@article {pmid41381084,
year = {2025},
author = {Kashkouli, M and Khajehali, J},
title = {Effects of antibiotic treatments on symbiotic bacteria and life history traits of Bemisia tabaci and Trialeurodes vaporariorum (Hemiptera: Aleyrodidae): implications for pest control strategies.},
journal = {Journal of economic entomology},
volume = {118},
number = {6},
pages = {3190-3201},
doi = {10.1093/jee/toaf136},
pmid = {41381084},
issn = {1938-291X},
mesh = {Animals ; *Hemiptera/microbiology/growth & development/drug effects/physiology ; *Symbiosis/drug effects ; *Anti-Bacterial Agents/pharmacology ; *Life History Traits ; *Bacteria/drug effects ; Female ; Insect Control ; Male ; Nymph/growth & development/microbiology ; *Bacterial Physiological Phenomena/drug effects ; },
abstract = {Bemisia tabaci Gennadius and Trialeurodes vaporariorum Westwood are damaging agricultural pests, with control complicated by their high reproduction and resistance to treatments. This study investigates the effects of antibiotic treatments on the symbiotic bacteria and life history traits of these whitefly species using primer-specific PCRs, quantitative PCRs (qPCRs), and life table analyses. Results revealed that B. tabaci (isolate IUT1) hosts a diverse set of symbionts, including Portiera, Hamiltonella, Arsenophonus, and Rickettsia, while T. vaporariorum (isolate IUT2) carries only Portiera and Arsenophonus. The antibiotic treatments-tetracycline, rifampicin, and a cocktail of ampicillin, cefotaxime, and gentamicin-significantly altered the abundance of specific symbionts, with notable reductions of Rickettsia in B. tabaci and Arsenophonus in T. vaporariorum. In addition, ampicillin, cefotaxime, gentamicin, and tetracycline treatments resulted in significant decreases and increases of Portiera in both whiteflies, respectively. Antibiotic exposure also led to profound effects on whitefly preadult durations, fecundity, life expectancy, and some biological parameters including r, R0, and gross reproductive rate of whiteflies. Specifically, B. tabaci treated with rifampicin lost its ability to mature into adulthood, while T. vaporariorum treated with rifampicin was unable to lay eggs. Furthermore, treatment with ampicillin, cefotaxime, and gentamicin rendered both species of whiteflies incapable of egg-laying. A negative r value was also recorded in B. tabaci following tetracycline treatment. These results highlight the critical role of symbiotic bacteria in whitefly biology and provide insight into the potential consequences of disrupting these associations.},
}

Animals
*Hemiptera/microbiology/growth & development/drug effects/physiology
*Symbiosis/drug effects
*Anti-Bacterial Agents/pharmacology
*Life History Traits
*Bacteria/drug effects
Female
Insect Control
Male
Nymph/growth & development/microbiology
*Bacterial Physiological Phenomena/drug effects

@article {pmid41381056,
year = {2025},
author = {Wei, Y and Liu, Q and Zhang, J and Ren, M and Luo, X},
title = {Transforming Barriers into Opportunities: Saline-Alkali-Tolerant Plants for Sustainable Agriculture Expansion.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c10327},
pmid = {41381056},
issn = {1520-5118},
abstract = {Global soil salinization and alkalization affect 10.7% of terrestrial ecosystems, critically threatening food security and ecological stability. Contemporary remediation strategies have evolved from traditional land reclaiming approaches to innovative biological solutions focusing on saline-alkali-tolerant (SAT) plant development, offering dual benefits of enhanced agricultural productivity and arable land expansion in marginal environments. However, significant knowledge gaps persist, especially regarding the systematic classification of SAT plant resources, their multilevel adaptation mechanisms, the identification of exploitable gene pools for precision breeding, and the synergistic interactions between microalgae and plants in soil amelioration. This perspective provides a comprehensive synthesis of the field spanning from fundamental research to practical applications. Notably, we propose a "microalgae-SAT plants-crop" tripartite symbiosis model that simultaneously facilitates ecological restoration through microbial-plant interactions, enables economic valorization of degraded lands, and promotes sustainable intensification of saline agriculture. By integrating molecular technologies with ecological engineering principles, this work provides both theoretical frameworks and implementable solutions for managing global saline-alkali land and promoting sustainable agricultural development.},
}

@article {pmid41380661,
year = {2025},
author = {Pitsillides, F and Salem, H},
title = {An earful of fungi: Hearing organ repurposed for symbiosis.},
journal = {Cell host & microbe},
volume = {33},
number = {12},
pages = {1999-2000},
doi = {10.1016/j.chom.2025.11.005},
pmid = {41380661},
issn = {1934-6069},
mesh = {*Symbiosis ; Animals ; *Fungi/physiology ; Female ; Wasps/physiology ; *Heteroptera/microbiology ; Biological Evolution ; },
abstract = {In a recent publication in Science, Nishino et al.[1] reveal the evolutionary co-option of an auditory structure into a newly identified type of symbiotic organ. This organ, found on the hindlegs of female stinkbugs, houses fungi that act as defensive symbionts by protecting eggs from parasitism by wasps.},
}

*Symbiosis
Animals
*Fungi/physiology
Female
Wasps/physiology
*Heteroptera/microbiology
Biological Evolution

@article {pmid41380570,
year = {2025},
author = {Bleil, BM and Granek, EF and Kirk, NL and Hladik, ML},
title = {Chronic, low concentration pesticide exposure alters reproduction and behavior in the intertidal sea anemone, Anthopleura elegantissima.},
journal = {Marine pollution bulletin},
volume = {224},
number = {},
pages = {119118},
doi = {10.1016/j.marpolbul.2025.119118},
pmid = {41380570},
issn = {1879-3363},
abstract = {Widespread pesticide and herbicide use paired with frequent transport away from application sites has led to pesticide presence in nearly all terrestrial and aquatic environments globally. Pesticides have unintentional toxic effects on non-target organisms by interfering with cellular processes, behavior, feeding, reproduction, and disrupting endocrine processes. The aggregating anemone, Anthopleura elegantissima, is an important species along the North American Pacific coast due to its symbiotic relationships that contribute to high productivity, and its clonal abundance that structures the rocky intertidal habitat. Commonly used pesticides, atrazine, diuron, and carbendazim were previously detected in coastal waters of Oregon, U.S.A. This study examined the potential effects of these pesticides at environmentally relevant concentrations on reproduction, symbionts, and behavior of A. elegantissima over an eight-week period. Pesticides significantly decreased gonad development in all treatments, having the most significant effect in individual treatments of atrazine (p = 0.003), carbendazim (p = 0.003), and the mixture of all three pesticides (p = 0.008). All pesticide treatments significantly increased cloning behavior compared to the control, suggesting that cloning could be a stress response. Pesticide exposure also significantly increased tentacle retraction movement, suggesting possible metabolic or energy impairments. While other studies have previously found behavioral changes in anemones due to pollutants, our study is the first to document behavioral changes in anemones from pesticide exposure. All three pesticides significantly impacted a non-target marine invertebrate at environmentally relevant concentrations, which underscores the value of studies that focus on effects on marine invertebrates, paired with comprehensive pesticide monitoring in coastal areas.},
}

@article {pmid41380105,
year = {2025},
author = {Montiel, J and García-Soto, I and Monroy-Morales, E and Lace, B and Robledo-Gamboa, M and Vestergaard, M and Sandal, N and Ott, T and Stougaard, J},
title = {The Lotus japonicus alpha-expansin EXPA1 is recruited during intracellular and intercellular rhizobial colonization.},
journal = {The Plant journal : for cell and molecular biology},
volume = {124},
number = {5},
pages = {e70639},
doi = {10.1111/tpj.70639},
pmid = {41380105},
issn = {1365-313X},
support = {IA200125//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; IA200723//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; 403222702//Deutsche Forschungsgemeinschaft/ ; 414136422//Deutsche Forschungsgemeinschaft/ ; CBF2023-2024-834//Secretaría de Ciencia, Humanidades, Tecnología e Innovación/ ; 834221//H2020 European Research Council/ ; OPP11772165//Bill and Melinda Gates Foundation/ ; },
mesh = {*Lotus/microbiology/genetics/metabolism/physiology ; *Plant Proteins/metabolism/genetics ; Symbiosis ; Gene Expression Regulation, Plant ; Root Nodules, Plant/microbiology/genetics/metabolism ; *Mesorhizobium/physiology ; Agrobacterium/physiology ; Plant Roots/microbiology/genetics/metabolism ; Cell Wall/metabolism ; *Rhizobium/physiology ; },
abstract = {Most legumes establish a mutualistic association with rhizobia, a group of nitrogen-fixing bacteria. In Lotus japonicus, the symbiotic colonization occurs intracellularly, via root hair infection threads by Mesorhizobium loti, or intercellularly, with Agrobacterium pusense IRBG74. In both mechanisms, cell wall remodeling is presumably an essential process. In plants, α-expansins (EXPA) promote cell wall loosening by non-enzymatically triggering a pH-dependent relaxation. In this study, we show that LjEXPA1 is critical for the intracellular and intercellular symbiotic program in L. japonicus. Promoter activity and subcellular localization analyses revealed that EXPA1 is recruited at essential compartments and structures of epidermal and cortical cells in both mechanisms of rhizobial infection, such as the infection chambers, infection pockets, and transcellular infection threads. Additionally, EXPA1-YFP abundantly accumulated in dividing cortical cells during nodule formation. The expression profile of EXPA1 correlates with the symbiotic phenotype observed in homozygous mutants disrupted in the EXPA1 gene (expA1-1 and expA1-2). Infection thread formation and intercellular colonization were drastically reduced in expA1-1 and expA1-2 mutants, compared with wild-type plants. Similarly, nodule formation was significantly reduced in these mutants after M. loti or IRBG74 inoculation. Our results indicate that non-enzymatic cell wall remodeling by the α-expansin EXPA1 is crucial for the successful establishment of Lotus-rhizobia symbiosis, regardless of the infection mechanism.},
}

*Lotus/microbiology/genetics/metabolism/physiology
*Plant Proteins/metabolism/genetics
Symbiosis
Gene Expression Regulation, Plant
Root Nodules, Plant/microbiology/genetics/metabolism
*Mesorhizobium/physiology
Agrobacterium/physiology
Plant Roots/microbiology/genetics/metabolism
Cell Wall/metabolism
*Rhizobium/physiology

@article {pmid41379853,
year = {2025},
author = {Sankari, S and Arnold, MFF and Babu, VMP and Deutsch, M and Walker, GC},
title = {Exploiting peptide chirality and transport to dissect the complex mechanism of action of host peptides on bacteria.},
journal = {PLoS genetics},
volume = {21},
number = {12},
pages = {e1011892},
doi = {10.1371/journal.pgen.1011892},
pmid = {41379853},
issn = {1553-7404},
abstract = {Elucidation of the complex mechanisms of action of antimicrobial peptides (AMPs) is critical for improving their efficacy. A major challenge in AMP research is distinguishing AMP effects resulting from various protein interactions from those caused by membrane disruption. Moreover, since AMPs often act in multiple cellular compartments, it is challenging to pinpoint where their distinct activities occur. Nodule-specific cysteine-rich (NCR) peptides secreted by some legumes, including NCR247, have evolved from AMPs to regulate differentiation of their nitrogen-fixing bacterial partner during symbiosis as well as to exert antimicrobial actions. At sub-lethal concentrations, NCR247 exhibits strikingly pleiotropic effects on Sinorhizobium meliloti. We used the L- and D-enantiomeric forms of NCR247 to distinguish between phenotypes resulting from stereospecific, protein-targeted interactions and those caused by non-specific interactions such as membrane disruption. In addition, we utilized an S. meliloti strain lacking BacA, a transporter that imports NCR peptides into the cytoplasm. The bacterial protein BacA, plays critical symbiotic roles by possibly reducing periplasmic peptide accumulation and fine-tuning symbiotic signaling. Use of the BacA-deficient strain made it possible to distinguish between phenotypes resulting from peptide interactions in the periplasm and those occurring in the cytoplasm. At high concentrations, both L- and D-NCR247 permeabilize bacterial membranes, consistent with nonspecific cationic AMP activity. In the cytoplasm, both NCR247 enantiomers sequester heme and trigger iron starvation in a chirality-independent but BacA-dependent manner. However, only L-NCR247 activates bacterial two-component systems via stereospecific periplasmic interactions. By combining stereochemistry and genetics, this work disentangles the spatial and molecular complexity of NCR247 action. This approach provides critical mechanistic insights into how host peptides with pleiotropic functions modulate bacterial physiology.},
}

@article {pmid41379245,
year = {2025},
author = {Namadara, S and Pragadeesh, ARU and Uthandi, S and Rangasamy, A and Malaichamy, K and Venkatesan, M and Narayanan, MB and Murugaiyan, S},
title = {Comparative metagenomic analysis of bacterial communities associated with two mealybug species, Phenacoccus saccharifolii and Dysmicoccus carens infesting sugarcane in Tamil Nadu, India.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {12},
pages = {504},
pmid = {41379245},
issn = {1573-0972},
support = {DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; },
mesh = {*Saccharum/parasitology ; Animals ; India ; *Bacteria/classification/genetics/isolation & purification ; *Hemiptera/microbiology ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; DNA, Bacterial/genetics ; },
abstract = {This study presents a comparative metagenomic analysis of the gut bacterial communities of two sugarcane-infesting mealybug species, Phenacoccus saccharifolii (WR) and Dysmicoccus carens (RR), from Tamil Nadu, India. Using Oxford Nanopore sequencing of the 16s rRNA gene spanning the hypervariable regions V1 - V9 and predictive metagenomics, differences in microbial diversity, taxonomy, and functional potential were assessed to explore the ecological adaptations of the gut microbiota in mealybugs. The D. carens gut microbiome showed higher species richness than P. saccharifolii (WR) (125 vs. 45 species, p < 0.05) but lower community evenness (0.43 vs. 0.61, p < 0.05), resulting in similar overall Shannon diversity (2.08 vs. 2.30) despite markedly different community structures, which may be influenced by their different feeding niches, including the sugarcane crown region, leaf sheath tissues, and basal stem and root portions. Both mealybug species exhibited contrasting bacterial community structures. D. carens (RR) harbored high abundances of endosymbionts (43.8%), Gilliamella (22.3%), Enterobacter (18.3%), and Candidatus Tremblaya (9.3%), representing a symbiont-dominated microbiome typical of many hemipteran insects. P. saccharifolii (WR) displayed a distinct profile with Serratia as the dominant genus (43.2%), followed by Enterobacter (20.1%), Klebsiella (14.6%), and substantially reduced endosymbiont abundances (14.8%). Beta diversity analysis revealed distinct community clustering of species, highlighting the variation driven by feeding habitat and host genotype. Functional profiling indicated largely conserved metabolic capabilities dominated by amino acid and carbohydrate metabolism, which was a key to compensate the nutrient-poor phloem sap diet. The core microbiome identified several genera that form complex ecological networks, emphasizing their importance in community stability. These findings provide insights into the role of symbiotic bacteria in mealybug adaptation to different ecological niches within the sugarcane agroecosystem. Understanding these host-microbiome interactions may facilitate the development of targeted, microbiome-based biocontrol strategies for sustainable mealybug management in sugarcane cultivation.},
}

*Saccharum/parasitology
Animals
India
*Bacteria/classification/genetics/isolation & purification
*Hemiptera/microbiology
RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
Phylogeny
DNA, Bacterial/genetics

@article {pmid41378770,
year = {2025},
author = {Huang, P and Sardina, J and Lu, H and Bruner-Montero, G and Currie, CR and Li, L},
title = {Proteome-Wide Analysis and Surface Protein Isolation for Secretome Characterization Reveal Insights into the Biology of the Leaf-Cutter Ant Acromyrmex echinatior.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.5c05220},
pmid = {41378770},
issn = {1520-6882},
abstract = {Characterizing the proteome of an organism can provide critical insights into the proteins that regulate key biological processes such as development, physiology, and environmental interactions. While proteome-wide analyses reveal broad protein dynamics, spatially resolved approaches can uncover specific, localized functions. For example, the leaf-cutter ant Acromyrmex echinatior secretes a unique protein layer that coats its exoskeleton and interacts with biotic and abiotic factors, including its symbiotic bacterium Pseudonocardia. In this study, to characterize both the whole-body proteome and the externally secreted cuticular protein layer of A. echinatior, we utilize a dual-layered proteomic approach. Using diaPASEF, we quantified 4,428 proteins across four early adult ages, uncovering distinct age-dependent protein clusters enriched in muscle development, lipid metabolism, and immune-related responses. We then developed an acid-based extraction method to isolate the externally secreted protein layer, identifying 323 secreted proteins via the ddaPASEF acquisition. Many of these proteins exhibited temporal abundance changes and were associated with functions, such as environmental stress response, microbial defense, and cuticle sclerotization. Notably, tropomyosin-family proteins were highly enriched in the external secretome and exhibited significant changes across early adult time points, potentially linking these ion-binding molecules to metal-enrichment processes occurring during this crucial stage. Together, this work reveals dynamic changes in the internal and surface proteomes of young adult A. echinatior ants and provides a methodological framework for further probing localized extra-cuticular protein function in complex biological systems.},
}

@article {pmid41377505,
year = {2025},
author = {Huberman, LB and Villalobos-Escobedo, JM and Skerker, JM and Shi, R and Rico-Ramírez, AM and Adams, C and Arkin, AP and Deutschbauer, AM and Glass, NL},
title = {Construction of a randomly barcoded insertional mutant library in the filamentous fungus Trichoderma atroviride.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.30.691285},
pmid = {41377505},
issn = {2692-8205},
abstract = {Filamentous fungi play key roles in ecosystems, agriculture, biotechnology, symbiosis, and disease, yet the large-scale characterization of gene function in these organisms remains limited by low transformation efficiencies and their multinucleate, syncytial cells, which complicate high-throughput screening strategies. To address the challenge of high-throughput screening in filamentous fungi, we developed methods to construct a genome-wide barcoded insertional mutant library in Trichoderma atroviride , a filamentous fungus widely used as a biocontrol agent against bacterial and fungal plant pathogens. Our strategy leveraged randomly barcoded transfer DNA insertions from plasmid libraries containing hundreds of millions of unique DNA barcodes and a broad host-range drug resistance marker delivered via Agrobacterium tumefaciens into T. atroviride . By optimizing transformation conditions, we achieved up to 600 independent transformants per infection event, resulting in a library of over 31,000 mapped insertions disrupting 7,104 of the 11,863 predicted genes in the T. atroviride genome. This resource establishes a scalable platform for high-throughput functional genomics in filamentous fungi, enabling both fundamental investigations of fungal biology and engineering approaches toward improved medical applications, biotechnology, and sustainable agriculture.},
}

@article {pmid41375325,
year = {2025},
author = {Li, Y and Hossain, MS and Libault, M},
title = {Single-Cell Omics in Legumes: Research Trends and Applications.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {23},
pages = {},
doi = {10.3390/plants14233615},
pmid = {41375325},
issn = {2223-7747},
support = {2414183, 2425989//U.S. National Science Foundation (NSF)/ ; 2022-67013-36144//U.S. Department of Agriculture - National Institute of Food and Agriculture (USDA-NIFA)/ ; },
abstract = {Legumes are important food crops and play a central role in sustainable agriculture through their ability to form symbiosis with rhizobia, soil bacteria that fix atmospheric nitrogen. Recent advances in single-cell and spatial transcriptomics, along with single-cell epigenomics, have enabled high-resolution analysis of gene expression dynamics and the prediction of cell-type-specific regulatory networks. In this review, we highlight recent progress in the use of single-cell omics in legumes, with a particular focus on how genes functioning in distinct cell types contribute to plant development, responses to pathogens, stress-induced plasticity, and the establishment of root nodule symbioses. Case studies in Medicago truncatula, Lotus japonicus, Glycine max, and Arachis hypogaea illustrate the shift from bulk to single-cell multi-omics. We conclude by outlining current limitations and future directions for building integrated legume cell atlases that will support translational research and crop improvement.},
}

@article {pmid41375270,
year = {2025},
author = {Veršulienė, A and Garbaras, A and Kadžienė, G and Shamshitov, A and Toleikienė, M},
title = {Mycorrhizal Abundance and Its Interaction with Cereal Root Traits and Crop Productivity in Organically Managed Cereal/Legume Intercropping.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {23},
pages = {},
doi = {10.3390/plants14233561},
pmid = {41375270},
issn = {2223-7747},
support = {S-PD-24-39//Research Council of Lithuania/ ; },
abstract = {Mixed cropping may positively affect soil fertility and soil biological activities, such as those related to mycorrhizal colonization intensity (M%), which plays a vital role in the plant nutrient cycle and can improve tolerance to drought and pathogens. This plant and soil fungi symbiosis helps to reduce dependency on chemical fertilizers, promotes sustainable agricultural practices, and minimizes environmental impacts. However, field studies that clearly assess the effects of cereal/legume intercropping on mycorrhizal intensity and relate it to plant productivity, yield quality, and plant adaptation to climate change are lacking. This field experiment was conducted to assess the effects of cereals/legume intercropping on mycorrhizal colonization, and to explore its interaction with physical cereal root parameters and crop yield. Three main crops, spring barley, oat, and field pea, were grown as monocultures. For the spring barley and oat, the study also included two different fertilization levels (with and without organic fertilizers) and legume intercropping (field pea and red clover). The intercropping had a significant impact on spring barley and oat root length, diameter, and specific root length. The general average of root length and diameter was higher in oat-pea and barley-pea cropping systems. The most significant effect in root architecture parameters observed in red clover was when it was intercropped with barley or oat. The establishment of field pea intercrop significantly increased M% in spring barley and had a positive effect on the grain yields of both spring barley and oat. Meanwhile, red clover intercropping enhanced M% and grain yield in oats but had no such effect in barley. In both spring barley and oat, M% was positively correlated with grain yield.},
}

@article {pmid41373797,
year = {2025},
author = {Bustos, D and Morales-Quintana, L and Urra, G and Arriaza-Rodríguez, F and Pollmann, S and Méndez-Yáñez, A and Ramos, P},
title = {Modulation of α-Mannosidase 8 by Antarctic Endophytic Fungi in Strawberry Plants Under Heat Waves and Water Deficit Stress.},
journal = {International journal of molecular sciences},
volume = {26},
number = {23},
pages = {},
doi = {10.3390/ijms262311650},
pmid = {41373797},
issn = {1422-0067},
support = {Fondecyt 1250346; Fondecyt 1240771; ANILLO #ATE220014//Agencia Nacional de Investigación y Desarrollo/ ; },
mesh = {*alpha-Mannosidase/metabolism/genetics/chemistry ; *Fragaria/microbiology/enzymology/genetics ; *Endophytes/physiology ; Molecular Docking Simulation ; Plant Proteins/metabolism/genetics/chemistry ; Hot Temperature ; Molecular Dynamics Simulation ; *Stress, Physiological ; Plant Roots/microbiology ; },
abstract = {Plant-microbe interactions exert a significant influence on host stress responses; however, the molecular mechanisms underlying these effects remain inadequately understood. In this study, we characterize FaMAN8, an α-mannosidase from Fragaria × ananassa, to explore its role in adaptation to heat waves and water deficit, as well as its modulation by fungal endophytes. Transcriptomic analysis identified FaMAN8 as the sole α-mannosidase isoform highly conserved across reported sequences, with root-specific induction under conditions of heat stress, deficient irrigation, and endophytic colonization. Structural modeling revealed that FaMAN8 exhibits the canonical domain organization of glycoside hydrolase family 38 (GH38) enzymes, featuring a conserved catalytic architecture and metal-binding site. Molecular docking and dynamics simulations with the Man3GlcNAc2 ligand indicated a stable binding pocket involving key catalytic residues and strong electrostatic complementarity. MM-GBSA and free energy landscape analyses further supported the thermodynamic stability of the protein-ligand complex. Cavity analysis revealed a larger active site in FaMAN8 compared to its homolog JbMAN, suggesting broader substrate accommodation. Collectively, these findings identify FaMAN8 as a stress-responsive glycosidase potentially involved in glycan remodeling during beneficial root-fungus interactions. This work provides molecular insights into plant-microbe symbiosis and lays the groundwork for microbiome-informed strategies to enhance crop stress resilience.},
}

*alpha-Mannosidase/metabolism/genetics/chemistry
*Fragaria/microbiology/enzymology/genetics
*Endophytes/physiology
Molecular Docking Simulation
Plant Proteins/metabolism/genetics/chemistry
Hot Temperature
Molecular Dynamics Simulation
*Stress, Physiological
Plant Roots/microbiology

@article {pmid41373681,
year = {2025},
author = {Moskal, K and Tomaszewski, B and Boczkowska, M},
title = {Epigenomics and Non-Coding RNAs in Soybean Adaptation to Abiotic Stresses.},
journal = {International journal of molecular sciences},
volume = {26},
number = {23},
pages = {},
doi = {10.3390/ijms262311527},
pmid = {41373681},
issn = {1422-0067},
mesh = {*Glycine max/genetics/physiology ; *Stress, Physiological/genetics ; Gene Expression Regulation, Plant ; *RNA, Untranslated/genetics ; *Epigenomics/methods ; *Adaptation, Physiological/genetics ; Plant Proteins/genetics/metabolism ; Epigenesis, Genetic ; },
abstract = {This review presents soybean responses to drought, heat, and salinity within a signal-transcript-chromatin framework. In this framework, calcium/reactive oxygen species and abscisic acid cues converge on abscisic acid-responsive element binding factor (ABF/AREB), dehydration-responsive element binding protein (DREB), NAC, and heat shock factor (HSF) families. These processes are modulated by locus-specific chromatin and non-coding RNA layers. Base-resolved methylomes reveal a high level of CG methylation in the gene body, strong CHG methylation in heterochromatin, and dynamic CHH 'islands' at the borders of transposable elements. CHH methylation increases over that of transposable elements during seed development, and GmDMEa editing is associated with seed size. Chromatin studies in soybean and model species implicate the reconfiguration of salt-responsive histone H3 lysine 27 trimethylation (H3K27me3) in G. max and heat-linked H2A.Z dynamics at thermoresponsive promoters characterized in Arabidopsis and other plants, suggesting that a conserved chromatin layer likely operates in soybean. miR169-NF-YA, miR398-Cu/Zn Superoxide Dismutases(CSD)/copper chaperone of CSD(CCS), miR393-transporter inhibitor response1/auxin signaling F-box (TIR1/AFB), and miR396-growth regulating factors (GRF) operate across leaves, roots, and nodules. Overexpression of lncRNA77580 enhances drought tolerance, but with context-dependent trade-offs under salinity. Single-nucleus and spatial atlases anchor these circuits in cell types and microenvironments relevant to stress and symbiosis. We present translational routes, sentinel epimarkers (bisulfite amplicons, CUT&Tag), haplotype-by-epigenotype prediction, and precise cis-regulatory editing to accelerate marker development, genomic prediction and the breeding of resilient soybean varieties with stable yields.},
}

*Glycine max/genetics/physiology
*Stress, Physiological/genetics
Gene Expression Regulation, Plant
*RNA, Untranslated/genetics
*Epigenomics/methods
*Adaptation, Physiological/genetics
Plant Proteins/genetics/metabolism
Epigenesis, Genetic

@article {pmid41369003,
year = {2025},
author = {Lidoy, J and Minchev, Z and España-Luque, L and Benítez-González, AM and Ramos, A and García, J and Berrio, E and Nesterenko, O and Díaz-Ortiz, P and Meléndez-Martínez, AJ and Pozo, MJ and López-Ráez, JA},
title = {Carotenoid Biofortification in Field-Grown Tomato Fruits by Early Inoculation with Arbuscular Mycorrhizal Fungi.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c14198},
pmid = {41369003},
issn = {1520-5118},
abstract = {Carotenoids are bioactive compounds with relevant health-promoting properties. Thus, a carotenoid-rich diet is essential for improving human health. Beneficial soil microorganisms are used in agriculture as biostimulants to promote plant growth and development and increase their tolerance/resistance to stress. However, their effects on fruit quality have been less studied. In the present study, we assess the impact of early inoculation of tomato seedlings with the arbuscular mycorrhizal (AM) fungus Rhizophagus irregularis on carotenoid content in fruits under real agronomic production settings. We show that early inoculation of seedlings with AM fungi provides long-lasting benefits that impact fruit quality, increasing the content of the carotenoids lycopene and β-carotene. We also show that this increase is related to transcriptional upregulation of key genes of their biosynthesis pathway. Our results show that AM fungi, commonly used as biostimulants in agriculture, can also be used as a sustainable strategy for carotenoid biofortification in tomato production systems, contributing to the production of healthy "functional products".},
}

@article {pmid41365928,
year = {2025},
author = {Liao, Z and Yang, H},
title = {Historical change and spatial relation of cultural memory in Guangzhou from the perspective of heritage representation.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {43506},
doi = {10.1038/s41598-025-21055-w},
pmid = {41365928},
issn = {2045-2322},
support = {2023GZGJ314//the Philosophy and Social Sciences of Guangzhou in the 14th Five-year Period(2023GZGJ314)/ ; No.910108005//a grant from the Guangzhou Huashang College(No.910108005)/ ; No.HSRHKC2024127//a grant from the Guangzhou Huashang College(No.HSRHKC2024127)/ ; },
abstract = {UNLABELLED: Cultural memory fundamentally shapes urban collective identity, , yet it is seldom quantified at fine spatial scales. This study proposes the Heritage–Memory Symbiosis Loop (HMSL) as an analytical framework to examine Guangzhou, a historic trading hub in China with 446 state-listed heritage units. Each heritage unit is systematically classified within a “two representations–six memory-space” matrix, and a Cultural Memory Index (CMI) is computed and visualized as a spatialfield-energy surface. Subsequently, Kernel-density estimation, Moran’s I, and LISA analyses illuminate memory hotspots centered around the Yuexiu–Liwan core, while revealing the attenuation of spirituality-based memories in fringe districts undergoing gentrification. Field-energy gradients underpin the delineation of three protection zones: high-intensity “living museums” along dynastic trade routes, medium-intensity multipurpose belts, and low-intensity rural nodes. The CMI map constitutes the first point-level quantification of cultural memory for Guangzhou, elucidates the interplay between material and spiritual domains within the human–land system, and supplies a replicable methodology—including heritage inventory, memory zoning, and field-energy mapping— tailored for conservation strategies in rapidly urbanizing Asian cities.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-21055-w.},
}

@article {pmid41367418,
year = {2025},
author = {Li, Z and Kuang, X and Shan, G and Wu, J},
title = {Repeated Aedes albopictus bites reshape gut microbiota and repattern inflammatory readouts in a murine colitis model.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1702365},
pmid = {41367418},
issn = {1664-302X},
abstract = {The gut microbiota represents a stable and dynamic symbiotic community that maintains host health and shapes immune homeostasis. Environmental exposures can disturb this symbiosis, yet the impact of repeated vector biting on host microbial communities has not been explored. Here, we investigated how repeated Aedes albopictus mosquito bites influence gut microbiota composition and stability in a murine model of dextran sulfate sodium (DSS)-induced colitis. Mice were repeatedly exposed to mosquito bites over several weeks prior to DSS treatment, and fecal microbiota were profiled using 16S rRNA sequencing at baseline, during inflammation (day 7), and recovery (day 14). Mosquito biting acted as a "press disturbance," increasing microbial richness and community dispersion at baseline compared to unbitten controls. During DSS challenge, mosquito-exposed mice exhibited distinct microbial trajectories relative to DSS-only mice, including altered relative abundance of taxa such as Lactobacillus. These microbiota shifts were associated with changes in host inflammatory readouts, including elevated IL-6 during induction and partial normalization by day 14, as well as modest hematological adjustments. Our findings demonstrate that repeated vector exposure can reshape the gut microbiota, modulating the stability and composition of this core host symbiosis under inflammatory stress. These results highlight the sensitivity of symbiotic microbial communities to ecological perturbations and suggest that vector-host interactions may represent an underappreciated factor influencing host-microbe partnerships.},
}

@article {pmid41366724,
year = {2025},
author = {Papachristos, K and Miller, WJ and Klasson, L},
title = {A co-speciation dilemma and a lifestyle transition with genomic consequences in Wolbachia of Neotropical Drosophila.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-025-12340-z},
pmid = {41366724},
issn = {1471-2164},
abstract = {BACKGROUND: Long-term persistent symbiotic associations may result in co-speciation and can be inferred if species trees of hosts and symbionts are congruent in topology and divergence times. Co-speciation has been seen to occur relatively frequently in obligate associations, but is less common in parasitic or facultative ones, mainly due to the difference in horizontal transmission rates. The long-term vertical inheritance and close host association of obligate endosymbionts also generally result in smaller genomes than in facultative endosymbionts. Here, we investigate co-speciation and genome reduction using highly similar strains of the endosymbiont Wolbachia infecting Drosophila species from the willistoni and saltans groups, where only one strain, wPau, infecting D. paulistorum, is obligate.

RESULTS: We sequenced the Wolbachia genomes from five species of the willistoni and saltans groups and constructed phylogenies. Topological congruence was found between these Wolbachia strains and the nuclear DNA of their hosts, except for wPau and D. paulistorum, but full topological congruence was observed between Wolbachia and the host mitochondrial DNA. However, assuming temporal congruence, we estimated extremely low evolutionary rates in Wolbachia of 10[- 10]-10[- 11] changes/site/year. Additionally, the obligate wPau strain was found to have a larger genome than closely related facultative strains, mainly due to an ongoing expansion of an IS4 element. Furthermore, wPau has lost a large proportion of its prophage WO genes, but the cif genes, known to be involved in the CI phenotype, are intact. Finally, nine of the eleven genes from the prophage WO-associated Undecim cluster are uniquely duplicated.

CONCLUSIONS: The congruent topologies between Wolbachia and their willistoni and saltans group hosts indicate co-speciation. However, the high similarity between Wolbachia strains, which results in low mutation rate estimates, challenges this interpretation. Contrary to the expectations of the genome reduction theory, we observed an increase in genome size in the obligate wPau strain, potentially driven by a decreased population size. Finally, the duplication of the Undecim cluster, despite a major loss of other prophage-associated genes, suggests that the genes in the Undecim cluster are under strong selection and potentially play a role in the obligate association between wPau and their D. paulistorum hosts.},
}

@article {pmid41366253,
year = {2025},
author = {Breselge, S and de Paula Dias Moreira, L and Skibinska, I and Yin, X and Brennan, L and Kilcawley, K and Porcellato, D and Cotter, PD},
title = {Water kefir multi-omics reveals functional redundancies despite taxonomic differences and the underappreciated contribution of yeast.},
journal = {NPJ science of food},
volume = {9},
number = {1},
pages = {265},
pmid = {41366253},
issn = {2396-8370},
support = {818368//European Union's Horizon 2020/ ; 818368//European Union's Horizon 2020/ ; SFI/12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; SFI/12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; USIRL-2019-1//HRB/SFI/ ; USIRL-2019-1//HRB/SFI/ ; SFI/16/RC/3835//Irish Department of Agriculture, Food and the Marine/ ; TC/2018/0025//Food for Health Ireland/ ; NA-AGFOODDEVELAUTH20201216//Institute for the Advancement of Food and Nutritional Sciences/ ; 101060218//European Union's Horizon Europe/ ; },
abstract = {Water kefir (WK) is a fermented beverage produced by a complex symbiotic community of microbes, including yeasts, lactic acid bacteria (LAB), and acetic acid bacteria (AAB). Here, we combined shotgun metagenomics, NMR metabolomics, GC-MS volatile organic compound (VOC) analysis, and metaproteomics to investigate microbial succession, functional dynamics, and the roles of yeasts and Zymomonas in WK fermentations representative of two WK types, i.e., one dominated by yeast-LAB-AAB and another by Zymomonas. Metagenomic profiling revealed that yeast-LAB-AAB communities exhibited dynamic microbial succession, whereas Zymomonas-dominated communities remained stable. Despite differing microbial compositions, both fermentations maintained consistent global metabolic functions, although specialized metabolic pathways and VOC profiles diverged. Metaproteomic analysis revealed a strong underappreciation of yeast contributions in metagenomic datasets, with yeasts representing a larger fraction of the proteome than predicted by DNA-based abundance. Lentilactobacillus hilgardii was enriched on WK grains, suggesting a specialized niche role. Our findings highlight the value of integrating multi-omics approaches to uncover microbial activity and community function in fermented foods and offer insights for the design of tailored WK starter cultures.},
}

@article {pmid41365119,
year = {2025},
author = {Fallah, SF and Afshar-Mohammadian, M},
title = {The physiological impacts of three AMF species and Bacillus thuringiensis (vegetative and endospore forms) in strawberry under different phosphorus availability.},
journal = {Plant physiology and biochemistry : PPB},
volume = {230},
number = {},
pages = {110901},
doi = {10.1016/j.plaphy.2025.110901},
pmid = {41365119},
issn = {1873-2690},
abstract = {The interactions between arbuscular mycorrhizal fungi (AMFs) and Bacillus thuringiensis can enhance plant growth, yet their combined effects under varying phosphorus (P) conditions remain unclear. This study evaluated three AMF species, Funneliformis mosseae (AMF1), Funneliformis caledonium (AMF2), and Acaulospora langula (AMF3), in combination with vegetative and endospore forms of B. thuringiensis in strawberry grown under no P addition, insoluble P, and P-available conditions. Under insoluble P, vegetative B. thuringiensis produced the greatest growth improvements, particularly with AMF3 (up to 89 % above the uninoculated control) and AMF2 (up to 80 %). Dual inoculation with vegetative cells increased root length to 29.3 cm, biomass to 1.45 g DW, and total protein content to 2.1 mg g[-1] FW, though root P sometimes decreased (0.13 %), suggesting a growth-dilution effect. In contrast, In P-available soil, dual inoculation reduced AMF colonization (11 %), root length (16 cm), and biomass (0.45 g DW), but increased root P (0.19 %), reflecting indicating downregulation of symbiosis when external P is sufficient. PAL and POD activities were modulated by both P availability and bacterial form. FTIR analyses showed that vegetative cells enhanced polysaccharide deposition, whereas endospores increased lignin-associated features. Multivariate analyses (PCA, NMDS) identified P availability as the primary driver of plant-microbe interaction outcomes. Overall, the benefits of AMF-B. thuringiensis were most evident under conditions of insoluble P, emphasizing their potential to enhance nutrient uptake in low P soil.},
}

@article {pmid41363624,
year = {2025},
author = {Gellért, C and Ebrahimkhalili, N and Siwakoti, S and Zhu, H and Kereszt, A},
title = {Not All Allies Are Welcome: Partner Discrimination in Legume-Rhizobium Symbiosis.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {},
number = {},
pages = {},
doi = {10.1094/MPMI-08-25-0108-FI},
pmid = {41363624},
issn = {0894-0282},
abstract = {The nitrogen-fixing symbiosis between leguminous plants and soil bacteria, collectively termed rhizobia, is a major contributor of fixed nitrogen to the biosphere. The ability of legumes to secure nitrogen from the atmosphere underlies their ecological success and has made them important crops in both traditional and modern sustainable agriculture. Many genes directing the establishment and functioning of this beneficial interaction have been identified under laboratory conditions using a limited number of bacterial strains and plant species in pairwise combinations. Under natural and field conditions, however, plants encounter numerous potential partners, as soil microbiomes contain diverse bacteria equipped with the necessary toolkit for symbiosis. Consequently, legumes must possess mechanisms to select for or against specific partners. This review highlights how legumes employ elements of their immune system for the negative selection of rhizobia via processes resembling the gene-for-gene model of effector-triggered immunity in plant-pathogen interactions.},
}

@article {pmid41362231,
year = {2025},
author = {Sánchez-Cañizares, C and Ledermann, R and McKenna, J and Underwood, TJ and Mendoza-Suárez, M and Green, R and Ramakrishnan, K and East, AK and Webb, I and Kirchhelle, C and Jorrín, B and Saalbach, G and James, EK and Moreira-Leite, F and Terpolilli, J and Poole, PS},
title = {Developmental fates and N2-fixing efficiency of terminally-differentiated versus undifferentiated bacteroids from legume nodules.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/plphys/kiaf613},
pmid = {41362231},
issn = {1532-2548},
abstract = {Within legume root nodules, rhizobia differentiate into bacteroids, which reduce N2 into NH3 for secretion to the plant. Bacteroids may be swollen and terminally differentiated or non-swollen and can regenerate outside nodules. It is unclear why these different endosymbiotic lifestyles exist and whether they differ in symbiotic efficiency. Here, we compared N2 fixing bacteroids of the near isogenic strains Rhizobium leguminosarum bv. phaseoli 4292 (Rlp4292) and R. leguminosarum bv. viciae A34 (RlvA34), nodulating Phaseolus vulgaris (common bean) and Pisum sativum (pea), respectively. The larger bean plants fixed more N2, but peas fixed 1.6-3-fold more per unit nodule mass. Values per unit volume were similar between bean and pea because bean nodules are 2.7-fold denser (i.e., mass per unit volume). Bean nodules have higher numbers of smaller (∼1/5 the volume) bacteroids than peas. Bean bacteroids are denser (i.e., 2.5-fold protein per unit volume) although less closely packed than pea bacteroids (i.e. more space between bean bacteroids). Critically, pea bacteroids, fix N2 at higher rates versus bean per unit bacteroid protein, as protein expression is skewed towards N2 fixation and TCA-cycle enzymes. Pea bacteroids infect 1.6 times the percentage of nodule volume of beans (i.e., 14.2% versus 9.1%). Overall, the increased packing density of pea bacteroids, as well as the bias of their proteome to nitrogenase, associated N2 fixation processes, and dicarboxylate metabolism, contributes to their greater symbiotic efficiency, which is likely driven by plant antimicrobial peptides.},
}

@article {pmid41361370,
year = {2025},
author = {Liu, J and Su, B and Miao, J and Li, S and Zhang, Q and Wang, F and Lin, Y and Lin, L},
title = {Whole-genome sequencing and analysis of the symbiotic Mycena sp. L02 with Gastrodia Elata.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-025-12405-z},
pmid = {41361370},
issn = {1471-2164},
support = {CB22144SO29A//Major Science and Technology Projects in Yunnan Province/ ; },
abstract = {BACKGROUND: Mycena is a widespread genus of mushroom capable of decomposing various dead plant substrates. Gastrodia elata is a fully mycoheterotrophic orchid whose seed germination depends on specific Mycena strains. However, only a few Mycena species are capable of inducing germination, necessitating the identification of novel germinating fungal resources.

RESULTS: The genome of Mycena sp. L02 was sequenced using the Illumina NovaSeq and Oxford Nanopore Technologies (ONT) platforms. The final assembly spanned 160.06 Mb, with 36,246 genes predicted and repetitive sequences accounting for 31.90% (46,496,154 bp) of the genome. A total of 1,339 CAZyme genes were annotated, along with 3,772 genes involved in host-pathogen interactions, 88.33% of which were associated with loss of pathogenicity, reduced virulence, or unaffected pathogenicity. Comparative genomic analysis between germinating and non-germinating Mycena strains revealed that their CAZymes and PHI gene characteristics represent common traits shared across the Mycena genus, with no distinctive features identified. Furthermore, pathways enriched in unique gene families of the germinating fungi-such as glutathione metabolism, sulfur metabolism, phosphatidylinositol signaling system, and inositol phosphate metabolism-may contribute to the germination of G. elata seeds.

CONCLUSIONS: The abundance of CAZymes and low-virulence genes in L02 ensures sufficient nutrient acquisition and may facilitate hyphal penetration of the lignin-rich seed coat of G. elata, thereby enabling successful symbiosis. Additionally, KEGG pathways enriched in the unique gene families of the germinating fungi may contribute to the stimulation of seed germination in G. elata. Overall, this study provides a valuable genomic foundation for screening high-performance germinating fungi and further investigating the molecular mechanisms underlying the symbiosis with G. elata.},
}

@article {pmid41361240,
year = {2025},
author = {Vondrák, J and Svoboda, S and Říha, P and Hauser, T and Kantnerová, V and Škaloud, P and Kubásek, J},
title = {Semilichen, an unjustly neglected symbiotic system between green biofilms and true lichens.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-30542-z},
pmid = {41361240},
issn = {2045-2322},
support = {67985939//Akademie Věd České Republiky/ ; },
abstract = {Symbiotic systems of photosynthetic microorganisms and fungi are widespread in terrestrial biomes and lichens are probably the most advanced and complex. Conversely, the least complex systems are "green biofilms" with a completely unexplored mycobiome. We describe here a new system intermediate between green biofilms and lichens-semilichens. Light and fluorescence microscopy, eDNA sequencing, molecular phylogeny, Chlorophyll a fluorescence and [13]C labelling/metabolomics were used to study algal and fungal identity, morphology and physiology of the symbiosis. Tight contact between algae and a single predominant fungus (mycobiont) is revealed in semilichens. The algae are from the symbiotic lineages of Trebouxiophyceae and Ulvophyceae, the fungi belong to Arthoniomycetes, Dothideomycetes, Eurotiomycetes, Lecanoromycetes and Lichinomycetes. Algae are alive and perform substantial photosynthetic activity. [13]C labelled photosynthates are partially converted into specific fungal polyols (arabitol, mannitol) demonstrating the C-flow from algae to fungi. The new symbiotic system was defined and compared with other terrestrial algal-fungal symbioses. It is characterized by minimalist environmental requirements and extremely low production of biomass. As a result, it also inhabits environments unfavourable for lichens. Our research supports the hypothesis that the long-term existence of algae and fungi in terrestrial conditions affected by frequent and repeated drying is likely dependent on their mutual coexistence.},
}

@article {pmid41361211,
year = {2025},
author = {Lange, K and Blanckaert, A and Marcus Do Noscimiento, MI and Grover, R and Fine, M and Reynaud, S and Ferrier-Pagès, C},
title = {Extracellular enzymatic activities of octocorals and scleractinian corals under environmental stress.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {43351},
pmid = {41361211},
issn = {2045-2322},
mesh = {*Anthozoa/enzymology/physiology/microbiology ; Animals ; *Stress, Physiological ; Nitrogen/metabolism ; Phosphorus/metabolism ; Alkaline Phosphatase/metabolism ; Coral Reefs ; Carbon/metabolism ; Leucyl Aminopeptidase/metabolism ; Symbiosis ; Ecosystem ; },
abstract = {Extracellular enzymes, released by coral holobionts (coral host, symbiotic dinoflagellates and associated microorganisms) are involved in nutrient cycling and can serve as diagnostic indicators of coral health and reef ecosystem functionality. For example, α-glucosidases (α-Glu), Leucine-aminopeptidases (LAP) and alkaline phosphatases (APA), hydrolyze large molecules into assimilable nutrients containing carbon, nitrogen and phosphorus, respectively. This study investigated the extracellular activity (EEA) of these three enzymes in octocoral and hexacoral species under different environmental conditions. Results revealed that EEA from mucus-associated microbes was low, while entire coral holobionts exhibited significant activity. Furthermore, under identical environmental conditions and substrate concentrations, LAP activity was the highest, followed by APA and α-Glu, suggesting nitrogen and phosphorus limitation rather than carbon. Heat and light stress significantly influenced enzyme activities, with APA showing the strongest increase, reflecting an increased demand for phosphorus and adaptive strategies to mitigate phosphorus limitation. Finally, all three EEAs were much lower in octocorals than in hexacorals. By investigating the mechanisms controlling enzymatic activities in corals, this research contributes to a deeper understanding of coral physiology and nutrient metabolism in response to changing environmental conditions.},
}

*Anthozoa/enzymology/physiology/microbiology
Animals
*Stress, Physiological
Nitrogen/metabolism
Phosphorus/metabolism
Alkaline Phosphatase/metabolism
Coral Reefs
Carbon/metabolism
Leucyl Aminopeptidase/metabolism
Symbiosis
Ecosystem

@article {pmid41358334,
year = {2025},
author = {Benjamin, G and Pacoud, M and Boutet, S and Clement, G and Brouquisse, R and Gatti, JL and Poirié, M and Frendo, P},
title = {Nitrogen-fixing symbiosis induces differential accumulation of Medicago truncatula leaf defence metabolites in response to pea aphid infestation.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1670344},
pmid = {41358334},
issn = {1664-462X},
abstract = {Legume symbiosis with rhizobial nitrogen-fixing bacteria enables legumes to grow in nitrate-depleted soils. Rhizobial symbioses also induce systemic plant defence against bioaggressors. We investigated how nitrogen-fixing symbiosis (NFS) in the legume Medicago truncatula can prime plant defence against the pea aphid Acyrthosiphon pisum. We analysed metabolite modification using both gas chromatography/mass spectrometry (GC-MS) and liquid chromatography/mass spectrometry (LC-MS) and defence pathway gene expression using qPCR in the leaves of both NFS and nitrate-fed [non-inoculated (NI)] plants after aphid infestation (Amp). The accumulation of primary and secondary metabolites was modulated by both NFS and aphid infestation. Sixty-two defence-related metabolites, such as salicylate, pipecolate, gentisic acid, and several soluble sugars, were differentially regulated by aphid infestation under both NFS and NI conditions. Nineteen metabolites, including triterpenoid saponins, accumulated specifically under NFS_Amp conditions. Gene expression analysis showed that aphid-infested plants exhibited significantly higher expression of chalcone isomerase, flavonol synthase, hydroxyisoflavone-O-methyl transferase, and pterocarpan synthase, while D-pinitol dehydrogenase was only significantly induced in NI-infested leaves. Our data suggest that NFS, in addition to being a plant nitrogen provider, stimulates specific legume defences upon pest attack and should also be considered a potential tool in Integrated Pest Management strategies.},
}

@article {pmid41358162,
year = {2025},
author = {Nicolas-Asselineau, L and Speth, DR and Zeller, LM and Woodcroft, BJ and Singleton, CM and Liu, L and Dueholm, MKD and Milucka, J},
title = {Occurrence and temporal dynamics of denitrifying protist endosymbionts in the wastewater microbiome.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf209},
pmid = {41358162},
issn = {2730-6151},
abstract = {Effective wastewater treatment is of critical importance for preserving public health and protecting natural environments. Key processes in wastewater treatment, such as denitrification, are performed by a diverse community of prokaryotic and eukaryotic microbes. However, the diversity of the microbiome and the potential role of the different microbial taxa in some wastewater treatment plant setups is not fully understood. We aimed to investigate the presence and diversity of denitrifying bacteria of the candidate family Azoamicaceae that form obligate symbioses with protists in wastewater treatment plants. Our analyses showed that denitrifying endosymbionts belonging to the Ca. Azoamicus genus are present in 20%-50% of wastewater treatment plants worldwide. Time-resolved amplicon data from four Danish WWTPs showed high temporal fluctuations in the abundance and composition of the denitrifying endosymbiont community. Twelve high-quality metagenome-assembled genomes of denitrifying endosymbionts, four of which were circular, were recovered. Genome annotation showed that a newly described, globally widespread species, Ca. Azoamicus parvus, lacked a nitrous oxide reductase, suggesting that its denitrification pathway is incomplete. This observation further expands the diversity of metabolic potentials found in denitrifying endosymbionts and indicates a possible involvement of microbial eukaryote holobionts in wastewater ecosystem dynamics of nitrogen removal and greenhouse gas production.},
}

@article {pmid41356942,
year = {2025},
author = {Alasbily, H and Mohamed, HH and Asheibi, A and Bazina, MS and Alkaseh, A and Ghaith, HM and Ali Fahmi, F},
title = {Probiotics in Periodontal Diseases: Mechanisms, Evidence Mapping, Limitations, and Future Directions.},
journal = {Cureus},
volume = {17},
number = {11},
pages = {e96042},
pmid = {41356942},
issn = {2168-8184},
abstract = {Periodontal disease represents a spectrum of inflammatory disorders that impact the teeth's supporting tissues. It is initiated by the buildup of microbial plaque and sustained by dysbiosis, an imbalance in the oral microbiome that causes tissue damage and disturbs host-microbe homeostasis. These diseases can range from reversible inflammation of the gingiva (gingivitis) to irreversible destruction of the periodontal apparatus (periodontitis). While scaling and root planing, with or without antimicrobials, can effectively reduce bacterial burden, mechanical debridement by itself may not restore microbial symbiosis and may allow disease-associated microbial populations to persist. Incomplete pathogen clearance from deep pockets, residual calculus, or inaccessible root surfaces frequently results in bacterial regrowth and disease progression. Probiotics have emerged as a possible alternative or supplement in periodontal therapy. Their possible benefits include microbial balance restoration in the oral cavity, as well as anti-inflammatory, immunomodulatory, and bone-preserving actions. Nonetheless, the strain-specific effects, dosage regimen, safety profile especially in certain patients and the absence of large-scale, long‑term randomized controlled trials to definitively establish their efficacy remain as concerns. This review discusses the mechanisms through which probiotics may influence periodontal diseases, systematically maps preclinical and clinical evidence, and highlights current limitations and future directions for their application in periodontal therapy.},
}

@article {pmid41356629,
year = {2025},
author = {Lee, JH and Kim, Y and Park, JT and Lee, DH and Hee-Young, J},
title = {Morphological and Phylogenetic Characterization of Raffaelea xyleboricola sp. nov. from Xyleborus Beetles in Korea.},
journal = {Mycobiology},
volume = {53},
number = {6},
pages = {867-876},
pmid = {41356629},
issn = {1229-8093},
abstract = {A fungal isolate was obtained from ambrosia beetles (Xyleborus sp.) collected using beetle traps placed in an apple orchard in Gunwi-gun, Daegu, Republic of Korea. Cytochrome oxidase I (COI) gene sequencing confirmed that the beetles belonged to the genus Xyleborus. The fungal isolate, designated ARI-25-A12, was subjected to morphological and molecular identification and characterization. On malt extract agar (MEA), colonies exhibited a white, fur-like surface, and hyphae penetrated the medium along the margins. As the colony matured, the center became dull yellow, and after 20 days of incubation, the colony diameter reached 49.6-56.0 mm. Morphologically, conidiophores were hyaline, simple or occasionally branched, and conidia were hyaline, thin-walled, unicellular, and globose. Conidia produced yeast-like sprout cells through a budding-like process, and the average conidial size was 5.2 × 5.2 μm (n = 100). Molecular phylogenetic analyses based on ITS, LSU, SSU, and β-TUB gene sequences indicated that ARI-25-A12 is classified within the genus Raffaelea. Phylogenetic trees constructed from ITS sequences and a combined dataset of LSU, SSU, and β-TUB gene sequences consistently classified the isolate as a distinct lineage, clearly separated from previously reported Raffaelea species, with additional morphological differences supporting its distinct classification. Based on these results, ARI-25-A12 is described herein as Raffaelea xyleboricola sp. nov.},
}

@article {pmid41356477,
year = {2025},
author = {Chakraborty, A and Roy, A and He, S and Castellano-Hinojosa, A and Asiegbu, FO and Coutinho, TA},
title = {Editorial: Forest microbiome: dynamics and interactions in the anthropocene era.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1729625},
pmid = {41356477},
issn = {1664-302X},
}

@article {pmid41356475,
year = {2025},
author = {Wang, L and Liu, W and Wang, L and Zhang, K and Li, D and Ji, J and Luo, J and Zhu, X and Cui, J and Gao, X},
title = {Cross-generational ripples: sublethal fipronil exposure alters Binodoxys communis microbiome without lethal consequences.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1637234},
pmid = {41356475},
issn = {1664-302X},
abstract = {INTRODUCTION: Fipronil, a broad-spectrum phenylpyrazole insecticide, demonstrates high efficacy against Aphis gossypii (cotton aphid). However, its potential effects on Binodoxys communis, a key natural enemy of A. gossypii, remain largely unexplored. This study comprehensively assessed the safety of fipronil for B. communis, with particular emphasis on sublethal effects and associated microbiome alterations.

METHODS: We evaluated the sublethal effects of fipronil on the development of B. communis across parental (F0) and offspring (F1) generations. Furthermore, the alterations in the microbial diversity and community structure of B. communis were analyzed using 16S rRNA sequencing. Functional prediction of the microbiota was performed via PICRUSt2.

RESULTS: Indirect fipronil exposure significantly prolonged larval development in the parental generation (F0, p = 0.017), while showing no statistically significant impact on the offspring generation (F1). 16S rRNA sequencing revealed apparent alterations in the microbial community. In adults, the dominant genus shifted from Akkermansia to Muribaculum after 1 h exposure, while the dominant phylum showed significantly reduced abundance after 3 d. In larvae, the major phylum (Proteobacteria) remained unchanged, but the major genus shifted from Brevitalea to Vicinamibacter. Functional prediction indicated that the predicted genes were predominantly enriched in metabolic pathways (75% of the functional repertoire).

DISCUSSION: These results suggest that fipronil exposure induces previously unrecognized sublethal effects on a key natural enemy insect, primarily by disrupting its symbiotic microbiota, which may play a major role in host metabolism. Our findings highlight the ecological risks of fipronil and emphasize the need for pesticide risk assessments that consider sublethal effects on beneficial insects and their microbiota.},
}

@article {pmid41356471,
year = {2025},
author = {Shigeta, K and Shiraishi, K and Schroll, M and Lauer, R and Keppler, F and Sakai, Y and Yurimoto, H},
title = {Methylotrophic yeast Candida boidinii enhances the colonization of plant growth-promoting yeast Papiliotrema laurentii in the phyllosphere.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1677102},
pmid = {41356471},
issn = {1664-302X},
abstract = {Methanol-utilizing microbes are ubiquitous in the phyllosphere, where they assimilate methanol released from pectin, the major component of the plant cell wall. While methylotrophic bacteria Methylobacterium spp. are well studied for their symbiotic relationships with the host plants, the ecology and functional roles of methylotrophic yeasts on plants remain poorly understood. In the effort to isolate yeasts from 26 phyllosphere samples, we identified Candida boidinii as the only methylotrophic yeast, while the remaining isolates, categorized into 17 species in 12 genera, lacked this metabolic trait. To obtain insight into the role of methylotrophic yeasts in the phyllosphere, we investigated the interaction of C. boidinii with a plant growth-promoting yeast (PGPY), Papiliotrema laurentii, one of the identified yeast species during isolation. We found that the colonization of P. laurentii was enhanced by the presence of C. boidinii on Arabidopsis thaliana leaves. Co-cultivation assays revealed that the cell yield of P. laurentii was enhanced by C. boidinii during cultivation on pectin and that the methanol-utilizing ability and pectin methylesterase (PME) activity of C. boidinii contributed to this enhancement. Stable carbon isotope labeling of pectin methylester groups unambiguously confirmed their assimilation by C. boidinii, but not by P. laurentii. These findings suggest that C. boidinii not only survives in the phyllosphere by utilizing pectin-derived methanol but also contributes to the fitness of other yeast species through metabolic cooperation. This study provides new insights into the niche construction and survival strategies of phyllosphere methylotrophic yeasts, highlighting their potential role in shaping microbial community dynamics and promoting beneficial plant-microbe interactions.},
}

@article {pmid41353278,
year = {2025},
author = {Guibert, I and Conti-Jerpe, IE and Pons, L and Tayaban, K and Sayco, SL and Cabaitan, P and Conaco, C and Baker, DM},
title = {Trophic niche partitioning in giant clams.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-025-09313-z},
pmid = {41353278},
issn = {2399-3642},
abstract = {Ecosystems are influenced by competition for limited resources, a driver of niche partitioning. Over time, the emergence of novel traits facilitating new resource exploitation can reduce competition. However, additional layers of complexity, like symbiosis, complicate our understanding of the patterns shaping reef communities. Therefore, empirical evidence of niche partitioning reducing competition in symbiotic benthic communities is limited. Using a unique common garden experiment, we examined the nutritional strategies of six giant clam holobionts and characterized their symbiont assemblages. Variation in trophic strategies confirmed trophic niche partitioning, as species fell along a continuum from highly heterotrophic to highly autotrophic. Tridacna gigas and T. derasa, listed as critically endangered and endangered, respectively, were the most autotrophic and fast-growing species. We found significant phylogenetic signals in trophic niche scores, growth rate, and shell length, indicating the role of natural selection in shaping giant clam nutritional ecology. We conclude that niche partitioning is a driver of giant clam evolution with benefits and costs; high autotrophy reliance results in greater growth rates yet may increase vulnerability to disturbances. Given the impact of human activities on giant clams, conservation efforts should focus on these ecosystem engineers, especially highly autotrophic and geographically constrained species.},
}

@article {pmid41352734,
year = {2025},
author = {Li, X and Zhang, Z and Chen, D and Chen, Z and Li, L and Song, Z and Li, J and Li, W and Wang, E and Wang, R and Huang, R and Zhao, P and Sun, H and Cai, J and Zhang, L and Hu, H and Li, Y and Kang, Y and Ou, H and Xu, H and Cheng, X},
title = {Microbial mediators of environmental change in the Yellow River basin: Flavobacterium and pollution dynamics during the dry season.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123509},
doi = {10.1016/j.envres.2025.123509},
pmid = {41352734},
issn = {1096-0953},
abstract = {The Yellow River basin, densely populated and characterized by intensive industrial and agricultural activities, faces significant water quality concerns. However, the impact of different pollution sources (e.g., industrial, domestic, and mixed wastewater) on the microbial spectrum in sections of the Yellow River during the dry season remains unclear. This research seeks to address this knowledge gap by examining the variations of microbial community structure and ecology influenced by different pollution sources. Our results showed that pH, NO3-N, TP and turbidity differed significantly among the different pollution groups. Industrial pollution increased species richness, while domestic wastewater reduced microbial diversity. Flavobacterium abundance increased significantly with domestic pollution but decreased dramatically with industrial pollution. Specific genera linked to domestic pollution included Pseudarcicella and Denitratisoma, while industrial pollution was associated with Sulfurimonas Trichococcus, Halomonas, and fungal genera such as Fusarium. Network analysis revealed the pollutants disrupted the community structure and dissolved symbiotic interactions, thereby promoting the emergence of new dominant microorganisms. KEGG analysis found that domestic sources were associated with amino acid metabolism and secondary metabolite biosynthesis, while industrial sources enhanced activity in isoflavonoid biosynthesis and carbohydrate metabolism. Our findings provide a comprehensive microbial ecological analysis of the sediment-rich core industrial area of the Yellow River, shedding light on the impacts of different pollution sources and river section locations on microbial networks, offering valuable insights for ecological safety and protection.},
}

@article {pmid41352522,
year = {2025},
author = {Torres de Farias, S and José, M},
title = {The Natural history of the transition between RNA to DNA in the early stages of life.},
journal = {Bio Systems},
volume = {},
number = {},
pages = {105671},
doi = {10.1016/j.biosystems.2025.105671},
pmid = {41352522},
issn = {1872-8324},
abstract = {In this work we examine different hypotheses for the fixation of DNA as the principal informational molecule. The emergence of protein RNA-dependent RNA polymerases heralded the beginning of a process that ultimately culminated in the transition from RNA to DNA as the primary informational molecule. To understand this pivotal transition, it is necessary to examine the evolutionary history of nucleic acid polymerases, with particular emphasis on RNA-dependent RNA polymerases, RNA-dependent DNA polymerases, and DNA-dependent DNA polymerases. Instead of resolving the debates over single versus multiple origins of DNA, we adhere to the need to conceptualize early evolution as a dynamic network, driven by horizontal transfer, molecular innovation, and symbiosis between cells and viruses.},
}

@article {pmid41352348,
year = {2025},
author = {Wagner, JM and Wong, JH and Millar, JG and Haxhimali, E and Brückner, A and Naragon, TH and Boedicker, JQ and Parker, J},
title = {Enforced specificity of an entrenched symbiosis.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.10.066},
pmid = {41352348},
issn = {1879-0445},
abstract = {The Metazoa encompasses inordinate lineages of symbionts and ecological specialists that obligately depend on particular hosts. The maintenance and fidelity of these lifestyles are often posited to hinge on sensory tuning to host-derived cues, a paradigm supported by studies of neural function in host-specific models. We experimentally reconstituted a socially complex relationship between an obligately symbiotic rove beetle and its single, natural host ant species, permitting us to probe its sensory basis. We show that cuticular hydrocarbons-the ant's nestmate recognition pheromones-elicit host recognition by the beetle and the execution of ant grooming behavior, enabling the beetle to chemically mimic its host and infiltrate the nest as a parasitic impostor. The beetle also follows host trail pheromones, permitting inter-colony dispersal. Yet the beetle also performs these symbiotic behaviors with non-host ants separated by up to ∼95 million years, is able to socially assimilate into their colonies, and shows minimal sensory preference for its natural host over non-host species. Agent-based modeling reveals that the specificity of the beetle emerges not from sensory tuning but from physiological limits on dispersal and negative fitness interactions with alternative hosts, constraining the otherwise promiscuous beetle to its natural host. Recreating the in silico model with living insects empirically demonstrates specificity arising from these enforcing barriers. Our findings show how entrenched symbioses can obviate selection for taxonomically precise host recognition, with specificity emerging from forces external to the symbiont. Chance realization of latent compatibilities with alternative hosts may facilitate host switching, explaining the diversification and deep-time success of such taxa.},
}

@article {pmid41352302,
year = {2025},
author = {Zhang, J and An, M and Chen, Y and Li, X and Qu, G and Liang, J},
title = {Terpenoids are associated with cytokinin and auxin signaling during mycorrhiza formation in the Suillus bovinus-Pinus yunnanensis symbiosis.},
journal = {Plant physiology and biochemistry : PPB},
volume = {230},
number = {},
pages = {110852},
doi = {10.1016/j.plaphy.2025.110852},
pmid = {41352302},
issn = {1873-2690},
abstract = {Suillus bovinus is an ecologically significant wild ectomycorrhizal fungus that forms symbiotic associations with pine trees. Terpenoids are known to play a key role in interactions between fungi and plants. However, the molecular mechanisms underlying the effects of terpenoids on the formation of symbiotic associations with S. bovinus remain poorly understood. Here, we investigated the effect of S. bovinus terpenoids on root development and mycorrhizal formation in Pinus yunnanensis using physiological, transcriptomic, and phytohormone assays. Our findings revealed that terpenoids from S. bovinus were associated with alterations in the synthesis and signaling of cytokinin in P. yunnanensis, evidenced by changes in the expression of specific genes in the mevalonate synthesis pathway and signaling transduction, such as CKXs, AHP, and A-ARRs. Similarly, these terpenoids correlated with changes in auxin synthesis and signaling, indicated by modulated tryptophan levels and the expression of specific enzyme genes, such as GH3, AUX1, AUX/IAA, and SAUR. This suggests that terpenoids from S. bovinus may contribute to lateral root development and mycorrhizal formation in P. yunnanensis, potentially by influencing the relative levels of cytokinin and auxin. These results shed light on the potential involvement of terpenoids produced by S. bovinus in establishing symbiotic interactions between ectomycorrhizal fungi and their host plants, warranting further direct functional validation.},
}

@article {pmid41352299,
year = {2025},
author = {Lin, J and Zhang, J and Guo, P and Jia, B and Chen, Y and Zhang, Z and Guo, W},
title = {Arbuscular mycorrhizal fungi enhance maize tolerance to combined La-NaCl stress by restructuring the rhizosphere bacterial community.},
journal = {Plant physiology and biochemistry : PPB},
volume = {230},
number = {},
pages = {110849},
doi = {10.1016/j.plaphy.2025.110849},
pmid = {41352299},
issn = {1873-2690},
abstract = {Arbuscular mycorrhizal fungi (AMF) and plant rhizosphere microbes help alleviate the combined abiotic stress of plants. However, the microbial mechanisms by which AMF symbiosis improves plant tolerance to combined rare earth-salt stress remain unclear. We conducted a pot experiment to assess the effects of AMF on maize growth, nutrient contents, toxic ion accumulation, and rhizosphere bacterial community in La or combined La-NaCl stress (La-NaCl). The results revealed that in La and La-NaCl, AMF significantly increased plant biomass, P, Mg, and La contents (35.14 %-468.79 %), significantly decreased soil available P and K concentrations (6.52 %-28.30 %). In La-NaCl, AMF significantly increased Na[+] content (41.41 %-305.75 %) and decreased the concentrations and translocation rates of La and Na[+] of plants (13.50 %-56.55 %). Additionally, AMF significantly altered the rhizosphere bacterial community structure and significantly increased the Firmicutes abundance by 15.97 % (La) and 62.51 % (La-NaCl). Moreover, AMF increased the modularity of networks in La and La-NaCl, altered biomarkers and keystones in La (e.g., Noviherbaspirillum) and La-NaCl (e.g., Ramlibacter), thus reshaping the key microorganisms. Molecular ecological networks revealed that AMF strengthened the key microorganisms' positive correlation with plant indices in La-NaCl. The structural equation model further indicated that AMF can affect plant growth by regulating the composition, diversity, and network characteristics of rhizosphere bacterial community in La-NaCl. To summarize, the findings of this study improved our understanding of the underlying microbial mechanisms by which AMF promote plant resistance to combined La-NaCl stress.},
}

@article {pmid41352032,
year = {2025},
author = {Fu, M and Xu, Y and Liu, X and Huang, T and Ma, B and Li, F and Shi, W and Zhang, H},
title = {Water lifting aerators control algal growth in drinking water reservoirs: Performance, mechanism and application.},
journal = {Water research},
volume = {290},
number = {},
pages = {125022},
doi = {10.1016/j.watres.2025.125022},
pmid = {41352032},
issn = {1879-2448},
abstract = {Artificial mixing has gained extensive attention owing to its strong applicability and effective inhibition of algae. However, few studies have explored the mechanisms by which water lifting aerators (WLAs) control algae growth. Here, a laboratory simulation of vertical light and temperature conditions in a reservoir was conducted to explore the mechanisms affecting algal growth. The mechanism of artificial mixing in controlling algae growth was investigated in situ. The results revealed that algal cell growth was inhibited under low temperature (15 °C, 5 °C) and lightless (0 lx) conditions, leading to suppressed synthesis of Chlorophylla and carotenoids, as well as reduced photosynthetic activity. Soluble microbial products content remained largely unchanged, whereas soluble protein content increased. After artificial mixing, nutrient and pollutant concentrations in the water, as well as algae density, were significantly reduced, and changes in algal community structure were observed. The interspecific relationships among the algae were primarily mutualistic symbiosis, which weakened at the action point after artificial mixing. Phosphorus (p < 0.05) and carbon (p < 0.05) contents significantly influenced algae community structure at the action point, with carbon (p < 0.05) content being a significant factor affecting algae abundance. The results provide a solid theoretical foundation for exploring the mechanism by which artificial mixing inhibits algae growth and proliferation, and offer scientific support for applying WLAs to control algae growth in drinking water reservoirs.},
}

@article {pmid41351674,
year = {2025},
author = {Hikosaka, A and Nishimoto, A and Takeda, N and Hikosaka-Katayama, T},
title = {Occurrence of 12 Acoela Species in the Seto Inland Sea.},
journal = {Zoological science},
volume = {42},
number = {6},
pages = {540-555},
doi = {10.2108/zs240106},
pmid = {41351674},
issn = {0289-0003},
mesh = {Animals ; Phylogeny ; Japan ; RNA, Ribosomal, 18S/genetics ; Oceans and Seas ; Electron Transport Complex IV/genetics ; *Animal Distribution ; Species Specificity ; },
abstract = {The Acoela is a notable taxon in terms of the early evolution of bilaterians and the photosynthetic symbiosis between animals and microalgae. There are approximately 416 described species of Acoela worldwide, which are classified into 16 families. In total, 21 species have been reported in Japan, of which five have been reported in the Seto Inland Sea. We surveyed acoels in the intertidal zone of beaches along the Seto Inland Sea coast of Hiroshima Prefecture and collected specimens. A comparison of mitochondrial cytochrome oxidase subunit I (COI) sequences and molecular phylogenetic analysis suggested that they could be divided into 12 species. Molecular phylogenetic analysis using 18S rRNA sequences suggested that these species belonged to five families: Convolutidae, Otocelididae, Dakuidae, Actinoposthiidae, and Isodiametridae. There have been no previous reports of Dakuidae or Actinoposthiidae in Japan and no reports of Isodiametridae in the Seto Inland Sea. These results suggested that the diversity of Acoela in Japan and the Seto Inland Sea is far richer than is currently known.},
}

Animals
Phylogeny
Japan
RNA, Ribosomal, 18S/genetics
Oceans and Seas
Electron Transport Complex IV/genetics
*Animal Distribution
Species Specificity

@article {pmid41351672,
year = {2025},
author = {Ikuta, T and Sugimura, M and Yuasa, A and Amari, Y},
title = {Successful Maintenance of Chemosynthetic Symbiotic Bacterial Abundance in Hydrothermal Mussels During Long-Term Rearing Experiments Exceeding 1000 Days.},
journal = {Zoological science},
volume = {42},
number = {6},
pages = {521-531},
doi = {10.2108/zs250041},
pmid = {41351672},
issn = {0289-0003},
mesh = {Animals ; *Symbiosis/physiology ; *Bacteria/classification/genetics ; *Mytilidae/microbiology/physiology ; Gills/microbiology/anatomy & histology ; *Bivalvia/microbiology ; Phylogeny ; },
abstract = {Symbiosis with chemosynthetic bacteria is a biological phenomenon that has enabled animals to adapt to deep-sea environments. The deep-sea vent mussel Bathymodiolus septemdierum harbors sulfur-oxidizing symbionts in its gills, which serve as its main source of nutrients. However, the establishment and maintenance of this symbiosis process remain poorly understood, partly because culturing deep-sea mussels and their symbionts is difficult and experimental studies are rare. In the present study, we aimed to establish a rearing method for B. septemdierum and investigate the effects of sodium sulfide (Na2S) addition and gas concentration control in rearing tanks. Three tanks were prepared: a normal tank (tank N), one with Na2S (tank S), and one with Na2S and control dissolved oxygen (tank SO). Mussels were maintained for more than 1000 days, and host survival, gill histology, and the abundance of symbionts were investigated. In tanks N and S, symbionts were depleted within a short period, whereas in tank SO, gill morphology and symbiont abundance were maintained at levels comparable to those of freshly collected individuals, even after 1000 days. However, the survival rate of the host did not correspond to symbiont maintenance. Phylogenetic analysis revealed that the symbiont RuBisCO exists in Form II, which is generally adapted to low-O2 and high-CO2 environments. These results suggest that the long-term maintenance of B. septemdierum symbionts is possible by adding Na2S and controlling the dissolved gas concentration. Further improvements in rearing methods could contribute to a deeper understanding of host-symbiont interactions in this unique deep-sea organism.},
}

Animals
*Symbiosis/physiology
*Bacteria/classification/genetics
*Mytilidae/microbiology/physiology
Gills/microbiology/anatomy & histology
*Bivalvia/microbiology
Phylogeny

@article {pmid41351265,
year = {2025},
author = {Wu, J and Zhang, X and Fan, Z and Huang, Y and Cao, Y and Ren, J and Yang, L and Tian, J and Yu, Y and Kong, Z},
title = {Symbiosome membrane-localized cationic amino acid transporters support symbiotic nitrogen fixation in Medicago truncatula.},
journal = {Plant communications},
volume = {},
number = {},
pages = {101636},
doi = {10.1016/j.xplc.2025.101636},
pmid = {41351265},
issn = {2590-3462},
abstract = {Legumes engage in nitrogen-fixing symbiosis with rhizobia, wherein it is well established that host legumes supply dicarboxylates as a carbon source to rhizobia, while rhizobia reciprocate by providing ammonium to the host plants. Apart from the classical model, accumulating evidence suggests that amino acid exchange is also essential to legume-rhizobium symbiosis. However, it remains unclear whether amino acid transporters are present on the symbiosome membrane (SM) to mediate amino acid exchange in symbiotic nitrogen fixation (SNF). In this study, we identified three amino acid transporters in Medicago truncatula-MtCAT1a, MtCAT1b, and MtCAT1c-belonging to a clade of the plant Cationic Amino acid Transporter (CAT) family known for transporting a wide range of amino acids. Notably, MtCAT1b and MtCAT1c are predominantly expressed in infected cells of nodules and are localized to the SM. Genetic analyses further demonstrate that both MtCAT1b and MtCAT1c are required for amino acid exchange on the SM, with additional evidence indicating that metabolism of bacteroids is disturbed in the mutant. Transport assays reveal that both MtCAT1b and MtCAT1c exhibit broad substrate specificity. Collectively, our findings identify MtCAT1b and MtCAT1c as key mediators of cross-kingdom amino acid exchange, essential for maintaining efficient SNF in root nodules.},
}

@article {pmid41350987,
year = {2025},
author = {Du, E and Li, P and Chen, Y and Lin, H and Xu, Q and Huang, X and Gui, F},
title = {Positive feedback effect of rhizosphere Bacillus on the growth and defense of Ageratina adenophora.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1686},
pmid = {41350987},
issn = {1471-2229},
support = {2024J0428//he Scientific Research Foundation of Education Department of Yunnan Province/ ; 202401AS070003//Yunnan Fundamental Research Projects/ ; },
mesh = {*Rhizosphere ; *Bacillus/physiology ; *Ageratina/growth & development/microbiology/physiology ; Soil Microbiology ; Animals ; Symbiosis ; Herbivory ; },
abstract = {BACKGROUND: The formation of symbiotic relationships between invasive plants and soil microorganisms in invaded regions, which enhances their adaptive capacity has been extensively studied. Bacillus, as a representative soil beneficial microorganism, can be recruited by invasive plants to their rhizosphere to promote growth. However, it remains unclear how dominant Bacillus species in the rhizosphere changes, and what feedback effects these changes may have, when invasive plants encounter biotic resistance in the invaded region, particularly from plant competition and insect herbivory.

RESULTS: This study investigated the contents of Bacillus idriensis, B. mycoides, B. thuringiensis in the rhizosphere soil of Ageratina adenophora under different biotic resistance. It showed that B. idriensis exhibited the highest increase in the rhizosphere during plant competition, whereas B. thuringiensis showed the most significant increase under Aphis gossypii infestation. The effect of these Bacillus species on the competitive interactions between A. adenophora and native plant Rabdosia amethystoides were assessed. Inoculation with B. idriensis led to an 185.66% increase in biomass for monocultured A. adenophora and a 175.83% increase in mixed culture, thereby enhancing the positive effect of interspecific competition on the growth of A. adenophora. Additionally, the responses of A. adenophora to infestation by the generalist herbivorous A . gossypii following Bacillus inoculation were examined. B.thuringiensis inoculated significantly increased the levels of jasmonic acid, total phenols, flavonoids in A. adenophora infested by A. gossypii by 49.38%, 20.78%, 18.59%, while significantly reducing the survival rate and nymph density of A. gossypii, indicating enhanced resistance to the herbivore. B. idriensis improved the tolerance of A. adenophora to A. gossypii through growth promotion.

CONCLUSION: Our findings demonstrate that the abundance of distinct Bacillus species in the rhizosphere of A. adenophora varies in response to diverse biotic resistance encountered in the invaded region. These rhizobacterial interactions generate specific feedback effects that collectively enhance the invasiveness of the species.},
}

*Rhizosphere
*Bacillus/physiology
*Ageratina/growth & development/microbiology/physiology
Soil Microbiology
Animals
Symbiosis
Herbivory

@article {pmid41349338,
year = {2025},
author = {Bastías, DA and Johnson, LJ and Jáuregui, R and Applegate, ER and Liu, X and Mace, WJ and Card, SD},
title = {Paenibacillus taichungensis strain E222: Mother and progeny plant growth promotion and association with an Epichloë fungal endophyte.},
journal = {Plant physiology and biochemistry : PPB},
volume = {230},
number = {},
pages = {110851},
doi = {10.1016/j.plaphy.2025.110851},
pmid = {41349338},
issn = {1873-2690},
abstract = {There are limited publications evaluating the effects of bacteria on plant-fungal symbioses. We evaluated the effects of a bacterium (designated strain E222) on perennial ryegrass (Lolium perenne) symbiotically associated with an Epichloë endophyte. Within this tripartite symbiosis, E222 was characterised as an ectosymbiont of Epichloë sp. AR135, the latter a mutualistic endophytic fungus of L. perenne. We hypothesised that (i) E222 would promote host plant growth and not interfere with the in planta production of AR135-derived antiherbivore alkaloids and AR135 growth and (ii) the Epichloë hyphal colonisation of plant seeds would facilitate the E222 entry into the progeny seeds. Via whole genome analysis, E222 was identified as Paenibacillus taichungensis and predicted to possess plant growth-promoting traits. E222 was inoculated on seeds of perennial ryegrass associated with AR135 and the bacterium was systemically present in the subsequent seedlings. E222 promoted the growth of AR135-associated plants, as expected, but reduced AR135-derived alkaloid concentrations and decreased the AR135 biomass at an early plant stage. AR135, but not E222, was detected in the progeny seeds and in line with the absence of E222, growth of progeny seedlings was not affected by the bacterial inoculation of mother plants. The bacterial effects on plants and Epichloë may be explained by the predicted abilities of E222 to promote plant growth (e.g., auxin production) and compete with AR135 for alkaloid precursors (e.g., tryptophan).},
}

@article {pmid41349301,
year = {2025},
author = {Li, C and Sun, H and Xi, Y and Li, Y and Wang, X and Huang, Z and Li, W and Zeng, X and Jia, Y},
title = {Phycosphere bacterial communities mediate arsenic accumulation and speciation in coastal macroalgae: Evidence from field investigation.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140647},
doi = {10.1016/j.jhazmat.2025.140647},
pmid = {41349301},
issn = {1873-3336},
abstract = {Macroalgae are known to efficiently accumulate arsenic, however, the role of their phycosphere bacterial communities in modulating arsenic uptake and transformation remains poorly understood. This study investigates the impact of phycosphere bacterial communities on arsenic accumulation and speciation in three coastal macroalgae species: Laminaria japonica (brown alga), Ulva pertusa Kjellman (green alga), and Mazzaella japonica (red alga). Among the three, L. japonica exhibited higher total arsenic content than M. japonica and U. pertusa. Phycosphere bacterial communities differed significantly among the macroalgae species in both α- and β-diversity and were strongly correlated with variations in intracellular arsenic species. Functional gene predictions indicated enrichment of pst and GST genes in L. japonica and M. japonica, associated with enhanced arsenic uptake and detoxification, while arsC was more abundant in the U. pertusa phycosphere, suggesting a preference for arsenate reduction pathways. These findings reveal the distinct roles of phycosphere bacterial communities among different macroalgae and their influence on the conversion of inorganic to organic arsenic, providing new insights into arsenic biogeochemistry in marine macroalgae-bacteria symbiotic systems.},
}

@article {pmid41347882,
year = {2025},
author = {Xu, Y and Zhang, F and Chen, X and Zhang, M and Chen, Z},
title = {Synergistic Interactions between Nitrogen Fixation and Phosphorus Uptake in Legumes: Insights from the Root Nodule Bacterium En1.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c08432},
pmid = {41347882},
issn = {1520-5118},
abstract = {The synergistic interaction between symbiotic nitrogen (N) fixation and phosphorus (P) nutrition in legumes remains poorly understood yet critical for mitigating grassland degradation under nutrient limitations. Using 16S rRNA sequencing, we compared bacterial communities in root nodules, rhizosphere, and bulk soils of three wild legumes (Trifolium repens L., Medicago sativa L., and Indigofera amblyantha Craib). Nodules showed reduced bacterial diversity but shared core microbes derived from soil reservoirs, including Ensifer. We isolated an Ensifer strain (En1) and genomic analysis revealed genes specifically involved in nitrogen fixation and phosphate uptake. Functionally, En1 solubilized and mineralized phosphate (calcium phytate and calcium phosphate). Inoculation experiments confirmed that En1 enhances plant P acquisition. Our findings demonstrate a mechanism whereby nitrogen-fixing rhizobia directly facilitate P uptake, establishing a self-sustaining N-P coprovision system in legume-microbe symbiosis, offering a novel strategy for grassland restoration by concurrently addressing N and P limitations.},
}

@article {pmid41347246,
year = {2025},
author = {Mishra, S and Shukla, AC and Craven, KD},
title = {Editorial: Microbial symbionts of lower plants.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1727008},
doi = {10.3389/fmicb.2025.1727008},
pmid = {41347246},
issn = {1664-302X},
}

@article {pmid41346372,
year = {2025},
author = {Villanueva-Castañeda, M and Antunez-Mojica, M and Tapia-Maruri, D and Ramírez, OCM and Delgado, RD and Barrera-Molina, AI},
title = {Development and Morphological/Microstructural Characterization of a Novel Synergic Synbiotic Co-Encapsulated Lactobacillus spp. Consortium and Kale Powder.},
journal = {Food science & nutrition},
volume = {13},
number = {12},
pages = {e71314},
pmid = {41346372},
issn = {2048-7177},
abstract = {Kale, a nutrient-dense leafy green rich in bioactive compounds, has emerged as a promising prebiotic candidate for enhancing probiotic viability and functionality. This study investigated the effects of kale powder and its polyphenolic compounds on the growth and stability of a Lactobacillus spp. consortium. Growth kinetics experiments revealed that 1% kale powder significantly enhanced bacterial growth, with a pronounced increase observed after 5 h of incubation compared to the control. Furthermore, a synergistic synbiotic was successfully co-encapsulated using a 1.3% alginate-based matrix combined with 1% kale powder and Lactobacillus spp. consortium. Morphological characterization under varying temperature conditions demonstrated that co-encapsulated particles maintained structural integrity at 4°C and during freezing, while dehydration led to significant size reduction due to moisture loss. Encapsulation efficiency reached 93%, with the alginate matrix effectively protecting bacterial viability, as evidenced by only a 13% reduction in viability after storage at 4°C. Microscopic analyses confirmed the presence of polyphenols within the co-encapsulated system, with confocal microscopy revealing distinct autofluorescence attributed to phenolic compounds. Electron microscopy further showed that co-encapsulated particles remained intact under refrigeration and freezing but exhibited morphological changes after dehydration. Growth kinetics of the Lactobacillus spp. consortium in medium supplemented with kale-derived polyphenols indicated optimal growth at 0.4% concentration, while higher concentrations (0.6%) led to reduced growth, suggesting substrate inhibition. These findings highlight the dual role of kale polyphenols as prebiotic substrates and protective agents, underscoring their potential in developing stable and functional synbiotic delivery systems for probiotic applications.},
}

@article {pmid41345699,
year = {2025},
author = {Yilmaz, A and Kasap, OE},
title = {Prevalence of Wolbachia in natural sand fly (diptera: psychodidae) populations from Türkiye and its potential role in mitochondrial divergence.},
journal = {Parasites & vectors},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13071-025-07157-4},
pmid = {41345699},
issn = {1756-3305},
support = {2211-A National PhD Scholarship Program//TÜBİTAK/ ; 101057690//European Commission/ ; 10038150 and 10038150//UK Research and Innovation/ ; TBAG 105T205 and SBAG 114S999//Türkiye Bilimsel ve Teknolojik Araştırma Kurumu/ ; 09D01601002 and 01001601001//Hacettepe University Scientific Research Unit/ ; W911QY-16-C-0160//AFHSB-GEIS/ ; },
abstract = {BACKGROUND: Phlebotomine sand flies are vectors of various pathogens, most notably Leishmania spp. Symbiotic bacteria have recently gained considerable attention owing to their effects on hosts and on other organisms co-infecting the same host. In this study, we investigated the natural Wolbachia infection status of sand fly taxa distributed in Türkiye and examined its potential role in driving the deep mitochondrial divergence observed within certain taxa.

METHODS: We analysed 858 sand fly specimens, mostly collected between 2005 and 2016, with additional samples obtained in 2023. Specimens were morphologically identified, and the mitochondrial cox1 gene was sequenced for DNA barcoding. For selected taxa showing marked mitochondrial divergence, species delimitation methods were applied, and genetic diversity indices and neutrality tests were calculated. Wolbachia infection was detected via PCR amplification of the wsp gene, and strain diversity was characterised using multilocus sequence typing (MLST) of five housekeeping genes. Logistic regression was used to evaluate associations between infection status and mitochondrial lineage, sex or collection period.

RESULTS: Wolbachia infection was detected in 16.67% of specimens, occurring exclusively in Phlebotomus papatasi, Ph. major s.l., Ph. tobbi, Ph. economidesi and Sergentomyia minuta. Analyses of wsp and MLST data identified all sequences as belonging to Supergroup A, with multiple strains present within and across host taxa. Infection among the five Ph. major s.l. lineages delineated by species delimitation was significantly associated with lineage, with lineages 3-5 showing a higher probability of infection. The reduced haplotype and nucleotide diversity, along with a significant negative deviation from neutrality observed in lineage 5, suggest a selective sweep likely driven by Wolbachia infection.

CONCLUSIONS: This study represents the first comprehensive screening of Wolbachia infection in sand fly taxa distributed across Türkiye, during which several novel Wolbachia strains were identified. Our findings suggest a potential role of Wolbachia infection in driving lineage differentiation within certain sand fly taxa. However, further detailed investigations are required to elucidate the mechanisms by which Wolbachia influences sand fly diversification and to assess the broader epidemiological implications related to sand fly-borne diseases (SFBDs).},
}

@article {pmid41344242,
year = {2025},
author = {Araújo, AS and Cavalcanti, IMF and de Almeida Campos, LA and de Souza, FRA and Gonçalves, DA and Teixeira, JAC and Nobre, C and Stamford, TCM},
title = {Enhancing coconut-based beverages with symbiotic microcapsules: Evaluation of physical-chemical traits and probiotic stability during gatrointestinal digestion.},
journal = {Food chemistry},
volume = {499},
number = {},
pages = {147359},
doi = {10.1016/j.foodchem.2025.147359},
pmid = {41344242},
issn = {1873-7072},
abstract = {This study highlights the effectiveness of ionic gelation combined with vibratory extrusion and chitosan hydrochloride coating as a robust strategy for the microencapsulation of Lacticaseibacillus rhamnosus GG intended for application in complex food matrices. The developed symbiotic microcapsules demonstrated desirable morphological and structural characteristics and provided significant protection to the encapsulated probiotic under simulated gastrointestinal conditions. When incorporated into a coconut water-soluble extract, the microcapsules influenced the physicochemical properties of the food matrix, promoting increased acidity, soluble solids content, and lightness, while preserving probiotic viability above the critical threshold of 6 log CFU/mL throughout storage. The additional chitosan hydrochloride coating further enhanced the protective capacity of the capsules, improving resistance to extreme pH and bile salts during simulated gastrointestinal digestion. These results support the potential of this encapsulation approach to enhance the stability and functionality of probiotics in functional foods.},
}

@article {pmid41344091,
year = {2025},
author = {Yuan, H and Yang, W and Ali, S and Behan, AA and Chen, L and Li, W and Gao, W and Arain, MA and Nabi, F and Buzdar, JA and Li, Z},
title = {From ponds to pastures: Azolla as a functional and climate-smart feed resource for poultry and livestock.},
journal = {Poultry science},
volume = {105},
number = {1},
pages = {106168},
doi = {10.1016/j.psj.2025.106168},
pmid = {41344091},
issn = {1525-3171},
abstract = {The escalating challenge of securing sustainable, climate-resilient feed resources necessitates the exploration of novel alternatives. This review critically evaluates the potential of Azolla, a small aquatic fern, as a functional and climate-smart feed ingredient for livestock and poultry. Owing to its symbiotic association with the nitrogen-fixing cyanobacterium Anabaena azollae, Azolla achieves rapid biomass accumulation without external nitrogen input, thereby offering a uniquely low-carbon low-cost cultivation system. Nutritionally, Azolla contains 15-35 % crude protein (dry matter), and serve as a valuable source of essential amino acids, vitamins, minerals, and diverse bioactive compounds that may contribute to improved animal health and product quality. Evidence from feeding trials in poultry and other livestock species consistently demonstrate that Azolla supplementation significantly enhance growth performance, feed efficiency, egg and milk production, immune functions, and overall product attributes, while simultaneously lowering feed cost. Notably, its bioactive profile supports gut integrity, antioxidant capacity, and methane mitigation, emphasizing its dual potential to improve productivity and reduce the environmental footprint of animal agriculture. Azolla's adaptability across agro-climatic zones and capacity for year-round cultivation further reinforce its suitability as a climate-smart feed resource. Despite these advantages, constraints related to large-scale production, preservation, nutrient variability, and the presence of anti-nutritional factors highlight the need for standardized cultivation protocols and innovative processing technologies. This review consolidates current evidence on the nutritional, functional, and ecological value of Azolla and identifies key research priorities to support its broader adoption as a sustainable feed resource for livestock and poultry.},
}

@article {pmid41343712,
year = {2025},
author = {Su, C and Wan, Y and He, D and Cai, T and He, S and Li, J and Wan, H},
title = {Acetobacter Protects DmDuox-Deficient Drosophila melanogaster from Impaired Detoxification.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c12535},
pmid = {41343712},
issn = {1520-5118},
abstract = {Dual oxidase (Duox) is essential for host physiological homeostasis. Loss of Duox disrupts host physiology and alters microbiota composition, potentially affecting the host tolerance to environmental stress. However, whether symbiotic bacteria can influence these detrimental effects remains unclear. This study investigated the role of symbiotic bacteria and DmDuox in regulating host detoxification gene expression in Drosophila melanogaster. Bioassays showed that silencing DmDuox increased D. melanogaster sensitivity to neonicotinoid insecticides, while axenic D. melanogaster displayed an even greater sensitivity. Moreover, 16S rRNA gene amplicons sequencing revealed DmDuox silencing significantly increased Acetobacter abundance, and reintroduction of the isolated Acetobacter oryzifermentans strain to axenic DmDuoxRNAi D. melanogaster reduced host insecticide sensitivity. Further studies showed that DmDuox and A. oryzifermentans regulated P450 gene expression and enzyme activity. These findings demonstrate that A. oryzifermentans protects DmDuox-deficient D. melanogaster from impaired detoxification and enriches the mechanism underlying the host-symbiont synergistic response to xenobiotic toxins.},
}

@article {pmid41342927,
year = {2025},
author = {Vaessen, L and Russ, K and Kirchmair, M and Neuhauser, S and Schlick-Steiner, BC and Steiner, FM},
title = {How carton-nest fungi of the ant Lasius fuliginosus interact with each other and with the root-rot fungus Armillaria mellea.},
journal = {Mycologia},
volume = {},
number = {},
pages = {1-9},
doi = {10.1080/00275514.2025.2568230},
pmid = {41342927},
issn = {1557-2536},
abstract = {Lasius fuliginosus, a fungus-growing ant species distributed across Europe, hosts various fungi inside its carton nests in trees, including the nest fungus SP1 of the order Chaetothyriales, as well as the nest fungi SP5 and SP4 of the order Venturiales. The goal of this study was to gain a better understanding of the fungal interactions inside the L. fuliginosus nests as well as of potential interactions around the nests, including the effects of Armillaria mellea-a root-rot fungus infecting potential host trees. We performed two types of confrontation experiments on Petri dishes between the isolated nest fungi and A. mellea. Firstly, using de Wit experiments, we tested the fungal species in pairwise combinations at three different initial confrontation concentrations. Secondly, a linear confrontation setup focused on differences in directional growth of the fungal species in pairwise combinations as well as on the development of A. mellea rhizomorphs. For the fungi SP1, SP5, and SP4, we found positive influences on each other (SP1 on SP5, SP4 on SP1 and SP5, and SP5 on SP1) alongside no influence (SP1 on SP4, SP5 on SP4). SP1 had a significantly negative impact on the surface growth and directional growth of A. mellea, and SP5 triggered the strongest rhizomorph development of A. mellea, possibly a stress reaction of the root-rot fungus. Armillaria mellea did not negatively impact any of the nest fungi and even promoted the surface growth of SP1. The de Wit setup and the linear setup turned out to be complementary and together facilitated first insights into potential roles of the nest fungi in this association of ants and fungi in trees. Follow-up studies will need to assess how these findings under Petri dish conditions transfer to conditions in natural habitat, in the presence of both the ant and the tree host.},
}

@article {pmid41342399,
year = {2025},
author = {Xiang, T and Peak, SL and Huitt, EC and Grossman, AR},
title = {Distinct transcriptomic strategies underlie differential heat tolerance in Symbiodiniaceae symbionts.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf268},
pmid = {41342399},
issn = {1751-7370},
abstract = {Dinoflagellate algae in the family Symbiodiniaceae, symbionts of many marine cnidarians are critical for the metabolic integrity of reef ecosystems, which are increasingly threatened by environmental stress. The resilience of the cnidarian-dinoflagellate symbiosis depends on thermotolerance of the partner organisms; coral hosts that harbor heat-resistant symbionts exhibit greater resistance to bleaching. Although coral responses to heat stress are well-documented, transcriptomic adaptation/acclimation of Symbiodiniaceae to elevated temperatures are limited. Here, we compare thermal responses of two species representing two genera of Symbiodiniaceae, Symbiodinium linucheae (strain SSA01; ITS2 type A4) and Breviolum minutum (strain SSB01; ITS2 type B1). SSA01 in culture maintained photosynthetic function at elevated temperatures and mounted a rapid transcriptomic response characterized by early downregulation of a JMJ21-like histone demethylase coupled with prompt upregulation of transcripts associated with DNA repair and oxidative stress, which would likely contribute to enhanced resilience to heat stress. In contrast, SSB01 experienced a decline in photosynthetic efficiency and a delayed transcriptomic response that included upregulation of transcripts encoding proteasome subunits and reduced transcripts encoding proteins involved in photosynthesis and metabolite transport. These findings indicate that a rapid and moderate transcriptomic response that results in increased expression of genes related to the synthesis and repair of biomolecules might be crucial for thermal tolerance in the Symbiodiniaceae whereas sensitivity to elevated temperatures may be reflected by increased protein turnover and a marked decline in anabolic processes. Understanding these differences is vital for predicting coral responses to warming seas and developing strategies to mitigate heat-stress impacts on reefs.},
}

@article {pmid41342220,
year = {2025},
author = {Misaki, A and Suzuki, S and Maeno, S and Endo, A and Sasaki, Y and Enomoto, G and Yokota, K and Kajikawa, A},
title = {The response regulator FpsR controls the flagella-pili transition and mucosal colonization in Ligilactobacillus ruminis.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2596807},
doi = {10.1080/19490976.2025.2596807},
pmid = {41342220},
issn = {1949-0984},
mesh = {Animals ; *Flagella/genetics/metabolism/physiology ; Mice ; *Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; *Fimbriae, Bacterial/genetics/metabolism ; *Intestinal Mucosa/microbiology ; Flagellin/metabolism/genetics ; Toll-Like Receptor 5/metabolism/genetics ; Bacterial Adhesion ; Humans ; Female ; },
abstract = {Ligilactobacillus ruminis is a flagellated lactic acid bacterium found in the intestines of various mammals, including humans. Although this species harbors a complete flagellar gene cluster, flagella formation has not been observed in human-derived strains, and the underlying regulatory mechanisms remain unknown. Here, we isolated a motility-acquired mutant of L. ruminis ATCC 25644 that exhibited full flagellation and a measurable chemotactic response under acidic conditions (pH 3.0). Whole-genome sequencing revealed a ~35 kb deletion encompassing multiple regulatory genes. Functional complementation identified a single response regulator, designated FpsR (flagellation-piliation switchover regulator), as a central switch that suppresses flagella formation while promoting pilus expression. The motility-acquired mutant displayed reduced pilus production, diminished adhesion to murine intestinal mucus and fibronectin, and increased susceptibility to acid (pH 3.0) and bile (0.25-0.5%), resulting in a complete loss of intestinal colonization in a murine model. Furthermore, while flagellin from the motile strain activated TLR5 and induced proinflammatory responses comparable to those of pathogenic bacteria, no such inflammation was observed in vivo, likely due to the strain's colonization failure. These findings reveal FpsR as a previously unrecognized genetic mechanism that coordinates motility and mucosal colonization in a human commensal bacterium and provide insight into how flagella are regulated and silenced in the gut environment to support host-microbe symbiosis.},
}

Animals
*Flagella/genetics/metabolism/physiology
Mice
*Bacterial Proteins/genetics/metabolism
Gene Expression Regulation, Bacterial
*Fimbriae, Bacterial/genetics/metabolism
*Intestinal Mucosa/microbiology
Flagellin/metabolism/genetics
Toll-Like Receptor 5/metabolism/genetics
Bacterial Adhesion
Humans
Female

@article {pmid41341309,
year = {2025},
author = {Chang, OC and Lin, WY},
title = {Genotype-specific modulation of drought tolerance by arbuscular mycorrhizal symbiosis in foxtail millet.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1696600},
pmid = {41341309},
issn = {1664-462X},
abstract = {Drought stress is a major environmental factor limiting crop productivity. Arbuscular mycorrhizal fungi (AMF), as beneficial soil microbes, can improve plant growth and stress resilience; however, the effectiveness of this symbiosis is often influenced by the host plant's genetic background. In this study, we investigated the interaction between AM symbiosis and drought tolerance in two foxtail millet (Setaria italica) accessions with contrasting drought responses: the drought-tolerant ISE42 and the drought-sensitive TT8. Following a 14-day drought treatment, both accessions exhibited wilting, but AMF-colonized plants reduced malondialdehyde accumulation, indicating alleviated oxidative stress. Notably, only colonized ISE42 plants recovered upon rewatering. Although AMF colonization was confirmed by staining and qRT-PCR, AM symbiosis-conserved genes were strongly induced in ISE42 and TT8 only at 7 days post-treatment. Transcriptomic analysis further revealed that AM symbiosis significantly enhanced the expression of genes involved in nitrogen transport, assimilation, lignin metabolism, and cellulose biosynthesis in ISE42, suggesting improved nutrient uptake and cell wall reinforcement as key mechanisms underlying enhanced drought tolerance. In addition, drought-induced stress hormone signaling pathways were downregulated in colonized ISE42 roots, pointing to AM symbiosis-mediated stress alleviation. Together, these results demonstrate genotype-specific effects of AMF on drought tolerance and recovery capability, and highlight the importance of considering host genetic variation in the application of AMF for crop improvement.},
}

@article {pmid41341062,
year = {2025},
author = {Tan, EX and Nguyen, LBT and Jin, Y and Lv, Y and Phang, IY and Ling, XY},
title = {SERS Cheminformatics: Opportunities for Data-Driven Discovery and Applications.},
journal = {ACS central science},
volume = {11},
number = {11},
pages = {2034-2052},
pmid = {41341062},
issn = {2374-7943},
abstract = {Surface-enhanced Raman scattering (SERS) is a powerful analytical technique offering ultrasensitive, nondestructive molecular fingerprinting. However, challenges such as spectral overlap, noise, and signal variability, especially in complex mixtures, limit its reliability and reproducibility. With increasing volumes of complex SERS data, there is a pressing need for advanced tools to manage and interpret this information. Cheminformatics amalgamates chemical knowledge with computational methods to deliver solutions for spectral preprocessing, database management, molecular modeling, pattern recognition, and multimodal data integration. This Outlook presents a vision for uniting SERS and cheminformatics to enhance the reliability of (bio)-chemical analysis and discovery. We propose a conceptual framework built upon four interconnected pillars: (1) centralized SERS databases, (2) molecular modeling for mechanistic insights, (3) machine learning (ML) for spectral analysis, and (4) automation and artificial intelligence for expanding the SERS chemical space. Together, these four pillars form a dynamic, feedback-driven system that enhances interpretability, accelerates data-driven discovery, and facilitates real-time SERS analysis. The symbiotic relationship between SERS and cheminformatics positions this integration at the forefront of data-driven chemical research with transformative applications in materials science, catalysis, biomedical diagnostics, and environmental monitoring.},
}

@article {pmid41340927,
year = {2025},
author = {Samuel David, AV and María Del Rocío, PR},
title = {Termites and their gut microbiome in animal nutrition: Advances and biotechnological applications.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {23},
number = {},
pages = {527-534},
pmid = {41340927},
issn = {2405-6383},
abstract = {Since the late 20th century, termites have attracted attention due to the vast potential of their gut microbiome and digestive enzymes, which enable them to efficiently degrade lignocellulosic biomass, making them a promising resource for animal nutrition, particularly for recovering fibrous waste. Termite gastrointestinal symbionts and enzymes are highly effective at decomposing plant fiber, thus positioning them as natural bioreactors with significant biotechnological potential. This review examines the evolving applications of termites in animal feed, including their incorporation as protein sources in diets for monogastric animals and fish, as well as the utilization of bacteria, fungi, and enzymes derived from their guts as additives to enhance the digestibility of agricultural byproducts in both ruminants and non-ruminants. Furthermore, recent developments have demonstrated the identification and heterologous expression of lignocellulolytic enzymes and metabolites with prebiotic and detoxifying properties. The diversity of termite species offers an exceptional source of microbial communities. These communities highly adaptable to various fibrous substrates due to their diet, which enhances their potential despite existing limitations in cultivation and process standardization. However, their gut microbiota remains an untapped resource with immense potential to improve feed efficiency, promote sustainability, and reduce reliance on conventional inputs. It is concluded that at larger scale in vivo studies are needed to fully realize the potential of these symbiotic systems in animal nutrition.},
}

@article {pmid41338748,
year = {2025},
author = {Zeng, Y and Shen, Z and Cao, Y and Luo, X and Yang, L and Lu, Q and Li, R},
title = {Deciphering the regulatory mechanisms of color formation in Naematelia sinensis fruiting bodies through multi-omics approaches.},
journal = {Fungal biology},
volume = {129},
number = {8},
pages = {101667},
doi = {10.1016/j.funbio.2025.101667},
pmid = {41338748},
issn = {1878-6146},
mesh = {*Fruiting Bodies, Fungal/genetics/metabolism ; *Pigments, Biological/metabolism ; Gene Expression Regulation, Fungal ; Transcriptome ; Metabolomics ; *Basidiomycota/genetics/metabolism ; *Agaricales/genetics/metabolism ; Gene Expression Profiling ; Metabolome ; Metabolic Networks and Pathways ; Color ; Multiomics ; },
abstract = {Naematelia sinensis fruiting bodies, a complex composed of Naematelia sinensis and Stereum hirsutum, exhibit unique characteristics due to the symbiosis of these two fungi and their distinct color features. However, the regulatory mechanisms underlying the coloration of N. sinensis fruiting bodies and the interactions between the two fungi remain poorly understood. In this study, we integrated transcriptomic and non-targeted metabolomic data from three variants of N. sinensis fruiting bodies-white fruiting bodies (control), yellow variant (treatment_1), and yellow fruiting bodies (treatment_2)-to investigate the relationship between the two fungi and color accumulation. Principal component analysis (PCA) revealed that the transcriptomic and metabolomic data showed overlap between control and treatment_1 but a clear separation from treatment_2, indicating the reliability of the data. Integrated analysis of the transcriptome and metabolome has unveiled key metabolic pathways associated with pigment accumulation in N. sinensis fruiting bodies. These pathways include the biosynthesis of cofactors, phenylalanine, tyrosine, and tryptophan, as well as the metabolism of tryptophan. In riboflavin metabolism, one gene (NAU27003364) was identified in N. sinensis, while three genes (STEHIDRAFT_95968, STEHIDRAFT_153579, and STEHIDRAFT_86958) were identified in S. hirsutum. The quantification of riboflavin and qRT-PCR results also indicated that most of them exhibited differences. This study represents the first multi-omics investigation into the functional pathways underlying color transformation in the fruiting bodies of N. sinensis, elucidating the regulatory interactions between N. sinensis and S. hirsutum. Our findings provide a theoretical foundation for understanding the molecular mechanisms of color transformation and the selective cultivation of fungal strains.},
}

*Fruiting Bodies, Fungal/genetics/metabolism
*Pigments, Biological/metabolism
Gene Expression Regulation, Fungal
Transcriptome
Metabolomics
*Basidiomycota/genetics/metabolism
*Agaricales/genetics/metabolism
Gene Expression Profiling
Metabolome
Metabolic Networks and Pathways
Color
Multiomics

@article {pmid41338345,
year = {2025},
author = {Dong, T and Cui, Y and Zhang, L and Yang, J and Yang, C and Qian, W and Peng, Y},
title = {Photocatalyst-driven microalgal-bacterial symbiosis enables organic carbon-free and energy-efficient nitrogen removal in a pilot-scale wastewater treatment.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133744},
doi = {10.1016/j.biortech.2025.133744},
pmid = {41338345},
issn = {1873-2976},
abstract = {The sustainability of simultaneous nitrification-denitrification (SND) is hindered by high aeration demands and external carbon input. Here, a g-C3N4-driven microalgal-bacterial symbiotic SND system was deployed in an 8 m[3] pilot-scale reactor for low-C/N practical wastewater. Photocatalyst-driven spatially structured bacterial-algal cooperation facilitated > 92.50 % total nitrogen removal, eliminating external carbon addition and reducing aeration energy by 38.10 %. Photocatalysis selectively enriched phototrophic Sphingomonadaceae, boosting EPS secretion by 2.77-2.99-fold. The resulting adhesive, oxygen-diffusion-limiting EPS matrix immobilized g-C3N4 and supported stratified biofilms hosting anaerobic denitrifiers, phototrophs, and microalgae. Oxygenic microalgae colonized the aerobic exterior, whereas denitrifiers occupied the anoxic core, mitigating oxygen-induced antagonism. Furthermore, photocatalysis potentially shifted algal metabolism to preferentially assimilate ammonium over nitrate, minimizing substrate competition with denitrifiers. This algal-bacterial synergy supported nitrification via algal oxygen. Meanwhile, denitrifiers, fueled exclusively by photogenerated electrons, activated narGHI and the tricarboxylic acid (TCA) cycle to enable organic carbon-independent nitrogen removal.},
}

@article {pmid41338199,
year = {2025},
author = {Yamada, T and Palm, NW},
title = {A host-centric view of the microbiota metabolome.},
journal = {Immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.immuni.2025.11.006},
pmid = {41338199},
issn = {1097-4180},
abstract = {Host-associated microbes produce thousands of metabolites that influence diverse aspects of mammalian physiology, including the immune system. However, the organizing principles governing these interactions remain largely unclear. Here, we propose a host-centric teleological framework for classifying microbiota metabolites based on their impacts on host biology and co-evolutionary principles of host-microbiota symbiosis. We outline three broad functional categories of metabolite-mediated impacts on the host-niche expansion, perception, and (maladaptive) noise. We then discuss transitions between these categories over short and long-term timescales and define specific microbial features that may influence these transitions. Finally, because most microbial metabolites remain uncharacterized, we review approaches to discover novel bioactive microbial metabolites with a view toward comprehensive mapping of small molecule-mediated host-microbe interactions.},
}

@article {pmid41337959,
year = {2025},
author = {Dong, D and Xie, Z and Wang, B and Ou, W and Tang, Y and Yang, J and Guo, Y and Fa, X},
title = {Effects of a forage-native multi-PGPM consortium symbiotic system on rhizosphere ecology and microbial regulation for remediating PAHs-contaminated very-high-altitude coal mines.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140653},
doi = {10.1016/j.jhazmat.2025.140653},
pmid = {41337959},
issn = {1873-3336},
abstract = {The very-high-altitude coal mines face polycyclic aromatic hydrocarbons (PAHs) pollution, yet studies on microbial degradation of PAHs in this region remain scarce. In this study, a native multi-plant growth-promoting microorganism consortium (N-M-PGPM-C, comprising four Tibetan Plateau strains: Trichoderma, Bacillus, Pseudomonas, and Floccularia luteovirens) was constructed. Their effects on forage growth, PAHs degradation, rhizosphere microbes, and soil metabolites were systematically investigated via high-throughput sequencing and LC-MS/MS metabolomics. The results showed that the N-M-PGPM-C significantly improved forage growth (93.81 %-120.05 % increase in dry weight compared to single PGPM treatment), degraded aromatic compounds in the rhizosphere soil, and enriched seven plant-beneficial microorganisms (e.g., Lysinibacillus, Solibacillus). In addition, it promoted the colonization and proliferation of two strains from the N-M-PGPM-C (i.e., Trichoderma by 3.20-fold and Bacillus by 9.41-fold) by reshaping the rhizosphere microbial community. According to the metabolomic analysis, the N-M-PGPM-C modulated 114 metabolites, enriching pathways for bisphenol, toluene, and benzoate degradation. The metabolite 2'-deoxyguanosine was strongly correlated with the enrichment of seven plant-beneficial microorganisms such as Lysinibacillus and Solibacillus and synergized with Trichoderma and Bacillus. Laboratory validations confirmed that Trichoderma and Bacillus possess intrinsic PAH-degrading capabilities, and exogenous application of 2'-deoxyguanosine significantly alleviated PAH stress in forages. These findings reveal the mechanism by which the N-M-PGPM-C remediates PAH contamination through the forage- native multi-PGPM consortium symbiotic system, providing a promising strategy for ecological restoration in the very-high-altitude regions.},
}

@article {pmid41334814,
year = {2025},
author = {López-Gutiérrez, JC and López-Hernández, D and Toro, M},
title = {Arbuscular Mycorrhizal Fungi and Phosphorus-mobilizing Microorganisms Mediate Organic Phosphorus Cycling in Tropical Savanna Soils.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf135},
pmid = {41334814},
issn = {1574-6968},
abstract = {In highly weathered tropical soils, organic phosphorus (Po) constitutes a primordial reservoir for plant P-nutrition. We studied the dynamics of Po fractions, soil phosphatase activity and P-mobilizing microflora in root compartments of non-mycorrhizal (rhizosphere and bulk soil) and mycorrhizal (mycorrhizosphere and hyphosphere) Urochloa brizantha plants growing in rhizoboxes with a low P-sorbing Entisol and a high P-sorbing Ultisol from native neotropical savannas. Inoculation with native arbuscular mycorrhizal fungi resulted in an improvement in plant P-status, particularly in the high P-sorbing soil, that coincided with transformations in more recalcitrant P fractions, a higher phosphatase activity and a higher proportion of P-solubilizing and P-mineralizing organisms in mycorrhizal compartments. We provide evidence for a mycorrhizospheric effect in low P-fertility soils that allows plants to access specific P-pools via symbiosis with arbuscular mycorrhizal fungi.},
}

@article {pmid41333292,
year = {2025},
author = {Turudu, V and Kutlu, I and Gulmezoglu, N},
title = {Biochemical and molecular responses of maize to low and high temperatures in symbiosis with mixed arbuscular mycorrhizal fungi cultures.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20419},
pmid = {41333292},
issn = {2167-8359},
mesh = {*Zea mays/microbiology/metabolism/genetics/physiology ; *Mycorrhizae/physiology ; *Symbiosis/physiology ; *Hot Temperature ; Lipid Peroxidation ; *Cold Temperature ; Temperature ; Plant Proteins/metabolism/genetics ; Minerals/metabolism ; },
abstract = {In this study, changes in mineral element concentrations, physiological parameters, and gene expression of heat shock proteins were investigated in maize plants subjected to mycorrhiza under low and high temperature stress. The application of seven different temperatures (5 °C, 10 °C, 15 °C, 25 °C, 35 °C, 40 °C, and 45 °C) under five different mixed arbuscular mycorrhizal fungi (AMF) culture treatments (M0, M1, M2, M3, and M4) constituted the factors of the experiment. With the application of mycorrhiza, the plant dry weight was found to be the highest at 25 °C, and the M3 group was applied. The highest values in mineral element concentrations were detected at 25 °C in the maize plant, where M4 had N, P, K, Ca, and Fe concentrations; M3 had Cu and Mn concentrations; and M2 had Mg and Zn concentrations. Lipid peroxidation gradually increased with temperature changes in all the applications, and the protective effect of proline was more pronounced at high temperatures than at low temperatures. Antioxidant enzyme activities were altered by applications of mycorrhiza and temperature. For all mycorrhiza applications, the expression of HSP70 and HSP90 reached a maximum at 10 °C, 40 °C, and 45 °C. It has been revealed that low- and high-temperature applications in maize plants cause serious changes in the mycorrhizal symbiosis on the basis of investigated parameters, and these changes occur at different levels depending on the temperature changes and the differences between mixed AMF cultures. However, it can be said that the M3 application has the capacity to facilitate the growth of maize even in conditions of low (-10 °C) and high (45 °C) temperature.},
}

*Zea mays/microbiology/metabolism/genetics/physiology
*Mycorrhizae/physiology
*Symbiosis/physiology
*Hot Temperature
Lipid Peroxidation
*Cold Temperature
Temperature
Plant Proteins/metabolism/genetics
Minerals/metabolism

@article {pmid41331913,
year = {2025},
author = {Jannesar, M and Bassami, B and Dalir, G and Sheikhzadeh, S and Tabrizchi, J and Seyedi, SM},
title = {Rice miRNA-mediated trans-kingdom gene regulation in pathogenic and symbiotic fungal interactions.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-025-12386-z},
pmid = {41331913},
issn = {1471-2164},
}

@article {pmid41331875,
year = {2025},
author = {Kong, L and Mao, Y and Zheng, R and Feng, Y and Chen, B and Wu, X and Zhu, Q and Feng, J and Liu, S},
title = {Overlooked siderophore producers favor ammonium oxidation in global wastewater treatment plants.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02290-9},
pmid = {41331875},
issn = {2049-2618},
support = {523B2095//National Natural Science Foundation of China/ ; Nos. 52270016//National Natural Science Foundation of China/ ; 2022YFC3203003//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Iron is essential for biological nitrogen removal in wastewater treatment plants (WWTPs), as a significant portion of microbial nitrogen-transforming enzymes require iron. However, iron bioavailability is a global challenge for nitrogen removal microbes in WWTPs, where it often exists in insoluble forms due to its complexation with various wastewater constituents.

RESULTS: Combined laboratory experiment and metagenomic analysis of 52 global WWTPs, we found that siderophore-producing bacteria (SPB) were previously uncharacterized dominant members in activated sludge. SPB enhance the iron uptake of activated sludge microbial communities by facilitating the transport of iron ions from insoluble sources into the cells. Of the 1328 total recovered metagenome-assembled genomes (MAGs) from global WWTPs, 6.2% were identified as SPB, while 79.3% of MAGs could utilize siderophores, indicating widespread sharing of siderophores in WWTPs. Interestingly, nearly all ammonium-oxidizing bacteria (AOB) from WWTPs lacked siderophore-producing capacity, and exogenous siderophore (20 µM pyochelin) addition boosted ammonium oxidation rates by 28.2%. Moreover, strong indications were found for an association between AOB and the SPB in global WWTPs, suggesting their symbiotic interaction is a common and critical process to maintain ammonium oxidation performance. SPB in WWTPs were predominantly aerobic or facultative anaerobic heterotrophic bacteria, exhibiting low taxonomic diversity but high abundance.

CONCLUSIONS: This study reveals SPB as previously overlooked but crucial contributors to biological nitrogen removal in global WWTPs, providing foundational insights into iron-based microbial cooperation within engineered systems. Modulating SPB activity based on their metabolic characteristics is a promising strategy to cope with low iron bioavailability issue for biological processes in WWTPs. Video Abstract.},
}

@article {pmid41331684,
year = {2025},
author = {Núñez-Pons, L and Cusano, LM and Chiarore, A and Mirasole, A and Teixidó, N and Efremova, J and Mazzella, V},
title = {Too hot for my bugs: mediterranean heatwave disrupts associated microbiomes in the sponge Petrosia ficiformis.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00830-2},
pmid = {41331684},
issn = {2524-6372},
support = {CN_00000033//National Biodiversity Future Center - NBFC/ ; CN_00000033//National Biodiversity Future Center - NBFC/ ; P05//EuroMarine-EMBRC 2020 call/ ; },
abstract = {BACKGROUND: Global climate change exacerbates the incidence of marine heatwaves (MHWs), which have increased in intensity and frequency over the past years, causing severe impacts on marine coastal ecosystems. MHWs have already triggered mass mortalities of habitat-forming species, including corals, sponges and gorgonians, in temperate, tropical and polar seas. In the Mediterranean, these high peaks of temperature have been shown to affect several sponge species, and likely, their symbiotic microbial communities. During the summer of 2022, populations of the sponge Petrosia ficiformis (Poiret, 1789) were conspicuously observed with signs of thermal stress linked to a MHW around the Gulf of Naples (Tyrrhenian Sea, Italy). These included depigmentation spots and tissue texture alterations, which often evolved in necrotic processes and eventual death. At the peak of the MHW, however, apparently thermoresistant sponges co-occurred with sensitive unhealthy specimens. In order to explore potential microbial drivers correlated with these divergent thermal-stress tolerances, Healthy and Unhealthy individuals were sampled along the coast of Ischia Island in early September 2022.

RESULTS: Prokaryotic community characterization based on the 16 S rRNA gene revealed dissimilar compositions in Unhealthy versus apparently Healthy sponges. Increased alpha diversity richness and low evenness in thermosensitive sponges were due to an extensive presence of rare taxa, and to the introduction of potentially pathogenic groups (e.g., Vibrio spp.). Major microbial families regularly associated with P. ficiformis - SAR202, Caldilineaceae, Poribacteria or TK17, were replaced in thermosensitive specimens by professed opportunistic groups within Lentimicrobiaceae, Rhodobacteraceae or Flavobacteriaceae. In turn, conservancy of hub microbes and thermotolerant symbionts (e.g., Rhodothermaceae, Thermoanaerobaculaceae) in Healthy sponges were observed during this disrupting event. Unhealthy microbiomes reflected lower network stability with respect to Healthy holobionts, due to the inconsistency of functional keystone taxa and prevalence of transient microbes.

CONCLUSIONS: Dysbiotic shifts due to colonization of scavenger groups and opportunistic microbes, and interconnectivity loss characterized thermally stressed sponges. In contrast, resistant specimens retained keystone symbionts that could have ensured functional cooperation, and maintenance of prokaryotic community cohesion under thermal stress. The existence of stress-resistant phenotypes in sponge holobionts offers a glimmer of hope for species persistence, and their study may identify potential source populations for ecosystem recovery.},
}

@article {pmid41331417,
year = {2025},
author = {Fiege, K and Asbun, AA and Boeren, S and Engelmann, JC and Villanueva, L},
title = {Membrane changes during syntrophic interactions of an archaeal-bacterial coculture.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04509-z},
pmid = {41331417},
issn = {1471-2180},
support = {735929LPI//Moore-Simons Project on the Origin of the Eukaryotic Cell/ ; 735929LPI//Moore-Simons Project on the Origin of the Eukaryotic Cell/ ; 024.002.002//Soehngen Institute for Anaerobic Microbiology (SIAM)/ ; 024.002.002//Soehngen Institute for Anaerobic Microbiology (SIAM)/ ; },
abstract = {Syntrophic interactions between bacteria and archaea are vital for anaerobic processes, relying on close cell-to-cell contact for efficient metabolite and electron transfer. Membrane-associated proteins and lipids likely play key roles in stabilizing these contacts, though little is known about membrane changes during syntrophy. These interactions are also central to theories of eukaryogenesis, where a symbiosis between an archaeal host - likely an Asgard archaeon - and a bacterial partner may have arisen from prior syntrophic interactions. Model systems of syntrophic microbes provide valuable insights into how such intimate associations could have led to the emergence of eukaryotic life. Here, we used syntrophic cocultures of the sulfate-reducing bacterium Desulfovibrio vulgaris and the methanogenic archaeon Methanococcus maripaludis to investigate membrane changes during a syntrophic interaction involving cell-to-cell contact. Evolved cocultures after several generations under syntrophic conditions were analyzed by proteomics and transcriptomics to identify differentially expressed proteins connected to cell-to-cell interactions, as well as by lipid analyses to determine changes in the cell membrane of both syntrophic partners. These data suggest a higher impact on the archaeon M. maripaludis, affecting transmembrane, signaling, and lipid biosynthesis proteins. To investigate the impact of evolutionary adaptation, both partners were re-isolated from a non-evolved ancestral coculture (coculture after mixing species), as well as from evolved (several generations) cocultures. While lipid profiles had changed in the coculture due to evolutionary adaptation, isolates were found to revert their lipid composition to the wildtype profile when growing independent again. This in-depth analysis of a model syntrophic coculture provides clues on how interdomain cell-to-cell interactions might have led to membrane changes during early eukaryogenesis.},
}

@article {pmid41330321,
year = {2025},
author = {McMillan, CK},
title = {Climate change: Nitrogen fixing trees contribute to permafrost thaw.},
journal = {Current biology : CB},
volume = {35},
number = {23},
pages = {R1149-R1151},
doi = {10.1016/j.cub.2025.10.057},
pmid = {41330321},
issn = {1879-0445},
mesh = {*Permafrost ; *Climate Change ; *Nitrogen Fixation/physiology ; Symbiosis ; Arctic Regions ; Root Nodules, Plant/physiology/microbiology ; Tundra ; },
abstract = {Siberian alder (Alnus hirsuta) is expanding into Arctic tundra, and a new study shows it can heat permafrost through symbiotic nitrogen-fixing root nodules. This discovery introduces a biologically mediated feedback in which plant-microbe partnerships actively engineer soil thermal balance.},
}

*Permafrost
*Climate Change
*Nitrogen Fixation/physiology
Symbiosis
Arctic Regions
Root Nodules, Plant/physiology/microbiology
Tundra

@article {pmid41329233,
year = {2025},
author = {Guarino, M and Di Ciaula, A and Portincasa, P and De Giorgio, R},
title = {Narrative review on microbiota and sepsis: the host's betrayal?.},
journal = {Internal and emergency medicine},
volume = {},
number = {},
pages = {},
pmid = {41329233},
issn = {1970-9366},
abstract = {Sepsis remains a leading cause of morbidity and mortality worldwide. Increasing evidence suggests that the gut microbiota, long considered a "less relevant" to human body health, it plays a crucial role in the pathophysiology of sepsis. Disruption of the host-microbe balance contributes to impaired barrier integrity, microbial translocation, and dysregulated immune responses. This perspective raises the possibility that dysbiosis is not merely a consequence of critical illness, rather an active driver of septic progression. This narrative review explores the relationship between sepsis and gut microbiome. PubMed, Scopus, and EMBASE were searched from inception to September 2025. Recent studies have highlighted the triangular interplay between the intestinal barrier, gut microbiota, and immune system. Altered microbial composition and increased permeability foster systemic inflammation and immune dysfunction. Biomarkers such as diamine oxidase and intestinal fatty acid-binding protein are emerging as promising indicators of gut injury. Experimental therapies (i.e., faecal microbiota transplantation, targeted probiotics, prebiotics, postbiotics, and personalized antibiotic regimens guided by microbial profiling) provide potential to modulate host-microbe interactions. Integration of microbiome analysis with multi-omics and advanced bioinformatics may enable stratification of septic patients by microbial signatures, paving the way for precision medicine approaches. Modulation of gut microbiota represents a novel therapeutic frontier in sepsis. Conceptualizing sepsis as a disease of disrupted host-microbe symbiosis may unravel new diagnostic and therapeutic strategies. Future research should aim at prioritizing high-quality trials, innovative designs, and equitable implementation to target microbiota to improve survival and recovery in patients with sepsis.},
}

@article {pmid41328923,
year = {2025},
author = {Cazalé, A-C and Navarro, M and Doin de Moura, GG and Hoarau, D and Bellvert, F and Valière, S and Baroukh, C and Remigi, P and Guidot, A and Capela, D},
title = {Disruption of putrescine export in experimentally evolved Ralstonia pseudosolanacearum enhances symbiosis with Mimosa pudica.},
journal = {mBio},
volume = {},
number = {},
pages = {e0122525},
doi = {10.1128/mbio.01225-25},
pmid = {41328923},
issn = {2150-7511},
abstract = {Polyamines are essential molecules across all domains of life, but their role as signaling molecules in host-microbe interactions is increasingly recognized. However, because they are produced by both the host and the microbe, their dual origin makes their functional dissection challenging. The plant pathogen Ralstonia pseudosolanacearum GMI1000 secretes large amounts of putrescine both in vitro and in the xylem sap of host plants. In this study, we investigated the genetic changes underlying its experimental evolution into a legume symbiont. We showed that the paeA gene (RSc2277), which was repeatedly mutated during this process, encodes a putrescine exporter. Mutations in paeA completely abolished putrescine excretion in vitro and enhanced bacterial proliferation within nodules during interaction with the legume Mimosa pudica. When these mutations occurred in symbionts already capable of intracellular infection, they further increased bacterial load in nodules and allowed the detection of nitrogenase activity. In addition, paeA-mutated symbionts modulated host gene expression toward a more functional symbiotic state by repressing defense-related genes and inducing nodule development genes. These nodule development genes include genes encoding leghemoglobins and an arginine decarboxylase, a key enzyme in plant putrescine biosynthesis. These results indicate that bacterial and plant putrescine have distinct functions in legume symbiosis and highlight the complex role of polyamines in plant-microbe interactions.IMPORTANCERhizobia, the nitrogen-fixing symbionts of legumes, emerged through repeated and independent horizontal transfers of some essential symbiotic genes. However, these transfers alone are often insufficient to convert the recipient bacterium into a functional legume symbiont. In a laboratory experiment, we evolved the plant pathogen Ralstonia pseudosolanacearum into a nodulating and intracellularly infecting symbiont of Mimosa pudica. This transition required genomic modifications in the recipient bacterium to activate its acquired symbiotic potential. Here, we demonstrated that one of these key adaptive modifications is the inactivation of bacterial putrescine export. This polyamine, when produced by the microsymbiont, appears to act as a negative signal for the plant. This study provides new insights into the distinct roles of bacterial- and plant-derived putrescine in plant-microbe interactions, highlighting their functional divergence despite being produced by both organisms.},
}

@article {pmid41327776,
year = {2025},
author = {Sokolova, IM and Sokolov, EP and Piontkivska, H and Timm, S and Amorim, K and Zettler, ML},
title = {Unravelling Hypoxia Tolerance: Transcriptomic and Metabolic Insights From Lucinoma capensis in an Oxygen Minimum Zone.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70194},
doi = {10.1111/mec.70194},
pmid = {41327776},
issn = {1365-294X},
support = {03V01279//Bundesministerium für Bildung und Forschung/ ; GZ INST 264/125-1FUGG//Hochschul-Bau-Förderungsgesetz/ ; //Mare Balticum Fellowship, Universität Rostock/ ; RPIV00812019//National Commission on Research, Science and Technology/ ; },
abstract = {The lucinid clam Lucinoma capensis thrives at the oxygen minimum zone margins in the Benguela Upwelling System, where oxygen levels fluctuate dramatically. Understanding its adaptation to such extreme conditions provides key insights into survival strategies under fluctuating oxygen availability. We investigated the transcriptomic and metabolomic responses of L. capensis under normoxia, hypoxia, and recovery, focusing on the gills and digestive gland. Our findings highlight distinct organ-specific responses, with the gills showing strong transcriptional changes to oxygen fluctuations, in contrast to the more stable profile observed in the digestive gland. Under hypoxic conditions, the gills exhibited coordinated downregulation of protein synthesis, transposable element activity, and immune function, suggesting a tightly regulated energy conservation strategy and mechanisms to preserve symbiont stability and genomic integrity. Activation of prokaryotic metabolism in the gills supports the symbionts' role in host energy acquisition and sulfide detoxification during hypoxia. In contrast, the digestive gland showed minimal transcriptional shifts during anoxia, with upregulation of pathways supporting structural maintenance. Upon reoxygenation, the gills displayed an active and asymmetric recovery, characterised by rapid restoration of protein synthesis and gradual normalisation of protein degradation and immune functions. Despite significant transcriptomic changes, the metabolome remained largely stable, reflecting L. capensis's resilience to oxygen fluctuations. However, an overshoot in TCA cycle intermediates and derepression of previously downregulated pathways indicate that reoxygenation involves active metabolic reprogramming, not merely a return to baseline. This study highlights the specialised tissue responses and symbiotic contributions that enable L. capensis to thrive in one of the ocean's most challenging environments.},
}

@article {pmid41326395,
year = {2025},
author = {Zhao, L and Sun, Y and Ren, J and Gao, H and Xiao, G},
title = {Construction of waste-to-resource knowledge graph for industrial symbiosis identification using large language models.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66599-7},
pmid = {41326395},
issn = {2041-1723},
support = {RG10/23//Ministry of Education - Singapore (MOE)/ ; },
abstract = {Circular Economy offers a promising approach to achieve sustainability goals by circulating resources and closing resource loops. Industrial Symbiosis adopts similar concept in industrial systems that reduces raw material consumption and waste production through collaborative waste-to-resource exchanges. While waste-to-resource databases provide valuable knowledge for IS opportunity identification, existing databases are mainly constructed manually and are restricted by their sizes and scalability. In this work, we propose an automated framework to construct a Waste-to-Resource Knowledge Graph (W2RKG) from pertinent research papers using Large Language Models, which enhances coverage, scalability, and standardisation of the resulting database. The framework comprises a Retrieving Module, an Extraction Module, and a Fusion Module, that collectively transform unstructured text into a well-organised knowledge graph. The final constructed database contains 3518 waste entities, 4471 resource entities and 33,679 waste-to-resource relationships. Extensive experiments and evaluation results demonstrate the efficacy of the proposed method and the overall high quality of the constructed database. The study, thereby, contributes an automatic framework for waste-to-resource database construction and provides a readily accessible W2RKG to support Industrial Symbiosis practitioners in identification applications.},
}

@article {pmid41326106,
year = {2026},
author = {Chantab, K and Rao, Z and Zheng, X and Ngamhui, N and Han, R and Cao, L},
title = {Ascaroside-mediated modulation of host microbiota and survival in galleria mellonella by symbiotic bacteria of entomopathogenic nematode.},
journal = {Pesticide biochemistry and physiology},
volume = {216},
number = {Pt 1},
pages = {106744},
doi = {10.1016/j.pestbp.2025.106744},
pmid = {41326106},
issn = {1095-9939},
mesh = {Animals ; Symbiosis ; *Moths/microbiology/drug effects ; Larva/microbiology/drug effects ; Photorhabdus/physiology ; Gastrointestinal Microbiome/drug effects ; *Nematoda ; *Microbiota/drug effects ; Hemolymph/microbiology ; Bacteria ; Quorum Sensing/drug effects ; },
abstract = {Microbial symbionts and host pheromones are recognized as important mediators in the interactions between insect and entomopathogenic nematodes (EPNs). However, the influence of EPN-derived ascarosides and associated symbiotic bacteria on the insect's microbial community remains poorly understood. In this study, Galleria mellonella larvae were injected with nematode ascarosides (ascr#9 and ascr#11) and/or symbiotic bacteria (Photorhabdus luminescens) to investigate changes in the bacterial communities of larval haemolymph and gut. The result showed that the haemolymph was dominated by Gammaproteobacteria and Bacteroidia, while the gut microbiota was enriched with Bacilli. Burkholderiaceae and Enterococcaceae were the predominant families in the haemolymph and gut, respectively. Significant differences in bacterial community composition were observed across treatments. Notably, co-injection of ascarosides and P. luminescens significantly reduced the bacterial abundance of Ralstonia (commensal bacteria) and Photorhabdus (invader bacteria). The co-injection with ascarosides and symbiotic bacteria significantly contributed to prolonged host survival and sustained physiological stability compared to being exposed to bacteria alone. Mechanistically, ascarosides selectively upregulated the quorum sensing gene luxD in P. luminescens, suggesting that nematode pheromones modulate bacterial communication and collective behavior to regulate population dynamics. These findings indicate that ascarosides function as key microbial modulators, suppressing harmful bacterial growth and fostering a balanced community that supports host viability.},
}

Animals
Symbiosis
*Moths/microbiology/drug effects
Larva/microbiology/drug effects
Photorhabdus/physiology
Gastrointestinal Microbiome/drug effects
*Nematoda
*Microbiota/drug effects
Hemolymph/microbiology
Bacteria
Quorum Sensing/drug effects

@article {pmid41326105,
year = {2026},
author = {Li, S and Li, S and Yang, D and Wen, C and Wen, J},
title = {Wolbachia-mediated regulation of EscrGST1 modulates pesticide resistance in Eucryptorrhynchus scrobiculatus.},
journal = {Pesticide biochemistry and physiology},
volume = {216},
number = {Pt 1},
pages = {106743},
doi = {10.1016/j.pestbp.2025.106743},
pmid = {41326105},
issn = {1095-9939},
mesh = {Animals ; *Wolbachia/physiology/drug effects ; Neonicotinoids/pharmacology ; *Insecticides/pharmacology ; *Insecticide Resistance/genetics ; *Insect Proteins/genetics/metabolism ; *Weevils/microbiology/drug effects/genetics ; Pyrethrins/pharmacology ; Cytochrome P-450 Enzyme System/metabolism/genetics ; Nitro Compounds/pharmacology ; Glutathione Transferase/metabolism/genetics ; Symbiosis ; RNA Interference ; Tetracycline/pharmacology ; },
abstract = {Wolbachia, a maternally transmitted intracellular symbiont widely distributed in arthropods, regulates diverse host functions including detoxification. Eucryptorrhynchus scrobiculatus Motschulsky (Coleoptera: Curculionidae) as a specialist borer pest of Ailanthus altissima (Mill.) Swingle, it exclusively damages the host tree through larval boring and adult supplemental feeding, constituting a major wood-boring insect in China's forestry ecosystems. This study investigated the role of Wolbachia in modulating the detoxification capacity of E. scrobiculatus. Fluorescence in situ hybridization (FISH) and quantitative PCR (qPCR) analyses demonstrated that 21-day tetracycline treatment (15 mg/mL) effectively eliminated Wolbachia (99.96 % reduction). Compared to symbiotic controls, Wolbachia-depleted weevils exhibited significantly reduced activities of cytochrome P450 monooxygenases (P450) and glutathione S-transferase (GST), while carboxylesterase (CES) activity increased. Subsequently, transcriptomic analysis further revealed that Wolbachia-depleted weevils exhibited diminished expression of the detoxification gene EscrGST1 and reduced tolerance to the insecticides imidacloprid and cypermethrin. RNA interference (RNAi) silencing of EscrGST1 induced a compensatory increase in Wolbachia abundance during gene suppression, demonstrating a bidirectional regulatory mechanism between symbiont dynamics and host detoxification pathways. These findings demonstrate that Wolbachia mediates pesticide resistance in E. scrobiculatus by modulating EscrGST1 activity, providing novel strategies for controlling E. scrobiculatus, and offering new perspectives for developing pest control approaches through targeted disruption of symbiotic relationships.},
}

Animals
*Wolbachia/physiology/drug effects
Neonicotinoids/pharmacology
*Insecticides/pharmacology
*Insecticide Resistance/genetics
*Insect Proteins/genetics/metabolism
*Weevils/microbiology/drug effects/genetics
Pyrethrins/pharmacology
Cytochrome P-450 Enzyme System/metabolism/genetics
Nitro Compounds/pharmacology
Glutathione Transferase/metabolism/genetics
Symbiosis
RNA Interference
Tetracycline/pharmacology

@article {pmid41324084,
year = {2025},
author = {Zheng, P and Ding, P and Gao, WZ and Chen, X and Shi, L},
title = {The Jarman-Bell principle revisited: Gut microbiota facilitate body size-dependent nutritional strategies in herbivores.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100508},
pmid = {41324084},
issn = {2666-5174},
abstract = {Body size is a key determinant of nutritional strategies in herbivores, yet the role of gut microbiota in mediating these strategies remains insufficiently explored. To address this gap, we examined two sympatric ungulates of contrasting body sizes in an arid ecosystem-red deer (Cervus elaphus, large-bodied) and goitered gazelle (Gazella subgutturosa, small-bodied)-to test three predictions derived from the Jarman-Bell principle (JBP). We applied dietary DNA metabarcoding, plant nutritional profiling, and 16S rRNA sequencing of gut microbiota to assess how body size shapes macronutrient intake, microbial composition, and functional adaptations. Both species exhibited similar macronutrient ratios dominated by carbohydrates (∼88-90 %), supporting the nutritional balancing hypothesis. However, they differed in nutrient targets and microbial profiles: red deer consumed more non-structural carbohydrates and fats, with enriched gut microbial taxa (Paludibacter, Turicibacter) linked to energy metabolism, reflecting an energy maximization strategy. In contrast, goitered gazelles ingested more crude protein and harbored microbial taxa (Prevotella) associated with protein digestion, alongside immune-supporting microbes (Butyricicoccus, Coprococcus, and Victivallis), consistent with a protein maximization strategy. Red deer also demonstrated a greater microbial capacity for fiber degradation (Fibrobacter, Ruminococcus albus) and detoxification of plant secondary metabolites (Clostridium, Desulfovibrio, Prevotella, Variovorax). Functional pathway analysis revealed enrichment in lignocellulose and terpenoid metabolism, indicating an adaptation to low-quality forage. In contrast, goitered gazelles showed limited microbial associations with fiber or phytotoxin regulation, suggesting weaker microbial-mediated adaptation to low-quality diets. These results demonstrate that body size governs distinct nutritional strategies in sympatric herbivores, mediated through differential gut microbiota composition and function. Larger species, such as red deer, exhibit enhanced microbial capacity for fiber and toxin regulation, allowing them to utilize lower-quality forage more efficiently.},
}

@article {pmid41322278,
year = {2025},
author = {Hao, T and Su, H and Quan, Z and Zhang, R and Yu, M and Xu, J and Li, J and Li, S and Warren, A and Al-Farraj, SA and Yi, Z},
title = {Distinct evolutionary origins and mixed-mode transmissions of methanogenic endosymbionts are revealed in anaerobic ciliated protists.},
journal = {Marine life science & technology},
volume = {7},
number = {4},
pages = {700-716},
pmid = {41322278},
issn = {2662-1746},
abstract = {UNLABELLED: Methanogenic endosymbionts are the only known intracellular archaeans and are especially common in anaerobic ciliated protists. Studies on the evolution of associations between anaerobic ciliates and their methanogenic endosymbionts offer an excellent opportunity to broaden our knowledge about symbiosis theory and adaptation of eukaryotes to anoxic environments. Here, the diversity of methanogenic endosymbionts was analyzed with the addition of nine anaerobic ciliate populations that were newly studied by various methods. Results showed that diverse anaerobic ciliates host methanogenic endosymbionts that are limited to a few genera in orders Methanomicrobiales, Methanobacteriales, and Methanosarcinales. For the first time, anaerobic ciliates of the classes Muranotrichea and Prostomatea were found to host methanogenic endosymbionts. Distinct origins of endosymbiosis were revealed for classes Armophorea and Plagiopylea. We posit that armophoreans and plagiopyleans might have harbored Methanoregula (order Methanomicrobiales) and Methanocorpusculum (order Methanomicrobiales), respectively, as methanogenic endosymbionts at the beginning of their evolution. Subsequently, independent endosymbiont replacement events occurred in methanogen-ciliate associations, probably due to ecological transitions, species radiation of ciliate hosts, and vertical transmission bottlenecks of endosymbionts. Our results shed light on the evolution of associations between anaerobic ciliates and methanogens, and identifies the necessary preconditions for illustrating mechanisms by which endosymbioses between these partners were established.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00295-9.},
}

@article {pmid41322272,
year = {2025},
author = {Kim, JM and Choi, BJ and Bayburt, H and Lee, JK and Jeon, CO},
title = {Identifying potential keystone bacterial species within the phycosphere of marine algae and unveiling their metabolic characteristics.},
journal = {Marine life science & technology},
volume = {7},
number = {4},
pages = {989-1007},
pmid = {41322272},
issn = {2662-1746},
abstract = {UNLABELLED: Metabolic interactions between microbiomes and algal hosts within the phycosphere of marine macroalgae are drawing increasing attention due to their roles in food webs, global nutrient cycles, industries, and their potential as food resources. However, these relations remain poorly understood. In this study, 43 marine macroalgae, including red, brown, and green algae, were collected from the coastal areas of Korea. We identified the bacterial communities within the loosely and tightly attached environments (LAEs and TAEs, respectively) of the phycosphere, along with those in the surrounding seawater, using 16S rRNA gene sequencing. β-Diversity analysis revealed significant differences between the bacterial communities among the three, with minimal variation related to sampling location or algal color. Indicator value analysis identified Pseudoalteromonas (in the LAE and TAE), Psychromonas (in the LAE), Marinomonas (in the LAE), and Litorimonas (in the TAE) as the dominant taxa in the phycosphere, in contrast to seawater. Network analysis suggested positive correlations among taxa within the same environments and negative correlations between those in the LAE and TAE, highlighting their distinct ecological conditions. Analysis using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States and Kyoto Encyclopedia of Genes and Genomes pathways revealed functional variations between the phycosphere- and seawater-residing microbes. The microbial taxa-function relationships were assessed through Spearman's rank-order correlation. Additionally, bacterial species belonging to the core taxa were isolated and their genomes sequenced. Their metabolic traits were analyzed via bioinformatics, recognizing key metabolic features essential for symbiotic interactions with algal hosts and survival within the phycosphere. The findings of this study advance our understanding of the marine algal phycosphere microbiome by detailing the metabolic characteristics of potential keystone species.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00325-6.},
}

@article {pmid41321819,
year = {2025},
author = {Jiang, J and Zhou, S and Song, J and Xia, C and Yang, X and Yang, K and Li, F},
title = {Diet-microbiome coevolution: the core mechanism for semi-aquatic adaptation and cross-habitat niche coexistence of the web-footed shrew (Nectogale elegans).},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1711143},
pmid = {41321819},
issn = {1664-302X},
abstract = {The adaptation of mammals to semi-aquatic niches represents a pivotal ecological transition, in which the coevolution of dietary specialization and gut microbiome is regarded as playing a fundamental role. However, the general mechanisms that link these traits to survival across habitats remain insufficiently investigated, particularly in small mammals with high metabolic constraints. Using the web-footed shrew (Nectogale elegans), a rare small mammal with extreme semi-aquatic specialization, this study supplements the understanding of host-microbe symbiosis in the process of small mammals adapting to new ecosystem. To address how diet facilitates semi-aquatic adaptation, we integrated benthic community surveys and dietary DNA metabarcoding. Our results showed that the web-footed shrew primarily utilizes benthic macroinvertebrates (Diptera, Ephemeroptera, and Trichoptera), consistent with the composition of local benthic biomass, and supplemented by Cypriniformes fish. Comparative analysis of DNA metabarcoding with sympatric terrestrial rodents further revealed that semi-aquatic shrews achieve niche differentiation through two complementary mechanisms: habitat partitioning (aquatic vs. terrestrial) and trophic level differentiation (secondary consumers of invertebrates vs. consumers of plants). This discovery extends niche theory, demonstrating how habitat-specific resource utilization shapes trophic stratification. Compared to the terrestrial group, the gut microbiome of the semi-aquatic shrew exhibited significant differences in both microbiome composition and functional potential: dominance of Proteobacteria and Firmicutes, reduced abundances of carbohydrate-active enzymes (CAZymes), as well as selective enrichment of genes involved in fatty acid metabolism. These results reflect the high-fat, high-protein niche of semi-aquatic shrews. Additionally, the seasonal stability of the microbiome of the semi-aquatic shrew mirrors the consistency of benthic resources, and maintaining metabolic homeostasis is key to long-term adaptation to fluctuating environments. Overall, this study demonstrates a framework for semi-aquatic adaptation in small mammals: dietary specialization drives niche differentiation, which in turn selects for gut microbiome adaptation, optimizing habitat-specific resource utilization. This research underscores the role of diet-microbiome coevolution in enabling semi-aquatic adaptation, offering novel insights into ecological niche differentiation and specialization mechanisms in small mammals.},
}

@article {pmid41320831,
year = {2025},
author = {Abbot, B and Field, S and Carneal, L and White Iii, RA and Buchan, A and West, C and Lee, L and Carter, ME},
title = {Comparative genomics reveals multipartite genomes undergoing loss in the fungal endosymbiotic genus Mycetohabitans.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf231},
pmid = {41320831},
issn = {1759-6653},
abstract = {Endosymbiotic bacteria extensively impact phenotypes of their eukaryotic hosts, while experiencing dramatic changes to their own genome as they become more host-restricted in lifestyle. Understanding the trajectory of such a genome has largely been done through study of animal-associated bacteria, especially insect endosymbionts. Yet, endofungal bacteria provide another natural experimental model for investigating how microbial genomes change when living inside of a host cell. Mycetohabitans spp. are culturable bacterial endosymbionts of the Mucoromycota fungus Rhizopus microsporus. To investigate the genome dynamics resulting from the endohyphal nature of this emerging model genus, we long-read sequenced and assembled new complete genomes to combine with previous assemblies, creating a global dataset of 28 complete Mycetohabitans genomes. All genomes were between 3.3 and 3.9 Mbp in size and were multipartite, structured into two conserved replicons with some strains having an additional plasmid. Based on evolutionary rate and gene content analysis of the different replicons, we termed the two major ones a chromosome and chromid. The differential presence of a third, mobilome-rich plasmid in some strains and the proliferation of transposable elements provide putative mechanisms for recombination or gene loss. The conservation of intact prophage and putative toxin-antitoxin systems, and extensive enrichment of secondary metabolite clusters in the Mycetohabitans genomes highlight the dynamic nature of this reducing genome. With fungal-bacterial symbioses becoming increasingly apparent phenomena, lessons learned from this symbiosis will inform our understanding of bacterial adaptation to novel hosts, and the process of microbe-microbe coevolution.},
}

@article {pmid41320684,
year = {2025},
author = {Moraes, MP and Paraginski, JA and Mayer, NA and Bianchi, VJ},
title = {Effect of Substrate Type and Arbuscular Mycorrhizal Fungi on Growth and Quality of Own-Rooted 'Koroneiki' Olive Nursery Trees.},
journal = {Current microbiology},
volume = {83},
number = {1},
pages = {51},
pmid = {41320684},
issn = {1432-0991},
mesh = {*Olea/microbiology/growth & development ; *Mycorrhizae/growth & development/physiology ; Plant Roots/microbiology/growth & development ; Soil Microbiology ; Soil/chemistry ; Fertilizers/analysis ; Biomass ; Symbiosis ; Trees/growth & development/microbiology ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) are known to improve nutrient uptake and growth of perennial crops, including olive trees. In nursery systems, substrate type and microbial associations can strongly influence the establishment and quality of own-rooted plants. Evaluate the effects of different growing media and Rhizophagus intraradices inoculation on the growth and early vigor of own-rooted nursery trees of Olea europaea 'Koroneiki'. A completely randomized design was used with six treatments consisting of different substrate compositions - commercial substrates (Carolina Soil[®], Turfa Fértil[®], and Beifort[®] S-10B) - combined with two fertilizer doses (1 and 3 g dm[- 3] of controlled-release fertilizer), either with or without R. intraradices inoculation. Growth parameters assessed included plant height, stem diameter, leaf number, root volume and length, shoot and root fresh and dry biomass, shoot/root ratio, and Dickson Quality Index. Mycorrhizal colonization parameters (frequency and intensity) were also evaluated. Nursery tree height, root development, and biomass accumulation were significantly influenced by substrate composition and AMF inoculation (p < 0.05). Turfa Fértil[®] and Beifort[®] S-10B promoted greater height growth, while Carolina Soil[®] enhanced root volume and length. AMF inoculation improved dry biomass accumulation, particularly in Turfa Fértil[®]. The highest Dickson Quality Index values were observed in Carolina Soil[®] and Beifort[®] S-10B treatments, indicating greater structural robustness. Mycorrhizal colonization intensity was highest in Carolina Soil[®], suggesting favorable conditions for AMF symbiosis. Carolina Soil[®], with or without R. intraradices inoculation, and Beifort[®] S-10B proved to be the most effective substrates for enhancing early vigor and structural quality in 'Koroneiki' olive nursery trees.},
}

*Olea/microbiology/growth & development
*Mycorrhizae/growth & development/physiology
Plant Roots/microbiology/growth & development
Soil Microbiology
Soil/chemistry
Fertilizers/analysis
Biomass
Symbiosis
Trees/growth & development/microbiology

@article {pmid41319642,
year = {2025},
author = {Li, XH and Wang, XD and Song, H and Chen, S},
title = {Endophyte synergistic phytoremediation is a sustainable solution for the removal of heavy metals and organic pollutants.},
journal = {Journal of environmental management},
volume = {396},
number = {},
pages = {128126},
doi = {10.1016/j.jenvman.2025.128126},
pmid = {41319642},
issn = {1095-8630},
abstract = {In recent decades, rapid economic growth has exacerbated environmental pollution, necessitating sustainable remediation strategies. Phytoremediation, an eco-friendly biotechnology leveraging plant microbe interactions, has emerged as a promising solution. Endophytes, the symbiotic microorganisms inhabiting plants, play a pivotal role in enhancing phytoremediation efficiency by promoting plant growth, improving stress tolerance, and facilitating pollutant degradation. This review systematically examines the mechanisms by which endophytes synergistically enhance phytoremediation, focusing on: (1) growth promotion and nutrient acquisition mediated by phytohormones; (2) restructuring of soil microbial communities to improve soil health; (3) boosting metal tolerance and bioaccumulation in plants; and (4) enzymatic degradation of organic contaminants. Furthermore, we critically evaluate recent advancements in endophyte synergistic phytoremediation, highlighting its potential for large-scale application in mitigating heavy metals and organic pollutants. Despite its promise, challenges such as scalability, environmental variability, and mechanistic uncertainties remain. In this review, we identify key research gaps and propose future directions to optimize the interactions between endophytes and plants for sustainable environmental remediation. By integrating theoretical insights with practical applications, this review provides a comprehensive foundation for advancing phytoremediation technologies.},
}

@article {pmid41319531,
year = {2025},
author = {Rodríguez-Caballero, G and Torres, P and Díaz, G and Roldán, A and Caravaca, F},
title = {Lower specificity of mycorrhizal associations in the invader Nicotiana glauca could mediate adaptive advantages over the native plant species during the drought season.},
journal = {The Science of the total environment},
volume = {1009},
number = {},
pages = {181053},
doi = {10.1016/j.scitotenv.2025.181053},
pmid = {41319531},
issn = {1879-1026},
abstract = {Mycorrhizal associations involving arbuscular mycorrhizal fungi (AMF) can play a critical role in the success of plant invasion processes, particularly under environmental stress conditions such as drought. This study investigated the effects of plant invasiveness, seasonal soil moisture (wet vs. dry seasons), and characteristics of invaded sites on AMF communities associated with the roots of the invasive species Nicotiana glauca and co-occurring native plants in Mediterranean semiarid ecosystems. High-throughput MiSeq sequencing identified 546 amplicon sequence variants (ASVs) of AMF, with members of the family Glomeraceae predominating in all samples. Native plants exhibited significantly greater AMF richness (the Chao1 richness estimator ranged from 21.8 under wet conditions to 40.4 under dry conditions) and diversity (the Shannon-Weaver diversity index ranged from 2.4 under wet conditions to 2.9 under dry conditions), whereas the AMF communities associated with N. glauca were less diverse and characterized by generalist taxa independently soil moisture (the Shannon-Weaver diversity index ranged from 2.0 under wet conditions to 2.1 under dry conditions). The rhizosphere of invasive plants exhibited higher enzymatic activities-including dehydrogenase, urease, and alkaline phosphomonoesterase (approximately 70 %, 33 %, and 26 % higher, respectively, than those in the rhizosphere of native plants)-with enzyme values remaining more stable across seasons. Canonical correspondence analysis (CCA) revealed that the AMF community composition was influenced by soil biochemical parameters, particularly the alkaline phosphomonoesterase activity related to phosphorus cycling. Moreover, rhizospheric soils of N. glauca displayed greater structural stability, especially during the dry season. These findings indicate that N. glauca supports resilient and functionally efficient AMF associations under varying water availability, which may enhance its ecological success in drought-affected environments.},
}

@article {pmid41318663,
year = {2025},
author = {Liu, S and Zhao, Z and Ji, Y and Zhu, H and Sun, Y and Li, M and Yu, Q},
title = {Synthetic bacterium-facilitated colonization of nitrogen-fixing bacteria for remodeling the rhizosphere microbiome and improving plant yield.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02189-5},
pmid = {41318663},
issn = {2049-2618},
support = {32170102//National Natural Science Foundation of China/ ; 2024YFD1701100//National Key R&D Program of China/ ; U23A20158//Joint Funds of the National Natural Science Foundation of China/ ; NCC2022-PY-09//Foundation of Nankai University-Cangzhou Bohai New Area Green Chemical Research Institute/ ; 63253191//Fundamental Research Funds for the Central Universities/ ; },
abstract = {BACKGROUND: Nitrogen-fixing bacteria (NFBs) play a critical role in biological nitrogen fixation for supplying essential nitrogen nutrients to plants in agriculture and natural ecosystems. Especially, these bacteria and Leguminosae plants form symbiosis to improve plant growth and soil fertility. Theoretically, the inoculation of NFBs into soils increases biological nitrogen fixation, but the efficiency of NFBs is frequently compromised by the low capacity of NFB root colonization. In this study, we introduced the synthetic bacterium EcCMC, which was genetically engineered to express the surface-displayed artificial polysaccharide (PS)-recognizing protein Cmc, to test if it can improve NFBs root colonization in representative Leguminosae plants, including Astragalus sinicus and Medicago sativa. Rhizosphere microbiomes, biochemical indicators, and plant yields were evaluated after 28 days in the three treatments, i.e., the control group without addition of any exogenous bacterium, the NFBs plus EcM (bacteria only expressing mCherry rather than Cmc) group, and the NFBs plus EcCMC group (n = 3).

RESULTS: Owing to its polysaccharide-binding capacity, EcCMC strongly bound to the surface of A. sinicus roots. This binding was followed by the increased recruitment of the exogenous NFBs, Sinorhizobium meliloti and Sphingomonas endophytica, on the roots. As revealed by amplicon sequencing of the 16S rRNA gene, a combined inoculation of EcCMC and the NFBs increased the relative abundance of both Rhizobiales and Sphingomonadales, two important bacterial groups involved in nitrogen fixation. Consistently, metabolomic analysis showed that the metabolites involved in nitrogen fixation remarkably accumulated in the rhizosphere soils inoculated with NFBs plus EcCMC. Moreover, inoculation of NFBs plus EcCMC increased the activity of nitrogenase from 10.8 ~ 11.3 to 16.2 nmol/min/g (significant difference, p < 0.05, t-test), together with the total soil nitrogen levels from 217 ~ 258 to 414 mg/kg (significant difference, p < 0.05), and the soil organic matter levels from 19.5 ~ 20.8 to 23.6 mg/kg (significant difference, p < 0.05). Consequently, the yield of A. sinicus was remarkably improved by the inoculation of NFBs plus EcCMC. Similar results were observed in the experiments using Medicago sativa.

CONCLUSIONS: This study sheds a novel light on a synthetic biology-assisted regulation of rhizosphere microbiomes for enhanced nitrogen fixation and soil fertility in Leguminous plants. The designed polysaccharide-binding protein may be used as a universal tool to promote plant growth and enhance crop resilience in the future. Video Abstract.},
}

@article {pmid41315966,
year = {2025},
author = {Huang, R and Li, K and Wang, D and Meng, W and Wei, X},
title = {Dual gradient dynamics: morpho-anatomical and symbiotic fungal communities in Fraxinus Mandshurica fine roots across root order and habitats.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-025-07675-4},
pmid = {41315966},
issn = {1471-2229},
support = {145309629//Basic Research Business Fee Project for Provincial Undergrad-uate Universities in Heilongjiang Province/ ; },
abstract = {BACKGROUND: The cooperation between fine roots and mycorrhizal fungi is of great significance in terms of adapting to harsh environments and acquiring resources. Nevertheless, how this cooperative relationship responds in different environments remains unclear. To understand the mechanisms of the interaction between root order structure and morphology and endophytic fungi in different habitats, we investigated the anatomical and chemical traits of first five order roots, as well as the percentage of mycorrhizal colonization and the community structure of root-inhabiting fungi of Fraxinus mandshurica in the semi-arid and humid habitats of Northeast China.

RESULTS: In contrast to humid habitats, the fine roots of F. mandshurica in semi-arid habitats exhibited more conservative resource-acquisition traits, characterized by greater root diameter and tissue density alongside reduced specific root length, specific root surface area and nitrogen and phosphorus concentrations. Concurrently, anatomical traits showed adaptations for symbiotic fungi association: cortical cell thickness, cell size and the ratio of cortical thickness to half of the stele diameter were higher in absorptive roots. The diversity of symbiotic fungi, represented by arbuscular mycorrhizal fungi (AMF), and the percentage of mycorrhizal colonization were significantly higher than those in humid habitats, enhancing resource acquisition. It is worth noting that in semi-arid habitats, not only do the absorptive roots of F. mandshurica habour a higher proportion of AMF, but AMF hyphae and vesicles were also observed in the transport roots. Moreover, AMF extending from absorptive roots to transport roots was detected, representing a novel resource-acquisition strategy.

CONCLUSIONS: The semi-arid habitat promotes the development of conservative resource-acquisition traits in the fine roots of F. mandshurica and expands the spatial extent of root nutrient exchange. It also enhances the ability of fine roots to recruit symbiotic fungi and facilitates the extension of mycorrhizal fungal hyphae from absorptive roots to transport roots, thereby strengthening the response of roots and mycorrhizal fungi to adverse conditions.},
}

@article {pmid41314145,
year = {2025},
author = {Li, X and Lin, X and Dong, Z and Zhou, R and Niu, Q},
title = {Biomass ratio regulates methane conversion and carbon fixation in a methanotrophs-microalgae symbiotic system: Efficiency optimization and mechanisms driven by co-metabolism.},
journal = {Water research},
volume = {290},
number = {},
pages = {125016},
doi = {10.1016/j.watres.2025.125016},
pmid = {41314145},
issn = {1879-2448},
abstract = {The methanotrophs-microalgae symbiotic system for greenhouse gas treatment is a novel biological carbon fixation technology. However, practical applications are limited by low conversion efficiency, which arises from metabolic heterogeneity in growth rates and carbon-nitrogen resource utilization within the system. To improve metabolic stability of such symbiotic systems, this study systematically assessed CH4 metabolic fluxes by regulating the methanotrophs-microalgae biomass ratio, and further revealed synergistic mechanisms that enhance system stability. Experimental results indicated that at a methanotrophs to microalgae ratio of 1:5, the CH4 consumption rate peaked at 1.1 L CH4/d/g biomass. The extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory and the laser confocal revealed that the co-aggregation force of methanotrophs and microalgae was significantly enhanced at the optimal ratio. This enhancement was crucial for regulating the spatial mutualistic growth and metabolic interactions within the methanotrophs-microalgae symbiotic community. Structural equation modeling (SEM) indicated that poly-β-hydroxybutyrate (PHB) exerts a significant negative effect on methane consumption (-0.68***). Metagenomics results indicated that at the optimal methanotrophs-microalgae ratio, the relative abundance of genes associated with the methane oxidation center metabolic pathway increased by 1.38 times. This significantly enriched Type I methanotrophs (1.89 times) and Type II methanotrophs (1.51 times), while the relative abundance of genes involved in the PHB production pathway decreased by 16 %. This change accelerated the conversion and assimilation of methane carbon, ultimately improving the carbon fixation efficiency by 16 %. This study provided theoretical foundations and technical support for advancing the engineering application of methanotrophs and microalgae symbionts to achieve efficient, stable methane conversion and simultaneous carbon sequestration.},
}

@article {pmid41313925,
year = {2025},
author = {Mechri, B and Guesmi, A and Tekaya, M and Chehab, H and Ben Hamadi, N},
title = {Mycorrhizal symbiosis drives a carbon-dependent metabolic reprogramming in olive tree rhizosphere and leaves.},
journal = {Journal of plant physiology},
volume = {316},
number = {},
pages = {154661},
doi = {10.1016/j.jplph.2025.154661},
pmid = {41313925},
issn = {1618-1328},
abstract = {We investigated the effect of arbuscular mycorrhizal (AM) symbiosis on the triacylglycerol fatty acids (TAGFA) profile in the rhizosphere of olive trees colonized by Rhizophagus (R.) irregularis. The TAGFA 16:1ω5 was used as a marker of AM fungal storage structures, whereas TAGFA 18:2ω6 was used as a marker of saprotrophic fungal storage structures. Our results showed that the rhizospheres of AM and non-mycorrhizal (NM) plants differed significantly in their TAGFA composition, a finding reported here for the first time. In particular, root colonization by R. irregularis increased TAGFA 16:1ω5 by 76 % and decreased TAGFA 18:2ω6 by 45 %, suggesting that less carbon was allocated to saprotrophic fungal storage structures. This redistribution of carbon in AM plant rhizospheres strongly influenced the content of cyclopropyl fatty acids in microbial cytomembranes, which are widely used as classical indicators of nutritional stress in soil microorganisms. The cyclopropyl-to-precursor ratio decreased significantly in AM rhizospheres, indicating that AM symbiosis effectively alleviates microbial stress in olive rhizospheres. These marked changes in the AM rhizosphere were associated with metabolic rearrangements in olive leaves. AM symbiosis generally had a positive impact on amino acid levels, particularly those of the glutamate family (glutamic acid, arginine, ornithine, and glutamine). Metabolic reprogramming also enhanced other pathways of secondary metabolism, notably flavonoids (luteolin 7-O-glucoside and luteolin 7-O-rutinoside) and the secoiridoid oleuropein. Taken together, our results highlight the pivotal role of AM fungi in regulating the allocation of photosynthates from aboveground tissues to belowground structures, including roots and their associated mycorrhizal partners, thereby driving rhizospheric changes and priming the accumulation of defensive compounds in olive leaves. This may (1) decrease leaf water potential, making it more negative and thereby facilitating water movement from the stem to the leaves, and (2) enhance tolerance to environmental stresses.},
}

@article {pmid41312132,
year = {2025},
author = {S, CB and Mahto, RK and Singh, RK and V, R and Singh, KK and Kushwah, S and Lavanya, GR and Kudapa, H and Kumar Valluri, V and Vemula, AK and Yadav, RR and Yadav, LB and Upadhyaya, HD and Hamwieh, A and Kumar, R},
title = {Genome-wide association studies identified novel SNPs associated with efficient biological nitrogen fixation in chickpea (Cicer arietinum L.).},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1652315},
pmid = {41312132},
issn = {1664-462X},
abstract = {Chickpea (Cicer arietinum L.) is the second most important food legume crop, capable of converting atmospheric nitrogen (N2) into ammonia (NH3) in symbiotic association with Mesorhizobium cicero through a process called biological nitrogen fixation (BNF). BNF shows promise in effectively diminishing reliance on exogenous nitrogen applications, enhancing soil sustainability and productivity in pulse crops. Notably, there are limited studies on the molecular basis of root nodulation in chickpea. In order to identify new sources of highly nodulating genotypes and gain deep insights into genomic regions governing BNF, a diverse chickpea global germplasm collection (284) was evaluated for nodulation and yield traits in four different environments in an augmented randomized block design. The genotypes exhibited significant trait variation, encompassing all traits under study. Correlation analysis revealed a significant positive correlation of nodulation traits on yield within the chickpea population. The genotypes ICC 7390, ICC 15, ICC 8348, and ICC 2474 were identified as high nodulating across the locations. Genome-wide association studies (GWAS) identified noteworthy and stable marker-trait associations (MTAs) linked to the traits of interest. For the traits number of nodules (NON) and nodule fresh weight (NFW), 65 and 109 significant MTAs were identified, respectively. In addition, two SNPs, Ca1pos289.52482.1 and 6_33340878, identified in our earlier studies were validated by independent population studies, which are crucial in evaluating the accuracy and reliability of the projections. Subsequent analysis revealed that a substantial proportion of these MTAs were situated within intergenic regions, with the potential to modulate genes associated with the focal traits. The candidate genes identified could be converted to Kompetitive allele-specific PCR (KASP) markers and exploited in marker-assisted breeding, accentuating their impact on future chickpea breeding efforts.},
}

@article {pmid41312105,
year = {2025},
author = {Ye, K and Zheng, J and Dong, Z and Wang, S and Huang, S},
title = {Harnessing omics to decode the mechanisms of symbiotic nitrogen fixation.},
journal = {aBIOTECH},
volume = {6},
number = {4},
pages = {602-617},
pmid = {41312105},
issn = {2662-1738},
abstract = {UNLABELLED: Symbiotic nitrogen fixation is predominantly observed in legumes, which form specialized structures termed nodules on their roots that contain symbiotic rhizobia. This mutualistic association provides reciprocal benefits: rhizobia convert atmospheric nitrogen into bioavailable forms, supplying essential nitrogen to their host plants, while obtaining reduced carbon in return. The increasing reliance on nitrogen fertilizers to satisfy escalating demands for food has prompted various approaches aimed at unravelling the mechanisms underlying symbiotic nodulation, seeking to transfer this capacity to non-nodulating crops. Transcriptome-based analyses have revealed that nodulation is a complex developmental program involving many genes. To comprehensively investigate this phenomenon, multiple omics technologies have been deployed and integrated, yielding exciting breakthroughs. In this review, we outline how omics have accelerated research in this area and discuss how advancements in technologies, such as artificial intelligence, could further deepen our understanding of nodulation.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42994-025-00208-5.},
}

@article {pmid41312095,
year = {2025},
author = {Liu, Q and Dong, Q and Chen, ZC},
title = {Nutrient storage and release in uninfected cells of soybean nodules support symbiotic nitrogen fixation in infected cells.},
journal = {aBIOTECH},
volume = {6},
number = {4},
pages = {790-802},
pmid = {41312095},
issn = {2662-1738},
abstract = {UNLABELLED: Symbiotic nitrogen fixation (SNF) between legumes and rhizobia contributes to sustainable agriculture. In root nodules, infected cells (ICs) are the primary sites of rhizobial colonization and nitrogen fixation. However, the function of the neighboring uninfected cells (UCs) has received little attention and is poorly understood. In this study, we employed a symplastic tracing approach to elucidate the role of UCs in nutrient storage and transport within root nodules. We uncovered an extensive network of plasmodesmata connecting ICs and UCs, while direct IC-IC connections were absent. By artificially inducing callose deposition at plasmodesmata, we demonstrate that plasmodesmata permeability between ICs and UCs regulates nutrient import into ICs, thereby influencing nutrient homeostasis and the SNF ability of nodules. Furthermore, high nitrogen levels triggered callose deposition at plasmodesmata, restricting nutrient transport, which may represent one mechanism by which excessive nitrogen inhibits SNF. These findings provide insights into the regulatory mechanisms of SNF and underscore the crucial role of UCs in optimizing nitrogen fixation efficiency.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42994-025-00247-y.},
}

@article {pmid41312060,
year = {2025},
author = {Kim, IH and Wang, J and Ivanenko, VN},
title = {A new Hemicyclops (Copepoda, Cyclopoida, Clausidiidae) associated with the scleractinian coral Galaxea from the South China Sea.},
journal = {ZooKeys},
volume = {1260},
number = {},
pages = {93-109},
pmid = {41312060},
issn = {1313-2989},
abstract = {The genus Hemicyclops Boeck, 1873 is known for its association with various marine invertebrates, including cnidarians, crustaceans, polychaetes, and sponges, with some species also occurring in planktonic communities. Here, we report the first association of Hemicyclops with the scleractinian coral Galaxea fascicularis (Linnaeus, 1767) (Scleractinia, Euphylliidae). Hemicyclops cyanus sp. nov. is described based on a female specimen collected from this coral host in the lagoon (depth 10 m) of Dongsha Atoll, Pratas Islands, South China Sea. The new species is readily distinguished from its congeners by its characteristic genital double-somite, which bears prominent anterolateral expansions, and by the flexed, elongated exopodal segment of leg 5, which is more than three times longer than wide. In H. cyanus sp. nov., the paired spermatophores attached to the female are fused into a butterfly-shaped, highly modified complex with large lateral wings and a central tube into which the female urosome is inserted. To aid in species identification, we present the first comparative plate with schematic illustrations of the genital double-somites for the group of 25 species, including the type species.},
}

@article {pmid41310464,
year = {2025},
author = {Batool, A and Wang, C and Xia, Y and Xiao, L and Ahmad, J and Liu, L and Ge, L and Chen, C},
title = {Transcriptional profiles of endophyte Serendipita indica associated with plant growth improvement in watermelon.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-025-07659-4},
pmid = {41310464},
issn = {1471-2229},
support = {CARS-25-17//Earmarked Fund for China Agriculture Research System/ ; CARS-25-17//Earmarked Fund for China Agriculture Research System/ ; CARS-25-17//Earmarked Fund for China Agriculture Research System/ ; CARS-25-17//Earmarked Fund for China Agriculture Research System/ ; CARS-25-17//Earmarked Fund for China Agriculture Research System/ ; CARS-25-17//Earmarked Fund for China Agriculture Research System/ ; CARS-25-17//Earmarked Fund for China Agriculture Research System/ ; CARS-25-17//Earmarked Fund for China Agriculture Research System/ ; },
abstract = {BACKGROUND: Endophytes play an important role in improving the nutrient regime and growth status of host plants via symbiosis. Considering the importance of endophytes for maintaining good plant growth and development, we executed current study and investigated the effect of S. indica on watermelon plant growth, nutrient uptake efficiency and spatiotemporal variations in root-specific characteristics. Briefly, the surface sterilized seeds of three watermelon accessions were sowed on peat, perlite, and vermiculite media (3:2:1) in dark at 25 °C, the photosynthetic photon flux density 880 µmol/m[2]/s, 28[◦]C/21[◦]C day/night temperature and 68% relative humidity was maintained. The plants were inoculated with the endophyte S. indica at one-to two-leaf stage except the control plants. Serendipita indica was cultivated on Potato Dextrose Agar at 28 °C, and mass multiplied in 200 ml Potato Dextrose Broth after inoculating mycelial discs from freshly grown PDA and incubated at 28 °C with constant shaking at 150-200 rpm. After filtration, the viable fungal homogenate was used as inoculant, two weeks later the root fungal structures were observed. The morphological/physiological and molecular perspectives were determined as described in material method section.

RESULTS: The ZJU-accession (ZJU-197) with maximum colonization capacity has better plant growth (60.54%) and photosynthetic assimilation rate with maximum chlorophyll contents and more nutrients acquisition (N, P), thus making this symbiotic association helpful for watermelon plant physiological and morphological attributes. The endophyte S. indica upregulated Phosphomethylethanolamine N-methyltransferase domain proteins which are essential for the synthesis of secondary metabolites and participate in plant growth and nutrient uptake. Additionally, the colonized watermelon plants showed overexpression of dual affinity NRT1/PTR 7.3/6.3, similar to nitrate reductase and other metabolizing enzymes, thus making absorbed nutrients efficiently assimilated in the leaves to increase photosynthetic efficiency, resulting in biomass accumulation. Overexpression of genes facilitating nutrient uptake confirmed the influence of endophytes on nutrient acquisition in treated watermelon plants compared to that in untreated plants. The shared gene module enabled us to identify various auxin and secondary metabolite-regulated interlinked genes that contributed to watermelon plant growth induced by the S. indica inoculation.

CONCLUSION: Improved watermelon plant growth and nutrients availability have been elucidated from different physiological and molecular perspectives, and the phenotypic and genotypic variations in various plant traits are the definitive explanations for our hypothesis. These results emphasize the synergistic effects of S. indica on the nutritional status and growth characteristics of watermelon plants through the upregulation of certain secondary metabolites and other plant processes.},
}

@article {pmid41309565,
year = {2025},
author = {Ma, YX and Li, WH and Zhang, MY and Zhao, S and Lv, ZJ and Lin, HT and Liao, LS and Wang, XD},
title = {Organic parallel grouping crystals without grain boundary.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10647},
pmid = {41309565},
issn = {2041-1723},
support = {52173177//National Natural Science Foundation of China (National Science Foundation of China)/ ; 524B2169//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Organic crystal-based micro/nanostructures with morphology-driven photons/electrons transport characteristics demonstrate exceptional potential for the development of optoelectronic functional materials. However, the construction of continuities and lossless interfaces within multicomponent structures remains a significant challenge, primarily due to inherent material differences and current technology limits. Herein, organic parallel grouping crystals (OPGCs), which devoid of grain boundaries between crystals via a solution viscosity-induced binuclear co-growth strategy, are designed to enhance photon transmission efficiency. Notably, the symbiotic phenomenon among components within OPGCs is precisely regulated by manipulating the solvent viscosity to exceed 0.5 mPa·s through adjustments in factors such as the cooling rate, solvent type, concentration. Compared with the low photon transmission efficiency (2.1%) caused by the discontinuous splicing interface, the elimination of grain boundaries significantly enhances the interlayer photon transmission efficiency of OPGCs, resulting in an overlap degree-dependent adjustable transmission efficiency ranging from 21.3% to 54.9%. This symbiotic strategy demonstrates universality to small molecules, coordination compounds, and cocrystals, enabling the construction of parallel grouping structures comprising single- or multi-component crystals.},
}

@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.},
}