Ui-Ju Lee, Joo-Han Gwak, Christiana Abiola, Seongjun Lee, Jin-Sun Yoo, Ok-Ja Si, Hyo Je Cho, Zhe-Xue Quan, Katharina Kitzinger, Holger Daims, Michael Wagner, Man-Young Jung, Sung-Keun Rhee
Nitrite-oxidizing bacteria (NOB) use either periplasmic (pNXR) or cytoplasmic (cNXR) nitrite oxidoreductase to oxidize nitrite, and this distinction influences nitrite affinity and energy yield. cNXR-containing NOB have historically been considered low-affinity, copiotrophic nitrifiers adapted to high nitrite and neutral pH. Here, we report a previously uncharacterized pH- and substrate-dependent modulation of nitrite affinity in cNXR NOB that is not observed in pNXR NOB and is not a universal microbial trait. Nitrobacter winogradskyi Nb-255, grown at low nitrite (1 mM), had a high apparent affinity (Km(app) = 25.9 μM; specific affinity ao = 440.5 l g cells−1 h−1) comparable to oligotrophic pNXR NOB. However, when grown at high nitrite (10 mM), these cells showed a low affinity at pH 7.5 (Km(app) = 388.0 μM) but exhibited a rapid increase in affinity upon immediate exposure to pH 5.5 (Km(app) = 19.2 μM) without prior acid adaptation. In contrast, pNXR NOB exhibited consistent kinetic behavior across different pH conditions, underscoring that this kinetic plasticity is unique to cNXR NOB. Kinetic inhibition assays revealed that this plasticity is mechanistically underpinned by a shift from a low-affinity nitrite/nitrate antiporter (NarK) to a high-affinity nitrite channel (NirC), coupled with enhanced HNO2 diffusion at low pH, together increasing intracellular nitrite availability. These findings establish that cNXR NOB can dynamically tune nitrite affinity via transporter-level regulation in response to nitrite concentration and pH. This novel mechanism provides a mechanistic explanation for the unexpected prevalence of Nitrobacter in acidic, low-nitrite environments, highlighting its ecological relevance.
{"title":"Kinetic Plasticity of Nitrite-Oxidizing Bacteria Containing Cytoplasmic Nitrite Oxidoreductase","authors":"Ui-Ju Lee, Joo-Han Gwak, Christiana Abiola, Seongjun Lee, Jin-Sun Yoo, Ok-Ja Si, Hyo Je Cho, Zhe-Xue Quan, Katharina Kitzinger, Holger Daims, Michael Wagner, Man-Young Jung, Sung-Keun Rhee","doi":"10.1093/ismejo/wrag040","DOIUrl":"https://doi.org/10.1093/ismejo/wrag040","url":null,"abstract":"Nitrite-oxidizing bacteria (NOB) use either periplasmic (pNXR) or cytoplasmic (cNXR) nitrite oxidoreductase to oxidize nitrite, and this distinction influences nitrite affinity and energy yield. cNXR-containing NOB have historically been considered low-affinity, copiotrophic nitrifiers adapted to high nitrite and neutral pH. Here, we report a previously uncharacterized pH- and substrate-dependent modulation of nitrite affinity in cNXR NOB that is not observed in pNXR NOB and is not a universal microbial trait. Nitrobacter winogradskyi Nb-255, grown at low nitrite (1 mM), had a high apparent affinity (Km(app) = 25.9 μM; specific affinity ao = 440.5 l g cells−1 h−1) comparable to oligotrophic pNXR NOB. However, when grown at high nitrite (10 mM), these cells showed a low affinity at pH 7.5 (Km(app) = 388.0 μM) but exhibited a rapid increase in affinity upon immediate exposure to pH 5.5 (Km(app) = 19.2 μM) without prior acid adaptation. In contrast, pNXR NOB exhibited consistent kinetic behavior across different pH conditions, underscoring that this kinetic plasticity is unique to cNXR NOB. Kinetic inhibition assays revealed that this plasticity is mechanistically underpinned by a shift from a low-affinity nitrite/nitrate antiporter (NarK) to a high-affinity nitrite channel (NirC), coupled with enhanced HNO2 diffusion at low pH, together increasing intracellular nitrite availability. These findings establish that cNXR NOB can dynamically tune nitrite affinity via transporter-level regulation in response to nitrite concentration and pH. This novel mechanism provides a mechanistic explanation for the unexpected prevalence of Nitrobacter in acidic, low-nitrite environments, highlighting its ecological relevance.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"52 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147292651","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}
Yi Wang, David Schleheck, Elena Marinova, Martin Wessels, Sebastian Schaller, Flavio S Anselmetti, Antje Schwalb, Mikkel Winther Pedersen, Laura S Epp
Bacteria and archaea are under-characterized in palaeoecological studies, despite their ubiquity, high diversity, and tight integration with the abiotic, biotic, and human-influenced environments. The complexity of their assemblages and difficulties in separating living- from paleo-prokaryotes render research challenging. Here we present an ancient metagenomic time-series of prokaryotes from a sediment core of Lake Constance, spanning the last 13 500 years of natural and anthropogenic impact. We mapped DNA to reference genomes and characterised the DNA damage of taxa as collectively increasing with time. By constructing co-abundance networks, we recognize major assemblage groups, containing both dead and living microbes, that show specific dynamics: Short-term and often low-abundance assemblages are linked to the Pleistocene–Holocene transition, floods, and human activities. Noticeably, certain lineages harbouring microbes common in human-impacted environments expanded during the Middle Ages and Modern time. Some abundant taxa associated with various freshwater and soil environments persisted through millennia. By extricating different sources and trajectories of change, we demonstrate the power of prokaryotic sedimentary DNA in revealing nature- and human-caused long-term eco-evolutionary consequences.
{"title":"Prokaryotic assemblages recovered by sedimentary DNA record natural and human-driven disturbances over the past 13 500 years in a cultural landscape","authors":"Yi Wang, David Schleheck, Elena Marinova, Martin Wessels, Sebastian Schaller, Flavio S Anselmetti, Antje Schwalb, Mikkel Winther Pedersen, Laura S Epp","doi":"10.1093/ismejo/wrag031","DOIUrl":"https://doi.org/10.1093/ismejo/wrag031","url":null,"abstract":"Bacteria and archaea are under-characterized in palaeoecological studies, despite their ubiquity, high diversity, and tight integration with the abiotic, biotic, and human-influenced environments. The complexity of their assemblages and difficulties in separating living- from paleo-prokaryotes render research challenging. Here we present an ancient metagenomic time-series of prokaryotes from a sediment core of Lake Constance, spanning the last 13 500 years of natural and anthropogenic impact. We mapped DNA to reference genomes and characterised the DNA damage of taxa as collectively increasing with time. By constructing co-abundance networks, we recognize major assemblage groups, containing both dead and living microbes, that show specific dynamics: Short-term and often low-abundance assemblages are linked to the Pleistocene–Holocene transition, floods, and human activities. Noticeably, certain lineages harbouring microbes common in human-impacted environments expanded during the Middle Ages and Modern time. Some abundant taxa associated with various freshwater and soil environments persisted through millennia. By extricating different sources and trajectories of change, we demonstrate the power of prokaryotic sedimentary DNA in revealing nature- and human-caused long-term eco-evolutionary consequences.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147292415","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}
Shiri Graff van Creveld, Sacha N Coesel, Ellen Lavoie, Vaughn Iverson, Rhonda Morales, Megan J Schatz, Alexandra E Jones-Kellett, Jesse McNichol, Rebecca S Key, Jed Fuhrman, Bryndan P Durham, E Virginia Armbrust
Phytoplankton are the base of marine food webs. They form intricate interactions with heterotrophic bacteria ranging from mutualistic to pathogenic that together impact oceanic carbon and nutrient cycling. Our understanding of these interactions in marine environments remains primarily limited to laboratory-based studies of model organisms. Here, we report the discovery and characterization of Ekhidna algicida sp. nov. strain To15, isolated from the oligotrophic Pacific Ocean (16°N, 140°W) based on its algicidal effect on the pelagic diatom Thalassiosira oceanica. Subsequent co-culture experiments demonstrate that E. algicida is lethal within days to a diverse array of diatoms, including diatoms isolated from similar locations, with the effect mediated by bacterial exudates produced during co-culture with susceptible diatoms. Exudates of E. algicida monoculture are not algicidal, suggesting a pathogenic shift upon interaction with susceptible diatoms. The genome of E. algicida To15 encodes for a type IX secretion system (T9SS), together with candidate secreted proteases, suggesting a potential protein-mediated pathogenicity. Twenty additional algicidal Ekhidna strains were subsequently isolated from the Pacific Ocean. All these algicidal bacteria pass through 0.2 μm pore-size filters, highlighting the importance of the often-overlooked group of “filterable” marine bacteria. Our findings reveal E. algicida as a Pacific Ocean diatom pathogen, with potential impacts on microbial community composition dynamics in pelagic ecosystems.
{"title":"Induced pathogenicity toward open-ocean diatoms by a filterable bacterium Ekhidna algicida sp. nov.","authors":"Shiri Graff van Creveld, Sacha N Coesel, Ellen Lavoie, Vaughn Iverson, Rhonda Morales, Megan J Schatz, Alexandra E Jones-Kellett, Jesse McNichol, Rebecca S Key, Jed Fuhrman, Bryndan P Durham, E Virginia Armbrust","doi":"10.1093/ismejo/wrag038","DOIUrl":"https://doi.org/10.1093/ismejo/wrag038","url":null,"abstract":"Phytoplankton are the base of marine food webs. They form intricate interactions with heterotrophic bacteria ranging from mutualistic to pathogenic that together impact oceanic carbon and nutrient cycling. Our understanding of these interactions in marine environments remains primarily limited to laboratory-based studies of model organisms. Here, we report the discovery and characterization of Ekhidna algicida sp. nov. strain To15, isolated from the oligotrophic Pacific Ocean (16°N, 140°W) based on its algicidal effect on the pelagic diatom Thalassiosira oceanica. Subsequent co-culture experiments demonstrate that E. algicida is lethal within days to a diverse array of diatoms, including diatoms isolated from similar locations, with the effect mediated by bacterial exudates produced during co-culture with susceptible diatoms. Exudates of E. algicida monoculture are not algicidal, suggesting a pathogenic shift upon interaction with susceptible diatoms. The genome of E. algicida To15 encodes for a type IX secretion system (T9SS), together with candidate secreted proteases, suggesting a potential protein-mediated pathogenicity. Twenty additional algicidal Ekhidna strains were subsequently isolated from the Pacific Ocean. All these algicidal bacteria pass through 0.2 μm pore-size filters, highlighting the importance of the often-overlooked group of “filterable” marine bacteria. Our findings reveal E. algicida as a Pacific Ocean diatom pathogen, with potential impacts on microbial community composition dynamics in pelagic ecosystems.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"42 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146222802","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}
Xingsheng Yang, Bo Zhao, Kai Feng, Jie Wang, Mingqian Liu, Xi Peng, Qing He, Yanjuan Lu, Hassan Waseem, Shang Wang, Mari-Karoliina H Winkler, Joana Falcão Salles, Ye Deng
Anaerobic digestion (AD) is a cornerstone technology for sustainable waste treatment and renewable energy recovery, yet its complex microbe-metabolite interactions remain poorly understood. Here, we combined high-resolution molecular profiling and microbial community sequencing in a three-month study across seven full-scale digesters to resolve dissolved organic matter (DOM) and microbiome dynamics. A total of 28,925 DOM molecules, including a conserved core of 1,154 metabolites, were identified. By disentangling metabolic pathways, we observed complex transformation patterns that extend beyond simple substrate breakdown. Molecules within a mass window (183.57–390.81 m/z) exhibited high persistence, strong microbial associations, and distinct transformation trajectories. Within this mass window, microbial community composition and feedstock input, together explained ~30.1%–43.4% of the observed spatiotemporal variation. In each digester, 1,260–2,108 molecules were closely associated with microbial metabolism, forming 7.77–24.52 microbe-metabolite associations on average. The accumulation and turnover of these microbial metabolites were strongly linked to methane production and system performance, highlighting microbial processing of DOM as a significant factor shaping microbe-metabolite interactions. This perspective emphasizes the importance of microbe-metabolite interplay in AD, providing a conceptual framework for predictive monitoring and optimization of engineered biotechnologies.
{"title":"Microbial synthesis structures organic compound composition in anaerobic digestion","authors":"Xingsheng Yang, Bo Zhao, Kai Feng, Jie Wang, Mingqian Liu, Xi Peng, Qing He, Yanjuan Lu, Hassan Waseem, Shang Wang, Mari-Karoliina H Winkler, Joana Falcão Salles, Ye Deng","doi":"10.1093/ismejo/wrag036","DOIUrl":"https://doi.org/10.1093/ismejo/wrag036","url":null,"abstract":"Anaerobic digestion (AD) is a cornerstone technology for sustainable waste treatment and renewable energy recovery, yet its complex microbe-metabolite interactions remain poorly understood. Here, we combined high-resolution molecular profiling and microbial community sequencing in a three-month study across seven full-scale digesters to resolve dissolved organic matter (DOM) and microbiome dynamics. A total of 28,925 DOM molecules, including a conserved core of 1,154 metabolites, were identified. By disentangling metabolic pathways, we observed complex transformation patterns that extend beyond simple substrate breakdown. Molecules within a mass window (183.57–390.81 m/z) exhibited high persistence, strong microbial associations, and distinct transformation trajectories. Within this mass window, microbial community composition and feedstock input, together explained ~30.1%–43.4% of the observed spatiotemporal variation. In each digester, 1,260–2,108 molecules were closely associated with microbial metabolism, forming 7.77–24.52 microbe-metabolite associations on average. The accumulation and turnover of these microbial metabolites were strongly linked to methane production and system performance, highlighting microbial processing of DOM as a significant factor shaping microbe-metabolite interactions. This perspective emphasizes the importance of microbe-metabolite interplay in AD, providing a conceptual framework for predictive monitoring and optimization of engineered biotechnologies.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"18 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146222803","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}
Lauren N Hart, Reagan Errera, Casey Godwin, Keith A Loftin, Zachary R Laughrey, Leon R Katona, Emma C Johnson, Rose M Cory, E Anders Kiledal, Paul Den Uyl, Jenan J Kharbush, David H Sherman, Gregory J Dick
Toxic cyanobacterial harmful algal blooms (cyanoHABs) threaten freshwater resources globally and are intensifying with increasing eutrophication. Bloom toxicity is strongly influenced by intraspecific variation in the biosynthetic repertoires of toxic cyanobacteria, yet few studies examine the diversity of cyanobacterial cyanopeptides beyond hepatotoxic microcystins. To understand the dynamics and drivers of cyanopeptide diversity in cyanoHABs, we analyzed temporal patterns of cyanobacteria, metabolites, and their biosynthetic gene clusters (BGCs) in western Lake Erie using a seven-year time series (2016–2022) of metagenomic and metabolomic data. Our findings demonstrate that shifts from Microcystis to Dolichospermum occur later in the bloom season, coinciding with lower temperatures. Modules of co-varying BGCs (biosynthesis modules) from these genera were identified with hierarchical clustering, with uncharacterized BGCs among the most abundant. Biosynthesis modules rich in nonribosomal peptide synthetases (NRPS) peaked in early August, coinciding with elevated levels of inorganic nitrogen, warmer temperatures, and high Microcystis abundance. In contrast, modules rich in polyketide synthases (PKS) and ribosomally synthesized and post-translationally modified peptides (RiPPs) peaked following the Microcystis maximum in mid-August. Metabolomic analyses confirmed that metabolites followed shared seasonal patterns with their associated biosynthesis modules, forming three phases characterized by (1) microcystins, (2) anabaenopeptins and aeruginosins, and (3) aerucyclamides. These phases co-varied with bottom-up and top-down pressures, with later phases coinciding with increased microbially processed organic nitrogen and reduced detection of grazers. This study demonstrates consistent seasonal patterns of cyanobacterial metabolite succession and co-occurrence beyond microcystins, suggesting tradeoffs between biosynthetic resource demands and ecological controls.
{"title":"Diverse Cyanopeptides Follow Distinct Temporal Succession Patterns in Freshwater Harmful Algal Blooms","authors":"Lauren N Hart, Reagan Errera, Casey Godwin, Keith A Loftin, Zachary R Laughrey, Leon R Katona, Emma C Johnson, Rose M Cory, E Anders Kiledal, Paul Den Uyl, Jenan J Kharbush, David H Sherman, Gregory J Dick","doi":"10.1093/ismejo/wrag026","DOIUrl":"https://doi.org/10.1093/ismejo/wrag026","url":null,"abstract":"Toxic cyanobacterial harmful algal blooms (cyanoHABs) threaten freshwater resources globally and are intensifying with increasing eutrophication. Bloom toxicity is strongly influenced by intraspecific variation in the biosynthetic repertoires of toxic cyanobacteria, yet few studies examine the diversity of cyanobacterial cyanopeptides beyond hepatotoxic microcystins. To understand the dynamics and drivers of cyanopeptide diversity in cyanoHABs, we analyzed temporal patterns of cyanobacteria, metabolites, and their biosynthetic gene clusters (BGCs) in western Lake Erie using a seven-year time series (2016–2022) of metagenomic and metabolomic data. Our findings demonstrate that shifts from Microcystis to Dolichospermum occur later in the bloom season, coinciding with lower temperatures. Modules of co-varying BGCs (biosynthesis modules) from these genera were identified with hierarchical clustering, with uncharacterized BGCs among the most abundant. Biosynthesis modules rich in nonribosomal peptide synthetases (NRPS) peaked in early August, coinciding with elevated levels of inorganic nitrogen, warmer temperatures, and high Microcystis abundance. In contrast, modules rich in polyketide synthases (PKS) and ribosomally synthesized and post-translationally modified peptides (RiPPs) peaked following the Microcystis maximum in mid-August. Metabolomic analyses confirmed that metabolites followed shared seasonal patterns with their associated biosynthesis modules, forming three phases characterized by (1) microcystins, (2) anabaenopeptins and aeruginosins, and (3) aerucyclamides. These phases co-varied with bottom-up and top-down pressures, with later phases coinciding with increased microbially processed organic nitrogen and reduced detection of grazers. This study demonstrates consistent seasonal patterns of cyanobacterial metabolite succession and co-occurrence beyond microcystins, suggesting tradeoffs between biosynthetic resource demands and ecological controls.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"121 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146215800","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}
Baozhan Wang, Ping Gao, Ping Zhang, Yue Zheng, Xu Liu, Ning Ling, Jun Shan, Rongjiang Yao, Shuai Zhao, Zhiguo Zhang, Guibing Zhu, Man-Young Jung, Jianwen Zou, Xiaoyuan Yan, Sungeun Lee, Christina Hazard, Graeme W Nicol, Jizhong Zhou, Yunfeng Yang, Yongguan Zhu, David A Stahl, Michael Wagner, Yanzheng Gao, Jiandong Jiang, Wei Qin
Global heatwave intensification under climate change will impact the nitrogen cycle, yet its effect on active nitrifier groups or their interactions with viruses remains unclear. Using 13CO2-DNA-based stable-isotope probing coupled with metagenomics, we show that elevated temperatures under heatwave conditions fundamentally restructure active nitrifying communities and their associated viruses in Yangtze River estuary upper tidal flats and adjacent agricultural soils. In tidal flats, sustained high temperature constrained nitrification by reducing the abundance of active ammonia-oxidizing archaea and bacteria (AOA, AOB) and canonical nitrite-oxidizing bacteria (NOB). This was accompanied by a shift in the active community from marine to more thermotolerant but less salt-tolerant terrestrial ecotypes. Conversely, heatwave conditions in agricultural soils suppressed AOB but enhanced nitrification activity in thermotolerant terrestrial AOA ecotypes. Across both ecosystems, inferred virus-nitrifier interactions were temperature dependent. 13C-labeled nitrifier-infecting viruses exhibited coordinated shifts in virus-to-host abundance ratios and predicted lifestyles with their hosts, with sustained high temperatures reducing virus-to-host abundance ratios and favoring temperate infections, relative to higher abundance ratios and a greater proportion of predicted lytic cycles at lower temperatures. We identified AOA-infecting viruses that carry plastocyanin (pcy), encoding a key copper-dependent electron carrier in the AOA respiratory chain, with conserved active sites and a predicted protein fold that supports its capacity for electron transfer, potentially augmenting host energy metabolism. Together, our findings demonstrate that prolonged heatwaves drive coupled shifts in nitrifier community composition and virus–host interaction strategies in a land-use–dependent manner, with implications for nitrogen transformations and ecosystem feedbacks under climate extremes.
{"title":"Elevated Temperature Simulating Heatwaves Restructures Active Nitrifying Communities and Associated Viruses in Tidal Flats and Agricultural Soils","authors":"Baozhan Wang, Ping Gao, Ping Zhang, Yue Zheng, Xu Liu, Ning Ling, Jun Shan, Rongjiang Yao, Shuai Zhao, Zhiguo Zhang, Guibing Zhu, Man-Young Jung, Jianwen Zou, Xiaoyuan Yan, Sungeun Lee, Christina Hazard, Graeme W Nicol, Jizhong Zhou, Yunfeng Yang, Yongguan Zhu, David A Stahl, Michael Wagner, Yanzheng Gao, Jiandong Jiang, Wei Qin","doi":"10.1093/ismejo/wrag037","DOIUrl":"https://doi.org/10.1093/ismejo/wrag037","url":null,"abstract":"Global heatwave intensification under climate change will impact the nitrogen cycle, yet its effect on active nitrifier groups or their interactions with viruses remains unclear. Using 13CO2-DNA-based stable-isotope probing coupled with metagenomics, we show that elevated temperatures under heatwave conditions fundamentally restructure active nitrifying communities and their associated viruses in Yangtze River estuary upper tidal flats and adjacent agricultural soils. In tidal flats, sustained high temperature constrained nitrification by reducing the abundance of active ammonia-oxidizing archaea and bacteria (AOA, AOB) and canonical nitrite-oxidizing bacteria (NOB). This was accompanied by a shift in the active community from marine to more thermotolerant but less salt-tolerant terrestrial ecotypes. Conversely, heatwave conditions in agricultural soils suppressed AOB but enhanced nitrification activity in thermotolerant terrestrial AOA ecotypes. Across both ecosystems, inferred virus-nitrifier interactions were temperature dependent. 13C-labeled nitrifier-infecting viruses exhibited coordinated shifts in virus-to-host abundance ratios and predicted lifestyles with their hosts, with sustained high temperatures reducing virus-to-host abundance ratios and favoring temperate infections, relative to higher abundance ratios and a greater proportion of predicted lytic cycles at lower temperatures. We identified AOA-infecting viruses that carry plastocyanin (pcy), encoding a key copper-dependent electron carrier in the AOA respiratory chain, with conserved active sites and a predicted protein fold that supports its capacity for electron transfer, potentially augmenting host energy metabolism. Together, our findings demonstrate that prolonged heatwaves drive coupled shifts in nitrifier community composition and virus–host interaction strategies in a land-use–dependent manner, with implications for nitrogen transformations and ecosystem feedbacks under climate extremes.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"402 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146222806","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}
Self-organizing spatial patterns are ubiquitous in microbial ecosystems, yet their sensitivity to environmental conditions remains poorly understood. Understanding spatial pattern sensitivity is particularly relevant for surface-associated microbial systems, as their functioning depends on how different cell-types self-organize across space as a consequence of their traits and environmental conditions. Here, we integrate principles from microbial systems ecology with self-organization theory to understand how environmental conditions and biotic interactions shape the sensitivity of emergent spatial intermixing, which is a critical feature of spatial patterns. Using denitrifying strains of the bacterium Stutzerimonas stutzeri that engage in negative (competitive) or positive (cross-feeding) interactions, we demonstrate that spatial intermixing emerging from positive interactions is more sensitive to environmental conditions than that emerging from negative interactions. We further develop and quantify the spatial intermixing strength as a key descriptor of spatial pattern sensitivity, revealing that high short-range dispersal and strong biotic interdependence promote persistent spatial intermixing. Our findings highlight that ecosystem sensitivity to environmental conditions can be inferred from features of emergent spatial patterns, providing a quantitative framework for understanding how environmental and biological factors jointly govern ecosystem assembly and dynamics.
{"title":"Sensitivity of microbial spatial self-organization to surface friction depends on metabolic interactions","authors":"Philipp Tandler, David R Johnson, Guram Gogia","doi":"10.1093/ismejo/wrag035","DOIUrl":"https://doi.org/10.1093/ismejo/wrag035","url":null,"abstract":"Self-organizing spatial patterns are ubiquitous in microbial ecosystems, yet their sensitivity to environmental conditions remains poorly understood. Understanding spatial pattern sensitivity is particularly relevant for surface-associated microbial systems, as their functioning depends on how different cell-types self-organize across space as a consequence of their traits and environmental conditions. Here, we integrate principles from microbial systems ecology with self-organization theory to understand how environmental conditions and biotic interactions shape the sensitivity of emergent spatial intermixing, which is a critical feature of spatial patterns. Using denitrifying strains of the bacterium Stutzerimonas stutzeri that engage in negative (competitive) or positive (cross-feeding) interactions, we demonstrate that spatial intermixing emerging from positive interactions is more sensitive to environmental conditions than that emerging from negative interactions. We further develop and quantify the spatial intermixing strength as a key descriptor of spatial pattern sensitivity, revealing that high short-range dispersal and strong biotic interdependence promote persistent spatial intermixing. Our findings highlight that ecosystem sensitivity to environmental conditions can be inferred from features of emergent spatial patterns, providing a quantitative framework for understanding how environmental and biological factors jointly govern ecosystem assembly and dynamics.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146215801","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}
Marie-Katherin Zühlke, Alexandra Bahr, Daniel Bartosik, Vipul Solanki, Michelle Teune, Norma Welsch, Frank Unfried, Tristan Barbeyron, Elizabeth Ficko-Blean, Paula Schoppmeier, Laurie Schiller, Nahja Busse, Disha Banerjee, Lionel Cladière, Alexandra Jeudy, Anne Susemihl, Fabian Hartmann, Diane Jouanneau, Murielle Jam, Matthias Höhne, Mihaela Delcea, Greta Reintjes, Uwe T Bornscheuer, Dörte Becher, Jan-Hendrik Hehemann, Mirjam Czjzek, Thomas Schweder
Fructans are ubiquitous in terrestrial ecosystems, however, these glycans are underexplored in the marine environment. We have discovered that the Antarctic gammaproteobacterium Pseudoalteromonas distincta is highly adapted to the degradation of fructose-containing substrates. This is enabled by proteins encoded in several genomic regions, including a fructan polysaccharide utilization locus (PUL). In addition to a glycoside hydrolase from family 32 (GH32), the fructan PUL encodes two proteins that have been described as specific for the phylum Bacteroidota and were previously unknown for the class Gammaproteobacteria (phylum Pseudomonadota): a glycan-binding SusD-like protein and a SusC-like TonB-dependent transporter (TBDT), which work as a complex in glycan import in Bacteroidota. Proteome, biochemical, sequence, and structural analyses indicate that the SusD-like protein and SusC-like TBDT of P. distincta mediate the uptake of inulin-type fructans, followed by degradation by a periplasmic exo-active GH32. In contrast, P. distincta likely degrades levan-type fructans via an extracellular endo-acting GH32 that is not encoded in the fructan PUL. Comparative genomics identified further SusD-like proteins and SusC-like TBDTs in Gammaproteobacteria, most of which are co-encoded with GH32s, indicative of fructan PULs, and are frequently associated with the marine habitat. Our study thus suggests that SusC/D-like complexes are not exclusive to the phylum Bacteroidota. It further shows that fructans contribute to the marine glycan pool and are targeted by specialized marine communities.
{"title":"Fructan utilization by members of marine Gammaproteobacteria involves SusC/D-like proteins","authors":"Marie-Katherin Zühlke, Alexandra Bahr, Daniel Bartosik, Vipul Solanki, Michelle Teune, Norma Welsch, Frank Unfried, Tristan Barbeyron, Elizabeth Ficko-Blean, Paula Schoppmeier, Laurie Schiller, Nahja Busse, Disha Banerjee, Lionel Cladière, Alexandra Jeudy, Anne Susemihl, Fabian Hartmann, Diane Jouanneau, Murielle Jam, Matthias Höhne, Mihaela Delcea, Greta Reintjes, Uwe T Bornscheuer, Dörte Becher, Jan-Hendrik Hehemann, Mirjam Czjzek, Thomas Schweder","doi":"10.1093/ismejo/wrag030","DOIUrl":"https://doi.org/10.1093/ismejo/wrag030","url":null,"abstract":"Fructans are ubiquitous in terrestrial ecosystems, however, these glycans are underexplored in the marine environment. We have discovered that the Antarctic gammaproteobacterium Pseudoalteromonas distincta is highly adapted to the degradation of fructose-containing substrates. This is enabled by proteins encoded in several genomic regions, including a fructan polysaccharide utilization locus (PUL). In addition to a glycoside hydrolase from family 32 (GH32), the fructan PUL encodes two proteins that have been described as specific for the phylum Bacteroidota and were previously unknown for the class Gammaproteobacteria (phylum Pseudomonadota): a glycan-binding SusD-like protein and a SusC-like TonB-dependent transporter (TBDT), which work as a complex in glycan import in Bacteroidota. Proteome, biochemical, sequence, and structural analyses indicate that the SusD-like protein and SusC-like TBDT of P. distincta mediate the uptake of inulin-type fructans, followed by degradation by a periplasmic exo-active GH32. In contrast, P. distincta likely degrades levan-type fructans via an extracellular endo-acting GH32 that is not encoded in the fructan PUL. Comparative genomics identified further SusD-like proteins and SusC-like TBDTs in Gammaproteobacteria, most of which are co-encoded with GH32s, indicative of fructan PULs, and are frequently associated with the marine habitat. Our study thus suggests that SusC/D-like complexes are not exclusive to the phylum Bacteroidota. It further shows that fructans contribute to the marine glycan pool and are targeted by specialized marine communities.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146215709","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}
Alexandre Desparmet, Bruno Jesus, Tony Robinet, Thierry Dufour, Cédric Hubas
Diatom-dominated intertidal microphytobenthic biofilms experience daily fluctuations in irradiance, which can lead to oxidative stress within the photosynthetic apparatus through the production and accumulation of reactive oxygen species. To maintain photosynthetic efficiency, benthic diatoms have developed protective strategies, including mobilization of the antioxidant xanthophyll cycle and the ability to migrate vertically through sediments. However, mechanistic understanding of signaling pathways underlying migration remains poorly characterized. This study investigated the triggering effect of reactive oxygen species on behavioral and photophysiological responses through the analysis of lipophilic pigments and fluorescence parameters. To this end, two microphytobenthic communities, one with sediment allowing vertical migration and another without sediment restricting it, were exposed to irradiance, cold atmospheric plasma, and hydrogen peroxide stresses. Results showed a consistent downward migration response under all oxidative stresses, highlighting the key role of reactive oxygen species, especially hydrogen peroxide, in triggering this microphytobenthic behavior. Moreover, a difference was observed between the pathways involved in vertical migration and those underlying photoprotective responses. Hydrogen peroxide and cold atmospheric plasma stresses highlighted the necessity for substantial microphytobenthic migration, whereas irradiance induced a specific and controlled response involving engagement of the xanthophyll cycle, acting in synergy with the migration strategy by showing stronger activation when migration was impaired. By establishing that a rapid and efficient migration could be induced by reactive oxygen species and could act in synergy with the xanthophyll cycle in epipelic cells, this study provides key insights into the molecular basis of microphytobenthic responses to cellular and environmental oxidative stresses.
{"title":"Reactive oxygen species trigger downward vertical migration in diatom microphytobenthic biofilms as a strategy to cope with oxidative stress","authors":"Alexandre Desparmet, Bruno Jesus, Tony Robinet, Thierry Dufour, Cédric Hubas","doi":"10.1093/ismejo/wrag034","DOIUrl":"https://doi.org/10.1093/ismejo/wrag034","url":null,"abstract":"Diatom-dominated intertidal microphytobenthic biofilms experience daily fluctuations in irradiance, which can lead to oxidative stress within the photosynthetic apparatus through the production and accumulation of reactive oxygen species. To maintain photosynthetic efficiency, benthic diatoms have developed protective strategies, including mobilization of the antioxidant xanthophyll cycle and the ability to migrate vertically through sediments. However, mechanistic understanding of signaling pathways underlying migration remains poorly characterized. This study investigated the triggering effect of reactive oxygen species on behavioral and photophysiological responses through the analysis of lipophilic pigments and fluorescence parameters. To this end, two microphytobenthic communities, one with sediment allowing vertical migration and another without sediment restricting it, were exposed to irradiance, cold atmospheric plasma, and hydrogen peroxide stresses. Results showed a consistent downward migration response under all oxidative stresses, highlighting the key role of reactive oxygen species, especially hydrogen peroxide, in triggering this microphytobenthic behavior. Moreover, a difference was observed between the pathways involved in vertical migration and those underlying photoprotective responses. Hydrogen peroxide and cold atmospheric plasma stresses highlighted the necessity for substantial microphytobenthic migration, whereas irradiance induced a specific and controlled response involving engagement of the xanthophyll cycle, acting in synergy with the migration strategy by showing stronger activation when migration was impaired. By establishing that a rapid and efficient migration could be induced by reactive oxygen species and could act in synergy with the xanthophyll cycle in epipelic cells, this study provides key insights into the molecular basis of microphytobenthic responses to cellular and environmental oxidative stresses.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"90 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146222804","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}
Ina Wasmuth, Anan Ibrahim, Phil Köhler, Hrant Hovhannisyan, Marina Marcet-Houben, Toni Gabaldón, Soninkhishig Tsolmon, Christina Warinner, Pierre Stallforth
Milk has a rich microbiota that engages in complex interactions. These interactions can be mutualistic or antagonistic, shaping the microbial composition of dairy products and affecting fermentation, preservation, and product quality. In this study, we investigate the interaction between Pseudomonas bacteria and the yeast Candida zeylanoides in the context of traditional dairy fermentation. We identified a collection of cyclic lipopeptides (CLPs) from Pseudomonas sp. SM4, isolated from the traditional Mongolian dairy product öröm and elucidated the structure of six CLPs belonging to the amphisin family using a combination of bioinformatic predictions, mass spectrometry, Marfey’s analysis, NMR spectroscopy, and X-ray crystallography. Milk-based bioassays and 16S rRNA gene amplicon sequencing analyses revealed changes in the microbial composition of milk due to the addition of the CLP tensin A and allowed us to identify its function in promoting the growth of C. zeylanoides, a yeast commonly found in dairy environments. Through transcriptomic analysis, we obtained preliminary insights into the potential metabolic pathways that may contribute to the growth-promoting effect, which indicates a role for the glyoxylate metabolism. This represents the first report of a CLP directly stimulating yeast growth. Understanding how Pseudomonas-derived lipopeptides modulate microbial communities, particularly by supporting yeasts relevant to dairy fermentations, could inform strategies for optimizing dairy fermentation processes like kefir production and improving the stability and quality of fermented dairy products.
{"title":"Growth Promotion of Milk-Associated Candida zeylanoides by a cyclic-lipopeptide produced by Pseudomonas","authors":"Ina Wasmuth, Anan Ibrahim, Phil Köhler, Hrant Hovhannisyan, Marina Marcet-Houben, Toni Gabaldón, Soninkhishig Tsolmon, Christina Warinner, Pierre Stallforth","doi":"10.1093/ismejo/wrag033","DOIUrl":"https://doi.org/10.1093/ismejo/wrag033","url":null,"abstract":"Milk has a rich microbiota that engages in complex interactions. These interactions can be mutualistic or antagonistic, shaping the microbial composition of dairy products and affecting fermentation, preservation, and product quality. In this study, we investigate the interaction between Pseudomonas bacteria and the yeast Candida zeylanoides in the context of traditional dairy fermentation. We identified a collection of cyclic lipopeptides (CLPs) from Pseudomonas sp. SM4, isolated from the traditional Mongolian dairy product öröm and elucidated the structure of six CLPs belonging to the amphisin family using a combination of bioinformatic predictions, mass spectrometry, Marfey’s analysis, NMR spectroscopy, and X-ray crystallography. Milk-based bioassays and 16S rRNA gene amplicon sequencing analyses revealed changes in the microbial composition of milk due to the addition of the CLP tensin A and allowed us to identify its function in promoting the growth of C. zeylanoides, a yeast commonly found in dairy environments. Through transcriptomic analysis, we obtained preliminary insights into the potential metabolic pathways that may contribute to the growth-promoting effect, which indicates a role for the glyoxylate metabolism. This represents the first report of a CLP directly stimulating yeast growth. Understanding how Pseudomonas-derived lipopeptides modulate microbial communities, particularly by supporting yeasts relevant to dairy fermentations, could inform strategies for optimizing dairy fermentation processes like kefir production and improving the stability and quality of fermented dairy products.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"122 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146222808","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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