@article {pmid40777375,
year = {2025},
author = {Dupuis, S and Lingappa, UF and Purvine, SO and Chiang, L and Gallaher, SD and Nicora, CD and Lipton, MS and Merchant, SS},
title = {Mono-mix strategy enables comparative proteomics of a cross-kingdom microbial symbiosis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.07.22.666210},
pmid = {40777375},
issn = {2692-8205},
abstract = {Cross-kingdom microbial symbioses, such as those between algae and bacteria, are key players in biogeochemical cycles. The molecular changes during initiation and establishment of symbiosis are of great interest, but quantitatively monitoring such changes can be challenging, particularly when the microorganisms differ greatly in size or are intimately associated. Here, we analyze output from data-dependent acquisition (DDA) LC-MS/MS proteomics experiments investigating the well-studied interaction between the alga Chlamydomonas reinhardtii and the heterotrophic bacterium Mesorhizobium japonicum . We found that detection of bacterial proteins decreased in coculture by 50% proteome-wide due to the abundance of algal proteins. As a result, standard differential expression analysis led to numerous false-positive reports of significantly downregulated proteins, where it was not possible to distinguish meaningful biological responses to symbiosis from artifacts of the reduced protein detection in coculture relative to monoculture. We show that data normalization alone does not eliminate the impact of altered detection on differential expression analysis of the cross-kingdom symbiosis. We assessed two additional strategies to overcome this methodological artifact inherent to DDA proteomics. In the first, we combined algal and bacterial monocultures at a relative abundance that mimicked the coculture, creating a "mono-mix" control to which the coculture could be compared. This approach enabled comparable detection of bacterial proteins in the coculture and the monoculture control. In the second strategy, we enhanced detection of lowly abundant bacterial proteins by using sample fractionation upstream of LC-MS/MS analysis. When these simple approaches were combined, they allowed for meaningful comparisons of nearly 10,000 algal proteins and over 4,000 bacterial proteins in response to symbiosis by DDA. They successfully recovered expected changes in the bacterial proteome in response to algal coculture, including upregulation of sugar-binding proteins and transporters. They also revealed novel proteomic responses to coculture that guide hypotheses about algal-bacterial interactions.},
}

@article {pmid40777051,
year = {2025},
author = {Kramer, N and Galindo-Martínez, CT and Jacques, SL and Tresguerres, M and Loya, Y and Wangpraseurt, D},
title = {Depth-dependent microskeletal features modify light harvesting in Turbinaria reniformis corals.},
journal = {iScience},
volume = {28},
number = {8},
pages = {113137},
pmid = {40777051},
issn = {2589-0042},
abstract = {Coral skeletal morphology modulates light exposure in symbiotic algae, especially in light-limited environments like mesophotic reefs. However, quantifying light capture within complex coral structures remains challenging. Here, we used optical coherence tomography and high-resolution X-ray scanning to explore depth-dependent bio-optical properties of shallow and mesophotic Turbinaria reniformis corals from the Gulf of Eilat/Aqaba, Red Sea. We identified two distinct skeletal layers: a highly scattering superficial layer and a deeper, more light-penetrating layer. Mesophotic corals showed higher scattering coefficients and a lower anisotropy of scattering values, yielding increased reflectivity. Regardless of depth, coenosteum grooves facilitated forward scattering, while protruding features such as spines and septa increased surface reflectivity and isotropic scattering. Light simulations demonstrated an enhanced fluence rate at the skeleton-water interface, with mesophotic corals enhancing the available light up to 2.7-fold. These findings suggest that microskeletal heterogeneity fine-tunes light capture at the microenvironmental scale, thereby enhancing light-harvesting efficiency across depth.},
}

@article {pmid40774854,
year = {2025},
author = {Ding, W and Dong, S and Lambers, H},
title = {Phosphorus acquisition and pathogen defense: synergies versus trade-offs.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.07.010},
pmid = {40774854},
issn = {1878-4372},
abstract = {During their life cycle, plants encounter simultaneous biotic and abiotic stresses. A low availability of inorganic phosphorus (P) commonly limits plant growth in natural and agricultural ecosystems. Pathogen attacks pose risks to plant productivity and biodiversity, causing yield loss and ecosystem degradation. Plants evolved various strategies to cope with P limitation, which, in turn, affect their resistance to pathogens. However, a comprehensive understanding of how efficient plant P-acquisition strategies influence their pathogen resistance under P-limited conditions remains elusive. We highlight how these P-acquisition strategies can enhance or decrease pathogen resistance through multiple mechanisms. We advocate using this information to design more sustainable agricultural systems and explain species turnover in natural ecosystems, especially in the context of global change.},
}

@article {pmid40774824,
year = {2025},
author = {Lee, I and Kim, BS and Suk, KT and Lee, SS},
title = {Gut Microbiome-Based Strategies for the Control of Carbapenem-Resistant Enterobacteriaceae.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2406017},
doi = {10.4014/jmb.2406.06017},
pmid = {40774824},
issn = {1738-8872},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Carbapenem-Resistant Enterobacteriaceae/drug effects/physiology ; Humans ; Fecal Microbiota Transplantation ; *Enterobacteriaceae Infections/prevention & control/microbiology/therapy ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Animals ; Carbapenems/pharmacology ; Antimicrobial Stewardship ; },
abstract = {Carbapenem-resistant Enterobacteriaceae (CRE) represent a critical antimicrobial resistance threat due to their resistance to last-resort antibiotics and high transmission potential. While conventional strategies-such as infection control, antimicrobial stewardship, and novel antibiotic development-remain essential, growing attention has shifted toward the gut microbiome, which plays a central role in mediating colonization resistance against CRE. Disruption of the intestinal microbiota-primarily driven by antibiotic exposure and further exacerbated by non-antibiotic drugs such as proton pump inhibitors-reduces microbial diversity and impairs functional integrity, facilitating CRE acquisition, prolonged carriage, and horizontal transmission. In response, microbiome-based strategies-including microbiome disruption indices (MDIs), fecal microbiota transplantation (FMT), and rationally designed symbiotic microbial consortia-are being explored as novel approaches for CRE prevention and decolonization. Mechanistic studies have shown that colonization resistance is mediated by both direct mechanisms (e.g., nutrient competition, short-chain fatty acid production) and indirect mechanisms (e.g., immune modulation via IL-36 signaling). Advances in metagenomics, metabolomics, and culturomics have enabled high-resolution profiling of gut microbial communities and their functional roles. Emerging preclinical and clinical evidence supports the potential of microbiome-informed interventions to predict infection risk, enhance antimicrobial stewardship, and guide the development of next-generation probiotics targeting CRE. Longitudinal studies continue to evaluate the efficacy of FMT and synthetic microbial consortia in eradicating intestinal CRE colonization. Collectively, these insights underscore the promise of gut microbiome science as a complementary and innovative strategy for CRE control in the post-antibiotic era.},
}

*Gastrointestinal Microbiome/drug effects
*Carbapenem-Resistant Enterobacteriaceae/drug effects/physiology
Humans
Fecal Microbiota Transplantation
*Enterobacteriaceae Infections/prevention & control/microbiology/therapy
Anti-Bacterial Agents/pharmacology/therapeutic use
Animals
Carbapenems/pharmacology
Antimicrobial Stewardship

@article {pmid40773571,
year = {2025},
author = {Nahrendorf, M and Ginhoux, F and Swirski, FK},
title = {Immune system influence on physiology.},
journal = {Science (New York, N.Y.)},
volume = {389},
number = {6760},
pages = {594-599},
doi = {10.1126/science.adx4380},
pmid = {40773571},
issn = {1095-9203},
mesh = {Animals ; Humans ; Cell Communication ; Homeostasis ; *Immune System/physiology ; Leukocytes/physiology/immunology ; Phagocytosis ; Nervous System ; },
abstract = {The immune system's central function is to maintain homeostasis by guarding the organism against dangerous external and internal stressors. Immunity's operational toolbox contains diverse processes, such as phagocytosis, antigen recognition, cell killing, and secretion of cytokines and antibodies. Although immune cells interact with each other, they also communicate with cells typically associated with other organ systems, including the nervous, circulatory, metabolic, musculoskeletal, endocrine, and hematopoietic. This abundant cross-talk shows that immunity transcends defense and homeostasis: It is a network that participates in many physiological processes necessary for life. By accessing the circulation and inhabiting every tissue, leukocytes sense, interpret, and regulate biological processes. In this Review, we highlight recent studies that illustrate the often bidirectional and symbiotic relationships through which the immune system regulates physiology.},
}

Animals
Humans
Cell Communication
Homeostasis
*Immune System/physiology
Leukocytes/physiology/immunology
Phagocytosis
Nervous System

@article {pmid40772886,
year = {2025},
author = {Qiu, P and Liu, X and Wei, D},
title = {Iron acquisition in the mutualistic fungus Penicillium herquei: implications of mineral elements in insect-fungus symbiosis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0105125},
doi = {10.1128/spectrum.01051-25},
pmid = {40772886},
issn = {2165-0497},
abstract = {Mutualistic interactions between insects and fungi are pivotal in ecosystem dynamics, yet the underlying molecular mechanisms remain largely unexplored. This study investigates iron acquisition strategies of the mutualistic Penicillium herquei, revealing the involvement of mineral elements in insect-fungus symbiosis. Comparative transcriptomics of weevil-farming strain (WFS) and soil free-living strain (SFS) revealed distinct transcriptional profiles, with 4,357 upregulated genes in WFS. Enrichment analyses highlighted a significant upregulation of genes linked to oxidoreductase activity, iron and heme binding, with a notable prevalence of cytochrome P450 (CYP450). qRT-PCR confirmed differential expression of CYP450 and siderophore-related genes, indicating enhanced iron absorption in WFS. Comparative analysis of iron content further demonstrated significantly higher iron levels in WFS than in SFS and weevil host plant leaves, suggesting a nutritional adaptation for symbiotic lifestyle. These findings provide novel insights into the role of iron metabolism in insect-fungus mutualism, highlighting potential evolutionary mechanisms that bolster symbiotic fitness.IMPORTANCEUnraveling the complex interplay between insects and fungi is crucial for deciphering the intricate dynamics of ecosystems. In this study, a notable upregulation of genes associated with iron and heme binding, as well as a significant increase in iron content within WFS was revealed, suggesting a specialized adaptation strategy to enhance iron acquisition, potentially enabling the fungus to efficiently provide essential nutrients, including bioavailable iron, to weevil host. This research not only advances our understanding of the molecular mechanisms governing insect-fungus mutualism but also highlights the potential evolutionary mechanisms that bolster symbiotic fitness and contribute to the co-evolution of these interacting species.},
}

@article {pmid40772389,
year = {2025},
author = {Dauphin, B and de Freitas Pereira, M and Croll, D and Cardoso Anastácio, T and Fauchery, L and Guinet, F and Dutra Costa, M and Martin, F and Peter, M and Kohler, A},
title = {Genetic variation among progeny shapes symbiosis in a basidiomycete with poplar.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70395},
pmid = {40772389},
issn = {1469-8137},
support = {//Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG)/ ; //Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)/ ; ANR-11-LABX-0002-01//Laboratory of Excellence ARBRE/ ; //Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; //CNPq Research Grant/ ; },
abstract = {Forest trees rely on ectomycorrhizal (ECM) fungi for acquiring scarce resources such as water and nutrients. However, the molecular mechanisms governing ECM traits remain inadequately understood, particularly the role of intraspecific fungal variation in root-tip colonisation and trophic interactions. This study examined six ECM traits using Pisolithus microcarpus, an ECM fungus capable of forming ECM rootlets in poplar. A collection of 40 sibling monokaryons and their parental dikaryon was analysed through genome and transcriptome sequencing to examine quantitative trait loci, gene expression and mating-type loci. These findings revealed a pronounced phenotypic continuum in poplar root colonisation by sibling monokaryons, ranging from incompatible to fully compatible strains. Genetic recombination among monokaryons was demonstrated, and genomic regions potentially involved in ECM fungal traits were identified. Transcriptomic analysis revealed greater differentiation in transcriptomic profiles between fungal strains than between fungal tissues, and uncovered tissue-specific functional responses for ECM and free-living mycelia. Poplar exhibited distinct transcriptomic responses when interacting with different sibling monokaryons and the parental dikaryon. Allele sorting at 11 mating-type loci confirmed the species' heterothallic tetrapolar system. This study advances understanding of the genetic and transcriptomic mechanisms underlying ECM symbioses, highlighting intraspecific fungal diversity's role in forest ecosystem functioning.},
}

@article {pmid40772380,
year = {2025},
author = {Duan, Y and Zhang, W and Liu, H and Wang, M and Zhong, L and Liu, J and Chen, X and Zhang, S},
title = {Insights into the molecular response mechanisms of fasting stress and refeeding in channel catfish (Ictalurus punctatus) through transcriptome and histological analysis.},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70164},
pmid = {40772380},
issn = {1095-8649},
support = {JATS [2023] 374//Jiangsu Agricultural Industry Technology System/ ; CARS-46//China Agriculture Research System of MOF and MARA/ ; PZCZ201741//Important New Varieties Selection Project of Jiangsu Province/ ; },
abstract = {Throughout their life cycles, many fish alternate between periods of fasting and feeding due to the temporal and geographical variability of food availability in aquatic environments. The ability to adapt to fasting and restore internal balance after refeeding is fundamental to the long-term survival and symbiotic relationships of aquatic species. However, our understanding of the mechanisms by which the fish adapt to fasting and refeeding remains limited. We looked at the growth performance, intestinal and liver histology, and liver gene expression patterns of channel catfish, a significant commercial species, during three weeks of fasting stress and three weeks of refeeding, respectively, in order to clarify the molecular response mechanisms to these two events. Our study revealed that fasting significantly impacts growth, histological characteristics and physiological metabolism. During the fasting period, catfish growth performance was greatly inhibited, but growth compensation was observed after refeeding. Histological analysis showed that liver and intestinal tissues experienced varying degrees of apoptotic injury during fasting, with a modest number of TUNEL-positive cells still present in the liver after refeeding. We identified 787 significant differentially expressed genes (DEGs) in the control group in three weeks (CG3) groups versus the fasting-refeeding group inthree week (EG3) group, while only 35 DEGs were defined in the CG6 group versus the EG6 group. Gene Ontology functional annotation and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses suggested that fasting stress affected gene expression related to the mitotic cell cycle, cell cycle processes, amino acid metabolism, steroid biosynthesis, fatty acid metabolism and immune responses. Metabolism and cellular process response genes were significantly downregulated in the fasting group. Significant alterations in the expression levels of genes related to metabolism and apoptosis were validated by quantitative Real-time PCR (qRT-PCR). This study provides insights into the physiological mechanisms underlying fish adaptation to fasting or nutritional deficiency stress, shedding light on how channel catfish respond to fasting stress and refeeding.},
}

@article {pmid40772276,
year = {2025},
author = {Adil, G and Liu, S and Bao, X and Mamut, R},
title = {The chloroplast genome of the Peltigera elisabethae photobiont Chloroidium sp. W5 and its phylogenetic implications.},
journal = {Frontiers in genetics},
volume = {16},
number = {},
pages = {1602048},
pmid = {40772276},
issn = {1664-8021},
abstract = {INTRODUCTION: Lichens are globally distributed symbiotic organisms comprising fungi (mycobionts) and photosynthetic partners (photobionts), with exceptional adaptability to extreme environments. Despite growing interest in lichen symbiosis, chloroplast genome data for photobionts remain scarce, hindering insights into symbiotic coevolution and genomic architecture.

METHODS: To address this gap, we characterized the chloroplast genome of Chloroidium sp. W5, a photobiont of the lichen Peltigera elisabethae, using next-generation sequencing. The circular genome (190,579 bp) was assembled and annotated using a combination of bioinformatics tools, including GetOrganelle for genome assembly and GeSeq for annotation. We conducted a comprehensive analysis of the genome's structure, gene content, and repetitive elements. Codon usage patterns were assessed using MEGA 11, and phylogenetic relationships were inferred using maximum likelihood analysis with IQ-tree.

RESULTS: The circular genome (190,579 bp) lacks the canonical quadripartite structure (LSC/IR/SSC) and exhibits a strong AT bias (56.1%). Annotation identified 110 functional genes, including 79 protein-coding genes, 28 tRNAs, and 3 rRNAs. Repetitive sequence analysis revealed 5,000 dispersed repeats (2.62% of the genome), predominantly forward and palindromic types, with SSR loci showing a significant A/T preference. Codon usage analysis demonstrated a pronounced bias toward A/U-ending codons (RSCU > 1), suggesting translational adaptation to symbiotic nutrient constraints. Phylogenetic reconstruction robustly placed Chloroidium sp. W5 within the Watanabeales clade (ML = 100), while synteny analysis revealed extensive genomic rearrangements compared to close relatives.

DISCUSSION: These findings enrich the chloroplast genome database for lichen photobionts, shedding light on symbiosis-driven genomic plasticity and providing a foundation for studying host-photobiont coevolution and lichen ecological adaptation.},
}

@article {pmid40771817,
year = {2025},
author = {Lai, X and Huang, J and Li, Y and Dong, L},
title = {Symbiotic bacteria-mediated imbalance and repair of immune homeostasis: exploring novel mechanisms of microbiome-host interactions in atopic dermatitis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1649857},
pmid = {40771817},
issn = {1664-3224},
mesh = {Humans ; *Dermatitis, Atopic/immunology/microbiology/therapy/metabolism ; *Homeostasis/immunology ; Dysbiosis/immunology ; Animals ; *Microbiota/immunology ; *Symbiosis/immunology ; *Skin/microbiology/immunology ; *Host Microbial Interactions/immunology ; *Bacteria/immunology/metabolism ; Gastrointestinal Microbiome/immunology ; },
abstract = {The skin surface is colonised by a rich microbiome, and intricate interactions between this microenvironment and microbial communities are critical for maintaining skin homeostasis. Atopic dermatitis (AD), a chronic inflammatory skin disease characterised by skin barrier dysfunction and aberrant immune activation, exhibits a rising global incidence. While conventional therapeutic strategies offer short-term symptom control, their long-term use is limited by adverse effects including skin atrophy, metabolic disorders, and increased infection risk. Critically, these approaches fail to cure AD or reverse the underlying immune imbalance. Recent research has firmly established the skin microbiome as a central driver in AD pathogenesis. The molecular mechanisms underpinning microbiome-host interactions, including the potential for remote regulation via the gut-skin axis, are now being actively investigated. This review systematically analyses how microbial dysbiosis in AD promotes Th2/Th17 immune polarization through three key pathways: microbial metabolites, immune signalling, and barrier integrity. Building on these mechanistic insights and recent advances, we propose novel multimodal therapeutic strategies targeting the microbial-immune axis. We further elucidate the role of commensal bacteria in maintaining immune homeostasis. Ultimately, this synthesis aims to bridge fundamental research with clinical applications, providing a robust theoretical foundation for future therapeutic development and clinical studies in AD management.},
}

Humans
*Dermatitis, Atopic/immunology/microbiology/therapy/metabolism
*Homeostasis/immunology
Dysbiosis/immunology
Animals
*Microbiota/immunology
*Symbiosis/immunology
*Skin/microbiology/immunology
*Host Microbial Interactions/immunology
*Bacteria/immunology/metabolism
Gastrointestinal Microbiome/immunology

@article {pmid40771681,
year = {2025},
author = {Lethielleux-Juge, C},
title = {Review: roles of mycorrhizal symbioses and associated soil microbiomes in ecological restoration.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1456041},
pmid = {40771681},
issn = {1664-302X},
abstract = {The ecological roles of Arbuscular Mycorrhizal Fungi (AMF) are diverse, providing essential nutrients to host plants, tolerance to stress, and regulation of metabolic pathways, greatly involved in soil C dynamics, unlocking minerals and promoting reactive Fe minerals. Although spores dispersal modes are still not clearly understood, a strong positive relationship exists between intra-and extraradical mycelium at the ecosystem level. AMF are essential in ecosystem restoration by improving soil attributes, above and belowground biodiversity, seedlings survival, growth, and establishment on stressed soils, driving plant succession and preventing plant invasion. AMF inoculants from native and early seral instead of exotics and late seral, consortia instead of few or single species, are more efficient. Plant and AMF communities evolve together after revegetation, fine fescues are among the most resilient species, especially Festuca rubra, whose fungal strategies have been recently finely studied. Distinct AMF communities are associated with functionally different plants, which are related to differences in P and C transportomes and genetic variations within the AMF symbiont. Ligneous species react differently to forest soil inoculations according to their arbuscular mycorrhizal symbiosis (AM) or ectomycorrhizal symbiosis (EM) status, and in dual-mycorrhizal plants, costs and benefits are context-dependent, with mycorrhizal switch occurring under various abiotic or biotic factors and resource availability. In mine restoration, root colonization is generally very low during the first year post-reclamation, then increases rapidly before stabilizing. Parallel to plant successions, increased soil parameters, and decreased contaminants, AMF diversity increased and changed, affiliated Glomus genera with small spores being completed by Acaulospora or Gigaspora larger spores under southern climates. A similar recovery period was observed for fungal communities in forest restoration, where ectomycorrhizal mycorrhizal fungi (EMF) species dominate, and diversity increased with time post-revegetation, influenced by edaphic variables and tree species. Under heavy metal (HM) contamination, microorganism classes, enzymes, and AMF efficiency vary with time, soil parameters, restoration treatments, plant species, and levels of soil contamination, with Proteobacteria and Actinobacteria being often predominant. Dual applications of specific microbial and AMF species induced synergistic effects on plant growth and soil resilience. Under other contaminants, several AMF and microbial consortia proved to favorize plant growth and nutrient availability and decrease soil toxicity. New quality indicators to compare rehabilitation studies are proposed.},
}

@article {pmid40770989,
year = {2025},
author = {Javaux, EJ},
title = {A diverse Palaeoproterozoic microbial ecosystem implies early eukaryogenesis.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {380},
number = {1931},
pages = {20240092},
pmid = {40770989},
issn = {1471-2970},
support = {//Fonds De La Recherche Scientifique - FNRS/ ; //Belgian Federal Science Policy Office/ ; },
mesh = {*Fossils ; *Biological Evolution ; *Eukaryota/physiology ; *Microbiota ; *Ecosystem ; Symbiosis ; },
abstract = {Microbial interactions may lead to major events in life and planetary evolution, such as eukaryogenesis, the birth of complex nucleated cells. In synergy with microbiology, cellular palaeobiology may shed some light on this very ancient and debated affair and its circumstances. The 1.78-1.73 Ga McDermott Formation, McArthur Basin (Australia), preserves a microfossil assemblage that provides unique insights into the evolution of early eukaryotes. The fossil cells display a level of morphological complexity, disparity and plasticity requiring a complex cytoskeleton and an endomembrane system, pushing back the minimum age of uncontested eukaryotic fossils by more than 100 million years (Ma). They also document an earlier appearance of reproduction by budding, simple multicellularity and diverse programmed openings of cyst wall implying a life cycle, as well as possible evidence for microbial symbiosis and behaviour, including eukaryovory and ectosymbiosis. This microbial community that also includes cyanobacterial cells preserving thylakoids, microbial mats and other microfossils, thrived in supratidal to intertidal marine environments with heterogeneous but mostly suboxic to anoxic redox conditions. Taken together, these observations imply early eukaryogenesis, including mitochondrial endosymbiosis in micro-/nano-oxic niches, and suggest a >1.75 Ga minimum age for the Last Eukaryotic Common Ancestor (LECA), preceded by a deeper history of the domain Eukarya, consistent with several molecular clocks and the fossil record.This article is part of the discussion meeting issue 'Chance and purpose in the evolution of biospheres'.},
}

*Fossils
*Biological Evolution
*Eukaryota/physiology
*Microbiota
*Ecosystem
Symbiosis

@article {pmid40770786,
year = {2025},
author = {Galambos, N and Parisot, N and Vallier, A and Bevilacqua, C and Balmand, S and Vincent-Monégat, C and Rebollo, R and Gillet, B and Hughes, S and Heddi, A and Zaidman-Rémy, A},
title = {Dual-transcriptomics on microdissected cells reveals functional specialisation of symbiont-bearing-cells and contrasted responses to nutritional stress in the cereal weevil.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {182},
pmid = {40770786},
issn = {2049-2618},
support = {ANR-19-CE20-0010//Agence Nationale de la Recherche/ ; ANR-19-CE20-0010//Agence Nationale de la Recherche/ ; ANR-19-CE20-0010//Agence Nationale de la Recherche/ ; ANR-19-CE20-0010//Agence Nationale de la Recherche/ ; ANR-19-CE20-0010//Agence Nationale de la Recherche/ ; ANR-19-CE20-0010//Agence Nationale de la Recherche/ ; ANR-19-CE20-0010//Agence Nationale de la Recherche/ ; },
mesh = {Animals ; *Symbiosis/genetics ; *Weevils/microbiology/genetics/physiology/metabolism ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Gene Expression Profiling ; *Transcriptome ; Stress, Physiological ; Laser Capture Microdissection ; },
abstract = {BACKGROUND: Insects thriving on a nutritionally imbalanced diet often establish long-term relationships with intracellular symbiotic bacteria (endosymbionts), which complement their nutritional needs and improve their physiological performances. Endosymbionts are in host specialised cells, called the bacteriocytes, which in many insects group together to form a symbiotic organ, the bacteriome. The cereal weevil Sitophilus oryzae houses multiple bacteriomes at the adult mesenteric caeca.

RESULTS: Using microscopic cell imaging, we revealed that bacteriomes consist of several cell types, including progenitor cells, peripheral bacteriocytes, central bacteriocytes and epithelial cells. By combining laser capture microdissection and dual RNA-sequencing, we showed that both host cell types and their associated endosymbionts express distinct transcriptional profiles. The comparison between peripheral bacteriocytes and midgut cells from insects artificially deprived from endosymbionts (aposymbiotic) unravelled cellular pathways modulated by the presence of endosymbionts. The cell-specific response to endosymbionts in peripheral bacteriocytes includes a boost of fatty-acid and amino acid metabolisms. We found that central bacteriocytes overexpress transport and G-protein signalling-related genes when compared to peripheral bacteriocytes, indicating a signalling and/or transport function of these cells. Diet composition strongly impacts host and endosymbiont gene expression and reveals a molecular trade-off among metabolic pathways.

CONCLUSIONS: This study provides evidence on how endosymbionts interfere and enhance metabolic performances of insect bacteriocytes and highlights key genes involved in the bacteriocyte differentiation and metabolic pathways. Video Abstract.},
}

Animals
*Symbiosis/genetics
*Weevils/microbiology/genetics/physiology/metabolism
*Bacteria/genetics/classification/metabolism/isolation & purification
Gene Expression Profiling
*Transcriptome
Stress, Physiological
Laser Capture Microdissection

@article {pmid40770781,
year = {2025},
author = {Boulenger, A and Aires, T and Engelen, AH and Muyzer, G and Marengo, M and Gobert, S},
title = {Microbiome matters: how transplantation methods and donor origins shape the successful restoration of the seagrass Posidonia oceanica.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {99},
pmid = {40770781},
issn = {2524-6372},
support = {STARECAPMED//Territorial Collectivity of Corsica/ ; STARECAPMED//Territorial Collectivity of Corsica/ ; STARECAPMED//Rhone-Mediterranean and Corsican Water Agency/ ; STARECAPMED//Rhone-Mediterranean and Corsican Water Agency/ ; FSR2021//University of Liege/ ; FSR2021//University of Liege/ ; ASP 40006932//Fonds National de la Recherche Scientifique - FNRS/ ; UIDB/04326/2020//Portuguese national funds FCT/ ; UIDB/04326/2020//Portuguese national funds FCT/ ; RESTORESEAS//Biodiversa/ ; },
abstract = {BACKGROUND: Posidonia oceanica forms extensive seagrass meadows in the Mediterranean Sea, providing key ecosystem services. However, these meadows decline due to anthropogenic pressures like anchoring and coastal development. Transplantation-based restoration has been explored for decades, yet the role of the plant-associated microbiome in restoration success remains largely unknown.

RESULTS: 16 S rRNA gene amplicon sequencing was used to investigate how different transplantation methods and donor origins influence the bacterial communities of P. oceanica cuttings two years post-transplantation. We tested three transplantation methods, iron staples, coconut fiber mats, and BESE elements, and compared them with control meadows and donor populations from two different origins: naturally uprooted storm-fragments and intermatte cuttings manually harvested from established meadows. Our results show that transplantation methods strongly shape bacterial communities in seagrass roots. Iron staples promoted microbial assemblages most similar to natural meadows, likely due to direct sediment contact enhancing recruitment of key functional bacterial orders such as Chromatiales and Desulfobacterales. In contrast, BESE elements and coconut fiber mats displayed dissimilar bacterial communities compared to control meadows, likely due to material composition and physical separation between the cuttings and the sediment. Donor origin had only subtle effects on bacterial communities' structure, although intermatte cuttings showed higher abundances of Candidatus Thiodiazotropha, a genus thought to be involved sulfur oxidation and nitrogen fixation.

CONCLUSION: Our results demonstrate that transplantation methods strongly influence root-associated bacterial communities. Limited sediment contact in elevated substrates delayed the establishment of key functional bacteria, highlighting the importance of direct interaction with the sediment microbial pool. These results imply that restoration strategies should prioritize methods enhancing sediment-root interactions to support microbial recovery. Incorporating microbiome considerations, such as optimized substrates or microbial inoculation, could improve the resilience and long-term success of P. oceanica restoration.},
}

@article {pmid40770683,
year = {2025},
author = {Pu, Z and Zhang, R and Zhang, C and Wang, H and Wang, XX},
title = {The balance between rhizosphere carboxylates and arbuscular mycorrhizal symbiosis in wheat phosphorus acquisition.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1031},
pmid = {40770683},
issn = {1471-2229},
support = {2021YFD1901001//National Key R&D Program of China/ ; },
mesh = {*Triticum/microbiology/metabolism/genetics/growth & development ; *Mycorrhizae/physiology ; *Phosphorus/metabolism ; *Rhizosphere ; *Symbiosis ; *Carboxylic Acids/metabolism ; Plant Roots/metabolism/microbiology ; Plant Shoots/metabolism ; },
abstract = {BACKGROUND: Changes in plant growth and root traits in wheat (Triticum aestivum L.) vary depending on the level of phosphorus (P) supply. Two important strategies for P acquisition in wheat are the release of carboxylates into the rhizosphere and the presence of arbuscular mycorrhizal fungi (AMF). However, the relationship between root exudates and P concentration in the shoot and root, as well as the role of AMF in this process, is not yet fully understood. This study was conducted utilizing three P supply rates (0, 50, and 200 mg P kg[-1] soil) in conjunction with AMF inoculation. We examined the effects of AMF on amount of rhizosphere carboxylates and plant P uptake for nine P contrasting wheat genotypes.

RESULTS: AMF decreased carboxylates, root biomass, root P content of wheat, and AMF reduced wheat root P allocation of wheat under all P levels. Notably, at 50 mg kg[-1] P level, the shoot P concentration of AMF-inoculated wheat exceeded that of other P levels, having a positive mycorrhizal responsiveness in all wheat genotypes. Furthermore, analysis revealed that wheat root morphology and acid phosphatase activity significantly influenced mycorrhizal growth responsiveness, while root carboxylates played a significant role in mycorrhizal P responsiveness.

CONCLUSIONS: The P acquisition of wheat was found to be contingent upon the interplay of root morphology, AMF, and carboxylate levels, with AMF and carboxylate playing a more crucial role in enhancing P absorption. Consequently, the current research provides important insights for nutrient management in wheat agricultural cultivation.},
}

*Triticum/microbiology/metabolism/genetics/growth & development
*Mycorrhizae/physiology
*Phosphorus/metabolism
*Rhizosphere
*Symbiosis
*Carboxylic Acids/metabolism
Plant Roots/metabolism/microbiology
Plant Shoots/metabolism

@article {pmid40770490,
year = {2025},
author = {Liu, Y and Zhou, Z and Jarman, JB and Chen, H and Miranda-Velez, M and Terkeltaub, R and Dodd, D},
title = {Gut bacteria degrade purines via the 2,8-dioxopurine pathway.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40770490},
issn = {2058-5276},
support = {K08-DK110335//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01-AT011396//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
abstract = {Approximately one-third of urate, which at elevated levels contributes to hyperuricaemia and gout, is excreted into the intestinal tract of healthy individuals where bacteria aid its elimination. However, the molecular details of purine metabolism in the gut microbiome are unclear. Here we uncovered the 2,8-dioxopurine pathway, an anaerobic route for purine degradation in the gut bacteria, Clostridium sporogenes and Escherichia coli. Reconstitution with purified enzymes and mutational analysis combined with isotope tracking and mass spectrometry identified a selenium-dependent enzyme, 2,8-dioxopurine dehydrogenase (DOPDH), and seven additional enzymes that connect purine metabolism to short-chain fatty acid synthesis and ATP generation (measured via luciferase assay). Competition experiments in gnotobiotic mice showed that bacteria harbouring this pathway exhibit a fitness advantage, with wild-type bacteria rapidly outcompeting a DOPDH-deficient strain. Widespread presence of these genes across host-associated microbiomes suggests a host-microbe symbiosis, where host-secreted urate fosters a metabolic niche for bacteria that break it down. These findings could have therapeutic implications for the modification and enhancement of intestinal elimination of urate.},
}

@article {pmid40769503,
year = {2025},
author = {Thomas, T and Garritano, AN},
title = {Symbiotic Ammonia Oxidation in the Marine Environment.},
journal = {Annual review of marine science},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-marine-040824-032008},
pmid = {40769503},
issn = {1941-0611},
abstract = {Ammonia oxidation is a fundamental step in the marine nitrogen cycle, catalyzing the conversion of ammonia to nitrite or nitric oxide and generating reductive power for the autotrophic growth of microorganisms. The ecology, diversity, and properties of ammonia-oxidizing microbes in the ocean's plankton have been extensively studied, but these microbes can also live in association or symbiosis with marine hosts such as sponges, corals, jellyfish, bivalves, and crustaceans. Sequencing-based studies have revealed that ammonia-oxidizing archaea of the family Nitrosopumilaceae are prevalent in various marine hosts, although other taxa are also found and coexist within the same host. Ammonia oxidation rates are highly variable between host species, even between closely related taxa. Limited knowledge is available on the metabolic interactions that ammonia-oxidizing microbes have, but theoretical considerations indicate that they could make significant contributions to carbon fixation for their hosts. Additionally, ammonia-oxidizing microbes appear to also have undergone specific genomic adaptations to their host environment, and the hosts may also enable ammonia oxidation to occur in habitats where planktonic counterparts might be limited. This review identifies key knowledge gaps and highlights the need for further research to fully understand the ecological significance of symbiotic ammonia oxidation in marine ecosystems.},
}

@article {pmid40769480,
year = {2025},
author = {Dong, X and Zhang, Q and Li, M and Al-Dhabi, NA and Chen, J and He, J and Wang, H and Tang, W},
title = {Metagenomic analysis of algal-bacteria symbiosis system (ABSS) under aniline stress: Synergistic optimization of aniline degradation and nitrogen metabolism.},
journal = {Environmental research},
volume = {285},
number = {Pt 3},
pages = {122510},
doi = {10.1016/j.envres.2025.122510},
pmid = {40769480},
issn = {1096-0953},
abstract = {As an energy-efficient and environmentally friendly algae-bacteria symbiotic system (ABSS), the underlying mechanisms governing its response to aniline remained inadequately explored. To address this, our research conducted a metagenomics-bathe superior performance of an ABSS (R2) over conventional activated sludge (R1) for aniline wastewater treatment. Specifically, R2 exhibited more stable aniline and COD removal capabilities compared to R1, with a 20 % significant increase in total nitrogen removal efficiency. Metagenomic analysis revealed that microbial growth and metabolism in R2 were more vigorous. The abundance of functional genes associated with aniline degradation, ammonia assimilation, and nitrification in R2 was significantly higher than in R1. Notably, OLB12 in R2 made prominent contributions to aniline degradation and nitrogen metabolism. The introduction of microalgae reshaped the functional microbial community structure, collaboratively promoting the efficient operation of the system. These findings provided valuable guidance for the management of aniline wastewater.},
}

@article {pmid40768754,
year = {2025},
author = {Akhtar, JR and O'Connor, EK and Chung, KC},
title = {Parallel Advancements in Art and Anatomy.},
journal = {Annals of plastic surgery},
volume = {},
number = {},
pages = {},
doi = {10.1097/SAP.0000000000004456},
pmid = {40768754},
issn = {1536-3708},
abstract = {The relationship between art and medicine is symbiotic, and one of its foundations is the anatomical dissection. Dissections simultaneously contributed to an advancement of scientific understanding of the human body and the creation of artwork that depicted accurate human anatomy and body movements, specifically in European painting. Dissections became a standard component of both medical education and art training during the Renaissance, which introduced new expectations for artists to acquire a deep understanding of anatomy and reflect this in their work. With each art movement following the Renaissance, artists continued to strengthen their mastery of illustrating the human body and push the boundaries of artistic representation of the body. This paper outlines a brief history of how cadaver dissections became a cornerstone of both medical education and training for artists in European contexts, and the ways in which medical understanding and anatomical accuracy in art developed simultaneously. This is illustrated through close visual analyses of works from 3 time periods and art movements that exhibit increasing anatomical accuracy leading to mastery and artistic freedom.},
}

@article {pmid40767474,
year = {2025},
author = {Sui, J and Wang, L and Zhou, Y and Chen, F and Wang, T and Chen, SH and Cui, X and Yang, Y and Zhang, W},
title = {Resolving the Dilemma of Dicarboximide Fungicides Residue Contamination: Promises and Challenges of Microbial Degradation.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c04153},
pmid = {40767474},
issn = {1520-5118},
abstract = {Dicarboximide fungicides are widely used due to their low toxicity, broad spectrum, and high efficacy. However, their extensive accumulation in the environment can alter the composition of soil microbial communities, reduce the complexity of symbiotic networks within these communities, and pose potential threats to ecosystems and human health. Therefore, removing dicarboximide fungicide residues from various environmental media is of great practical significance. Microbial degradation has become a key focus in pollutant remediation research. To date, several microorganisms, including Providencia stuartii, Brevundimonas naejangsanensis, Rhodococcus, and Arthrobacter, have been identified as capable of degrading dicarboximide fungicides, with degradation rates ranging from 50% to 80%. This paper reviews the current research and challenges in microbial degradation of dicarboximide fungicide residues, focusing on fungicidal mechanisms, environmental fate, nontarget organism toxicity, potential degrading microorganisms, and molecular mechanisms. The findings serve as a reference for the rational use and bioremediation of dicarboximide fungicides, helping to mitigate their negative impact on the environment and living organisms while promoting sustainable agriculture and environmental conservation.},
}

@article {pmid40766715,
year = {2025},
author = {Van Vlaenderen, L and Conner, WR and Shropshire, JD},
title = {Counting cytoplasmic incompatibility factor mRNA using digital droplet PCR.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.07.30.667682},
pmid = {40766715},
issn = {2692-8205},
abstract = {Wolbachia bacteria inhabit over half of all insect species and often spread through host populations via efficient maternal transmission and cytoplasmic incompatibility (CI), killing aposymbiotic embryos when fertilized by symbiotic males. Wolbachia 's cifB gene triggers CI in males, while cifA , expressed in females, rescues embryos from CI-induced lethality. In some systems, cifA also contributes to CI induction. CI strength-the percentage of embryos that die from CI-is a key determinant of Wolbachia 's prevalence in host populations, and cifB mRNA levels in testes generally correlate with CI strength. Yet, cifB 's rarity can hamper precise quantification, necessitating tissue pooling for reverse transcription quantitative PCR (RT-qPCR) to achieve reliable measurements, obscuring variation at the level of individual insect tissues. Here, we present four RT digital droplet PCR (RT-ddPCR) assays to count rare cifA and cifB mRNA from w Mel Wolbachia in Drosophila melanogaster . These assays count cif transcripts alongside a synthetic spike-in RNA or a D. melanogaster housekeeping gene to normalize for technical or biological variation. These assays have a limit of detection of about 1 cifA and 3 cifB copies per reaction. We expect these methods to be useful for mosquito-control programs that use w Mel to block the spread of pathogens from Aedes aegypti to humans. Moreover, the oligos were designed with homology to cifA and cifB sequences from at least 33 Wolbachia strains, suggesting utility beyond w Mel. These methods will allow researchers to measure cif mRNA levels from individual insect tissues, enabling efforts to pair molecular and phenotypic data at unprecedented resolutions.},
}

@article {pmid40765519,
year = {2025},
author = {Uchida, T and Li, Y and Yamashita, H and Shimada, G and Shinzato, C},
title = {Microbiome of the Boring Giant Clam Provides Insights Into Holobiont Resilience Under Coral Reef Environmental Stress.},
journal = {Environmental microbiology},
volume = {27},
number = {8},
pages = {e70161},
pmid = {40765519},
issn = {1462-2920},
support = {20H03235//Japan Society for the Promotion of Science/ ; 21H04742//Japan Society for the Promotion of Science/ ; 24KJ0896//Japan Society for the Promotion of Science/ ; 24K01847//Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; *Coral Reefs ; *Microbiota ; Symbiosis ; *Bivalvia/microbiology/physiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Stress, Physiological ; Anthozoa/microbiology ; Phylogeny ; },
abstract = {Giant clams are key denizens of coral reef ecosystems, forming holobionts through symbiotic relationships with algae of the family Symbiodiniaceae, as in reef-building corals. In this study, we performed a tissue-specific microbiome analysis of the boring giant clam, Tridacna crocea and evaluated the impact of dark-induced bleaching on its outer mantle bacterial community. Using 16S rRNA metabarcoding, Endozoicomonas was identified as the dominant bacterial genus in most tissues, particularly in gills, implying an important contribution to the giant clam holobiont. In contrast, in the outer mantle, where algal symbionts reside, the microbiome exhibited greater diversity, with a significant presence of carotenoid-producing bacteria such as Rubritalea (Rubritaleaceae) and Muricauda (Flavobacteriaceae). These bacteria may protect symbiotic algae from light and thermal stresses, potentially enhancing holobiont resilience in coral reef environments. Although dark-induced bleaching significantly reduced algal cell density, bacterial diversity remained largely unaffected, suggesting a robust bacterial association, independent of algal dynamics. This study highlights the potential ecological significance of Endozoicomonas and carotenoid-producing bacteria in sustaining giant clam holobiont health and provides insights into microbial mechanisms that support stress tolerance in coral reef organisms.},
}

Animals
*Coral Reefs
*Microbiota
Symbiosis
*Bivalvia/microbiology/physiology
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification/metabolism
Stress, Physiological
Anthozoa/microbiology
Phylogeny

@article {pmid40765126,
year = {2025},
author = {Li, L and Tang, L},
title = {Gut Microbiota in Exercise-Regulated Development, Progression, and Management of Type 2 Diabetes Mellitus: A Review of the Role and Mechanisms.},
journal = {Medical science monitor : international medical journal of experimental and clinical research},
volume = {31},
number = {},
pages = {e947511},
doi = {10.12659/MSM.947511},
pmid = {40765126},
issn = {1643-3750},
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/therapy/physiopathology ; *Gastrointestinal Microbiome/physiology ; *Exercise/physiology ; Disease Progression ; Insulin Resistance/physiology ; Dysbiosis ; Animals ; },
abstract = {Imbalance of the gut microbiota is considered a possible factor in the rapid progression of insulin resistance in type 2 diabetes mellitus (T2DM). Dysbiosis of the gut microbiota can alter intestinal barrier function and host metabolism, as well as signaling pathways in T2DM patients, which are directly or indirectly associated with insulin resistance. Additionally, symbiotic fungi and opportunistic bacteria can stimulate the local immune system, increasing intestinal permeability and leading to gut leakage. This, in turn, activates systemic inflammation and contributes to insulin resistance. Exercise is known to play a crucial role in disease prevention and blood glucose control, as well as in managing diabetes-related organ complications. Aerobic exercise, in particular, is commonly used to prevent and control diabetes by enhancing skeletal muscle responsiveness to insulin through the upregulation of enzymes involved in cellular glucose utilization. Various forms of exercise can also alter the composition and function of the gut microbiota. This paper focuses on the relationship between the gut microbiota and T2DM, the impact of exercise on gut microbiota, and the role of the gut microbiota in exercise-induced improvement of T2DM, aiming to review the role and mechanisms of the gut microbiota in exercise-regulated development, progression, and management of T2DM.},
}

Humans
*Diabetes Mellitus, Type 2/microbiology/therapy/physiopathology
*Gastrointestinal Microbiome/physiology
*Exercise/physiology
Disease Progression
Insulin Resistance/physiology
Dysbiosis
Animals

@article {pmid40764272,
year = {2025},
author = {Peng, Q and Jiang, P and Yi, L and Li, Y and Yang, Q and Wan, X and He, J and Mo, Z and Niu, H and Lan, Q and Jia, H and Xu, D and Wang, C and Yang, H and Liu, Z and Chen, WH},
title = {In vivo systematic analysis of microbiota-prebiotic crosstalk reveals a synbiotic that effectively ameliorates DSS-induced colitis in mice.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2541028},
pmid = {40764272},
issn = {1949-0984},
mesh = {Animals ; *Synbiotics/administration & dosage ; *Colitis/chemically induced/microbiology/therapy ; *Gastrointestinal Microbiome/drug effects ; Dextran Sulfate/adverse effects ; Mice ; Humans ; *Prebiotics/administration & dosage ; Disease Models, Animal ; Mice, Inbred C57BL ; Male ; Bacteria/classification/genetics/isolation & purification ; Female ; Akkermansia ; },
abstract = {Systematic identification of prebiotic-microbe interactions is essential for developing precision microbiome-targeted interventions to improve human health. In this study, we developed an in vivo systematic screening platform to evaluate microbiota-prebiotic crosstalk and applied it to identify a synbiotic combination effective against dextran sulfate sodium (DSS)-induced colitis in mice. Specifically, we first established a humanized gut microbiota mouse model by colonizing mice with 73 microbial strains, which showed highly abundant and prevalent in the human gut. Concurrently, we administered the mice with 28 different prebiotic or prebiotic candidates, including polyphenols, polysaccharides, vitamins, and minerals common in the market. Following the DSS-induced colitis, we evaluated the protective effects of each microbiota-prebiotic pairing. Fourteen prebiotic or prebiotic candidates, designated as the ESS group, significantly alleviated colitis, partly by enriching specific beneficial microbes such as Bacteroides thetaiotaomicron, Akkermansia muciniphila, and Erysipelatoclostridium ramosum prior to disease onset. Further experiments revealed two symbiotic combinations with the strongest anti-inflammatory effects: calcium-magnesium tablets (CMT) combined with either B. thetaiotaomicron or A. muciniphila. Mechanistically, CMT promoted the growth of B. thetaiotaomicron and alleviated inflammation by upregulating genes associated with probiotic activity. Finally, in an intervention trial involving healthy human volunteers, CMT selectively increased B. thetaiotaomicron abundance without altering the overall gut microbiota composition. Together, our study presents a systematic framework for elucidating microbe-prebiotic interactions, identifying synbiotic combinations with therapeutic potential, and advancing precision microbiome-based strategies for disease prevention and treatment.},
}

Animals
*Synbiotics/administration & dosage
*Colitis/chemically induced/microbiology/therapy
*Gastrointestinal Microbiome/drug effects
Dextran Sulfate/adverse effects
Mice
Humans
*Prebiotics/administration & dosage
Disease Models, Animal
Mice, Inbred C57BL
Male
Bacteria/classification/genetics/isolation & purification
Female
Akkermansia

@article {pmid40763899,
year = {2025},
author = {Ahmad, F and Bodawatta, K and Poulsen, M and Zhu, D},
title = {Advancing approaches to cultivate industrially and ecologically relevant microorganisms from termite guts.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {108676},
doi = {10.1016/j.biotechadv.2025.108676},
pmid = {40763899},
issn = {1873-1899},
abstract = {The termite gut harbours a remarkably dense and diverse consortium of symbiotic microbes, encompassing archaeal, bacterial, and eukaryotic taxa. These symbiotic communities hold intricate ecological processes and a pronounced potential for exploitation across multifaceted domains, including industrially important enzymes, biofuels, pharmaceuticals, and bioremediation. Despite the conspicuous richness, a substantial portion of microbial assemblages inhabiting the termite gut remains undiscovered and inadequately characterized. Although traditional culture-based and culture-independent molecular-based technologies are broadly used to study termite gut microbiota, they frequently encounter limitations in the isolation, culturing, and characterization of less prevalent microbial lineages and are biased toward certain taxa. The rapid development of molecular techniques has greatly promoted the identification and genomic potential of microbes in termite guts, revealing hidden diversity and application potential. However, limitations in culture-based approaches to build on genomic insights have hampered our understanding of the ecology of most of these microbes and the capitalisation on their properties. To help improve culturomics approaches for termite gut microbes, we provide an overview of past and emerging methodologies for isolation and cultivation of symbiotic microbes. In doing so, we highlight future directions and current challenges that need to be overcome to advance these approaches.},
}

@article {pmid40763740,
year = {2025},
author = {Chen, K and Wang, X and Pang, R and Chen, L and Chen, J and Ren, Z and Wang, S and Wang, Y and Li, X and Su, C},
title = {The sucrose transporter GmSWEET3c drives soybean nodulation by regulating root sucrose allocation.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.07.032},
pmid = {40763740},
issn = {1879-0445},
abstract = {Symbiotic nitrogen fixation in legumes, driven by the interaction between rhizobia and host plants, provides essential nitrogen for plant growth but demands substantial energy. Sucrose, the principal product of photosynthesis, is critical in supporting this process. Despite its importance, the mechanisms underlying sucrose allocation following rhizobia inoculation remain poorly understood. Here, we identified and characterized GmSWEET3c, a rhizobia-induced sucrose transporter that is critical for sucrose allocation to the root susceptible zone. Functional analysis of the Gmsweet3c mutant revealed impaired sucrose allocation and a significant reduction in nodule formation, underscoring its critical role in symbiotic nodulation. Using a GmSWEET3c-GFP fusion protein, we found that the protein is located in both the plasma membrane of root cells and the membranes of infection threads, suggesting dual roles of GmSWEET3c in facilitating sucrose transport to the root susceptible zone and directing sucrose toward infection threads. Moreover, we demonstrated that GmNSP1, a key symbiotic transcription factor, directly binds to the promoter region of GmSWEET3c, activating its expression. Collectively, our findings highlight GmSWEET3c as a key mediator of sucrose distribution in soybean roots after rhizobia inoculation, enhancing our understanding of carbohydrate allocation in legume-rhizobia symbioses.},
}

@article {pmid40762940,
year = {2025},
author = {Wang, Y and Zhao, Z and Liu, J and Yang, A and Jacquemyn, H and Yang, L and Qian, X and Li, T and Ding, G and Xing, X},
title = {Contribution of orchids to the carbon budget of fungi in germinating seeds of Gymnadenia conopsea.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {40762940},
issn = {1869-1889},
abstract = {Orchids critically rely on mycorrhizal fungi for seed germination and seedling development, but the extent to which the fungus benefits from the orchid is less clear. Recent work in arbuscular mycorrhizae has suggested that plants can provide fatty acids (FAs) to fungi, but empirical evidence in orchids remains limited. Here, we combine lipidomic and transcriptomic analyses to test the hypothesis that the germination-promoting fungus Ceratobasidium sp. GS2 receives carbon in the form of FAs from Gymnadenia conopsea seeds during symbiotic germination. Confocal and transmission electron microscopy confirmed the potential of FA transfer from seeds to the fungus. Symbiosis resulted in significant changes in the lipid composition of the fungus, with increased concentrations of FAs in the external mycelium. RNA-seq showed upregulation of genes associated with FA synthesis in seeds and downregulation of de novo FA synthesis genes in fungi 12 d post-symbiosis, indicating that the increased amounts of FAs in the fungus may originate from the seeds. These results indicate that FAs absorbed by hyphae in the colonized inner cortex cells support hyphal growth, providing evidence for directional carbon flow from the orchid seeds to the fungus and supporting a "give now and get now" model of mutualism in orchid-fungus symbioses.},
}

@article {pmid40761278,
year = {2025},
author = {Boyno, G and Rezaee Danesh, Y and Çevik, R and Teniz, N and Demir, S and Demirer Durak, E and Farda, B and Mignini, A and Djebaili, R and Pellegrini, M and Porcel, R and Mulet, JM},
title = {Synergistic benefits of AMF: development of sustainable plant defense system.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1551956},
pmid = {40761278},
issn = {1664-302X},
abstract = {Arbuscular mycorrhizal fungi (AMF) are a ubiquitous group of soil microorganisms that form symbiotic relationships with the roots of over 80% of terrestrial plant species. These beneficial fungi are crucial in plant growth, nutrition enhancement, and abiotic and biotic stress resilience. This review explores the AMF synergistic benefits including their capacity to interact with plant roots system to enhance nutrient absorption, improve stress resilience, and confer disease resistance, and their potential applications in sustainable agriculture. The Review integrates recent insights illustrating the molecular processes responsible for improving plant defense mechanisms by AMF, including the modulation of signaling pathways. It highlights the importance of AMF-induced systemic resistance in enhanced abiotic and biotic stress resistance. Moreover, the article provides an integrative perspective on applying AMF toward sustainable plant protection. Within this context, we discussed how these fungi improve plant performance, including enhanced nutrient acquisition, increased tolerance to environmental stressors, and enhanced protection against pathogens by improving plant resistance to biotic stress through the activation of the plant immune system. We also examine the ecological significance of AMF in maintaining soil health and fertility and highlight the importance of incorporating their management into sustainable agricultural practices. Future research directions and innovative applications are also presented. The literature survey demonstrated these fungi's versatility in improving plant tolerance to several biotic and abiotic stresses. At the scientific level, these abilities are supported by several open-field experiments on different plant species. Available commercial formulations and positive ongoing research of AMF, in combination with other sustainable tools, highlight the solid research outline on these beneficial fungi.},
}

@article {pmid40759634,
year = {2025},
author = {Lee, H and Kim, B and Park, J and Park, S and Yoo, G and Yum, S and Kang, W and Lee, JM and Youn, H and Youn, B},
title = {Cancer stem cells: landscape, challenges and emerging therapeutic innovations.},
journal = {Signal transduction and targeted therapy},
volume = {10},
number = {1},
pages = {248},
pmid = {40759634},
issn = {2059-3635},
support = {RS-2023-00207904//National Research Foundation of Korea (NRF)/ ; No. RS-2023-00301938//National Research Foundation of Korea (NRF)/ ; },
mesh = {Humans ; *Neoplastic Stem Cells/pathology/metabolism/immunology ; *Tumor Microenvironment/genetics ; *Neoplasms/genetics/therapy/pathology/metabolism/immunology ; Drug Resistance, Neoplasm/genetics ; Animals ; },
abstract = {Cancer stem cells (CSCs) constitute a highly plastic and therapy-resistant cell subpopulation within tumors that drives tumor initiation, progression, metastasis, and relapse. Their ability to evade conventional treatments, adapt to metabolic stress, and interact with the tumor microenvironment makes them critical targets for innovative therapeutic strategies. Recent advances in single-cell sequencing, spatial transcriptomics, and multiomics integration have significantly improved our understanding of CSC heterogeneity and metabolic adaptability. Metabolic plasticity allows CSCs to switch between glycolysis, oxidative phosphorylation, and alternative fuel sources such as glutamine and fatty acids, enabling them to survive under diverse environmental conditions. Moreover, interactions with stromal cells, immune components, and vascular endothelial cells facilitate metabolic symbiosis, further promoting CSC survival and drug resistance. Despite substantial progress, major hurdles remain, including the lack of universally reliable CSC biomarkers and the challenge of targeting CSCs without affecting normal stem cells. The development of 3D organoid models, CRISPR-based functional screens, and AI-driven multiomics analysis is paving the way for precision-targeted CSC therapies. Emerging strategies such as dual metabolic inhibition, synthetic biology-based interventions, and immune-based approaches hold promise for overcoming CSC-mediated therapy resistance. Moving forward, an integrative approach combining metabolic reprogramming, immunomodulation, and targeted inhibition of CSC vulnerabilities is essential for developing effective CSC-directed therapies. This review discusses the latest advancements in CSC biology, highlights key challenges, and explores future perspectives on translating these findings into clinical applications.},
}

Humans
*Neoplastic Stem Cells/pathology/metabolism/immunology
*Tumor Microenvironment/genetics
*Neoplasms/genetics/therapy/pathology/metabolism/immunology
Drug Resistance, Neoplasm/genetics
Animals

@article {pmid40758735,
year = {2025},
author = {Chen, CL and Zeng, KW and Chen, HC and Deng, YY and Lee, CF and Huang, DC and Liu, LC},
title = {Secure and efficient graduate employment: A consortium blockchain framework with InterPlanetary file system for privacy-preserving resume management and efficient talent-employer matching.},
journal = {PloS one},
volume = {20},
number = {8},
pages = {e0315277},
pmid = {40758735},
issn = {1932-6203},
mesh = {Humans ; *Employment ; *Blockchain ; *Personnel Selection/methods ; Job Application ; *Privacy ; *Computer Security ; Students ; },
abstract = {In recent years, the unemployment situation of teenagers has become increasingly serious, and many college students face the problem of unemployment upon graduation. Concurrently, Companies need more support in their talent acquisition processes, including high costs, security concerns, inefficiencies, and time-consuming sourcing procedures. Moreover, job applicants frequently confront risks associated with potentially compromising their personal information during the application process. Since blockchain technology has the characteristics of non-tampering, traceability, and non-repudiation, it has outstanding significance for solving the trust problem between organizations. Blockchain has emerged as a powerful tool for tackling talent acquisition campaigns. This study proposes a novel approach utilizing consortium chain technology in conjunction with the InterPlanetary File System (IPFS) to develop a decentralized talent recruitment system. This approach enables students, educational institutions, and potential employers to encrypt and upload data to the blockchain through consortium chain technology, with strict access controls requiring student authorization for resume data retrieval. The proposed system facilitates a symbiotic relationship between educational institutions and industry partners, allowing students to identify suitable employment opportunities while enabling companies to source candidates with requisite expertise efficiently. Finally, the system could meet the characteristic requirements of various blockchains, perform well in terms of communication cost, computing cost, throughput, and transaction delay in the blockchain, and contribute to solving talent recruitment.},
}

Humans
*Employment
*Blockchain
*Personnel Selection/methods
Job Application
*Privacy
*Computer Security
Students

@article {pmid40758630,
year = {2025},
author = {Klamert, L and Brockett, C and Craike, M and Shrestha, N and Parker, AG},
title = {The imperative of planetary mental health: insights, recommendations, and a call to action.},
journal = {Global public health},
volume = {20},
number = {1},
pages = {2541220},
doi = {10.1080/17441692.2025.2541220},
pmid = {40758630},
issn = {1744-1706},
mesh = {Humans ; *Mental Health ; *Global Health ; *Environmental Health ; },
abstract = {An alarming progression of human-centred and environmental concerns has marked the Anthropocene, including climatic changes and the inextricably linked deterioration of human mental health. Expanding on the 2015 Rockefeller Foundation-Lancet Commission on Planetary Health, we propose that mental health be explicitly included within the planetary health approach. This inclusion acknowledges the importance of population mental health as part of planetary health and addresses the symbiotic deterioration of global mental health and environmental health. As part of this approach, we conceptualise several types of interventions, including symbiocentric and transformative mental health interventions, with the latter combining active environmentalism with the aim of simultaneously improving mental health and wellbeing. We further identify several areas of opportunity in which transformative interventions could be translated to practice and implemented across a range of settings, including workplaces, educational contexts, and organised sport. Making a call to action, we highlight the urgency of shifting from individualised to collective environmental responsibility, including collective transformative reflection, with different stakeholders coming together to scale up transformative interventions and working towards true planetary (mental) health. Finally, we give recommendations to promote symbiocentric and transformative interventions in policy and reform.},
}

Humans
*Mental Health
*Global Health
*Environmental Health

@article {pmid40756436,
year = {2025},
author = {Priya Reddy, YN and Johnson, JM and Oelmüller, R},
title = {A cell wall extract of a Fusarium incarnatum strain requires the mitochondrial POLY(A)-SPECIFIC RIBONUCLEASE AtPARN for inducing cytoplasmic calcium elevation in Arabidopsis roots.},
journal = {Physiology and molecular biology of plants : an international journal of functional plant biology},
volume = {31},
number = {6},
pages = {851-861},
pmid = {40756436},
issn = {0971-5894},
abstract = {UNLABELLED: Cytoplasmic Ca[2+] ([Ca[2+]]cyt) elevation is a rapid response of roots to colonizing beneficial and pathogenic fungi. We have previously demonstrated that the elicitor-active compound cellotriose from a cell wall (CW) extract of the beneficial fungus Piriformospora indica requires the MALECTIN-DOMAIN CONTAINING CELLOOLIGOMER RECEPTOR KINASE1 (CORK1) and the mitochondrial POLY(A)-SPECIFIC RIBONUCLASE AtPARN for [Ca[2+]]cyt elevation in Arabidopsis roots. Here, we show that CW extracts from beneficial and pathogenic Fusarium strains, in particular Fusarium incarnatum strain K23, require AtPARN, but not CORK1 for [Ca[2+]]cyt elevation and the activation of Ca[2+]-dependent downstream responses. [Ca[2+]]cyt elevation by the F. incarnatum strain K23 extract does not require the BRASSINOSTEROID INSENSITIVE1-ASSOCIATED RECEPTOR KINASE1 (BAK1) co-receptor or the TWO-PORE Ca[2+] CHANNEL1 (TPC1) but operates synergistically with the cellotriose- and chitin-induced signaling pathways. We propose a convergence of the signaling pathways induced by the CW extracts from P. indica and K23 at AtPARN prior to the increase in [Ca[2+]]cyt ~ 90 s after the stimulus. Furthermore, the elevated [Ca[2+]]cyt levels activate a mild defense response which might be used by the roots to restrict fungal propagation and to balance beneficial and non-beneficial traits in the symbiosis.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-025-01600-7.},
}

@article {pmid40754665,
year = {2025},
author = {Zhang, X and Gu, L and Yang, G and Liu, C and Huang, K and Chen, Q},
title = {Effects of isaria cateniannulata on the colonization process and enzyme activity of fagopyrum tataricum seeds during germination.},
journal = {Virulence},
volume = {},
number = {},
pages = {2543062},
doi = {10.1080/21505594.2025.2543062},
pmid = {40754665},
issn = {2150-5608},
abstract = {Endophytic colonization of entomopathogenic fungi has garnered significant attention for its role in promoting plant growth. Specifically, Isaria cateniannulata has shown a positive effect on the germination of F. tataricum (buckwheat) seeds, but the mechanisms underlying this promotion remain unclear. This study aimed to elucidate the colonization process of I. cateniannulata in F. tataricum seeds during germination stages, quantify the colonization efficiency and tissue specificity of the fungus, and investigate the temporal dynamics of antioxidant enzyme activities and malondialdehyde content triggered by fungal colonization. Furthermore, we evaluated the potential of I. cateniannulata-colonized seedlings to suppress T. urticae populations through oviposition inhibition. The results demonstrated for the first time that I. cateniannulata could successfully colonize germinating F. tataricum seeds during the seed imbibition and germination stages, either by forming dissolution zones with its spores or by germinating and forming mycelia. Initial colonization of all tissues was observed within 16 h, with colonization rates peaking after 5 days, with a preferential colonization rate observed as endosperm > embryo > seed coat. Furthermore, the colonization by I. cateniannulata enhanced peroxidase (POD) activity in the embryo and reduced malondialdehyde (MDA) content. Seedlings grown after colonization were also found to effectively reduce the number of eggs laid by T. urticae. These findings provide both theoretical insights and practical foundation for developing a symbiotic system between I. cateniannulata and F. tataricum seeds.},
}

@article {pmid40753811,
year = {2025},
author = {Xu, Y and Wang, SP and Zhang, WS and Sun, ZY and Gou, M and Wang, ST and Tang, YQ},
title = {Modified biochar mitigates nitrogen loss in distilled grain waste composting by modulating microbial community assembly and function.},
journal = {Environmental research},
volume = {285},
number = {Pt 3},
pages = {122495},
doi = {10.1016/j.envres.2025.122495},
pmid = {40753811},
issn = {1096-0953},
abstract = {Pristine biochar (DB)-assisted composting can enhance product maturity and mitigate nitrogen loss, but its efficacy varies and is limited by feedstock variability and preparation conditions, highlighting the need for surface modifications to optimize performance. This study systematically investigated the effects of DB and KOH-modified biochar (DBK) on compost maturity, nitrogen loss, and the related microbial mechanisms during the composting of distilled grain waste, using a group without biochar addition (D) as the control. Results indicated that DBK exhibited a specific surface area of 644.33 m[2]/g and was rich in pore structures and functional groups. DBK significantly promoted compost maturity, with the seed germination index (GI) reaching 70 % by 23 d and biological nitrification occurring earlier (16 d). Additionally, compared to D and DB, DBK reduced nitrogen loss by 34.13 % and 10.47 %, respectively. DBK accelerates critical nitrogen transformation processes by increasing the abundance of nitrogen-fixing bacteria and associated functional genes. Neutral community modeling and symbiotic networks indicated higher microbial community complexity and stochasticity, thereby promoting functional redundancy and improving nitrogen retention. Furthermore, Actinomadura and Chryseolinea were identified as key microbial drivers of nitrogen transformation, with their nxrABC and hao genes playing crucial roles in establishing efficient 'microbe-gene' synergistic mechanisms. Finally, economic analysis indicated that DBK generated a net profit of up to 63.63 RMB/t. These findings provide a theoretical basis for using modified biochar to promote maturity and control nitrogen loss during composting.},
}

@article {pmid40753805,
year = {2025},
author = {Ai, L and Wei, M and Ma, J and Dai, Y and Zhang, J and Chen, F and Qin, Y and Yang, H},
title = {Occurrence patterns and ecological implications of microplastic contamination in citrus orchard soils on Karst Sloping Terrains, South China.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139391},
doi = {10.1016/j.jhazmat.2025.139391},
pmid = {40753805},
issn = {1873-3336},
abstract = {Microplastics have emerged as pervasive pollutants in soil ecosystems, posing threats to fragile karst environments. However, their occurrence characteristics and ecological consequences remain poorly understood. In the present study, we investigated the pollution characteristics, ecological risks, and relationships among soil environment indicators and microplastics in citrus-cultivated soils in the Lijiang karst sloping terrains, South China. The average concentration of soil microplastics was 3160 ± 342 items/kg, and the particle abundance and pollution load index increased with cultivation years and declined with slope position. Moreover, we detected significant correlations among the abundance, shape, and composition of microplastics and key soil parameters. Notably, microplastics were observed to have significant effects on the structure, network relationships, and functionalities of soil microbial communities. Positive relationships were identified between the soil microplastic abundance and the energy-sourcing function of bacteria and the symbiotic mode of nutrition in fungi. Shape differences of microplastics were significantly positively correlated with saprophytic nutrition in fungi. Our findings provide valuable insights into the ecological risks posed by microplastics and highlight the urgent necessity of implementing sustainable strategies for plastic waste management to mitigate adverse impacts on ecologically sensitive regions, including agricultural soils in the karst sloping terrains of South China.},
}

@article {pmid40752570,
year = {2025},
author = {Igamberdiev, AU},
title = {The development of code systems during eukaryogenesis and the rise of multicellularity.},
journal = {Bio Systems},
volume = {255},
number = {},
pages = {105546},
doi = {10.1016/j.biosystems.2025.105546},
pmid = {40752570},
issn = {1872-8324},
abstract = {The expansion of the set of biological codes associated with the appearance and complexification of eukaryotic cells (eukaryogenesis) and the evolution of multicellularity is based on the development of higher codes operating over the genetic system. In the course of evolution, the perception-action functional cycles described by Jakob von Uexküll become complemented by the secondary meta-cycles, which perceive the work of the primary cycles, and finally by tertiary cycles of meta-reflexivity, which perceive and evaluate the previous activity of the secondary functional cycles and generate a new field of meanings associated with conscious experience. The development of secondary and tertiary cycles forms the basis of higher-level codes operating over the genetic system and resulting in the evolutionary separation between unikonts and bikonts, in the divergence between protostomes and deuterostomes, in all events of cellular differentiation manifested as differentiation trees, and finally in the appearance of consciousness. The expansion of codes associated with the rise of eukaryotic organelles and with the cytoskeleton rearrangements in the ontogenesis of multicellular organisms determines the course of the evolutionary process toward complexification. The internally controlled recombination process, in particular, in the course of meiotic cell division and ontogenetic differentiation, becomes the driving factor of progressive evolution. It corresponds to the growing role of the epigenome and epigenetic regulation in the complexification of biological organization. It is concluded that the evolutionary process unfolds as a propagating non-deducible construction following the generation of functional redundancy, which is achieved through gene duplication, symbiosis, and cell-cell interactions, and becomes an important precondition for the appearance of new evolutionary acquisitions.},
}

@article {pmid40749845,
year = {2025},
author = {Lu, YZ and Di, C and Sun, J and Wang, L and Li, X and Zhu, GC},
title = {Bentazone stress resistance in Methylocystis-Tetradesmus symbiosis: Biochemical and communicative exchanges.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133053},
doi = {10.1016/j.biortech.2025.133053},
pmid = {40749845},
issn = {1873-2976},
abstract = {Methane-oxidizing bacteria (MOB)-microalgae symbiosis is vital for greenhouse gas and carbon regulation in shallow aquatic ecosystems (e.g., rice paddies). However, the effects of pesticide exposure on these non-target species and their stress-induced microbial interactions remain poorly understood. In this study, the widely used pesticide bentazone (BTZ), known to occur at concentrations ranging from background levels to higher values (e.g., up to 100 mg/L) in specific contaminated scenarios like agricultural wastewater, was employed as a model stressor to investigate its effects on the symbiotic system formed by Methylocystis bryophila (M. bryophila) and Tetradesmus obliquus (T. obliquus). Results showed that while BTZ exposure (tested at 10-30 mg/L) inhibited key processes like cell proliferation, methane oxidation, and photosynthesis in individual species, the symbiotic system exhibited significantly enhanced resilience. This resilience stemmed from synergistic interactions, including: facilitated gas exchange promoting metabolic recovery; altered metabolic coupling (e.g., MOB porphyrin supporting algal chlorophyll, algal use of MOB-derived acetate); enhanced intercellular exchange of nutrients and protective extracellular polymeric substances formation; and strengthened physical association via algal metabolites promoting bacterial aggregation and mass transfer. This study elucidates key biochemical and communication mechanisms driving enhanced stress tolerance in MOB-microalgae symbiosis, highlighting the crucial role of microbial interactions in mitigating pesticide impacts in aquatic environments.},
}

@article {pmid40749791,
year = {2025},
author = {Li, M and Zhao, G and Li, MM},
title = {Regulatory mechanisms of quorum sensing in microbial communities and their potential applications in ruminant livestock production.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.07.055},
pmid = {40749791},
issn = {2090-1224},
abstract = {BACKGROUND: Quorum sensing (QS) is a cell-to-cell communication system that enables microbial communities to dynamically regulate their metabolism and physiological activities according to the surrounding cell density. The rumen's diverse microbial ecosystem represents a classic example of host-microbiome symbiosis. Despite significant progress in understanding the composition and function of ruminal microbial communities, the underlying communication mechanisms in the rumen ecosystem remain largely enigmatic. Gaining insight into these regulatory mechanisms is crucial for developing knowledge-based strategies to improve animal productivity, health, and sustainability in ruminant livestock production.

AIM OF REVIEW: This review aims to provide an overview of microbial QS communication systems mediated by diverse signaling molecules, including bacterial intraspecies and interspecies QS, fungal QS, and archaeal QS. We conducted a structured review by searching multiple scientific databases, synthesizing data from relevant studies, and critically evaluating the roles of QS systems in microbial communities. This approach ensures a comprehensive analysis of the current understanding of QS mechanisms and their implications for ruminant livestock. Specifically, we elucidate the identification and potential mechanisms of the QS system facilitated by three prevalent signaling molecules (N-acyl homoserine lactones, autoinducing peptides, and autoinducer 2) in ruminants. Recent advances in understanding the effects of QS on microbial fermentation, immune function, biofilm formation, and virulence factor production are summarized in detail, providing a scientific basis for applying QS in ruminant livestock production.

The rumen harbors various QS signaling molecules that modulate microbial community dynamics, impacting composition, structure, and function. The versatility of QS allows it to regulate ruminal fermentation and inhibit pathogen growth, thereby improving productivity and reducing disease risk in ruminants. This review synthesizes recent advances in QS mechanisms, crucial for disease prevention, combating antibiotic resistance, and promoting sustainable livestock production. Future research should investigate QS pathways and networks in the rumen microbiome through in vivo experiments and multi-omics analyses to gain a deeper understanding of microbial community regulation.},
}

@article {pmid40749676,
year = {2025},
author = {Qian, JM and Li, K and Liu, W and Zhang, J and Wylie, A and Arnall, B and Krzmarzick, MJ and Wang, E and Oldroyd, GED and Bai, Y and Feng, F and Zhang, J},
title = {Chitooligosaccharide receptors modulate root microbiota to enhance symbiosis and growth in Medicago.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.07.010},
pmid = {40749676},
issn = {1879-0445},
abstract = {Plant roots interact with beneficial microbes, such as arbuscular mycorrhizal fungi (AMF), to aid in nutrient uptake. The interaction with AMF is initiated by plant Lysin motif (LysM) receptor-like kinases, CERK1 and LYR4 in Medicago truncatula, that detect AMF signals such as chitooligosaccharides (COs). However, the broader role of AMF-detecting receptors in shaping the root microbial community is largely unknown, and the impact of these receptor-mediated microbial communities on the AMF symbiosis is yet to be determined. This study examines the effects of CERK1 and LYR4 mutations on the root bacterial community, showing that these receptors have significant effects on shaping the bacterial community. Using bacteria isolated from wild-type roots, we created a synthetic bacterial community (SynCom), CO-SynCom. Plants inoculated with CO-SynCom exhibited significantly enhanced growth and AMF colonization in a manner dependent on the CO receptors LYR4 and CERK1, likely due to CERK1- and LYR4-mediated changes in hormone-related pathways and activation of symbiosis signaling. Our results highlight the essential role of plant symbiotic receptors in shaping root microbiota and offer valuable insights into optimizing plant-microbe interactions to enhance symbiosis and support sustainable agriculture.},
}

@article {pmid40749035,
year = {2025},
author = {Gómez de Las Heras, MM and Carrasco, E and Pérez-Manrique, M and Inohara, N and Delgado-Pulido, S and Fernández-Almeida, Á and Gálvez-Castaño, MI and Francos-Quijorna, I and Simó, C and García-Cañas, V and Escrig-Larena, JI and Aranda, JF and Soto-Heredero, G and Gabandé-Rodríguez, E and Blanco, EM and Días-Almeida, J and Núñez, G and Mittelbrunn, M},
title = {CD4 T cell therapy counteracts inflammaging and senescence by preserving gut barrier integrity.},
journal = {Science immunology},
volume = {10},
number = {110},
pages = {eadv0985},
doi = {10.1126/sciimmunol.adv0985},
pmid = {40749035},
issn = {2470-9468},
mesh = {Animals ; Mice ; *Inflammation/immunology ; *Gastrointestinal Microbiome/immunology ; *Aging/immunology ; *CD4-Positive T-Lymphocytes/immunology/transplantation ; Mice, Inbred C57BL ; *Intestinal Mucosa/immunology ; T-Lymphocytes, Regulatory/immunology ; Adoptive Transfer ; Cellular Senescence ; },
abstract = {Healthy aging relies on a symbiotic host-microbiota relationship. The age-associated decline of the immune system can pose a threat to this delicate equilibrium. In this work, we investigated how the functional deterioration of T cells can affect host-microbiota symbiosis and gut barrier integrity and the implications of this deterioration for inflammaging, senescence, and health decline. Using the Tfam[fl/fl]Cd4[Cre] mouse model, we found that T cell failure compromised gut immunity leading to a decrease in T follicular cells and regulatory T cells (Treg cells) and an accumulation of highly proinflammatory and cytotoxic T cells. These alterations were associated with intestinal barrier disruption and gut dysbiosis. Microbiota depletion or adoptive transfer of total CD4 T cells or a Treg cell-enriched pool prevented gut barrier dysfunction and mitigated premature inflammaging and senescence, ultimately enhancing the health span in this mouse model. Thus, a competent CD4 T cell compartment is critical to ensure healthier aging by promoting host-microbiota mutualism and gut barrier integrity.},
}

Animals
Mice
*Inflammation/immunology
*Gastrointestinal Microbiome/immunology
*Aging/immunology
*CD4-Positive T-Lymphocytes/immunology/transplantation
Mice, Inbred C57BL
*Intestinal Mucosa/immunology
T-Lymphocytes, Regulatory/immunology
Adoptive Transfer
Cellular Senescence

@article {pmid40748298,
year = {2025},
author = {Cersosimo, A and Longo Elia, R and Condello, F and Colombo, F and Pierucci, N and Arabia, G and Matteucci, A and Metra, M and Adamo, M and Vizzardi, E and LA Fazia, VM},
title = {Cardiac rehabilitation in patients with atrial fibrillation.},
journal = {Minerva cardiology and angiology},
volume = {},
number = {},
pages = {},
doi = {10.23736/S2724-5683.25.06885-1},
pmid = {40748298},
issn = {2724-5772},
abstract = {Cardiovascular diseases (CVD) remain the leading cause of morbidity and mortality worldwide, accounting for significant public health and economic burdens. Cardiac rehabilitation (CR) is a comprehensive, multidisciplinary program designed to aid patients in recovering from cardiac events and to prevent further complications. The aim of CR is to improve their quality of life and prognosis. It involves continued prognostic stratification, clinical stabilization, optimization of pharmacological and non-pharmacological therapy, management of comorbidities, treatment of disabilities, reinforcement of secondary prevention interventions, and maintenance of adherence to therapy. The most recent European Society of Cardiology guidelines for the diagnosis and management of atrial fibrillation (AF) emphasize the importance of cardiorespiratory fitness, recommending that patients engage in moderate-intensity exercise and remain physically active to prevent AF incidence or recurrence. Through this symbiotic relationship, CR addresses all aspect of cardiac fitness in AF management. The program's structured exercise regimens are specifically tailored to address the challenges associated with AF, promoting overall cardiovascular health and reducing the risk for cardiac death. CR is also crucial for emotional well-being, offering support and coping mechanisms for the psychological impact of AF, beyond the physical training program. CR programs involve a multidisciplinary approach that is carried out collaboratively by a team of healthcare professionals, including nurses, physiotherapists, psychologists, and dietitians. Moreover, CR in AF patients aims to carry out comprehensive patient support through clinical stabilization and therapy optimization interventions, prescription and implementation of physical activity, educational support on lifestyle risk factors and social-emotional distress, and periodic assessment of outcomes. This narrative review aims to elucidate the role of CR in AF patients, shedding light on the potential benefits and challenges associated with integrating rehabilitation programs into the care of individuals with AF.},
}

@article {pmid40747421,
year = {2025},
author = {Ansaldo, E and Yong, D and Carrillo, N and McFadden, T and Abid, M and Corral, D and Rivera, C and Farley, T and Bouladoux, N and Gribonika, I and Belkaid, Y},
title = {T-bet expressing Tr1 cells driven by dietary signals dominate the small intestinal immune landscape.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.30.662190},
pmid = {40747421},
issn = {2692-8205},
abstract = {UNLABELLED: Intestinal immunity defends against enteric pathogens, mediates symbiotic relationships with the resident microbiota, and provides tolerance to food antigens, safeguarding critical nutrient absorption and barrier functions of this mucosal tissue. Despite the abundance of tissue resident activated T cells, their contributions to these various roles remains poorly understood. Here, we identify a dominant population of IL-10 producing, T-bet expressing CD4+ Tr1 T cells, residing in the small intestinal lamina propria at homeostasis. Remarkably, these intestinal Tr1 cells emerge at the time of weaning and accumulate independently of the microbiota displaying similar abundance, function and TCR repertoire under germ-free conditions. Instead, the small intestinal T-bet+ Tr1 program is driven and shaped by dietary antigens, and accumulates in a cDC1-IL-27 dependent manner. Upon activation, these cells robustly express IL-10 and multiple inhibitory receptors, establishing a distinct suppressive profile. Altogether, this work uncovers a previously unappreciated dominant player in homeostatic small intestinal immunity with the potential to play critical suppressive roles in this tissue, raising important implications for the understanding of immune regulation in the intestine.

SIGNIFICANCE STATEMENT: Establishing immunological tolerance to self and environmental antigens is critical to preserve tissue homeostasis and function. In the intestine, both dietary and microbiota derived antigens are routinely encountered by the immune system, which deploys a variety of mechanisms to maintain tolerance to these innocuous antigens. Understanding how immunological tolerance is established is critical, a when this process goes awry it can lead to severe inflammatory and autoimmune diseases such as food allergy and inflammatory bowel disease. However, how tolerance is established in the intestine is still poorly understood. In this study we describe a novel dominant T cell population in the small intestine shaped by dietary components with the potential to play important roles in immune tolerance at this site. back # IntroductionBarrier surfaces such as the gut and skin represent the first line of defense against the environment. These organs must strike a delicate balance between providing protection against environmental and infectious agents, maintaining tissue function, and establishing a homeostatic symbiotic relationship with resident microbes collectively known as the microbiota (1). The immune system plays a critical role in establishing these dynamic and carefully regulated relationships, as evidenced by the large number of immune cells present at these sites. Of particular note, activated T cells are very abundant at barrier tissues, where they orchestrate immune effector functions geared towards these varied tasks (1, 2). In the small intestine, the intraepithelial compartment harbors innate like natural CD8aa⁺ IELs, many of which are self reactive; as well as CD4⁺CD8aa⁺ and CD8ab⁺ IELs responding to dietary and microbial antigens (3). The underlying lamina propria (SILP) harbors predominantly CD4⁺ T cells, which participate in responses to commensal-derived and dietary antigens (2, 4). Despite the abundance of small intestinal CD4 T cells, only a handful of cognate immune interactions focusing on Type 17 and T regulatory helper subsets have been described. Thus, whether immune responses in this tissue are truly limited to a small number of antigenic triggers and effector functions remains to be fully elucidated. The small number of gut homeostatic CD4 T cell responses described thus far have been shown to primarily respond to specific commensal bacteria or dietary antigens (1, 2, 5-8): Among other examples, SFB induces cognate Th17 cells in the small intestine (9, 10), a consortium human commensal bacteria induces CD8b⁺ cells in the colon (11), and Akkermansia muciniphila indices T FH and other effector cells in the Peyer's patches and lamina propria, respectively (12). Furthermore most regulatory T cells in the colon are induced in response to commensal or pathobiont species at homeostasis, providing critical regulatory functions (13, 14). Cognate immune responses to SFB help contain this commensal species in the intestine (15), but also have systemic impacts on the susceptibility to autoimmune disease (16, 17). Interestingly, despite presenting a classical Th17 effector profile, a subset of SFB-induced Th17 cells possess IL-10 secretion capabilities and suppress cognate immune responses without the expression of Foxp3 (18), suggesting immunoregulatory functions reminiscent of Tr1 cells. Whether these competing capabilities are unique to SFB-specific immune responses or a general hallmark of small intestinal immunity remains unknown. The description of SFB-specific Tr1-like cells in the small intestine was surprising, as this CD4⁺ T cell subset, characterized by abundant IL-10 secretion in the absence of Foxp3 expression, has only been described in the context of chronic antigen stimulation, such as chronic infection or cancer (19). The Tr1 cell program is controlled by a variety of transcription factors and upstream signaling pathways, including IL-27 signaling, MAF and AHR (20). AHR-ligands are abundant in the intestine, and MAF is a hallmark of other regulatory commensal-specific responses (21, 14). Furthermore, IL-27, which can induce both proinflammatory and immunoregulatory functions, is abundant in the small intestine (22, 23). This raises the possibility that the Tr1 program is a more general feature of small intestinal immunity, not uniquely restricted to SFB-specific responses. In this study we explore the breadth of CD4⁺ T cell responses in the small intestine, and uncover a previously uncharacterized CD4⁺T-bet⁺ T cell immune response that is dominant in this tissue. Unexpectedly, these SILP CD4⁺T-bet⁺ T cells are independent of the microbiota, maintaining a similar functional profile and shared antigen specificities in germ-free conditions. Instead, we reveal that dietary components drive the accumulation, function, and clonal selection of this T cell population. Finally, we show that, contrary to classical Th1 cells, SILP CD4⁺T-bet⁺ T cells adopt a Tr1 immunoregulatory functional program during activation, suggesting that this is a general feature of CD4⁺ T cell immunity in the small intestine wired towards immune regulation and tissue homeostasis.},
}

@article {pmid40746883,
year = {2025},
author = {Alvarado-Ortiz, E and Sarabia-SáNCHEZ, MA},
title = {Hypoxic link between cancer cells and the immune system: The role of adenosine and lactate.},
journal = {Oncology research},
volume = {33},
number = {8},
pages = {1803-1818},
pmid = {40746883},
issn = {1555-3906},
mesh = {Humans ; *Adenosine/metabolism ; *Neoplasms/immunology/metabolism/pathology ; Tumor Microenvironment/immunology ; *Lactic Acid/metabolism ; Animals ; *Immune System/metabolism/immunology ; Tumor Escape ; },
abstract = {The tumor microenvironment (TME) is characterized by a symbiosis between cancer cells and the immune cells. The scarcity of oxygen generates hostility that forces cancer cells to alter their biological features in solid tumors. In response to low oxygen availability, the Hypoxia Inducible Factors (HIF-1/2/3α) act as metabolic mediators, producing extracellular metabolites in the tumor microenvironment that influence the immune cells. The modulation of lactate and adenosine on immune evasion has been widely described; however, under hypoxic conditions, it has been barely addressed. Evidence has demonstrated an interplay between cancer and the immune cells, and the present review explores the findings that support HIFs bridging the gap between the rise of these metabolites and the immunosurveillance failure in a hypoxic context. Moreover, new insights based on systemic oxygen administration are discussed, which might counterbalance the effect mediated by lactate and adenosine, to recover anti-tumor immunity. Thus, the disruption of anti-tumor immunity has been the focus of recent research and this novel avenue opens therapeutic vulnerabilities that can be useful for cancer patients.},
}

Humans
*Adenosine/metabolism
*Neoplasms/immunology/metabolism/pathology
Tumor Microenvironment/immunology
*Lactic Acid/metabolism
Animals
*Immune System/metabolism/immunology
Tumor Escape

@article {pmid40744917,
year = {2025},
author = {van Galen, LG and Stewart, JD and Qin, C and Corrales, A and Manley, BF and Kiers, ET and Crowther, TW and Van Nuland, ME},
title = {Global divergence in plant and mycorrhizal fungal diversity hotspots.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6702},
pmid = {40744917},
issn = {2041-1723},
mesh = {*Mycorrhizae/physiology/classification ; *Biodiversity ; Soil Microbiology ; *Plants/microbiology ; Symbiosis ; Forests ; Grassland ; Ecosystem ; *Fungi/classification ; },
abstract = {Environmental protection strategies often rely on aboveground biodiversity indicators for prioritising conservation efforts. However, substantial biodiversity exists belowground, and it remains unclear whether aboveground diversity hotspots are indicative of high soil biodiversity. Using geospatial layers of vascular plant, arbuscular mycorrhizal fungi, and ectomycorrhizal fungi alpha diversity, we map plant-fungal diversity associations across different scales and evaluate evidence for potential correlation drivers. Plant-fungal diversity correlations are weak at the global scale but stronger at regional scales. Plant-arbuscular mycorrhizal fungal correlations are generally negative in forest biomes and positive in grassland biomes, whereas plant-ectomycorrhizal fungal correlations are mostly positive or neutral. We find evidence that symbiosis strength, environmental covariation, and legacy effects all influence correlation patterns. Only 8.8% of arbuscular mycorrhizal and 1.5% of ectomycorrhizal fungal diversity hotspots overlap with plant hotspots, indicating that prioritising conservation based solely on aboveground diversity may fail to capture diverse belowground regions.},
}

*Mycorrhizae/physiology/classification
*Biodiversity
Soil Microbiology
*Plants/microbiology
Symbiosis
Forests
Grassland
Ecosystem
*Fungi/classification

@article {pmid40744203,
year = {2025},
author = {Fu, H and Chen, W and Guo, T and Huang, W and Xu, H and Qu, Z and Yan, N},
title = {Mitigation of waste sulfur acid in lead smelting: Substance flow analysis of a case study in China.},
journal = {Environmental research},
volume = {285},
number = {Pt 3},
pages = {122472},
doi = {10.1016/j.envres.2025.122472},
pmid = {40744203},
issn = {1096-0953},
abstract = {The migration and conversion of sulfur resources throughout the entire production process of lead smelting (LS), a key process in non-ferrous heavy metal production, underscores the significance of analyzing its flow characteristics. This study elucidates the sulfur flow dynamics during the lead smelting process based on production data from a representative group company in China in 2020. We found a predominantly singular structure of sulfur products, resulting in a low corresponding sulfur utilization index (∼89.23 %). Conversely, the sulfur waste index was notably high (∼9.68 %). Here we propose a three-phase optimization strategy: optimizing the structure of raw materials and products in the initial stage, augmenting the scale and structure of primary processes in the middle stage, and advancing industrial symbiosis technology, alongside adjusting industry scale, product structures, and promoting pollutant end-treatment technologies in the latter stages. Through the implementation of these measures, it is anticipated that approximately 180,000 tons of waste acid can be mitigated in the non-ferrous heavy metal industry while 257,600 tons of sulfur resources can be recycled in lead smelting annually in China.},
}

@article {pmid40743974,
year = {2025},
author = {Qin, S and Deng, L and Lin, Y and Jiang, L and Liu, X and Zhang, Q},
title = {Quorum sensing signaling molecules enhance the treatment performance of the HN-AD bacteria-Chlorella symbiotic system in MABR.},
journal = {Journal of environmental management},
volume = {392},
number = {},
pages = {126783},
doi = {10.1016/j.jenvman.2025.126783},
pmid = {40743974},
issn = {1095-8630},
abstract = {To enhance the stability of membrane aerated biofilm reactor (MABR) and accelerate the formation of biofilm, this study introduced a symbiotic system composed of heterotrophic nitrification-aerobic denitrification (HN-AD) bacteria and Chlorella into the MABR, and compared it with a control system inoculated with HN-AD bacteria and activated sludge. The effects of adding 0.8 μM exogenous C8-HSL on biofilm formation and the efficiency of nitrogen and phosphorus removal were investigated by comparing systems with and without the signaling molecule. Results showed that 0.8 μM C8-HSL enhanced the removal efficiencies of ammonia nitrogen, total nitrogen (TN), and total phosphorus (TP) by 25.17 %, 36.22 %, and 38.74 %, respectively, and increased extracellular polymeric substances (EPS) production by 68.62 %. High-throughput sequencing identified Desulfomicrobium and Aliidiomarina as the dominant microorganisms involved in nitrogen and phosphorus removal. The nirB gene played a key role in the denitrification process, and phoBR gene was essential for phosphorus removal. This study provides theoretical support for the application of quorum sensing in MABR systems, offering a novel strategy to improve the efficiency and stability of high ammonia wastewater treatment.},
}

@article {pmid40741765,
year = {2025},
author = {Baatsen, J and Hosaka, GK and Mondin, M and Azevedo, JL and Hungria, M and Quecine, MC},
title = {Benzoxazinoids stimulate chemotaxis and act as a signaling molecule in Azospirillum brasilense Ab-V5, while showing minor effects on Pseudomonas protegens Pf-5.},
journal = {mBio},
volume = {},
number = {},
pages = {e0141425},
doi = {10.1128/mbio.01414-25},
pmid = {40741765},
issn = {2150-7511},
abstract = {UNLABELLED: Root colonization by plant growth-promoting bacteria (PGPB) involves recruiting beneficial partners from the rhizosphere. Among well-studied PGPB, Azospirillum brazilense Ab-V5 and Pseudomonas protegens Pf-5 are two well-known bacterial strains renowned for their growth-enhancing capacity and extensively used as bio-inputs. Many cereals, such as maize, produce indole-derived benzoxazinoids (BXs), specialized metabolites that shape root-associated microbiomes to promote colonization by plant-growth-promoting bacteria (PGPB). Although the mechanisms by which BXs recruit PGPB remain unclear, we hypothesize that BXs directly facilitate root colonization by favoring bacteria adapted to these metabolites in the soil environment. In this study, we investigated the impact of the relatively stable lactam BX-derivative, 6-methoxy-2-benzoxazolinone (MBOA), on two PGPB strains: Azospirillum brasilense Ab-V5 and Pseudomonas protegens Pf-5. Transcriptomic analysis revealed that MBOA had minimal effects on Pf-5, but triggered extensive gene expression changes in Ab-V5, particularly in pathways related to energy metabolism, chemotaxis, and biofilm formation. Subsequent assays confirmed that MBOA acts as a chemoattractant for Ab-V5 and, at moderate concentrations, enhances both biofilm formation and colonization of Arabidopsis roots. We propose that the chemotactic property of MBOA on Ab-V5 can enhance its establishment in the rhizosphere and that this metabolite can trigger the metabolic transition required for root colonization.

IMPORTANCE: In this paper, we studied the impact of benzoxaziniods on root colonization mechanisms of two potent plant-growth- promoting bacterial strains. We explored these mechanisms by an RNA sequencing experiment and by microscopy. The paper highlights how biofilm is particularly affected and reports on chemotactic responses. Most of the results we obtained we could validate with phenotypic assays. We show that benzoxazinoids, produced by many cereals, profoundly affect bacterial behavior related to plant-bacterial interactions. The bacteria in this study are known for their ecological roles in the soil, being either in plant protection or as biofertilizers. Thus, this work holds significant socio-economic value for society.},
}

@article {pmid40740717,
year = {2025},
author = {Parmentier, T and Wybouw, N},
title = {Lasius flavus ants protect root aphid eggs from predators and pathogens during winter hibernation.},
journal = {Royal Society open science},
volume = {12},
number = {7},
pages = {250217},
pmid = {40740717},
issn = {2054-5703},
abstract = {Cooperative brood care is key to the ecology and evolution of social insects. Interestingly, social insects may also care for the brood of other species that dwell in their nests. This study explores how the yellow meadow ant Lasius flavus cares for the eggs of the root aphid Anoecia zirnitsi and how this service affects the resistance of aphid eggs to predators and pathogens. In winter, A. zirnitsi eggs were found exclusively in L. flavus nest chambers near the ant brood. Laboratory experiments showed that L. flavus detects, transports, piles and grooms the aphid eggs. We could recapitulate these caring behaviours in L. flavus using glass beads coated with chemical cues extracted from the aphid egg surface. Other ant species did not collect or nurse the eggs, suggesting a specific interaction between L. flavus and the eggs of A. zirnitsi. We further demonstrated that L. flavus strongly increased the aphid eggs' protection against predators and fungal pathogens. Ants, however, were not essential for the eggs to hatch, and aphid nymphs were capable of independently colonizing grass roots. Our research highlights the crucial protection services L. flavus ants provide to root aphids in winter, while the potential costs and delayed benefits (honeydew provision) of this protection for the ants should be further explored.},
}

@article {pmid40740338,
year = {2025},
author = {Mancabelli, L and Tarracchini, C and Longhi, G and Alessandri, G and Ventura, M and Turroni, F},
title = {Dissecting the molecular interactions between botanical extracts and the human gut microbiota.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1610170},
pmid = {40740338},
issn = {1664-302X},
abstract = {Over millions of years, humans and their gut microbes have developed a symbiotic relationship that benefits both organisms. Many plants and herbs consumed as food by humans, such as aloe vera gel and dandelion root extracts, contain bioactive compounds with recognized therapeutic or preventive effects. However, the impact of these botanicals on the composition and functionality of the human gut microbiota is not yet understood. In this study, the molecular impact of these botanicals on reconstructed human gut microbiota was assessed by in-vitro bioreactor experiments followed by metagenomics and transcriptomic approaches, highlighting both taxonomic and functional changes in the human gut microbiome. Furthermore, cross-feeding activities established by common human gut microbial taxa like Bacteroides spp. when cultivated on these extracts were assessed. In conclusion, the results show that botanicals affect intestinal populations that are highly dependent on the microbial taxa present and that trophic interactions are established in few key gut members.},
}

@article {pmid40740254,
year = {2025},
author = {English, EL and Krueger, JM},
title = {Bacterial peptidoglycan levels have brain area, time of day, and sleep loss-induced fluctuations.},
journal = {Frontiers in neuroscience},
volume = {19},
number = {},
pages = {1608302},
pmid = {40740254},
issn = {1662-4548},
abstract = {Sleep-inducing bacterial cell wall components isolated from brain and urine of sleep deprived animals were identified as peptidoglycan (PG) and muropeptides in the 1980s. Following host detection of PG/muropeptides, downstream signaling mechanisms include release of effector molecules, e.g., cytokines involved in sleep regulation. Understanding of physiological brain PG changes has remained limited, in part due to the historic difficulties of PG quantitation. Herein, we report murine brain PG levels in multiple brain areas within the context of animals' rest-wake cycles and after sleep loss. Significant time-of-day changes in brain PG levels occurred in all brain areas; lowest levels occurred during the transition from rest to wake periods, at zeitgeber time 12 (ZT12). Highest levels of PG were in brainstem while olfactory bulb, hypothalamic, and cortical PG levels were lower. After 3 h of sleep disruption, PG levels increased in the somatosensory cortex, but decreased in brainstem, and hypothalamus. After 6 h of sleep disruption, PG increased in the brainstem and olfactory bulb compared to control levels. Further, RNA-seq analyses of somatosensory cortical tissue was used to assess sleep loss-dependent changes in genes previously linked to PG. Multiple PG-related genes had altered expression with sleep loss including PG binding and signaling molecules, e.g., Pglyrp1 and Nfil3. In summary, brain PG levels were dependent on time of day, brain area, and sleep history. Further, sleep loss altered brain gene expression for PG-linked genes. Collectively, these data are consistent with the hypothesis that microbe-host symbiotic interactions are involved in murine sleep regulatory mechanisms.},
}

@article {pmid40739833,
year = {2025},
author = {Fan, JW and Chen, M and Tian, F and Yao, R and Turner, NC and Yang, L and Fang, WY and Abbott, L and Li, FM and Du, YL},
title = {Arbuscular mycorrhizal fungi enhance alfalfa production by changing root morphology and physiology.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraf335},
pmid = {40739833},
issn = {1460-2431},
abstract = {Soil phosphorus (P) deficiency can severely limit crop and forage productivity. With limited P resources, breeding programs to select high-P efficiency (HPE) genotypes have been developed, but the role of arbuscular mycorrhizal fungi (AMF) in altering root morphology and physiology to increase P use efficiency and production remains poorly understood. In this study, we compared mycorrhizal responsiveness, and plasticity of root morphological and physiological traits between two low-P efficiency (LPE) and two HPE alfalfa genotypes under low and high P treatments. Plants were grown either in soil with naturally occurring AMF or in sterilized soil added with AMF-free bacteria. The results indicated that the AMF symbiosis significantly increased alfalfa productivity and physiological P use efficiency by enhancing total root length and root surface area while reducing carboxylate release. Under low P conditions, HPE genotypes with AMF symbiosis showed higher shoot dry weight, greater mycorrhizal responsiveness, thicker and more robust roots, as well as increased carboxylate release compared to LPE genotypes. We conclude that exploitation of the dominant species in indigenous AMF populations and breeding of crop genotypes with high mycorrhizal responsiveness show promising avenues with which to improve forage productivity and alleviate P-limitation in modern agricultural ecosystems.},
}

@article {pmid40739792,
year = {2025},
author = {Faghihkhorasani, F and Moosavi, M and Rasool Riyadh Abdulwahid, AH and Kavei, M and Karimi, S and Seyed Karimi, M and Vezvaei, P and Manafi Varkiani, M and Aref, AR and Ebrahimi, N},
title = {Role of monocarboxylate transporters in cancer immunology and their therapeutic potential.},
journal = {British journal of pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1111/bph.70110},
pmid = {40739792},
issn = {1476-5381},
abstract = {Monocarboxylate transporters (MCTs) affect cancer metabolism and the regulation of immune responses, making them targets for cancer therapy. This study examines the roles of MCTs, specifically MCT1 and MCT4, in various cancer types and their influence on the advancement of tumours, metastasis and patient prognosis. We analyse the interaction among MCTs, tumour microenvironments (TMEs) and the immune system, as biomarkers and targets for therapy. Initial clinical trials have demonstrated encouraging outcomes with MCT inhibitors, including AZD3965. The combination of MCT inhibition and immunotherapy, such as immune checkpoint blockade, has shown synergistic effects in boosting the antitumour responses of the body's immune system. This study reviews the importance of MCTs and their potential as new targets for enhancing cancer therapy efficacy, especially when used in conjunction with current medicine treatment regimes. In numerous malignancies, tumour cells form a metabolic symbiosis wherein glycolytic cells, marked by elevated MCT4 expression, secrete lactate into the TME, while oxidative cancer cells, expressing MCT1, absorb this lactate as a metabolic substrate for the tricarboxylic acid cycle. Disrupting this lactate shuttle through targeted inhibition of MCTs is a promising strategy to overcome immune evasion and enhance the efficacy of immunotherapies. Targeting monocarboxylate transporters (MCTs) in glycolytic and oxidative tumour cells enhances antitumour immunity. Combinational therapy using MCT1 inhibitors (e.g. AZD3965), MCT4 inhibitors and immune checkpoint blockade can suppress lactate-mediated immunosuppression in the TME. By disrupting lactate shuttling between glycolytic and oxidative tumour cells, this strategy promotes T cell function and improves cancer treatment outcomes.},
}

@article {pmid40738088,
year = {2025},
author = {Zhang, H and Yin, J and Jiang, H and Zeng, W and Cheng, Y and Yang, J and Lin, D and Bai, L and Liang, H},
title = {Reduction of antibiotics and antibiotic resistance genes in simulated-sunlight-supported counter-diffusion bacteria-Algae biofilms: Interface properties and functional gene responses.},
journal = {Water research},
volume = {286},
number = {},
pages = {124285},
doi = {10.1016/j.watres.2025.124285},
pmid = {40738088},
issn = {1879-2448},
abstract = {A novel bacteria-algae symbiotic counter-diffusion biofilm system integrated within simulated-sunlight (designated UV-MABAR) was engineered to simultaneously address antibiotic residuals and antibiotic resistance genes (ARGs) while maintaining functional microbial consortia under simulated solar irradiation. The non-algal control system (UV-MABR) demonstrated elevated repulsion energy barriers accompanied by significant suppression of ATP synthase (p < 0.01) and DNA repair-related gene clusters, leading to biofilm homeostasis disruption and subsequent sulfamethoxazole (SMX) effluent accumulation peaking at 138.11±2.34 μg/L. In contrast, the UV-MABAR configuration exhibited dynamic quenching of tyrosine-associated fluorescence moieties within extracellular polymeric substances, thereby diminishing complexation potential with SMX aromatic rings and achieving 70.75 %±3.21 % abiotic photodegradation efficiency, which substantially curtailed ARG proliferation pathways, promoting a significant downregulation of sul1 (-1.9 log2 fold-change) and sul2 (-1.1 log2 fold-change) expression compared to conventional MABR controls. Besides, algal in UV-MABAR attenuated the irradiation-induced α-helix/(β-sheet + random coil) conformational shift, moderating biofilm matrix compaction. Crucially, algal proliferation up-regulated bacterial recA expression (1.7-fold increase), thereby preserving catabolic gene integrity and preventing endogenous substances release. These protective measures kept effluent concentrations of SMX, NH4[+]-N, total nitrogen, and COD in UV-MABAR at 19.84 μg/L, 3.88 mg/L, 12.76 mg/L, and 34.97 mg/L, respectively, during 150 days of operation.},
}

@article {pmid40737754,
year = {2025},
author = {Torralbo, F and López, CM and Alseekh, S and Martínez-Rivas, FJ and Reyes, MR and Fernie, AR and Alamillo, JM},
title = {The source of nitrogen conditions transcriptomic responses to water deficit in common bean roots.},
journal = {Plant physiology and biochemistry : PPB},
volume = {228},
number = {},
pages = {110264},
doi = {10.1016/j.plaphy.2025.110264},
pmid = {40737754},
issn = {1873-2690},
abstract = {Drought stress reduces plant growth and yield of crops. Common bean (Phaseolus vulgaris L.) establishes symbiosis with rhizobia, ensuring an adequate nitrogen supply without fertilizers. However, the relationship with rhizobia is constrained by limited water availability which inhibits both nitrogen fixation and plant growth. In addition, physiological and molecular responses of common bean to drought are conditioned by the form of nitrogen assimilated. Therefore, understanding the molecular mechanism(s) triggered in common bean under water-deficit conditions is relevant to identify the best strategies to resist drought stress. With the objective of understanding the molecular responses of roots and nodules from common bean to water-deficit stress, plants cultivated under N2-fixation or nitrate fertilization were exposed to ten days of water deprivation. Afterwards, transcriptomic analysis was performed in roots, while metabolome profiling was carried out in roots and nodules. Physiological results showed that under water-deficit, N2-fixing plants increased their root biomass more than nitrate-fertilized plants. Furthermore, water-deficit stress induced more transcriptional changes in nitrate-fertilized plants than in N2-fixing plants, including a larger number of transcription factors in these plants compared with the N2-fixing plants. On the other hand, roots from N2-fixing plants accumulated more metabolites with potential protective functions such as allantoin, proline, raffinose, abscisic acid, and flavonoids in response to water-deficit stress than plants fertilized with nitrate, indicating that symbiosis might facilitate a faster and more efficient response to water-deficit stress. Moreover, common bean nodules exposed to water-deficit stress accumulated proline and erythritol, but reduced their content of maltose, pyruvic acid and allantoin compared to their respective controls. Taken collectively, these findings suggest that, despite the inhibition of nodule activity, N2-fixing plants respond better to water-deficit stress than nitrate-fertilized plants.},
}

@article {pmid40736480,
year = {2025},
author = {Martin, F},
title = {[Fungal communities in forest soils under climate change].},
journal = {Comptes rendus biologies},
volume = {348},
number = {},
pages = {167-181},
doi = {10.5802/crbiol.179},
pmid = {40736480},
issn = {1768-3238},
mesh = {*Soil Microbiology ; *Climate Change ; *Forests ; *Fungi/physiology/classification ; Mycorrhizae/physiology ; Trees/microbiology ; Symbiosis ; Ecosystem ; Soil ; },
abstract = {Forest fungi are crucial for the function and sustainability of forest ecosystems. This article reviews the current understanding of the biology and ecology of two main fungal guilds in forests: saprotrophic fungi, which decompose plant detritus and soil organic matter, and symbiotic mycorrhizal fungi, which promote tree growth. I will explore the factors influencing the diversity and dynamics of fungal communities in forest soils under climate change conditions. Finally, I briefly discuss research programs aimed at defining the conditions for utilising tree microbiota, particularly mycorrhizal symbionts, in planting and assisted migration projects for forestry species. Controlled mycorrhiza formation allows for the production of young forest seedlings mycorrhized with selected fungal strains, thereby enhancing the mineral and water nutrition of seedlings, stimulating juvenile growth, and increasing resistance to drought and pathogens. It is also used for truffle cultivation and edible mushroom production.},
}

*Soil Microbiology
*Climate Change
*Forests
*Fungi/physiology/classification
Mycorrhizae/physiology
Trees/microbiology
Symbiosis
Ecosystem
Soil

@article {pmid40736419,
year = {2025},
author = {Li, X and Li, H and Wang, S and Zhang, H and Shao, Y and Chen, Y and Yuan, Z},
title = {Distinct strategies of soil bacterial generalists and specialists in temperate deciduous broad-leaved forests.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0099225},
doi = {10.1128/aem.00992-25},
pmid = {40736419},
issn = {1098-5336},
abstract = {UNLABELLED: Based on global biotic homogenization, habitat generalists and specialists play an important role in maintaining the stability of ecosystems. However, limited information is available about the assembly processes and co-occurrence patterns of soil bacterial habitat specialists and generalists in forest ecosystems, particularly their response mechanisms to environmental factors. In this study, high-throughput sequencing technology was used to investigate the role of the ecological assemblage processes of soil bacterial habitat specialists and generalists and their role in maintaining the stability of the symbiotic network in temperate deciduous broad-leaved forests (China). The results showed that compared with specialists, the diversity of bacterial habitat generalists was lower, but their distribution ranges and environmental niche breadth were wider. Results from the null and neutral models indicate that, compared to deterministic processes, the community assembly of habitat generalists and specialists is more strongly influenced by stochastic processes, with generalists exhibiting a higher degree of stochasticity than specialists. Network analysis results showed that habitat specialists played a greater role in maintaining the stability of the bacterial co-occurrence network than the generalists. In addition, bacterial habitat specialists were more likely to be affected by light and spatial feature vectors than generalists. These findings provide a novel perspective for understanding the assembly processes and diversity maintenance mechanisms of the forest soil bacterial community.

IMPORTANCE: Limited information is available about bacterial specialists and generalists in forests. Generalists were more affected by stochastic processes than specialists. Specialists played a more important role in network stability than generalists. Light and spatial vectors had stronger effects on specialists than generalists.},
}

@article {pmid40736175,
year = {2025},
author = {Shi, Q and Wei, Z and Pang, J and Qudsi, AI and Wei, M and Zhang, Z and Zhang, Y and Wang, Z and Chen, K and Xu, X and Lu, X and Liang, Q},
title = {Achromobacter in the Conjunctival Sac Microbiota: Potential Association With Acanthamoeba Keratitis Related to Orthokeratology Lenses.},
journal = {Investigative ophthalmology & visual science},
volume = {66},
number = {9},
pages = {71},
pmid = {40736175},
issn = {1552-5783},
mesh = {Humans ; Male ; Female ; *Microbiota ; *Acanthamoeba Keratitis/microbiology/etiology ; *Conjunctiva/microbiology ; Adult ; *Achromobacter/isolation & purification/genetics/physiology ; In Situ Hybridization, Fluorescence ; RNA, Ribosomal, 16S/genetics ; *Orthokeratologic Procedures/adverse effects/instrumentation ; Acanthamoeba ; *Contact Lenses/adverse effects ; Young Adult ; DNA, Bacterial/genetics/analysis ; Dysbiosis/microbiology ; Middle Aged ; },
abstract = {PURPOSE: Acanthamoeba keratitis (AK) is a severe infection linked to orthokeratology lens use, whereas the involvement of conjunctival microbiota in AK remains poorly understood. This study investigates microbiota dysbiosis in AK pathogenesis to inform microbiota-based interventions.

METHODS: Conjunctival swabs from 14 patients with AK and 10 healthy controls underwent 16S rRNA sequencing. Microbiome analysis compared diversity, taxa, and metabolic pathways. Functional assays quantified Achromobacter-enhanced Acanthamoeba adhesion and migration. Metagenomics and fluorescence in situ hybridization (FISH) with species-specific probes confirmed endosymbiosis.

RESULTS: Patients with AK showed reduced bacterial diversity compared with the healthy controls (P < 0.001) but similar richness. Relative abundance of Achromobacter in the AK group was higher compared to the healthy control group (P < 0.001). Achromobacter dominated microbiota among the AK group, being identified as a key biomarker via the linear discriminant analysis effect size (LEfSe). In vitro, Achromobacter increased Acanthamoeba adhesion (P = 0.007) and the migration area (P < 0.05). Metagenomic analysis and FISH further showed Achromobacter spp. as potential endosymbionts of Acanthamoeba. Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed upregulated phenylalanine, fatty acid, and propanoate metabolism in the AK group (all P < 0.001). MetaCyc highlighted enriched pyruvate fermentation to isobutanol, aerobic respiration I, and L-isoleucine biosynthesis II in the AK group (P < 0.001).

CONCLUSIONS: AK-associated conjunctival dysbiosis features Achromobacter dominance, reduced diversity, and altered metabolism. Achromobacter is associated with enhanced adhesion and migration of Acanthamoeba, indicating a possible symbiotic interaction and its potential as a biomarker and therapeutic target.},
}

Humans
Male
Female
*Microbiota
*Acanthamoeba Keratitis/microbiology/etiology
*Conjunctiva/microbiology
Adult
*Achromobacter/isolation & purification/genetics/physiology
In Situ Hybridization, Fluorescence
RNA, Ribosomal, 16S/genetics
*Orthokeratologic Procedures/adverse effects/instrumentation
Acanthamoeba
*Contact Lenses/adverse effects
Young Adult
DNA, Bacterial/genetics/analysis
Dysbiosis/microbiology
Middle Aged

@article {pmid40736111,
year = {2025},
author = {Goginyan, V and Harutyunyan, S and Stepanyan, T and Khachatryan, G and Bagiyan, V and Hovhannisyan, R and Harutyunyan, B and Kinosyan, M and Ghazanchyan, N and Davidyan, T and Verdyan, A and Chitchyan, K},
title = {Effect of complex microbial preparation of free-living and symbiotic nitrogen-fixing bacteria for agricultural crops.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {85},
number = {},
pages = {e292171},
doi = {10.1590/1519-6984.292171},
pmid = {40736111},
issn = {1678-4375},
mesh = {*Crops, Agricultural/microbiology/growth & development ; *Symbiosis/physiology ; *Nitrogen-Fixing Bacteria/physiology/metabolism ; *Nitrogen Fixation/physiology ; *Fertilizers/microbiology ; *Soil Microbiology ; Nitrogen/metabolism ; },
abstract = {The aim of this work was to study the newly developed biofertilizer and plant growth-promoting activity of a consortium of bacterial strains Azotobacter chroococcum MDC 6111, Paenibacillus polymyxa MDC 280 and symbiotic nitrogen-fixing bacteria Rhizobium leguminosarum MDC 5609, Mesorhizobium ciceri MDC 6048 and Bradyrhizobium japonicum MDC 5789. It should be noted that in the biofertilizer formula, the strains A. chroococcum and P. polymyxa are unaltered components, and the nodule bacteria are included depending on the type of crop, taking into account the specificity of these bacteria to plants. In this case, both the nitrogen-fixing capacity and the phosphate-mobilizing activity of these bacteria were taken into account. It was found that the increase in the organic layer content from 2.73 to 5.79% occurs with the active participation of microbial strains introduced into the soil. During the plant growth period, an increase in mobile nitrogen forms (NO3-) to 71.9 mg-eq/100 g and soil saturation with molecular nitrogen to 16.2 mg/100 g were detected. A decrease in the content of phosphorus salts (Р2О5, РО43-) and potassium (K+) to 2.86, 3.82 and 5.86 mg-eq/100 g, respectively, was shown. Thus, the content of the immobile form of potassium (K2O) decreases approximately 3 times, and the amount of immobile phosphorus (P2O5) - 3.63 times. These processes in the soil are due to the active activity of nitrogen-fixing and phosphate-solubilizing bacteria, as well as the use of these ions by plants. At the same time, the nitrogen (N) content increases by 2.38 times, and its mineralized form - NO3- by 3.0 times, respectively. As a result of the field experiments, it was found that the tested soil rhizobacteria actively adhere to seeds and seedlings, spreading in the rhizosphere of plants, contributing to the effective action of the biopreparation, thereby fixing more nitrogen. Microorganisms in the process of metabolism increase the efficiency of obtaining soluble salts of phosphorus, potassium and calcium by plants. In general, it was found that joint inoculation of rhizobacteria strains demonstrated higher growth parameters and plant biomass, and crop ripening is achieved 12-20 days earlier compared to the control options. The use of biopreparation in agriculture allows to improve the content of the organic component of the soil, thereby contributing to the restoration of the ecological balance of the soil.},
}

*Crops, Agricultural/microbiology/growth & development
*Symbiosis/physiology
*Nitrogen-Fixing Bacteria/physiology/metabolism
*Nitrogen Fixation/physiology
*Fertilizers/microbiology
*Soil Microbiology
Nitrogen/metabolism

@article {pmid40735137,
year = {2025},
author = {Yin, M and Yang, M and Han, X and Yin, L and Peng, H and Huang, L},
title = {Spatial metabolic heterogeneity in Poria cocos (Schw.) Wolf (Fushen): Insights from quantitative analysis and widely targeted metabolomics.},
journal = {Food chemistry: X},
volume = {29},
number = {},
pages = {102802},
pmid = {40735137},
issn = {2590-1575},
abstract = {Poria cocos (Schw.) Wolf (Fushen) is valued for its nutritional and therapeutic properties. Fushen is commonly processed into slices of different shapes and sizes. We quantified alkali-soluble and water-soluble polysaccharides, total amino acids, and triterpenoids in Fushen slices of varying geometries (square: 1-9 cm width; round: 1-6 cm radii). Results showed that triterpenes and water-soluble polysaccharides initially decreased and then stabilized with increasing slice size, while total amino acids accumulated progressively, indicating spatial metabolic heterogeneity in Fushen. To map metabolite distribution, we segmented the Fushen into seven concentric zones and profiled the metabolites using a widely targeted metabolomics approach. A total of 359 metabolites were identified. The fungal symbiotic matrix exhibited metabolic profiles similar to the intermediate regions, while peripheral regions maintained comparable levels of triterpenes, saccharides, and amino acid derivatives. This study provides a detailed metabolomic blueprint of Fushen and offers insights for standardized processing and optimized medicinal use.},
}

@article {pmid40734651,
year = {2025},
author = {Liao, IJ and Sakagami, T and Lewin, TD and Bailly, X and Hamada, M and Luo, YJ},
title = {Animal-chlorophyte photosymbioses: evolutionary origins and ecological diversity.},
journal = {Biology letters},
volume = {21},
number = {7},
pages = {20250250},
pmid = {40734651},
issn = {1744-957X},
support = {//KAKENHI/ ; //National Science and Technology Council/ ; //Royal Society/ ; //Academia Sinica/ ; },
mesh = {Animals ; *Symbiosis ; *Biological Evolution ; *Chlorophyta/physiology/genetics ; *Photosynthesis ; *Cnidaria/physiology ; *Mollusca/physiology ; Phylogeny ; },
abstract = {Photosynthetic symbiosis occurs across diverse animal lineages, including Porifera, Cnidaria, Xenacoelomorpha and Mollusca. These associations between animal hosts and photosynthetic algae often involve the exchange of essential macronutrients, supporting adaptation to a wide range of aquatic environments. A small yet taxonomically widespread subset of animals host photosymbionts from the core chlorophytes, a phylogenetically expansive clade of green algae. These rare instances of 'plant-like' animals have arisen independently across distantly related lineages, resulting in striking ecological and physiological diversity. Although such associations provide valuable insights into the evolution of symbiosis and adaptation to novel ecological niches, animal-chlorophyte photosymbioses remain relatively understudied. Here, we present an overview of photosymbioses between animals and chlorophytes, highlighting their independent evolutionary origins, ecological diversity and emerging genomic resources. Focusing on Porifera, Cnidaria and Xenacoelomorpha, we review shared and lineage-specific adaptations underlying these associations. We also contrast them with dinoflagellate-based systems to demonstrate their distinct ecological and cellular features. Our work sets the stage for elucidating the molecular mechanisms underlying these associations, enhancing our understanding of how interspecies interactions drive adaptation to unique ecological niches through animal-chlorophyte symbiosis.},
}

Animals
*Symbiosis
*Biological Evolution
*Chlorophyta/physiology/genetics
*Photosynthesis
*Cnidaria/physiology
*Mollusca/physiology
Phylogeny

@article {pmid40733477,
year = {2025},
author = {Leng, J and Xu, R and Liu, Y and Jiang, T and Hu, H and Ding, Z and Dai, S},
title = {Genome-Wide Analysis of GmMYB S20 Transcription Factors Reveals Their Critical Role in Soybean Nodulation.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {14},
pages = {},
pmid = {40733477},
issn = {2223-7747},
support = {32441006//National Natural Science Foundation of China/ ; 32070300//National Natural Science Foundation of China/ ; 17DZ2252700//Shanghai Engineering Research Center of Plant Germplasm Resources of China/ ; },
abstract = {Soybean relies on symbiotic nitrogen fixation (SNF) to support sustainable agriculture. In this study, we conducted a comprehensive analysis of the GmMYB transcription factor subfamily 20, with a focus on GmMYB62a and GmMYB62b. Phylogenetic and structural analyses revealed that these genes are evolutionarily conserved among legumes and possess distinct domain architectures. Expression profiling and GUS staining showed that GmMYB62a and GmMYB62b are constitutively expressed in nodules. Functional analyses revealed that loss of GmMYB62s function significantly reduced nodule density, while overexpression promoted nodulation. Transcriptomic analysis (RNA-seq) further demonstrated that GmMYB62s regulate key pathways, including hormone signaling, immune responses, and cell wall metabolism, thereby coordinating symbiotic interactions. Collectively, our findings identify GmMYB62a and GmMYB62b as critical molecular regulators of nodulation in soybean, providing promising targets for improving symbiotic nitrogen fixation efficiency in legume crops.},
}

@article {pmid40733334,
year = {2025},
author = {Radi, H and Koufan, M and Belkoura, I and Koussa, T and Mazri, MA},
title = {In Vitro Mycorrhization for Plant Propagation and Enhanced Resilience to Environmental Stress: A Review.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {14},
pages = {},
pmid = {40733334},
issn = {2223-7747},
abstract = {Arbuscular mycorrhizal fungi (AMF) play a key role in enhancing plant stress tolerance, nutrient uptake, and overall health, making them essential for sustainable agriculture. Their multifaceted contributions to the rhizosphere-through biofertilization, bioprotection, and biostimulation-have led to growing interest in their application. In recent years, in vitro mycorrhization has emerged as a promising approach for the rapid propagation of economically and ecologically important plant species, offering improved agronomic and physiological traits as well as increased resilience to environmental stressors. However, challenges remain in achieving consistent AMF-plant symbiosis under in vitro conditions across diverse species. This review highlights the potential of in vitro mycorrhization as a controlled system for investigating AMF interactions and their impact on plant development. Various in vitro mycorrhization systems are described and discussed, along with their applications in the mass production of AMF propagules and mycorrhizal plants, and their role in enhancing the acclimatization of micropropagated plantlets to ex vitro conditions. The role of in vitro mycorrhization as an effective tissue culture approach that integrates plant propagation with enhanced resilience to environmental stress is emphasized. The factors influencing the success of in vitro mycorrhization and strategies for the large-scale production of AMF propagules and mycorrhizal plants are explored. Although research in this area is still limited, existing studies underscore the potential of in vitro mycorrhization to enhance plant tolerance to abiotic and biotic stresses-an increasingly urgent goal in the context of climate change and global food security.},
}

@article {pmid40732484,
year = {2025},
author = {Ahangar, MN and Farhat, ZA and Sivanathan, A},
title = {AI Trustworthiness in Manufacturing: Challenges, Toolkits, and the Path to Industry 5.0.},
journal = {Sensors (Basel, Switzerland)},
volume = {25},
number = {14},
pages = {},
pmid = {40732484},
issn = {1424-8220},
support = {123456789//Innovate Uk/ ; },
abstract = {The integration of Artificial Intelligence (AI) into manufacturing is transforming the industry by advancing predictive maintenance, quality control, and supply chain optimisation, while also driving the shift from Industry 4.0 towards a more human-centric and sustainable vision. This emerging paradigm, known as Industry 5.0, emphasises resilience, ethical innovation, and the symbiosis between humans and intelligent systems, with AI playing a central enabling role. However, challenges such as the "black box" nature of AI models, data biases, ethical concerns, and the lack of robust frameworks for trustworthiness hinder its widespread adoption. This paper provides a comprehensive survey of AI trustworthiness in the manufacturing industry, examining the evolution of industrial paradigms, identifying key barriers to AI adoption, and examining principles such as transparency, fairness, robustness, and accountability. It offers a detailed summary of existing toolkits and methodologies for explainability, bias mitigation, and robustness, which are essential for fostering trust in AI systems. Additionally, this paper examines challenges throughout the AI pipeline, from data collection to model deployment, and concludes with recommendations and research questions aimed at addressing these issues. By offering actionable insights, this study aims to guide researchers, practitioners, and policymakers in developing ethical and reliable AI systems that align with the principles of Industry 5.0, ensuring both technological advancement and societal value.},
}

@article {pmid40732102,
year = {2025},
author = {Liu, Y and Ren, J and Yu, B and Liu, S and Cao, X},
title = {Metagenomic and Metabolomic Perspectives on the Drought Tolerance of Broomcorn Millet (Panicum miliaceum L.).},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071593},
pmid = {40732102},
issn = {2076-2607},
support = {YDZJSX2022A044//the Central Guiding Local Science and Technology Development Funds/ ; CARS-06-14.5-A16//the earmarked fund for CARS/ ; 2025CYJSTX03-23//the earmarked fund for Modern Agro-Industry Technology Research System/ ; },
abstract = {Drought stress is an important abiotic stress factor restricting crop production. Broomcorn millet (Panicum miliaceum L.) has become an ideal material for analyzing the stress adaptation mechanisms of crops due to its strong stress resistance. However, the functional characteristics of its rhizosphere microorganisms in response to drought remain unclear. In this study, metagenomics and metabolomics techniques were employed to systematically analyze the compositional characteristics of the microbial community, functional properties, and changes in metabolites in the rhizosphere soil of broomcorn millet under drought stress. On this basis, an analysis was conducted in combination with the differences in functional pathways. The results showed that the drought treatment during the flowering stage significantly altered the species composition of the rhizosphere microorganisms of broomcorn millet. Among them, the relative abundances of beneficial microorganisms such as Nitrosospira, Coniochaeta, Diversispora, Gigaspora, Glomus, and Rhizophagus increased significantly. Drought stress significantly affects the metabolic pathways of rhizosphere microorganisms. The relative abundances of genes associated with prokaryotes, glycolysis/gluconeogenesis, and other metabolic process (e.g., ribosome biosynthesis, amino sugar and nucleotide sugar metabolism, and fructose and mannose metabolism) increased significantly. Additionally, the expression levels of functional genes involved in the phosphorus cycle were markedly upregulated. Drought stress also significantly alters the content of specific rhizosphere soil metabolites (e.g., trehalose, proline). Under drought conditions, broomcorn millet may stabilize the rhizosphere microbial community by inducing its restructuring and recruiting beneficial fungal groups. These community-level changes can enhance element cycling efficiency, optimize symbiotic interactions between broomcorn millet and rhizosphere microorganisms, and ultimately improve the crop's drought adaptability. Furthermore, the soil metabolome (e.g., trehalose and proline) functions as a pivotal interfacial mediator, orchestrating the interaction network between broomcorn millet and rhizosphere microorganisms, thereby enhancing plant stress tolerance. This study sheds new light on the functional traits of rhizosphere microbiota under drought stress and their mechanistic interactions with host plants.},
}

@article {pmid40732090,
year = {2025},
author = {da Silva, IA and de Andrade, JLS and Barbosa, FLA and Almeida, MS and Araújo, MLH and de Souza, AJ and Araujo, ASF and Pereira, APA and Garcia, KGV},
title = {Co-Application of Seaweed Extract (Solieria filiformis) and Silicon: Effect on Sporulation, Mycorrhizal Colonization, and Initial Growth of Mimosa caesalpiniaefolia.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071581},
pmid = {40732090},
issn = {2076-2607},
abstract = {Seaweed extracts (SEs) and silicon (Si) are known to enhance plant growth under adverse conditions. However, their combined effects on arbuscular mycorrhizal fungi (AMF) are not yet fully understood. This study evaluated the effect of the co-application of an SE and Si on the AMF spore abundance, mycorrhizal colonization, and early growth of Mimosa caesalpiniaefolia. Plants were grown in a greenhouse for 70 days in soil with or without an SE (Solieria filiformis) and three Si levels (0, 150, and 300 mg kg[-1]). Growth parameters, AMF spore abundance, mycorrhizal colonization, and plant/soil chemical composition were assessed. SE and Si increased the plant height, stem diameter, number of leaves, and shoot dry mass, while higher Si levels reduced the root dry mass and length. Mycorrhizal colonization was highest (64%) at 150 mg kg[-1] Si with SE, whereas AMF spore abundance decreased as Si increased. SE and 300 mg kg[-1] Si raised the Si levels in the shoot, while root Si increased only at 300 mg kg[-1] Si. Shoot Na increased at 300 mg kg[-1] Si without SE, whereas K was highest at 150 mg kg[-1] Si with SE. The soil pH, electrical conductivity, and Na increased at 300 mg kg[-1] Si, while K and P decreased at this level without SE. These findings indicate that SE and Si co-application benefits early growth and may modulate mycorrhizal symbiosis, highlighting the importance of proper management to maximize plant and soil benefits.},
}

@article {pmid40732061,
year = {2025},
author = {Alahmari, AN and Hassoubah, SA and Alaidaroos, BA and Al-Hejin, AM and Bataweel, NM and Farsi, RM and Algothmi, KM and Alshammari, NM and Ashour, ATK},
title = {Antimicrobial Metabolites Isolated from Some Marine Bacteria Associated with Callyspongia crassa Sponge of the Red Sea.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071552},
pmid = {40732061},
issn = {2076-2607},
abstract = {The Red Sea is rich in symbiotic microorganisms that have been identified as sources of bioactive compounds with antimicrobial, antifungal, and antioxidant properties. In this study, we aimed to explore the potential of marine sponge-associated bacteria as sources of antibacterial compounds, emphasizing their significance in combating antibiotic resistance (AMR). The crude extracts of Micrococcus, Bacillus, and Staphylococcus saprophyticus exhibited significant antibacterial activity, with inhibition zones measuring 12 mm and 14 mm against Escherichia coli, Staphylococcus aureus, Candida albicans, and other infectious strains. The DPPH assay showed that the bacterial isolates AN3 and AN6 exhibited notable antioxidant activity at a concentration of 100 mg/mL. To characterize the chemical constituents responsible for the observed bioactivity, a GC-MS analysis was performed on ethyl acetate extracts of the potent strains. The analysis identified a range of antimicrobial compounds, including straight-chain alkanes (e.g., Tetradecane), cyclic structures (e.g., Cyclopropane derivatives), and phenolic compounds, all of which are known to disrupt microbial membranes or interfere with metabolic pathways. The bioprospecting and large-scale production of these compounds are challenging. In conclusion, this study underscores the potential for marine bacteria associated with sponges from the Red Sea to be a source of bioactive compounds with therapeutic relevance.},
}

@article {pmid40732002,
year = {2025},
author = {Jin, Y and Chen, Z and Malik, K and Li, C},
title = {Achnatherum inebrians Bacterial Communities Associated with Epichloë gansuensis Endophyte Infection Under Low-Concentration Urea Treatment: Links to Plant Growth and Root Metabolite.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071493},
pmid = {40732002},
issn = {2076-2607},
support = {32201445, 2021M701525, 2024M761243, 22JR5RA434, 22ZSCQD01, 22JR5RA532, lzujbky-2022-kb02, lzujbky-2023-49 and [2021]794.//the National Science Foundation of China , the China Postdoctoral Science Foundation, Gansu Province Outstanding Doctoral Students Project , Intellectual Property Plan (Targeted Organization) Project of Gansu Administration for Market Regulation, Gansu Pr/ ; },
abstract = {Despite chemical exchange often serving as the first step in plant-microbe interactions, the specialized chemical metabolites produced by grass-Epichloë endophyte symbiosis as mediators of host growth, nutrient acquisition, and modulators of the rhizosphere community under low-nitrogen conditions are areas lacking in knowledge. In this study, we investigated the plant growth-promoting effects of the Epichloë endophyte strain and identified the growth of the Epichloë strain under different types of nitrogen source treatments. In addition to the in vitro test, we evaluated growth performance for Epichloë endophyte-infected plants (E+) and Epichloë endophyte-free plants (E-) in a pot trial under 0.01 mol/L urea treatment. Seedlings from E+ and E- groups were collected to analyze the plant bacterial microbiome and root metabolites. The E. gansuensis endophyte strain was found not to produce indoleacetic acid (IAA), pectinase, or contain ferritin. The nitrogenase gene, essential for nitrogen fixation, was also absent. These results suggest that E. gansuensis endophyte strains themselves do not contain attributes to promote plant growth. Concerning N fertilization, it was observed an increase in the colony diameter of E. gansuensis strain was observed only in the NO3[-]-N (NN) treatment, while inhibition was observed in the urea-N (UN) treatment. E. gansuensis endophyte symbiosis significantly increased tiller number and plant dry weight. Overall, our results suggest that the E+ plants had more root forks and greater average root diameter compared to E- plants under the UN treatment. In a pot experiment using UN, data from 16S rRNA amplicon sequencing revealed that E. gansuensis endophyte infection significantly altered the bacterial community composition in shoot and root, and significantly increased Shannon (p < 0.001) and Chao 1 (p < 0.01) indexes. The relative abundance of Acidobacteriota, Actinomycetota, Cyanobacteriota, Fibrobacterota, Myxococcota, and Patescibacteria in the shoot, and Cyanobacteriota, Pseudomonadota, and Verrucomicrobiota in the root were significantly increased by E. gansuensis endophyte infection. Similarly, E. gansuensis endophyte symbiosis shifted the metabolite composition of the host plants, with the E+ plants showing a higher number of metabolites than the E- plants. In addition, co-metabolism network analysis revealed that the positive relevance between exudates and microorganisms in the root of the E+ plants is higher than that of the E- plants. These findings provide valuable insights into the knowledge of the effects of the symbiotic relationship between host plants and Epichloë endophyte on interspecific interactions of plant microbiome, beneficial for harnessing endophytic symbiosis, promoting plant growth.},
}

@article {pmid40731996,
year = {2025},
author = {Asimakis, E and Galiatsatos, I and Apostolopoulou, G and Savvidou, EC and Balatsos, G and Karras, V and Evangelou, V and Dionyssopoulou, E and Augustinos, A and Papadopoulos, NT and Michaelakis, A and Stathopoulou, P and Tsiamis, G},
title = {The Symbiotic Bacterial Profile of Laboratory-Reared and Field-Caught Aedes albopictus Mosquitoes from Greece.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071486},
pmid = {40731996},
issn = {2076-2607},
support = {«moSquITo»: Innovative approaches for monitoring and management of the Asian tiger mosquito with emphasis on the Sterile Insect Technique (ΤΑΕΔΚ06173)//National Recovery and Resilience Plan, "Greece 2.0" & EU Funding - Next Generation EU/ ; },
abstract = {The Asian tiger mosquito Aedes albopictus is a highly invasive species capable of transmitting human pathogens. For population management, the sterile insect technique (SIT) is considered an effective and sustainable alternative to conventional methods, such as insecticides and reducing or eliminating breeding sites. The use of symbiotic bacteria to improve the application of SIT or design combined SIT/incompatible insect technique (IIT) approaches is currently considered. In this context, exploring the microbiota of local mosquito populations is crucial for identifying interesting components. This study employed 16S rRNA sequencing and microbiological methods to characterize the diversity of laboratory and wild Ae. albopictus in Greece. Differences were recorded between wild and lab-reared mosquitoes, with laboratory samples exhibiting higher diversity. Laboratory treatment, sex, and developmental stage also resulted in variations between communities. Populations reared in the same facility developed mostly similar bacterial profiles. Two geographically distant wild populations displayed similar bacterial profiles, characterized by seasonal changes in the relative abundance of Pantoea and Zymobacter. Wolbachia was dominant in most groups (63.7% relative abundance), especially in field-caught mosquitoes. It was identified with two strains, wAlbA (21.5%) and wAlbB (42.2%). Other frequent taxa included Elizabethkingia, Asaia, and Serratia. Blood feeding favored an increase in Serratia abundance. Various Enterobacter, Klebsiella, Aeromonas, and Acinetobacter strains were isolated from larval and adult mosquito extracts and could be further characterized as diet supplements. These findings suggest that the microbiota of local populations is highly variable due to multiple factors. However, they retain core elements shared across populations that may exhibit valuable nutritional or functional roles and could be exploited to improve SIT processes.},
}

@article {pmid40731987,
year = {2025},
author = {Zhu, F and Liu, Y and Wu, C and Li, K and Hu, Y and Liu, W and Yu, S and Li, M and Dong, X and Yu, H},
title = {Microbial Corrosion Behavior of L245 Pipeline Steel in the Presence of Iron-Oxidizing Bacteria and Shewanella algae.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071476},
pmid = {40731987},
issn = {2076-2607},
abstract = {Microbiologically influenced corrosion (MIC) poses significant challenges in oilfield water injection environments, leading to substantial socioeconomic losses. L245 steel, a low-alloy steel widely used in oil and gas pipelines due to its excellent mechanical properties and cost-effectiveness, remains highly vulnerable to MIC during long-term service. This study uses surface characterization and electrochemical techniques to investigate the corrosion behavior of L245 pipeline steel under short-cycle conditions in a symbiotic environment of iron-oxidizing bacteria (IOB) and Shewanella algae (S. algae). Key findings revealed that localized corrosion of L245 steel was markedly exacerbated under coexisting IOB and S. algae conditions compared to monoculture systems. However, the uniform corrosion rate under symbiosis fell between the rates observed in the individual IOB and S. algae systems. Mechanistically, the enhanced corrosion under symbiotic conditions was attributed to the synergistic electron transfer interaction: IOB exploited electron carriers secreted by S. algae during extracellular electron transfer (EET), which amplified the microbial consortium's capacity to harvest electrons from the steel substrate. These results emphasize the critical role of interspecies electron exchange in accelerating localized degradation of carbon steel under complex microbial consortia, with implications for developing targeted mitigation strategies in industrial pipelines exposed to similar microbiological environments.},
}

@article {pmid40731978,
year = {2025},
author = {Garcia, M and Bruna, P and Duran, P and Abanto, M},
title = {Cyanobacteria and Soil Restoration: Bridging Molecular Insights with Practical Solutions.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071468},
pmid = {40731978},
issn = {2076-2607},
abstract = {Soil degradation has been accelerating globally due to climate change, which threatens food production, biodiversity, and ecosystem balance. Traditional soil restoration strategies are often expensive, slow, or unsustainable in the long term. In this context, cyanobacteria have emerged as promising biotechnological alternatives, being the only prokaryotes capable of performing oxygenic photosynthesis. Moreover, they can capture atmospheric carbon and nitrogen, release exopolysaccharides (EPSs) that stabilize the soil, and facilitate the development of biological soil crusts (biocrusts). In recent years, the convergence of multi-omics tools, such as metagenomics, metatranscriptomics, and metabolomics, has advanced our understanding of cyanobacterial dynamics, their metabolic potential, and symbiotic interactions with microbial consortia, as exemplified by the cyanosphere of Microcoleus vaginatus. In addition, recent advances in bioinformatics have enabled high-resolution taxonomic and functional profiling of environmental samples, facilitating the identification and prediction of resilient microorganisms suited to challenging degraded soils. These tools also allow for the prediction of biosynthetic gene clusters and the detection of prophages or cyanophages within microbiomes, offering a novel approach to enhance carbon sequestration in dry and nutrient-poor soils. This review synthesizes the latest findings and proposes a roadmap for the translation of molecular-level knowledge into scalable biotechnological strategies for soil restoration. We discuss approaches ranging from the use of native biocrust strains to the exploration of cyanophages with the potential to enhance cyanobacterial photosynthetic activity. By bridging ecological functions with cutting-edge omics technologies, this study highlights the critical role of cyanobacteria as a nature-based solution for climate-smart soil management in degraded and arid ecosystems.},
}

@article {pmid40731227,
year = {2025},
author = {Chen, CY and Chang, YH and Leong, YK and Chang, JS},
title = {Application of algae-bacteria symbiosis system for ammonia nitrogen wastewater treatment.},
journal = {Journal of bioscience and bioengineering},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jbiosc.2025.06.011},
pmid = {40731227},
issn = {1347-4421},
abstract = {In industrial processes, the primary sources of ammonia nitrogen emissions are organic matter and nitrogen-containing chemicals. When released directly into the environment, these nitrogen compounds elevate aquatic toxicity and reduce dissolved oxygen levels, significantly affecting aquatic ecosystems. This review introduces both traditional and novel ammonia nitrogen wastewater treatment technologies. Traditional methods include physical, chemical, and biological processes. The focus of this review is on novel ammonia nitrogen wastewater treatment technology based on algae-bacteria symbiosis systems. The review discusses key environmental factors influencing the algae-bacteria symbiosis system, such as temperature, light intensity, carbon dioxide concentration, and bioflocculation. Furthermore, it presents innovative large-scale algae-bacteria symbiosis system designed to achieve high carbon dioxide removal efficiency while effectively treating ammonia nitrogen wastewater with low energy consumption. This review aims to provide valuable insights that support the future development of efficient and commercially viable novel technologies for treating ammonia-nitrogen wastewater.},
}

@article {pmid40729388,
year = {2025},
author = {Riaz, MR and Sosa Marquez, I and Lindgren, H and Levin, G and Doyle, R and Romero, MC and Paoli, JC and Drnevich, J and Fields, CJ and Geddes, BA and Marshall-Colón, A and Heath, KD},
title = {Mobile gene clusters and coexpressed plant-rhizobium pathways drive partner quality variation in symbiosis.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {31},
pages = {e2411831122},
doi = {10.1073/pnas.2411831122},
pmid = {40729388},
issn = {1091-6490},
support = {IOS-1645875//NSF (NSF)/ ; DBI-2022049//NSF (NSF)/ ; IOS-2243821//NSF (NSF)/ ; na//Consejo Nacional de Humanidades, Ciencias y Tecnologías (Conahcyt)/ ; na//UofI | UIUC | Carl R. Woese Institute for Genomic Biology (IGB)/ ; IOS- 2243818//NSF (NSF)/ ; },
mesh = {*Symbiosis/genetics ; *Sinorhizobium meliloti/genetics ; *Multigene Family ; Root Nodules, Plant/microbiology/genetics ; Genetic Variation ; Transcriptome ; *Rhizobium/genetics ; Gene Regulatory Networks ; },
abstract = {Plant-microbe symbioses such as the legume-rhizobium mutualism are vital in the web of ecological relationships within both natural and managed ecosystems, influencing primary productivity, crop yield, and ecosystem services. The outcome of these interactions for plant hosts varies quantitatively and can range from highly beneficial to even detrimental depending on natural genetic variation in microbial symbionts. Here, we take a systems genetics approach, harnessing the genetic diversity present in wild rhizobial populations to predict genes and molecular pathways crucial in determining partner quality, i.e., the benefits of symbiosis for legume hosts. We combine traits, dual-RNAseq of both partners from active nodules, pangenomics/pantranscriptomics, and Weighted Gene Co-expression Network Analysis (WGCNA) for a panel of 20 Sinorhizobium meliloti strains that vary in symbiotic partner quality. We find that genetic variation in the nodule transcriptome predicts host plant biomass, and WGCNA reveals networks of genes in plants and rhizobia that are coexpressed and associated with high-quality symbiosis. Presence-absence variation of gene clusters on the symbiosis plasmid (pSymA), validated in planta, is associated with high or low-quality symbiosis and is found within important coexpression modules. Functionally our results point to management of oxidative stress, amino acid and carbohydrate transport, and NCR peptide signaling mechanisms in driving symbiotic outcomes. Our integrative approach highlights the complex genetic architecture of microbial partner quality and raises hypotheses about the genetic mechanisms and evolutionary dynamics of symbiosis.},
}

*Symbiosis/genetics
*Sinorhizobium meliloti/genetics
*Multigene Family
Root Nodules, Plant/microbiology/genetics
Genetic Variation
Transcriptome
*Rhizobium/genetics
Gene Regulatory Networks

@article {pmid40729385,
year = {2025},
author = {Chen, P and Geng, H and Ma, B and Zhang, Y and Zhu, Z and Li, M and Chen, S and Wang, X and Sun, C},
title = {Integrating spatial omics and single-cell mass spectrometry imaging reveals tumor-host metabolic interplay in hepatocellular carcinoma.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {31},
pages = {e2505789122},
doi = {10.1073/pnas.2505789122},
pmid = {40729385},
issn = {1091-6490},
support = {82404587//the National Natural Science Foundation of China/ ; 82273888//the National Natural Science Foundation of China/ ; tsqn202403096//the Taishan Scholars Program of Shandong Province/ ; tstp20221138//the Taishan Scholar Progarm of Shandong Province/ ; 2024QZJH04//the Youth Excellent Talents Program of Qilu University of Technology (Shandong Academy of Sciences)/ ; },
mesh = {*Carcinoma, Hepatocellular/metabolism/pathology/diagnostic imaging ; *Liver Neoplasms/metabolism/pathology/diagnostic imaging ; Humans ; Tumor Microenvironment ; Single-Cell Analysis/methods ; Cancer-Associated Fibroblasts/metabolism/pathology ; Mass Spectrometry/methods ; Macrophages/metabolism ; Glycolysis ; Metabolomics/methods ; Cell Communication ; Cell Line, Tumor ; },
abstract = {Metabolic crosstalk among diverse cellular populations contributes to shaping a competitive and symbiotic tumor microenvironment (TME) to influence cancer progression and immune responses, highlighting vulnerabilities that can be exploited for cancer therapy. Using a spatial multiomics platform to study the cell-specific metabolic spectrum in hepatocellular carcinoma (HCC), we map the metabolic interactions between different cells in the HCC TME and identify a unique tumor-immune-cancer-associated fibroblast (CAF) "interface" zone, where cell-cell interactions are enhanced and accompanied by significant upregulation of lactic acid and long-chain polyunsaturated fatty acids. Further combining single-cell mass spectrometry imaging of patient-derived tumor organoids, cocultured CAFs, and macrophages, we demonstrate that CAFs increase glycolysis and secrete lactic acid to the surrounding microenvironment to drive immunosuppressive macrophage M2 polarization. These findings facilitate the understanding of cancer-associated metabolic interactions in complex TME and provide clues for targeted clinical therapies.},
}

*Carcinoma, Hepatocellular/metabolism/pathology/diagnostic imaging
*Liver Neoplasms/metabolism/pathology/diagnostic imaging
Humans
Tumor Microenvironment
Single-Cell Analysis/methods
Cancer-Associated Fibroblasts/metabolism/pathology
Mass Spectrometry/methods
Macrophages/metabolism
Glycolysis
Metabolomics/methods
Cell Communication
Cell Line, Tumor

@article {pmid40728918,
year = {2025},
author = {Vannette, RL and Williams, NM and Peterson, SS and Martin, AN},
title = {Pollen diet, more than geographic distance, shapes provision microbiome composition in two species of cavity-nesting bees.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf067},
pmid = {40728918},
issn = {1574-6941},
abstract = {The microbial composition of stored food can influence its stability and determine the microbial species consumed by the organism feeding on it. Many bee species store nectar and pollen in provisions constructed to feed developing offspring. Yet whether microbial composition is determined by the pollen types within provisions, variation between bee species at the same nesting sites, or geographic distance was unclear. Here, we sampled two species of co-occurring cavity nesting bees in the genus Osmia at 13 sites in California and examined the composition of pollen, fungi and bacteria in provisions. Pollen composition explained 15% of variation in bacterial composition and ∼30% of variation in fungal composition, whereas spatial distance among sites explained minimal additional variation. Symbiotic microbe genera Ascosphaera, Sodalis and Wolbachia showed contrasting patterns of association with pollen composition, suggesting distinct acquisition and transmission routes for each. Comparing provisions from both bee species comprised of the same pollens points to environmental acquisition rather than bee species as a key factor shaping the early stages of the bee microbiome in Osmia. The patterns we observed also contrast with Apilactobacillus-dominated provision microbiome in other solitary bee species, suggesting variable mechanisms of microbial assembly in stored food among bee species.},
}

@article {pmid40728316,
year = {2025},
author = {Armitage, DW and Alonso-Sánchez, AG and Coy, SR and Cheng, Z and Hagenbeek, A and López-Martínez, KP and Phua, YH and Sears, AR},
title = {Adaptive pangenomic remodeling in the Azolla cyanobiont amid a transient microbiome.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf154},
pmid = {40728316},
issn = {1751-7370},
abstract = {Plants fix nitrogen in concert with diverse microbial symbionts, often recruiting them from the surrounding environment each generation. Vertical transmission of a microbial symbiont from parent to offspring can produce extreme evolutionary consequences, including metabolic codependence, genome reduction, and synchronized life cycles. One of the few examples of vertical transmission of N-fixing symbionts occurs in Azolla ferns, which maintain an obligate mutualism with the cyanobacterium Trichormus azollae-but the genomic consequences of this interaction, and whether the symbiosis involves other vertically transmitted microbial partners, are currently unknown. We generated high-coverage metagenomes across the genus Azolla and reconstructed metagenome assembled genomes to investigate whether a core microbiome exists within Azolla leaf cavities, and how the genomes of T. azollae diverged from their free-living relatives. Our results suggest that T. azollae is the only consistent symbiont across all Azolla accessions, and that other bacterial groups are transient or facultative associates. Pangenomic analyses of T. azollae indicate extreme pseudogenization and gene loss compared to free-living relatives-especially in defensive, stress-tolerance, and secondary metabolite pathways-yet the key functions of nitrogen fixation and photosynthesis remain intact. Additionally, differential codon bias and intensified positive selection on photosynthesis, intracellular transport, and carbohydrate metabolism genes suggest ongoing evolution in response to the unique conditions within Azolla leaf cavities. These findings highlight how genome erosion and shifting selection pressures jointly drive the evolution of this unique mutualism, while broadening the taxonomic scope of genomic studies on vertically transmitted symbioses.},
}

@article {pmid40726432,
year = {2025},
author = {Hua, R and Ding, N and Hua, Y and Wang, X and Xu, Y and Qiao, X and Shi, X and Bai, T and Xiong, Y and Zhuo, X and Fan, C and Zhou, J and Wu, Y and Liu, J and Yuan, Z and Li, T},
title = {Ligilactobacillus Murinus and Lactobacillus Johnsonii Suppress Macrophage Pyroptosis in Atherosclerosis through Butyrate-GPR109A-GSDMD Axis.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e01707},
doi = {10.1002/advs.202501707},
pmid = {40726432},
issn = {2198-3844},
support = {2021YFA1301201//National Key R&D Program of China/ ; 2021YFA0805400//National Key R&D Program of China/ ; 2024YFA1307004//National Key R&D Program of China/ ; 82000474//National Science Foundation of China/ ; 82370458//National Science Foundation of China/ ; 82370875//National Science Foundation of China/ ; 82430019//National Science Foundation of China/ ; 2021KJXX-04//Innovative Talents Promotion Plan of Shaanxi Province of China/ ; xzy012019093//Xi'an Jiaotong University/ ; 2020JM-383//Natural Science Foundation of Shaanxi Province/ ; },
abstract = {Gut microbiota and their metabolites are remarkable regulators in atherosclerosis. Oral drugs such as aspirin have recently been found to modulate the gut microbiome. However, the roles of drug-microbiota-metabolite interactions in atherosclerosis have not been explored. Herein, two gut probiotics, Ligilactobacillus murinus (L. murinus) and Lactobacillus johnsonii (L. johnsonii), are identified from mouse models and human cohorts, which are positively correlated with aspirin usage. Specifically, the eradication of these two species eliminated aspirin's anti-atherosclerotic effects, while their transplantation exhibited therapeutic effects against atherosclerosis. Integrative analysis of metagenomic and metabolomic data showed that elevated levels of butyrate are associated with these two species. Mechanically, L. murinus and L. johnsonii form symbiotic networks with butyrate-producing bacteria such as Allobaculum. This study confirmed that gut microbes produce butyrate, which helps preserve the gut barrier and prevents the leakage of lipopolysaccharides. By integrating molecular biology and single-cell sequencing data, G protein-coupled receptor 109A (GPR109A) is confirmed as the direct target of butyrate. Through the activation of GPR109A, butyrate produced by L. murinus and L. johnsonii suppressed the expression of Gasdermin D (GSDMD) in the pyroptosis of macrophages during atherosclerosis. These findings offer novel insights into the drug-microbiota axis that can be targeted to improve the treatment of atherosclerosis.},
}

@article {pmid40725467,
year = {2025},
author = {Ye, S and Wei, X and Chen, J and Luo, S and Jiang, T and Yang, J and Zheng, R and Chen, S},
title = {Research on Key Genes for Flowering of Bambusaoldhamii Under Introduced Cultivation Conditions.},
journal = {Genes},
volume = {16},
number = {7},
pages = {},
pmid = {40725467},
issn = {2073-4425},
support = {2021YFD2200501301//National Key Research and Development Program of China during the 14th Five-Year Plan Period, "Geographical Differentiation of Biomass Formation in Bambusaoldhamii Germplasm"/ ; },
mesh = {*Flowers/genetics/growth & development ; Gene Expression Regulation, Plant ; Transcriptome/genetics ; *Plant Proteins/genetics ; Gene Regulatory Networks ; Gene Expression Profiling ; Genes, Plant ; *Bambusa/genetics/growth & development ; *Poaceae/genetics/growth & development ; },
abstract = {BACKGROUND: Bambusaoldhamii is an important economic bamboo species. However, flowering occurred after its introduction and cultivation, resulting in damage to the economy of bamboo forests. Currently, the molecular mechanism of flowering induced by introduction stress is still unclear. This study systematically explored the key genes and regulatory pathways of flowering in Bambusaoldhamii under introduction stress through field experiments combined with transcriptome sequencing and weighted gene co-expression network analysis (WGCNA), with the aim of providing a basis for flower-resistant cultivation and molecular breeding of bamboo.

RESULTS: The study conducted transcriptome sequencing on flowering and non-flowering Bambusaoldhamii bamboo introduced from Youxi, Fujian Province for 2 years, constructed a reference transcriptome containing 213,747 Unigenes, and screened out 36,800-42,980 significantly differentially expressed genes (FDR < 0.05). The results indicated that the photosensitive gene CRY and the temperature response gene COR413-PM were significantly upregulated in the flowering group; the expression level of the heavy metal detoxification gene MT3 increased by 27.77 times, combined with the upregulation of the symbiotic signaling gene NIN. WGCNA analysis showed that the expression level of the flower meristem determination gene AP1/CAL/FUL in the flowering group was 90.38 times that of the control group. Moreover, its expression is regulated by the cascade synergy of CRY-HRE/RAP2-12-COR413-PM signals.

CONCLUSIONS: This study clarifies for the first time that the stress of introducing Bambusaoldhamii species activates the triad pathways of photo-temperature signal perception (CRY/COR413-PM), heavy metal detoxification (MT3), and symbiotic regulation (NIN), collaboratively driving the AP1/CAL/FUL gene expression network and ultimately triggering the flowering process.},
}

*Flowers/genetics/growth & development
Gene Expression Regulation, Plant
Transcriptome/genetics
*Plant Proteins/genetics
Gene Regulatory Networks
Gene Expression Profiling
Genes, Plant
*Bambusa/genetics/growth & development
*Poaceae/genetics/growth & development

@article {pmid40725341,
year = {2025},
author = {López-Hernández, MG and Rincón-Rosales, R and Rincón-Molina, CI and Manzano-Gómez, LA and Gen-Jiménez, A and Maldonado-Gómez, JC and Rincón-Molina, FA},
title = {Diversity and Functional Potential of Gut Bacteria Associated with the Insect Arsenura armida (Lepidoptera: Saturniidae).},
journal = {Insects},
volume = {16},
number = {7},
pages = {},
pmid = {40725341},
issn = {2075-4450},
support = {19337.24-P and 19414.24-P//Tecnológico Nacional de México/ ; },
abstract = {Insects are often associated with diverse microorganisms that enhance their metabolism and nutrient assimilation. These microorganisms, residing in the insect's gut, play a crucial role in breaking down complex molecules into simpler compounds essential for the host's growth. This study investigates the diversity and functional potential of symbiotic bacteria in the gut of Arsenura armida (Lepidoptera: Saturniidae) larvae, an edible insect from southeastern Mexico, using culture-dependent and metagenomic approaches. Bacterial strains were isolated from different gut sections (foregut, midgut, and hindgut) and cultured on general-purpose media. Isolates were identified through 16S rRNA gene sequencing and genomic fingerprinting. Metagenomics revealed the bacterial community structure and diversity, along with their functional potential. A total of 96 bacterial strains were isolated, predominantly Gram-negative bacilli. Rapidly growing colonies exhibited enzymatic activity, cellulose degradation, and sugar production. Phylogenetic analysis identified eight genera, including Acinetobacter, Bacillus, Enterobacter, Pseudomonas, and others, with significant cellulose-degrading capabilities. Metagenomics confirmed Bacillota as the most abundant phylum. These complementary methods revealed abundant symbiotic bacteria with key metabolic roles in A. armida, offering promising biotechnological applications in enzymatic bioconversion and cellulose degradation.},
}

@article {pmid40725334,
year = {2025},
author = {Gao, H and Yin, XJ and Fan, ZH and Gu, XH and Su, ZQ and Luo, BR and Qiu, BL and Zhang, LH},
title = {Effects of Endosymbionts on the Nutritional Physiology and Biological Characteristics of Whitefly Bemisia tabaci.},
journal = {Insects},
volume = {16},
number = {7},
pages = {},
pmid = {40725334},
issn = {2075-4450},
support = {Grant No.KJQN202400533//Science and Technology Research Program of Chongqing Municipal Education Commission/ ; Grant No.23XLB031//Chongqing Normal University Foundation/ ; CSTB2024TIAD-KPX0015//Chongqing Technological Innovation and Application Development Project/ ; },
abstract = {Insects and their endosymbionts have a close mutualistic relationship. However, the precise nature of the bacterial endosymbiont-mediated interaction between host plants and whitefly Bemisia tabaci MEAM1 is still unclear. In the present study, six populations of Bemisia tabaci MEAM1 sharing the same genetic background were established by rearing insects for ten generations on different host plants, including poinsettia, cabbage, cotton, tomato, and tobacco, and an additional population was reared on cotton and treated with antibiotics. The physiological and nutritional traits of the insects were found to be dependent on the host plant on which they had been reared. Systematic analysis was conducted on the endosymbiont titers, the amino acid molecules and contents, as well as developmental and oviposition changes in the MEAM1 populations reared on each host plant tested. The results indicate that B. tabaci contained the primary symbiont Portiera and the secondary symbionts Hamiltonella and Rickettsia. In addition, the titer of endosymbiotic bacteria in females is higher than that in males. Among the MEAM1 populations reared on each host plant, the variation pattern of Portiera titer generally corresponded with changes in biological characteristics (body length, weight and fecundity) and AA contents. This suggests that changes in the amino acid contents and biological characteristics of different B. tabaci populations may be due to changes in the Portiera content and the differences in the nutrition of the host plants themselves. Our findings were further confirmed by the reduction in Portiera with antibiotic treatment. The amino acids, body size, body weight, and fecundity of B. tabaci were all reduced with the decrease in the Portiera titer after antibiotic treatment. In summary, our research revealed that host plants can affect the content of symbiotic bacteria, particularly Portiera, and subsequently affect the nutrition (i.e., the essential amino acids content) of host insects, thus changing their biological characteristics.},
}

@article {pmid40725318,
year = {2025},
author = {Prieto, SV and Dho, M and Orrù, B and Gonella, E and Alma, A},
title = {Symbiont-Targeted Control of Halyomorpha halys Does Not Affect Local Insect Diversity in a Hazelnut Orchard.},
journal = {Insects},
volume = {16},
number = {7},
pages = {},
pmid = {40725318},
issn = {2075-4450},
support = {//Regione Piemonte/ ; },
abstract = {Harmless crop-associated insect communities are a fundamental part of the agroecosystem. Their potential as a reservoir of natural enemies of pests has encouraged their conservation through the development of low-impact pest management programs. The brown marmorated stink bug, Halyomorpha halys, represents a serious threat to Italian hazelnut production. Laboratory and field experiments confirmed the susceptibility of this pest to the disruption of the obligated symbiotic interaction with gut bacteria, paving the way for the development of the symbiont-targeted control strategy. Here we present the results of a three-year field assessment of symbiont-targeted control in a hazelnut orchard in northwestern Italy. The use of a biocomplex to disrupt symbiont acquisition by H. halys nymphs was compared to the use of lambda-cyhalothrin insecticide. The effects on the local entomofauna were assessed, as were the trend of H. halys population and the damage caused by stink bugs to harvested hazelnuts. The insecticide consistently reduced the insect diversity in the field, while the anti-symbiont biocomplex had no effect. However, the control of the H. halys population and the stink bug-induced damage to hazelnuts varied over the years in the field plot submitted to the symbiont-targeted approach. Our results indicate that the symbiont-targeted control does not interfere with local insect communities. Key aspects for improving the effectiveness of this tactic are discussed.},
}

@article {pmid40725284,
year = {2025},
author = {Wang, Y and Zhang, Y and Li, R and Li, Y and Cha, M and Yi, X},
title = {Host Plant Dependence of the Symbiotic Microbiome of the Gall-Inducing Wasp Trichagalma acutissimae.},
journal = {Insects},
volume = {16},
number = {7},
pages = {},
pmid = {40725284},
issn = {2075-4450},
support = {ZR2024MC092//Natural Science Foundation of Shandong Province/ ; },
abstract = {Symbiotic bacteria play a pivotal role in the biology and ecology of herbivorous insects, affecting host growth and adaptation. However, the effects of host identity on the symbiotic microbiota of gall-inducing insects remain less explored. In this study, we utilized high-throughput sequencing to investigate the effects of different oak hosts on the structure and diversity of the symbiotic microbial community in the asexual larvae of the gall-inducing wasp Trichagalma acutissimae. Host plant species significantly altered the alpha and beta diversity of symbiotic microbiota of T. acutissimae. At the phylum level, Proteobacteria was the predominant microflora in both groups, with significantly higher abundance in larvae parasitizing Quercus acutissima than in those parasitizing Q. variabilis. Pseudomonas, which has been identified as responsible for tannin decomposition, was the most dominant genus in T. acutissimae larvae infesting both hosts. LEfSe analysis revealed substantial differences in the symbiotic microbial communities between the two hosts while also highlighting some commonalities. Functional prediction analysis indicated no significant difference in the functional roles of symbiotic bacteria between larvae infesting the two hosts. These findings suggest that the symbiotic microbiome of T. acutissimae larvae is influenced by host plant species, yet different microbial compositions may perform similar functions, implying the potential role of symbiotic microbiota in the adaptation to high-tannin oak leaves. This research enhances our understanding of the symbiotic relationship between forest pests and their associated microbes.},
}

@article {pmid40725114,
year = {2025},
author = {Wilgan, R},
title = {Phylogenetic Determinants Behind the Ecological Traits of Relic Tree Family Juglandaceae, Their Root-Associated Symbionts, and Response to Climate Change.},
journal = {International journal of molecular sciences},
volume = {26},
number = {14},
pages = {},
pmid = {40725114},
issn = {1422-0067},
support = {N.A.//Institute of Dendrology Polish Academy of Sciences/ ; 2020/37/N/NZ8/01403//National Science Center/ ; },
mesh = {*Symbiosis ; *Phylogeny ; *Plant Roots/microbiology/genetics ; *Mycorrhizae/physiology/genetics ; *Climate Change ; *Trees/microbiology/genetics ; },
abstract = {Dual mycorrhizal symbiosis, i.e., the association with both arbuscular and ectomycorrhizal fungal symbionts, is an ambiguous phenomenon concurrently considered as common among various genetic lineages of trees and a result of bias in data analyses. Recent studies have shown that the ability to form dual mycorrhizal associations is a distinguishing factor for the continental-scale invasion of alien tree species. However, the phylogenetic mechanisms that drive it remain unclear. In this study, all the evidence on root-associated symbionts of Juglandaceae from South and North America, Asia, and Europe was combined and re-analysed following current knowledge and modern molecular-based identification methods. The Juglandaceae family was revealed to represent a specific pattern of symbiotic interactions that are rare among deciduous trees and absent among conifers. Closely related phylogenetic lineages of trees usually share the same type of symbiosis, but Juglandaceae contains several possible ones concurrently. The hyperdiversity of root symbionts of Juglandaceae, unlike other tree families, was concurrently found in Central and North America, Asia, and Europe, indicating its phylogenetic determinants, which endured geographical isolation. However, for many Juglandaceae, including the invasive Juglans and Pterocarya species, this was never studied or was studied only with outdated methods. Further molecular research on root symbionts of Juglandaceae, providing long sequences and high taxonomic resolutions, is required to explain their ecological roles.},
}

*Symbiosis
*Phylogeny
*Plant Roots/microbiology/genetics
*Mycorrhizae/physiology/genetics
*Climate Change
*Trees/microbiology/genetics

@article {pmid40724547,
year = {2025},
author = {Golaz, D and Bürgi, L and Egli, M and Bigler, L and Pessi, G},
title = {The Siderophore Phymabactin Facilitates the Growth of the Legume Symbiont Paraburkholderia phymatum in Aluminium-Rich Martian Soil.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
pmid = {40724547},
issn = {2075-1729},
support = {310030_215282/SNSF_/Swiss National Science Foundation/Switzerland ; 4000144510//prodex/ ; },
abstract = {Beneficial interactions between nitrogen-fixing soil bacteria and legumes offer a solution to increase crop yield on Earth and potentially in future Martian colonies. Paraburkholderia phymatum is a nitrogen-fixing beta-rhizobium, which enters symbiosis with more than 50 legumes and can survive in acidic or aluminium-rich soils. In a previous RNA-sequencing study, we showed that the beta-rhizobium P. phymatum grows well in simulated microgravity and identified phymabactin as the only siderophore produced by this strain. Here, the growth of the beta-rhizobium P. phymatum was assessed in Martian simulant soil using Enhanced Mojave Mars Simulant 2 (MMS-2), which contains a high amount of iron (18.4 percent by weight) and aluminium (13.1 percent by weight). While P. phymatum wild-type's growth was not affected by exposure to MMS-2, a mutant strain impaired in siderophore biosynthesis (ΔphmJK) grew less than P. phymatum wild-type on gradient plates in the presence of a high concentration of MMS-2 or aluminium. This result suggests that the P. phymatum siderophore phymabactin alleviates aluminium-induced heavy metal stress. Ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS) showed that phymabactin can bind to aluminium more efficiently than iron. These results not only deepen our understanding of the behaviour of rhizobia in simulated extraterrestrial environments but also provide new insights into the potential use of P. phymatum for bioremediation of aluminium-rich soils and the multiple roles of the siderophore phymabactin.},
}

@article {pmid40724335,
year = {2025},
author = {Cánovas, BM and Pérez-Novas, I and García-Viguera, C and Domínguez-Perles, R and Medina, S},
title = {Assessment of Winery By-Products as Ingredients as a Base of "3S" (Safe, Salubrious, and Sustainable) Fermented Beverages Rich in Bioactive Anthocyanins.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {14},
pages = {},
pmid = {40724335},
issn = {2304-8158},
support = {PRTR-C17.I1//Ministerio de Ciencia e Innovación/ ; PID2023-148254OB-C21 (FERMISANO) funded by MICIU/AEI/10.13039/501100011033 and by "ERDF/EU"//Ministerio de Ciencia, Innovación y Universidades/ ; 22300/FPI/23//Fundación Séneca-Agencia de Ciencia y Tecnología de la Región de Murcia/ ; },
abstract = {Oenological residues may cause environmental pollution when processing does not significantly reduce volume and/or harmful conditions. The lack of proper valorisation alternatives entails high disposal costs and resource inefficiency that jeopardise the sustainability and competitiveness of the industry. Interestingly, wine by-products are underappreciated sources of multipurpose bioactive compounds, such as anthocyanins, associated with health benefits. Alternatively, transforming oenological by-products into valuable co-products will promote sustainability and thus, create new business opportunities. In this context, the present study has assessed the applicability of winery by-products (grape pomace and wine lees) as ingredients to develop new functional kombucha-analogous beverages "3S" (safe, salubrious, and sustainable) by the Symbiotic Culture of Bacteria and Yeast (SCOBY). Concerning the main results, during the kombucha's development, the fermentation reactions modified the physicochemical parameters of the beverages, namely pH, total soluble solids, acetic acid, ethanol, and sugars, which remained stable throughout the monitored shelf-life period considered (21 days). The fermented beverages obtained exhibited high anthocyanin concentration, especially when using wine lees as an ingredient (up to 5.60 mg/L at the end of the aerobic fermentation period (10 days)) compared with the alternative beverages produced using grape pomace (1.69 mg/L). These findings demonstrated that using winery by-products for the development of new "3S" fermented beverages would provide a dietary source of bioactive compounds (mainly anthocyanins), further supporting new valorisation chances and thus contributing to the competitiveness and sustainability of the winery industries. This study opens a new avenue for cross-industry innovation, merging fermentation traditions with a new eco-friendly production of functional beverages that contribute to transforming oenological residues into valuable co-products.},
}

@article {pmid40723480,
year = {2025},
author = {Zhou, C and Ding, F},
title = {Analysis of the Alterations in Symbiotic Microbiota and Their Correlation with Intestinal Metabolites in Rainbow Trout (Oncorhynchus mykiss) Under Heat Stress Conditions.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {14},
pages = {},
pmid = {40723480},
issn = {2076-2615},
abstract = {Global warming represents one of the most pressing environmental challenges to cold-water fish farming. Heat stress markedly alters the mucosal symbiotic microbiota and intestinal microbial metabolites in fish, posing substantial barriers to the healthy artificial breeding of rainbow trout (Oncorhynchus mykiss). However, the relationship between mucosal commensal microbiota, intestinal metabolites, and host environmental adaptability under heat stress remains poorly understood. In this study, rainbow trout reared at optimal temperature (16 °C) served as controls, while those exposed to maximum tolerated temperature (24 °C, 21 d) comprised the heat stress group. Using 16S rRNA amplicon sequencing and ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS), we analysed the mucosal commensal microbiota-including gastrointestinal digesta, gastrointestinal mucosa, skin mucus, and gill mucosa-and intestinal metabolites of rainbow trout under heat stress conditions to explore adaptive and regulatory mechanisms. Analysis of microbial composition and diversity revealed that heat stress exerted the greatest impact on the diversity of gill and skin mucus microbiota, followed by gastrointestinal digesta, with relatively minor effects on the gastrointestinal mucosa. At the phylum level, Proteobacteria, Firmicutes, and Bacteroidetes were predominant in the stomach, intestine, and surface mucosa. At the genus level, Acinetobacter showed the greatest increase in abundance in skin and gill mucosa under heat stress, while Enterobacteriaceae exhibited the most pronounced increase in intestinal digesta, gastric digesta, and gastric mucosa. Differential metabolites in the intestinal digesta under heat stress were predominantly enriched in pathways associated with amino acid metabolism, particularly tryptophan metabolism. This study provides a comprehensive characterisation of microbiota and metabolic profile alterations in rainbow trout under heat stress condition, offering a theoretical foundation for understanding the response mechanisms of fish commensal microbiota to thermal stress.},
}

@article {pmid40723436,
year = {2025},
author = {Maimaitiyiming, M and Huang, Y and Jia, L and Wu, M and Chen, Z},
title = {Epichloë Endophyte Alters Bacterial Nitrogen-Cycling Gene Abundance in the Rhizosphere Soil of Perennial Ryegrass.},
journal = {Biology},
volume = {14},
number = {7},
pages = {},
pmid = {40723436},
issn = {2079-7737},
support = {2014CB138702//National Basic Research Program of China/ ; 32201445//National Science Foundation of China/ ; 2021M701525//China Postdoctoral Science Foundation/ ; IRT17R50//Program for Changjiang Scholars and Innovative Research Team in University, China/ ; 22JR5RA532//Gansu Provincial Youth Science and Technology Fund Program/ ; 22JR5RA434//Gansu Province Outstanding Doctoral Students Project/ ; B12002//111 Project (B12002)/ ; },
abstract = {Perennial ryegrass (Lolium perenne), an important forage and turfgrass species, can establish a mutualistic symbiosis with the fungal endophyte Epichloë festucae var. lolii. Although the physiological and ecological impacts of endophyte infection on ryegrass have been extensively investigated, the response of the soil microbial community and nitrogen-cycling gene to this relationship has received much less attention. The present study emphasized abundance and diversity variation in the AOB-amoA, nirK and nosZ functional genes in the rhizosphere soil of the endophyte-ryegrass symbiosis following litter addition. We sampled four times: at T0 (prior to first litter addition), T1 (post 120 d of 1st litter addition), T2 (post 120 d of 2nd litter addition) and T3 (post 120 d of 3rd litter addition) times. Real-time fluorescence quantitative PCR (qPCR) and PCR amplification and sequencing were used to characterize the abundance and diversity of the AOB-amoA, nirK and nosZ genes in rhizosphere soils of endophyte-infected (E+) plants and endophyte-free (E-) plants. A significant enhancement of total Phosphorus (P), Soil Organic Carbon (SOC), Ammonium ion (NH4[+]) and Nitrate ion (NO3[-]) contents in the rhizosphere soil was recorded in endophyte-infected plants at different sampling times compared to endophyte-free plants (p ≤ 0.05). The absolute abundance of the AOB-amoA gene at T0 and T1 times was higher, as was the absolute abundance of the nosZ gene at T0, T1 and T3 times in the E+ plant rhizophere soils relative to E- plant rhizosphere soils. A significant change in relative abundance of the AOB-amoA and nosZ genes in the host rhizophere soils of endophyte-infected plants at T1 and T3 times was observed. The experiment failed to show any significant alteration in abundance and diversity of the nirK gene, and diversity of the AOB-amoA and nosZ genes. Analysis of the abundance and diversity of the nirK gene indicated that changes in soil properties accounted for approximately 70.38% of the variation along the first axis and 16.69% along the second axis, and soil NH4[+] (p = 0.002, 50.4%) and soil C/P ratio (p = 0.012, 15.8%) had a strong effect. The changes in community abundance and diversity of the AOB-amoA and nosZ genes were mainly related to soil pH, N/P ratio and NH4[+] content. The results demonstrate that the existence of tripartite interactions among the foliar endophyte E. festucae var. Lolii, L. perenne and soil nitrogen-cycling gene has important implications for reducing soil losses on N.},
}

@article {pmid40723404,
year = {2025},
author = {Fan, Y and Tian, M and Hu, D and Xiong, Y},
title = {Exploring the Biocultural Nexus of Gastrodia elata in Zhaotong: A Pathway to Ecological Conservation and Economic Growth.},
journal = {Biology},
volume = {14},
number = {7},
pages = {},
pmid = {40723404},
issn = {2079-7737},
support = {81960654//the National Natural Science Foundation of China/ ; 101520250000030//the Yunnan Minzu University Talent Introduction Program/ ; },
abstract = {Gastrodia elata, known as Tianma in Chinese, is a valuable medicinal and nutritional resource. The favorable climate of Zhaotong City, Yunnan Province, China, facilitates its growth and nurtures rich biocultural diversity associated with Tianma in the region. Local people not only cultivate Tianma as a traditional crop but have also developed a series of traditional knowledge related to its cultivation, processing, medicinal use, and culinary applications. In this study, field surveys employing ethnobotanical methods were conducted in Yiliang County, Zhaotong City, from August 2020 to May 2024, focusing on Tianma. A total of 114 key informants participated in semi-structured interviews. The survey documented 23 species (and forms) from seven families related to Tianma cultivation. Among them, there were five Gastrodia resource taxa, including one original species, and four forms. These 23 species served as either target cultivated species, symbiotic fungi (promoting early-stage Gastrodia germination), or fungus-cultivating wood. The Fagaceae family, with 10 species, was the most dominant, as its dense, starch-rich wood decomposes slowly, providing Armillaria with a long-term, stable nutrient substrate. The cultural importance (CI) statistics revealed that Castanea mollissima, G. elata, G. elata f. flavida, G. elata f. glauca, G. elata f. viridis, and Xuehong Tianma (unknown form) exhibited relatively high CI values, indicating their crucial cultural significance and substantial value within the local community. In local communities, traditionally processed dried Tianma tubers are mainly used to treat cardiovascular diseases and also serve as a culinary ingredient, with its young shoots and tubers incorporated into dishes such as cold salads and stewed chicken. To protect the essential ecological conditions for Tianma, the local government has implemented forest conservation measures. The sustainable development of the Tianma industry has alleviated poverty, protected biodiversity, and promoted local economic growth. As a distinctive plateau specialty of Zhaotong, Tianma exemplifies how biocultural diversity contributes to ecosystem services and human well-being. This study underscores the importance of biocultural diversity in ecological conservation and the promotion of human welfare.},
}

@article {pmid40721058,
year = {2025},
author = {Gerlin, L and Gaget, K and Lapetoule, G and Quivet, Y and Baa-Puyoulet, P and Rahioui, I and Lopes, MR and Da Silva, P and Calevro, F and Charles, H},
title = {Quantifying supply and demand in the pea aphid-Buchnera symbiosis reveals the metabolic Achilles' heels of this interaction.},
journal = {Metabolic engineering},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ymben.2025.07.011},
pmid = {40721058},
issn = {1096-7184},
abstract = {Many herbivorous insects feed on unbalanced diets and rely on bacterial endosymbionts to meet all their nutritional needs. This is the case for the pea aphid (Acyrthosiphon pisum), a plant pest whose remarkable growth and reproductive capacities cannot be sustained by its sole nutritional resource, the plant phloem sap, and which relies on a symbiotic relationship maintained over millions of years with the intracellular bacterium Buchnera aphidicola for the biosynthesis of amino acids and vitamins. Exploiting original experimental data and metabolic reconstructions, we have built a quantitative genome-scale metabolic model of B. aphidicola and used it to quantify amino acid exchanges between the bacterium and its host. We found metabolites that can rewire pathways, influencing the balance between selfish (growth-focused) and mutualist (amino acid synthesis) behavior. Among the products synthesized by Buchnera, phenylalanine, tyrosine and leucine are the main matter sinks and consume more than 60% of imported glucose and serine. Finally, we compared the predicted bacterial supply to the aphid demand in amino acids. We found that the pea aphid may efficiently regulate its symbiont population density depending on its metabolic requirements, but that embryos are quantitatively not self-sustaining, with embryonic bacteria supply falling short of demand by 50%. Overall, our study highlights candidate compounds and pathways to target for destabilizing this symbiosis or predicting its resilience to environmental or nutritional perturbations.},
}

@article {pmid40719630,
year = {2025},
author = {Kelleher, LA and Ramalho, MO},
title = {Impact of rising temperatures on the bacterial communities of Aphaenogaster ants.},
journal = {Biology open},
volume = {},
number = {},
pages = {},
doi = {10.1242/bio.062145},
pmid = {40719630},
issn = {2046-6390},
abstract = {Studies have shown that biodiversity will be impacted by global climate change, with the effect on ants just beginning to be documented. However, this influence on ant symbiotic bacterial communities remains understudied. Aphaenogaster Mayr, 1853, are seed dispersing ants in deciduous forests and their bacterial communities have just been uncovered; however, much is unknown. We aim to determine the impact that warming temperatures will have on Aphaenogaster survival and on their bacterial communities. Ants from four colonies were collected from West Chester, Pennsylvania, USA and entire colonies were subjected to a control temperature (22 °C). After 6-12 months the same colonies were subjected to an experimental temperature (32 °C). DNA was then extracted from ants of all development stages and the 16S rRNA gene was amplified and sequenced following the NGS amplicon approach. The findings revealed that Aphaenogaster ant mortality rates increased, and their symbiotic bacterial communities changed in warmer temperatures. This resulted in a decrease in the presence of Wolbachia spp. and an increase in the presence of Corynebacterium sp. This study reveals important information about the impact of warming temperature on Aphaenogaster ants, and we suggested methods to help protect these ants and other insects in the future.},
}

@article {pmid40716373,
year = {2025},
author = {Liu, Z and Lei, J and Yang, R and Cheng, L and Du, Y and Zhang, Y and Wang, J and Liu, Y},
title = {An artificial intelligence modeling framework based on microbial community structure prediction enhances the pollutant removal efficiency of the algae-bacteria granular sludge system.},
journal = {Journal of environmental management},
volume = {392},
number = {},
pages = {126648},
doi = {10.1016/j.jenvman.2025.126648},
pmid = {40716373},
issn = {1095-8630},
abstract = {Algae-bacteria granular sludge (ABGS) technology is a new energy-saving and low-carbon water treatment technology based on the algae-bacteria symbiotic system. However, due to its complex internal microbial system, the regulation mechanism of ABGS is unclear. To address this issue, the present study constructed a two-stage optimal control model for the ABGS system, which includes prediction of microbial community structure and planning of pollutant removal efficiency. This model enabled intelligent optimization of the system's pollutant removal efficiency through the regulation of operational parameters. In the first stage, seven machine learning (ML) algorithms were compared to predict the succession process of microbial community structure under the different conditions (R[2] > 0.94). In the second stage, six ML algorithms were compared to predict the pollutant removal efficiency of the ABGS system, combining regulatory indicators and microbial community structure (R[2] > 0.94). Finally, the non-dominated sorting genetic algorithm was used to integrate the prediction models of the two stages, and the microbial community structure was selectively shaped to enhance the removal efficiency of any two of the carbon, nitrogen, and phosphorus pollutants in the ABGS system (removal rate >90 %). The results of this study provided a universally applicable and quantitative intelligent guidance model for the performance optimization of ABGS technology and other biological systems.},
}

@article {pmid40718908,
year = {2025},
author = {Sun, G and Zhang, Y and Jin, C and Jia, Y},
title = {Ultrasound-CT Symbiosis in Pediatric Lung Abscess Volume Tracking.},
journal = {Journal of ultrasound in medicine : official journal of the American Institute of Ultrasound in Medicine},
volume = {},
number = {},
pages = {},
doi = {10.1002/jum.70015},
pmid = {40718908},
issn = {1550-9613},
}

@article {pmid40717827,
year = {2024},
author = {Hui, F and Lin, YT and Perez, M and Qiu, JW and Sun, Y},
title = {A New Species of Natsushima (Annelida: Chrysopetalidae) Living in the Mantle Cavity of a Deep-Sea Solemyid Clam.},
journal = {Zoological studies},
volume = {63},
number = {},
pages = {e41},
pmid = {40717827},
issn = {1810-522X},
abstract = {Natsushima is a genus of deep-sea Chrysopetalidae (Annelida) characterized by numerous bifurcate chaetae. It is poorly known, with three species living in the mantle cavity of bivalves in chemosynthetic habitats. Here we describe Natsushima nanhaiensis n. sp. based on an integrative morphological and molecular phylogenetic analysis of specimens collected from the Haima cold seep in the South China Sea. Morphologically, the new species can be distinguished from its congeneric species by the shape and number of the neuropodial hooks and bifurcate chaetae, the shape of the parapodia, and the long dorsal cirri. Sequence comparison and phylogenetic analysis based on the mitochondrial COI and 16S rRNA gene sequences supported the placement of Natsushima nanhaiensis n. sp. in Natsushima and its status as a distinct species. We also present a key to species of Natsushima and discuss their biogeography.},
}

@article {pmid40717644,
year = {2025},
author = {Gobetti, A and Cornacchia, G and Tomasoni, G and Ramorino, G},
title = {The environmental benefits of industrial symbiosis: A case study on substituting sand with steel slag as filler in epoxy mortar.},
journal = {Waste management & research : the journal of the International Solid Wastes and Public Cleansing Association, ISWA},
volume = {},
number = {},
pages = {734242X251350543},
doi = {10.1177/0734242X251350543},
pmid = {40717644},
issn = {1096-3669},
abstract = {Electric arc furnace (EAF) slag, a by-product of steelmaking commonly utilized as artificial aggregate, still faces significant landfilling despite extensive reuse. This study explores sustainable alternatives to minimize landfilling by investigating the environmental benefits of incorporating EAF slag as filler in epoxy mortar, as a substitute for a natural material such as river sand. Experimental results demonstrate that slag-filled mortar exhibits comparable or superior mechanical performance to sand-filled mortar, making it a technically feasible substitute. Moreover, the heavy metals leaching of slag, which is one of the major concerns about the reuse of this material, is reduced thanks to the incorporation into the polymeric matrix, ensuring a safe reuse. To quantify these sustainability benefits, a comparative life cycle assessment is conducted for two scenarios involving the production of a functional unit of 1 m[2] of epoxy mortar, typically applied in epoxy screeds, using sand or slag at equal volume fraction. Scenario 1 encompasses slag landfilling and sand extraction, while scenario 2 involves slag reuse as a filler, avoiding landfilling and sand extraction. Life cycle impact assessment using the Environmental Footprint 3.0 method reveals across-the-board reductions. The majority of analyzed impact categories experience a reduction of over 90% attributed to the avoidance of slag disposal and landfill inertization. Overall, reusing slag as an epoxy filler presents significant sustainability benefits compared to disposal, promoting the adoption of this industrial symbiosis application.},
}

@article {pmid40717481,
year = {2025},
author = {Larkin, J and Kassam, R and Crow, W and Hajihassani, A},
title = {Exploring the diversity of turfgrass-associated entomopathogenic nematodes and their symbiotic bacteria for root-knot and sting nematode biocontrol.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70077},
pmid = {40717481},
issn = {1526-4998},
support = {//US Department of agriculture/ ; 2022-51102-38143//Methyl Bromide Transitions Program/ ; },
abstract = {BACKGROUND: Symbiotic bacteria from the genera Xenorhabdus and Photorhabdus associated with Steinernema and Heterorhabditis entomopathogenic nematodes (EPNs), respectively, show nematicidal properties against plant-parasitic nematodes. This study investigated the diversity of EPNs in Floridian turfgrass systems and the effect of secondary metabolites of their symbiotic bacteria against grass root-knot (Meloidogyne graminis) and sting (Belonolaimus longicaudatus) nematodes, major pests in turfgrass systems.

RESULTS: Six isolates of H. indica, four of S. glaseri, and two of S. diaprepesi were isolated and identified molecularly from three turfgrass locations. Additionally, their symbiotic bacteria, X. poinarii, X. griffiniae, X. doucetiae, X. indica, P. akhurstii and P. luminescens were isolated and molecularly identified. Nematicidal efficacy of bacterial secondary metabolites (crude extracts) was tested against M. graminis and B. longicaudatus nematodes in vitro. Bioassays demonstrated a concentration-dependent increase in nematode mortality. The isolates X. poinarii 733 and X. griffiniae 1050 exhibited high mortality against M. graminis after 24, 48 and 72 h of exposure at 25% concentration (>87%) (P < 0.05). In addition to these isolates, two others, P. akhurstii 846 and P. luminescens 1189, exhibited high mortality (44-100%) against B. longicaudatus after 72 h at 25%, 50% and 100% concentrations (P < 0.05).

CONCLUSION: These findings indicate that Florida turfgrass soils harbor a high diversity of EPNs and associated bacteria. Furthermore, our results suggest for the first time that Xenorhabdus and Photorhabdus-derived secondary metabolites offer a promising biocontrol approach for managing M. graminis and B. longicaudatus. © 2025 Society of Chemical Industry.},
}

@article {pmid40714542,
year = {2025},
author = {Cáceres-Mago, K and Salazar, MJ and Becerra, AG},
title = {Glomalin-related soil protein produced by arbuscular mycorrhizal fungi: its role in Pb stabilization at heavily contaminated sites.},
journal = {Chemosphere},
volume = {385},
number = {},
pages = {144589},
doi = {10.1016/j.chemosphere.2025.144589},
pmid = {40714542},
issn = {1879-1298},
abstract = {Glomalin-related soil protein (GRSP), produced by arbuscular mycorrhizal fungi (AMF), plays a key role in stabilizing potentially toxic elements. This study evaluated the impact of Pb contamination on GRSP content in rhizosphere soil and its contribution to Pb binding at heavily contaminated sites. AMF colonization, spore density, and AMF species richness and diversity were also assessed. Additionally, methodological tests were conducted to evaluate the suitability of protocols for quantifying the amount of Pb bound to GRSP. Soil and root samples were collected from three dominant plant species at 20 locations near an abandoned Pb smelter, along with three uncontaminated locations. A Pb concentration gradient (149.28-77,588.77 mg kg[-1]) was identified. GRSP, classified into easily extractable (EE-GRSP: 0.46-1.75 mg g[-1]) and total (T-GRSP: 1.22-3.89 mg g[-1]), was detected at all sites. GRSP content was not directly affected by Pb contamination, but showed a positive association with AMF richness and diversity. The abundance of the morphospecies Acaulospora rehmii, A. scrobiculata, Entrophospora infrequens, Funneliformis geosporus, and Racocetra fulgida correlated positively with T-GRSP. Reliable quantification of Pb bound to GRSP required protein precipitation followed by dialysis. Pb bound to T-GRSP (2.03-548.54 mg g[-1]) increased with soil Pb, while the percentage of soil Pb retained by GRSP decreased (23.13-1.04 %). Nevertheless, the same amount of T-GRSP bound 77 times more Pb in the most contaminated location compared to the least. Therefore, enhancing the GRSP pool, particularly through AMF morphospecies related to higher GRSP content, may be a key strategy for AMF-assisted phytoremediation.},
}

@article {pmid40713930,
year = {2025},
author = {Escudero-Leyva, E and Belle, M and DadkhahTehrani, A and Culver, JN and Araya-Salas, M and Kutza, JP and Goldson, N and Chavarría, M and Chaverri, P},
title = {Genomic insights reveal community structure and phylogenetic associations of endohyphal bacteria and viruses in fungal endophytes.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {95},
pmid = {40713930},
issn = {2524-6372},
support = {IOS-2321265//National Science Foundation/ ; IOS-2321265//National Science Foundation/ ; IOS-2321265//National Science Foundation/ ; IOS-2321265//National Science Foundation/ ; IOS-2321265//National Science Foundation/ ; },
abstract = {BACKGROUND: Endohyphal microbial communities, composed of bacteria and viruses residing within fungal hyphae, play important roles in shaping fungal phenotypes, host interactions, and ecological functions. While endohyphal bacteria have been shown to influence fungal pathogenicity, secondary metabolism, and adaptability, much remains unknown about their diversity and host specificity. Even less is known about endohyphal viruses, whose ecological roles and evolutionary dynamics are poorly understood. This study integrates genomic and transcriptomic approaches to (1) characterize the diversity of endohyphal bacterial and viral communities in fungal endophytes isolated from Fagus grandifolia leaves, and (2) assess potential host specialization through phylogenetic signal analyses.

RESULTS: We analyzed 19 fungal isolates spanning eight fungal orders (Amphisphaeriales, Botryosphaeriales, Diaporthales, Glomerellales, Mucorales, Pleosporales, Sordariales, and Xylariales). Bacterial communities were highly diverse and showed significant phylogenetic signal, with core taxa-such as Bacillales, Burkholderiales, Enterobacterales, Hyphomicrobiales, and Pseudomonadales-shared across hosts. Several bacterial groups were associated with specific fungal orders, suggesting host specialization: Moraxellales, Sphingomonadales, and Streptosporangiaceae in Amphisphaeriales; Enterobacterales, Hyphomicrobiales, and Micrococcales in Glomerellales; and Cytophagales in Diaporthales. In contrast, viral communities were less diverse and dominated by double-stranded DNA viruses, primarily Bamfordvirae and Heunggongvirae. No core viral taxa were detected in metatranscriptomic data, and only a few reads of double-stranded RNA viruses were found.

CONCLUSIONS: Overall, our results indicate potential host specialization in bacterial endophytes and limited viral diversity in fungal hosts, with dsDNA viruses dominating the endohyphal virome. These findings provide new insights into the ecological and evolutionary dynamics of fungal-associated microbiota. Future work expanding taxonomic reference databases and exploring the functional roles of these microbial symbionts will be essential to understanding their contributions to fungal biology, host interactions, and broader ecosystem processes.},
}

@article {pmid40712359,
year = {2025},
author = {Liu, Y and Li, S and Song, X and Bartlam, M and Wang, Y},
title = {Differential responses of bacterial and archaeal communities to biodegradable and non-biodegradable microplastics in river.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139327},
doi = {10.1016/j.jhazmat.2025.139327},
pmid = {40712359},
issn = {1873-3336},
abstract = {Microplastics are widespread environmental pollutants that pose risks to ecosystems, yet their effects on bacterial and archaeal communities in aquatic ecosystems remain understudied. In this study, we performed a 14-day microcosm experiment combined with metagenomic sequencing to compare bacterial and archaeal responses to a biodegradable microplastic (polylactic acid, PLA) and a non-biodegradable microplastic (polyvinyl chloride, PVC). Microplastics selectively enriched distinct microbial assemblages, with Pseudomonadota and Euryarchaeota identified as the dominant bacterial and archaeal phyla, accounting for 67.83 % and 15.95 %, respectively. Archaeal community in surrounding water were more sensitive to colonization time than bacterial community. Compared to the surrounding water, the plastisphere displayed simpler and more loosely connected microbial networks. Notably, co-occurrence networks of both bacteria and archaea in the PVC plastisphere were predominantly shaped by symbiotic interactions. Both bacteria and archaea carried diverse antibiotic resistance genes (ARGs), but PLS-PM indicated that bacteria were the primary drivers of ARG dissemination (path coefficient = 0.952). While the PVC plastisphere showed higher ARG abundance than the PLA plastisphere, elevated intI1 expression in the PLA plastisphere suggests a potentially greater risk of ARG dissemination associated with PLA microplastics. These findings reveal the distinct effects of PLA and PVC microplastics on microbial communities and highlight the role of microplastics in ARG dissemination, emphasizing their ecological risks in aquatic ecosystems.},
}

@article {pmid40712336,
year = {2025},
author = {Thirunavukkarasu, S and Rajendran, P and Hwang, JS},
title = {Adaptations of Xenograpsus testudinatus to shallow hydrothermal vent environments in the western Pacific: A comprehensive review.},
journal = {Marine pollution bulletin},
volume = {221},
number = {},
pages = {118467},
doi = {10.1016/j.marpolbul.2025.118467},
pmid = {40712336},
issn = {1879-3363},
abstract = {The grapsoid crab Xenograpsus testudinatus, Ng et al. (2000) inhabits unique ecosystems of active shallow-water hydrothermal vents of the western Pacific volcanic rises as the dominant vent metazoan. This species provides a valuable model to explore population expansion, evolutionary ecology, metabolic regulation, genetic adaptation, and meta-population dynamics. A comprehensive literature review revealed that X. testudinatus, a dominant vent metazoan, has evolved robust metabolic strategies driven by mechanisms of acid-base regulation, allowing it to preserve its eco-physiological balance under extreme conditions. The species' physiology and metabolism are intricately linked to symbiotic relationships with beneficial microbiomes, which play a crucial role in its adaptive strategies. The genetic masterpiece of the genomic constitution of vent crabs showed extreme sulfur toxic tolerance through a specified genetic mechanism to H2S detoxification through epithelial and pillar cells of the gill filaments. Furthermore, the isotopic analyses of δ[13]C and δ1[5]N values suggest extensive ingestion of dead zooplankton with microbes forming marine snow in the shallow vents, facilitating a highly efficient recycling trophic system. The overall review highlights critical advancements in our understanding of the eco-physiology, symbiotic relationships, and evolutionary adaptations of marine organisms thriving in one of the earth's most extreme environments.},
}

@article {pmid40711997,
year = {2025},
author = {Hansen, AK and Percy, DM and Mao, S and Degnan, PH},
title = {Effect of oceanic islands on an insect symbiont genome in transition to a host-restricted lifestyle.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf153},
pmid = {40711997},
issn = {1759-6653},
abstract = {Islands offer unique opportunities to study adaptive radiations and their impacts on host genome evolution. In Hawaiian Pariaconus psyllids, all species harbor the ancient nutritional symbiont Carsonella, while only free-living and open-gall species on younger islands host a second stable co-symbiont, Makana. In contrast, a third co-symbiont, Malihini, appears to be in an early-stage of host restriction and genome degradation, making it a valuable model for understanding symbiont evolution during island radiations. Here, we examine Malihini genome evolution across multiple Pariaconus lineages using 16S rRNA sequencing, metagenomics, phylogenetic reconstruction, and microscopy. We find that Malihini is co-diversifying with its hosts on the oldest island Kaua'i (kamua group; open- and closed-gall makers) and on the younger islands only in free-living species (bicoloratus group). Comparison of five Malihini genomes-including three newly assembled in this study-shows ongoing genome reduction from a large-genome ancestor (>3,900 protein-coding genes), likely driven by relaxed selection, vertical transmission bottlenecks, and island dispersal over the past 5-million-years. On Kaua'i, the galling psyllids appear to depend more heavily on co-symbiont (Malihini) for the biosynthesis of amino acids and B-vitamins than galling species on younger islands-especially closed-gall species, which only have Carsonella. Surprisingly, free-living psyllids on younger islands with all three symbionts, show metabolic reliance similar to Kaua'i gall-makers. Together, our results demonstrate that island biogeography and host plant ecology shape symbiont losses and co-diversification patterns. Malihini represents an early-stage of symbiont genome degradation during host restriction, in sharp contrast to its more stable co-residents, Carsonella and Makana.},
}

@article {pmid40711302,
year = {2025},
author = {Yu, Y and Jin, F and Wang, L and Cheng, J and Pan, S},
title = {Role of Gut Microbiota and Metabolite Remodeling on the Development and Management of Rheumatoid Arthritis: A Narrative Review.},
journal = {Veterinary sciences},
volume = {12},
number = {7},
pages = {},
pmid = {40711302},
issn = {2306-7381},
support = {32072809//National Natural Science Foundation of China/ ; BK20211119//Natural Science Foundation of Jiangsu Province/ ; G2023014067L//National Foreign Experts Project (High-end Foreign Experts Introduction Programs of Ministry of Science and Technology)/ ; 22-R-17//Open Fund of Meat Processing Key Laboratory of Sichuan Province/ ; SJCX23_2016//Research and Practice Innovation Plan for Postgraduates in Jiangsu Province/ ; 202411117163Y//Innovation and Entrepreneurship Training Program for College Students of Higher Education In-stitutions in Jiangsu Province/ ; SBJC23007//Special Project of Cross-cooperation of Northern Jiangsu People's Hospital/ ; },
abstract = {Rheumatoid arthritis (RA) is a chronic autoimmune disease that has a serious impact on both human health and animal production. The gut microbiota is a large and complex symbiotic ecosystem in animals, and the imbalance of gut microbiota is closely related to the pathogenesis of numerous diseases, including RA. The interactions among the gut microbiota, intestinal barrier, and immune system play key roles in maintaining intestinal homeostasis and affecting the development of RA. Regulating intestinal flora and metabolites provides new ideas for the prevention and treatment of RA. Probiotics can regulate the balance of intestinal flora and metabolites, improve the immune environment, and provide novel therapeutic strategies against RA. In order to summarize the role of gut microbiota and metabolite remodeling in the development and management of RA, this review will elaborate on the role of intestinal flora imbalance in the pathogenesis of RA and assess prospective therapeutic approaches that target the gut flora. Understanding the interaction among intestinal flora, metabolites, and RA will help to clarify the pathogenesis of RA and develop innovative and personalized therapeutic interventions against chronic autoimmune diseases.},
}