ISME Journal最新文献

Heterologous expression in E. coli reveals that bicarbonate transporter BicA2 mediates carbon uptake in marine Prochlorococcus spp. 大肠杆菌中的异源表达揭示了碳酸氢盐转运体BicA2介导海洋原绿球藻的碳吸收。

IF 10.2 1区环境科学与生态学

ISME Journal Pub Date : 2026-08-27 DOI: 10.1093/ismejo/wrag222

Loraine M Rourke, Caitlin S Byrt, G Dean Price, Benedict M Long

{"title":"Heterologous expression in E. coli reveals that bicarbonate transporter BicA2 mediates carbon uptake in marine Prochlorococcus spp.","authors":"Loraine M Rourke, Caitlin S Byrt, G Dean Price, Benedict M Long","doi":"10.1093/ismejo/wrag222","DOIUrl":"https://doi.org/10.1093/ismejo/wrag222","url":null,"abstract":"The widespread oceanic cyanobacterial Prochlorococcus genus is a major contributor to global carbon fixation, yet mechanisms enabling this lineage to elevate intracellular inorganic carbon as a substrate for photosynthesis remain unresolved. Cyanobacterial CO2-concentrating mechanisms typically rely on membrane-bound bicarbonate (HCO3-) transporters SbtA1, SbtA2, BicA and BCT1, and CO2-to-HCO3- conversion uptake systems (CO2 pumps; NDH-I3 and NDH-I4), to elevate a cellular HCO3- pool for use by Rubisco-containing carboxysomes. Evidence suggests Prochlorococcus harbours carboxysomes with a low-CO2-specificity Rubisco, implying a functional CCM dependent on active HCO3- uptake. However, canonical CO2 pumps are absent, leaving distant HCO3- transporter homologues, BicA2 and SbtA2, as prime candidates for HCO3- transport in this group. Yet these have not been functionally characterised. Here we demonstrate that BicA2 from P. marinus CCMP1375 mediates Na+-dependent HCO3- uptake in E. coli, whereas BicA2 from P. marinus CCMP1986 is inactive in its native form but acquired transport function through a single amino acid substitution during adaptive laboratory evolution. These findings confirm BicA2 as a low-affinity, Na+-dependent bicarbonate transporter with variable flux, revealing a previously uncharacterized CCM component in Prochlorococcus. This mechanistic insight reshapes our understanding of carbon acquisition strategies in the most abundant photosynthetic organism on Earth and highlights evolutionary plasticity in transporter function with implications for global biogeochemical cycles.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148842003","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Differential aggregation properties among Baltic Sea picocyanobacterial strains impact their export. 波罗的海picocyanobacter菌株之间的不同聚集特性影响了它们的出口。

IF 10.2 1区环境科学与生态学

ISME Journal Pub Date : 2026-08-27 DOI: 10.1093/ismejo/wrag214

Martin Ekman, Elina Viinimäki, Anders Svensson, Ryan W Paerl, Anders F Andersson, Helena Höglander, Jakob Walve, Rachel A Foster

{"title":"Differential aggregation properties among Baltic Sea picocyanobacterial strains impact their export.","authors":"Martin Ekman, Elina Viinimäki, Anders Svensson, Ryan W Paerl, Anders F Andersson, Helena Höglander, Jakob Walve, Rachel A Foster","doi":"10.1093/ismejo/wrag214","DOIUrl":"https://doi.org/10.1093/ismejo/wrag214","url":null,"abstract":"Picocyanobacteria contribute significantly to carbon export but the mechanism by which their biomass is transported to depth is unclear. By analysing16S rRNA gene sequences from sediment trap material and size fractionated water samples from different depths in the Baltic Sea, we show that picocyanobacterial contribution to phytoplankton biomass export was largely proportional (70-90%) to their surface water abundances. However, we also found that both cell aggregation (enrichment in >10 μm fraction) and sedimentation (trap enrichment) varied among Synechococcus ASVs (amplicon sequence variants). A robust linear relationship was identified between ASV enrichment in traps and ASV enrichment in the >10 μm fraction, suggesting that cell aggregation is a direct determinant of Synechococcus sedimentation. Seasonal abundance patterns were similar among the dominant aggregate-forming ASVs but distinct from those of single cell ASVs, suggesting aggregate/colony-formation being an important trait in determining distribution of Synechococcus strains and their response to environmental conditions. Correlating microscopy- and sequence-based abundances further allowed us to propose genotypes for the dominant Baltic Sea colonial picocyanobacterial morphotypes. Our results provide in situ data linking phenotypic characteristics of picocyanobacteria with sedimentation properties and several lines of evidence for a quantitative dependency between surface water picocyanobacterial aggregate/colony formation and sinking. These findings are important for our understanding of mechanisms involved in export of pico-sized phytoplankton biomass from the photic zone to depth and emphasize the need to investigate occurrence and environmental regulation of cell aggregation in other picophytoplankton dominated waters (eg, open ocean gyres).","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148841958","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Carbon substrate type shapes spatial self-organization in a multi-species biofilm community. 碳基质类型决定了多物种生物膜群落的空间自组织。

IF 10.2 1区环境科学与生态学

ISME Journal Pub Date : 2026-08-27 DOI: 10.1093/ismejo/wrag223

Deyong Zhu, Anna J Svagan, Nan Yang, Mads Frederik Hansen, Michael Kühl, Mette Burmølle

{"title":"Carbon substrate type shapes spatial self-organization in a multi-species biofilm community.","authors":"Deyong Zhu, Anna J Svagan, Nan Yang, Mads Frederik Hansen, Michael Kühl, Mette Burmølle","doi":"10.1093/ismejo/wrag223","DOIUrl":"https://doi.org/10.1093/ismejo/wrag223","url":null,"abstract":"Spatial organization is a defining feature of multispecies biofilms and critically influences microbial interactions and emergent community properties. However, understanding and manipulating how microbes assemble into spatially structured biofilms remains challenging because most experimental frameworks emphasize species composition and pairwise interactions, while often overlooking the spatial constraints on biofilms imposed by the environment. In this study, we focus on how carbon substrate type, distinguishing between diffusible sugars and polymeric substrates, affects biofilm self-organization in a four-member synthetic bacterial community (SynCom). Across all tested conditions, the SynCom consistently formed more biofilm biomass than any of its subsets, indicating a robust synergistic phenotype. Using chemically defined, 3D-printed hydrogel substrates with consistent physical properties, we varied carbon source composition to identify its impact on biofilm assembly. Microscopic imaging showed that carbon substrate type strongly influenced biofilm self-organization with diffusible simple carbon substrates yielding relatively intermixed communities, whereas polymer-rich carbon substrates promoted a highly structured biofilm organization characterized by the dominance and peripheral localization of polymer-degrading species. Bioinformatic analyses of carbohydrate-active enzyme (CAZyme) repertoires and genome-scale metabolic modeling suggested bidirectional metabolite exchange among the SynCom members, which was also supported by analysis of biofilm formation in conditioned community supernatants. Together, our findings suggest carbon substrate type as an important ecological determinant of biofilm self-organization, highlighting the need to integrate environmental factors alongside species composition and metabolic potential to fully understand and manipulate natural and engineered multispecies biofilms.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148841967","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Enrichment and Characterization of a Haloalkaline-tolerant Anammox Bacterium. 耐卤碱厌氧氨氧化菌的富集与特性研究。

IF 10.2 1区环境科学与生态学

ISME Journal Pub Date : 2026-08-27 DOI: 10.1093/ismejo/wrag221

Han-Yin Chuang, Jer-Horng Wu, Shan-Hua Chen, Wei-Yu Chen, Li-Jin Fong, Yi-Ting Lin

{"title":"Enrichment and Characterization of a Haloalkaline-tolerant Anammox Bacterium.","authors":"Han-Yin Chuang, Jer-Horng Wu, Shan-Hua Chen, Wei-Yu Chen, Li-Jin Fong, Yi-Ting Lin","doi":"10.1093/ismejo/wrag221","DOIUrl":"https://doi.org/10.1093/ismejo/wrag221","url":null,"abstract":"Metagenomic surveys have substantially expanded the known diversity of anaerobic ammonium-oxidizing (anammox) bacteria. However, the physiological traits of newly proposed anammox genera remain largely hypothetical due to the lack of cultured representatives. Although niche differentiation driven by salinity, organic substrates, and oxygen is well documented in anammox bacteria, adaptations to alkaline environments remain uncharacterized. Moreover, no anammox lineage has been identified as an alkaline specialist. Herein, we report the enrichment (>80% relative abundance) of an anammox bacterium, provisionally named Candidatus Loosdrechtia alkalitolerans, which represents the cultured member of the genus Ca. Loosdrechtia. Ca. L. alkalitolerans exhibits marked haloalkaline tolerance, outcompeting other freshwater anammox genera under long-term saline-alkaline stress conditions (0.5% NaCl; pH~9.13). Comparative genomics revealed that among freshwater anammox lineages, only Ca. L. alkalitolerans encodes a complete multiple resistance and pH adaptation (Mrp) cation/proton antiporter operon. Batch assays with transcriptional profiling demonstrated that sodium addition upregulated mrp expression and recovered anammox activity under alkaline stress, suggesting that Mrp-mediated cation/proton exchange may contribute to pH homeostasis in Ca. L. alkalitolerans. Furthermore, database mining revealed that the habitat of Ca. L. alkalitolerans is not restricted to haloalkaline environments, but extends to diverse freshwater and wastewater ecosystems. These findings provide mechanistic insight into saline-alkaline tolerance in anammox bacteria, expanding understanding of their physiological plasticity and ecological roles.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148842035","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Soil amelioration impacts viral ecology in saline-alkali lands. 盐碱地土壤改良对病毒生态的影响

IF 10.2 1区环境科学与生态学

ISME Journal Pub Date : 2026-08-26 DOI: 10.1093/ismejo/wrag217

Junxi Liu, Guixiang Zhou, Lin Chen, Yu Xiao, Yakov Kuzyakov, Congzhi Zhang, Ping Huang, Donghao Ma, Jiabao Zhang

{"title":"Soil amelioration impacts viral ecology in saline-alkali lands.","authors":"Junxi Liu, Guixiang Zhou, Lin Chen, Yu Xiao, Yakov Kuzyakov, Congzhi Zhang, Ping Huang, Donghao Ma, Jiabao Zhang","doi":"10.1093/ismejo/wrag217","DOIUrl":"https://doi.org/10.1093/ismejo/wrag217","url":null,"abstract":"The continuous expansion of saline-alkali lands under climate change threatens food security and reduces soil carbon stocks. A common mitigation strategy is soil amelioration, which converts degraded soils back into an arable state. Microbes play critical roles in soil health and recovery. However, the viruses that infect these microbial communities, and their potential impacts during saline-alkali soil restoration, remain largely unknown. Here, we combined total soil metagenomics and viromics to investigate host-linked viral ecology across four major saline-alkali regions in China, each encompassing two soil amelioration statuses: saline-alkali and reclaimed. We found that viral community structure was shaped by both geography and soil amelioration status, with salinity and alkalinity emerging as key environmental factors. Viral populations were sensitive to soil restoration, showing strong amelioration-status endemism with functional adaptations. Virus-host dynamics ranged from reduced temperate viruses to abundance mismatches in those infecting key carbon-cycling microorganisms, including carbohydrate degraders. 13C-cellulose DNA-SIP experiments provided further support for this mismatch by tracing assimilated carbon transfer between active host and virus populations. Compared with saline-alkali soils, the relative abundance of hosts in restored soils increased from 39.0% to 61.0%, whereas the linked viruses decreased from 60.6% to 39.4%. Together, these findings reveal an underappreciated role of viruses in shaping saline-alkali soil amelioration trajectories, and could improve management strategies for degraded land recovery and carbon storage.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148820010","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Site-specific recombination and purifying selection influence Cry toxin formation and specialization. 位点特异性重组和纯化选择影响Cry毒素的形成和特化。

IF 10.2 1区环境科学与生态学

ISME Journal Pub Date : 2026-08-26 DOI: 10.1093/ismejo/wrag218

Anton E Shikov, Ruslan O Alagov, Maria E Belousova, Anton A Nizhnikov, Kirill S Antonets

{"title":"Site-specific recombination and purifying selection influence Cry toxin formation and specialization.","authors":"Anton E Shikov, Ruslan O Alagov, Maria E Belousova, Anton A Nizhnikov, Kirill S Antonets","doi":"10.1093/ismejo/wrag218","DOIUrl":"https://doi.org/10.1093/ismejo/wrag218","url":null,"abstract":"In bacteria, multi-domain toxins represent a universal tool for determining the host range, being a cornerstone for public health and agriculture. Given high host specificity and potency, Cry toxins represent the most widely used bioinsecticides in agriculture. Their worldwide application grows annually; thus, the rational design of bioinsecticides requires a deeper understanding of the processes that orchestrate the origin and evolution of Cry toxins. The accepted views on how Cry toxins exchange domains postulate that homologous recombination sparks domain III swapping, altering host specificity and broadening strains' activities. This perspective, however, stems from laboratory experiments and has never been studied in nature. Here, we leveraged all available Cry sequences and uncovered the mechanism of the evolution of Cry toxins via site-specific recombination guided by XerCD recombinases that target insertions and conserved blocks between domain borders. The emergence of specialists from generalists is sparked by the purifying selection of specialized hybrids. Therefore, our model of domain shuffling caused by site-specific recombination of cry loci, followed by selection-driven specialization, illustrates how multi-domain toxins evolve and attune to specific hosts.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148819984","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Metabolic division of labour drives estuarine-coastal N2O emissions. 代谢分工驱动河口-沿海N2O排放。

IF 10.2 1区环境科学与生态学

ISME Journal Pub Date : 2026-08-26 DOI: 10.1093/ismejo/wrag216

Enquan Zhang, Shengjie Li, Ehui Tan, Qiuyun Jiang, Yunxuan Li, Ziqi Wu, Jiaxin Chen, Xianhui Wan, Xianbiao Lin, Nengwang Chen, Yu Cong, Nianzhi Jiao, Xiyang Dong, Qiang Zheng

{"title":"Metabolic division of labour drives estuarine-coastal N2O emissions.","authors":"Enquan Zhang, Shengjie Li, Ehui Tan, Qiuyun Jiang, Yunxuan Li, Ziqi Wu, Jiaxin Chen, Xianhui Wan, Xianbiao Lin, Nengwang Chen, Yu Cong, Nianzhi Jiao, Xiyang Dong, Qiang Zheng","doi":"10.1093/ismejo/wrag216","DOIUrl":"https://doi.org/10.1093/ismejo/wrag216","url":null,"abstract":"Estuarine and coastal systems are global hotspots of marine nitrous oxide (N2O) emissions, where microbial nitrification and denitrification are the primary processes regulating N2O dynamics. However, how interactions among different N2O-associated microorganisms influence ecosystem-scale N2O emissions remains poorly understood. This study combined in situ N2O concentrations, 15N-based potential rates, metagenomics, metatranscriptomics, and genome-scale metabolic model analysis to explore N2O production and reduction processes in estuarine and coastal systems. Potential N2O production and reduction rates, together with in situ concentrations, the relative abundance, and the transcriptional activity of associated genes, were significantly higher at low salinity and declined toward coastal regions. Based on the gene content of 974 recovered N2O-associated genomes, microorganisms were classified into three functional groups: net N2O producers, net N2O consumers, and self-sustaining N2O players. The abundance, composition, and activity of these functional groups shifted along estuarine-coastal gradients. A larger NO/N2O exchange gap, reflecting the imbalance between model-inferred NO and N2O handoff potentials, was found at low salinity and was associated with elevated bottom-water N2O concentrations. Together, community-level division of labour and the associated exchange gap provide a conceptual framework for linking N2O-related functional groups to N2O accumulation in estuarine-coastal ecosystems.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148820112","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Model-guided design of defined microbial community reveals interactions underpinning plant growth and stress tolerance. 定义微生物群落的模型引导设计揭示了植物生长和抗逆性的相互作用。

IF 10.2 1区环境科学与生态学

ISME Journal Pub Date : 2026-08-26 DOI: 10.1093/ismejo/wrag219

Shinichi Yamazaki, Masaru Nakayasu, Keiko Kanai, Rie Mizuno, Rumi Kaida, Sachiko Masuda, Arisa Shibata, Ken Shirasu, Atsushi J Nagano, Yoshiharu Fujii, Akifumi Sugiyama, Yuichi Aoki

{"title":"Model-guided design of defined microbial community reveals interactions underpinning plant growth and stress tolerance.","authors":"Shinichi Yamazaki, Masaru Nakayasu, Keiko Kanai, Rie Mizuno, Rumi Kaida, Sachiko Masuda, Arisa Shibata, Ken Shirasu, Atsushi J Nagano, Yoshiharu Fujii, Akifumi Sugiyama, Yuichi Aoki","doi":"10.1093/ismejo/wrag219","DOIUrl":"https://doi.org/10.1093/ismejo/wrag219","url":null,"abstract":"Defined microbial communities (DMCs; also known as SynComs) offer a promising strategy to enhance plant growth and stress tolerance by harnessing beneficial plant-associated microbes. However, the rational design and efficient exploration of complex DMC configurations remain challenging. Here, we present an interpretable model-guided framework that integrates plant phenotyping, microbial genomics, and machine learning to optimize DMC outcomes and identify microbial interactions relevant to plant performance. Using tomato as a model, we evaluated diverse DMC, temperature, and metabolite combinations in growth experiment and used a quality-controlled dataset comprising 301 plants representing 102 DMC compositions for predictive modeling. An Elastic Net regression model trained on plant biomass data and DMC composition features enabled prediction of unseen DMC outcomes, and incorporating genomic features substantially improved predictive performance, supporting the importance of functional potential in modeling community effects. We applied the model to prioritize and design improved DMCs, which were validated in laboratory assays and field trials. One model-guided DMC significantly enhanced plant growth in the field and improved heat stress tolerance under controlled conditions. Model interpretation and multi-omics analyses highlighted specific microbial interactions, including metabolite-associated relationships involving Sphingobium sp. and tomatine, that were linked to host stress-responsive gene expression. Together, our results demonstrate a scalable framework for predicting and prioritizing DMCs and identify candidate metabolite-associated microbial interactions that may contribute to plant growth promotion and abiotic stress tolerance.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148819634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Oxygen-dependent metabolism of dissolved organic matter in hypoxic marine environments. 海洋缺氧环境中溶解有机物的氧依赖性代谢。

IF 10.2 1区环境科学与生态学

ISME Journal Pub Date : 2026-08-26 DOI: 10.1093/ismejo/wrag220

Benjamin N Daniels, Sarah Wolf, Qi Chen, Fabian Wittmers, Kayla Stanley, Clare Jayawickrama, Edward W Davis, Abzer K Pakkir Shah, Craig A Carlson, Daniel Petras, Francis Chan, Stephen J Giovannoni

{"title":"Oxygen-dependent metabolism of dissolved organic matter in hypoxic marine environments.","authors":"Benjamin N Daniels, Sarah Wolf, Qi Chen, Fabian Wittmers, Kayla Stanley, Clare Jayawickrama, Edward W Davis, Abzer K Pakkir Shah, Craig A Carlson, Daniel Petras, Francis Chan, Stephen J Giovannoni","doi":"10.1093/ismejo/wrag220","DOIUrl":"https://doi.org/10.1093/ismejo/wrag220","url":null,"abstract":"Low-oxygen marine environments are dynamic hotspots where microbial activity and dissolved organic matter (DOM) cycling are altered, with implications for understanding ecosystem responses to intensifying anthropogenic pressures. The hypoxic barrier hypothesis (HBH) proposed a mechanism by which DOM cycling could be altered under hypoxia by the inhibition of non-respiratory oxidase enzymes, whereas respiration continued. To investigate oxygen-dependent changes in DOM composition and consequences of the HBH, we combined controlled mesocosm experiments with non-targeted metabolomics to identify classes of compounds that accumulate in hypoxic treatments. Many of these compounds require non-respiratory oxidase enzymes for catabolism in KEGG metabolic maps, and when tested in experiments with microbial communities, their catabolism was inhibited by hypoxia, validating the concept of oxygen-dependent dissolved organic matter (ODDOM). The identified ODDOM molecules displayed chemical characteristics associated with increased DOM stability, including increased aromaticity, carbon oxidation state, and decreased saturation. In a meta-analysis of FT-ICR-MS datasets from three oceanographic cruises that included samples collected across oxygen gradients and within oxygen minimum zone (OMZ) waters, molecules with chemical properties similar to the mesocosm-derived ODDOM accumulated within the oxycline of the North Pacific Ocean. In the mesocosm experiments, the growth of many microbial taxa was unaffected by hypoxia, and others were either stimulated or inhibited by hypoxia, suggesting unexplored complexity in microbial adaptations to oxygen concentrations in this range. These findings suggest that hypoxia can mechanistically constrain enzymatic pathways determining DOM bioavailability, with implications for microbial carbon cycling and microbial evolution in expanding ocean oxygen minimum zones.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148819988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Adaptations of gummivorous primate gut-associated bifidobacteria to type-II arabinogalactan utilisation. 粘食性灵长类肠道相关双歧杆菌对ii型阿拉伯半乳聚糖利用的适应性。

IF 10.2 1区环境科学与生态学

ISME Journal Pub Date : 2026-08-19 DOI: 10.1093/ismejo/wrag210

Yuki Sasaki, Tomoya Kozakai, Moe Inoue, Mikiyasu Sakanaka, Toshihiko Katoh, Hiroki Kaneko, Hiroo Imai, Toshitaka Odamaki, Kiyotaka Fujita, Takane Katayama

{"title":"Adaptations of gummivorous primate gut-associated bifidobacteria to type-II arabinogalactan utilisation.","authors":"Yuki Sasaki, Tomoya Kozakai, Moe Inoue, Mikiyasu Sakanaka, Toshihiko Katoh, Hiroki Kaneko, Hiroo Imai, Toshitaka Odamaki, Kiyotaka Fujita, Takane Katayama","doi":"10.1093/ismejo/wrag210","DOIUrl":"https://doi.org/10.1093/ismejo/wrag210","url":null,"abstract":"Bifidobacteria inhabiting the primate gut exhibit host-dependent genetic diversification, particularly in their gene repertoire related to carbohydrate metabolism, suggesting adaptation to host diets. However, these diverse genetic traits remain poorly associated with specific dietary components. Here, through enzymatic and genetic analyses, we demonstrate that several Bifidobacterium species residing in the gut of gummivorous primates, such as marmosets, possess previously uncharacterised pathways for the efficient utilisation of type-II arabinogalactan (AG), the major polysaccharide component of tree gums. The assimilation pathways comprises two key components: a bifunctional β-1,3-galactanase that cleaves the AG backbone via both endo- and exo-mode actions and an ATP-binding cassette transporter that internalises the released arabinogalactan oligosaccharides (AGOs) into cells. Data mining of deposited metagenomic datasets suggested that the endo/exo-β-1,3-galactanase and the AGO transporter contribute to cross-feeding interactions within Bifidobacterium communities in the gut of gummivorous primates. Our study not only highlights molecular strategies employed by certain Bifidobacterium species to adapt to the dietary habits of a host but may also inform probiotic intervention strategies for the health and welfare of these primates in captive settings.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148800945","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0