Lauren M Hemara, Mark T Andersen, Haileigh R Patterson, Marion Wood, Matthew D Templeton, Jay Jayaraman
Host specificity of a plant pathogen is defined by its effector complement. However, it remains unclear whether the full complement is required for pathogenicity. Pseudomonas syringae pv. actinidiae (Psa) is an emerging model pathogen of kiwifruit with over 30 functional effectors, providing a unique opportunity to understand how host-mediated selection shapes pathogen evolution. The majority of Psa’s effectors previously appeared non-essential in single knockout contexts. Why, then, does Psa maintain such a large repertoire? We sought to examine effector requirements, redundancies, and repertoire refinement across host genotypes through a mutated effector-leveraging evolution experiment (MELEE), serially passaging competitive populations of effector knockout strains. Competition suggests that all effectors are collectively required for successful virulence, demonstrated by the dominance of wild-type. Host-specific effector requirements identified may further explain the maintenance of this large effector repertoire, providing important insights into the dynamics of effector redundancy following incursions.
{"title":"Individually redundant effectors are collectively required for bacterial pathogen virulence","authors":"Lauren M Hemara, Mark T Andersen, Haileigh R Patterson, Marion Wood, Matthew D Templeton, Jay Jayaraman","doi":"10.1093/ismejo/wraf262","DOIUrl":"https://doi.org/10.1093/ismejo/wraf262","url":null,"abstract":"Host specificity of a plant pathogen is defined by its effector complement. However, it remains unclear whether the full complement is required for pathogenicity. Pseudomonas syringae pv. actinidiae (Psa) is an emerging model pathogen of kiwifruit with over 30 functional effectors, providing a unique opportunity to understand how host-mediated selection shapes pathogen evolution. The majority of Psa’s effectors previously appeared non-essential in single knockout contexts. Why, then, does Psa maintain such a large repertoire? We sought to examine effector requirements, redundancies, and repertoire refinement across host genotypes through a mutated effector-leveraging evolution experiment (MELEE), serially passaging competitive populations of effector knockout strains. Competition suggests that all effectors are collectively required for successful virulence, demonstrated by the dominance of wild-type. Host-specific effector requirements identified may further explain the maintenance of this large effector repertoire, providing important insights into the dynamics of effector redundancy following incursions.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145599051","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Organismal life cycles are influenced by Earth’s rotation and orbit, generating daily and seasonal light cycles that vary with latitude, especially in temperate and polar zones. Photoperiodism relies on organisms’ ability to measure time via the circadian clock and detect light through specific photoreceptors. Molecular basis of photoperiodism is well-characterized in plants, but photoperiod adaptation in phytoplankton remain largely unexplored. Here, we investigated circadian clock components, photoreceptors, and associated effectors in eukaryote picoalga species from Ostreococcus, Bathycoccus, and Micromonas. We showed that the investigated species shared a conserved set of homologous circadian clock-related genes that appeared in the early evolution of Mamielalles order. Furthermore, gene duplication events account for the specific occurrences and uneven gene copy numbers among these genera. Through metagenomic and metatranscriptomic analyses, we assessed the gene expression profiles of candidate photoperiod-related genes across the global ocean. Our findings reveal an unexpected diversity in photoreceptors, particularly within Micromonas, and highlight the CCT domain family, a key group of transcription factors governing circadian rhythms (TOC1 family) and photoperiodism (CONSTANS family) in plants. TOC1, a central component of the circadian clock in Ostreococcus tauri, is either absent or truncated in tropical species. Functional assays further indicate that the TOC1/CCA1 oscillator is non-functional in the tropical strain of Ostreococcus sp. RCC809. These results imply that certain circadian mechanisms may be dispensable at low latitudes, underscoring the diversity of photoperiod adaptations in marine phytoplankton. These results provide valuable insights into the molecular evolution of cosmopolitan plankton groups, particularly their mechanisms of local adaptation.
{"title":"Latitudinal Diversity in Circadian and Light-Sensing Genes in an Ecologically Vital Group of Marine Picoeukaryote Algae","authors":"Janaina Rigonato, Jean-Claude Lozano, Valérie Vergé, Olivier Jaillon, François-Yves Bouget","doi":"10.1093/ismejo/wraf263","DOIUrl":"https://doi.org/10.1093/ismejo/wraf263","url":null,"abstract":"Organismal life cycles are influenced by Earth’s rotation and orbit, generating daily and seasonal light cycles that vary with latitude, especially in temperate and polar zones. Photoperiodism relies on organisms’ ability to measure time via the circadian clock and detect light through specific photoreceptors. Molecular basis of photoperiodism is well-characterized in plants, but photoperiod adaptation in phytoplankton remain largely unexplored. Here, we investigated circadian clock components, photoreceptors, and associated effectors in eukaryote picoalga species from Ostreococcus, Bathycoccus, and Micromonas. We showed that the investigated species shared a conserved set of homologous circadian clock-related genes that appeared in the early evolution of Mamielalles order. Furthermore, gene duplication events account for the specific occurrences and uneven gene copy numbers among these genera. Through metagenomic and metatranscriptomic analyses, we assessed the gene expression profiles of candidate photoperiod-related genes across the global ocean. Our findings reveal an unexpected diversity in photoreceptors, particularly within Micromonas, and highlight the CCT domain family, a key group of transcription factors governing circadian rhythms (TOC1 family) and photoperiodism (CONSTANS family) in plants. TOC1, a central component of the circadian clock in Ostreococcus tauri, is either absent or truncated in tropical species. Functional assays further indicate that the TOC1/CCA1 oscillator is non-functional in the tropical strain of Ostreococcus sp. RCC809. These results imply that certain circadian mechanisms may be dispensable at low latitudes, underscoring the diversity of photoperiod adaptations in marine phytoplankton. These results provide valuable insights into the molecular evolution of cosmopolitan plankton groups, particularly their mechanisms of local adaptation.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"150 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145610940","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yang Zhou, Yongqiang Yang, Yuqi Mao, Zhangqun Hou, Yiyang Xu, Kelei Zhao, Yiwen Chu, Xinrong Wang, Can Wang, Shun Li, Fei Xu, Likai Hao, Binbin Xie, Jiafu Lin, Tao Song
Macrolide antibiotics are vital for controlling infections in humans, animals, and agriculture, yet their effectiveness is increasingly compromised by antimicrobial resistance. Macrolide esterases (MLEs) are key mediators of macrolide resistance but have only been detected in Gram-negative bacteria, with no evidence in Gram-positive species. Here, we mined over 500,000 Gram-positive genomes and identified 8,707 candidate proteins. Six representative MLEs were functionally validated, conferring resistance to 16-membered macrolides and increasing minimum inhibitory concentrations up to 16-fold in Escherichia coli and 128-fold in Bacillus subtilis. Moreover, two exhibited broad-spectrum activity against all clinically and veterinary relevant 16-membered macrolides. Temporal analysis revealed that Gram-positive MLEs originated at least 2.7 million years ago, contrasting with their emergence in Gram-negative bacteria after the introduction of antibiotics. Genomic surveys further demonstrated the global distribution of MLE-carrying Gram-positive bacteria across 97 countries and diverse ecosystems, including clinical, food, agricultural, and natural environments. These findings highlight Gram-positive MLEs as an underrecognized risk and underscore the need for a One Health–oriented strategy to monitor, assess, and mitigate the spread of macrolide resistance across interconnected ecosystems.
{"title":"Global distribution of α/β hydrolase family macrolide esterases in Gram-positive bacteria","authors":"Yang Zhou, Yongqiang Yang, Yuqi Mao, Zhangqun Hou, Yiyang Xu, Kelei Zhao, Yiwen Chu, Xinrong Wang, Can Wang, Shun Li, Fei Xu, Likai Hao, Binbin Xie, Jiafu Lin, Tao Song","doi":"10.1093/ismejo/wraf261","DOIUrl":"https://doi.org/10.1093/ismejo/wraf261","url":null,"abstract":"Macrolide antibiotics are vital for controlling infections in humans, animals, and agriculture, yet their effectiveness is increasingly compromised by antimicrobial resistance. Macrolide esterases (MLEs) are key mediators of macrolide resistance but have only been detected in Gram-negative bacteria, with no evidence in Gram-positive species. Here, we mined over 500,000 Gram-positive genomes and identified 8,707 candidate proteins. Six representative MLEs were functionally validated, conferring resistance to 16-membered macrolides and increasing minimum inhibitory concentrations up to 16-fold in Escherichia coli and 128-fold in Bacillus subtilis. Moreover, two exhibited broad-spectrum activity against all clinically and veterinary relevant 16-membered macrolides. Temporal analysis revealed that Gram-positive MLEs originated at least 2.7 million years ago, contrasting with their emergence in Gram-negative bacteria after the introduction of antibiotics. Genomic surveys further demonstrated the global distribution of MLE-carrying Gram-positive bacteria across 97 countries and diverse ecosystems, including clinical, food, agricultural, and natural environments. These findings highlight Gram-positive MLEs as an underrecognized risk and underscore the need for a One Health–oriented strategy to monitor, assess, and mitigate the spread of macrolide resistance across interconnected ecosystems.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145599050","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jibing Li, Xixi Cai, Menghui Li, Dayi Zhang, Bei Li, Ling N Jin, Chunling Luo, Gan Zhang
Fungi play critical but underappreciated roles comparing to bacteria in the bioremediation of organic pollutants, particularly emerging contaminants. Numerous fungal species, along with their functional genes and metabolic pathways, remain largely unexplored. Here, we integrate single-cell Raman-activated cell sorting with stable isotope probing to identify and characterize in situ active fungi involved in emerging contaminant degradation. This approach enabled the isolation of a Penicillium sp. strain LJD-20, previously unreported, which acts as an active degrader of 2-methylnaphthalene, a model emerging pollutant. Genomic analyses revealed that LJD-20 harbors a diverse repertoire of degradation-related genes, including those encoding dioxygenases, methylhydroxylases, and cytochrome P450 monooxygenases, highlighting its versatile metabolic potential. Single-cell genome sequencing also uncovered a potential close fungal–bacterial co-occurrence, suggesting possible ecological or metabolic interactions. In bioaugmentation trials, strain LJD-20 independently degraded 2-methylnaphthalene and simultaneously promoted the enrichment of other microorganisms involved in its removal. These findings highlight the metabolic versatility and ecological importance of fungi in pollutant degradation and demonstrate the utility of combining single-cell and isotopic approaches to explore microbial function and interaction in complex environments.
{"title":"In situ Degradation of 2-Methylnaphthalene by a Soil Penicillium Strain Associated with Fungal-Bacterial Interactions","authors":"Jibing Li, Xixi Cai, Menghui Li, Dayi Zhang, Bei Li, Ling N Jin, Chunling Luo, Gan Zhang","doi":"10.1093/ismejo/wraf260","DOIUrl":"https://doi.org/10.1093/ismejo/wraf260","url":null,"abstract":"Fungi play critical but underappreciated roles comparing to bacteria in the bioremediation of organic pollutants, particularly emerging contaminants. Numerous fungal species, along with their functional genes and metabolic pathways, remain largely unexplored. Here, we integrate single-cell Raman-activated cell sorting with stable isotope probing to identify and characterize in situ active fungi involved in emerging contaminant degradation. This approach enabled the isolation of a Penicillium sp. strain LJD-20, previously unreported, which acts as an active degrader of 2-methylnaphthalene, a model emerging pollutant. Genomic analyses revealed that LJD-20 harbors a diverse repertoire of degradation-related genes, including those encoding dioxygenases, methylhydroxylases, and cytochrome P450 monooxygenases, highlighting its versatile metabolic potential. Single-cell genome sequencing also uncovered a potential close fungal–bacterial co-occurrence, suggesting possible ecological or metabolic interactions. In bioaugmentation trials, strain LJD-20 independently degraded 2-methylnaphthalene and simultaneously promoted the enrichment of other microorganisms involved in its removal. These findings highlight the metabolic versatility and ecological importance of fungi in pollutant degradation and demonstrate the utility of combining single-cell and isotopic approaches to explore microbial function and interaction in complex environments.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145594092","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Bathyarchaeia, among the most ancient and abundant microbial lineages on Earth, dominate diverse anoxic subsurface ecosystems and play a pivotal role in global carbon cycling. This review synthesizes current understanding of their physiological, metabolic, and evolutionary foundations underlying their ecological significance and environmental effects over geological timescales. Despite their global distribution in the deep biosphere, the phylogenetic diversity and total cellular abundance of Bathyarchaeia remain substantially underestimated. As uncultivated metabolic generalists, Bathyarchaeia exhibit remarkable metabolic versatility, including anaerobic organic degradation, dark carbon fixation, and putative methane and alkane metabolism. Specifically, genus Baizosediminiarchaeum has been demonstrated to adopt organomixotrophy by coupling anaerobic lignin degradation with inorganic carbon assimilation. These metabolic strategies likely enable them to thrive in energy-limited subsurface environments with dynamic geochemical fluctuation. The early evolutionary history of Bathyarchaeia appears closely linked to major geological events, including tectonic activity and plant evolution, whereas more recent lineage expansions reflect physiological adaptations to host-associated and anthropogenically influenced environments, highlighting their on-going co-evolution with Earth's modern environments. Overall, we propose carbon metabolic innovation as the central driver behind the ecological and evolutionary significance of Bathyarchaeia, putatively linking microbial ecological functions to planetary biogeochemical processes. Future efforts in isolation and cultivation remains essential for elucidating their unknown physiological and metabolic mechanisms. In parallel, advances in ecological modeling and the development of lineage-specific lipid biomarkers hold great promise for quantifying their contributions to global carbon budgets and reconstructing paleoenvironmental and paleoclimate conditions.
{"title":"Carbon metabolic versatility underpins Bathyarchaeia ecological significance across the global deep subsurface.","authors":"Jialin Hou 侯佳林,Chen Yang 杨琛,Fengping Wang 王风平","doi":"10.1093/ismejo/wraf259","DOIUrl":"https://doi.org/10.1093/ismejo/wraf259","url":null,"abstract":"Bathyarchaeia, among the most ancient and abundant microbial lineages on Earth, dominate diverse anoxic subsurface ecosystems and play a pivotal role in global carbon cycling. This review synthesizes current understanding of their physiological, metabolic, and evolutionary foundations underlying their ecological significance and environmental effects over geological timescales. Despite their global distribution in the deep biosphere, the phylogenetic diversity and total cellular abundance of Bathyarchaeia remain substantially underestimated. As uncultivated metabolic generalists, Bathyarchaeia exhibit remarkable metabolic versatility, including anaerobic organic degradation, dark carbon fixation, and putative methane and alkane metabolism. Specifically, genus Baizosediminiarchaeum has been demonstrated to adopt organomixotrophy by coupling anaerobic lignin degradation with inorganic carbon assimilation. These metabolic strategies likely enable them to thrive in energy-limited subsurface environments with dynamic geochemical fluctuation. The early evolutionary history of Bathyarchaeia appears closely linked to major geological events, including tectonic activity and plant evolution, whereas more recent lineage expansions reflect physiological adaptations to host-associated and anthropogenically influenced environments, highlighting their on-going co-evolution with Earth's modern environments. Overall, we propose carbon metabolic innovation as the central driver behind the ecological and evolutionary significance of Bathyarchaeia, putatively linking microbial ecological functions to planetary biogeochemical processes. Future efforts in isolation and cultivation remains essential for elucidating their unknown physiological and metabolic mechanisms. In parallel, advances in ecological modeling and the development of lineage-specific lipid biomarkers hold great promise for quantifying their contributions to global carbon budgets and reconstructing paleoenvironmental and paleoclimate conditions.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145559199","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Qing-Lian Wu, Tian Lan, Lin Deng, Jing-Wen Jia, Wei-Tong Ren, Hua-Zhe Wang, Juan-Shan Du, Nan-Qi Ren, Wan-Qian Guo
Widespread aromatic pollutants such as benzene, toluene, ethylbenzene, and xylene are traditionally considered to drive soil carbon loss through mineralisation and ecotoxicity. Contrary to this view, our study reveals that low concentrations of these pollutants stimulate microbial carbon chain elongation—a previously overlooked carbon conversion pathway producing medium-chain fatty acids, thereby reshaping soil carbon dynamics. Using phased amplicon sequencing, metagenomics, and metaproteomics of soil microcosms amended with these compounds, we demonstrate that aromatic pollutants bidirectionally regulate carbon chain elongation at both taxonomic and molecular levels. These pollutants selectively enrich Clostridium_sensu_stricto_12 and Rummelibacillus while suppressing Acinetobacter, a key elongation taxon in natural soils. Simultaneously, they inhibit Petrimonas, a syntrophic fatty acid degrader, promoting the accumulation of medium-chain fatty acids. Carbon chain-elongating bacteria cooperate with aromatic degraders, redirecting pollutant-derived carbon towards chain elongation rather than complete mineralisation to CO₂. Among them, Bacillus occupies a pivotal niche bridging aromatic degradation and carbon elongation. At the molecular level, aromatic pollutants enhance chain elongation by accelerating substrate uptake and channelling the key intermediate acetyl-CoA into the reverse β-oxidation pathway. Additionally, aromatic pollutants restrain fatty acid biosynthesis pathway by upregulating fabR, whereas inhibiting acrR and fadR. They also maintain NADH availability to alleviate Rex-mediated repression of bcd, a critical gene in the β-oxidation pathway. However, high concentrations of aromatic pollutants disrupt metabolic homeostasis and suppress chain elongation activity. Our findings redefine the ecological impact of aromatic hydrocarbon contamination in soil, demonstrating their role in modulating anaerobic carbon fixation and retention within soil microbial communities.
{"title":"Aromatic Pollutants Rewire Soil Microbial Carbon Fixation via Chain Elongation","authors":"Qing-Lian Wu, Tian Lan, Lin Deng, Jing-Wen Jia, Wei-Tong Ren, Hua-Zhe Wang, Juan-Shan Du, Nan-Qi Ren, Wan-Qian Guo","doi":"10.1093/ismejo/wraf254","DOIUrl":"https://doi.org/10.1093/ismejo/wraf254","url":null,"abstract":"Widespread aromatic pollutants such as benzene, toluene, ethylbenzene, and xylene are traditionally considered to drive soil carbon loss through mineralisation and ecotoxicity. Contrary to this view, our study reveals that low concentrations of these pollutants stimulate microbial carbon chain elongation—a previously overlooked carbon conversion pathway producing medium-chain fatty acids, thereby reshaping soil carbon dynamics. Using phased amplicon sequencing, metagenomics, and metaproteomics of soil microcosms amended with these compounds, we demonstrate that aromatic pollutants bidirectionally regulate carbon chain elongation at both taxonomic and molecular levels. These pollutants selectively enrich Clostridium_sensu_stricto_12 and Rummelibacillus while suppressing Acinetobacter, a key elongation taxon in natural soils. Simultaneously, they inhibit Petrimonas, a syntrophic fatty acid degrader, promoting the accumulation of medium-chain fatty acids. Carbon chain-elongating bacteria cooperate with aromatic degraders, redirecting pollutant-derived carbon towards chain elongation rather than complete mineralisation to CO₂. Among them, Bacillus occupies a pivotal niche bridging aromatic degradation and carbon elongation. At the molecular level, aromatic pollutants enhance chain elongation by accelerating substrate uptake and channelling the key intermediate acetyl-CoA into the reverse β-oxidation pathway. Additionally, aromatic pollutants restrain fatty acid biosynthesis pathway by upregulating fabR, whereas inhibiting acrR and fadR. They also maintain NADH availability to alleviate Rex-mediated repression of bcd, a critical gene in the β-oxidation pathway. However, high concentrations of aromatic pollutants disrupt metabolic homeostasis and suppress chain elongation activity. Our findings redefine the ecological impact of aromatic hydrocarbon contamination in soil, demonstrating their role in modulating anaerobic carbon fixation and retention within soil microbial communities.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"109 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145594093","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Maximilian Lehenberger, Yu Pan, Stefanie Ungerer, Michael Reichelt, Daniela Pemp, Christian Paetz, Josef Lehenberger, Niklas Gentsch, Felix Feistel, Peter Gros, Leane Lehmann, Jonathan Gershenzon
Wood-colonizing beetles are associated with a diversity of microbes many of which are thought to act as mutualists with their beetle hosts, but the evidence is usually anecdotal. The ship-timber beetle Elateroides dermestoides, one of the few fungus-farming but non-social ambrosia beetles, is described to have a mutualistic relationship with the yeast-like fungus Alloascoidea hylecoeti. Here, we tested the hypothesis that A. hylecoeti has a high nutrient content thus allowing it to function as a valuable food source for the solitary larvae of E. dermestoides, which bore into the wood of dead trees, an extremely nutrient-poor substrate. Our analyses revealed that A. hylecoeti is rich in soluble sugars, free amino acids, ergosterol, phosphorus, and potassium compared to the other fungi measured, and also accumulates high amounts of fatty acids, B vitamins and nitrogen. We also tested whether A. hylecoeti possesses chemical mechanisms to suppress antagonistic microbes. Extracts from A. hylecoeti and chemical compounds produced or accumulated by this fungus were found to significantly inhibit the growth of potentially competing fungi. The active substances include fungal-produced monoterpenes and acetic acid, as well as phenolic compounds accumulated from host tree tissues. Moreover, sufficient acetic acid was released by A. hylecoeti to drop the medium pH to as low as 3.6, which inhibited all tested competitors, whereas the growth of A. hylecoeti was promoted. Taken together, the nutritional properties and competitive ability of A. hylecoeti may make a major contribution to the success of its insect partner, the ship-timber beetle under natural conditions.
{"title":"Fungal symbiont of an ambrosia beetle possesses high nutrient content and suppresses competing fungi with antimicrobial compounds","authors":"Maximilian Lehenberger, Yu Pan, Stefanie Ungerer, Michael Reichelt, Daniela Pemp, Christian Paetz, Josef Lehenberger, Niklas Gentsch, Felix Feistel, Peter Gros, Leane Lehmann, Jonathan Gershenzon","doi":"10.1093/ismejo/wraf258","DOIUrl":"https://doi.org/10.1093/ismejo/wraf258","url":null,"abstract":"Wood-colonizing beetles are associated with a diversity of microbes many of which are thought to act as mutualists with their beetle hosts, but the evidence is usually anecdotal. The ship-timber beetle Elateroides dermestoides, one of the few fungus-farming but non-social ambrosia beetles, is described to have a mutualistic relationship with the yeast-like fungus Alloascoidea hylecoeti. Here, we tested the hypothesis that A. hylecoeti has a high nutrient content thus allowing it to function as a valuable food source for the solitary larvae of E. dermestoides, which bore into the wood of dead trees, an extremely nutrient-poor substrate. Our analyses revealed that A. hylecoeti is rich in soluble sugars, free amino acids, ergosterol, phosphorus, and potassium compared to the other fungi measured, and also accumulates high amounts of fatty acids, B vitamins and nitrogen. We also tested whether A. hylecoeti possesses chemical mechanisms to suppress antagonistic microbes. Extracts from A. hylecoeti and chemical compounds produced or accumulated by this fungus were found to significantly inhibit the growth of potentially competing fungi. The active substances include fungal-produced monoterpenes and acetic acid, as well as phenolic compounds accumulated from host tree tissues. Moreover, sufficient acetic acid was released by A. hylecoeti to drop the medium pH to as low as 3.6, which inhibited all tested competitors, whereas the growth of A. hylecoeti was promoted. Taken together, the nutritional properties and competitive ability of A. hylecoeti may make a major contribution to the success of its insect partner, the ship-timber beetle under natural conditions.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"172 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145553961","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Fraser Kennedy, Matthieu Bressac, Philip Butterworth, Svenja Halfter, Philip W Boyd
Mesopelagic microbes and zooplankton, degrade, and attenuate >90% of the 10 billion tonnes of particulate organic carbon that sinks into the oceans’ interior annually. Approaches such as particle interceptors/incubators (called c-respire) can isolate the microbial assemblage attached to particles from that of zooplankton, enabling quantification of microbially mediated particulate organic carbon flux attenuation. This metric yields patterns of particulate organic carbon degradation by microorganisms through the upper mesopelagic (200-500 m depth). Here, we investigate the temporal sequence of particulate organic carbon degradation in two steps. First, we intercept sinking particle assemblages from different depths (180-300 m) and hence with varying degrees of exposure to microbial activity. Second, we incubate these intercepted particles shipboard for 12 h (short-term) and track degradation using apparent respiratory quotients (dDIC/dDO2). We also conducted a 12-hour shipboard incubation on a particle assemblage that had already undergone a 36-hour in situ c-respire (long-term) incubation. At a subantarctic and two polar sites, ARQs from short-term incubations exhibited a significant decrease with depth, consistent with particles deeper in the upper mesopelagic being exposed to a longer period of degradation and flux attenuation (as they settle). ARQs from all long-term incubations had significantly lower ARQs, and smaller depth-dependent gradients, than the short-term incubations. We interpret these trends as being driven in part by sequential changes in the stoichiometry of the microbially altered POC substrates. ARQs of <0.5 (less than the theoretical minimum) were observed in long-term incubations suggesting a role for incomplete oxidation of dissolved substrates. This temporal sequence is used to conceptually explore what sets the limits on microbially mediated degradation of POC.
{"title":"Respiratory quotients of particle-associated microbes track carbon flux attenuation in the mesopelagic Southern Ocean","authors":"Fraser Kennedy, Matthieu Bressac, Philip Butterworth, Svenja Halfter, Philip W Boyd","doi":"10.1093/ismejo/wraf255","DOIUrl":"https://doi.org/10.1093/ismejo/wraf255","url":null,"abstract":"Mesopelagic microbes and zooplankton, degrade, and attenuate &gt;90% of the 10 billion tonnes of particulate organic carbon that sinks into the oceans’ interior annually. Approaches such as particle interceptors/incubators (called c-respire) can isolate the microbial assemblage attached to particles from that of zooplankton, enabling quantification of microbially mediated particulate organic carbon flux attenuation. This metric yields patterns of particulate organic carbon degradation by microorganisms through the upper mesopelagic (200-500 m depth). Here, we investigate the temporal sequence of particulate organic carbon degradation in two steps. First, we intercept sinking particle assemblages from different depths (180-300 m) and hence with varying degrees of exposure to microbial activity. Second, we incubate these intercepted particles shipboard for 12 h (short-term) and track degradation using apparent respiratory quotients (dDIC/dDO2). We also conducted a 12-hour shipboard incubation on a particle assemblage that had already undergone a 36-hour in situ c-respire (long-term) incubation. At a subantarctic and two polar sites, ARQs from short-term incubations exhibited a significant decrease with depth, consistent with particles deeper in the upper mesopelagic being exposed to a longer period of degradation and flux attenuation (as they settle). ARQs from all long-term incubations had significantly lower ARQs, and smaller depth-dependent gradients, than the short-term incubations. We interpret these trends as being driven in part by sequential changes in the stoichiometry of the microbially altered POC substrates. ARQs of &lt;0.5 (less than the theoretical minimum) were observed in long-term incubations suggesting a role for incomplete oxidation of dissolved substrates. This temporal sequence is used to conceptually explore what sets the limits on microbially mediated degradation of POC.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"28 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145553962","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Miniaturization, i.e., reduction in body size, happens in different organisms as an adaptation strategy under environmental stress such as warming. However, whether phytoplankton miniaturization occurs in coastal waters remains understudied due to complex environmental factors and strong spatiotemporal variability. Here, we comprehensively investigated the long-term changes in phytoplankton body size over 20 years in the coastal waters of Hong Kong through monthly sampling at 25 stations across the region. We employed a framework distinguishing two drivers of community miniaturization: (1) intraspecific size reduction (species miniaturization) and (2) shifts in community composition toward a higher proportion of small species. At the species level, miniaturization was widespread, more in diatoms than dinoflagellates, primarily driven by temperature, supporting the temperature-size relation. In contrast, community-level miniaturization was negligible across most stations (except in a semi-closed bay), which was attributed to the decreased proportion of small species. This could be explained by the declined phosphate concentration which not only directly reduced the proportion of small species but also diminished the temperature sensitivity of phytoplankton community. Our findings provide multi-scale insights into coastal phytoplankton miniaturization, with critical implications for food web dynamics and the biological carbon pump. Moreover, we highlight that anthropogenic nutrient reduction may significantly mitigate community-level phytoplankton miniaturization, though localized effects in semi-enclosed systems warrant further investigation.
{"title":"Decadal scale phytoplankton species miniaturization in subtropical coastal waters","authors":"Zhimeng Xu, Xiaodong Zhang, Mingjue Li, Wenzhao Liang, Yu Ma, Lixia Deng, Jiawei Chen, Kailin Liu, Hongbin Liu","doi":"10.1093/ismejo/wraf257","DOIUrl":"https://doi.org/10.1093/ismejo/wraf257","url":null,"abstract":"Miniaturization, i.e., reduction in body size, happens in different organisms as an adaptation strategy under environmental stress such as warming. However, whether phytoplankton miniaturization occurs in coastal waters remains understudied due to complex environmental factors and strong spatiotemporal variability. Here, we comprehensively investigated the long-term changes in phytoplankton body size over 20 years in the coastal waters of Hong Kong through monthly sampling at 25 stations across the region. We employed a framework distinguishing two drivers of community miniaturization: (1) intraspecific size reduction (species miniaturization) and (2) shifts in community composition toward a higher proportion of small species. At the species level, miniaturization was widespread, more in diatoms than dinoflagellates, primarily driven by temperature, supporting the temperature-size relation. In contrast, community-level miniaturization was negligible across most stations (except in a semi-closed bay), which was attributed to the decreased proportion of small species. This could be explained by the declined phosphate concentration which not only directly reduced the proportion of small species but also diminished the temperature sensitivity of phytoplankton community. Our findings provide multi-scale insights into coastal phytoplankton miniaturization, with critical implications for food web dynamics and the biological carbon pump. Moreover, we highlight that anthropogenic nutrient reduction may significantly mitigate community-level phytoplankton miniaturization, though localized effects in semi-enclosed systems warrant further investigation.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145554090","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nicholas J Reichart, Sheryl Bell, Vanessa A Garayburu-Caruso, Natalie Sadler, Sharon Zhao, Kirsten S Hofmockel
Soil organic matter decomposition is a complex process reflecting microbial composition and environmental conditions. Moisture can modulate the connectivity and interactions of microbes. Due to heterogeneity, a deeper understanding of the influence of soil moisture on the dynamics of organic matter decomposition and resultant phenotypes remains a challenge. Soils from a long-term field experiment exposed to high and low moisture treatments were incubated in the laboratory to investigate organic matter decomposition using chitin as a model substrate. By combining enzymatic assays, biomass measurements, and microbial enrichment via activity-based probes, we determined the microbial functional response to chitin amendments and field moisture treatments at both the community and cell scales. Chitinolytic activities showed significant responses to the amendment of chitin, independent of differences in field moisture treatments. However, for other measurements of carbon metabolism and cellular functions, soils from high moisture field treatments had greater potential enzyme activity than soils from low moisture field treatments. A cell tagging approach was used to enrich and quantify bacterial taxa that are actively producing chitin-degrading enzymes. By integrating organism, community, and soil core measurements we show that 1) a small subset of taxa compose the majority (>50%) of chitinase production despite broad functional redundancy, 2) the identity of key chitin degraders varies with moisture level, and 3) extracellular enzymes that are not cell-associated account for most potential chitinase activity measured in field soil.
{"title":"Impact of Moisture on Microbial Decomposition Phenotypes and Enzyme Dynamics","authors":"Nicholas J Reichart, Sheryl Bell, Vanessa A Garayburu-Caruso, Natalie Sadler, Sharon Zhao, Kirsten S Hofmockel","doi":"10.1093/ismejo/wraf250","DOIUrl":"https://doi.org/10.1093/ismejo/wraf250","url":null,"abstract":"Soil organic matter decomposition is a complex process reflecting microbial composition and environmental conditions. Moisture can modulate the connectivity and interactions of microbes. Due to heterogeneity, a deeper understanding of the influence of soil moisture on the dynamics of organic matter decomposition and resultant phenotypes remains a challenge. Soils from a long-term field experiment exposed to high and low moisture treatments were incubated in the laboratory to investigate organic matter decomposition using chitin as a model substrate. By combining enzymatic assays, biomass measurements, and microbial enrichment via activity-based probes, we determined the microbial functional response to chitin amendments and field moisture treatments at both the community and cell scales. Chitinolytic activities showed significant responses to the amendment of chitin, independent of differences in field moisture treatments. However, for other measurements of carbon metabolism and cellular functions, soils from high moisture field treatments had greater potential enzyme activity than soils from low moisture field treatments. A cell tagging approach was used to enrich and quantify bacterial taxa that are actively producing chitin-degrading enzymes. By integrating organism, community, and soil core measurements we show that 1) a small subset of taxa compose the majority (&gt;50%) of chitinase production despite broad functional redundancy, 2) the identity of key chitin degraders varies with moisture level, and 3) extracellular enzymes that are not cell-associated account for most potential chitinase activity measured in field soil.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"54 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145515621","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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