaxis over random motility alone. We find that chemotaxis can substantially decrease search times for small phytoplankton, but this advantage is highly sensitive to variations in bacterial phenotypes or phytoplankton leakage rates. By contrast, chemotaxis toward large phytoplankton cells reduces the search time more modestly, but this benefit is more robust to variations in search or environmental parameters. Applying our findings to marine phytoplankton communities, we find that, in productive waters, chemotaxis toward phytoplankton smaller than 2 μm provides little to no benefit, but can decrease average search times for large phytoplankton (∼20 μm) from 2 wk to 2 d, an advantage that is robust to variations and favors bacteria with higher swimming speeds. By contrast, in oligotrophic waters, chemotaxis can reduce search times for picophytoplankton (∼1 μm) up to 10-fold, from a week to half a day, but only for bacteria with low swimming speeds and long sensory timescales. This asymmetry may promote the coexistence of diverse search phenotypes in marine bacterial populations.},
}

*Phytoplankton/physiology
*Chemotaxis/physiology
Bacteria/metabolism
Bacterial Physiological Phenomena
Models, Biological

@article {pmid39789151,
year = {2025},
author = {Frasca, S and Alabiso, A and D'Andrea, MM and Migliore, L},
title = {Uncovering the Fungal Community Composition of Alive and Dead Posidonia oceanica Matte.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {170},
pmid = {39789151},
issn = {1432-184X},
mesh = {*Alismatales/microbiology ; Ascomycota/genetics/classification/metabolism/growth & development ; Mycobiome ; Fungi/genetics/classification/metabolism/isolation & purification ; DNA, Fungal/genetics ; Seawater/microbiology ; Biodegradation, Environmental ; Geologic Sediments/microbiology ; Phylogeny ; },
abstract = {Posidonia oceanica retains a large amount of carbon within its belowground recalcitrant structure, the 'matte,' which is characterized by low oxygen availability and biodegradation. Fungi may play a pivotal role in carbon sequestration within the matte, even if little/no information is available. To fill this gap, we profiled fungal communities from the upper and lower layers of alive and dead matte, by using an ITS2-5.8S rDNA metabarcoding approach. The study was conducted in a shallow coastal stretch of the Aegean Sea (Crete). Then, 184 operational taxonomic units were identified, predominantly belonging to Ascomycota, in alive and dead matte. Nevertheless, their composition significantly differed: the host-specific Posidoniomyces atricolor was dominant in alive but not in dead matte, while fast-growing saprotrophs, potentially accelerating the decomposition rate, increased in dead matte. These findings lay the groundwork for future investigations on the possible increase of biodegradation under the changing environmental conditions.},
}

*Alismatales/microbiology
Ascomycota/genetics/classification/metabolism/growth & development
Mycobiome
Fungi/genetics/classification/metabolism/isolation & purification
DNA, Fungal/genetics
Seawater/microbiology
Biodegradation, Environmental
Geologic Sediments/microbiology
Phylogeny

@article {pmid39788196,
year = {2025},
author = {Kim, YT and Huang, YP and Ozturk, G and Hahn, J and Taha, AY and Wang, A and Barile, D and Mills, DA},
title = {Characterization of Bifidobacterium bifidum growth and metabolism on whey protein phospholipid concentrate.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2024-25885},
pmid = {39788196},
issn = {1525-3198},
abstract = {Whey protein phospholipid concentrate (WPPC) is a co-product generated during the manufacture of whey protein isolate. WPPC is depleted of simple sugars but contains numerous glycoconjugates embedded in the milk fat globule membrane, suggesting this fraction may serve as a carbon source for growth of bifidobacteria commonly enriched in breast fed infants. In this work, we demonstrate that WPPC can serve as a sole carbon source for the growth of Bifidobacterium bifidum, a species common to the breastfed infant and routinely used as a probiotic. Growth on WPPC fractions resulted in expression of key extracellular glycosyl hydrolases in B. bifidum associated with the catabolism of glycoproteins. Interestingly, this included induction of fucosidase genes in B. bifidum linked to catabolism of fucosylated human milk oligosaccharides even though the WPPC glycan possesses little fucose. Additional growth studies revealed that WPPC-glycan components N-acetylglucosamine or N-acetylgalactosamine were required for pre-activation of B. bifidum toward rapid growth on the fucosylated human milk oligosaccharides. Growth on WPPC fractions also resulted in expression of extracellular sialidases in B. bifidum which promoted a consistent release of sialic acid, a well-known component of bovine milk oligosaccharides and glycoconjugates with potential impacts on gut microbial ecology and host cognition. These studies suggest WPPC may serve as a promising bioactive component to facilitate probiotic activity for use in infant formulas and other synbiotic applications.},
}

@article {pmid39787750,
year = {2025},
author = {Zhang, S and Wang, J and Liu, Z and Xia, X and Wu, X and Li, X and Liu, Y and Xu, Z and Marzadri, A and McDowell, WH and Cai, Y and Yang, Z},
title = {Temperature has an enhanced role in sediment N2O and N2 fluxes in wider rivers.},
journal = {Water research},
volume = {273},
number = {},
pages = {123095},
doi = {10.1016/j.watres.2025.123095},
pmid = {39787750},
issn = {1879-2448},
abstract = {Riverine N2O and N2 fluxes, key components of the global nitrogen budget, are known to be influenced by river size (often represented by average river width), yet the specific mechanisms behind these effects remain unclear. This study examined how environmental and microbial factors influenced sediment N2O and N2 fluxes across rivers with varying widths (2.8 to 2,000 m) in China. Sediment acted as sources of both N2O and N2 emissions, with both N2 (0.2 to 20.8 mmol m[-2] d[-1]) and N2O fluxes (0.7-54.2 μmol m[-2] d[-1]) decreasing significantly as river width increased. N2 fluxes were positively correlated with denitrifying bacterial abundance, whereas N2O fluxes, when normalized by the abundance of denitrifying bacteria, were negatively correlated with the abundance of N2O-reducing microbes. Water physicochemical factors, particularly temperature and nitrate, were more important drivers of these fluxes than sediment factors. Nitrate significantly increased denitrifying bacterial abundance, whereas higher temperatures enhanced cell-specific activity. Lower N2O and N2 emissions in wider rivers were attributed to decreased denitrifying microbial abundance and lower denitrification rates, in addition to the commonly assumed reduction in exogenous N2O and N2 inputs. Rolling regression analysis showed that nitrate concentration had a stronger effect on sediment N2O and N2 fluxes in narrower rivers, whereas temperature was more influential in wider rivers. This difference is attributed to more stable nitrate concentrations and decreased nitrogen removal efficiency in wider rivers, while temperature variation remained consistent across all river widths. Beyond sediments, temperature had a greater effect on excess N2O concentrations than nitrate in the overlying water of wider rivers (>165 m), highlighting its broader impact. This study provides new biogeochemical insights into how river width influences sediment N2O and N2 fluxes and highlights the importance of incorporating temperature into flux predictions, particularly for wider rivers.},
}

@article {pmid39786593,
year = {2025},
author = {Xu, Y and Liang, J and Qin, L and Niu, T and Liang, Z and Li, Z and Chen, B and Zhou, J and Yu, K},
title = {The Dynamics of Symbiodiniaceae and Photosynthetic Bacteria Under High-Temperature Conditions.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {169},
pmid = {39786593},
issn = {1432-184X},
support = {42090041//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 2018GXNSFAA281328//Guangxi scientific projects/ ; 2018GXNSFAA281328//Guangxi scientific projects/ ; 2018GXNSFAA281328//Guangxi scientific projects/ ; 2018GXNSFAA281328//Guangxi scientific projects/ ; 2018GXNSFAA281328//Guangxi scientific projects/ ; 2018GXNSFAA281328//Guangxi scientific projects/ ; },
mesh = {*Photosynthesis ; *Symbiosis ; *Anthozoa/microbiology/physiology ; China ; *Hot Temperature ; *Dinoflagellida/physiology ; Animals ; *Seasons ; Bacteria/classification/metabolism/genetics ; Cyanobacteria/physiology ; Chlorophyll A/metabolism ; },
abstract = {Coral thermal tolerance is intimately linked to their symbiotic relationships with photosynthetic microorganisms. However, the potential compensatory role of symbiotic photosynthetic bacteria in supporting Symbiodiniaceae photosynthesis under extreme summer temperatures remains largely unexplored. Here, we examined the seasonal variations in Symbiodiniaceae and photosynthetic bacterial community structures in Pavona decussata corals from Weizhou Island, Beibu Gulf, China, with particular emphasis on the role of photosynthetic bacteria under elevated temperature conditions. Our results revealed that Symbiodiniaceae density and Chlorophyll a concentration were lowest during the summer and highest in the winter. Notably, the summer bacterial community was predominately composed of the proteorhodopsin bacterium BD 1-7 _clade, alongside a significant increase in Cyanobacteria, particularly Synechococcus_CC9902 and Cyanobium_PCC-6307, which represented 61.85% and 31.48% of the total Cyanobacterial community, respectively. In vitro experiments demonstrated that Cyanobacteria significantly enhanced Symbiodiniaceae photosynthetic efficiency under high-temperature conditions. These findings suggest that the increased abundance of photosynthetic bacteria during summer may mitigate the adverse physiological effects of reduced Symbiodiniaceae density, thereby contributing to coral stability. Our study highlights a potential synergistic interaction between Symbiodiniaceae and photosynthetic bacteria, emphasizing the importance of understanding these dynamic interactions in sustaining coral resilience against environmental stress, although further research is necessary to establish their role in preventing coral bleaching.},
}

*Photosynthesis
*Symbiosis
*Anthozoa/microbiology/physiology
China
*Hot Temperature
*Dinoflagellida/physiology
Animals
*Seasons
Bacteria/classification/metabolism/genetics
Cyanobacteria/physiology
Chlorophyll A/metabolism

@article {pmid39786575,
year = {2024},
author = {McNeal, R and Wells, JD and Tomberlin, JK},
title = {Bernard Greenberg: a legacy in medical, veterinary, and forensic entomology.},
journal = {Journal of medical entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jme/tjae158},
pmid = {39786575},
issn = {1938-2928},
abstract = {Bernard Greenberg was a ground-breaking scientist in the worlds of medical-veterinary and forensic entomology, studying the ability of flies to serve as a vector of human and other vertebrate pathogens. His work also extended beyond these topics, creating key studies on flies and their associated microbial ecology. These efforts led to numerous research publications and two books on flies and their associated microorganisms. Greenberg served a pioneering role in establishing the field of forensic entomology in the USA later in his career, publishing key papers and a book that are highly cited to this day. We present a review of Dr Greenberg's scientific contributions concerning flies and disease, insect/microbe interactions, and insects as forensic indicators.},
}

@article {pmid39777550,
year = {2025},
author = {Byers, AK and Wakelin, SA and Condron, L and Black, A},
title = {Land Use Change Disrupts the Network Complexity and Stability of Soil Microbial Carbon Cycling Genes Across an Agricultural Mosaic Landscape.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {167},
pmid = {39777550},
issn = {1432-184X},
mesh = {*Soil Microbiology ; *Carbon Cycle ; New Zealand ; *Agriculture ; *Soil/chemistry ; *Microbiota ; *Bacteria/genetics/classification/metabolism ; Carbon/metabolism ; Gene Regulatory Networks ; Forests ; Ecosystem ; },
abstract = {To understand the effects of agricultural land use change and management on soil carbon (C) cycling, it is crucial to examine how these changes can influence microbial soil C cycling. Network analysis can offer insights into the structure, complexity, and stability of the soil microbiome in response to environmental disturbances, including land use change. Using SparCC-based co-occurrence networks, we studied how land use change impacts the connectivity, complexity, and stability of microbial C-cycling gene networks across an agricultural mosaic landscape in Canterbury, New Zealand. The most densely connected networks were found in land uses that were under the most intensive agricultural management, or under naturally regenerating vegetation. The microbial C-cycling gene networks from both land uses presented high network connectivity, low modularity, and a low proportion of negative gene interactions. In contrast, microbial C-cycling genes from native forests, which had the most stable and undisturbed plant cover, had the lowest network connectivity, highest modularity, and a greater proportion of negative gene interactions. Although the differences in total soil C content between land uses were small, the large effects of land use on the network structure of microbial C-cycling genes may have important implications for long-term microbial soil C cycling. Furthermore, this research highlights the value of using microbial network analysis to study the metabolic gene interactions shaping the functional structure of soil microbial communities in a manner not typically captured by more traditional forms of microbial diversity analysis.},
}

*Soil Microbiology
*Carbon Cycle
New Zealand
*Agriculture
*Soil/chemistry
*Microbiota
*Bacteria/genetics/classification/metabolism
Carbon/metabolism
Gene Regulatory Networks
Forests
Ecosystem

@article {pmid39779689,
year = {2025},
author = {Cottin, A and Dequiedt, S and Djemiel, C and Prévost-Bouré, NC and Tripied, J and Lelièvre, M and Terreau, L and Régnier, T and Karimi, B and Jolivet, C and Bispo, A and Saby, N and Maron, PA and Ranjard, L and Terrat, S},
title = {Harmonized Datasets of microbiological parameters from a French national-scale soil monitoring survey.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {34},
pmid = {39779689},
issn = {2052-4463},
support = {2021PRE00370//Conseil régional de Bourgogne-Franche-Comté (Regional Council of Burgundy)/ ; },
abstract = {Microbiological datasets and associated environmental parameters from the French soil quality monitoring network (RMQS) offer an opportunity for long-term and large-scale soil quality monitoring. Soils supply important ecosystem services e.g. carbon dynamics/storage or mineral element recycling, supported by the soil microbial diversity (bacteria, archaea and fungi). Based on the 2,240 sites of the 2000-2015 RMQS, molecular tools were applied to characterize soil microbiota. Soil DNA analysis yielded molecular microbial biomass for 2,168 sites, bacterial and fungal qPCR for 2,073 sites, and high-throughput amplicon sequencing of targeted 16S rDNA bacterial and archaeal genes for 1,842 sites. All these datasets were partially or completely unavailable, so raw results files from RMQS microbiological studies were harmonized and published in a Dataverse repository to facilitate their reusability. Altogether, these datasets allow for in-depth studies of soil microbial ecology and biogeography, and will be updated with fungal datasets and the second currently ongoing monitoring campaign (2016-2027).},
}

@article {pmid39779584,
year = {2025},
author = {Roy, A and Ray, S},
title = {Molecular Evolution of Paralogous Cold Shock Proteins in E. coli: A Study of Asymmetric Divergence and Protein Functional Networks.},
journal = {Molecular biotechnology},
volume = {},
number = {},
pages = {},
pmid = {39779584},
issn = {1559-0305},
abstract = {Nine homologous Cold Shock Proteins (Csps) have been recognized in the E.coli Cold Shock Domain gene family. These Csps function as RNA chaperones. This study aims to establish the evolutionary relationships among these genes by identifying and classifying their paralogous counterparts. It focuses on the physicochemical, structural, and functional analysis of the genes to explore the phylogeny of the Csp gene family. Computational tools were employed for protein molecular modeling, conformational analysis, functional studies, and duplication-divergence assessments. The research also examined amino acid conservation, protein mutations, domain-motif patterns, and evolutionary residue communities to better understand residual interactions, evolutionary coupling, and co-evolution. H33, M5, W11 and F53 residues were highly conserved within the protein family. It was further seen that residues M5, G17, G58, G61, P62, A64, V67 were intolerant to any kind of mutation whereas G3, D40, G41, Y42, S44, T54, T68, S69 were most tolerable towards substitutions. The study of residue communities displayed that the strongest residue coupling was observed in N13, F18, S27, F31, and W11. It was observed that all the gene pairs except CspF/CspH had new motifs generated over time. It was ascertained that all the gene pairs underwent asymmetric expression divergence after duplication. The Ka/ Ks ratio also revealed that all residues undertook neutral and purifying selection pressure. New functions were seen to develop in gene pairs evident from generation of new motifs. The discovery of new motifs and functions in Csps highlights their adaptive versatility, crucial for E. coli's resilience to environmental stressors and valuable for understanding bacterial stress response mechanisms. These findings will pave the way for future investigations into Csp evolution, with potential applications in microbial ecology and antimicrobial strategy development.},
}

@article {pmid39779304,
year = {2025},
author = {Diakaki, M and Jimenez, BA and de Lange, E and Butterbach, P and van der Heijden, L and Köhl, J and de Boer, W and Postma, J},
title = {Spinach Seed Microbiome Characteristics Linked to Suppressiveness Against Globisporangium ultimum Damping-Off.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf004},
pmid = {39779304},
issn = {1574-6941},
abstract = {Recently we demonstrated that the seed microbiome of certain spinach (Spinacia oleracea) seed lots can confer disease suppression against Globisporangium ultimum damping-off (previously known as Pythium ultimum). We hypothesised that differences in the microbial community composition of spinach seed lots correlate with the levels of damping-off suppressiveness of each seed lot. Here, we show that a large proportion of variance in seed-associated bacterial (16S) and fungal (ITS1) amplicon sequences was explained by seed lot identity, while 9.8% of bacterial and 7.1% of fungal community variance correlated with disease suppression. More specifically, a higher relative abundance of basidiomycetous dimorphic yeasts such as Vishniacozyma, Filobasidium and Papiliotrema and of the bacterial genus Massilia was a key feature of suppressive seed microbiomes. We suggest that the abundance of these genera is indicative of seed lot suppressive potential. Seed processing and treatment can become more targeted with indicator taxa being used to evaluate the presence of beneficial seed-associated microbial functions. This process in turn could contribute to the sustainable management of seedling diseases. Finally, this study highlights the ubiquity of yeasts in spinach seed microbiota and their potential beneficial roles for seed health.},
}

@article {pmid39777152,
year = {2024},
author = {Liao, H and Wang, X and Wang, X and Zhang, M and Zhang, Y and Huang, S and Wang, H and Jin, H and Wang, J and Li, X and Yan, J and Schubert, T and Löffler, FE and Yang, Y},
title = {Organohalide respiration: retrospective and perspective through bibliometrics.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1490849},
doi = {10.3389/fmicb.2024.1490849},
pmid = {39777152},
issn = {1664-302X},
abstract = {Organohalide-respiring bacteria (OHRB) play a pivotal role in the transformation of organohalogens in diverse environments. This bibliometric analysis provides a timely overview of OHRB research trends and identifies knowledge gaps. Publication numbers have steadily increased since the process was discovered in 1982, with fluctuations in total citations and average citations per publication. The past decade witnessed a peak in publications, underscoring heightened research activity and extensive collaboration. Thematic analysis identified two primary research foci: mechanistic exploration of OHRB and their interplay with environmental factors. Future research should prioritize elucidating the roles OHRB's play in biogeochemical cycling, utilizing synthetic biology tools for enhanced biotransformation, deciphering OHRB's ecological interactions, unraveling their evolutionary pathways, and investigating dehalogenation capabilities in other microorganisms, including archaea. These research directions promise to advance our understanding of microbially-driven organohalide transformations, microbial ecology, and genetic engineering potential, ultimately informing natural organohalide cycling and environmental management strategies.},
}

@article {pmid39775407,
year = {2025},
author = {Sun, X and Armstrong, M and Moradi, A and Bhattacharya, R and Antão-Geraldes, AM and Munthali, E and Grossart, HP and Matsuzaki, SS and Kangur, K and Dunalska, JA and Stockwell, JD and Borre, L},
title = {Impacts of climate-induced drought on lake and reservoir biodiversity and ecosystem services: A review.},
journal = {Ambio},
volume = {},
number = {},
pages = {},
pmid = {39775407},
issn = {1654-7209},
support = {RGPIN-2019-04315//Natural Sciences and Engineering Research Council of Canada/ ; 1638679//U.S. National Science Foundation (NSF) Macrosystems Biology Program/ ; 722518//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; 722518//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; 722518//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; LA/P/0007/2020//SusTEC/ ; PRG 1266//Estonian Research Council/ ; JPMEERF20232002//Environmental Restoration and Conservation Agency/ ; 1702991//National Science Foundation/ ; UIDB/00690/2020//CIMO/ ; UIDP/00690/2020//CIMO/ ; PIDDAC//Fundação para a Ciência e a Tecnologia/ ; },
abstract = {Intensifying extreme droughts are altering lentic ecosystems and disrupting services provisioning. Unfortunately, drought research often lacks a holistic and intersectoral consideration of drought impacts, which can limit relevance of the insights for adaptive management. This literature review evaluated the current state of lake and reservoir extreme drought research in relation to biodiversity and three ecosystem services. The study findings demonstrated that few articles linked or discussed drought implications with one or more ecosystem services, instead focusing primarily on biodiversity. Drought effects on biodiversity varied among species and taxonomic groups. In the limited literature that included ecosystem service provisioning, droughts had a general negative effect. Drinking water supply can decrease and become more costly. Decreasing water flow and volume can reduce hydropower generation. Degraded water quality can also impact recreation. Future intersectoral collaborations and research on intensifying droughts should support adaptive management efforts in mitigating drought impacts.},
}

@article {pmid39774713,
year = {2025},
author = {Dobrzyński, J and Kulkova, I and Jakubowska, Z and Wróbel, B},
title = {Non-native PGPB Consortium Altered the Rhizobacterial Community and Slightly Stimulated the Growth of Winter Oilseed Rape (Brassica napus L.) Under Field Conditions.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {168},
pmid = {39774713},
issn = {1432-184X},
support = {DDD.6509.00267.2022.15.//The research was funded by the European Agricultural Fund under the Rural Development Programme for 2014-2020/ ; DDD.6509.00267.2022.15.//The research was funded by the European Agricultural Fund under the Rural Development Programme for 2014-2020/ ; DDD.6509.00267.2022.15.//The research was funded by the European Agricultural Fund under the Rural Development Programme for 2014-2020/ ; DDD.6509.00267.2022.15.//The research was funded by the European Agricultural Fund under the Rural Development Programme for 2014-2020/ ; },
mesh = {*Brassica napus/microbiology/growth & development ; *Soil Microbiology ; Pseudomonas/growth & development/metabolism ; Plant Roots/microbiology/growth & development ; Phosphorus/metabolism ; Bacteria/classification/genetics/isolation & purification/growth & development ; Nitrogen/metabolism ; Rhizosphere ; Microbial Consortia ; Indoleacetic Acids/metabolism ; Microbiota ; Azotobacter/growth & development/metabolism ; },
abstract = {Plant growth-promoting bacteria (PGPB) are among the most promising alternatives to mineral fertilizers. However, little is known about the effects of applied bacteria on the native microbiota, including the rhizobacterial community, which plays a crucial role in bacteria-plant interactions. Therefore, this study is aimed at assessing the effects of PGPB not only on plants but also, importantly, on the native rhizobacterial community of winter oilseed rape. The bacterial consortium, consisting of Pseudomonas sp. KR227 and Azotobacter PBC1 (P2A), slightly promoted plant growth, increasing the root weight by 21.95% and seed yield by 18.94%. This likely results from its ability to produce indole-3-acetic acid (IAA), solubilize phosphorus, and fix nitrogen, as indicated by a 35.76% increase in N-NH4 and a 35.05% increase in available phosphorus (AP). The introduced PGPB altered the rhizobacterial community of rapeseed, increasing the relative abundance of the phylum Proteobacteria and the genus Pseudomonas while decreasing the relative abundance of phylum Verrucomicrobiota (3 weeks after inoculation). Moreover, Proteobacteria were positively correlated with AP, while Verrucomicrobiota were correlated with N-NH4. At the genus level, Flavobacterium and Pseudomonas were positively correlated with AP, whereas Candidatus Udaeobacter showed a positive correlation with N-NH4 and a negative correlation with pH. Importantly, the P2A consortium did not significantly affect the diversity of native rapeseed rhizobacteria. These findings suggest that the tested P2A consortium has potential as a biostimulant in rapeseed cultivation.},
}

*Brassica napus/microbiology/growth & development
*Soil Microbiology
Pseudomonas/growth & development/metabolism
Plant Roots/microbiology/growth & development
Phosphorus/metabolism
Bacteria/classification/genetics/isolation & purification/growth & development
Nitrogen/metabolism
Rhizosphere
Microbial Consortia
Indoleacetic Acids/metabolism
Microbiota
Azotobacter/growth & development/metabolism

@article {pmid39774673,
year = {2025},
author = {Chen, SC and Chen, S and Musat, N and Kümmel, S and Ji, J and Lund, MB and Gilbert, A and Lechtenfeld, OJ and Richnow, HH and Musat, F},
title = {Author Correction: Back flux during anaerobic oxidation of butane support archaea-mediated alkanogenesis.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {453},
doi = {10.1038/s41467-024-55458-6},
pmid = {39774673},
issn = {2041-1723},
}

@article {pmid39772705,
year = {2025},
author = {Zhou, J and Liu, Z and Wang, S and Li, J and Zhang, L and Liao, Z},
title = {A novel framework unveiling the importance of heterogeneous selection and drift on the community structure of symbiotic microbial indicator taxa across altitudinal gradients in amphibians.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0419223},
doi = {10.1128/spectrum.04192-23},
pmid = {39772705},
issn = {2165-0497},
abstract = {UNLABELLED: Existing analytical frameworks for community assembly have a noticeable knowledge gap, lacking a comprehensive assessment of the relative contributions of individual or grouped microbial distinct sampling units (DSUs) and distinct taxonomic units (DTUs) to each mechanism. Here, we propose a comprehensive framework for identifying DTUs/DSUs that remarkably contribute to the various mechanisms sustaining microbial community structure. Amphibian symbiotic microbes along an altitudinal gradient from Sichuan Province, China, were employed to examine the proposed statistical framework. In different altitude groups, we found that heterogeneous selection governed the community structure of symbiotic microbes across DSUs, while stochastic processes tended to increase with altitude. For DTUs at phylum and family levels, drift emerged as the dominant mechanism driving the community structure in the most symbiotic microbial taxa, while heterogeneous selection governs the most dominant or indicator taxa. Notably, the relative contribution of heterogeneous selection was significantly positively correlated with the relative abundance and niche breadth of taxa, and negatively correlated with drift. We also detected that community assembly processes remarkably regulate the structure of symbiotic microbial communities and their correlation with environmental variables. Altogether, our modeling framework is a robust and valuable tool that further enlarges our insight into microbiota community assembly.

IMPORTANCE: Distinguishing the drivers regulating microbial community assembly is essential in microbial ecology. We propose a novel modeling framework to partition the relative contributions of each individual or group of microbial DSUs and DTUs into different underpinning mechanisms. An empirical study on amphibian symbiotic microbes notably enlarges insight into community assembly patterns in the herpetological symbiotic ecosystem and demonstrates that the proposed statistical framework is an informative and sturdy tool to quantify microbial assembly processes at both levels of DSUs and DTUs. More importantly, our proposed modeling framework can provide in-depth insights into microbiota community assembly within the intricate tripartite host-environment-microbe relationship.},
}

@article {pmid39772204,
year = {2024},
author = {Obong'o, BO and Ogutu, FO and Hurley, SK and Okiko, GM and Mahony, J},
title = {Exploring the Microbial Ecology of Water in Sub-Saharan Africa and the Potential of Bacteriophages in Water Quality Monitoring and Treatment to Improve Its Safety.},
journal = {Viruses},
volume = {16},
number = {12},
pages = {},
doi = {10.3390/v16121897},
pmid = {39772204},
issn = {1999-4915},
mesh = {Africa South of the Sahara ; *Bacteriophages/physiology ; *Water Quality ; *Water Microbiology ; *Water Purification/methods ; Bacteria/virology ; Humans ; Food Safety/methods ; Biodegradation, Environmental ; },
abstract = {Access to safe water and food is a critical issue in sub-Saharan Africa, where microbial contamination poses significant health risks. Conventional water treatment and food preservation methods have limitations in addressing water safety, particularly for antibiotic-resistant bacteria and other pathogenic microorganisms. This review explores the potential application of bacteriophages as an innovative solution for water treatment and food safety in the region. Bacteriophages specifically infect bacteria and offer a targeted approach to reducing bacterial load, including multidrug-resistant strains, without the drawbacks of chemical disinfectants. This review also highlights the advantages of phage bioremediation, including its specificity, adaptability, and minimal environmental impact. It also discusses various case studies demonstrating its efficacy in different water systems. Additionally, we underscore the need for further research and the development of region-specific phage applications to improve water quality and public health outcomes in sub-Saharan Africa. By integrating bacteriophage strategies into water treatment and food production, the region can address critical microbial threats, mitigate the spread of antimicrobial resistance, and advance global efforts toward ensuring safe water for all.},
}

Africa South of the Sahara
*Bacteriophages/physiology
*Water Quality
*Water Microbiology
*Water Purification/methods
Bacteria/virology
Humans
Food Safety/methods
Biodegradation, Environmental

@article {pmid39771075,
year = {2024},
author = {Tapia, Y and Salazar, O and Seguel, O and Suazo-Hernández, J and Urdiales-Flores, D and Aponte, H and Urdiales, C},
title = {Optimizing Heavy Metal Uptake in Carpobrotus aequilaterus Through Electrokinetic Treatment: A Comprehensive Study on Phytoremediation from Mine Tailings.},
journal = {Toxics},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/toxics12120860},
pmid = {39771075},
issn = {2305-6304},
support = {3220201//Agencia Nacional de Investigación y Desarrollo/ ; },
abstract = {Copper mining drives economic growth, with the global demand expected to reach 120 million metric tons annually by 2050. However, mining produces tailings containing heavy metals (HMs), which poses environmental risks. This study investigated the efficacy of phytoremediation (Phy) combined with electrokinetic treatment (EKT) to increase metal uptake in Carpobrotus aequilaterus grown in tailings from the Metropolitan Region of Chile. The plants were exposed to varying voltages and treatment durations. In the control (no EKT), the root metal contents were Fe (1008.41 mg/kg) > Cu (176.38 mg/kg) > Mn (103.73 mg/kg) > Zn (30.26 mg/kg), whereas in the shoots, the order was Mn (48.69 mg/kg) > Cu (21.14 mg/kg) > Zn (17.67 mg/kg) > Fe (27.32 mg/kg). The optimal EKT (15 V for 8 h) significantly increased metal uptake, with roots accumulating Fe (5997.24 mg kg[-1]) > Mn (672 mg kg[-1]) > Cu (547.68 mg kg[-1]) > Zn (90.99 mg kg[-1]), whereas shoots contained Fe (1717.95 mg kg[-1]) > Mn (930 mg kg[-1]) > Cu (219.47 mg kg[-1]) > Zn (58.48 mg kg[-1]). Although EKT enhanced plant growth and biomass, higher voltages stressed the plants. Longer treatments were more effective, suggesting that EK-Phy is a promising method for remediating metal-contaminated tailings.},
}

@article {pmid39770685,
year = {2024},
author = {Han, Y and He, J and Li, M and Peng, Y and Jiang, H and Zhao, J and Li, Y and Deng, F},
title = {Unlocking the Potential of Metagenomics with the PacBio High-Fidelity Sequencing Technology.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/microorganisms12122482},
pmid = {39770685},
issn = {2076-2607},
support = {SQ2023YFE0102739//National Key Research and Development Program of China/ ; 2022A1515110819//Youth project of Guangdong Foshan joint fund of the Guangdong Natural Science Foundation/ ; 32170430//National Natural Science Foundation of China/ ; },
abstract = {Traditional methods for studying microbial communities have been limited due to difficulties in culturing and sequencing all microbial species. Recent advances in third-generation sequencing technologies, particularly PacBio's high-fidelity (HiFi) sequencing, have significantly advanced metagenomics by providing accurate long-read sequences. This review explores the role of HiFi sequencing in overcoming the limitations of previous sequencing methods, including high error rates and fragmented assemblies. We discuss the benefits and applications of HiFi sequencing across various environments, such as the human gut and soil, which provides broader context for further exploration. Key studies are discussed to highlight HiFi sequencing's ability to recover complete and coherent microbial genomes from complex microbiomes, showcasing its superior accuracy and continuity compared to other sequencing technologies. Additionally, we explore the potential applications of HiFi sequencing in quantitative microbial analysis, as well as the detection of single nucleotide variations (SNVs) and structural variations (SVs). PacBio HiFi sequencing is establishing a new benchmark in metagenomics, with the potential to significantly enhance our understanding of microbial ecology and drive forward advancements in both environmental and clinical applications.},
}

@article {pmid39770645,
year = {2024},
author = {Neviani, E},
title = {The Natural Whey Starter Used in the Production of Grana Padano and Parmigiano Reggiano PDO Cheeses: A Complex Microbial Community.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/microorganisms12122443},
pmid = {39770645},
issn = {2076-2607},
abstract = {Natural whey starter (NWS) is an undefined complex culture used in the production of Grana Padano and Parmigiano Reggiano PDO cheeses. The aim of this review is to discuss, in light of the latest research results, the role of NWS as a primary player in the cheese-making process, considering the microbial community scenario. NWS is traditionally produced by fermenting part of the whey collected at the end of a previous cheese-making process. The method used to produce NWS, based on the back-slopping principle, favors the selection of a microbiota composed mainly of thermophilic lactic acid bacteria. This method of preparation induces the survival of several different species and biotypes. The presence of such a mixture of strains facilitates the development of a natural starter characterized by a remarkable ability to adapt to non-standardized cheese-making parameters. NWS is a microbial community whose activity is not simply the result of the sum of the activities of individual microorganisms, but rather the activity of the community as a whole, in which each individual bacterial cell responds to the presence of the others. According to this traditional protocol, the NWS becomes the 'microbiological bond' between cheeses over time.},
}

@article {pmid39770585,
year = {2024},
author = {Heczko, PB and Giemza, M and Ponikiewska, W and Strus, M},
title = {Importance of Lactobacilli for Human Health.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/microorganisms12122382},
pmid = {39770585},
issn = {2076-2607},
support = {RPMP.01.02.01-12-0413/17.//The National Centre for Research and Development/ ; },
abstract = {As an extraordinarily diverse group of bacteria, lactobacilli are now classified into several genera, many of which still include "Lactobacillus" in their names. Despite their names, this group of lactic acid bacteria comprises microorganisms that are crucial for human health, especially during the early development of the human microbiota and immune system. The interactions between lactobacilli and components of the mucosal immunity lead to its shaping and development, which is possibly considered a prime mover in the advancement of the human immune system. Although much of the evidence backing the pivotal role of lactobacilli in maintaining human health comes from studies on probiotics aiming to elucidate the mechanisms of their functional activities and studies on mucosal immunity in germ-free mice, it is justifiable to extend observations on the properties of the individual probiotic Lactobacillus that are related to health benefits onto other strains sharing common characteristics of the species. In this review, we will discuss the acquisition, presence, and functions of lactobacilli in different human microbiota throughout their whole life, including those arising in the amnion and their interactions with mucosal and immune cells. Examples of immune system modulation by probiotic lactobacilli include their colonic competition for available nutrients, interference with colonization sites, competition for binding sites on gut epithelial cells, bacteriocin production, reduction of colonic pH, and nonspecific stimulation of the immune system.},
}

@article {pmid39770454,
year = {2024},
author = {Atazhanova, GA and Levaya, YK and Badekova, KZ and Ishmuratova, MY and Smagulov, MK and Ospanova, ZO and Smagulova, EM},
title = {Inhibition of the Biofilm Formation of Plant Streptococcus mutans.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {17},
number = {12},
pages = {},
doi = {10.3390/ph17121613},
pmid = {39770454},
issn = {1424-8247},
support = {АР23488250//MINISTRY OF SCIENCE AND HIGHER EDUCATION OF REPUBLIC OF KAZAKHSTAN/ ; },
abstract = {This review is devoted to a systematic analysis of studies aimed at investigating plant extracts, essential oils and phytochemical compounds capable of inhibiting Streptococcus mutans biofilm formation. This paper investigates the effect of extracts, essential oils and individual plant compounds on inhibiting the biofilm formation of Streptococcus mutans, one of the major pathogens responsible for the development of dental caries. Using cultural microbiology and molecular biology techniques, the authors describe the mechanisms by which plant samples reduce Streptococcus mutans adhesion and growth. The results show that several plant components have antibacterial properties, contributing to the reduction of Streptococcus mutans colony numbers and inhibiting the synthesis of extract-exopolysaccharide matrices required for biofilm formation. This work highlights the potential of botanicals in inhibiting Streptococcus mutans biofilm formation, which can be applied as natural antimicrobial agents in the prevention and treatment of dental diseases. Views on the use of these plant extracts and their components in dental preparations such as toothpastes, rinses and gels aimed at preventing dental caries are evaluated. The review shows the relevance of the research to optimizing the use of plant extracts, essential oils, individual compounds and their active actions in the control of Streptococcus mutans biofilms.},
}

@article {pmid39769364,
year = {2024},
author = {Grzyb, T and Szulc, J},
title = {Deciphering Molecular Mechanisms and Diversity of Plant Holobiont Bacteria: Microhabitats, Community Ecology, and Nutrient Acquisition.},
journal = {International journal of molecular sciences},
volume = {25},
number = {24},
pages = {},
doi = {10.3390/ijms252413601},
pmid = {39769364},
issn = {1422-0067},
mesh = {*Microbiota ; *Bacteria/genetics/classification/metabolism ; *Plants/microbiology ; Biodiversity ; Ecosystem ; Phosphorus/metabolism ; Nitrogen/metabolism ; Symbiosis ; Nutrients/metabolism ; },
abstract = {While gaining increasing attention, plant-microbiome-environment interactions remain insufficiently understood, with many aspects still underexplored. This article explores bacterial biodiversity across plant compartments, including underexplored niches such as seeds and flowers. Furthermore, this study provides a systematic dataset on the taxonomic structure of the anthosphere microbiome, one of the most underexplored plant niches. This review examines ecological processes driving microbial community assembly and interactions, along with the discussion on mechanisms and diversity aspects of processes concerning the acquisition of nitrogen, phosphorus, potassium, and iron-elements essential in both molecular and ecological contexts. These insights are crucial for advancing molecular biology, microbial ecology, environmental studies, biogeochemistry, and applied studies. Moreover, the authors present the compilation of molecular markers for discussed processes, which will find application in (phylo)genetics, various (meta)omic approaches, strain screening, and monitoring. Such a review can be a valuable source of information for specialists in the fields concerned and for applied researchers, contributing to developments in sustainable agriculture, environmental protection, and conservation biology.},
}

*Microbiota
*Bacteria/genetics/classification/metabolism
*Plants/microbiology
Biodiversity
Ecosystem
Phosphorus/metabolism
Nitrogen/metabolism
Symbiosis
Nutrients/metabolism

@article {pmid39768235,
year = {2024},
author = {Riekeles, M and Santos, B and Youssef, SA and Schulze-Makuch, D},
title = {Viability and Motility of Escherichia coli Under Elevated Martian Salt Stresses.},
journal = {Life (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/life14121526},
pmid = {39768235},
issn = {2075-1729},
support = {Scholarship for Max Riekeles//Friedrich-Ebert-Stiftung e.V./ ; },
abstract = {This study investigates the effects of three Martian-relevant salts-sodium chlorate, sodium perchlorate, and sodium chloride-on the viability and motility of Escherichia coli, a model organism for understanding microbial responses to environmental stress. These salts are abundant on Mars and play a crucial role in forming brines, one of the few sources of stable liquid water on the planet. We analyze the survivability under different salt concentrations using colony plating. Additionally, we perform a semi-automated motility analysis, analyzing microbial speeds and motility patterns. Our results show that sodium perchlorate is the most toxic, followed by sodium chlorate, with sodium chloride being the least harmful. Both survivability and motility are affected by salt concentration and exposure time. Notably, we observe a short-lived increase in motility at certain concentrations, particularly under sodium chlorate and sodium perchlorate stress, despite rapid declines in cell viability, suggesting a stress response mechanism. Given that motility might enhance an organism's ability to navigate harsh and variable environments, it holds promise as a key biosignature in the search for life on Mars.},
}

@article {pmid39764393,
year = {2024},
author = {Russo, CJ and Husain, K and Murugan, A},
title = {Soft Modes as a Predictive Framework for Low Dimensional Biological Systems across Scales.},
journal = {ArXiv},
volume = {},
number = {},
pages = {},
pmid = {39764393},
issn = {2331-8422},
abstract = {All biological systems are subject to perturbations: due to thermal fluctuations, external environments, or mutations. Yet, while biological systems are composed of thousands of interacting components, recent high-throughput experiments show that their response to perturbations is surprisingly low-dimensional: confined to only a few stereotyped changes out of the many possible. Here, we explore a unifying dynamical systems framework - soft modes - to explain and analyze low-dimensionality in biology, from molecules to eco-systems. We argue that this one framework of soft modes makes non-trivial predictions that generalize classic ideas from developmental biology to disparate systems, namely: phenocopying, dual buffering, and global epistasis. While some of these predictions have been borne out in experiments, we discuss how soft modes allow for a surprisingly far-reaching and unifying framework in which to analyze data from protein biophysics to microbial ecology.},
}

@article {pmid39762141,
year = {2025},
author = {Nguyen, PN and Rehan, SM},
title = {Supporting wild bee development with a bacterial symbiont.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxae317},
pmid = {39762141},
issn = {1365-2672},
abstract = {AIMS: Wild bees foster diverse microbiota that may determine survival success of developing larvae. Here, we compare survivorship and microbial communities of Ceratina calcarata small carpenter bees reared from eggs across three treatments: maternally collected control provisions with diverse microbiota, sterile provisions, and probiotic provisions supplemented with a beneficial symbiont, Apilactobacillus kunkeei.

METHODS AND RESULTS: Survival probability and adult masses differed across treatments, with the probiotic treatment resulting in highest survivorship and masses. By comparing the bacterial (16S rRNA), fungal (ITS), and plant (rbcL) communities of adults reared across treatments, we characterized distinct microbial communities across each that suggest the microbiome may be sensitive to microbial succession and competition.

CONCLUSIONS: We describe positive implications for the usage of probiotics on wild bees. Furthermore, the sensitivity of bee microbiota's relationships to their host, floral resources, and the environment suggests that holistic approaches best encapsulate the complex network of interactions between bees and their microbes.},
}

@article {pmid39760916,
year = {2025},
author = {García-Bodelón, Á and Baković, N and Cano, E and Useros, F and Lara, E and González-Miguéns, R},
title = {Predators in the Dark: Metabarcoding Reveals Arcellinida Communities Associated with Bat Guano, Endemic to Dinaric Karst in Croatia.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {166},
pmid = {39760916},
issn = {1432-184X},
support = {PID2021-128499NB-I00//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-128499NB-I00//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-128499NB-I00//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-128499NB-I00//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-128499NB-I00//Spanish Ministry of Science, Innovation and Universities/ ; Garantía Juvenil CM 2021//Comunidad de Madrid (Spain)/ ; Garantía Juvenil CM 2021//Comunidad de Madrid (Spain)/ ; Class: UP/I-612-07/21-48/170, Ref. No.: 517-10-1-1-21-3, 16.07.2021//Croatian Ministry of Economy and Sustainable Development/ ; },
mesh = {Croatia ; Animals ; *Chiroptera/microbiology ; *Caves/microbiology ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Ecosystem ; Chironomidae/genetics ; Feces/microbiology ; Electron Transport Complex IV/genetics/analysis ; Geologic Sediments/microbiology ; Phylogeny ; },
abstract = {Karst caves, formed from the dissolution of soluble rocks, are characterized by the absence of photosynthetic activity and low levels of organic matter. Organisms evolve under these particular conditions, which causes high levels of endemic biodiversity in both macroorganism and microbes. Recent research has highlighted the presence of testate amoebae (Arcellinida) group in cave environments. This study investigates the diversity of Arcellinida in Dinaric karstic caves in Croatia, a global diversity hotspot, focusing on the influence of bat guano on community structure. Sediment samples were collected from two independent hydrosystems, and a metabarcoding approach was used to assess Arcellinida diversity at specific and intraspecific levels, using Arcellinid-specific primers to amplify the mitochondrial cytochrome oxidase subunit I (COI) region. Results reveal a significant impact of guano on both specific and intraspecific diversity of Arcellinida. Communities in guano-rich sites displayed higher diversity, abundance, and the presence of unique OTUs and genetic variants not observed in other habitats, highlighting the crucial role of bats as ecosystem engineers. In contrast, sites without guano hosted communities with low abundance and reduced biodiversity. These differences suggest the existence of guano-associated Arcellinida communities. This study provides new insights into the biodiversity of subterranean ecosystems and the ecological roles of Arcellinida in karstic environments.},
}

Croatia
Animals
*Chiroptera/microbiology
*Caves/microbiology
*Biodiversity
*DNA Barcoding, Taxonomic
Ecosystem
Chironomidae/genetics
Feces/microbiology
Electron Transport Complex IV/genetics/analysis
Geologic Sediments/microbiology
Phylogeny

@article {pmid39760871,
year = {2025},
author = {Mwaheb, MA and El-Aziz, BMA and Abd-Elhalim, BT and El-Kassim, NA and Radwan, TEE},
title = {Study of Different Cultivated Plants Rhizosphere Soil Fungi-Mediated Pectinase: Insights into Production, Optimization, Purification, Biocompatibility, and Application.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {165},
pmid = {39760871},
issn = {1432-184X},
mesh = {*Polygalacturonase/metabolism ; *Soil Microbiology ; *Rhizosphere ; Fungi/enzymology/metabolism/isolation & purification/classification/genetics ; Aspergillus/metabolism/enzymology/isolation & purification ; Egypt ; Fungal Proteins/metabolism ; },
abstract = {Microorganisms are preferred as an enzyme source due to their short lifespan, high production rate, affordability, and absence of harmful chemicals in enzymes generated from plant and animal sources. Fungi communities are biological factories for many bioactive compounds such as the important industrial enzyme pectinase. The current study dealt with production, optimization, purification, biocompatibility, and application of fungal pectinase obtained from five plant rhizospheres (banana, jarawa, lemon, tomato, and wheat) at Fayoum Governorate, Egypt. The highest pectinase degrading index (PDI) was scored for FB5, FJ2, and FW1 isolates. Pectinase production was also examined quantitively and the highest output of 1603.67, 1311.22, and 1264.83 U/ml was gained by FB5, FJ1, and FW1 fungal isolates, respectively. The most active pectinase-producing fungi were identified as Aspergillus niveus strain AUMC1624, A. niger strain AUMC16245, and A. brasiliensis strain AUMC16244, respectively. For pectinase production optimization, one factor at a time (OFAT) protocol was applied and revealed that A. niger, A. niveus, and A. brasiliensis reached maximum pectinase levels at 1% pectin after 5, 7, and 7 days, at 40, 45, and 45 °C, respectively. Obtained pectinases were partially purified using ammonium sulfate precipitation (ASP) and organic solvent precipitation (OSP) methods. The highest activity using the ASP method scored at 40-60% saturation with A. niger. The thermostability characterization of A. niger pectinase was reached with relative activities of 61.7, 69.0, 99.9, 91.3, and 90.6% at temperatures ranging between 30 and 70 °C. pH optimized at pH 5-7. The enzyme's molecular weight was approximately 30 kDa. The GC-mass analysis of pectinase end products included acetic acid ethyl ester, hexadecane carbonsaure methylase, and hexadecenoic acid. The biocompatibility was examined using a human skin cell line (HFb-4) for the first time, with a minimal half concentration (IC50) of 151.86 ± 0.76 U/ml. The biocompatible pectinase was applied as a clothes bioscouring agent with different concentrations of 1893.52 U/ml achieving the highest bioscouring with 20.0%.},
}

*Polygalacturonase/metabolism
*Soil Microbiology
*Rhizosphere
Fungi/enzymology/metabolism/isolation & purification/classification/genetics
Aspergillus/metabolism/enzymology/isolation & purification
Egypt
Fungal Proteins/metabolism

@article {pmid39760805,
year = {2025},
author = {Willemsen, A and Manzano-Marín, A and Horn, M},
title = {Novel High-Quality Amoeba Genomes Reveal Widespread Codon Usage Mismatch Between Giant Viruses and Their Hosts.},
journal = {Genome biology and evolution},
volume = {17},
number = {1},
pages = {},
doi = {10.1093/gbe/evae271},
pmid = {39760805},
issn = {1759-6653},
support = {//European Union's Horizon 2020 research and innovation programme/ ; 891572//Marie Sklodowska-Curie/ ; 101039843//European Union/ ; //European Research Council Executive Agency/ ; //Austrian Science Fund/ ; },
mesh = {*Giant Viruses/genetics ; *Codon Usage ; *Amoeba/virology/genetics ; Genome, Protozoan ; Host Specificity ; Phylogeny ; Acanthamoeba/virology/genetics ; },
abstract = {The need for high-quality protist genomes has prevented in-depth computational and experimental studies of giant virus-host interactions. In addition, our current knowledge of host range is highly biased due to the few hosts used to isolate novel giant viruses. This study presents 6 high-quality amoeba genomes from known and potential giant virus hosts belonging to 2 distinct eukaryotic clades: Amoebozoa and Discoba. We employ their genomic data to investigate the predictability of giant virus host range. Using a combination of long- and short-read sequencing, we obtained highly contiguous and complete genomes of Acanthamoeba castellanii, Acanthamoeba griffini, Acanthamoeba terricola, Naegleria clarki, Vermamoeba vermiformis, and Willaertia magna, contributing to the collection of sequences for the eukaryotic tree of life. We found that the 6 amoebae have distinct codon usage patterns and that, contrary to other virus groups, giant viruses often have different and even opposite codon usage with their known hosts. Conversely, giant viruses with matching codon usage are frequently not known to infect or replicate in these hosts. Interestingly, analyses of integrated viral sequences in the amoeba host genomes reveal potential novel virus-host associations. Matching of codon usage preferences is often used to predict virus-host pairs. However, with the broad-scale analyses performed in this study, we demonstrate that codon usage alone appears to be a poor predictor of host range for giant viruses infecting amoeba. We discuss the potential strategies that giant viruses employ to ensure high viral fitness in nonmatching hosts. Moreover, this study emphasizes the need for more high-quality protist genomes. Finally, the amoeba genomes presented in this study set the stage for future experimental studies to better understand how giant viruses interact with different host species.},
}

*Giant Viruses/genetics
*Codon Usage
*Amoeba/virology/genetics
Genome, Protozoan
Host Specificity
Phylogeny
Acanthamoeba/virology/genetics

@article {pmid39753761,
year = {2025},
author = {Peng, Z and van der Heijden, MGA and Liu, Y and Li, X and Pan, H and An, Y and Gao, H and Qi, J and Gao, J and Qian, X and Tiedje, JM and Wei, G and Jiao, S},
title = {Agricultural subsoil microbiomes and functions exhibit lower resistance to global change than topsoils in Chinese agroecosystems.},
journal = {Nature food},
volume = {},
number = {},
pages = {},
pmid = {39753761},
issn = {2662-1355},
abstract = {Soils play a critical role in supporting agricultural production. Subsoils, below 20 cm, underpin fundamental agroecosystem sustainability traits including soil carbon storage, climate regulation and water provision. However, little is known about the ecological stability of subsoils in response to global change. Here we conducted a microcosm experiment to determine whether subsoils were more sensitive to global changes across 40 agricultural ecosystems in China, in combination with a multiple global change factor experiment and an in situ field study. We found that subsoils exhibited greater fluctuation in species diversity, community composition, and complexity of microbial networks and ecosystem functions than topsoils, indicating lower resistance to global changes. Soil biodiversity was a major driver of ecosystem resistance, surpassing climate and soil parameters. A reciprocal microorganism transplant experiment showed that microorganisms isolated from the topsoil are more resistant to global changes than those from subsoil. Our study emphasizes that subsoil ecosystems are sensitive to global changes, underscoring the importance of including subsoils in predictions of agricultural sustainability and crop productivity under changing environmental conditions.},
}