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Complete xylan utilization pathway and regulation mechanisms involved in marine algae degradation by cosmopolitan marine and human gut microbiota ISME J. (IF 10.8) Pub Date : 2025-05-22 Hai-Ning Sun, Xiu-Lan Chen, Yan Wang, Yan-Ping Zhu, Zhao-Jie Teng, Hai-Yan Cao, Ting-Ting Xu, Yin Chen, Yu-Zhong Zhang, Fang Zhao
β-1,3-xylan, typically found in marine algae as a major cell wall polysaccharide, represents an overlooked pool of organic carbon in global oceans. Whilst our understanding of microbial catabolism of xylans has improved significantly, particularly from biotransformations of terrestrial plant biomass that are typically composed of β-1,4-xylans, knowledge on how microbes utilize β-1,3-xylan remains limited
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Vertical transport and spatiotemporal dynamics of giant viruses in the North Pacific Subtropical Gyre ISME J. (IF 10.8) Pub Date : 2025-05-22 Md Moinuddin Sheam, Elaine Luo
Nucleocytoplasmic large DNA viruses, or “giant viruses,” are prevalent in marine environments, infecting diverse eukaryotic lineages and influencing the marine carbon cycle. Their genomes harbor wide range of auxiliary metabolic genes that influence biogeochemical processes. This study integrates planktonic (5–4000 m) and particle-associated (4000 m) metagenomic samples in the North Pacific Subtropical
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Plant and soil biodiversity sustain root mycorrhizal fungal richness under drought stress. ISME J. (IF 10.8) Pub Date : 2025-05-22 Markus Bittlingmaier,Nathalie Séjalon-Delmas,Kezia Goldmann,David Johnson,Raoul Huys,Grégoire T Freschet
Mycorrhizal phenotypes arise from interactions among plants, soil biota, and environmental factors, but disentangling these drivers remains a key challenge in ecology. Understanding how these interactions shape mycorrhizal community assembly and stability is essential for predicting and managing these relationships in both natural and agricultural ecosystems. Here, we designed a fully factorial experiment
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Legume-specific recruitment of rhizobia by hyphae of arbuscular mycorrhizal fungi ISME J. (IF 10.8) Pub Date : 2025-05-21 Jiadong He, Judith Van Dingenen, Sofie Goormachtig, Maryline Calonne-Salmon, Stéphane Declerck
The legume-rhizobia symbiosis possesses great potential for sustainable agriculture because of its ability to fix atmospheric nitrogen, reducing crop dependence on nitrogen fertilizers. Rhizobia recognize the host legume through flavonoids released by the roots. These signals are detected by bacteria typically over a few millimeters. Recent research has shown that arbuscular mycorrhizal fungi extend
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Dynamics of diazotroph particle colonization in the Arctic Ocean ISME J. (IF 10.8) Pub Date : 2025-05-20 Arthur Coët, Cécile Carpaneto Bastos, Mathias Lechelon, Ruth Hawley, Oliver Flanagan, Maeve C Lohan, Pierre Ronceray, Joanne E Hopkins, Claire Mahaffey, Mar Benavides
Global warming is causing sea ice retreat and intensifying algal blooms in the Arctic Ocean, in turn increasing nitrogen limitation in surface waters. Dinitrogen fixation by diazotrophic microorganisms, usually favored in low reactive nitrogen systems, may become an increasingly important source of nitrogen in the Arctic. Previous studies have shown that non-cyanobacterial diazotrophs are dominant
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Distinct iron acquisition strategies in oceanic and coastal variants of the mixotrophic dinoflagellate Karlodinium ISME J. (IF 10.8) Pub Date : 2025-05-20 Se Hyeon Jang, YuanYu Lin, Adrian Marchetti
The availability of the micronutrient iron is important in regulating phytoplankton growth across much of the world’s oceans, particularly in the high-nutrient, low-chlorophyll regions. Compared to known mechanisms of iron acquisition and conservation in autotrophic protists (e.g., diatoms), those of dinoflagellates remain unclear, despite their frequent presence in offshore iron-limited waters. Here
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Spatially structured bacterial interactions alter algal carbon flow to bacteria ISME J. (IF 10.8) Pub Date : 2025-05-17 Hyungseok Kim, Vanessa L Brisson, John R Casey, Courtney Swink, Kristina A Rolison, Nathaniel McCall, Amber N Golini, Trent R Northen, Dušan Veličković, Peter K Weber, Cullen R Buie, Xavier Mayali, Rhona K Stuart
Phytoplankton account for nearly half of global photosynthetic carbon fixation, and the fate of that carbon is regulated in large part by microbial food web processing. We currently lack a mechanistic understanding of how interactions among heterotrophic bacteria impact the fate of photosynthetically fixed carbon. Here, we used a set of bacterial isolates capable of growing on exudates from the diatom
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Independently evolved extracellular electron transfer pathways in ecologically diverse Desulfobacterota ISME J. (IF 10.8) Pub Date : 2025-05-17 Dario R Shaw, Krishna P Katuri, Veerraghavulu Sapireddy, Olga Douvropoulou, Jeffrey A Gralnick, Pascal E Saikaly
Extracellular electron transfer plays a role in the biogeochemical cycling of carbon, metals, sulfur, and nitrogen, and has wide-ranging biotechnological applications. The metal-reducing (Mtr), outer-membrane cytochrome (Omc), and porin-cytochrome (Pcc) pathways facilitate electron transfer to insoluble electron acceptors via trans-outer membrane cytochrome complexes. Although these pathways perform
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Holocene and contemporary marine dinoflagellate community patterns predict expansion of generalist dinoflagellate blooms in warming oceans ISME J. (IF 10.8) Pub Date : 2025-05-14 Lemian Liu, Siqi Zhu, Yifan Gu, Shuqin Tao, Bernd Krock, Changyou Wang, Xinguo Shi, Qi Yan, Xiusong Pan, Jianfeng Chen, Senjie Lin, Zhaohe Luo
Existing data and models suggest increasing prominence of dinoflagellates and their blooms in future warmer ocean but supporting long-term data are sparse. Here, we used 18S rRNA gene sequencing to investigate sedimentary ancient dinoflagellate communities in northern South China Sea and compared them with contemporary dinoflagellate data from global oceans (TARA Oceans data) and 40 years of dinoflagellate
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Natural and lab-derived microbiomes differentially shape stressor interaction patterns of Daphnia magna ISME J. (IF 10.8) Pub Date : 2025-05-12 Shira Houwenhuyse, Lore Bulteel, Isabel Vanoverberghe, Anna Krzynowek, Marlies Van de Maele, Manon Coone, Silke Van den Wyngaert, Arne Sinnesael, Robby Stoks, Ellen Decaestecker
Organisms are facing multiple, potentially interacting stressors in natural populations. The ability of populations coping with combined stressors depends on their tolerance to individual stressors and how stressors interact, which may not be correctly captured in controlled laboratory settings. One reason for this is that the microbial communities in laboratory settings often differ from the natural
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Emergence and disruption of cooperativity in a denitrifying microbial community ISME J. (IF 10.8) Pub Date : 2025-05-11 Alex V Carr, Anne E Otwell, Kristopher A Hunt, Yan Chen, James Wilson, José P Faria, Filipe Liu, Janaka N Edirisinghe, Jacob J Valenzuela, Serdar Turkarslan, Lauren M Lui, Torben N Nielsen, Adam P Arkin, Christopher S Henry, Christopher J Petzold, David A Stahl, Nitin S Baliga
Anthropogenic perturbations to the nitrogen cycle, primarily through use of synthetic fertilizers, is driving an unprecedented increase in the emission of nitrous oxide (N2O), a potent greenhouse gas and an ozone depleting substance, causing urgency in identifying the sources and sinks of N2O. Microbial denitrification is a primary contributor to biotic production of N2O in anoxic regions of soil,
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Chromosomal capture of beneficial genes drives plasmids towards ecological redundancy ISME J. (IF 10.8) Pub Date : 2025-05-11 R Craig MacLean, Cédric Lood, Rachel M Wheatley
Plasmids are a ubiquitous feature of bacterial genomes, but the forces driving genes and phenotypes to become associated with plasmids are poorly understood. To address this problem, we compared the fitness effects of chromosomal and plasmid genes in the plant symbiont Rhizobium leguminosarum. The relative abundance of beneficial genes on plasmids was very low compared to the chromosome across niches
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Drug delivery dynamics dictate evolution of bacterial antibiotic responses ISME J. (IF 10.8) Pub Date : 2025-05-11 John C Crow, Hao Geng, Christopher J Geiger, Timothy J Sullivan, Shannon M Soucy, Daniel Schultz
Microbes inhabit natural environments that are remarkably dynamic. Therefore, microbes harbor regulated genetic mechanisms to sense shifts in conditions and induce the appropriate responses. Recent studies suggest that the initial evolution of microbes occupying new niches favors mutations in regulatory pathways. However, it is not clear how this evolution is affected by how quickly conditions change
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Millimeter-scale niche differentiation of N-cycling microorganisms across the soil-water interface has implications for N2O emissions from wetlands ISME J. (IF 10.8) Pub Date : 2025-05-03 Yu-Jia Cai, Hong-Yang Zhang, Xiao-Ran Hu, Yu-Chen Yang, Christina Hazard, Graeme W Nicol, Ji-Zheng He, Ju-Pei Shen, Zi-Yang He, Lu Zhang, Jing-Hui Zhang, Hao Liu, Sha Zhang, Zheng Chen
Wetlands can be a significant source of N2O under current global climate change regime with the soil-water interface representing a biogeochemical hotspot for microbial activity. However, the role of soil-water interface in controlling N2O emissions remains poorly understood. We hypothesized that the millimeter-scale redox gradient across the soil-water interface generates corresponding distinct niche
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Fungi shape genome evolution of bacteria even in the absence of major growth phenotypes ISME J. (IF 10.8) Pub Date : 2025-05-03 Emily E Putnam, Robert May, Nina Freeman, Dillon Arrigan, Andrew Boylan, Laura H Childs, Benjamin E Wolfe
Studies of microbial interactions often emphasize interactions with large, easily measurable growth differences and short-term ecological outcomes spanning just a few generations. However, more subtle interactions, such as those without obvious phenotypes, may play a significant role in shaping both the short-term ecological dynamics and the long-term evolutionary trajectories of microbial species
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Beneficial and detrimental fungi within the culturable mycobiome of the Red Sea coral Stylophora pistilatta ISME J. (IF 10.8) Pub Date : 2025-05-03 Lior Granit, Rotem Levi, Nofar Lifshitz, Guilhem Banc-Prandi, Einat Zelinger, Britt Ronen, Judith Kraut-Cohen, Ankur Naqib, Stefan J Green, Maoz Fine, Oded Yarden
The presence of fungi in the coral microbiome is increasingly recognized, yet their potential impact on the holobiont’s health, particularly under stress conditions, remains underexplored. To address this gap, we isolated over 200 strains (predominantly Ascomycota) from the common scleractinian Red Sea coral, Stylophora pistillata. Using conidia from a rare (Stachybotrys chlorohalonata) and a common
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Sea cucumber grazing linked to enrichment of anaerobic microbial metabolisms in coral reef sediments ISME J. (IF 10.8) Pub Date : 2025-04-30 Andrew J Maritan, Cody S Clements, Zoe A Pratte, Mark E Hay, Frank J Stewart
Sea cucumbers have been overharvested world-wide, making assessments of their ecological effects challenging, but recent research demonstrated that sea cucumbers increase coral survival via disease suppression and were therefore important for facilitating reef health. The mechanisms underpinning the sea cucumber-coral interaction therefore are not well understood but are likely mediated through sea
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Residence-colonization trade-off and niche differentiation enable coexistence of Escherichia coli phylogroups in healthy humans ISME J. (IF 10.8) Pub Date : 2025-04-30 Thibaut Morel-Journel, Sonja Lehtinen, Olivier Cotto, Rafika Amia, Sara Dion, Clarisse Figueroa, Jonathan N V Martinson, Pascal Ralaimazava, Olivier Clermont, Xavier Duval, Forough L Nowrouzian, Seth T Walk, Erick Denamur, François Blanquart
Despite abundant literature on pathogenicity and virulence of the opportunistic pathogen Escherichia coli, much less is known about its ecological and evolutionary dynamics as a commensal. Based on two detailed longitudinal datasets on the gut microbiota of healthy adults followed for months to years in France and the USA, we identified a robust trade-off between the ability to establish in a new host
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Polyhydroxybutyrate production by freshwater SAR11 (LD12) ISME J. (IF 10.8) Pub Date : 2025-04-30 Brittany D Bennett, David A O Meier, V Celeste Lanclos, Hasti Asrari, John D Coates, J Cameron Thrash
SAR11 bacteria (order Pelagibacterales) are oligotrophs and often the most abundant bacterioplankton in aquatic environments. A subset of sequenced SAR11 genomes, predominantly in the brackish and freshwater SAR11 subclades, contain homologs of pha genes, which in other organisms confer the ability to store carbon and energy via polyhydroxyalkanoate polymers. Here, we investigated the relevance of
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Host identity drives the assembly of phytoplankton microbiomes across a continental scale environmental gradient ISME J. (IF 10.8) Pub Date : 2025-04-30 P Signe White, Taryn Y Broe, Mirte C M Kuijpers, Jonathan R Dickey, Sara L Jackrel
Host-associated microbiomes often promote host health, yet the key drivers of microbiome assembly and its consequences for host fitness remain unclear. We aimed to determine the relative roles of host identity versus the environment in driving host-microbiome assembly and the consequences of this variation in assembly for host fitness, which may help predict the resilience of host-associated microbiomes
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Proportional relationship between transcript concentrations and carbon biomass for open ocean plankton groups ISME J. (IF 10.8) Pub Date : 2025-04-30 Sacha N Coesel, Shiri Graff van Creveld, Mathilde Dugenne, Fernanda Henderikx-Freitas, Angelicque E White, E Virginia Armbrust
Unicellular plankton form the foundation of the marine food web, driving carbon fixation and cycling essential biogeochemical elements in marine ecosystems. Carbon biomass, often measured as a bulk property, serves as a common “currency” for ecologists. The increasing availability of metatranscriptomic data presents an opportunity to add taxonomic and functional resolution to ecological models and
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Bifidobacterium breve synergizes with Akkermansia muciniphila and Bacteroides ovatus to antagonize Clostridioides difficile ISME J. (IF 10.8) Pub Date : 2025-04-30 Yanan Li, Wen Rui, Xiaoya Sheng, Xilong Deng, Xiaoqian Li, Lingtong Meng, He Huang, Jingpeng Yang
The development of ecologically based in vivo microecological formulations for treating Clostridioides difficile infection (CDI) is a current research focus. Here, we selected three microorganisms—Akkermansia muciniphila (AM), Bacteroides ovatus (BO), and Bifidobacterium breve (BB)—to formulate a mixed bacterial formulation (ABB). Subsequently, we evaluated the ecological interactions among these three
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Akkermansia muciniphila exacerbates acute radiation-induced intestinal injury by depleting mucin and enhancing inflammation ISME J. (IF 10.8) Pub Date : 2025-04-29 Yafang Wang, Xusheng Wang, Zhenhui Chen, Jihua Zheng, Xiangqiang Liu, Yilin Zheng, Zhihao Zheng, Zi Xu, Yaowei Zhang, Keli Chen, Yuqin Zhang, Lu Yu, Yi Ding
Dysbiosis of gut microbiota plays a crucial role in acute radiation-induced intestinal injury. However, studies on the influence of gut microbiota on acute radiation-induced intestinal injury are inconsistent. In this study, we established an acute radiation-induced intestinal injury mouse model and performed fecal microbiota transplantation to explore the role of the gut microbiota in acute radiation-induced
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Fireworms are a reservoir and potential vector for coral-infecting apicomplexans ISME J. (IF 10.8) Pub Date : 2025-04-23 Anthony M Bonacolta, Bradley A Weiler, Candace J Grimes, Morelia Trznadel, Mark J A Vermeij, Patrick J Keeling, Javier del Campo
Corals (Cnidaria; Anthozoa) play critical roles as habitat-forming species with a wide range, from warm shallow-water tropical coral reefs to cold-water ecosystems. They also represent a complex ecosystem as intricate holobionts made up of microbes from all domains of the Tree of Life that can play significant roles in host health and fitness. The corallicolids are a clade of apicomplexans that infect
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Synthetic microbial community improves chicken intestinal homeostasis and provokes anti-Salmonella immunity mediated by segmented filamentous bacteria ISME J. (IF 10.8) Pub Date : 2025-04-23 Meihong Zhang, Suxin Shi, Yimei Feng, Fengwenhui Zhang, Yuxuan Xiao, Xin Li, Xingliang Pan, Yuqing Feng, Dan Liu, Yuming Guo, Yongfei Hu
Applying synthetic microbial communities to manipulate the gut microbiota is a promising manner for reshaping the chicken gut microbial community. However, it remains elusive the role of a designed microbial community in chicken physiological metabolism and immune responses. In this study, we constructed a ten-member synthetic microbial community (SynComBac10) that recapitulated the phylogenetic diversity
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Treatment of antibiotic-manufacturing wastewater enriches for Aeromonas veronii, a zoonotic antibiotic-resistant emerging pathogen ISME J. (IF 10.8) Pub Date : 2025-04-21 Xingshuo Wang, Meilun Wang, Wei Zhang, Hui Li, James M Tiedje, Jizhong Zhou, Edward Topp, Yi Luo, Zeyou Chen
Antibiotic-manufacturing wastewater treatment plants primarily target chemical pollutants, but their processes may select for antibiotic-resistant pathogens and antibiotic resistance genes. Here, leveraging the combined strengths of deep metagenomic sequencing, 16S rRNA gene sequencing, qPCR, and bacterial culturing, we investigated bacterial communities and antibiotic resistomes across eleven treatment
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Heat-induced Stress Modulates Cell Surface Glycans and Membrane Lipids of Coral Symbionts ISME J. (IF 10.8) Pub Date : 2025-04-18 Giada Tortorelli, Sabrina L Rosset, Clarisse E S Sullivan, Sarah Woo, Erika C Johnston, Nia Symone Walker, Joshua R Hancock, Carlo Caruso, Alyssa C Varela, Kira Hughes, Christian Martin, Robert A Quinn, Crawford Drury
The susceptibility of corals to environmental stress is determined by complex interactions between host genetic variation and the Symbiodiniaceae family community. We exposed genotypes of Montipora capitata hosting primarily Cladocopium or Durusdinium symbionts to ambient conditions and an eight-day heat stress. Symbionts’ cell surface glycan composition differed between genera and was significantly
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Climate History Modulates Stress Responses of Common Soil Bacteria Under Experimental Drought ISME J. (IF 10.8) Pub Date : 2025-04-18 Nicholas J Bouskill, Stephany S Chacon, Daniela F Cusack, Lee H Dietterich, Liang Chen, Aizah Khurram, Jana Voriskova, Hoi-Ying N Holman
Soil drying challenges microbial viability and survival, with bacteria employing various mechanisms to respond to shifts in osmolarity, including dormancy or metabolic upregulation of osmoprotectants. However, the extent to which these responses are shaped by an organism’s phylogeny, or the climate history of a given environment is poorly understood. This study examines the responses of phylogenetically
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Muribaculum intestinale restricts Salmonella Typhimurium colonization by converting succinate to propionate ISME J. (IF 10.8) Pub Date : 2025-04-18 Zhenyu Wang, Shuaishuai Kang, Zhenhua Wu, Xiaoyi Liu, Xiangyu Zhang, Yujun Wu, Yang Wen, Xingjian Zhou, Guolong Zhang, Junjun Wang, Dandan Han
Insufficient dietary fiber intake is associated with dysbiosis and compromised colonization resistance to enteric infections. However, a detailed understanding of the relationship between dietary fiber insufficiency and colonization resistance remains elusive. Our study aimed to delineate the impact of fiber deprivation on gut microbiome and colonization resistance in a murine model with Salmonella
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Fungal-mediated soil aggregation as a mechanism for carbon stabilization ISME J. (IF 10.8) Pub Date : 2025-04-18 Steven P C de Goede, S Emilia Hannula, Boris Jansen, Elly Morriën
Soils can potentially be turned into net carbon sinks for atmospheric carbon to offset anthropogenic greenhouse gas emissions. Occlusion of soil organic carbon (SOC) in soil aggregates is a key mechanism which temporarily protects it from decomposition by soil organisms. Filamentous fungi are recognized for their positive role in the formation and stabilization of aggregates. In this review we assess
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Promiscuous and genome-wide recombination underlies the sequence-discrete species of the SAR11 lineage in the deep ocean ISME J. (IF 10.8) Pub Date : 2025-04-18 Jianshu Zhao, Maria Pachiadaki, Roth E Conrad, Janet K Hatt, Laura A Bristow, Luis M Rodriguez-R, Ramon Rossello-Mora, Frank J Stewart, Konstantinos T Konstantinidis
Surveys of microbial communities (metagenomics) or isolate genomes have revealed sequence-discrete species. That is, members of the same species show >95% Average Nucleotide Identity (ANI) of shared genes among themselves vs. <83% ANI to members of other species while genome pairs showing between 83-95% ANI are comparatively rare. In these surveys, aquatic bacteria of the ubiquitous SAR11 clade (Class
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Within-host competition causes pathogen molecular evolution and perpetual microbiota dysbiosis ISME J. (IF 10.8) Pub Date : 2025-04-17 Emily J Stevens, Jingdi D Li, Tobias E Hector, Georgia C Drew, Kim Hoang, Samuel T E Greenrod, Steve Paterson, Kayla C King
Pathogens newly invading a host must compete with resident microbiota. This. within-host microbial warfare could lead to more severe disease outcomes or constrain the evolution of virulence. By passaging a widespread pathogen (Staphylococcus aureus) and a native microbiota community across populations of nematode hosts, we show that the pathogen displaced microbiota and reduced species richness, but
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Tetrahymena predation drives adaptive evolution of Salmonella by disrupting O-antigen biosynthesis and upregulating transcriptional regulator csgD ISME J. (IF 10.8) Pub Date : 2025-04-14 Hao Huang, Jinzhu Geng, Yuhao Dong, Chen Yuan, Gang Li, Meng Nie, Jingjing Guo, Yongjie Liu
Protozoan predation is increasingly understood to be one of the main environmental factors driving bacterial virulence evolution and adaptation strategies. In this study, we reveal the adaptive evolution of Salmonella Enteritidis in phenotypic and genomic traits after passage through Tetrahymena thermophila. We identified a beneficial and fixed mutation that occurs at the coding region of rfbP, encoding
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Episomal virus maintenance enables bacterial population recovery from infection and promotes virus-bacterial coexistence ISME J. (IF 10.8) Pub Date : 2025-04-11 Rodrigo Sanchez-Martinez, Akash Arani, Mart Krupovic, Joshua S Weitz, Fernando Santos, Josefa Anton
Viruses are ubiquitous in aquatic environments with total densities of virus-like particles often exceeding 107/ml in surface marine oligotrophic waters. Hypersaline environments harbor elevated prokaryotic population densities of 108/ml that coexist with viruses at even higher densities, approaching 1010/ml. The presence of high densities of microbial populations and viruses challenge traditional
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Identification of stress-alleviating strains from the core drought-responsive microbiome of Arabidopsis ecotypes ISME J. (IF 10.8) Pub Date : 2025-04-08 Zewen Li, Zhenghong Wang, Yujie Zhang, Jianbo Yang, Kaixiang Guan, Yi Song
Plant genetic and metabolic cues are involved in assembling their “core microbiome” under normal growth conditions. However, whether there is a core “stress responsive microbiome” among natural plant ecotypes remains elusive. Drought is the most significant abiotic stress worldwide. Characterizing conserved core root microbiome changes upon drought stress has the potential to increase plant resistance
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Selection for toxin production in spatially structured environments increases with growth rate ISME J. (IF 10.8) Pub Date : 2025-04-08 Ave T Bisesi, Jeremy M Chacón, Michael J Smanski, Linda Kinkel, William R Harcombe
Microbes adopt a diversity of strategies to successfully compete with coexisting strains for space and resources. One common strategy is the production of toxic compounds to inhibit competitors, but the strength and direction of selection for this strategy varies depending on the environment. Existing theoretical and experimental evidence suggests growth in spatially structured environments makes toxin
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Genome-streamlined SAR202 bacteria are widely present and active in the euphotic ocean ISME J. (IF 10.8) Pub Date : 2025-04-08 Changfei He, Michael Gonsior, Jihua Liu, Nianzhi Jiao, Feng Chen
SAR202 bacteria are a diverse group of bacteria in the ocean. The SAR202 lineages dominate the bacterial community and evolve specialized metabolisms for oxidizing recalcitrant organic compounds in the dark ocean. SAR202 bacteria are also present in the euphotic oceans; however, their ecological roles and metabolic potential remain poorly understood. In this study, we collected 392 non-redundant metagenome-assembled
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Phage-phage competition and biofilms affect interactions between two virulent bacteriophages and Pseudomonas aeruginosa ISME J. (IF 10.8) Pub Date : 2025-04-06 Magdalena Bürkle, Imke H E Korf, Anne Lippegaus, Sebastian Krautwurst, Christine Rohde, Chantal Weissfuss, Geraldine Nouailles, Xavière Menatong Tene, Baptiste Gaborieau, Jean-Marc Ghigo, Jean-Damien Ricard, Andreas C Hocke, Kai Papenfort, Laurent Debarbieux, Martin Witzenrath, Sandra-Maria Wienhold, Gopinath Krishnamoorthy
Virulent bacteriophages (or phages) are viruses that specifically infect and lyse a bacterial host. When multiple phages co-infect a bacterial host, the extent of lysis, dynamics of bacteria-phage and phage-phage interactions are expected to vary. The objective of this study is to identify the factors influencing the interaction of two virulent phages with different Pseudomonas aeruginosa growth states
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Adaptive survival strategies of rumen microbiota with solid diet deficiency in early life cause epithelial mitochondrial dysfunction ISME J. (IF 10.8) Pub Date : 2025-04-06 Shiqiang Yu, Yuting Fu, Jinrui Qu, Kai Zhang, Weiyun Zhu, Shengyong Mao, Junhua Liu
With extreme nutritional substrate deficiency, the adaptive responses of the gastrointestinal microbiota and host metabolism are largely unknown. Here, we successfully established a microbial substrate deficiency model in the rumen without solid diet introduction in neonatal lambs. In the absence of solid diet, we observed a reduction in the Simpson Index of rumen bacteria, along with a marked decline
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Adaptive genomic plasticity in large-genome, broad-host-range vibrio phages ISME J. (IF 10.8) Pub Date : 2025-04-04 Charles Bernard, Yannick Labreuche, Carine Diarra, Pauline Daszkowski, Karine Cahier, David Goudenège, Martin G Lamarche, Gregory B Whitfield, Manon Lang, Jeffrey Valencia, Justine Groseille, Damien Piel, Yan-Jiun Lee, Peter Weigele, Yves V Brun, Eduardo P C Rocha, Frédérique Le Roux
The host range of a bacteriophage—the diversity of hosts it can infect—is central to understanding phage ecology and applications. Whereas most well-characterized phages have narrow host ranges, broad-host-range phages represent an intriguing component of marine ecosystems. The genetic and evolutionary mechanisms driving their generalism remain poorly understood. In this study, we analyzed Schizotequatroviruses
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Longitudinal dynamics and cross-domain interactions of eukaryotic populations in wastewater treatment plants ISME J. (IF 10.8) Pub Date : 2025-04-04 Yue Huang, Xuemei Mao, Xiawan Zheng, Yuxiang Zhao, Dou Wang, Mengying Wang, Yiqiang Chen, Lei Liu, Yulin Wang, Martin F Polz, Tong Zhang
Activated sludge is a large reservoir of novel microorganisms and microbial genetic diversity. While much attention has been given to the profile and functions of prokaryotes, the eukaryotic diversity remains largely unexplored. In this study, we analyzed longitudinal activated sludge samples spanning 13 years from the largest secondary wastewater treatment plants in Hong Kong, unveiling a wealth of
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Interplay of ecological processes modulates microbial community reassembly following coalescence ISME J. (IF 10.8) Pub Date : 2025-04-03 Luana Bresciani, Gordon F Custer, David Koslicki, Francisco Dini-Andreote
Microbial community coalescence refers to the mixing of entire microbial communities and their environments. Despite conceptually analogous to a multispecies invasion, the ecological processes driving this phenomenon remain poorly understood. Here, we developed and implemented a beta-diversity–based statistical framework to quantify the contribution of distinct donor communities to community reassembly
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Differential aggregation patterns of Endozoicomonas within tissues of the coral Acropora loripes ISME J. (IF 10.8) Pub Date : 2025-03-31 Cecilie R Gotze, Ashley M Dungan, Allison M L van de Meene, Katarina Damjanovic, Gayle K Philip, Justin Maire, Lone Høj, Linda L Blackall, Madeleine J H van Oppen
Bacteria in the genus Endozoicomonas are well-known coral symbionts commonly found as clusters within tissues of several coral species. Mapping the spatial distribution of these microbial communities is critical to gaining a holistic understanding of the potential role they may play within the coral host. This study focuses on characterizing bacterial aggregates associated with the common reef-building
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Extensive and diverse lanthanide-dependent metabolism in the ocean ISME J. (IF 10.8) Pub Date : 2025-03-23 Marcos Y Voutsinos, Jillian F Banfield, Harry-Luke O McClelland
To date, the only known Lanthanide (Ln)-dependent enzymes are pyrroloquinoline quinone-dependent alcohol dehydrogenases. When compared to their Ca dependent counterparts, there is an emerging picture that Ln-dependent versions of these enzymes are generally more efficient, are preferentially upregulated in the presence of Ln when there is functional redundancy, and may even be evolutionarily older
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Dietary protein source alters gut microbiota composition and function ISME J. (IF 10.8) Pub Date : 2025-03-23 J Alfredo Blakeley-Ruiz, Alexandria Bartlett, Arthur S McMillan, Ayesha Awan, Molly Vanhoy Walsh, Alissa K Meyerhoffer, Simina Vintila, Jessie L Maier, Tanner G Richie, Casey M Theriot, Manuel Kleiner
The source of protein in a person's diet affects their total life expectancy. However, the mechanisms by which dietary protein sources differentially impact human health and life expectancy are poorly understood. Dietary choices impact the composition and function of the intestinal microbiota that ultimately modulate host health. This raises the possibility that health outcomes based on dietary protein
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Dietary intake of enrofloxacin promotes the spread of antibiotic resistance from food to simulated human gut ISME J. (IF 10.8) Pub Date : 2025-03-23 Qing Wang, Changzhen Liu, Yan Sun, Xuli Li, Weimin Gu, Na Wang, Shaojing Sun, Yi Luo
Antibiotic residues are commonly found in food. The effect of dietary exposure to veterinary antibiotics on the transmission of antibiotic resistant bacteria and antibiotic resistance genes from food to humans is unknown. We found that dietary exposure to enrofloxacin reduced microbial diversity, interactions and the immune responses, weakened the colonization resistance of the resident microbiota
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Temperature influences outcomes of an environmentally acquired symbiosis ISME J. (IF 10.8) Pub Date : 2025-03-23 Patrick T Stillson, Kaisy Martinez, Johnathan Adamson, Arshya Tehrani, Alison Ravenscraft
Microbial symbioses are essential for many animals, but their outcomes are often context dependent. For example, rising temperatures can disrupt symbioses by eliminating thermally sensitive symbionts. The temperature tolerance of a symbiont may therefore limit the temperature range of its host, but switching to a more thermally tolerant partner could expand this range. Eastern leaf footed bugs (Leptoglossus
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Adaptive responses of Trichlorobacter lovleyi to nitrite detoxification reveal overlooked contributions of Geobacterales to nitrate ammonification ISME J. (IF 10.8) Pub Date : 2025-03-18 Marcela Tabares, Kazem Kashefi, Gemma Reguera
Poorly understood microorganisms “short-circuit” the nitrogen cycle via the dissimilatory nitrate reduction to ammonium to retain the element in agricultural lands and stimulate crop productivity. The prevalence of Geobacterales closely related to Trichlorobacter lovleyi in nitrate ammonification hotspots motivated us to investigate adaptive responses contributing to ammonification rates in the laboratory
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Bacillus subtilis ensures high spore quality in competition with Salmonella Typhimurium via the SigB-dependent pathway ISME J. (IF 10.8) Pub Date : 2025-03-18 Eli Podnar, Kristina Dendinovic, Tjaša Danevčič, Bram Lories, Eva Kovačec, Hans Steenackers, Ines Mandic-Mulec
The interactions between beneficial bacteria and pathogens are understudied. Here we investigate the interactions between the probiotic strain Bacillus subtilis PS-216 and the pathogen Salmonella Typhimurium SL1344. We show here that the sporulation of B. subtilis is impaired when it competes with S. Typhimurium in a nutrient-depleted medium. The sporulation impairment in B. subtilis is mediated by
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Long-term metagenomic insights into the roles of antiviral defense systems in stabilizing activated sludge bacterial communities ISME J. (IF 10.8) Pub Date : 2025-03-17 Qifeng Zhang, Jie Li, Jinhua Tuo, Shengnan Liu, Yang Liu, Peng Liu, Lin Ye, Xu-Xiang Zhang
Bacteria have evolved various antiviral defense systems to protect themselves, but how defense systems respond to the variation of bacteriophages in complex bacterial communities and whether defense systems function effectively in maintaining the stability of bacterial community structure and function remain unknown. Here, we conducted a long-term metagenomic investigation on the composition of bacterial
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Metabolism of CO and H2 by pioneer bacteria in volcanic soils and the phyllosphere ISME J. (IF 10.8) Pub Date : 2025-03-16 Nicola Fantom, Robin A Dawson, Edina Prondvai, Philippe Constant, Gary M King, Hendrik Schäfer, Marcela Hernández
Trace gas degradation is a widespread metabolic adaptation in microbial communities, driving chemosynthesis and providing auxiliary energy that enhances persistence during nutrient starvation. In particular, carbon monoxide and hydrogen degradation can be of crucial importance for pioneering microbial communities colonising new, oligotrophic environmental niches, such as fresh volcanic deposits or
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Strong segregation promotes self-destructive cooperation ISME J. (IF 10.8) Pub Date : 2025-03-16 Lingling Wen, Yang Bai, Yunquan Lan, Yaxin Shen, Xiaoyi She, Peng Dong, Teng Wang, Xiongfei Fu, Shuqiang Huang
Self-destructive cooperators, which sacrifice themselves for others, challenge traditional group selection theory, as costs often exceed individual benefits. We predict self-destructive cooperators can persist in highly segregated environments where populations are primarily divided into homogenous groups originating from one or two founders. In such contexts, the benefits of self-destructive cooperators
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Spatio-temporal pattern formation of living organisms at the edge of chaos ISME J. (IF 10.8) Pub Date : 2025-03-13 Johannes Werner, Hartmut Arndt
Understanding spatio-temporal dynamics is essential for predicting how populations fluctuate over time and space. Theoretical models have highlighted the ecological complexity of spatio-temporal dynamics, which can lead to the emergence of complex patterns, including nonlinear dynamics and chaotic behavior, important mechanisms for maintaining of biodiversity. However, these dynamics are difficult
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Cellular heterogeneity in metabolism and associated microbiome of a non-model phytoflagellate ISME J. (IF 10.8) Pub Date : 2025-03-09 Aditya Jeevannavar, Javier Florenza, Anna-Maria Divne, Manu Tamminen, Stefan Bertilsson
Single-cell transcriptomics is a key tool for unravelling metabolism and tissue diversity in model organisms. Its potential for elucidating the ecological roles of microeukaryotes, especially non-model ones, remains largely unexplored. This study employed the Smart-seq2 protocol on Ochromonas triangulata, a microeukaryote lacking a reference genome, showcasing how transcriptional states align with
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Ecological and evolutionary responses of earthworm holobionts to environmental changes ISME J. (IF 10.8) Pub Date : 2025-03-09 Michael Opoku Adomako, Jing Wu, Fei-Hai Yu
Global environmental change substantially affects soil detritivores, including earthworms, impacting host-microbiota interactions and altering key soil biogeochemical processes such as litter decomposition. As microbial communities are inherently capable of rapid evolution, responses of earthworms and associated microbiota (i.e., earthworm holobionts) to global environmental change may likely involve
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Laminarin stimulates single cell rates of sulfate reduction whereas oxygen inhibits transcriptomic activity in coastal marine sediment. ISME J. (IF 10.8) Pub Date : 2025-01-02 Melody R Lindsay,Timothy D'Angelo,Elizabeth Goodell,Jacob H Munson-McGee,Melissa Herring,Michael Budner,Julia M Brown,Gregory S Gavelis,Corianna Mascena,Laura C Lubelczyk,Nicole J Poulton,Ramunas Stepanauskas,Beth N Orcutt,David Emerson
The chemical cycles carried out by bacteria and archaea living in coastal sediments are vital aspects of benthic ecology. These ecosystems are subject to physical disruption, which may allow for increased respiration and complex carbon consumption-impacting chemical cycling in this environment often thought to be a terminal place of deposition. We use the redox-enzyme sensitive probe RedoxSensor Green
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Metabolic interdependence and rewiring in Radiolaria-microalgae Photosymbioses ISME J. (IF 10.8) Pub Date : 2025-03-06 Vera Nikitashina, Benjamin Bartels, Joost Samir Mansour, Charlotte LeKieffre, Johan Decelle, Christian Hertweck, Fabrice Not, Georg Pohnert
Marine planktonic Radiolaria harboring symbiotic microalgae are ubiquitous in the oceans and abundant in oligotrophic areas. In these low-nutrient environments, they are among the most important primary producers. Systematic studies of radiolarian biology are limited because Radiolaria are non-culturable and prone to damage during sampling. To obtain insight into the mechanistic basis of radiolarian
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Plant growth-promotion triggered by extracellular polymer is associated with facilitation of bacterial cross-feeding networks of the rhizosphere ISME J. (IF 10.8) Pub Date : 2025-03-05 Yian Gu, Wenhui Yan, Yu Chen, Sijie Liu, Liang Sun, Zhe Zhang, Peng Lei, Rui Wang, Sha Li, Samiran Banerjee, Ville-Petri Friman, Hong Xu
Despite the critical role rhizosphere microbiomes play in plant growth, manipulating microbial communities for improved plant productivity remains challenging. One reason for this is the lack of knowledge on how complex substrates secreted in the microbiome ultimately shape the microbe-microbe and plant-microbe interaction in relation to plant growth. One such complex substrate is poly-γ-glutamic acid
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Mice expressing the autism-associated neuroligin-3 R451C variant exhibit increased mucus density and altered distributions of intestinal microbiota ISME J. (IF 10.8) Pub Date : 2025-03-04 Madushani Herath, Joel C Bornstein, Elisa L Hill-Yardin, Ashley E Franks
The intestinal mucus layer protects the host from invading pathogens and is essential for maintaining a healthy mucosal microbial community. Alterations in the mucus layer and composition of mucus-residing microbiota in people diagnosed with autism may contribute to dysbiosis and gastrointestinal dysfunction. Although microbial dysbiosis based on sequencing data is frequently reported in autism, spatial
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Extracellular aminopeptidase regulates exopolysaccharide production of Pseudomonas aeruginosa via quorum sensing ISME J. (IF 10.8) Pub Date : 2025-03-04 Tianhu Zhao, Fanglin Lei, Zhenyu Zhang, Di Wang, Luyan Z Ma
The biofilm matrix primarily consists of proteins, exopolysaccharides, and extracellular DNA. Pseudomonas aeruginosa aminopeptidase is one of the most abundant matrix proteins in P. aeruginosa biofilms and plays a crucial role in modulating biofilm development. In a previous study, we have revealed that the loss of aminopeptidase enhances the attachment ability of P. aeruginosa. However, the mechanism