@article {pmid41308222,
year = {2025},
author = {Dorawa, P and Kolniak-Ostek, J},
title = {Green and roasted coffee as novel substrates for kombucha fermentation: Modulation of bioactivity and phenolic profile.},
journal = {Food chemistry},
volume = {498},
number = {Pt 2},
pages = {147162},
doi = {10.1016/j.foodchem.2025.147162},
pmid = {41308222},
issn = {1873-7072},
abstract = {Fermentation of coffee beverages with a symbiotic culture of bacteria and yeast (SCOBY) is an emerging alternative to traditional tea-based kombucha. This study examined the effects of SCOBY fermentation on the chemical composition and bioactivity of infusions prepared from green and roasted beans of Coffea arabica and Coffea canephora. Fermentation for 14 days markedly altered the phenolic profile and enhanced the antioxidant, antidiabetic, anti-inflammatory, and anticholinesterase activities. Green C. canephora showed the highest antidiabetic and neuroprotective potential, while roasted coffees exhibited stronger antioxidant effects. Multivariate analyses (PCA and Pearson correlation) revealed close associations between phenolic transformation, sugar metabolism and biological functions. The results demonstrate that coffee, particularly in its green form, is a promising substrate for SCOBY fermentation and may serve as a basis for developing novel functional beverages with targeted health-promoting properties.},
}

@article {pmid41307238,
year = {2025},
author = {Chen, Y and Liu, Y and Li, J and Yu, H and Yang, J and Li, Q and Lyu, L and Zhang, S},
title = {Adaptive Feeding Strategies Facilitate Resilience of Deep-Sea Cold Seep Molluscs Confronting Climate Change.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70190},
doi = {10.1111/mec.70190},
pmid = {41307238},
issn = {1365-294X},
support = {42494884//National Natural Science Foundation of China/ ; 42306171//National Natural Science Foundation of China/ ; SCSIO202202//Development fund of South China Sea Institute of Oceanology of the Chinese Academy of Sciences/ ; GML20190609//PI project of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; 2025A1515010932//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2023B1212060047//Science and Technology Planning Project of Guangdong Province, China/ ; },
abstract = {Molluscs living in dynamic deep-sea cold seep environments have evolved distinct feeding strategies for survival. Here, we present the chromosome-level genomes of two sympatric mollusc species with distinct feeding strategies, a symbiosis-dependent mussel Gigantidas haimaensis and a predatory snail Phymorhynchus buccinoides. Comparative genomic analysis revealed gene family expansions related to the bacterial component degradation (e.g., b4GalTs) in G. haimaensis, suggesting an adaptation to symbiotic life. Conversely, P. buccinoides exhibited gene family expansions associated with appetite regulation (e.g., ox2r) and the digestive system (e.g., sult1 and chst), indicating genetic modifications for deep-sea predation. Furthermore, we conducted an in situ experiment mimicking a scenario in which ocean warming and sea-level rise resulted in a mass methane leakage in deep-sea cold seeps. Interestingly, G. haimaensis increased its metabolic rate and exhibited transcriptional responses. However, P. buccinoides suppressed energy production and responses at translational and posttranslational levels, which is compatible with their distinct feeding strategies. Collectively, our results provide insights on the evolutionary basis and resilience mechanisms related to energy management, which may facilitate methane tolerance of molluscs in the deep-sea cold seeps threatened by climate change.},
}

@article {pmid41307056,
year = {2025},
author = {Allen-Waller, L and Glass, BH and Jones, KG and Dworetzky, AG and Barott, KL},
title = {The temperate coral Astrangia poculata maintains acid-base homeostasis through heat stress.},
journal = {Royal Society open science},
volume = {12},
number = {11},
pages = {251528},
pmid = {41307056},
issn = {2054-5703},
abstract = {Heat stress can disrupt acid-base homeostasis in reef-building corals and other tropical cnidarians, often leading to cellular acidosis that can undermine organismal function. Temperate cnidarians experience a high degree of seasonal temperature variability, leading us to hypothesize that temperate taxa have more thermally robust pH homeostasis than their tropical relatives. To test this, we investigated how elevated temperature affects intracellular pH and calcification in the temperate coral Astrangia poculata. Clonal pairs were exposed to elevated (30°C) or control (22°C) temperatures for 17 days. Despite causing damage to host tissues and symbiont cells, elevated temperature did not affect intracellular pH or inhibit calcification in A. poculata. These responses contrast with those of tropical cnidarians, which experience cellular acidification and decreased growth during heat stress. Astrangia poculata therefore appears to have thermally resilient cellular acid-base homeostasis mechanisms, possibly because of adaptation to large seasonal temperature variations. However, we also observed tissue damage and lower egg densities in heat-treated individuals, suggesting that increasingly severe marine heatwaves can still threaten temperate coral fitness. These results provide insight into corals' nuanced adaptive capacity across latitudes and biological scales.},
}

@article {pmid41306926,
year = {2025},
author = {Melis, S and Gammuto, L and Castelli, M and Nardi, T and Bisaglia, B and Duron, O and Cafiso, A and Botman, J and Lambert, O and Olivieri, E and Sprong, H and Plantard, O and Sassera, D},
title = {Genetic and genomic variability of Spiroplasma and Midichloria endosymbionts associated with the tick Ixodes frontalis.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf202},
pmid = {41306926},
issn = {2730-6151},
abstract = {Ixodes frontalis, an ornithophilic tick species, is widely distributed all over Europe exhibiting two genetically diverging haplogroups based on differences in the cytochrome c oxidase subunit 1 mitochondrial gene. Despite its broad distribution, little is known about the presence of symbiotic bacteria in I. frontalis, while symbionts are generally widespread in ixodid ticks and responsible for important effects on host fitness. We collected I. frontalis from France and Italy (n = 277) and assessed that the most prevalent haplogroup was A (73%). We then investigated the presence of the symbionts, Midichloria mitochondrii and Spiroplasma ixodetis. They were both found at a high prevalence in adult ticks (66% and 77% respectively), while the number of positive immature ticks was significantly lower (18% for both). The experimental analysis of larvae hatched from egg clutches obtained from four females hints at vertical transmission of both symbionts. We obtained three genomes of Spiroplasma and one of Midichloria, and used them to perform comparative genomic analysis. Average nucleotide identity among available Spiroplasma or Midichloria genomes from I. frontalis are all extremely high, suggesting low genetic variability for both symbionts. Gene presence/absence analysis confirmed the presence of B vitamin synthesis genes in the genome of M. mitochondrii, and also showed the presence of the ETX/MTX2 gene, the RIP family and a partial Spaid-like gene in S. ixodetis. This gene repertoire indicates a nutritional role for Midichloria, while for S. ixodetis we hypothesize a role of this bacterium as a defensive symbiont or a manipulator of the host reproduction.},
}

@article {pmid41305496,
year = {2025},
author = {Morgese, EA and Ferrell, BD and Toth, SC and Polson, SW and Wommack, KE and Fuhrmann, JJ},
title = {Comparative Analysis Reveals Host Species-Dependent Diversity Among 16 Virulent Bacteriophages Isolated Against Soybean Bradyrhizobium spp.},
journal = {Viruses},
volume = {17},
number = {11},
pages = {},
doi = {10.3390/v17111474},
pmid = {41305496},
issn = {1999-4915},
support = {1736030//U.S. National Science Foundation/ ; P20 GM103446/GM/NIGMS NIH HHS/United States ; 1S10OD028725-01A1/GM/NIGMS NIH HHS/United States ; },
mesh = {*Bradyrhizobium/virology ; *Glycine max/microbiology ; *Bacteriophages/genetics/isolation & purification/classification/physiology/pathogenicity ; Host Specificity ; Symbiosis ; Phylogeny ; Genome, Viral ; },
abstract = {Phages play a role in shaping ecosystems by controlling host abundance via cell lysis, driving host evolution via horizontal gene transfer, and promoting nutrient cycling. The genus Bradyrhizobium includes bacteria able to symbiotically nodulate the roots of soybean (Glycine max), providing the plant with a direct source of biologically fixed nitrogen. Optimizing this symbiosis can minimize the use of nitrogen fertilizers and make soybean production more sustainable. Phages targeting Bradyrhizobium may modify their hosts' genotype, alter phenotypic traits such as symbiotic effectiveness, and mediate competition among strains for nodulation sites. Sixteen phages were isolated against B. diazoefficiens strain USDA110 and B. elkanii strains USDA94 and USDA31. Comparative analyses revealed host species-dependent diversity in morphology, host range, and genome composition, leading to the identification of three previously undescribed phage species. Remarkably, all B. elkanii phages shared a siphophage morphology and formed a single species with >97% nucleotide identity, even when isolated from farms separated by up to ~70 km, suggesting genomic stability across geographic scales. In contrast, phages isolated against B. diazoefficiens had a podophage-like morphology, exhibited greater genetic diversity, and divided into two distinct species. Although no phages were recovered against the B. japonicum strains or native Delaware Bradyrhizobium isolates tested, some Delaware Bradyrhizobium isolates showed susceptibility in a host range assay. The phage genomes demonstrated features predicting phenotypes. The phage terminase genes predicted headful packaging which promotes generalized transduction. The B. elkanii phages all carried tmRNA genes capable of rescuing stalled ribosomes, and all but one of the phages isolated against the two host species carried DNA polymerase A indicating greater phage control of genome replication. State-of-the-art structural annotation of a hypothetical gene shared by the B. diazoefficiens phages, having a mean amino acid identity of ~25% and similarity of ~35%, predicted a putative tail fiber function. Together this work expands the limited knowledge available on soybean Bradyrhizobium phage ecology and genomics.},
}

*Bradyrhizobium/virology
*Glycine max/microbiology
*Bacteriophages/genetics/isolation & purification/classification/physiology/pathogenicity
Host Specificity
Symbiosis
Phylogeny
Genome, Viral

@article {pmid41305123,
year = {2025},
author = {Teng, S and Lin, X and Wang, Y},
title = {Robust Beamforming Design for Energy Efficiency and Spectral Efficiency Tradeoff in Multi-STAR-RIS-Aided C-HRSMA.},
journal = {Sensors (Basel, Switzerland)},
volume = {25},
number = {22},
pages = {},
doi = {10.3390/s25226917},
pmid = {41305123},
issn = {1424-8220},
abstract = {This paper investigates a simultaneous transmitting and reflecting reconfigurable intelligent surface (STAR-RIS)-assisted cognitive hierarchical rate-splitting multiple access (C-HRSMA) system to enhance the system performance under imperfect channel state information (ICSI). By exploiting the natural user grouping afforded by the STAR-RIS and its distinct channel manipulation capabilities for the transmission and reflection users, we effectively mitigate inter-group common stream interference within C-HRSMA, consequently facilitating the achievement of higher spectral efficiency. Subsequently, the design is formulated as a non-convex optimization problem that incorporates the phase-shift matrix of STAR-RIS, the beamforming vector of the base station, and the common rate allocation vector. To address this non-convex problem, an alternating optimization (AO) technique is employed to decouple the primary problem and solve the subproblems using S-procedure and successive convex approximation (SCA). The simulation results validate that the proposed algorithm exhibits superior SE and EE performance against benchmark algorithms.},
}

@article {pmid41304966,
year = {2025},
author = {Hontana-Moreno, N and Morales, D},
title = {Biological Activities of Novel Kombuchas Based on Alternative Ingredients to Replace Tea Leaves.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {18},
number = {11},
pages = {},
doi = {10.3390/ph18111722},
pmid = {41304966},
issn = {1424-8247},
abstract = {Background/Objectives: Traditional kombucha is produced by fermenting a sweetened infusion of Camellia sinensis leaves with a symbiotic consortium of bacteria and yeasts (SCOBY). The growing interest in this beverage has driven the exploration of alternative substrates, including a wide range of plant-based raw materials, such as leaves, fruits, flowers, and seeds. Consequently, numerous products are being investigated for their differential properties, not only organoleptic but also nutritional and bioactive. This review aims to summarize recent advances in alternative kombucha research, focusing on the substrates used, their physicochemical and biochemical characteristics, and the biological activities studied. Methods: A comprehensive literature search was conducted to select articles related to alternative kombuchas. A critical analysis of their current state was carried out through the Strengths, Weaknesses, Opportunities, and Threats (SWOT) methodology. Results: The SWOT analysis led to the identification of strengths, including promising in vitro results and growing consumer interest; weaknesses, including a lack of animal studies, clinical trials, and approved health claims, and an excessive focus on antioxidant activity and phenolic compounds; opportunities, including substrate diversity, innovation, and consumer education; and threats, including elaboration risks, misinformation, competitors, and potential consumer rejection. Conclusions: Despite the promising results achieved to date, it is essential that the scientific community and the food industry continue efforts to generate robust evidence, particularly through clinical validation, in order to draw reliable conclusions regarding the benefits of alternative kombuchas for human health.},
}

@article {pmid41304609,
year = {2025},
author = {Bojórquez-Armenta, YJ and Sarmiento-López, LG and Pozo, MJ and Castro-Martínez, C and Lopez-Meyer, M},
title = {Characterization of Endoglucanase (GH9) Gene Family in Tomato and Its Expression in Response to Rhizophagus irregularis and Sclerotinia sclerotiorum.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {22},
pages = {},
doi = {10.3390/plants14223458},
pmid = {41304609},
issn = {2223-7747},
support = {A1-S-31400//Secretaría de Ciencia, Humanidades, Tecnología e Innovación/ ; 20230746//Instituto Politécnico Nacional/ ; },
abstract = {In this study, we report bioinformatics analysis of the endoglucanase GH9 gene family in tomato (Solanum lycopersicum L.) using the SL5.0 genome, confirming the presence of 19 members that clustered into classes A, B, and C. To explore their potential role in plant-microbe interactions, we determined the transcriptional regulation of 10 SlGH9 gene members in tomato leaves and roots during interactions with the mutualistic root mycorrhizal fungus Rhizophagus irregularis and the foliar pathogen Sclerotinia sclerotiorum. The upregulation of several SlGH9 genes in the leaves of mycorrhizal plants suggests that they are involved in cellulose remodeling and biosynthesis rather than its degradation. This would be consistent with the observed increase in foliar area. On the other hand, downregulation of some SlGH9 genes in leaves of pathogen-infected mycorrhizal plants suggests that these genes may play a role in the enhanced resistance observed by reducing cellulose degradation, thereby maintaining cell wall integrity. The potential involvement of endoglucanase genes in expansive growth (foliar area) and in defense in mycorrhizal and pathogen-infected plants may reflect a growth-defense trade-off.},
}

@article {pmid41304310,
year = {2025},
author = {Ding, L and Zhang, J and Qiao, S and Xu, J and Li, J and Zhang, W and Yi, Q and Wu, Y and Wang, T and Bian, P},
title = {The Effects of Feeding ybfQ-Deficient Gut Bacteria on Radio-Tolerance in Symbiotic Caenorhabditis elegans: The Key Role of Isoscoparin.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112626},
pmid = {41304310},
issn = {2076-2607},
support = {12135016//the National Natural Science Foundation of China/ ; 12475335//the National Natural Science Foundation of China/ ; 12075275//the National Natural Science Foundation of China/ ; GXXT-2022-001//the University Synergy Innovation Program of Anhui Province/ ; 2022AH050727//the Natural Science Research Project of Anhui Educational Committee/ ; },
abstract = {It is inevitable for life on earth to be exposed to various types of ionizing and non-ionizing radiation, underscoring the importance of radioprotection. The symbiotic interaction between gut microbiota and the host provides a strategy for protecting the organism against these stressors. However, the genetic mechanisms underlying this interaction remain poorly understood due to the complexity and diversity of gut microbiota. In this study, we employed a symbiotic experimental system involving Caenorhabditis elegans and Escherichia coli to systemically investigate the effects of bacterial genetic alterations on host responses to radiation exposure. Our findings revealed that deletion of the bacterial ybfQ gene (ΔybfQ) significantly enhanced worm tolerance to UV-B radiation. Transcriptomic analysis demonstrated an enhanced antioxidant capacity in ΔybfQ-fed worms, as evidenced by reduced levels of reactive oxygen species (ROS) and restored oxidative homeostasis. Notably, ΔybfQ bacteria exhibited overproduction of isoscoparin, and exogenous supplementation with isoscoparin similarly enhanced worm radio-tolerance, underscoring its crucial role in ΔybfQ-mediated antioxidant of host worm. Both interventions retained their protective effects in IIS-deficient worms (daf-16). However, the protective effects of ΔybfQ feeding, but not isoscoparin treatment, were attenuated in daf-2 worms with a constitutively activated IIS pathway, accompanied by reduced bacteria gut colonization. Collectively, our results provide novel insights into the genetic basis of host-microbe interactions and propose a potential pharmacological strategy for radiation protection.},
}

@article {pmid41304279,
year = {2025},
author = {Zhou, M and Li, Q and Han, Y and Wang, Q and Yang, H and Li, H and Hu, C},
title = {Sulfur Cycling and Life Strategies in Successional Biocrusts Link to Biomass Carbon in Dryland Ecosystems.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112594},
pmid = {41304279},
issn = {2076-2607},
support = {32370125//National Natural Science Foundation of China/ ; 41877419//National Natural Science Foundation of China/ ; 41877339//National Natural Science Foundation of China/ ; XDA17010502//Strategic Priority Research Program at the Chinese Academy of Science/ ; },
abstract = {Examining the changing patterns and underlying mechanisms of soil biomass carbon stocks constitutes a fundamental aspect of soil biology. Despite the potential influence of the sulfur cycle and the life strategies of organisms on community biomass, these factors have rarely been studied in tandem. Biocrusts are model systems for studying soil ecosystems. In this study, metagenomic analysis of biocrusts related to different life strategies from five batches over four consecutive years demonstrated that, in free-living communities, microbial biomass carbon (MBC) synthesis, via assimilatory sulfate reduction (ASR), is primarily coupled with the 3-hydroxypropionate/4-hydroxybutyrate and Calvin-Benson-Bassham cycles. These pathways are affected by the oxidation-reduction potential (Eh), pH, electrical conductivity, and nutrient levels. The decomposition of organic carbon (OC) via dissimilatory sulfate reduction (DSR) was accompanied by the production of dimethyl sulfide (DMS), which was influenced by the C/S ratio and moisture, whereas the synthesis of MBC by symbiotic communities was found to be affected by Eh and pH, and decomposition was affected by the C/S ratio. The MBC stock was influenced by all strategies, with resource strategies having the greatest impacts during the growing season, and the contribution of chemotrophic energy was most significant in free-living communities. In conclusion, the MBC in biocrusts is associated with both ASR and DSR and is facilitated by the A-, S-, and P-strategies under the regulation of the stoichiometric C/S ratio. The exploration of microbial life strategies and sulfur cycling in biocrusts within arid ecosystems in this study offers a new perspective on the patterns of change in soil biomass carbon stocks.},
}

@article {pmid41304215,
year = {2025},
author = {Arruda, ISA and Cavalcante, CDS and Rubens, RS and Castro, LNPF and Nóbrega, YKM and Dalmolin, TV},
title = {Changes in the Gut Microbiota of Patients After SARS-CoV-2 Infection: What Do We Know?.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112529},
pmid = {41304215},
issn = {2076-2607},
support = {DPI/BCE nº 01/2025//University of Brasilia/ ; FAPDF nº 09/2023//Fundação de Apoio à Pesquisa do Distrito Federal/ ; },
abstract = {COVID-19 can cause long-term symptoms, such as a post-infection syndrome, known as Long-COVID. Among the symptoms present during this period, the most reported are gastrointestinal symptoms. This study discusses the effects of changes in the gut microbiota of post-COVID-19 patients. SARS-CoV-2 infection is associated with significant alterations in gut microbial composition, disturbing its homeostasis and promoting a reduction in the abundance of beneficial symbiotic bacteria and an increase in the abundance of opportunistic pathogens. Furthermore, the composition of the gut microbiota may play a role in the prognosis of patients with post-COVID-19 infection. The microbiota of the intestinal tract and the respiratory tract influence each other; therefore, the gut-lung axis has attracted increasing interest in understanding COVID-19. Moreover, the brain-gut axis has been studied, since there have been reports of anxiety and depression along with post-COVID-19 gastrointestinal symptoms. Treatments options for intestinal dysbiosis in Long-COVID patients include probiotics, prebiotics, and fecal microbiota transplantation. These treatments may serve as an approach to improve gastrointestinal symptoms during Long-COVID, increasing microbiome diversity, strengthening the integrity of intestinal barrier functions, and consequently influencing the treatment of COVID-19.},
}

@article {pmid41304149,
year = {2025},
author = {Msiza, LJ and Ngmenzuma, TY and Mohammed, M and Jaiswal, SK and Dakora, FD},
title = {Cross-Infectivity of 11 Different Legume Species by 15 Native Rhizobia Isolated from African Soils.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112463},
pmid = {41304149},
issn = {2076-2607},
abstract = {Selecting symbiotic rhizobia for use as inoculants in agriculture is a major challenge, though it is necessary for exploiting biological nitrogen fixation as an eco-friendly source of N in contrast to chemical N fertilizers which can pollute the environment. In addition to high symbiotic efficiency, bacterial strain ability to infect and effectively nodulate a wide range of host plants is also desired. Cross-infectivity studies are therefore important for identifying rhizobial strains that are highly effective with a broad host range. The legume/rhizobia symbiosis has the potential to contribute about 80% or more N to agricultural systems, thus providing a sustainable source of N in cropping systems. This study assessed the cross-nodulation, colony morphology, relative symbiotic effectiveness and N2 fixation of native rhizobial isolates from Africa that nodulate diverse legume species. The results showed that the rhizobial isolates differed significantly in symbiotic performance and relative symbiotic effectiveness. As a result, they differed markedly in nodulation and shoot DM induced in their host plants.},
}

@article {pmid41303664,
year = {2025},
author = {Ershova, NM and Sheshukova, EV and Kamarova, KA and Alimova, AR and Savchenko, YY and Antimonova, AA and Komarova, TV},
title = {Xyloglucan Endotransglycosylase/Hydrolase Downregulation Increases Nicotiana benthamiana Tolerance to Tobacco Mosaic Virus Infection.},
journal = {International journal of molecular sciences},
volume = {26},
number = {22},
pages = {},
doi = {10.3390/ijms262211183},
pmid = {41303664},
issn = {1422-0067},
support = {19-74-20031//Russian Science Foundation/ ; 125091010191-6//Ministry of Science and Higher Education of Russian Federation/ ; },
mesh = {*Nicotiana/virology/genetics/enzymology ; *Tobacco Mosaic Virus/physiology/pathogenicity ; *Glycosyltransferases/genetics/metabolism ; *Plant Diseases/virology/genetics ; *Plant Proteins/genetics/metabolism ; Gene Expression Regulation, Plant ; Down-Regulation ; Disease Resistance/genetics ; },
abstract = {The biological functions of the multiple members of the xyloglucan endotransglycosylase/hydrolase (XTH) protein family are rather diverse: XTHs are cell wall remodeling enzymes that participate in plant growth and development, are involved in responses to various environmental stresses and interactions with pathogenic and symbiotic microorganisms. However, XTHs' role upon viral infection remains poorly understood. Here we identified and characterized Nicotiana benthamiana XTH (NbXTH) which is involved in responses to viral infection. We demonstrated that NbXTH is a positive regulator of intercellular transport. NbXTH suppression leads to the inhibition of tobacco mosaic virus (TMV) local spread, resulting in the increased tolerance of N. benthamiana plants to TMV. Therefore, NbXTH could be regarded as a susceptibility factor.},
}

*Nicotiana/virology/genetics/enzymology
*Tobacco Mosaic Virus/physiology/pathogenicity
*Glycosyltransferases/genetics/metabolism
*Plant Diseases/virology/genetics
*Plant Proteins/genetics/metabolism
Gene Expression Regulation, Plant
Down-Regulation
Disease Resistance/genetics

@article {pmid41303524,
year = {2025},
author = {Valitova, JN and Khabibrakhmanova, VR and Babayev, VM and Khajrullina, AF and Gurjanov, OP and Gazizova, NI and Beckett, RP and Minibayeva, FV},
title = {Sterol Composition in the Lichens Lobaria pulmonaria and Lobaria retigera: Does Photobiont Matter?.},
journal = {International journal of molecular sciences},
volume = {26},
number = {22},
pages = {},
doi = {10.3390/ijms262211041},
pmid = {41303524},
issn = {1422-0067},
support = {22-14-00362P//Russian Science Foundation/ ; },
mesh = {*Lichens/chemistry/metabolism ; *Sterols/chemistry/analysis/metabolism ; *Ascomycota/chemistry/metabolism ; Symbiosis ; *Phytosterols/chemistry/analysis/metabolism ; Ergosterol ; Nostoc/chemistry/metabolism ; Cholesterol/analogs & derivatives ; },
abstract = {The lipid composition of the mycobint and photobiont symbiotic partners of lichenized ascomycetes varies greatly. The aim of this study was to compare the profile of the major sterols in two closely related lichens from the genus Lobaria with different photobionts. The three-component lichen Lobaria pulmonaria has two photobionts. While the main photobiont is the chlorophycean alga Symbiochloris reticulata, this lichen contains small amounts of the cyanobacterium Nostoc. By contrast, the cyanobacterium Nostoc is the main photobiont in Lobaria retigera. Relatively loosely bound sterols were extracted using a chloroform-methanol mixture, and subsequently, more tightly bound sterols by alkaline saponification. The initial chloroform-methanol extraction step indicated that ergosterol is the principal sterol in both species, with phytosterols constituting a minor fraction. However, the addition of an alkaline saponification step to the standard protocol of sterol extraction greatly increases the release of tightly bound phytosterols, such as campesterol, stigmasterol, and β-sitosterol from L. pulmonaria, but not from L. retigera. Therefore, the mycobionts and Nostoc mainly possess sterols extractable by the standard mixture of chloroform/methanol, while the chlorophycean algal photobiont contains tightly bound sterols. This observation could be important when studying the roles of sterols in the stress tolerance of lichens.},
}

*Lichens/chemistry/metabolism
*Sterols/chemistry/analysis/metabolism
*Ascomycota/chemistry/metabolism
Symbiosis
*Phytosterols/chemistry/analysis/metabolism
Ergosterol
Nostoc/chemistry/metabolism
Cholesterol/analogs & derivatives

@article {pmid41302914,
year = {2025},
author = {Bykov, R and Shatalova, E and Andreeva, I and Khodakova, A and Ryabinin, A and Demenkova, M and Ilinsky, Y},
title = {Endosymbiotic Bacteria Spiroplasma and Wolbachia in a Laboratory-Reared Insect Collection.},
journal = {Insects},
volume = {16},
number = {11},
pages = {},
doi = {10.3390/insects16111168},
pmid = {41302914},
issn = {2075-4450},
support = {24-24-00378//Russian Science Foundation/ ; },
abstract = {Many insect and other arthropod species are maintained as non-model laboratory stocks and are used for fundamental and applied studies. Their biology may be affected by symbionts, such as Wolbachia and Spiroplasma. Thirty stocks of different insect species that are maintained at the Laboratory of biological control of phytophagous and phytopathogens in the Siberian Federal Scientific Centre of Agro-BioTechnologies were screened to find Spiroplasma/Wolbachia-host associations. We used 16S rDNA and fusA loci for Spiroplasma characterization and five MLST genes for Wolbachia. Seven out of thirty stocks harbored symbionts. Five stocks were infected with only Wolbachia, one with only Spiroplasma, and one with both symbionts. Two stocks were occasionally characterized by false-positive signals of Spiroplasma infection that were explained by contamination from food sources, viz. infected insects. Five Wolbachia isolates belonged to supergroup B and one to supergroup A. Only the MLST haplotype of Nabis ferus was previously known (ST-522), while the other haplotypes contained new alleles. One Spiroplasma isolate was clustered in the Ixodetis clade and another was basal to the Apis clade. We noted the importance of non-model insects for fundamental studies of host-symbiont interactions and their significance for applied research and practice.},
}

@article {pmid41302872,
year = {2025},
author = {Mu, K and Zhang, B and Cai, Z and Chen, J and Zhang, J and Su, J},
title = {Diversity and Influencing Factors of Endosymbiotic Bacteria in Tetranychus truncatus Sourced from Major Crops in Xinjiang.},
journal = {Insects},
volume = {16},
number = {11},
pages = {},
doi = {10.3390/insects16111126},
pmid = {41302872},
issn = {2075-4450},
support = {2022B02043//Key Research and Development Project of Autonomous Region/ ; U2003112//the National Natural Science Foundation of China/ ; 2024B02003//Key Research and Development Project of the Xinjiang/ ; },
abstract = {The Xinjiang Uygur Autonomous Region, situated in northwest China, boasts a unique geographical position and a consequent variety of environmental characteristics. T. truncatus is prevalent throughout this region as the primary pest affecting various crops. In this study, we analyzed the microbial community structures of endosymbiotic bacteria in T. truncatus collected from 17 regions and three host plants in Xinjiang using 16S rRNA sequencing. Through composition analysis of the endosymbiotic bacteria in T. truncatus from Xinjiang, it was found that the dominant bacterial phyla were Pseudomonadota and Bacillota. At the genus level, in addition to Wolbachia, Cardinium, and Spiroplasma (common symbiotic bacteria in T. truncatus), the infection rate of Rickettsia in T. truncatus in Xinjiang was found to be 92.8%. The diversity of the endosymbiotic bacteria community in T. truncatus is shaped by both host plant species and geographical region. Specifically, the endosymbiotic bacterial diversity in T. truncatus populations on corn was significantly higher than that observed in populations on cotton and soybean (p < 0.05). Furthermore, we discovered the diversity of endosymbiotic bacteria in T. truncatus was significantly higher in southern Xinjiang than in northern Xinjiang (p < 0.05).},
}

@article {pmid41302101,
year = {2025},
author = {Tan, Y and Ning, Y and Wang, S and Li, F and Cao, X and Wang, Q and Ren, A},
title = {Multilayered Regulation of Fungal Phosphate Metabolism: From Molecular Mechanisms to Ecological Roles in the Global Phosphorus Cycle.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/life15111676},
pmid = {41302101},
issn = {2075-1729},
support = {GHYF2024012//International Science & Technology Cooperation Program of Hainan Province/ ; No. SCKJ-JYRC-2023-37//Project of Sanya Yazhou Bay Science and Technology City/ ; No. ZDYF2024KJTPY005//Hainan ProvinceScience and Technology Special Fund/ ; },
abstract = {Phosphates are essential nutrients for living organisms, and they are involved in various biological processes, including lipid metabolism, energy synthesis, and signal regulation. Recent studies have elucidated the fundamental components and transport proteins of phosphate signaling pathways, thereby providing a more profound understanding of phosphate metabolism in fungi. In this review, we concentrate on synthesizing the recent findings concerning phosphate metabolism in fungi over the past five years. These findings include the role of phosphates in the global phosphorus cycle, their effect on fungal growth and development, the variations in PHO signaling pathways among different species, and their pivotal role in symbiosis with plants. A mounting body of research substantiates the notion that phosphates play a pivotal role in regulating fungal life activities through a multifaceted mechanism. This regulatory function encompasses the promotion of growth and development, adaptation to environmental variations among different fungal species, and the evolution of distinct regulatory factors and transport proteins. Consequently, this fosters fungal diversity.},
}

@article {pmid41302095,
year = {2025},
author = {Shi, S and Yang, W and Tao, Z and Li, F and Wei, B and Yue, C and Deng, Y and Shang, L and Chai, Z and Tang, YZ},
title = {In Situ Harvesting and Molecular Identification for the Germinating Species Diversity of Dinoflagellate Resting Cysts in Jiaozhou Bay, China.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/life15111670},
pmid = {41302095},
issn = {2075-1729},
support = {42406210//the National Science Foundation of China/ ; KFJ-SWYW047//the Key Research Infrastructures in the CAS Field Stations of the Chinese Academy of Science/ ; 2024YFF0506901//the National Key R&D Program of China/ ; U23A203//the National Science Foundation of China/ ; ZR2024MD109//Shandong Provincial Natural Science Foundation/ ; },
abstract = {Dinoflagellate resting cysts are critical to dinoflagellate ecology, acting as a key seed source for initiating harmful algal blooms (HABs) through their germination. However, the in situ germination dynamics of these cysts remain poorly understood due to technical challenges. To overcome this, we utilized the Germlings Harvester (GEHA), an in situ germination device we designed, to collect water samples containing dinoflagellate cysts germinated from marine sediments in Jiaozhou Bay, China, after 5 and 20 days of incubation. By combining the GEHA with metabarcoding analysis targeting 28S rDNA-specific primers for dinoflagellates, we identified 44 dinoflagellate species spanning 31 genera, 18 families, and 7 orders. Of these, 12 species were linked to HABs or recognized as toxic, including Azadinium poporum, Alexandrium leei, Alexandrium pacificum, Akashiwo sanguinea, Karlodinium veneficum, Stoeckeria algicida, and Luciella masanensis. Additionally, five species were newly identified as cyst producers, and one symbiotic dinoflagellate, Effrenium voratum, was detected. Our results also found that germinated dinoflagellate species increased from 23 to 34 with extended incubation, and the ratio of mixotrophic to heterotrophic species was approximately 2:1 in the samples of in situ sediments and seawater outside GEHA, as well as across germination durations (Sg-5 d vs. Sg-20 d). These findings provide essential field evidence for the role of resting cysts in driving HAB formation in this region and highlight the efficacy of the GEHA-based approach for studying in situ cyst germination dynamics, offering a robust tool for monitoring, early warning, prevention, and forecasting of HABs.},
}

@article {pmid41301944,
year = {2025},
author = {Yuan, Z and Fei, J and Li, S and Wu, Y and Liu, P},
title = {From Compensation to Collapse: UVB-Driven Disruption of Host-Microbiota Homeostasis Exacerbates Amphibian Ecological Risk.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {22},
pages = {},
doi = {10.3390/ani15223236},
pmid = {41301944},
issn = {2076-2615},
support = {KXB202310//the Scientific and Technological Innovation Ascend Plan of Harbin Normal University/ ; },
abstract = {The synergistic effects of stratospheric ozone depletion and climate change are intensifying surface ultraviolet-B (UVB) radiation, posing a severe threat to amphibians-one of the most endangered vertebrate groups globally. Xenopus laevis, with its cutaneous respiration and limited photoprotective mechanisms, exhibits high sensitivity to UVB, making it a suitable model for ecotoxicological studies. While UVB is known to cause DNA damage, immune suppression, and microbial dysbiosis, its mechanisms in multi-organ interactions, dose-response thresholds, and host-microbiome regulatory networks remain poorly understood. This study employed a gradient UVB exposure regime integrated with histopathology, oxidative stress assays, and 16S rRNA sequencing to systematically evaluate the effects of UVB on (1) cascade damage across skin, liver, and intestinal barriers; (2) immune cell distribution; (3) redox dynamics; and (4) microbial community structure and function. Our findings demonstrate that low-dose UVB activated compensatory antioxidant defenses without structural disruption, whereas exposure beyond a critical threshold induced nonlinear redox collapse, microbial dysbiosis, and multi-organ barrier failure, collectively exacerbating ecological adaptation risks. These results reveal a cross-scale mechanism by which UVB impairs amphibian health via disruption of host-microbe homeostasis, providing a conceptual and empirical framework for assessing species vulnerability under ongoing climate change.},
}

@article {pmid41301093,
year = {2025},
author = {Pokharel, U and Neelgund, G and Ray, RL and Balan, V and Kumar, S},
title = {Biochar for Soil Amendment: Applications, Benefits, and Environmental Impacts.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/bioengineering12111137},
pmid = {41301093},
issn = {2306-5354},
support = {02D48123//U.S. Environmental Protection Agency/ ; },
abstract = {The excessive use of chemical fertilizers results in environmental issues, including loss of soil fertility, eutrophication, increased soil acidity, alterations in soil characteristics, and disrupted plant-microbe symbiosis. Here, we synthesize recent studies available from up to 2025, focusing on engineered biochar and its application in addressing issues of soil nutrient imbalance, soil pollution from inorganic and organic pollutants, soil acidification, salinity, and greenhouse gas emissions from fields. Application of engineered biochar enhanced the removal of Cr (VI), Cd[2+], Ni[2+], Zn[2+], Hg[2+], and Eu[3+] by 85%, 73%, 57.2%, 12.7%, 99.3%, and 99.2%, respectively, while Cu[2+] and V[5+] removal increased by 4 and 39.9 times. Adsorption capacities for Sb[5+], Tl[+], and F[-] were 237.53, 1123, and 83.05 mg g[-1], respectively, and the optimal proportion of polycyclic aromatic hydrocarbon (PAH) removal was 57%. Herbicides such as imazapyr were reduced by 23% and 78%. Low-temperature pyrolyzed biochar showed high cation exchange capacity (CEC) resulting from improved surface functional groups. Although biochar application led to a yield increase of 43.3%, the biochar-compost mix enhanced it by 155%. The analysis demonstrates the need for future studies on the cost-effectiveness of biochar post-processing, large-scale biochar aging studies, re-application impact, and studies on biochar-compost or biochar-fertilizer mix productivity.},
}

@article {pmid41300498,
year = {2025},
author = {Baldelli, S and Aiello, G and De Bruno, A and Castelli, S and Lombardo, M and Stocchi, V and Tripodi, G},
title = {Bioactive Compounds and Antioxidant Potential of Truffles: A Comprehensive Review.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/antiox14111341},
pmid = {41300498},
issn = {2076-3921},
support = {2022K272X8//Prin 2022/ ; },
abstract = {Truffles are edible symbiotic hypogeal fungi and highly prized worldwide for their unique aroma and rich nutritional profile. Belonging to the order Pezizales and family Tuberaceae, with the genus Tuber being the most notable, truffles contain a diverse array of bioactive compounds including phenols, terpenoids, polysaccharides, anandamide, fatty acids, and ergosterols. These compounds contribute to a wide range of biological activities such as antioxidant, antibacterial, anti-inflammatory, hepatoprotective, and anticancer effects. This review comprehensively summarizes current scientific evidence on the biochemical composition, nutritional and aromatic properties, and biological activities of truffles, with special emphasis on their antioxidant and anti-tumor potential. Additionally, factors influencing truffle productivity and quality as well as advanced extraction and storage techniques to preserve bioactivity are discussed, highlighting their potential as valuable functional foods and sources of natural antioxidants.},
}

@article {pmid41300412,
year = {2025},
author = {Liu, Q and Zheng, J and Xing, Y and Guo, X and Qu, Y and Dong, Z and Yu, W and Zhang, G},
title = {Organic Mulching Enhances Soil Health and Fungal Diversity to Promote Growth of Aralia continentalis Kitag: A Sustainable Alternative to Conventional Fertilization in Agroecosystems.},
journal = {Biology},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/biology14111624},
pmid = {41300412},
issn = {2079-7737},
support = {20250203140SF//Key R&D Project of the Natural Science Foundation of Jilin Province/ ; ZKP202202//Climbing Project of Changchun University/ ; },
abstract = {Soil degradation from long-term chemical fertilization poses serious challenges to the sustainability of black soil agroecosystems in Northeast China, particularly for the cultivation of medicinal plants such as Aralia continentalis Kitag. To evaluate eco-friendly alternatives, we compared decomposed leaf mulching (LM), conventional fertilization (CF), and an untreated control (CK) in a five-year field experiment. LM significantly improved soil structure by reducing bulk density by 12.8% (p < 0.05) and increasing porosity by 15.6% while enhancing organic carbon and humus fractions by 23.4% and 31.7%, respectively. These changes promoted microbial biomass carbon by 28.2% (p < 0.01) and enriched beneficial fungi such as Mortierella, which correlated with nutrient mobilization and plant growth. Fungal richness and diversity were higher under LM (+18.4% and +12.6%, respectively), whereas CF reduced evenness and favored dominance of stress-tolerant taxa. Functional predictions indicated that LM sustained saprotrophic and symbiotic guilds, while CF weakened mycorrhizal associations. Structural equation modeling identified microbial community composition as a central mediator linking soil properties, microbial diversity, and biomass (R[2] = 0.78), with LM exerting the strongest cascading effects. At the plant level, LM achieved the highest above- and belowground biomass, outperforming CF and CK by 26.3% and 34.5%, respectively. Overall, decomposed leaf mulching represents a sustainable strategy to restore soil quality, enhance microbial diversity, and support medicinal plant cultivation in cold-region agroecosystems.},
}

@article {pmid41300391,
year = {2025},
author = {Oberprieler, C},
title = {Towards a Research Programme Aiming at Causes and Consequences of Reticulate Evolution.},
journal = {Biology},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/biology14111601},
pmid = {41300391},
issn = {2079-7737},
abstract = {Evolution is reticulate. Reticulation increases diversity and complexity on the different levels of the evolutionary hierarchy. In addition to the tendency for diversity and complexity to increase in unchecked evolutionary systems by ongoing divergence ('Zero-Force Evolutionary Law', 'Biology's First Law'), reticulate evolution, therefore, acts as a second mechanism for the establishment of evolutionary novelty and the rise in biodiversity and biocomplexity ('Biology's Second Law'). This provides the raw material for subsequent diversity-confining drift and selection processes. In order to fully appreciate reticulation processes as part of an updated paradigm of evolutionary biology, a research programme on the topic should encompass the identification of the fundamental evolutionary entities as vertices and the study of the relationships among these vertices as edges in the resulting network architectures. Additionally, along with surveys on the underlying determinants, this will lead to the study of emergent boundary conditions for reticulations and for the porosity of evolutionary entities. Finally, the programme should address the question whether there are equilibrium conditions between the complete fusion and complete isolation of evolutionary entities ('Goldilocks Zones') that foster reticulate evolution. As tools in this research programme, machine learning and modelling approaches, along with methods in the field of network reconstruction, transcriptomics, epigenetics, and karyology, are identified.},
}

@article {pmid41299971,
year = {2025},
author = {Song, D and Zhong, X and Wu, Y and Guo, J and Song, L and Yang, L},
title = {From Artisan Experience to Scientific Elucidation: Preparation Processes, Microbial Diversity, and Food Applications of Chinese Traditional Fermentation Starters (Qu).},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {22},
pages = {},
doi = {10.3390/foods14223814},
pmid = {41299971},
issn = {2304-8158},
support = {No.QianKeHeJiChu- ZD[2025]018//Guizhou Provincial Basic Research Program (Natural Science)/ ; },
abstract = {BACKGROUND: Qu was the core starter of traditional Chinese fermentation and had long relied on artisan experience, which led to limited batch stability and standardization. This review organized the preparation processes, microbial diversity, and application patterns of qu in foods from experience to science perspective.

METHODS: This work summarized typical process parameters for daqu, xiaoqu, hongqu, wheat bran or jiangqu, douchi qu, and qu for mold curd blocks used for furu. Parameters covered raw material moisture, bed thickness, aeration or turning, drying, final moisture, and classification by peak temperature. Multi-omics evidence was used to analyze the coupling of temperature regime, community assembly, and functional differentiation. Indicators for pigment or enzyme production efficiency and safety control such as citrinin in hongqu were included.

RESULTS: Daqu showed low, medium, and high temperature regimes. Thermal history governed differences in communities and enzyme profiles and determined downstream fermentation fitness. Xiaoqu rapidly established a three-stage symbiotic network of Rhizopus, Saccharomyces, and lactic acid bacteria, which supported integrated saccharification and alcohol fermentation. Hongqu centered on Monascus and achieved coordinated pigment and aroma formation with toxin risk control through programmed control of temperature, humidity, and final moisture. Wheat bran or jiangqu served as an enzyme production engine for salt-tolerant fermentation, and the combined effects of heat and humidity during the qu period, aeration, and bed loading determined hydrolysis efficiency in salt. Douchi and furu mold curd blocks used thin-layer cultivation and near-saturated humidity to achieve stable mold growth and reproducible interfacial moisture.

CONCLUSIONS: Parameterizing and online monitoring of key variables in qu making built a process fingerprint with peak temperature, heating rate, and moisture rebound curve at its core. Standardization and functional customization guided by temperature regime, community, and function were the key path for the transition of qu from workshop practice to industry and from experience to science. This approach provided replicable solutions for flavor consistency and safety in alcoholic beverages, sauces, vinegars, and soybean products.},
}

@article {pmid41299080,
year = {2025},
author = {Wang, ZZ and Ma, RF and Gu, LC and Wang, LZ and Chen, T and Yang, P and Zou, JN and Zhu, JY and Wu, ZW and Zhou, YN and Shi, M and Shen, XX and Huang, JH and Chen, XX},
title = {Dual interference with host neuropeptide signaling allows parasitoid wasp to hijack host sugar metabolism.},
journal = {The EMBO journal},
volume = {},
number = {},
pages = {},
pmid = {41299080},
issn = {1460-2075},
support = {U22A20485//MOST | NSFC | National Natural Science Foundation of China-Zhejiang Joint Fund for the Integration of Industrialization and Informatization (NSFC-Zhejiang Joint Fund)/ ; 32272607//MOST | National Natural Science Foundation of China (NSFC)/ ; 2023YFD1400800//MOST | National Key Research and Development Program of China (NKPs)/ ; 226-2024-00070//MOE | Fundamental Research Funds for the Central Universities (Fundamental Research Fund for the Central Universities)/ ; },
abstract = {Changes in host carbohydrate metabolism determine the outcome of host-parasite relationships, but the underlying mechanistic basis remains elusive. Here, we show that the parasitoid wasp Cotesia vestalis induces trehalose accumulation in its host, the moth Plutella xylostella, largely independently of insulin/adipokinetic hormone signalling and food intake. Instead, parasitoids rewire host carbohydrate metabolism via two pathways activated by the evolutionarily conserved short neuropeptide F (sNPF), a functional analogue of mammalian neuropeptide Y. Parasitoid-derived teratocytes secrete sNPF that interacts with the sNPF receptor (sNPFR) on host cells, and contributes to host hypertrehalosemia by promoting glycogenolysis in the fat body. We further find that a parasitoid-symbiotic virus induces expression of host-encoded sNPF, which stimulates glycolysis in the host midgut. Furthermore, we show that the host sNPF-sNPFR complex stimulates Gq/Ca[2+] signalling, while the parasitoid sNPF, exhibiting higher receptor affinity, triggers Gi/cAMP signalling. Molecular docking analyses suggest that the observed distinct receptor activation properties may be attributed to structural variations in the sNPF-sNPFR binding pocket. Collectively, our findings uncover an unexpected role of peripheral sNPFs in the regulation of carbohydrate metabolism during host-parasite interactions.},
}

@article {pmid41298861,
year = {2025},
author = {Han, H and Zhang, K and Qian, Z},
title = {Adaptability analysis and spatial correlation characteristics of water-energy-food-ecology system in the Yellow River Basin from the perspective of symbiosis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {42266},
pmid = {41298861},
issn = {2045-2322},
support = {2025-ZZJH-052//2025 General Project of Humanities and Social Science Research of Universities in Henan Province/ ; 2024CJJ151//2024 Philosophy and Social Sciences Planning project in Henan Province/ ; 42301357//National Natural Science Foundation of China/ ; },
abstract = {Based on the symbiosis theory, the concept of compatibility within the regional water-energy-food-ecology (WEFE) system was proposed. An indicator system for adaptability analysis was constructed from three subsystems: coordination, stability, and sustainability. Using the co-evolution model and partial autocorrelation analysis, the spatiotemporal evolutionary patterns and spatial correlation patterns of WEFE adaptability in the Yellow River Basin (YRB) from 2011 to 2022 were assessed. The results indicated that: (1) The order of subsystem weights was: stability > sustainability > coordination. (2) The absolute adaptability of the indicator was significantly higher than the relative adaptability. The adaptability degree of the three subsystems increased to varying degrees. Overall, the adaptability of the WEFE system in the middle and lower reaches of the YRB was obviously higher than in the upper reaches. (3) In terms of system coordination, the coordination and stability subsystems improved, whereas the coordination of the sustainability subsystem gradually declined. (4) The adaptability levels of the WEFE system in the YRB had a random distribution. In terms of local spatial autocorrelation, there were significant spatial disparities and path dependencies in the WEFE system adaptability across the YRB. This study enhances the understanding of the symbiotic adaptability development among water resources, food, energy and ecology in the YRB and provides important insights for regional multi-resource collaborative management.},
}

@article {pmid41298464,
year = {2025},
author = {Ricci, F and Bay, SK and Nauer, PA and Wong, WW and Ni, G and Jimenez, L and Jirapanjawat, T and Leung, PM and Bradley, JA and Eate, VM and Hall, M and Stubbusch, AKM and Fernández-Marín, B and de Los Ríos, A and Cook, PLM and Schroth, MH and Chiri, E and Greening, C},
title = {Metabolically flexible microorganisms rapidly establish glacial foreland ecosystems.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66734-4},
pmid = {41298464},
issn = {2041-1723},
support = {APP1178715//Department of Health | National Health and Medical Research Council (NHMRC)/ ; DE230101346//Department of Education and Training | Australian Research Council (ARC)/ ; DE250101210//Department of Education and Training | Australian Research Council (ARC)/ ; 101115755//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PID2019-105469RB-C22//Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)/ ; },
abstract = {An overriding question in ecology is how new ecosystems form. This question can be tested by studying colonisation of environments with little to no pre-existing life. Here, we investigated the functional basis of microbial colonisation in the forelands of a maritime Antarctic and an alpine Swiss retreating glacier, by integrating quantitative ecology, metagenomics, and biogeochemical measurements. Habitat generalists and opportunists rapidly colonise both forelands and persist across soil decadal chronosequences serving as proxies for temporal community dynamics. These microbes are metabolically flexible chemotrophic aerobes that overcome oligotrophic conditions by using organic and inorganic compounds, including atmospheric trace gases and sulphur substrates, for energy and carbon acquisition. They co-exist with metabolically flexible early-colonising opportunists and metabolically restricted later-colonising specialists, including Cyanobacteria, ammonia-oxidising archaea, and obligate predatory and symbiotic bacteria, that exhibit narrower habitat distributions. Analysis of 589 species-level metagenome-assembled genomes reveals early colonisation by generalists and opportunists is strongly associated with metabolic flexibility. Field- and laboratory-based biogeochemical measurements reveal the activity of metabolically flexible microbes rapidly commenced in the forelands. Altogether, these findings suggest primary succession in glacial foreland soils is driven by self-sufficient metabolically flexible bacteria that mediate chemosynthetic primary production and likely provide a more hospitable environment for subsequent colonisation.},
}

@article {pmid41297937,
year = {2025},
author = {Endo, K and Mutoh, A and Satoh, M and Ogawa, K and Shimatani, K and Suzuki, N},
title = {Urban veterinary accessibility and community well-being in Japan: a cross-sectional analysis using regional indicators.},
journal = {The Journal of veterinary medical science},
volume = {},
number = {},
pages = {},
doi = {10.1292/jvms.25-0396},
pmid = {41297937},
issn = {1347-7439},
abstract = {Access to medical care is important not only for humans, but also for companion animals. However, the distribution of veterinary services and their potential benefits to human well-being remain unclear. This study examined the relationship between veterinary clinics and community well-being in urban areas of Japan. The dataset included total 191 wards in Tokyo (a metropolitan city) and 19 ordinance-designated cities. Veterinary clinical locations were obtained from a high-resolution commercial database provided by ZENRIN Marketing Solutions Co., Ltd. Community well-being scores were obtained from the Digital Agency of Japan. Multiple linear regression analysis was conducted to predict the well-being scores based on the number of veterinary or human clinics per 100,000 residents. The results of veterinary clinics showed positive satisfaction with environmental symbiosis (β=1.17), natural disasters (β=1.04), community connections (β=1.00), self-efficacy (β=1.18), health status (β=1.32), employment and income (β=0.89), recreation and entertainment (β=0.91), culture and arts (β=1.53), abundance of educational opportunities (β=1.34), and business creation (β=1.03), while the results of human clinics showed negative satisfaction with public spaces (β=-0.69). Findings suggest that residents who place a high value on pets and the care they require may be attracted to areas with high concentrations of art, entertainment, education, and business resources. Although unmeasured confounding factors were related, this study posits a new assumption that the enrichment of animal welfare services is associated with regional well-being.},
}

@article {pmid41297850,
year = {2025},
author = {Dell'Aglio, E and Ferrarini, MG and Rebollo, R},
title = {Epigenetics and non-coding RNAs in host-endosymbiont interactions: insights from Wolbachia and beyond.},
journal = {Current opinion in insect science},
volume = {},
number = {},
pages = {101464},
doi = {10.1016/j.cois.2025.101464},
pmid = {41297850},
issn = {2214-5753},
abstract = {Symbioses are widespread in nature and are among major evolutionary forces. Insects have recurrently established intracellular symbioses with bacteria, balancing between immune responses and homeostasis. The processes involved in endosymbiosis establishment, maintenance, and control have recently been associated with epigenetic pathways and non-coding RNAs, which are known to regulate a wide range of cellular processes, including development, differentiation, immune response, and metabolism. Using the well-studied Wolbachia-Aedes aegypti model as a reference, we summarize how these mechanisms influence host gene expression, endosymbiont maintenance, and antiviral defence. Beyond Wolbachia, only a few examples have provided functional evidence of the role of epigenetics in regulating natural insect-bacteria associations. Collectively, these studies demonstrate that epigenetic factors can act as mediators of host-endosymbiont coordination; however, determining if such factors are drivers or by-products of symbiosis establishment will require further investigation.},
}

@article {pmid41297327,
year = {2025},
author = {Fuad, MTI and Dong, Y and Li, Z and Ge, M and Sharifuzzaman, SM and Liu, X and Zhang, X and Xu, Q},
title = {Seasonal gut microbiota and functional dynamics in brittle star (Ophiothrix exigua) from the Yellow Sea, China.},
journal = {Marine environmental research},
volume = {213},
number = {},
pages = {107734},
doi = {10.1016/j.marenvres.2025.107734},
pmid = {41297327},
issn = {1879-0291},
abstract = {The gut microbiota forms a complex symbiotic community that performs essential functions for the host, including metabolism, nutrient absorption, and environmental adaptation, while being shaped by both environmental and intrinsic host factors. This study represents the first comprehensive investigation of seasonal gut microbiota diversity in brittle stars, examining Ophiothrix exigua from the Yellow Sea using full-length 16S rRNA gene metabarcoding. A total of 565 amplicon sequence variants were identified from gut samples, distributed across 20 phyla, 135 genera, and 46 species. The dominant phyla included Proteobacteria, and Spirochaetota, with Salinispira identified as the core genus. Seasonal variations in microbiota diversity were evident, with Caulobacter predominating in summer, and Kistimonas and Trichococcus driving winter community shift. Corresponding seasonal changes in gut microbiota functions and functional pathways were observed. Fatty acid biosynthesis pathways were enriched in winter, while aromatic compound degradation pathways showed elevated activity in summer. Although seawater microbiota exerted relatively minor influence on gut microbial diversity, correlations with abiotic factors such as pH were observed. This study highlights the intricate relationship between gut microbiota, environmental microbiota, and abiotic factors in shaping the seasonal gut microbiota diversity of O. exigua, contributing to a better understanding of the host-microbiome ecology of invertebrates.},
}

@article {pmid41297304,
year = {2025},
author = {Ding, J and Wang, D and Ji, B and Li, A and Li, XY},
title = {Effect of Nitrosomonas europaea on Chlorella vulgaris in bio-hydrogels for startup of microalgal-bacterial granular sludge: Performance and microscopic mechanism.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {125023},
doi = {10.1016/j.watres.2025.125023},
pmid = {41297304},
issn = {1879-2448},
abstract = {Algal-bacterial granular sludge technology holds significant promise for treating municipal wastewater with carbon emission reduction. However, its practical application has been constrained by the long startup period. In this study, bio-hydrogels co-encapsulating autotrophic ammonia-oxidizing bacteria (Nitrosomonas europaea) and photomixotrophic microalgae (Chlorella vulgaris) were used in a microalgal-bacterial granules system (MBGS) for the treatment of low C/N wastewater. The operating conditions of the MBGS system included inoculation volume ratio of 1:6 (bio-hydrogel granules: wastewater), initial biomass of 0.33 g suspended solids (SS) /L, light intensity of 300 μmol/m[2]·s, and no aeration. The results showed that this strategy reduced the typical MBGS startup period to just 6 days, with biomass accumulation (1.53 g SS/L, >4 g SS/L after running 120 days) and efficient chemical oxygen demand (COD) and total nitrogen (TN) removal (effluent COD <20.00 mg/L and TN <2.50 mg/L). Transcriptomic analysis revealed that the symbiosis with Nitrosomonas significantly upregulated the expression of the PetH gene, which encodes a reductase (EC:1.18.1.2) in the photosynthetic system of Chlorella (log2 fold change=13.63), thereby enhancing the supply of NADPH required for the Calvin cycle. Concurrently, the expression of the rbcL gene, encoding the large subunit of Rubisco in Chlorella, was upregulated by 1.4-fold, which promoted photosynthetic carbon fixation. The symbiosis also suppressed heterotrophic metabolism in Chlorella, as evidenced by downregulation of 72.5 % of genes in glycolysis and the tricarboxylic acid cycle, thereby mitigating the adverse effects of encapsulating material biodegradation on the bio-hydrogel structure. In addition, cell proliferation of Chlorella was stimulated (over 13-fold upregulation of DNA replication licensing factors MCM5 and MCM6), which increased biomass and nutrient removal efficiency. Furthermore, a higher light intensity of 400 μmol/m[2]/s promoted a significant increase in extracellular polymeric substances (EPS) content (106.76 mg/g SS), improved granule stability (integrity coefficient < 20 %), and enhanced biomass production (4.68 g SS/L after 120 days of operation). These findings highlight a promising strategy for sustainable wastewater treatment.},
}

@article {pmid41297084,
year = {2025},
author = {Cameron, CC and Gebbie, W and Bowman, C and Waters, ER and Kalyuzhnaya, MG},
title = {Characterization and description of plant-growth-promoting methanotrophic bacteria belonging to the genus of Methylocaldum.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {1},
pages = {126670},
doi = {10.1016/j.syapm.2025.126670},
pmid = {41297084},
issn = {1618-0984},
abstract = {Arid soil microbiomes present untapped resources of microbial diversity. Here, we describe twelve isolates, all belonging to the Methylocaldum genus. Based on metagenomic studies, the isolates represent the major clades of methanotrophic bacteria inhabiting the arid biomes of Southern California, comprising up to 0.03 % of the total soil microbiota. Phenotyping of isolates indicates that they are obligate methanotrophic bacteria, some capable of methanol utilization. All strains can fix nitrogen, use nitrate and ammonia as a N-source, and have key genetic signatures of autotrophy, methylotrophy, and N2O assimilation. Based on the 16S rRNA phylogeny and whole -genome analyses, all strains are assigned to the species M. gracile. Three isolates from the rhizosphere of native Californian plants (Strains 0917, YM2 and S3V3) and GT1B-W are set apart from the other M. gracile strains, despite sharing <98 % of average nucleotide identity. Microbes isolated from plant rhizosphere display 150 unique genetic features and a series of tandem gene duplications predicted to contribute to their interactions with plants, including the 20-gene polyketide biosynthesis cluster and the TRAP C4-dicarboxylate transport system. Consistent with the genetic properties that may indicate an enhancement of plant-cooperation functions, the rhizosphere isolates support the survival of plants, Boechera depauperata and Arabidopsis thaliana, under drought conditions. Based on genetic and phenotypic characteristics, we propose to designate strains 0917, YM2, S3V3, and GT1B-W as a new subspecies of Methylocaldum gracile - Methylocaldum gracile subspecies dēsertum, L.n. dēsertum - a desert, to represent the native habitat of the species. The amended description of the M.gracile species is provided.},
}

@article {pmid41295393,
year = {2025},
author = {Tame, A},
title = {Integrated Regulation of Immunity and Nutritional Symbiosis in Deep-Sea Mussels.},
journal = {Marine drugs},
volume = {23},
number = {11},
pages = {},
doi = {10.3390/md23110425},
pmid = {41295393},
issn = {1660-3397},
support = {JP24K18110//the Japan Society for the Promotion of Science (JSPS) through KAKENHI/ ; },
mesh = {Animals ; *Symbiosis/immunology ; *Bivalvia/immunology/microbiology ; Gills/immunology/microbiology ; Immunity, Innate ; Phagocytosis/immunology ; Hemocytes/immunology ; Bacteria ; },
abstract = {Deep-sea mussels of the genus Bathymodiolus exhibit adaptability to nutrient-poor deep-sea environments by establishing nutritional intracellular symbiosis with chemosynthetic bacteria harbored within the gill epithelial cells. However, this poses a conflict for the innate immune system of the host, which must balance the tolerance of beneficial symbiotic bacteria with the need to eliminate exogenous microbes. This review synthesizes existing knowledge and recent findings on Bathymodiolus japonicus to outline the cellular and molecular mechanisms governing this symbiotic relationship. In the host immune system, hemocytes are responsible for systemic defense, whereas gill cells are involved in local symbiotic acceptance. Central to the establishment of symbiosis is the host's phagocytic system, which non-selectively engulfs bacteria but selectively retains symbionts. We highlight a series of cellular events in gill cells involving the engulfment, selection, retention and/or digestion of symbionts, and the regulatory mechanism of phagocytosis through mechanistic target of rapamycin complex 1, which connects bacterial nutrient supply with host immune and metabolic responses. This integrated model of symbiosis regulation, which links immunity, metabolism, and symbiosis, provides a fundamental framework for understanding how hosts establish and maintain a stable coexistence with microbes, offering a new perspective on symbiotic strategies in diverse organisms.},
}

Animals
*Symbiosis/immunology
*Bivalvia/immunology/microbiology
Gills/immunology/microbiology
Immunity, Innate
Phagocytosis/immunology
Hemocytes/immunology
Bacteria

@article {pmid41295187,
year = {2025},
author = {Luna-Fontalvo, JA and Balocchi, O and Martínez, O and Alonso, M and Ferrada, E},
title = {Symbiosis Between Epichloë Fungi and Bromus Grasses: A Review of Current Knowledge and Future Directions.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/jof11110807},
pmid = {41295187},
issn = {2309-608X},
support = {1220448//Agencia Nacional de Investigación y Desarrollo/ ; },
abstract = {Epichloë is a genus of endophytic fungi that forms systemic, vertically transmitted, and asymptomatic mutualistic associations with grasses in the subfamily Pooideae. These symbioses are non-pathogenic and are of considerable importance in agronomic and livestock systems due to their roles in enhancing host fitness under biotic and abiotic stress. Several studies have reported associations between Epichloë endophytes and species of the genus Bromus, a taxonomically complex group characterized by varying ploidy levels and frequent hybridization. Among its sections, Bromopsis includes the highest number of species naturally colonized by Epichloë fungi, while sections Bromus and Ceratochloa show lower infection rates. In South America, endophytes such as E. pampeana, E. tembladerae, E. typhina, and morphotypes of Neotyphodium spp. have been documented in species including B. auleticus, B. brachyanthera, and B. setifolius, where they appear to contribute to stress resilience. Although most findings originate from Argentina, significant knowledge gaps remain regarding the diversity and distribution of these endophytes in native Bromus species across the continent. This review synthesizes the current understanding of Epichloë-Bromus interactions, emphasizing their ecological and agronomic relevance, particularly in South America. Key factors influencing the establishment of these symbioses are examined, and future research directions are proposed to advance the study of these associations.},
}

@article {pmid41295153,
year = {2025},
author = {Jiang, S and Cheng, Z and Pan, H and Liu, S and Qu, H and Gao, M and Yang, L and Zhou, J},
title = {High Fire Drives the Reorganization of Taiga Soil Fungal Communities with Ascomycota as the Dominant Phylum After Long-Term Recovery.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/jof11110772},
pmid = {41295153},
issn = {2309-608X},
support = {GZ2024066//Guidance Project of Heilongjiang Provincial Key Research and Development Plan/ ; GZCG2023-024//Forestry and Grassland Ecological Protection and Restoration Funds Project/ ; CZKYF2024-1-A008//the Financial Special Project of Heilongjiang Province/ ; },
abstract = {Forest fires are key disturbance factors in forest ecosystems, and soil fungi play an irreplaceable role in post-fire recovery. This study focused on forest areas burned in 2000 in the Daxing'anling region of China, targeting long-term recovery sites with different fire intensities. Illumina MiSeq sequencing was used to analyze the structural characteristics of fungal communities and their environmental drivers. Results showed that compared with the control check (CK), the Shannon index of the low fire group (L) increased significantly (p < 0.05), while moderate (M) and high (H) fire groups reduced fungal diversity significantly. PCoA indicated significant differences in community structure (R[2] = 0.97, p = 0.001). In highly burned areas, the relative abundance of Ascomycota reached 94.17%, and Basidiomycota lost its dominance. Spearman analysis showed that pH, available phosphorus, available potassium, soil fluorescein diacetate hydrolase, soil dehydrogenase, and soil urease were significantly positively correlated with fungal alpha diversity. RDA revealed that total nitrogen, available phosphorus, soil water content, alkaline nitrogen, active potassium, and dissolved organic carbon had extremely significant effects on soil fungal community composition (p < 0.01). Co-occurrence network analysis indicated that symbiotic relationships dominated all groups. Networks in L and M groups were more complex, while that in H group was simplified and severely damaged. This study indicated that after long-term recovery, soil fungal communities in low fire areas returned to pre-fire levels; those in moderate and high fire areas did not recover, with high fire burns causing severe damage and community structure reorganization.},
}

@article {pmid41295138,
year = {2025},
author = {Li, P and Liu, J and Zhang, S and Zhu, Y and Yin, X and Xing, L and Wei, D and Jin, L},
title = {Effects of Nitrogen and Phosphorus Levels on Arbuscular Mycorrhizal Symbiosis and Associated Bacterial Communities in Culture.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/jof11110757},
pmid = {41295138},
issn = {2309-608X},
support = {KJCX20230116; ZHS202306//Special Project for the Construction of Scientific and Technological Innovation Capacity of Beijing Academy of Agriculture and Forestry Sciences/ ; },
abstract = {Arbuscular mycorrhizal (AM) fungi establish mutualistic symbioses with plant roots, enhancing plant growth and improving soil fertility through nutrient exchange. Among these, soil nitrogen (N) and phosphorus (P) are critical for symbiosis formation, directly influencing nutrient uptake and translocation within the symbiotic system. This study aimed to examine the regulatory roles of N and P levels on AM fungal development and associated bacterial communities in culture. Sorghum was used as the host plant in pot experiments with two AM fungi, Rhizophagus irregularis and Funneliformis mosseae, under varying N and P concentrations. The analyzed parameters included mycorrhizal colonization, propagule production, plant biomass, nutrient contents (N, P, and K), and bacterial community diversity. N3P1 treatment (150 mg/L N, 30 mg/L P) yielded the highest colonization rate, spore production, and arbuscule abundance in both AM fungal symbionts. At equivalent N and P concentrations, the N, P, and K contents in inoculated plants were significantly higher than those in controls. AM fungal inoculation markedly increased the bacterial diversity in the culture (Shannon index raised by 15.2-28.7%) and enriched beneficial taxa, such as Bradyrhizobium and Pseudomonas. N and P concentrations substantially influenced AM fungal symbiosis, with optimal development observed under N3P1 conditions. By regulating AM symbiotic establishment, N and P levels reshaped microbial community composition, providing theoretical guidance for industrialized AM fungal cultivation and inoculant production.},
}

@article {pmid41294327,
year = {2025},
author = {Huang, J and Xu, S and Liu, J and Wang, Q and Han, L and Ji, M and Lei, C and Zhu, Q and Chen, H},
title = {The viral proteins of influenza A virus competitively bind to TRIM31 with MAVS to fine-tune the antiviral innate immunity.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0189325},
doi = {10.1128/jvi.01893-25},
pmid = {41294327},
issn = {1098-5514},
abstract = {UNLABELLED: The influenza A virus (IAV) continues to pose a serious threat to animals and humans, making it urgent to reveal more about IAV-host interactions. Tripartite motif protein 31 (TRIM31), an E3 ubiquitin ligase, has been identified as an agonist of the type-I interferon (IFN-I) response against RNA viruses by targeting mitochondrial antiviral signaling protein (MAVS). Here, we demonstrated that TRIM31 plays critical and novel roles in the life cycle of IAV. TRIM31 promoted the IFN-I signaling induced by IAV; however, it was surprisingly found that TRIM31 does not affect IAV replication. Instead, IAV replication was significantly promoted by TRIM31 in MAVS- or interferon receptor-deficient cells, suggesting TRIM31 may facilitate IAV replication in an interferon-independent manner. Mechanistically, TRIM31 interacted specifically with the basic polymerase 1 (PB1), acidic polymerase (PA), and hemagglutinin (HA) proteins of different subtypes of IAV. The interaction between TRIM31 and the PB1, PA, and HA proteins enhances the stability and polymerase and membrane fusion activities of these viral proteins by catalyzing the K63-linked ubiquitination. Further, the PB1, PA, and HA proteins competitively bind to TRIM31 for IAV replication, leading to the attenuation of the TRIM31-MVAS complex-mediated IFN-I signaling activation. Therefore, the antiviral and proviral effects of TRIM31 reach a balance in IAV-infected cells, resulting in no significant impact on IAV replication. Our novel findings revealed an IAV-specific mechanism that IAV exploits TRIM31 to fine-tune the antiviral innate response and maintain the homeostasis of viral replication.

IMPORTANCE: During the long-term symbiosis with the host, IAVs have evolved a series of unique mechanisms to adapt to the host and support their own replication. The MAVS-mediated IFN-I signaling pathway is crucial for host cells to defend against RNA virus invasion, with TRIM31 functioning as a specific agonist for the activation of IFN-I antiviral response. In the present study, we demonstrated that IAV exploits TRIM31 to promote the stability and activity of viral proteins and reduces the positive effect of TRIM31 on the IFN-I response, thereby preventing TRIM31 from inhibiting IAV replication. Therefore, our results revealed a novel mechanism employed by IAV to adapt to host antiviral response and expanded our understanding of virus-host interactions.},
}

@article {pmid41294280,
year = {2025},
author = {Ullah, I and Zhou, D and Khan, AR and Muhammad, M and Zhang, Q and Ma, J and Egamberdieva, D and Shurigin, V and Li, L},
title = {Unveiling the Adaptation Mechanisms of Symbiotic Microbial Communities in Glycyrrhiza glabra Under Extreme Environmental Conditions.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf291},
pmid = {41294280},
issn = {1365-2672},
abstract = {Glycyrrhiza glabra is a medicinal legume species that is adapted to arid and saline environments, as well as climate stressors such as drought, salinity and extreme heat. This review highlights the latest developments in understanding the microbial communities associated with G. glabra, which enhance stress tolerance through nutrient acquisition, phytohormone modification, the production of antioxidants and osmotic regulation. This review synthesizes research on the distribution, diversity, and functionality of these microbial communities including endophytes, rhizobacteria, and arbuscular mycorrhizal fungi within the ecological context of degraded and marginal soils, which functionally enhances G. glabra as a model plant for studying plant-microbial interactions in extreme environments. We specifically highlight the microbial regulation of glycyrrhizin biosynthesis, a critical defense-related secondary metabolite with known therapeutic applications. Finally, we present an overview of new and emerging multi-omics tools that elucidate the molecular mechanisms underpinning these beneficial microbial interactions, and their potential in developing bio-inoculants for climate-resilient agriculture and providing a blueprint for harnessing native microbial partnerships to enhance plant survival, productivity, and soil restoration under climate uncertainty.},
}

@article {pmid41293613,
year = {2025},
author = {Zecca, N and Lücking, L and van Dijk, HAJ and Manzolini, G},
title = {Techno-Economic Assessment of Industrial Symbiosis Between Steel and Urea Plants: The INITIATE Process.},
journal = {Energy & fuels : an American Chemical Society journal},
volume = {39},
number = {46},
pages = {22293-22310},
pmid = {41293613},
issn = {0887-0624},
abstract = {The steelmaking and fertilizer industries accounted for approximately 10% of global anthropogenic CO2 emissions in 2024. This study examines an industrial symbiosis concept, termed INITIATE, which integrates these two sectors to enhance resource efficiency and to reduce CO2 emissions. The proposed system utilizes process gases from steel production as a feedstock for urea synthesis, using the sorption enhanced water gas shift (SEWGS) technology for simultaneous CO2 capture and production of a H2-N2 mixture. This stream is suitable for ammonia synthesis, which subsequently reacts with part of captured CO2 in a downstream urea production process. Two sizes of fertilizer production are analyzed: a small-scale configuration producing 224 turea/day and a large-scale case with a production capacity of 1500 turea/day. Simulation results indicate that the integrated symbiotic configuration of the INITIATE system enables substantial reductions in both the natural gas consumption and direct CO2 emissions. Under scenarios utilizing renewable electricity, the level of CO2 avoidance can reach up to 68%. The specific primary energy consumption per unit of CO2 avoided (SPECCA) ranges from -2.5 to 2.5 GJ/tCO2 . Negative values reflect a net reduction in primary energy demand, resulting from process integration and efficient resource utilization. From an economic perspective, the cost of CO2 avoidance is estimated at 24 €/tCO2 for the small-scale plant, increasing to 130 €/tCO2 for the large-scale configuration. Sensitivity analyses reveal that these costs are highly dependent on the prices of electricity and natural gas, with lower electricity prices and higher natural gas prices improving the economic performance of the INITIATE system compared with the base and reference cases.},
}

@article {pmid41292562,
year = {2025},
author = {Ullah, F and Zaman, F and Ishfaq, M and Ullah, H and Wang, C and Zhifang, L and Geilfus, CM},
title = {Sustainable Greenhouse Tomato Production: Benefits of Inoculation With Arbuscular Mycorrhizal Fungi Under Low Nitrogen and Phosphorus Conditions.},
journal = {Plant-environment interactions (Hoboken, N.J.)},
volume = {6},
number = {6},
pages = {e70058},
pmid = {41292562},
issn = {2575-6265},
abstract = {The effects of overused chemical fertilizers, which threaten soil, plant, and human health, have always remained a topic of interest in theory and practice, emphasizing the judicious use of mineral nutrients. This study was aimed at reducing the harmful effects of excessive chemical fertilizer application and at exploring alternative approaches that can improve soil fertility without environmental and health damage. The experimental design involved a controlled greenhouse setup where tomato cultivars were inoculated with different AMF species under varying nitrogen (N) and phosphorus (P) doses. The tomato cultivars Rio Grande and Nadir were inoculated with arbuscular mycorrhizal fungi species, including Glomus claroideum, Glomus etunicatum, Glomus fasciculatum, and Glomus mosseae-within a commercial greenhouse. This study aimed to evaluate the potential effects of these fungi on tomato growth physiology, yield, and fruit quality when subjected to varying doses of N and P. Glomus mosseae significantly increased plant height by 14%, stem diameter by 22.25%, dry matter by 23.59%, yield by 38.57%, N uptake by 16.40%, P uptake by 37.5%, potassium (K) uptake by 18.55%, chlorophyll a (Chl a) content by 15.18%, and chlorophyll b (Chl b) content by 25.19% when compared to untreated controls. Additionally, Glomus mosseae improved fruit diameter by 9.98%, fruit firmness by 18.45%, juice content by 15.20%, titratable acidity (TA) by 10.42%, and ascorbic acid concentration by 16.75%. The interaction between the N and P levels of 140:42 mg L[-1] and the arbuscular mycorrhizal fungus (AMF) species Glomus mosseae resulted in the highest improvement in growth, yield, and fruit quality-related traits. Among the cultivars, Rio Grande exhibited the greatest root colonization, plant dry matter content, N, P, K uptake, plant height, Chl a, Chl b, and yield when compared to the control. In contrast, cultivar Nadir showed the highest stem diameter, fruit size, firmness, ascorbic acid, fruit juice contents, and TA. This study recommends that AMF inoculation in combination with a low N and P supply can be promising for improving tomato growth, productivity, and fruit quality on a commercial scale with minimum threats to the environment and human health. This study suggests the exploration of long-term sustainability and scalability of AMF inoculation methods in diverse agricultural settings.},
}

@article {pmid41292049,
year = {2025},
author = {Tian, Z and Zhang, K and Sheng, S and Kan, C and Han, F and Sun, X},
title = {The Role of Lactate Metabolism in Tumors: From Metabolic Byproduct to Signaling Molecule.},
journal = {American journal of clinical oncology},
volume = {},
number = {},
pages = {},
doi = {10.1097/COC.0000000000001276},
pmid = {41292049},
issn = {1537-453X},
abstract = {Lactate, once viewed as a metabolic by-product of glycolysis, is now recognized as a central regulator in cancer biology. Accumulating evidence reveals that lactate actively participates in tumor progression by functioning as a metabolic fuel, signaling mediator, epigenetic modifier, and immune modulator. Tumor cells exhibit elevated glycolytic flux through the Warburg effect, producing large quantities of lactate through LDHA and exporting it through MCTs, which acidifies the tumor microenvironment and drives metabolic symbiosis, angiogenesis, and immune evasion. Lactate also stabilizes HIF-1α and activates the receptor GPR81, triggering signaling pathways that promote proliferation, invasion, and immune checkpoint expression. Epigenetically, lactate regulates histone acetylation and lactylation, modulating gene expression and supporting adaptive transcriptional programs. Immune suppression is reinforced through direct inhibition of effector T and NK cells and expansion of Tregs and MDSCs. Given its multifaceted role, lactate metabolism has emerged as a promising therapeutic target. Inhibitors of LDHA, MCT1/4, and GPR81 are under active development and show synergistic potential with immunotherapy and chemoradiotherapy. This review summarizes current advances in lactate biology and therapeutic strategies, highlighting the need for personalized approaches that consider tumor-specific lactate dependencies and signaling contexts.},
}

@article {pmid41291109,
year = {2025},
author = {Cohen, DD and Faigenboim, A and Elingold, I and Sher, Y and Galpaz, N and Minz, D},
title = {Dynamics in Microbial Communities Associated with the Development of Soil Fatigue in Banana.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02637-7},
pmid = {41291109},
issn = {1432-184X},
abstract = {Soil fatigue, well documented in various crops, presents a significant challenge to banana production by causing fast and then gradual declines in plant growth and yield over years of cultivation. Despite its impact on profitability, the underlying mechanisms driving soil fatigue remain poorly understood; however, a strong link to shifts in the soil microbiome has been suggested. We investigated the dynamics of microbial communities in relation to soil fatigue, using a novel semi-controlled outdoor experimental system. Soil at different stages of fatigue (0 to 42 months of banana cultivation) was generated in large containers filled with initially healthy soil. Banana plants grown in these soils were replaced with new plants which showed soil age-dependent growth. Three months postplanting, soil and root samples were collected for analyses of soil parameters and microbial community composition using bacterial (16S) and fungal (ITS) amplicon sequencing. We identified minor age-related shifts in mainly pH, potassium, and organic matter in the soil. While alpha diversity remained unchanged, significant shifts in bacterial and fungal community composition were observed in fatigued soils. Notably, the relative abundance of bacterial families such as Flavobacteriaceae, Pseudomonaceae, and Acidibacter increased, as did some fungal taxa (many from groups with known pathogens)-Ceratobasidiaceae (including Rhizoctonia), Dothideomycetes, and Stachybotryaceae. Simultaneously, the relative abundance of bacterial families with known beneficial members, including Gemmatimonadaceae, Moraxellaceae, Sphingomonadaceae, and Azospirillaceae, as well as symbiotic fungal taxa such as Glomeraceae and Lasiosphaeriaceae, declined. Thus, soil fatigue may be correlated to the proliferation of pathogenic populations and a loss of beneficial microorganisms.},
}

@article {pmid41290716,
year = {2025},
author = {Caesar, L and Barksdale, C and Valiati, VH and Newton, I},
title = {Spatial segregation and cross-kingdom interactions drive stingless bee hive microbiome assembly.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66678-9},
pmid = {41290716},
issn = {2041-1723},
support = {2022049//National Science Foundation (NSF)/ ; 2005306//National Science Foundation (NSF)/ ; },
abstract = {Studying host-associated microbiome assembly is key to understanding microbial and host evolution and health. While honey bee microbiome have been a central model for such investigations among pollinators, they overlook the diversity of eusocial dynamics and multi-kingdom interactions. Stingless bees-a diverse group of highly eusocial insects that includes managed species, varies in colony biology, and harbors a symbiotic yeast essential for larval development in at least one species-offer a valuable complementary system to study microbiome assembly under an eco-evolutionary context. Using amplicon sequencing, metagenomics, and microbial experiments, we investigate the drivers of microbiome assembly in stingless bee colonies. We reveal a spatially structured, site-adapted microbiome, where high microbial influx hive components are segregated from the brood, which harbors a stable, multi-kingdom community. We show that the brood microbiome is not only physically protected but also maintained through selective bacterial-fungal interactions and abiotic conditions shaped by bees and their symbionts, such as temperature and pH. Our findings uncover multi-layered mechanisms shaping eusocial superorganism microbiomes, from host biology to cross-kingdom interactions, while providing critical insights into microbiome maintenance of important pollinators.},
}

@article {pmid41290652,
year = {2025},
author = {Lin, ZL and Gao, SM and Peng, SX and Tang, LY and Luo, ZH and Lao, XW and Zhang, SY and Shu, WS and Meng, F and Huang, LN},
title = {Biogeography and host interactions of CPR and DPANN viruses in acid mine drainage sediments.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10492},
pmid = {41290652},
issn = {2041-1723},
mesh = {*Geologic Sediments/virology/microbiology ; Genome, Viral/genetics ; China ; Virome/genetics ; Metagenomics ; Mining ; Metagenome ; Phylogeny ; Ecosystem ; Acids ; *Host Microbial Interactions ; },
abstract = {The CPR and DPANN superphyla are globally distributed in anoxic habitats including extreme environments. However, the biogeography and potential ecological functions of their viruses remain unexplored. Here, we recover diverse CPR/DPANN metagenomic viral genomes from 90 acid mine drainage (AMD) sediments sampled across southeast China. Our data reveal deterministic processes as the primary driver of virome assembly shaping the distinct distribution patterns of CPR and DPANN viruses. While lifestyle prediction shows higher lytic virus diversity associated with DPANN, both CPR/DPANN viruses likely use the Piggyback-the-winner (PtW) strategy to co-exist with hosts in AMD sediments, with CPR viromes exhibiting increased lysis in low host-density regimes under intensive acidity/salinity conditions. A subsequent metatranscriptomic analysis uncovers diverse functional genes encoded by CPR and DPANN viruses actively expressed in situ, potentially supplementing host metabolisms yet diverging in replication, transcription, and translation-related functions. Furthermore, partial correlation network analysis suggests that putative symbiotic hosts of the CPR/DPANN may confer protection against viral infection through enhanced antiviral defense. Our results highlight the complex interplays between viruses, DPANN and CPR organisms, and their symbiotic hosts.},
}

*Geologic Sediments/virology/microbiology
Genome, Viral/genetics
China
Virome/genetics
Metagenomics
Mining
Metagenome
Phylogeny
Ecosystem
Acids
*Host Microbial Interactions

@article {pmid41290153,
year = {2025},
author = {Spilmont, N and Zardi, GI and Nicastro, KR},
title = {Intertidal mussel-symbiont associations act as CO2 sinks during daily emersion.},
journal = {Biology letters},
volume = {21},
number = {11},
pages = {20250498},
doi = {10.1098/rsbl.2025.0498},
pmid = {41290153},
issn = {1744-957X},
support = {//EMIMA experimental platform (Lille University)/ ; //FEDER/ ; //ANR/ ; },
mesh = {Animals ; *Carbon Dioxide/metabolism ; *Symbiosis ; *Mytilus edulis/microbiology/physiology/metabolism ; *Cyanobacteria/physiology ; *Carbon Sequestration ; Carbon Cycle ; },
abstract = {Human activities have disrupted the global carbon cycle, reducing carbon dioxide (CO2) uptake by tidal wetlands and submerged vegetation. This exacerbates climate challenges, including rising temperatures and ocean acidification. Coastal systems such as mangroves and seagrasses serve as key carbon sinks, promising for CO2 removal (CDR). Growing attention is being given to bivalves, whose calcification and reef-building activities shape coastal carbon dynamics. Most studies reduce bivalve impacts to a balance between individual CO2 emissions and the carbon stored in their shells and tissues, often overlooking species interactions-such as symbioses-that may modulate carbon fluxes. Here, we examined the mussel-symbiont holobiont using Mytilus edulis under emersion in a controlled chamber to quantify CO2 exchange. Mussels hosting cyanobacterial symbionts exhibited net atmospheric CO2 uptake during daily air exposure, a critical phase of the tidal cycle. To evaluate the potential significance at larger ecological scales, we combined laboratory-derived CO2 uptake data with field-based estimates of symbiont prevalence to model carbon fluxes at the mussel bed scale and compared them with values of established blue carbon systems. This research highlights the importance of species interactions in coastal carbon cycling and underscores the need to incorporate the mussel-symbiont holobiont into CDR models.},
}

Animals
*Carbon Dioxide/metabolism
*Symbiosis
*Mytilus edulis/microbiology/physiology/metabolism
*Cyanobacteria/physiology
*Carbon Sequestration
Carbon Cycle

@article {pmid41289393,
year = {2025},
author = {He, T and Zhao, Y and Wang, X and Qiu, Y and Deng, J and Zhang, K and Xu, X and Zhao, Y and Qian, K and Wang, H and Bai, T and Zhang, Y and Feng, C and Guo, L and Chen, H and Guo, L and Wang, Y and Hu, S},
title = {Precipitation increase promotes soil organic carbon formation and stability via the mycorrhizal fungal pathway.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {48},
pages = {e2519072122},
doi = {10.1073/pnas.2519072122},
pmid = {41289393},
issn = {1091-6490},
support = {32371626//MOST | National Natural Science Foundation of China (NSFC)/ ; BK20240193//JST | Natural Science Foundation of Jiangsu Province (Jiangsu Natural Science Foundation)/ ; },
mesh = {*Mycorrhizae/metabolism/physiology ; *Carbon/metabolism ; *Soil/chemistry ; *Soil Microbiology ; Plant Roots/microbiology/metabolism ; *Rain ; Climate Change ; Grassland ; Biomass ; Symbiosis ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) form symbiotic relationships with roots of most terrestrial plants, playing a crucial role in regulating soil organic carbon (SOC) dynamics. While precipitation increase (Pi) is a major facet of climate change, its impacts on root- and AMF-mediated SOC formation and stability remain largely unexplored. Here, we combined a meta-analysis across global grasslands with a multiyear precipitation manipulation experiment in a semiarid grassland on the Loess Plateau to disentangle the relative effects of roots and their associated AMF on microbial communities and SOC as influenced by Pi. We show that Pi induced tradeoffs between roots and AMF, and promoted SOC formation and stability via the mycelium- rather than the root-pathway, leading to an increase of 136% (±40) and 297% (±90) in mycelium-derived C and mineral-associated organic C (MAOC), respectively. Pi altered plant community composition, favoring subshrubs and forbs over grasses. Also, Pi reduced specific root length, but increased root diameter, tissue density, and root colonization and extraradical biomass of AMF. Furthermore, Pi-induced change in AMF shifted the soil bacterial community by favoring K-strategists, increasing bacterial necromass C and promoting MAOC accumulation. Our findings provide direct evidence that Pi enhances AMF-driven SOC sequestration by expanding the mycorrhizosphere and promoting microbiota with high C use efficiency, highlighting a key mechanism by which mycorrhizal fungi mediate SOC formation and stability under shifting precipitation regimes.},
}

*Mycorrhizae/metabolism/physiology
*Carbon/metabolism
*Soil/chemistry
*Soil Microbiology
Plant Roots/microbiology/metabolism
*Rain
Climate Change
Grassland
Biomass
Symbiosis

@article {pmid41289084,
year = {2025},
author = {Chen, H and Li, M and Zhong, Z and Seim, I and Wang, M and Lian, C and Zhuo, L and Wan, X and Wang, H and Han, G and Zhou, L and Zhang, H and Cao, L and Li, C},
title = {Function and Development of Deep-sea Mussel Bacteriocytes Revealed by SnRNA-seq and Spatial Transcriptomics.},
journal = {Genomics, proteomics & bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1093/gpbjnl/qzaf109},
pmid = {41289084},
issn = {2210-3244},
abstract = {The deep-sea chemosynthetic ecosystems are among one of the most unusual ecosystems on Earth, where most megafauna form close symbiotic associations with chemosynthetic microbes to obtain nutrition and shelter from the toxic environment. Despite the diverse forms of symbiotic organs in these deep-sea holobionts, the function and development of bacteriocytes, the host cells harboring symbionts, are still largely uncharacterized. Here, we have conducted the in situ decolonization assay and state-of-the-art single-nucleus and spatial transcriptomics to reveal the function and development of deep-sea mussel bacteriocytes. The bacteriocytes appear to optimize immune processes to facilitate recognition, engulfment, and elimination of endosymbionts. They also interact directly with them in carbohydrate and ammonia metabolism by exchanging metabolic intermediates via transporters such as SLC37A2 and RHBG-A. Bacteriocytes arise from three different proliferating cell types, and their successive development trajectory was delineated by multi-omics data and 3D reconstruction analyses. The molecular functions and the developmental processes of bacteriocytes were found to be guided by the same set of molluscan-conserved transcription factors and may be influenced by endosymbionts through sterol metabolism. The coordination in the functions and development of bacteriocytes and between the host and symbionts highlights the phenotypic plasticity of symbiotic cells, and underpins host-symbiont interdependence in adaptation to the deep sea.},
}

@article {pmid41288984,
year = {2025},
author = {Hernandez-Benitez, EM and Martínez-Romero, E and Aguirre-Noyola, JL and Farias-Rico, JA and Ledezma-Tejeida, D},
title = {Computational inference of Rhizobium phaseoli transcriptional regulatory network predicts Transcription Factors involved in nodulation.},
journal = {Briefings in functional genomics},
volume = {24},
number = {},
pages = {},
doi = {10.1093/bfgp/elaf020},
pmid = {41288984},
issn = {2041-2657},
support = {IA204925//Universidad Nacional Autónoma de México, Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica/ ; 2057038//Programa de Maestría en Ciencias Bioquímicas, Universidad Nacional Autónoma de México/ ; //Secretaría de Ciencia, Humanidades, Tecnología e Innovación/ ; },
mesh = {*Transcription Factors/metabolism/genetics ; *Gene Regulatory Networks ; *Rhizobium/genetics ; *Plant Root Nodulation/genetics ; *Phaseolus/microbiology/genetics ; *Computational Biology/methods ; Bacterial Proteins/genetics/metabolism ; Symbiosis/genetics ; },
abstract = {Growth of the common bean plant Phaseolus vulgaris is tightly linked to its symbiotic relationship with diverse rhizobial species, particularly Rhizobium phaseoli, an alphaproteobacterium that forms root nodules and provides high levels of nitrogen to the plant. Molecular cross-talk is known to happen through plant-derived metabolites, but only flavonoids have been identified as nodulation signals, which act through the activation of the NodD Transcription Factor (TF). The identification of signals that mediate nodulation via TFs can aid in the rational design of biofertilizers that promote plant-bacteria symbiosis. Here, we identified 57 TFs in the R. phaseoli genome through sequence conservation from Escherichia coli, and predicted a transcriptional regulatory network comprising 16 TFs, and 1,371 target genes. We identified the regulatory interactions relevant to nodulation via transcriptome analysis, and hypothesize that PuuR is a TF involved in nodulation, potentially acting via its known binding metabolite putrescine. Sequence and structural evidence predict a model where putrescine acts as a signaling metabolite in nodulation via the TF PuuR, and the regulation of the nodI gene.},
}

*Transcription Factors/metabolism/genetics
*Gene Regulatory Networks
*Rhizobium/genetics
*Plant Root Nodulation/genetics
*Phaseolus/microbiology/genetics
*Computational Biology/methods
Bacterial Proteins/genetics/metabolism
Symbiosis/genetics

@article {pmid41288789,
year = {2025},
author = {Carrara, JE and Smith, AH and Heller, WP},
title = {Application of spent mushroom compost enhances wheat yield but reduces mycorrhizal associations and grain nutrient concentration.},
journal = {Mycorrhiza},
volume = {35},
number = {6},
pages = {67},
pmid = {41288789},
issn = {1432-1890},
support = {8072-12000-014-000-D//USDA-ARS in-house project/ ; },
mesh = {*Triticum/growth & development/microbiology/metabolism/chemistry ; *Mycorrhizae/physiology ; *Composting ; Soil Microbiology ; *Agaricales ; Nutrients/analysis/metabolism ; Soil/chemistry ; Edible Grain/chemistry/growth & development ; },
abstract = {Developing management practices that enhance crop yield while maintaining soil health is the foremost objective of the regenerative agriculture movement. One avenue to achieving this goal is using biofertilizers and alternative soil amendments to supplement or replace agrochemicals. Here we report the results of a pairwise field trial of spring wheat (Triticum aestivum) wherein we investigated individual and combined impacts of inoculation with arbuscular mycorrhizal fungi (AMF) and a spent mushroom compost amendment (herein mushroom compost). The symbiotic relationship between AMF and plants has been demonstrated to benefit the yield and nutritional quality of many crops by enhancing access to mineral nutrients and water. Mushroom compost, consisting of the devitalized residual substrate following harvest of edible mushrooms, is a byproduct of the mushroom industry and is comprised of a variety of nutrient-rich organic material inputs. Therefore, the objective of this study was to (1) determine the effect to which AMF and mushroom compost individually impact wheat yield and nutritional quality, and (2) examine if these effects are synergistic or antagonistic when both amendments are applied together. We found that mushroom compost addition, regardless of AMF inoculation, enhanced grain yield by ~ 40%, but reduced AMF root colonization level by ~ 25-40%. Additionally, despite yield increases, mushroom compost addition reduced grain phosphorus (P), potassium (K), and magnesium (Mg) concentrations by ~ 10% and boron concentration by ~ 45%. In fact, grain P, K, and Mg concentrations were all correlated with mycorrhizal colonization level. These results suggest that while spent mushroom compost additions enhanced grain yield, this may have led to a mineral nutrient 'dilution effect' exacerbated by negative impacts on AMF colonization and community composition.},
}

*Triticum/growth & development/microbiology/metabolism/chemistry
*Mycorrhizae/physiology
*Composting
Soil Microbiology
*Agaricales
Nutrients/analysis/metabolism
Soil/chemistry
Edible Grain/chemistry/growth & development

@article {pmid41288749,
year = {2025},
author = {Ndabankulu, KP and Zama, N and Suinyuy, TN and Magadlela, A},
title = {Soil Microbe Interaction and Extracellular Enzyme Activity Mediated by Encephalartos villosus in KwaZulu-Natal Scarp Forest Ecosystems.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {132},
pmid = {41288749},
issn = {1432-184X},
support = {129403//National Research Foundation, South Africa/ ; 138091//National Research Foundation/ ; },
mesh = {*Soil Microbiology ; South Africa ; Soil/chemistry ; Forests ; *Bacteria/classification/enzymology/genetics/isolation & purification/metabolism ; Rhizosphere ; Symbiosis ; Ecosystem ; Microbiota ; },
abstract = {Cycads are ancient gymnosperms that play a crucial role in the soil health of scarp forests through their symbiotic associations with nutrient-cycling bacteria. However, the abundance of cycads in scarp forests has been decreasing at an alarming rate, highlighting the importance of determining the role of these species in nutrient cycling, microbial dynamics, and soil health. This study examined soil nutrient and microbial dynamics associated with Encephalartos villosus across four scarp forest sites in KwaZulu-Natal, South Africa. Soil samples were collected from the rhizosphere and non-rhizosphere zones (3-5 m away from the canopy) of mature plants. Results show that collection point did not influence soil nutrient and properties statistically; however, site-level variation was evident, with Hlathikhulu showing higher pH and nutrient concentrations, while Vernon Crookes exhibited lower pH and nutrient availability. Rhizosphere soils supported a greater diversity of nutrient-cycling bacteria, particularly taxa from the genera Bacillus, Burkholderia, Enterobacter, Luteibacter, and Pseudomonas with N-fixing, P-solubilizing, and N-cycling functions. Non-metric multidimensional scaling (NMDS) revealed that site differences, mainly driven by Mg, Ca, K, Zn, pH, and total cations, were stronger predictors of soil nutrient and microbial community variation than collection point alone. Enzyme assays showed that glucosaminidase and acid phosphatase were associated with community differences. These findings indicate that E. villosus enhances soil nutrient enrichment and microbial functional diversity in scarp forests, although the strength of these effects depends on local site conditions. Conservation of E. villosus is therefore critical, not only for species survival but also for sustaining soil fertility and ecosystem functioning in nutrient-limited scarp forest habitats.},
}

*Soil Microbiology
South Africa
Soil/chemistry
Forests
*Bacteria/classification/enzymology/genetics/isolation & purification/metabolism
Rhizosphere
Symbiosis
Ecosystem
Microbiota

@article {pmid41288716,
year = {2025},
author = {Chatterjee, A and Ghosh, P and Das, S and Sharaff, M and Mandal, S and Bhattacharya, PM and Chaudhuri, T and Pal, H},
title = {Mangrove derived coactive bacterial inoculant triggered biochemical traits rejuvenating plant cell function under salt stress.},
journal = {Plant cell reports},
volume = {44},
number = {12},
pages = {280},
pmid = {41288716},
issn = {1432-203X},
support = {IGSTC/Call 2019/CirCulTex/19/2020-2021/165//Indo-German Science and Technology Centre/ ; },
mesh = {*Solanum lycopersicum/microbiology/physiology/metabolism/drug effects ; *Salt Stress/physiology ; Plant Roots/microbiology ; *Plant Cells/metabolism ; Salt Tolerance ; },
abstract = {Novel endophytic bacterial consortium promotes the growth of Solanum lycopersicum surviving salt stress by differentially regulating the primary and secondary metabolic pathways. Crop yield is being impacted by global warming, which threatens food security. Salinization of soil or irrigation water is becoming increasingly prevalent in most agricultural terrain, especially around the coast. In India, it is estimated that approximately 10% of additional area is getting salinized, and around 50% of the arable land would be salt-affected by the year 2050. Finding innovative techniques that enable farmers to sustain production in an increasingly saline environment is crucial given the world's population expansion and the depletion of natural resources used in agriculture. Biostimulants are naturally occurring compounds or microorganisms that are used to promote plant functions, such as nutrient absorption, nutrient utilisation efficiency, abiotic stress tolerance, and the overall quality of the resulting agricultural products. In the present work, we evaluated the agronomic effectiveness of a novel formulated biostimulant consisting of four strains of endophytic bacteria isolated from the roots of mangrove plants of Sundarbans in a crop of great interest (Tomato) under controlled conditions and salt stress. Our research has shown that our product had a positive effect on the biochemical parameters in tomato plants under salt stress. The application of our biostimulant also increased osmolyte production and maintained Na[+]/K[+] homeostasis under salt conditions. Similarly, when exposed to salinity, the biostimulant increased the concentration of signature molecules, including primary metabolites, phenolic compounds, polyamines, and phytohormones inside the plant cell. This study enriched our body of knowledge by providing novel perspectives on the mechanism of salt resistance that endophytic microbes provide through symbiosis.},
}

*Solanum lycopersicum/microbiology/physiology/metabolism/drug effects
*Salt Stress/physiology
Plant Roots/microbiology
*Plant Cells/metabolism
Salt Tolerance

@article {pmid41288338,
year = {2025},
author = {Kamel Urmia, H and Koosha, M and Yakhchali, B and Moosa-Kazemi, SH and Oshaghi, MA},
title = {Environmental persistence and transmission dynamics of Serratia AS1 in mosquito habitats: advancing paratransgenesis for malaria control.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0184025},
doi = {10.1128/aem.01840-25},
pmid = {41288338},
issn = {1098-5336},
abstract = {UNLABELLED: Malaria remains a major global health challenge, particularly in developing countries, necessitating innovative control strategies. With rising resistance of Plasmodium to drugs and Anopheles mosquitoes to insecticides, paratransgenesis-using engineered symbiotic bacteria to deliver anti-pathogen molecules-offers a promising alternative. Translating this approach to field applications requires rigorous evaluation under semi-field conditions. We evaluated the environmental stability and transmission dynamics of Serratia AS1-mCherry, a paratransgenesis candidate, in Anopheles stephensi habitats under semi-field conditions in Bandar Abbas, Iran. Serratia AS1 successfully colonized mosquito midguts and ovaries, persisted in larval breeding water for 14 days, and remained stable on sugar-soaked cotton pads for 4-6 days. Transmission routes include transstadial, venereal, and vertical transmission, in addition to adult acquisition from larval habitats (sipping), demonstrating robust colonization and dissemination. Water-based delivery effectively disseminates Serratia AS1 among mosquito populations, highlighting its potential for paratransgenesis-based malaria control. This study establishes the feasibility of using Serratia AS1 with effector molecules in field settings, offering a sustainable strategy for managing vector-borne diseases.

IMPORTANCE: Malaria remains a major health challenge, especially in developing countries where traditional control methods like insecticides and drugs are becoming less effective due to resistance. This study explores a promising new approach called paratransgenesis, which uses genetically modified bacteria to fight malaria. We tested a bacterium called Serratia AS1, which can live inside mosquitoes and spread through their populations. Our experiments showed that Serratia AS1 can survive in mosquito breeding sites and spread effectively among mosquitoes through multiple routes, such as larval water, sugar sources, and even from parent mosquitoes to their offspring. These findings suggest that Serratia AS1 could be used to deliver anti-malaria molecules to mosquitoes in the wild, offering a sustainable and innovative way to control the disease. This work brings us one step closer to using paratransgenesis as a practical tool to reduce malaria transmission and save lives.},
}

@article {pmid41287631,
year = {2025},
author = {Kranawetter, C and Sumner, LW},
title = {Differential root zone secretions and the role of root border cells in rhizosphere manipulation.},
journal = {Phytochemistry reviews : proceedings of the Phytochemical Society of Europe},
volume = {24},
number = {6},
pages = {5639-5658},
pmid = {41287631},
issn = {1568-7767},
abstract = {Root tissues are broadly divided into mature tissue, elongation zone (developing tissue), root tip, and border cells. While each zone contributes individually to the overall root secretion profile, border cells are emphasized in this review due to their specialized secretory functions. Border cells are often overlooked in plant root focused studies, thus excluding an important component of root functionality. Border cells are a specialized cell type surrounding the root apical meristematic region of most plant species, with the exception of the Brassicaceae family that possess border-like cells. Both cell types share the commonality of complete detachment from the root tip and reliance on internal starch reserves to perform metabolic processes. However, border cells release from the root tip as single/individual cells whereas border-like cells separate as cohesive sheets. Furthermore, border cells, but not border-like cells, secrete a complex matrix consisting of mucilage, proteins, DNA, and metabolites. Many of these secreted compounds are bioactive (e.g. secreted mucilage supports microbial growth and DNA physically entangles pathogens) thus mediating symbiosis and pathogen defense. We are interested in metabolites secreted from individual root regions, with a heavy emphasis on those specifically arising from border cells. Border cell metabolite secretion is in need of further investigation, as current research indicates they secrete symbiosis-inducing, allelopathic, and defense oriented metabolites. This review will summarize current literature regarding metabolite secretions by specific root cell types and regions. In particular, it will focus on border cell contributions to the rhizosphere chemistry relative to other root tissue types.},
}

@article {pmid41286654,
year = {2025},
author = {Benmrid, B and Idbella, M and Bonanomi, G and Khourchi, S and Gherardelli, M and Bargaz, A and Cherki, G},
title = {Drought-tolerant rhizobacterial consortia with diverse plant growth promoting traits enhance wheat and faba bean growth under water and low-P availability promising multi-traits.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {771},
pmid = {41286654},
issn = {1471-2180},
support = {AS1-UM6P-Anhalt//OCP Group/ ; AS1-UM6P-Anhalt//OCP Group/ ; AS1-UM6P-Anhalt//OCP Group/ ; },
mesh = {*Triticum/growth & development/microbiology/metabolism ; *Vicia faba/growth & development/microbiology/metabolism ; Droughts ; *Phosphorus/metabolism/deficiency ; Plant Roots/microbiology/growth & development ; Rhizosphere ; *Bacteria/metabolism/classification/genetics ; Water/metabolism ; *Microbial Consortia/physiology ; Soil Microbiology ; Stress, Physiological ; },
abstract = {BACKGROUND: Staple crops like wheat and faba bean are increasingly subjected to multiple and simultaneous stresses, resulting in substantial yield reduction. Although vast available knowledge about the role of root-rhizosphere microbes in enhancing crop tolerance to single stress, few is known about the potential of bacterial consortia rationally assembled from strains with defined and complementary ecological functions to improve crop tolerance to combined drought and phosphorus (P) deficiency. This study evaluated wheat (Triticum durum) or faba bean (Vicia faba) morpho-physiological response to three functionally diverse drought-tolerant bacterial consortia (C7, C8, C9), in greenhouse conditions, under low-P well-watered conditions (rock phosphate (RP), 80% field capacity (FC)) or low-P drought conditions (RP, 40% FC).

RESULTS: Assessment of agro-physiological parameters identified consortium C8 as particularly effective, leading to significant increases in root biomass, leaf area, and shoot inorganic P content, of both wheat and faba bean plants under combined drought and low-P availability. This improvement is likely driven by bacterial traits related to drought tolerance, increased root biomass allocation, and enhanced rhizosphere P availability, as indicated by enhanced physiological traits related to leaf area, photosynthetic efficiency (Fv/Fm ratio), and chlorophyll content. Additionally, soil P availability and acquisition improved in response to bacterial inoculation that positively influenced faba bean nodulation, indicating that these bacterial consortia plausibly increased faba bean symbiotic effectiveness through optimizing P use efficiency as a potential mechanism among others. Additionally, the ability of bacterial consortia to produce phytohormones (e.g. Auxins) could partially explain induced root development and nodulation under water stress, given the key role of these phytohormones in root growth and rhizobia-legume symbiosis establishment.

CONCLUSION: Our findings provide consistent evidence on the effectiveness of bacterial consortia - comprising functionally diverse PGP traits - in enhancing plant growth and nutrient acquisition under stressful conditions.},
}

*Triticum/growth & development/microbiology/metabolism
*Vicia faba/growth & development/microbiology/metabolism
Droughts
*Phosphorus/metabolism/deficiency
Plant Roots/microbiology/growth & development
Rhizosphere
*Bacteria/metabolism/classification/genetics
Water/metabolism
*Microbial Consortia/physiology
Soil Microbiology
Stress, Physiological

@article {pmid41286598,
year = {2025},
author = {Zhang, Y and Wen, H and Li, Q and Lu, Y and Zhang, Z and Sui, L},
title = {From function to omics: endophytic Beauveria bassiana promotes maize growth by activating phytohormone signaling pathways under elevated carbon dioxide.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-025-07763-5},
pmid = {41286598},
issn = {1471-2229},
support = {32271683//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Several entomopathogenic fungal (EPF) species can colonise and establish symbiotic relationships with plants as endophytes, which affects crop growth under elevated carbon dioxide (eCO2) concentrations. However, how EPF facilitates eCO2 in plants is poorly understood, especially at the transcriptional and metabolic levels. Here, the authors used transcriptomics and metabolomics to examine the effects of a widely used EPF, Beauveria bassiana, on maize growth under eCO2, and how it regulated enzyme activity and endogenous hormone metabolism.

RESULTS: Beauveria bassiana colonisation significantly enhanced maize growth across CO₂ concentrations. Key effects include: 39.64% greater leaf area than controls at ambient CO₂ during S3. Significant developmental divergence in leaf area between S3-S4 under eCO₂, 11.8% higher 100-grain weight in eCO₂+Bb vs. eCO₂ alone. Concurrent increases in stress-responsive enzymes and hormones aligned with omics-revealed activation of primary metabolic pathways (ZMA01100) and secondary metabolite biosynthesis pathways (ZMA01110).

CONCLUSIONS: These findings suggested that B. bassiana colonization modulates plant growth under eCO2 by regulating the expression of related genes, and in turn, enzyme activity and hormone metabolism. The findings of the present study offered a theoretical foundation for elucidating the interactions between EPFs and plants under climate change.},
}

@article {pmid41286473,
year = {2025},
author = {Wang, H and Yang, Y and Zhang, H and Chen, X and Zhang, R and Hou, W and Zhang, G},
title = {Symbiotic N-Fixing Bacteria in the Root and Leaf of Typical Alpine Grassland Plants.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {127},
pmid = {41286473},
issn = {1432-184X},
mesh = {Grassland ; *Plant Roots/microbiology ; *Symbiosis ; *Plant Leaves/microbiology ; RNA, Ribosomal, 16S/genetics ; Tibet ; *Nitrogen-Fixing Bacteria/classification/genetics/isolation & purification/physiology ; Nitrogen Fixation ; Phylogeny ; DNA, Bacterial/genetics ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Soil Microbiology ; },
abstract = {Alpine plants in nitrogen-deficient environments can acquire nitrogen by associating with endophytic nitrogen-fixing microorganisms that inhabit their roots and leaves to form symbiotic relationships. However, research is limited on nitrogen-fixing bacterial communities in the roots and leaves of alpine grassland plants, especially regarding the differences between various plant parts. In this study, we compared the root and leaf bacterial communities of four alpine plant families (Asteraceae, Leguminosae, Poaceae, and Rosaceae) in the alpine meadow ecosystem of Naqu, Tibet, using culture-based methods, 16S rRNA, and nifH gene pyrosequencing. The results showed greater bacterial diversity in the root compared to the leaf, and Fabaceae plants harbored a higher abundance of nitrogen-fixing bacteria. Interestingly, the roots and leaves of non-Fabaceae plants (Kobresia, Festuca ovina, and Leontopodium) also harbored abundant nitrogen-fixing communities such as Microbacterium, Curtobacterium, and Rhodococcus. Compared with subtropical environments, Cyanobacteria are important symbiotic nitrogen-fixing bacteria in plants of alpine ecosystems. These findings indicate that plant species and plant parts strongly influence the selection of bacterial populations. Understanding these microbial ecological functions in alpine grasslands provides scientific insights for optimizing agricultural practices and ecosystem management.},
}

Grassland
*Plant Roots/microbiology
*Symbiosis
*Plant Leaves/microbiology
RNA, Ribosomal, 16S/genetics
Tibet
*Nitrogen-Fixing Bacteria/classification/genetics/isolation & purification/physiology
Nitrogen Fixation
Phylogeny
DNA, Bacterial/genetics
*Bacteria/classification/genetics/isolation & purification/metabolism
Soil Microbiology

@article {pmid41286138,
year = {2025},
author = {Liu, XQ and An, XP and He, WX and Xu, XH and Hashem, A and Abd-Allah, EF and Wu, QS},
title = {Hairy Vetch Intercropping Attenuates Mycorrhizal Benefits to Walnut Growth and Soil Organic Carbon Sequestration via Glomalin.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {128},
pmid = {41286138},
issn = {1432-184X},
support = {SCXX-XZCG-22016//Hubei Province '14th Five-Year' Major Science and Technology Aid Tibet Project/ ; ORF-2025-356//Ongoing Research Funding program, King Saud University, Riyadh, Saudi Arabia/ ; },
mesh = {*Juglans/growth & development/microbiology ; *Mycorrhizae/physiology/growth & development ; *Soil/chemistry ; Soil Microbiology ; *Carbon Sequestration ; Plant Roots/microbiology/growth & development ; Carbon/metabolism/analysis ; Biomass ; *Agriculture/methods ; *Fungal Proteins/metabolism ; *Glycoproteins/metabolism ; },
abstract = {Intercropping is a prevalent soil management strategy within walnut orchards, while its impacts on the functionality of arbuscular mycorrhizal fungi (AMF) in walnuts (Juglans regia) remain unclear, especially concerning soil carbon (C) sequestration via glomalin-related soil protein (GRSP). This study aimed to explore the effects of inoculation with the AMF species Diversispora spurca and intercropping with hairy vetch (Vicia villosa) on walnut biomass accumulation, soil water-stable aggregate (WSA) stability, leaf and root C (Cleaf and Croot) content, soil organic carbon (SOC), GRSP, and GRSP-contained C (CGRSP), in addition to the contribution rate of CGRSP to SOC. The intercropping treatment significantly inhibited root mycorrhizal colonization rate, soil hyphal length, and spore density in AMF-inoculated walnut plants. Individual AMF inoculation, rather than individual intercropping, significantly promoted shoot and root biomass accumulation, WSA stability, SOC, Cleaf and Croot, the levels of purified easily extractable (EEG), difficultly extractable (DEG), and total GRSP (TG), as well as their C contents. The combination treatment (AMF inoculation + intercropping) displayed limited benefits, improving just WSA stability without yielding synergistic advantages over individual treatments. Arbuscular mycorrhizal fungal inoculation significantly increased CGRSP, especially CDEG, while individual intercropping resulted in a reduction of CDEG. The combination treatment elevated both CDEG and CTG, albeit to a lesser extent than AMF alone. The contribution rates of CEEG, CDEG, and CTG to SOC were 0.33% - 0.53%, 1.16% - 1.78%, and 1.49% - 2.31%, respectively. Although AMF inoculation significantly increased the contribution rates of CDEG and CTG to SOC, this effect was diminished when combined with intercropping. Notably, CDEG, rather than CEEG, exhibited a significantly positive correlation with SOC and WSA stability. The findings provide new insights into the mechanisms of SOC sequestration in walnuts grown in controlled environments and offer a theoretical basis for the application of AMF in walnut cultivation.},
}

*Juglans/growth & development/microbiology
*Mycorrhizae/physiology/growth & development
*Soil/chemistry
Soil Microbiology
*Carbon Sequestration
Plant Roots/microbiology/growth & development
Carbon/metabolism/analysis
Biomass
*Agriculture/methods
*Fungal Proteins/metabolism
*Glycoproteins/metabolism

@article {pmid41285821,
year = {2025},
author = {Karimzadeh, S and Safaie, N and Mojerlou, S and Ebrahimi, L},
title = {Identity and diversity of culturable endophytic fungi associated with Capparis spinosa L. in Iran.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {41502},
pmid = {41285821},
issn = {2045-2322},
mesh = {*Endophytes/classification/isolation & purification/genetics ; Iran ; *Fungi/classification/isolation & purification/genetics ; *Biodiversity ; Phylogeny ; Plant Roots/microbiology ; },
abstract = {Endophytic fungi play a crucial role in plant health, contributing to stress tolerance, disease resistance, and ecological adaptation. However, the diversity and richness of endophytic fungal communities associated with Capparis spinosa L. in the Alborz, Tehran, and Qom provinces-ranging from semi-arid and slightly temperate to arid and desert climatic conditions-have not yet been investigated. Using morphological and molecular methods, we identified a diverse fungal assemblage comprising 3 phyla, 7 classes, 14 orders, 28 families, and 36 genera. Among the genera shared across all three provinces, Alternaria (28.8%) was the most dominant among the isolates, whereas Simplicillium (1.6%) was the least abundant. Analysis of the isolates using diversity indices revealed that species distribution in all three provinces tended toward evenness, with a similar pattern observed across different tissues. Qom exhibited the highest diversity and richness of fungal species. Additionally, a detailed comparison of different plant tissues revealed that roots consistently harbored the greatest variety and the highest number of isolates compared to stems, leaves, and fruits. Diversity metrics suggest a potential link between climatic gradients and endophyte diversity. These findings enhance our understanding of fungal-plant interactions and provide insights into the microbial contributions to C. spinosa resilience in harsh environmental conditions.},
}

*Endophytes/classification/isolation & purification/genetics
Iran
*Fungi/classification/isolation & purification/genetics
*Biodiversity
Phylogeny
Plant Roots/microbiology

@article {pmid41285752,
year = {2025},
author = {Schulz, F and Yan, Y and Weiner, AKM and Ahsan, R and Katz, LA and Woyke, T},
title = {Single-cell genomics reveals complex microbial and viral associations in ciliates and testate amoebae.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10336},
pmid = {41285752},
issn = {2041-1723},
mesh = {Single-Cell Analysis/methods ; Symbiosis/genetics ; *Amoeba/virology/microbiology/genetics ; *Microbiota/genetics ; Metagenomics/methods ; *Ciliophora/virology/microbiology/genetics ; Bacteria/genetics/classification ; Genomics/methods ; Giant Viruses/genetics ; Phylogeny ; Viruses/genetics/classification ; },
abstract = {Protists play important roles in nutrient cycling across ecosystems, yet the composition and function of their associated microbiomes remain poorly studied. Here, we use cultivation-independent single-cell isolation and genome-resolved metagenomics to investigate the microbiomes and viromes of more than 100 uncultivated ciliates and amoebae from diverse environments. Our findings reveal unique microbiome structures and complex associations with bacterial symbionts and viruses, with stark differences between ciliates and amoebae. We recover 117 microbial genomes affiliated with known eukaryotic endosymbionts, including Holosporales, Rickettsiales, Legionellales, Chlamydiae, and Babelota, and 258 genomes linked to host-associated Patescibacteriota. Many show genome reduction and genes related to toxin-antitoxin systems and nucleotide parasitism, indicating adaptation to intracellular lifestyles. We also identify more than 80 giant viruses from diverse lineages, some actively expressing genes in single-cell transcriptomes, along with other viruses predicted to infect eukaryotes or symbiotic bacteria. The frequent co-occurrence of giant viruses and microbial symbionts, especially in amoebae, suggests multipartite interactions. Together, our study highlights protists as hubs of microbial and viral associations and provides a broad view of the diversity, activity, and ecological importance of their hidden partners.},
}

Single-Cell Analysis/methods
Symbiosis/genetics
*Amoeba/virology/microbiology/genetics
*Microbiota/genetics
Metagenomics/methods
*Ciliophora/virology/microbiology/genetics
Bacteria/genetics/classification
Genomics/methods
Giant Viruses/genetics
Phylogeny
Viruses/genetics/classification

@article {pmid41284260,
year = {2025},
author = {Song, H and Dowdell, K and Delafont, V and Skerlos, S and Raskin, L},
title = {The Neglected Role of Heterotrophic Protists in Engineered Water Systems.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c04958},
pmid = {41284260},
issn = {1520-5851},
abstract = {Heterotrophic protists can be considered the dark matter of microbial communities in engineered water systems. They are ubiquitous and ecologically significant yet remain largely overlooked. Although a growing body of research demonstrates their pivotal roles (e.g., predation, symbiosis, and nutrient cycling) in microbial communities in natural ecosystems, their functions in engineered water systems are poorly characterized, and heterotrophic protists are frequently excluded from microbial analyses. This is largely due to methodological constraints that have only recently been overcome. Recent advances in imaging, high-throughput sequencing, and meta-omics approaches, combined with expanding reference databases, have revolutionized studies of protist diversity and functions in a wide range of natural environments. Drawing on research from the fields of protistology, microbial ecology, and environmental microbiology, this review explores how the well-documented ecological roles of heterotrophic protists in natural environments translate to engineered ecosystems, offering insights into their functions in water treatment. We critically evaluate recent literature to synthesize both beneficial roles and potential risks of heterotrophic protists in various water treatment systems, while identifying key knowledge gaps and proposing directions for future research. We advocate for a shift in perspective that recognizes heterotrophic protists as important players and call for their integration into microbial community characterization and ecological frameworks in microbial ecology studies of engineered water systems. This integration will transform our understanding of microbial communities in engineered water systems, ultimately enabling novel, mechanistic, and ecologically informed management strategies.},
}

@article {pmid41282262,
year = {2025},
author = {Geddes, B and Levin, G and Luu, C and Visich, N and Hoselton, S and Lipzen, A and Zhao, S and Li, L and diCenzo, G and Finan, T},
title = {Polyhydroxyalkanoate synthesis by Sinorhizobium meliloti drives a host-specific collapse in symbiosis with Medicago sativa.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-7715224/v1},
pmid = {41282262},
issn = {2693-5015},
abstract = {Naturally occurring root-nodule bacteria (rhizobia) vary substantially in their effectiveness at promoting growth of different plant hosts via symbiotic nitrogen fixation. These variations in rhizobial partner quality have important implications for the productivity of nitrogen-fixing symbioses in natural and agricultural ecosystems, yet we have a limited understanding of the genetic basis for this variation. In a case of host-specific reduction in symbiotic effectiveness (N 2 -fixation) with Medicago sativa , we identified the causative genetic elements from the pSymA replicon of Sinorhizobum meliloti HM006 and show them to be involved in polyhydroxyalkanoate (PHA) production in nitrogen-fixing bacteroids. Transfer of this gene region to a strain that forms an effective symbiosis with Medicago sativa resulted in a complete loss of symbiotic N 2 -fixation. We showed the mechanism for symbiotic collapse is the diversion of succinate semialdehyde pools in the bacteroid to gamma-hydroxybutyrate (GHB) by an iron-containing dehydrogenase, GhbD. These findings reveal unexpected impacts of carbon metabolism changes in nodules on symbiont performance and provide a rare example of mechanism for variation in rhizobium partner quality, suggesting that host-specific metabolic incompatibility may be a key player in the variations in partner quality observed in nature.},
}

@article {pmid41281664,
year = {2025},
author = {Lan, X and Zhang, F and Cui, G and Hu, B and Lai, Y and Lin, H and Huang, H and Zhou, D and Yu, M and Yao, G},
title = {Microbiota-directed lactic acid depleting nanoenzyme reactivates antitumor immunity and chemosensitivity in hypoxic tumor.},
journal = {Materials today. Bio},
volume = {35},
number = {},
pages = {102493},
pmid = {41281664},
issn = {2590-0064},
abstract = {The acidification of the tumor microenvironment (TME) remains a major obstacle contributing to malignant progression and impeding therapeutic development. While traditionally attributed to anaerobic glycolysis, increasing evidence suggests that hypoxia-induced colonization of intratumoral symbiotic microbiota, particularly anaerobes, produce lactic acid (LA) metabolites serves as a significant contributor to TME acidification. Although antibiotic-based combination therapies have been explored for the hypoxic tumor treatment, the efficiency was restricted in reversing acidification-induced immunosuppression and chemoresistance. To tackle this challenge, we engineered a delivery platform (TML NPs) for lactate oxidase (LOX) and chemotherapeutic drug tirapazamine (TPZ) by modifying the carrier with metronidazole (MTZ), an antibiotic bearing hypoxia-responsive functional group. By directly targeting the symbiotic anaerobic bacterial metabolism, this strategy introduces a novel paradigm for modulating TME acidification, reversing the LA-mediated suppression of anti-tumor immune responses and chemosensitivity. Our strategy offers a promising translational platform for the precise treatment of TNBC and other hypoxic malignancies.},
}

@article {pmid41280275,
year = {2026},
author = {Qi, X and Zhang, Y and Sun, Z and Wang, G and Ling, F},
title = {A simplified synthetic microbial community enhances resistance of crucian carp (Carassius auratus) to Aeromonas hydrophila infection through host immune activation.},
journal = {Synthetic and systems biotechnology},
volume = {11},
number = {},
pages = {407-418},
pmid = {41280275},
issn = {2405-805X},
abstract = {Bacterial diseases represent a major bottleneck in the sustainable development of aquaculture. The gut microbiota plays a vital role in host growth and health, including the enhancement of disease resistance. Although substantial progress has been made in elucidating the mechanisms of disease resistance in fish, the precise role of the gut microbiota in enhancing pathogen resistance in aquatic animals remains poorly understood. In this study, crucian carp (Carassius auratus) were used as a model to investigate the role of intestinal microbiota in modulating resistance to Aeromonas hydrophila. Individual crucian carp exhibited distinct clinical phenotypes following A. hydrophila infection. Specifically, significant differences were observed in the composition of the intestinal microbiota between fish displaying mild symptoms and those exhibiting severe phenotypic manifestations (α diversity: p < 0.01; β diversity: p = 0.001). Fecal microbiota transplantation (FMT) experiments demonstrated that fish with mild symptoms conferred enhanced resistance to A. hydrophila when their intestinal contents were transplanted into other individuals (p = 0.006). Further microbial analysis identified Cetobacterium (p = 0.013), Paraclostridium (p < 0.01), and Pseudomonas (p < 0.01) as key differential taxa. A simplified microbial community comprising these three strains was subsequently constructed. Feeding experiments confirmed that administration of this community significantly improved host resistance to A. hydrophila (p < 0.05) by activating intestinal immune responses and reinforcing the gut barrier. Overall, our findings underscore the potential of the microbial community as a novel strategy for disease prevention and control in aquaculture, providing a theoretical foundation for the development of microbiome-based therapies in fish health management.},
}

@article {pmid41279359,
year = {2025},
author = {Chi, X and Wang, CH and Parisotto, YF and Nyberg, WA and Cabric, V and Gelineau, A and Cao, Y and Owen, DL and Ambjörnsson, J and Mathis, D and Eyquem, J and Brown, CC and Benoist, C},
title = {Decoding Peripheral Tolerance: TCR Rules for pTreg differentiation in the Gut.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.20.683415},
pmid = {41279359},
issn = {2692-8205},
abstract = {Peripheral differentiation of regulatory T cells (pTregs) promoted by foreign antigens encountered in barrier tissues is considered a unique contributor to immunological tolerance to obligate non-self, like food or symbiotic microbes. The relative importance of adaptive recognition via the T cell receptor (TCR) vs environmental small-molecule or neuroimmune cues, is poorly understood. We leverage CRISPR-based TCR editing to perform in primary T cells in vivo , with a large panel of TCRs, a screen to assess pTreg differentiation induced by self, microbial, or dietary antigens. All antigen classes drive pTreg differentiation, which varies with the origin of the TCR: TCRs derived from Tregs enable pTreg differentiation much more effectively than those from Tconv. TCRs recognizing self, microbial, or dietary antigens elicit distinct pTreg phenotypes, Helios[+], RORγ[+], or both. Mechanistically, these trace to different types of antigen-presenting-cell involved. That Treg-derived TCRs preferentially drive tolerogenic fate speaks to preferential drivers of tolerogenic therapy.},
}

@article {pmid41279009,
year = {2025},
author = {Morgese, EA and Ferrell, BD and Toth, SC and Polson, SW and Wommack, KE and Fuhrmann, JJ},
title = {Comparative Analysis Reveals Host Species-Dependent Diversity Among 16 Virulent Bacteriophages Isolated Against Soybean Bradyrhizobium spp.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.06.680108},
pmid = {41279009},
issn = {2692-8205},
abstract = {Phages play a role in shaping ecosystems by controlling host abundance via cell lysis, driving host evolution via horizontal gene transfer, and promoting nutrient cycling. The genus Bradyrhizobium includes bacteria able to symbiotically nodulate the roots of soybean (Glycine max), providing the plant with a direct source of biologically fixed nitrogen. Optimizing this symbiosis can minimize the use of nitrogen fertilizers and make soybean production more sustainable. Phages targeting Bradyrhizobium may modify their hosts' genotype, alter phenotypic traits such as symbiotic effectiveness, and mediate competition among strains for nodulation sites. Sixteen phages were isolated against B. elkanii strains USDA94 and USDA31, and B. diazoefficiens strain USDA110. Comparative analyses revealed host species-dependent diversity in morphology, host range, and genome composition, leading to the identification of three previously undescribed phage species. Remarkably, all B. elkanii phages shared a siphophage morphology and formed a single species with >97% nucleotide identity, even when isolated from farms separated by up to ∼70 km, suggesting genomic stability across geographic scales. In contrast, phages isolated against B. diazoefficiens displayed podophage-like morphology, greater genetic diversity, and divided into two distinct species. Although no phages were recovered against B. japonicum strains or native Delaware Bradyrhizobium isolates tested, some Delaware isolates showed susceptibility during the host range assay. The phage genomes demonstrated features predicting phenotypes. Terminase genes predicted headful packaging among the phages which is critical for generalized transduction. The B. elkanii phages all carried tmRNA genes capable of recruiting stalled ribosomes and both phage groups carried DNA polymerase A indicating greater control of phage genome replication. State-of-the-art structural annotation revealed a tail fiber gene within a phage genome having the highest proportion (80.77%) of unknown genes. Together this work expands the limited knowledge available on soybean Bradyrhizobium phage ecology and genomics.},
}

@article {pmid41278752,
year = {2025},
author = {Lubin, MB and Teixeira, DH and Belin, BJ},
title = {Characterization of chemotaxis in soybean symbiont Bradyrhizobium diazoefficiens.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.14.682368},
pmid = {41278752},
issn = {2692-8205},
abstract = {UNLABELLED: Symbiotic relationships between nitrogen-fixing soil bacteria and legumes provide nearly half of all biologically fixed nitrogen on Earth, playing a crucial role in sustainable agriculture. These relationships rely on bacterial navigation of complex, dynamic soil environments to reach their plant hosts. Central to this behavior are bacterial motility and chemotaxis, the ability to sense and move toward host-derived signals in the rhizosphere. In the soybean symbiont Bradyrhizobium diazoefficiens USDA110, motility is controlled by dual flagellar systems, and this strain contains three putative but uncharacterized chemotaxis operons (che1 , che2 , and che3). Using targeted deletions of all three predicted cheA genes, we show that cheA2 is the primary driver of chemotaxis toward soybean seed exudate in soft agar assays, and that the greater contribution of cheA2 vs. cheA1 in soft agar chemotaxis is due to its genomic context. Interestingly, we also found that B. diazoefficiens mutants that are incapable of chemotaxis in semisolid media retain wild type-like swimming speeds in aqueous media. These findings provide insight into how the agricultural inoculant B. diazoefficiens coordinates its chemosensory systems to respond to its host plant.

IMPORTANCE: Chemotaxis is crucial for the establishment of beneficial plant-microbe associations, yet mechanistic studies of chemotaxis have been limited to a handful of soil bacterial models, namely Azospirillum brasilense , Sinorhizobium meliloti , and Rhizobium leguminosarum . These three models represent only a fraction of the diversity found among plant- beneficial bacteria and agricultural inoculants. The soybean symbiont Bradyrhizobium diazoefficiens USDA110 is a commonly used soybean inoculant with exceptional nitrogen fixation efficiency, but the genetic control of chemotaxis in B. diazoefficiens has not been examined. Establishing B. diazoefficiens as a model of chemotaxis provides an opportunity to understand how multiple chemotaxis systems coordinate root colonization in this major agricultural symbiont and can enable comparative analyses of plant-microbe recognition strategies across agricultural bacteria.},
}

@article {pmid41278148,
year = {2025},
author = {Dely, A and Racicot, R and Samples, R and Giddings, LA},
title = {Draft genome sequence and metabolomics data for Streptomyces sp. ADLamb9 isolated from the rhizosphere of Lavandula dentata.},
journal = {Data in brief},
volume = {63},
number = {},
pages = {112199},
pmid = {41278148},
issn = {2352-3409},
abstract = {Iron-chelating molecules or siderophores play pivotal roles in soil ecosystems, particularly in facilitating plant iron uptake as well as the phytoremediation of metal-polluted environments. Lavandula dentata, commonly referred to as French Lavender, is a valuable species for siderophore production due to its ability to thrive in iron-deficient Mediterranean soils by forming symbiotic relationships with siderophore-producing rhizosphere microbes. Here, we used a Chrome Azurol S (CAS) overlay assay to isolate a yellow-pigmented L. dentata rhizosphere siderophore-producing bacterium. This isolate also demonstrated antibacterial and antifungal activities against Bacillus subtilis and Aspergillus flavus, respectively. Genomic sequencing revealed that the isolate was Streptomyces sp. ADLamb9 with a genome size of 8.2 Mb and 71.77% GC content. antiSMASH analysis of the Streptomyces sp. ADLamb9 genome identified four putative siderophore biosynthetic gene clusters as well as the catecholate siderophore mirubactin. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) masses consistent with desferrioxamine B (561.3604 m/z), IC202C (517.3342 m/z), mirubactin (605.2207 m/z), as well as previously unreported desferrioxamine A1C. Notably, the presence of the rare earth element cerium differentially affected the accumulation of catecholate and hydroxamate siderophores, highlighting our incomplete understanding of the complex regulation and relationship between siderophore biosynthesis genes. These datasets, deposited at NCBI under the BioProject accession number PRJNA1224804, contribute to the broader scientific understanding of metabolite diversity and genomic features of Streptomyces sp. ADLamb9, providing insight into its use in bioremediation, especially in the presence of rare earth elements.},
}

@article {pmid41277186,
year = {2025},
author = {Sinha, A and Kumar, S},
title = {Symbiotic Relationships Between Arbuscular Mycorrhizal Fungi and Essential Oil-Producing Herbs: A Review of Recent Advances.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e70127},
doi = {10.1002/jobm.70127},
pmid = {41277186},
issn = {1521-4028},
support = {//The authors received no specific funding for this work./ ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) significantly impact on the growth, nutritional intake, and secondary metabolite synthesis of essential oil-producing plants by forming crucial symbiotic relationships with their roots. Recent research findings that demonstrate the diverse functions of AMF in improving the amount and chemical makeup of essential oils are compiled in this article. In sustainable agriculture, particularly in organic farming systems that utilize minimal synthetic inputs, AMF and medicinal herbs have demonstrated a positive relationship. AMF also supports ecological stability by promoting biodiversity and enhancing soil structure. The molecular and pharmacological mechanisms underlying these plant-fungal interactions are still not fully known, however. This study highlights the need for further research into the mechanisms of action of AMF, the development of effective inoculation methods, and the evaluation of novel herb-fungus combinations. It also reveals present research gaps. These revelations will open the door to more environmentally friendly farming methods and the efficient use of AMF in the manufacture of essential oils. AMF and medicinal plants have a promising interaction in sustainable agriculture, especially in organic farming systems that employ fewer synthetic inputs. Additionally, AMF improves soil structure and encourages biodiversity, both of which support ecological stability.},
}

@article {pmid41276973,
year = {2025},
author = {Luo, X and Yang, X and He, L and Wang, K and Gao, Y and Zhang, J and Yang, L and Li, Z and Zhao, X and Zhao, R and Zhao, S},
title = {Interaction Mechanisms between 6:2 Fluorotelomer Sulfonic Acid (6:2 FTSA) and Soil-Soybean System: Insight from Biodegradation, Phytotoxicity, and Microbial Shifts.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c11903},
pmid = {41276973},
issn = {1520-5118},
abstract = {As an important perfluorooctanesulfonate (PFOS) substitute, 6:2 fluorotelomer sulfonic acid (6:2 FTSA) has been widely detected in soil. However, the interaction mechanisms between 6:2 FTSA and the soil-plant system are still unknown. Here, we explored the biodegradation, phytotoxicity, and microbial impact of 6:2 FTSA in a soil-soybean system. The biodegradation of 6:2 FTSA in plants was mediated by both enzymes and coexisting microorganisms. 6:2 FTSA (2.97 nmol/g) inhibited soybean growth and caused oxidative damage, while soybeans enhanced their stress tolerance and metabolism of 6:2 FTSA by modulating genes involved in fatty acid metabolism, hormone signaling, oxidative stress, xenobiotic detoxification, and transmembrane transport. 6:2 FTSA affected rhizospheric and root endophytic microbial communities, with symbiotic fungi being more sensitive to 6:2 FTSA stress than bacteria. Five 6:2 FTSA-degrading rhizospheric and endophytic bacterial strains belonging to genera Acinetobacter, Rhodococcus, and Klebsiella were isolated and identified, with the rhizosphere bacteria exhibiting more effective degradation. Our findings reveal the ecological risks and detoxification mechanisms of emerging PFOS alternatives in soil-crop systems.},
}

@article {pmid41276563,
year = {2025},
author = {Thériault, V and De la Rosa, CMA and Miard, S and Taubert, S and Picard, F},
title = {Impact of bacterial inactivation methods on Caenorhabditis elegans feeding and healthspan.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-27444-5},
pmid = {41276563},
issn = {2045-2322},
support = {RGPIN-2024-06781//Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {Accurate bacterial inactivation methods are essential for nutritional and microbiota studies in Caenorhabditis elegans, to determine whether the observed effects arise from nutrients provided by ingested bacteria or from active symbiotic interactions. However, some inactivation methods alter bacterial palatability, complicating conclusions about their direct impact. We aimed to identify an effective method for inactivating the bacterial strain Escherichia coli OP50, the standard food source for most C. elegans experiments, that preserves normal behavior and physiology in C. elegans. We compared heat inactivation (65 °C for 35 min) with 0.5% paraformaldehyde (PFA) inactivation. Worms fed PFA-inactivated bacteria showed no food aversion, and maintained wild-type pharyngeal pumping levels, fertility rates, and lipid accumulation, closely resembling the behavior and physiology of worms fed alive E. coli OP50. In contrast, heat‑inactivated bacteria elicited strong food avoidance, reduced pumping activity, activation of the mitochondrial unfolded protein response (UPR[mt]), decreased lipid stores and fertility, and increased survival relative to the other groups. These findings demonstrate that 0.5% PFA inactivation more accurately preserves C. elegans physiological and behavioral traits than heat inactivation, making it a more suitable method for microbiota and nutritional studies.},
}

@article {pmid41276306,
year = {2025},
author = {Tian, L and Gupta, A and Li, W and Wang, G and Jiang, D and Yan, Y and Jia, Z and Tran, LP and Tian, C},
title = {Utilization of arbuscular mycorrhizal fungi symbiosis-related genes from host plants in biotechnology for sustainable agriculture.},
journal = {Critical reviews in biotechnology},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/07388551.2025.2581883},
pmid = {41276306},
issn = {1549-7801},
abstract = {In recent years, interest in the role of nutrient cycling in sustainable agriculture has significantly increased. The potential of arbuscular mycorrhizal (AM) fungi (AMFs) in nutrient cycling and plant growth improvement has long been recognized. However, there have been only a few studies on the identification and exploration of AM symbiosis-related plant genes for sustainable agriculture. We have developed a new constructive model for using host plant-derived AM symbiosis-related genes to improve breeding and AMF utilization for sustainable agriculture, particularly in the context of climate change. This model include: 1) the discovery of AM symbiosis-related genes in crop wild-relatives for molecular breeding and 2) the screening and propagation of AMFs that can help improve water-use efficiency and nutrient-use efficiency by crops, thereby reducing chemical fertilizer use in agricultural production. The first approach uniquely facilitates the identification of host plant-derived AM symbiosis-related genes, such as CHITIN ELICITOR RECEPTOR KINASE 1 (OsCERK1) from Dongxiang (DY) wild rice (Oryza rufipogon) (OsCERK1DY), MILDEW RESISTANCE LOCUS 1 (MLO1) from wild barley (Hordeum spontaneum), and WRKY60 from wild soybean (Glycine soja), for breeding purposes. The second one involves identifying soil-borne AMF species, such as Rhizophagus intraradices and Glomus mosseae for practical applications in the field. This suggestive model presents an emerging biotechnological potential for engineering climate-resilient crops.},
}

@article {pmid41275102,
year = {2025},
author = {Bruzzese, DJ and Gstöttenmayer, F and Weiss, BL and Khalil, H and Mach, RL and Abd-Alla, AMM and Aksoy, S},
title = {Comparative genomics and transcriptomics of the Spiroplasma glossinidia strain sGff reveal insights into host interaction and trypanosome resistance in Glossina fuscipes fuscipes.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-025-12351-w},
pmid = {41275102},
issn = {1471-2164},
support = {R21AI163969/NH/NIH HHS/United States ; R21AI163969/NH/NIH HHS/United States ; D42017//International Atomic Energy Agency/ ; },
}

@article {pmid41274117,
year = {2025},
author = {Imai, Y and Kimura, S and Kitajima, S and Sadato, N and Chiba, R and Hibino, H and Adachi-Akahane, S},
title = {Toward the promotion of "One Health" - part I: How do humans work to live together with humans, other organisms, and xenobiotics on Earth?.},
journal = {The journal of physiological sciences : JPS},
volume = {76},
number = {1},
pages = {100050},
doi = {10.1016/j.jphyss.2025.100050},
pmid = {41274117},
issn = {1880-6562},
abstract = {Thirty years from now, society will be transformed by dramatic advances in digital transformation, life infrastructure, and personalized medicine. People will communicate seamlessly in virtual spaces, and older adults will enjoy more fulfilling lives. Nevertheless, increasingly complex lifestyles will place immense pressure on ecosystems, affecting the environment and organisms and leading to serious health challenges. To address these issues, the Japanese Association of Anatomists, the Physiological Society of Japan (PSJ), and the Japanese Pharmacological Society have launched a collaborative initiative on "One Health". This framework aims to integrate the protection of flora and fauna with the health of humans, animals, and the planet, extending even to outer space. In the symposium held at 2025 APPW congress cohosted by PSJ, experts from multiple disciplines discussed how humans can coexist with microbes, xenobiotics, humans, and robots on Earth, fostering a sustainable and resilient future. This article summarizes this One Health symposium.},
}

@article {pmid41273130,
year = {2025},
author = {Zhang, XY and Li, DG},
title = {Immunoglobulin G and Aging: Biological Functions and Its Crosstalk with the Gut Microbiota.},
journal = {Rejuvenation research},
volume = {},
number = {},
pages = {},
doi = {10.1177/15491684251396176},
pmid = {41273130},
issn = {1557-8577},
abstract = {Aging is characterized by a progressive decline in physiological integrity, often accompanied by chronic inflammation and immune dysregulation. Immunoglobulin G (IgG), a key effector of humoral immunity, undergoes substantial structural and functional remodeling with age, particularly through changes in its glycosylation profile. These modifications shift IgG toward a proinflammatory state, linking it to inflammaging and multiple age-related diseases. This review synthesizes recent advances in understanding how IgG contributes to immune aging, with a specific focus on its glycosylation-dependent functions, tissue accumulation, and bidirectional crosstalk with the gut microbiota. We also highlight the potential of IgG as a biomarker and therapeutic target in aging-related interventions. We discuss the dual functional architecture of IgG and how age-related glycan shifts-namely, increased agalactosylation, afucosylation, and bisecting N-acetylglucosamine (GlcNAc)-enhance binding to activating Fcγ receptors, amplifying proinflammatory signaling. Experimental studies demonstrate that IgG accumulation in adipose tissue contributes to metabolic dysfunction via Neonatal Fc Receptor (FcRn)-dependent pathways. Additionally, sex hormones modulate IgG glycosylation patterns, partially explaining sex-specific differences in immune aging. The concept of "glycan clocks" has emerged as a tool to assess biological age and intervention responsiveness. Moreover, the gut microbiota plays a critical role in shaping the IgG repertoire, and aging disrupts this IgG-microbiota axis, resulting in altered mucosal immunity and systemic inflammation. Interventions targeting this axis-including microbiota modulation and glycoengineering-offer promising translational avenues for immune rejuvenation. Finally, we review emerging therapeutic strategies that leverage the gut-immune interface to mitigate aging-associated cardiovascular and metabolic diseases. IgG is not merely a biomarker but an active participant in the aging process, functioning at the intersection of immune regulation, microbial symbiosis, and systemic inflammation. Its age-associated transformation reflects broader changes in host immunity and highlights new opportunities for precision interventions in immunosenescence.},
}

@article {pmid41272488,
year = {2025},
author = {Wang, R and Pan, H},
title = {Identification and functional evaluation of cyclin-dependent kinase genes reveals that CDKB1;1 and CDKB2;2 contribute to the balance of mitosis and endoreduplication in Medicago truncatula nodule.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1617},
pmid = {41272488},
issn = {1471-2229},
mesh = {*Medicago truncatula/genetics/enzymology/microbiology ; *Mitosis/genetics ; *Root Nodules, Plant/genetics ; *Cyclin-Dependent Kinases/genetics/metabolism ; *Endoreduplication/genetics ; *Plant Proteins/genetics/metabolism ; Nitrogen Fixation/genetics ; Gene Expression Regulation, Plant ; Symbiosis ; Protein Interaction Maps ; },
abstract = {BACKGROUND: Cyclin-dependent kinases (CDKs) critically regulate plant cell cycle transitions, including mitosis-to-endoreduplication switches essential for growth and adaptation. In Medicago truncatula, nodules form through symbiotic nitrogen fixation with rhizobia. The terminal differentiation of bacteroids within nodule cells is critical for efficient nitrogen fixation. To maintain and optimize the functionality of these differentiated symbiosomes, host nodule cells undergo repeated rounds of endoreduplication. However, which CDKs are involved in regulating endoreduplication in nodule cells to support effective symbiotic nitrogen fixation remains largely unknown.

RESULTS: We identified and characterized 29 CDK genes (15 CDKs and 14 CDKLs) classified into eight conserved subgroups. These genes displayed diverse exon/intron structures and protein motifs, with CDKA, CDKB, and CDKL subfamilies showing strong conservation with Arabidopsis thaliana. Expression analysis revealed specific downregulation of CDKB1;1, CDKB2;2, and CDKL13 in nodule infection to fixation zones. Protein-protein interaction (PPI) network and Gene ontology (GO) analyses demonstrated CDKB1;1 and CDKB2;2 involvement in cell cycle regulation. Overexpression of CDKB1;1 or CDKB2;2 disrupted endoreduplication and nitrogen fixation, with CDKB1;1 having the most pronounced effect, while CDKL13 appeared dispensable for symbiosis.

CONCLUSION: Our study presents the comprehensive genome-wide analysis of the CDK gene family in M. truncatula, demonstrating that the essential role of CDKB1;1 and CDKB2;2 downregulation in symbiotic nitrogen fixation and endoreduplication offers new insights into cell cycle regulation in nodules. It also identifies potential targets for improving nitrogen fixation efficiency in legumes.},
}

*Medicago truncatula/genetics/enzymology/microbiology
*Mitosis/genetics
*Root Nodules, Plant/genetics
*Cyclin-Dependent Kinases/genetics/metabolism
*Endoreduplication/genetics
*Plant Proteins/genetics/metabolism
Nitrogen Fixation/genetics
Gene Expression Regulation, Plant
Symbiosis
Protein Interaction Maps

@article {pmid41271942,
year = {2025},
author = {Dmitrieva, M and Shelkovnikova, V and Morgunova, M and Malygina, E and Imidoeva, N and Belyshenko, A and Telnova, T and Vavilina, T and Konovalov, A and Batalova, A and Lipatova, O and Listopad, A and Axenov-Gribanov, D},
title = {Genetic and biotechnological potential of thermophilic Streptomyces sp. isolated from Baikal freshwater psychrophilic sponge.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {41403},
pmid = {41271942},
issn = {2045-2322},
support = {FZZE-2024-0003//Ministry of Science and Higher Education of the Russian Federation/ ; FZZE-2024-0013//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {*Streptomyces/genetics/isolation & purification/metabolism ; *Porifera/microbiology ; Animals ; Fresh Water/microbiology ; Biotechnology/methods ; Biological Products/metabolism/pharmacology ; Anti-Bacterial Agents/pharmacology ; Temperature ; Phylogeny ; },
abstract = {Microorganisms inhabiting extreme environmental conditions receive special attention because they possess different adaptations to adverse conditions. Currently, their biotechnological potential and ability to isolate biologically active metabolites have increased. The increasing mortality due to different diseases has become particularly important as one of the notable challenges in modern healthcare. This highlights the necessity of discovering new producers of natural products (NPs). The aim of this study was to evaluate the genetic and biotechnological potential through the assessment of NP synthesis and genome annotation of the thermophilic strain Streptomyces sp. LPB2020-019-1HS. The thermophilic strain was isolated from the Baikal endemic cold water sponge Lubomirskia baikalensis. Subsequently, Streptomyces sp. LPB2020-019-1HS was cultivated at six temperatures ([Formula: see text]C, [Formula: see text]C, [Formula: see text]C, [Formula: see text]C, [Formula: see text]C, and [Formula: see text]C) in twelve nutrient media with different compositions (nutrient rich and nutrient poor). Using high-performance liquid chromatography and mass spectrometry approaches, the synthesis of compounds by the strain was assessed at [Formula: see text]C, [Formula: see text]C, and [Formula: see text]C. Antimicrobial activity was evaluated at all temperatures (from [Formula: see text] to [Formula: see text]C). We demonstrated the presence of antibiotic activity against Bacillus subtilis for strains cultivated at 28 °C, [Formula: see text]C, and [Formula: see text]C. Additionally, we observed activity against Mycobacterium smegmatis when the strain was cultivated at [Formula: see text]C, [Formula: see text]C, [Formula: see text]C, and [Formula: see text]C. Furthermore, the strain exhibited activity against Escherichia coli, Pseudomonas putida, and Candida glabrata when cultured at [Formula: see text]C. Overall, we found that Streptomyces sp. LPB2020-019-1HS produces a family of NPs related to Nocardamine and hypothesized that freshwater Actinobacteria have mechanisms for chelating iron ions, making them available for plants/sponges or other symbiotic organisms. Therefore, our research findings underscore the importance of studying extremophilic microorganisms from Lake Baikal in the context of developing new pharmaceuticals and biotechnological solutions for contemporary healthcare challenges.},
}

*Streptomyces/genetics/isolation & purification/metabolism
*Porifera/microbiology
Animals
Fresh Water/microbiology
Biotechnology/methods
Biological Products/metabolism/pharmacology
Anti-Bacterial Agents/pharmacology
Temperature
Phylogeny

@article {pmid41271671,
year = {2025},
author = {Shahul Hameed, UF and Balakrishna, A and Wang, JY and Alvarez, D and Momin, AA and Schwarzenberg, A and Al-Babili, S and Arold, ST},
title = {Molecular Basis for Catalysis and Regulation of the Strigolactone Catabolic Enzyme CXE15.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10290},
pmid = {41271671},
issn = {2041-1723},
support = {BAS/1/1056-01-01//King Abdullah University of Science and Technology (KAUST)/ ; },
mesh = {*Lactones/metabolism ; *Arabidopsis/enzymology/genetics/metabolism ; *Arabidopsis Proteins/metabolism/chemistry/genetics ; Reactive Oxygen Species/metabolism ; Catalytic Domain ; Crystallography, X-Ray ; Gene Expression Regulation, Plant ; Catalysis ; *Plant Growth Regulators/metabolism ; Oxidation-Reduction ; Protein Multimerization ; },
abstract = {Strigolactones (SLs) are pivotal plant hormones involved in developmental, physiological, and adaptive processes. SLs also facilitate symbiosis with arbuscular mycorrhizal fungi and trigger germination of root parasitic Striga plants. The carboxylesterase CXE15, recently identified as the SL catabolic enzyme in Arabidopsis thaliana, plays a crucial role in regulating SL levels. Our study elucidates the structural and regulatory mechanisms of CXE15. We present four crystal structures capturing the conformational dynamics of CXE15, revealing a unique N-terminal extension (Nt) that transitions from a β-sheet in monomers to an intertwined helical structure in dimers. Only the dimeric form is catalytically active, as it forms a hydrophobic cavity for SLs between its two active sites. The moderate dimerisation affinity allows for genetic regulation through protein expression levels. Additionally, we identify an environment-controlled regulation mechanism. Under oxidising conditions, a disulphide bond forms between Cys14 of the two monomers, blocking the active site and inhibiting SL cleavage. This redox-sensitive inhibition of SL catabolism, triggered by reactive oxygen species (ROS) in response to abiotic stress, suggests a mechanism for maintaining high SL levels under beneficial conditions. Our findings provide molecular insights into the regulation of SL homeostasis and catabolism under stress conditions.},
}

*Lactones/metabolism
*Arabidopsis/enzymology/genetics/metabolism
*Arabidopsis Proteins/metabolism/chemistry/genetics
Reactive Oxygen Species/metabolism
Catalytic Domain
Crystallography, X-Ray
Gene Expression Regulation, Plant
Catalysis
*Plant Growth Regulators/metabolism
Oxidation-Reduction
Protein Multimerization

@article {pmid41270733,
year = {2025},
author = {Wei, Z and Lan, Y and Meng, L and Wang, H and Li, L and Li, Y and Zhang, N and Lu, R and Cui, Z and Song, Y and Wang, Y and Li, Y and Yue, Z and Fan, G and Li, Q and Gu, Y and Liu, S and Qian, PY and Meng, L and Shao, C},
title = {Hologenomic insights into the molecular adaptation of deep-sea coral Bathypathes pseudoalternata.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.10.020},
pmid = {41270733},
issn = {1934-6069},
abstract = {Deep-sea coral ecosystems support biodiversity and nutrient cycling through interactions with symbionts. However, their molecular mechanisms remain unexplored. Here, hologenomic analyses of Bathypathes pseudoalternata are applied to uncover molecular adaptations underpinning host-symbiont interactions. Genomic evidence reveals that B. pseudoalternata exhibits adaptations in nutrient transport, immune response, and lysosomal digestion, reflecting its genomic adjustments for a stable symbiosis. Candidatus Nitrosopumilus bathypathes (78.43% ± 3.65%) is inferred to oxidize host-derived ammonia to synthesize amino acids and vitamins to provision the host. The presence of CRISPR-Cas and restriction-modification (R-M) systems suggests that Ca. Bathyplasma bathypathes and Ca. Thalassoplasma bathypathes (10.68% ± 2.99%) may protect the host from viral infections. Ca. Bathybacter bathypathes (8.39% ± 1.53%) is hypothesized to synthesize heme, lipoic acid, and glutathione, which serve dual functions as antioxidants and nutrients. These findings collectively provide insights into how the hologenome contributes to the survival of B. pseudoalternata in the extreme environment.},
}

@article {pmid41267536,
year = {2025},
author = {Zhou, J and Zhang, W and Guo, Q and Liu, X and Wei, C},
title = {Initially Coexisting Endosymbionts Migrate Into Different Tissues During Ontogeny of Host Cicadas.},
journal = {Environmental microbiology},
volume = {27},
number = {11},
pages = {e70185},
doi = {10.1111/1462-2920.70185},
pmid = {41267536},
issn = {1462-2920},
support = {32270496//National Natural Science Foundation of China/ ; 2025KYCXZ05//Northwest A&F University Doctoral Candidates' Independent Innovation Research Project Funding/ ; },
mesh = {*Symbiosis ; *Hemiptera/microbiology/growth & development ; Animals ; *Fungi/physiology ; },
abstract = {Endosymbionts play pivotal roles in driving ecological and evolutionary diversification of many insects, yet the morphogenesis and evolutionary origin of their specialised symbiotic organs (e.g., bacteriomes) remain poorly understood. Here we investigated the bacteriome morphogenesis in Cicadidae using microscopy-based methods. We revealed that bacteriomes originate either from both the original bacteriocytes that emerged after anatrepsis and the novel bacteriocytes that appeared during katatrepsis, or solely from the latter. Bacteriomes expand via "budding" proliferation to increase the bacteriome unit number, and bacteriome developmental patterns closely correlate with the presence/absence of the yeast-like fungal symbionts (YLS) and their colonisation dynamics. The obligate endosymbiont Karelsulcia and YLS, coexisting in bacteriomes during early stages of host ontogeny, may compete for ecological niches, potentially resulting in translocation of YLS into fat bodies. This indicates that bacteriomes may have initially functioned as immune organs like fat bodies, but evolved specifically for accommodating bacterial endosymbionts. The translocation of YLS from bacteriomes to fat bodies during the later development of host cicadas indicates that immune-mediated regulation occurs in such symbiotic organs as host insects mature. This study sheds light on how symbiont-host interactions shape the symbiotic organogenesis, which provides insights into adaptive evolution of specialised symbiotic organs in plant sap-feeding insects.},
}

*Symbiosis
*Hemiptera/microbiology/growth & development
Animals
*Fungi/physiology

@article {pmid41266970,
year = {2025},
author = {Jin, L and Xu, Q and Miao, C and Zhan, J and Zhang, Y and Li, M and Cheng, J and Liu, P and Yang, Y and Zhou, H and Hu, Z and Li, F and Wu, C},
title = {Dynamic multi-omics analysis reveals the correlation between aroma compounds and symbiotic microbial community during tobacco leaf aging process.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-025-07765-3},
pmid = {41266970},
issn = {1471-2229},
support = {110202102033//the Key Grant of China National Tobacco Corporation, China/ ; },
}

@article {pmid41266614,
year = {2025},
author = {Wiles, EL and Kakumanu, ML and Schal, C},
title = {Wolbachia-supplemented B-vitamins are critical for blood digestion in the bed bug Cimex lectularius.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40962},
pmid = {41266614},
issn = {2045-2322},
support = {2023348287//National Science Foundation Graduate Research Fellowship Program/ ; NC02639//U.S. Department of Agriculture's National Institute of Food and Agriculture/ ; },
mesh = {Animals ; *Bedbugs/microbiology/physiology/metabolism ; *Wolbachia/physiology ; *Riboflavin/pharmacology/metabolism ; *Digestion ; Symbiosis ; *Vitamin B Complex/pharmacology ; Biotin/pharmacology ; Female ; },
abstract = {Wolbachia, a bacterial endosymbiont, acts as an obligate nutritional mutualist in the bed bug, Cimex lectularius. Wolbachia in C. lectularius (wCle) supplements B-vitamins, namely riboflavin (B2) and biotin (B7), which are deficient in the bed bug's diet of vertebrate blood. Experimental elimination of wCle significantly impairs fitness in bed bugs, resulting in slow development, low egg production and egg hatch rate, and smaller adult body size. Although this obligatory symbiosis has been well-documented, the specific physiological mechanisms by which wCle-supplemented B-vitamins promote bed bug fitness remain unclear. We hypothesized that B-vitamin deficiency impairs digestion in aposymbiotic bed bugs, and in this study we investigated the effects of wCle elimination on three digestive processes in the bed bug - diuresis, erythrocyte (red blood cell) lysis, and protein catabolism. Our results show that wCle elimination significantly slows both diuresis and protein catabolism. We also demonstrate that riboflavin is critical for the breakdown of hemoglobin, the main protein component of red blood cells, but not albumin, the main protein component of plasma. We propose that the lack of wCle-supplemented riboflavin results in systemic protein deficiency, driving various fitness-related deficits in aposymbiotic bed bugs. These findings enhance our understanding of bed bug digestive physiology and the wCle-bed bug nutritional mutualism, with broader implications for other blood-feeding arthropods.},
}

Animals
*Bedbugs/microbiology/physiology/metabolism
*Wolbachia/physiology
*Riboflavin/pharmacology/metabolism
*Digestion
Symbiosis
*Vitamin B Complex/pharmacology
Biotin/pharmacology
Female

@article {pmid41266521,
year = {2025},
author = {Zhou, Y and Zhu, P and Xia, Y and Hassan, Z},
title = {The mutualistic symbiosis of public and scientific attention in science communication.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {41151},
pmid = {41266521},
issn = {2045-2322},
support = {22YB013//Jiangxi Provincial Education Science '14th Five-Year Plan' 2022 General Topic: Research on Red Gene Inheritance of Contemporary College Students Based on Heart Stream Experience/ ; 2023JSYJC20//Public Security Ministry Technical Research Program/ ; G2024507002//Hebei Natural Science Foundation: Research on Modeling of Public Opinion Risks in Online Communities and Intelligent Governance Algorithms/ ; },
mesh = {Humans ; *Symbiosis ; *COVID-19/epidemiology ; Models, Theoretical ; *Communication ; *Information Dissemination/methods ; *Science ; *Scholarly Communication ; },
abstract = {This study examines the bidirectional tension between public and scientific attention amid informatization, analyzing their mutualistic symbiosis to address science communication challenges. We constructed a mathematical model of mutualistic symbiosis in their relationship was developed based on the Logistic Model. Subsequently, numerical simulations were employed to investigate the evolutionary trends and patterns of scientific attention, public attention, and the effectiveness of science communication under varying modes of public attention and initial values of scientific attention. Furthermore, using "COVID-19" as a case study, an empirical analysis was conducted on to assess the correlation between public attention and scientific attention and evaluate the constructed mathematical Model, verifying its scientific validity and effectiveness. This study underscores the critical role of science communication in fostering advantageous interactions between scientific and public attention. Nonetheless, it is imperative to adopt tailored science communication strategies that accommodate diverse public attention modes and initial levels of scientific attention while selecting appropriate symbiotic models for specific contexts. This proposed approach ensures the effective dissemination of scientific information and fosters a robust science communication ecosystem.},
}

Humans
*Symbiosis
*COVID-19/epidemiology
Models, Theoretical
*Communication
*Information Dissemination/methods
*Science
*Scholarly Communication

@article {pmid41266356,
year = {2025},
author = {Deng, Y and Zhao, H and Zhang, L and Yang, S and Zou, D and Ma, M and Hou, C},
title = {Symbiotic Enterococcus faecalis potentiates viral pathogenesis via fructose-1,6-bisphosphate-mediated insect gut epithelial damage.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {215},
pmid = {41266356},
issn = {2055-5008},
support = {32300418//National Natural Science Foundation of China/ ; 32300418//National Natural Science Foundation of China/ ; 2024RC1069//The Science and Technology of Innovation Program of Hunan Province/ ; CAAS-BRC-CB-2025-01//Agricultural Science and Technology Innovation Program/ ; GLKY-2022-16//Guangxi Forestry Science and Technology Promotion and Demonstration Project/ ; },
mesh = {Animals ; *Enterococcus faecalis/physiology/genetics ; Bees/virology/microbiology ; *Symbiosis ; Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Larva/virology/microbiology ; Apoptosis ; },
abstract = {Chinese sacbrood virus (CSBV) is highly lethal to Asian honey bee (Apis cerana) larvae. While gut symbionts are known to regulate viral infection, their role in CSBV pathogenesis remains poorly understood. Through 16S rRNA gene sequence analysis of the field-collected honey bees, we found that the larvae had a substantially higher relative abundance of Enterococcus than pupae or adults. Metagenome sequencing analysis of field-collected larvae demonstrated that CSBV infection significantly induced more than 45-fold enhancement in the abundance of Enterococcus faecalis, an opportunistic pathogen implicated in the development of purulent cystic lesions. In microbiota-free (MF) bees, colonization with E. faecalis markedly suppressed phospholipid metabolism and elevated levels of 4-guanidinobutyric acid and fructose-1,6-bisphosphate (FBP). These metabolic changes were associated with cytotoxicity and apoptosis, which worsened goblet cell damage and thereby facilitated CSBV infection, as indicated by metabolomics and pathological section analysis. Crucially, exogenous FBP administration directly enhanced cytotoxicity and apoptosis of gut in CSBV-infected MF bees, mirroring the CSBV susceptibility was mediated by E. faecalis. Our study unveiled a symbiotic bacteria's involvement in promoting RNA virus infection through metabolic reprogramming and epithelial barrier dysfunction, providing new insights into host-microbe-virus interactions in pollinators.},
}

Animals
*Enterococcus faecalis/physiology/genetics
Bees/virology/microbiology
*Symbiosis
Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
Larva/virology/microbiology
Apoptosis

@article {pmid41265612,
year = {2025},
author = {Ranjbar, M and Ahmadpour, M and Kiani, M and Govahi, M},
title = {Myco-macromolecular symbiosis: Chitosan-folate ZnO nanoplatforms from Trametes versicolor for dual-functional oncological and antibacterial therapy.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {149140},
doi = {10.1016/j.ijbiomac.2025.149140},
pmid = {41265612},
issn = {1879-0003},
abstract = {The increasing prevalence of antibiotic-resistant bacteria and cancer necessitates the development of novel, targeted therapeutic strategies. This study aimed to develop a multifunctional nanoplatform combining antibacterial and anticancer properties through green synthesis and strategic surface functionalization. Zinc oxide nanoparticles (ZnO NPs) were biosynthesized using Trametes versicolor extract as a reducing and capping agent, then surface-functionalized with chitosan (Cs) for enhanced biocompatibility and conjugated with folic acid (FA) for targeted delivery. The NPs were characterized using multiple analytical techniques and evaluated for antibacterial activity against Gram-positive (Bacillus subtilis, Staphylococcus aureus) and Gram-negative (Escherichia coli) bacteria. Cytotoxicity was assessed in cancer cells (MDA-MB-231) and normal cells (MCF-10 A), followed by gene expression analysis of key oncogenic and apoptotic markers. Characterization confirmed the formation of crystalline, core-shell structures with successful ligand attachment. Cs-ZnO NPs demonstrated significantly enhanced antibacterial activity against all tested bacterial strains compared to bare ZnO NPs. FA-Cs-ZnO NPs exhibited selective cytotoxicity toward cancer cells while maintaining biocompatibility with normal cells. Gene expression analysis revealed down-regulation of cancer stemness genes (CD44, SOX2) and proliferation markers (mTOR, β-catenin), coupled with up-regulation of the apoptotic marker Caspase 3. This green-synthesized, dual-functional nanoplatform demonstrates promising potential for combined antibacterial and targeted anticancer therapy, warranting further in vivo evaluation for clinical translation.},
}

@article {pmid41265272,
year = {2025},
author = {Jia, J and Xue, X and Wang, Z and Xiong, X and Hu, H and Wu, C},
title = {Phycosphere as a hotspot of antibiotic resistomes in aquatic environments.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140513},
doi = {10.1016/j.jhazmat.2025.140513},
pmid = {41265272},
issn = {1873-3336},
abstract = {Algal-bacterial interactions represent fundamental ecological processes in aquatic environments, crucially governing nutrient cycling and energy flow within food webs. Beyond their ecological roles, the algal phycosphere has recently been identified as a critical hotspot for the proliferation and enrichment of antibiotic resistance genes (ARGs). It's reported that the total abundance of ARGs in the phycosphere of microalgae is up to 47-fold higher than in the surrounding water. However, a systematic understanding of how the phycosphere drives ARG dynamics in aquatic ecosystems remains limited. This review synthesizes current evidence to evaluate the mechanisms by which algae influence ARG proliferation within aquatic ecosystems. Findings indicate that in the phycosphere, algal-bacterial interactions shape ARG fate by modulating bacterial community composition. The symbiotic bacteria are specifically enriched in the phycosphere and play important roles in the proliferation of ARGs. Furthermore, exogenous factors (e.g., nutrients, antibiotics, microplastics, and warming) alter these interactions, thereby changing the phycospheric bacterial community and further affecting ARG evolution. Algal blooms typically enhance the dominance of key ARG hosts, promoting aquatic ARG proliferation. The review concludes by outlining research priorities essential for advancing mechanistic insights into algal-associated ARG dynamics.},
}

@article {pmid41265199,
year = {2025},
author = {Li, X and Shi, F and Zhou, M and Su, H and Liu, X and Wei, Y and Wang, F},
title = {Arbuscular mycorrhizal fungi change toxic effects of different types of microplastics on Lactuca sativa L. by influencing plant metabolic processes.},
journal = {Ecotoxicology and environmental safety},
volume = {307},
number = {},
pages = {119443},
doi = {10.1016/j.ecoenv.2025.119443},
pmid = {41265199},
issn = {1090-2414},
abstract = {Soil microplastics (MPs) pollution is becoming more serious, and symbiotic microorganisms in soil-plant systems may influence the environmental behavior and related plant responses to MPs stress. In this study, common primary plastic products were broken down into MPs to investigate the toxic effects and migration behavior of MPs on lettuce (Lactuca sativa L.) in the presence of arbuscular mycorrhizal fungi (AMF). Our findings show that symbiotic AMF reduce the uptake and toxic effects of polyethylene terephthalate (PET) by increasing nucleotide metabolism and zeatin biosynthesis, resulting in a 20.64 % drop in PET uptake and an 11.43 % increase in lettuce biomass. In contrast, AMF promoted the absorption of polypropylene (PP) and polystyrene (PS) by lettuce, inhibiting ascorbate metabolism and lysine biosynthesis, and causing poorer lettuce growth. The positive regulatory effect of AMF on the nutritional quality and health status of plants under PET stress shows that AMF have the potential to alleviate the toxicity of MPs to lettuce in farmland and to remediate the MPs-related pollution in agricultural areas.},
}

@article {pmid41262929,
year = {2025},
author = {Asatulloev, T and Yusupov, Z and Cai, L and Chen, Q and Gurung, B and Tojibaev, KS and Sun, W},
title = {Comparative root associated microbial community analysis of Oreocharis mileensis, a resurrection plant species with extremely small populations.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1692695},
pmid = {41262929},
issn = {1664-302X},
abstract = {Plants dynamically interact with their microbiomes through phytohormonal signaling and defense responses, shaping microbial diversity and ecosystem function. While resurrection plants host growth-promoting and drought associated microbes, prior studies on different resurrection plants have been limited to localized sampling, potentially underestimating microbial diversity. We analyzed bacterial and fungal communities across five populations of Oreocharis mileensis, a resurrection plant, during hydrated and dehydrated states to examine population-level microbiome differences or affinity, identify microorganisms that may assist during plant desiccation, and assess their conservation across populations. We found that microbial composition was strongly influenced by compartment (bulk soil, rhizosphere, and endosphere) but exhibited only moderate drought-induced changes, suggesting that O. mileensis maintains a stable microbiome under stress. Core phyla (e.g., Proteobacteria, Actinobacteriota, Ascomycota) were conserved across populations, but genus-level core taxa varied relatively between populations, reflecting niche specialization and host genotype. Drought increased bacterial alpha diversity while reducing beta diversity, indicating homogenization driven by stress-tolerant taxa such as Actinobacteriota. Fungal responses differed, with increased beta diversity suggesting drought-enhanced compositional turnover. Key bacterial genera (e.g., Burkholderia-Caballeronia-Paraburkholderia, Bacillus, Rhizobium) dominated hydrated states, while drought enriched Actinobacteria (e.g., Microlunatus, Rubrobacter) and other drought-resistant taxa. Fungal communities shifted from saprotroph-dominated hydrated states to symbiotic taxa (e.g., Paraboeremia, Helotiales) under drought conditions. Functional profiling revealed compartment-specific metabolic specialization, with drought enriching stress-response pathways (e.g., secondary metabolite biosynthesis, signal transduction). These findings demonstrate that O. mileensis microbiomes are structured by compartmental filtering and exhibit drought-driven functional plasticity, with conserved stress-adapted taxa potentially supporting host resilience. Overall, this study expands our understanding of microbiome assembly in resurrection plants and highlights candidate microbes for microbiome engineering to enhance crop stress tolerance.},
}

@article {pmid41262890,
year = {2025},
author = {Chuang, PS and Hsu, TC and Lu, CY and Yu, SP and Liu, PY and Lim, SL and Chen, YH and Chiou, YJ and Yang, SH and Wang, PL and Tang, SL},
title = {Metabolic interactions between coral animal and endolithic bacterial communities.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf193},
pmid = {41262890},
issn = {2730-6151},
abstract = {Coral skeletons constitute sources of nutrients and energy for holobiont. Although bacteria predominate in endolithic microbiomes of corals, their ecological functions have long been masked by those of symbiotic microalgae. In the skeleton of Isopora palifera, previous studies showed the absence of microalgae and a green layer dominated by green sulfur bacteria. This system, which excludes a contribution from microalgae, provides a perfect model for studying the role of endolithic bacteria in corals. Using this model, we examined the metabolite profile and translocation of organic matter between coral tissue and skeleton. Chromatography-time-of-flight-mass spectrometry and ultra-high-performance liquid chromatography tandem mass spectrometry revealed distinct metabolic profiles in tissue and different skeletal layers. A stable isotope incubation experiment further demonstrated [13]C translocation between tissue and the green layer, but no translocation of [15]N. These findings suggest communication between the two compartments that is generally carbon-based, possibly in the form of carbohydrates and bioactive compounds, such as corticosterone and domoic acid. Nevertheless, some nitrogenous compounds appear to have an endolithic source, indicating a possible contribution of the skeleton to coral animal. Notably, antibiotic treatment greatly increased [15]N translocation in the tissue but not in the green layer. This highlights an important role of bacteria in nitrogen cycling in the holobiont and in establishing the nitrogen-limiting green layer. Altogether, this study provides the first data about coral skeletal metabolomes. Based on these findings, we propose a model of interactions between coral animal and skeletal bacterial communities, offering a new perspective on the ecological role of endolithic bacteria in corals.},
}

@article {pmid41261892,
year = {2025},
author = {Ma, M and Michalik, A and Deng, J and Hu, Y and Łukasik, P},
title = {Contrasting genomic trajectories of Bartonellaceae symbionts of planthoppers.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf216},
pmid = {41261892},
issn = {1759-6653},
abstract = {Symbioses with microorganisms have shaped the nutritional biology and evolution of many insects. For example, several ant clades have adapted to nutrient-poor diets through symbiosis with a specific clade of bacteria in the family Bartonellaceae (Hyphomicrobiales), notorious for also including virulent vertebrate pathogens. Here we show that Bartonellaceae phylogenetically placed within the clade that has only encompassed ant symbionts to date - Candidatus genus Tokpelaia - have established as symbionts in four different clades of planthoppers (Insecta: Hemiptera: Fulgoromorpha). Genome size and contents indicate different levels of integration of these strains into the planthopper biology and their diverse roles. Symbionts infecting one of the clades have some of the largest genomes among Bartonellaceae, at ca. 2 Mb, two others are under 700 kb, and the fourth is reduced to barely 158 kb. The planthopper-associated Tokpelaia strains with larger genomes, similarly to ant symbionts, encode multiple amino acid and vitamin biosynthesis genes, complementing the degraded nutritional capabilities of their hosts' ancient heritable endosymbionts. Strikingly, the smallest Tokpelaia genome lacks any genes linked to essential amino acid biosynthesis, in contrast to all other known insect-associated bacteria with genomes of comparable size. We identified a single vitamin biosynthesis gene and iron-sulfur cluster assembly genes as its only putative contributions to the host biology. Our results broaden the host spectrum of non-pathogenic Bartonellaceae, indicating that they have contributed to nutrition and symbiotic consortium function in diverse diet-restricted host clades. They also highlight an unexpectedly broad range of evolutionary outcomes for this important bacterial group.},
}

@article {pmid41261810,
year = {2025},
author = {Peng, L and Yang, Y and Martin, FM and Yuan, Z},
title = {Endophytes with mycorrhizal potentials: biological and ecological implications.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70772},
pmid = {41261810},
issn = {1469-8137},
support = {2022YFD2201900//National Key Research and Development Program of China/ ; 32471839//National Natural Science Foundation of China/ ; CAFYBB2023QC001-02//Fundamental Research Funds for the Central Nonprofit Research of Chinese Academy of Forestry/ ; Z25C010004//Zhejiang Provincial Natural Science Foundation of China/ ; },
abstract = {Generally, the root mycobiome is dominated by endophytic and mycorrhizal fungi with mutualistic potential to enhance plant fitness. In some cases, however, the distinction between the two biotrophic guilds is challenged by the ability of several endophytic fungi to colonize roots and transfer nutrients to the plants. With more research on harnessing plant-endophyte combinations using a gnotobiotic system, more endophytes endowed with mycorrhizal-like traits have been identified. They often benefit nonmycorrhizal plants by employing a set of responses to nutrient deficiency similar to those from mycorrhizal plants, orchestrate the development of ectomycorrhizal-like structures under controlled conditions, and share genetic traits with true mycorrhizal fungi, such as a lower content of plant cell wall-degrading enzymes and gene networks reminiscent of mutualistic interactions. Based on these characteristics, we propose the term 'mycorrhizal-like endophytes' to describe these fungi, which likely represent a transitional state along the endophyte-mycorrhizal mutualistic continuum.},
}

@article {pmid41261196,
year = {2025},
author = {Yu, WQ and Qiu, H and Sun, YP and Zhao, MW and Shi, L},
title = {Microorganisms' perception, scavenging, and adaptation to reactive oxygen species signals in microbe-plant interactions.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {12},
pages = {466},
pmid = {41261196},
issn = {1573-0972},
support = {No. CARS20//the China Agriculture Research System of the MOF and MARA/ ; (2024)171//the Project of Science and Technology Programs of Guizhou Province/ ; },
mesh = {*Reactive Oxygen Species/metabolism ; *Plants/microbiology/metabolism ; Symbiosis ; Signal Transduction ; Oxidative Stress ; Antioxidants/metabolism ; Oxidation-Reduction ; *Bacteria/metabolism ; Adaptation, Physiological ; Plant Immunity ; },
abstract = {Plant-microbial interactions represent a complex biological process in which reactive oxygen species (ROS) play central roles in both plant immunity and symbiosis establishment. ROS act as defense signaling molecules to activate immune responses and as symbiotic cues to regulate microbial colonization. To cope with plant-derived ROS, microbes have evolved sophisticated sensing and scavenging mechanisms; however, a systematic understanding of these responses remains limited. Recent advances in molecular biology and genetics have revealed that microbes can directly sense ROS via transcription factors or indirectly perceive oxidative stress through bio macromolecular damage. They maintain intracellular redox homeostasis through enzymatic antioxidant systems-including catalase (CAT), superoxide dismutase (SOD), and peroxiredoxin/thioredoxin (Prx/Trx)-as well as non-enzymatic mechanisms such as melanin and extracellular polysaccharides. This review systematically summarizes microbial ROS perception and scavenging strategies, highlighting functional distinctions and evolutionary adaptations in pathogenic infection versus symbiosis. These insights provide a theoretical framework for understanding plant-microbial interactions and suggest potential ROS-related strategies for improving agricultural productivity and ecological resilience.},
}

*Reactive Oxygen Species/metabolism
*Plants/microbiology/metabolism
Symbiosis
Signal Transduction
Oxidative Stress
Antioxidants/metabolism
Oxidation-Reduction
*Bacteria/metabolism
Adaptation, Physiological
Plant Immunity

@article {pmid41257969,
year = {2025},
author = {Arenas, F and Marqués-Gálvez, JE and Guarnizo, ÁL and Andreu-Ardil, L and Morte, A and Navarro-Ródenas, A},
title = {Winter soil mycelium dynamics of Terfezia claveryi are shaped by rainfall and temperature in Mediterranean shrublands.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40727},
pmid = {41257969},
issn = {2045-2322},
support = {145/MSJD/22//Ministerio de Ciencia, Innovación y Universidades/ ; 123/MTAI/22//Ministerio de Ciencia, Innovación y Universidades/ ; R.D. 103/2019//Universidad de Murcia/ ; MCIN/AEI/10.13039/50110001103//Ministerio de Ciencia e Innovación/ ; PRTR-C17.I1//Fundación Séneca/ ; },
abstract = {UNLABELLED: Shrubland ecosystems play a crucial role in Mediterranean forests, contributing to soil protection, biodiversity conservation, carbon sequestration, and ecosystem restoration. In semi-arid regions, mycorrhizal woody plants such as Helianthemum spp. form ectendomycorrhizal symbiosis with edible desert truffles, representing an emerging and sustainable crop with significant potential for rural development and economic diversification. Significant progress has been made in the breeding of Terfezia claveryi Chatin, but key aspects of its life cycle, such as the temporal and spatial behaviour of the soil mycelium, remain underexplored. This study aimed to investigate the seasonal dynamics of T. claveryi soil mycelium in plantations and wild areas of the Region of Murcia (Spain) using real-time quantitative PCR. The relationship between fungal biomass and host plant phenology and environmental parameters was also investigated. Our results showed that T. claveryi soil mycelium was higher in plantations than in wild areas, and in Xerolls than in Orthents soils. Fungal dynamics lacked seasonal or annual patterns; however winter mycelium showed a strong correlation with preceding agroclimatic variables, especially precipitation and maximum temperature. This research sheds light on the ecological processes underlying the desert truffle shrublands and offers practical implications for optimising T. claveryi cultivation strategies and promoting ecosystem restoration.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-24621-4.},
}

@article {pmid41259095,
year = {2025},
author = {Morel Revetria, MA and Sanjuan, J and Berriel, V and Velázquez, E},
title = {Bradyrhizobium monzae sp. nov. isolated from a root nodule of the introduced legume Crotalaria ochroleuca in Uruguay.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {75},
number = {11},
pages = {},
doi = {10.1099/ijsem.0.006973},
pmid = {41259095},
issn = {1466-5034},
mesh = {*Bradyrhizobium/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Phylogeny ; *Root Nodules, Plant/microbiology ; *Crotalaria/microbiology ; Uruguay ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Sequence Analysis, DNA ; Nucleic Acid Hybridization ; Base Composition ; Genome, Bacterial ; Fatty Acids/chemistry ; },
abstract = {A strain, namely Oc8[T], was isolated from a root nodule of Crotalaria ochroleuca in Uruguay. This strain induced effective nodules in roots of Crotalaria ochroleuca, Crotalaria juncea, Crotalaria spectabilis and Cajanus cajan. Oc8[T] belongs to the genus Bradyrhizobium according to the results of the 16S rRNA gene sequence analysis, and it forms an independent lineage within a cluster encompassing 13 described species of this genus. From them, the type strains closest related to the strain Oc8[T] with more than 99.5% similarity in 16S rRNA gene sequence were those of Bradyrhizobium ganzhouense, Bradyrhizobium cytisi, Bradyrhizobium guangdongense and Bradyrhizobium rifense (99.71%, 99.65%, 99.60% and 99.57%, respectively). A genome-based phylogeny showed that B. ganzhouense JCM 19881[T], B. cytisi CTAW11[T] and B. rifense CTAW71[T] were the closest type strains to the strain Oc8[T]. Values lower than the species cutoff of 95% and 70% were found after average nucleotide identity and digital DNA-DNA hybridization calculation between the genome of the strain Oc8[T] and those available genomes of the closest related Bradyrhizobium species. These results, together with those of the symbiotic nodC gene analysis, support the affiliation of this strain to the symbiovar cyanophyllae of a new species of Bradyrhizobium for which the name Bradyrhizobium monzae sp. nov. is proposed. The type strain is Oc8[T] (=LMG 33261[T]=CECT 30885[T]).},
}

*Bradyrhizobium/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
*Phylogeny
*Root Nodules, Plant/microbiology
*Crotalaria/microbiology
Uruguay
DNA, Bacterial/genetics
Bacterial Typing Techniques
Sequence Analysis, DNA
Nucleic Acid Hybridization
Base Composition
Genome, Bacterial
Fatty Acids/chemistry

@article {pmid41258495,
year = {2025},
author = {Gutiérrez-Sarmiento, W and Fosado-Mendoza, M and Lozano-Flores, C and Varela-Echavarría, A},
title = {The Body Wall Microbiome of the Terrestrial Slug Deroceras laeve Reveals Potential Endosymbionts and Shares Core Organisms with Other Mollusks.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02652-8},
pmid = {41258495},
issn = {1432-184X},
support = {CBF2023-2024-834//SECIHTI/ ; IN211322//DGAPA-UNAM PAPIIT/ ; },
abstract = {The marsh slug Deroceras laeve is an invasive mollusk found in gardens, field crops, and wetlands. It lacks a protective shell, suggesting that microbial communities are associated with its adaptability to the environment. Here, we used a whole shotgun metagenomic approach to analyse the complex microbiome of D. laeve and compared it to that of other mollusks. This demonstrated the presence in D. laeve of bacteriophages such as Erwinia phage, Certrevirus, and Machinavirus, which target plant pathogen bacteria. In the Archaea domain the halophilics Halovivax and Halobaculum predominated, but also present were the methanogens Methanobacterium, Methanobrevibacter, Methanocaldococcus, Methanococcus, and Methanosarcina, involved in phosphate solubilization and methanogenesis during decomposition of organic matter. The Bacteria domain was dominated by γ-Pseudomonadota such as Buttiauxella, Citrobacter, Enterobacter, Klebsiella, Kluyvera, Leclercia, and Pseudomonas which are producers of enzymes that degrade biomass and complex carbohydrates. Regarding the fungal community, filamentous or yeast ascomycetes predominated such as Debaryomyces, Puccina, and Pyricularia known as plant pathogens or associated with decaying organic matter. Consistent with these findings, functional analysis revealed enrichment in genes involved in fermentation and carbohydrate metabolism. Remarkably, regardless of species, ecosystem, and tissue type, we found that the core microbiome of the mollusks in this study is mainly structured by the Phyla Uroviricota, Euryarchaeaota, Pseudomonadota, and Ascomycota, with diversity at the genus level. This suggests ancient symbiotic interactions of these mollusks with specific types of microbes which may have been critical for adaptability to their environment.},
}

@article {pmid41257557,
year = {2025},
author = {Ehsanzadeh, P and Feizabadi, S and Razmjoo, J},
title = {Enhanced grain yield of mycorrhizae-inoculated modern and ancient wheats across different salinities: the gains stem from physiological, photosynthetic, and root attributes.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1597},
pmid = {41257557},
issn = {1471-2229},
mesh = {*Triticum/microbiology/growth & development/physiology/genetics ; *Mycorrhizae/physiology ; Photosynthesis ; Salinity ; Plant Roots/microbiology/physiology/growth & development ; Edible Grain/growth & development ; Symbiosis ; *Glomeromycota/physiology ; Genotype ; },
abstract = {The current salinization of soils and water resources not only reduces crop yield, but it may also alter the known beneficial symbiotic relationships in the rhizosphere of different plant species, including different types of wheat. Shedding light on the symbiotic association of the mycorrhizae (AMF) and ancient wheats under saline conditions may pave the way for tackling salt-induced penalties of wheat grain yield and, hence, solving the current global food security concerns. A two-year field experiment and a pot experiment were carried out, where 10 and 11 wheat genotypes (including modern bread and durum and ancient spelt and emmer wheats), respectively, were exposed to 0 -120 mM NaCl salinity and either left uninoculated or inoculated with AMF (Funnelliformis mosseae). Salinity suppressed plant chlorophylls by up to 20%, carotenoids by 33%, relative water content by 16%, K and P concentrations by 17 and 35%, respectively, grain yield by 19%, total plant dry mass by 7%, root length by 37%, volume by 49%, area by 35%, and root branching by 41%, while increasing Na accumulation by 35%, and proline concentration by 72%. The negative effects of salinity tended to be milder in some of the ancient emmer and spelt wheat genotypes. AMF inoculation ameliorated the adverse effects of salinity on photosynthetic attributes, rooting traits, grain yield components, total dry mass (7%), leaf relative water content (5%), K (21%) and P (23%) concentrations, while reducing the Na (6%) concentration under both saline and non-saline conditions. The maintained chlorophyll levels, root development, K and P concentrations, and total dry mass of the salt-stressed ancient emmer (and to a lesser extent spelt) genotypes were further sustained by AMF inoculation. Overall, findings from the field and pot experiments showed that AMF inoculation is effective in ameliorating salt damages in wheat. These findings depict AMF inoculation of ancient emmer, spelt, and Khorasan wheats as a promising practical strategy for tackling the ever-increasing threats of salt stress to wheat production and food security.},
}

*Triticum/microbiology/growth & development/physiology/genetics
*Mycorrhizae/physiology
Photosynthesis
Salinity
Plant Roots/microbiology/physiology/growth & development
Edible Grain/growth & development
Symbiosis
*Glomeromycota/physiology
Genotype

@article {pmid41256368,
year = {2025},
author = {Gao, A and Newhart, V and Flory, M and Alam, A},
title = {Pro-restitutive Bacteroides thetaiotaomicron reprograms the transcriptome of intestinal epithelial cells by modulating the expression of genes essential for proliferation and migration.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.30.679439},
pmid = {41256368},
issn = {2692-8205},
abstract = {The mammalian intestine harbors a highly complex, very diverse, and numerically vast community of symbiotic microorganisms, which profoundly influence the development and maintenance of the intestinal barrier function. Alterations in microbial composition, known as dysbiosis, are observed in Inflammatory Bowel Disease (IBD), colorectal cancer (CRC), and gastrointestinal infections; however, the exact causal relationship between these changes and the resolution of intestinal inflammation and the repair of damaged mucosa remains unclear. Notably, IBD is not only marked by dysbiosis but also by changes in microbial metabolic pathways and metabolite landscape in the intestinal lumen. The small molecules and microbial metabolites present in the intestinal lumen have emerged as potential regulators of gut pathology, cancer, and mucosal repair. Investigating how altered microbiota and microbial metabolic activities influence intestinal epithelial cells (IEC) can provide insights into their role in the regeneration of mucosal epithelia and restoration of gut barrier functions. This knowledge can be harnessed to promote intestinal homeostasis, prevent relapse, and prolong remission of IBD. To dissect the complex interplay between the gut microbiome and IEC, we focused on the overrepresented bacterium Bacteroides thetaiotaomicron . Here, we show that B. thetaiotaomicron and Akkermansia muciniphila , the dominant members of gut microbiota, expand during the repair & resolution phase of the chemically induced acute murine colitis. Furthermore, our bioinformatics analysis demonstrated that the elevated relative abundance of B. thetaiotamicron was also accompanied by rewiring of bacterial metabolic programs towards the essential amino acid metabolism, polyamine synthesis and utilization, stress response mechanisms, cell envelope biogenesis, and nutrient scavenging. Our RNA sequencing and transcriptomic analysis of primary human colonic epithelial cells cocultured with B. thetaiotaomicron showed that B. thetaiotaomicron stimulates the expression of genes and pathways involved in different cellular functions, including proliferation, differentiation, adhesion, lipid metabolism, migration, chemotaxis, and receptor expression. Our study emphasizes the crucial functions of the gut microbiome and metabolic activities in regulating the functions of intestinal epithelial cells during the repair of injured gut mucosa. Thus, these microorganisms and their metabolism hold promise as potential therapeutic agents.},
}

@article {pmid41254159,
year = {2025},
author = {Guo, J and Chu, L and Ye, X and King, WL and Shao, J and Wang, Z and Liu, J and Chen, C and Yu, M},
title = {Low soil phosphorus and high symbiotic fungal richness inhibits plant aboveground biomass in fragmented forests in China.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1598},
pmid = {41254159},
issn = {2399-3642},
support = {32101269//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31930073//National Natural Science Foundation of China (National Science Foundation of China)/ ; LQ22C030002//Science and Technology Department of Zhejiang Province/ ; },
mesh = {*Phosphorus/analysis ; China ; *Forests ; *Symbiosis ; *Soil/chemistry ; *Biomass ; *Soil Microbiology ; *Biodiversity ; *Fungi/physiology ; Rhizosphere ; },
abstract = {Habitat fragmentation is a major threat to biodiversity, and it usually leads to microclimate variations. Habitat quality (e.g. nutrients and moisture) and fungal symbioses play important roles in plant growth and ecosystem productivity. However, the impact of habitat fragmentation on plant aboveground biomass (AGB) is unclear. We examined the soil nutrients, rhizosphere fungal richness, and the AGB of 10 woody plant species on 10 islands of the same age but varying in size and isolation, in a land-bridge island system of subtropical China. Here we show that island size, soil nutrients, and fungal symbioses are key factors driving plant growth patterns in a fragmented island system. Plant AGB is positively correlated with soil phosphorus (P) but negatively correlated with richness of symbiotic fungi, suggesting that P content is more impactful than fungal symbiosis on plant growth in subtropical fragmented forests. Across all islands, low soil P and high symbiotic fungal richness lead to decreased plant AGB on small islands. These findings highlight the critical role of environmental filtering in shaping plant development within island fragments.},
}

*Phosphorus/analysis
China
*Forests
*Symbiosis
*Soil/chemistry
*Biomass
*Soil Microbiology
*Biodiversity
*Fungi/physiology
Rhizosphere

@article {pmid41254011,
year = {2025},
author = {Medina, S and Medrano-Padial, C and Guillén, S and Pérez-Través, L and Pérez-Novas, I and Periago, P and García-Viguera, C and Domínguez-Perles, R},
title = {SCOBY-based, innovative, and sustainable production of gallic acid from sucrose towards multipurpose applications.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40536},
pmid = {41254011},
issn = {2045-2322},
support = {MCIN/AEI/10.13039/501100011033//Ministerio de Ciencia e Innovación,Spain/ ; },
mesh = {*Gallic Acid/metabolism ; Fermentation ; *Sucrose/metabolism ; *Bacteria/metabolism ; *Kombucha Tea/microbiology ; *Yeasts/metabolism ; },
abstract = {Kombucha is a traditional beverage obtained from the fermentation of sugared tea by a symbiotic culture of bacteria and yeast (SCOBY), whose metabolism contributes significantly to the phytochemical composition and health-promoting properties of the final product. Among the phenolics present, gallic acid stands out as a multifunctional molecule with antioxidant, anti-inflammatory, and cardio-protective activities, making it a compound of growing interest for the development of functional foods, nutraceuticals and cosmetics. While gallic acid in kombucha has typically been attributed to plant-derived precursors, its potential de novo microbial origin has remained largely unexplored. In this work, robust evidence supports that SCOBY can synthesise gallic acid directly from sugars, without the contribution of tea or other plant materials. Metabolomic analyses combined with physicochemical characterisation (pH, ethanol, acetic acid, total soluble solids, sucrose, glucose, and fructose) revealed a linear increase in gallic acid production under standard fermentation conditions, associated with the microbial community's tolerance to high sugar concentrations and its metabolic capacity to generate bioactive phenolics. This finding highlights a previously unrecognised role of SCOBY as a natural cell factory for gallic acid production. In contrast to metabolic engineering approaches in model microorganisms such as Escherichia coli or Pseudomonas, our study demonstrates that a non-engineered microbial consortium can achieve this transformation simply and sustainably. These results open a novel route for the plant-free biosynthesis of gallic acid with potential applications across the food, cosmetic, and pharmaceutical industries.},
}

*Gallic Acid/metabolism
Fermentation
*Sucrose/metabolism
*Bacteria/metabolism
*Kombucha Tea/microbiology
*Yeasts/metabolism

@article {pmid41253823,
year = {2025},
author = {Zhou, J and Guo, Q and Han, X and Zhang, W and Huang, Z and Dietrich, CH and Wei, C},
title = {Genome degradation results in nested symbiosis and endosymbiont replacement in cicadas.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10104},
pmid = {41253823},
issn = {2041-1723},
mesh = {*Symbiosis/genetics ; *Hemiptera/microbiology/genetics ; Phylogeny ; Animals ; *Genome, Bacterial ; },
abstract = {Gradual genome degradation and fragmentation in primary nutritional endosymbionts have required symbiont-dependent hosts periodically to replace such symbionts over evolutionary timescales, yet the processes involved in de novo emergence of endosymbiosis and symbiont replacement are challenging to ascertain. Here we show that phylogenetic relationships of two ancient vertically-transmitted bacterial endosymbionts of cicadas, Hodgkinia and Karelsulcia, mirror host phylogeny, particularly indicating a single ancestral infection of cicadas by Hodgkinia with subsequent host-symbiont codiversification before being replaced by yeast-like fungal symbionts (YLS). We demonstrate a case of co-existence of Hodgkinia with Karelsulcia and a YLS, representing an advanced ongoing symbiont replacement process. In some individuals of the cicada Chremistica ochracea, the Hodgkinia is highly degenerated but colonizes (instead of neighboring) its partner Karelsulcia. The physical fusion of these two bacterial endosymbionts yields a nested symbiosis while the new YLS is recruited, probably preserving essential metabolic pathways necessary for host nutrition and facilitating continued vertical symbiont transmission. Such fusion may have provided refuge for the degrading bacterial endosymbiont and delayed symbiont replacement. Our study sheds light on adaptive and non-adaptive evolutionary mechanisms involved in symbiont loss and replacement, offering fresh insights into endosymbiotic origins of cellular organelles.},
}

*Symbiosis/genetics
*Hemiptera/microbiology/genetics
Phylogeny
Animals
*Genome, Bacterial

@article {pmid41253704,
year = {2025},
author = {Zecua-Ramirez, P and Dunken, N and Charura, NM and Llamas, E and De Quattro, C and Mandel, A and Langen, G and Dagdas, Y and Zuccaro, A},
title = {Autophagy restricts symbiosis-associated cell death and regulates colonization by Serendipita indica in Arabidopsis.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/plphys/kiaf590},
pmid = {41253704},
issn = {1532-2548},
abstract = {Endophytic colonization of Arabidopsis (Arabidopsis thaliana) by the beneficial root endophyte Serendipita indica is characterized by an initial biotrophic phase, followed by a confined host cell death phase that facilitates fungal accommodation. However, the host molecular pathways that restrict S. indica proliferation and regulate symbiosis-associated cell death remain largely unknown. Our study demonstrates that autophagy, a key cellular degradation pathway that maintains homeostasis, is locally activated during colonization and is required to limit fungal proliferation and immunometabolic stress. Autophagy-deficient mutants exhibit elevated basal root cell death, increased colonization, and hypersensitivity to the fungal-derived purine metabolite 2'-deoxyadenosine (dAdo), an immunometabolic signal that modulates host cell viability and reprograms immune and metabolic responses via ENT3 (equilibrative nucleoside transporter 3)-mediated uptake. In ent3 and atg5 ent3 mutants, suppression of dAdo import reduces S. indica-induced cell death, confirming the central role of ENT3-mediated uptake. Despite increased colonization and stress sensitivity, autophagy-deficient plants retain S. indica-mediated root growth promotion, indicating that mutualistic benefits can occur independently of immunometabolic stress resilience. Based on these findings, we propose that autophagy-mediated pro-survival responses are essential for maintaining symbiotic homeostasis by integrating immunometabolic signals and preserving host cell viability.},
}