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Function-Based Selection of Synthetic Communities Enables Mechanistic Microbiome Studies 基于功能的合成群落选择使机械微生物组研究成为可能
The ISME Journal Pub Date : 2025-09-17 DOI: 10.1093/ismejo/wraf209
Thomas C A Hitch, Johanna Bosch, Silvia Bolsega, Charlotte Deschamps, Lucie Etienne-Mesmin, Nicole Treichel, Stephanie Blanquet-Diot, Soeren Ocvirk, Marijana Basic, Thomas Clavel
{"title":"Function-Based Selection of Synthetic Communities Enables Mechanistic Microbiome Studies","authors":"Thomas C A Hitch, Johanna Bosch, Silvia Bolsega, Charlotte Deschamps, Lucie Etienne-Mesmin, Nicole Treichel, Stephanie Blanquet-Diot, Soeren Ocvirk, Marijana Basic, Thomas Clavel","doi":"10.1093/ismejo/wraf209","DOIUrl":"https://doi.org/10.1093/ismejo/wraf209","url":null,"abstract":"Understanding the complex interactions between microbes and their environment requires robust model systems such as synthetic communities (SynComs). We developed a functionally directed approach to generate SynComs by selecting strains that encode key functions identified in metagenomes. This approach enables the rapid construction of SynComs tailored to any ecosystem. To optimize community design, we implemented genome-scale metabolic models, providing in silico evidence for cooperative strain coexistence prior to experimental validation. Using this strategy, we designed multiple host-specific SynComs, including those for the rumen, mouse, and human microbiomes. By weighting functions differentially enriched in diseased versus healthy individuals, we constructed SynComs that capture complex host-microbe interactions. We designed an inflammatory bowel disease SynCom of 10 members that successfully induced colitis in gnotobiotic IL10-/- mice, demonstrating the potential of this method to model disease-associated microbiomes. Our study establishes a framework for designing functionally representative SynComs of any microbial ecosystem, facilitating mechanistic study.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"38 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145089630","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}
引用次数: 0
Two-step localization driven by peptidoglycan hydrolase in interbacterial predation 细菌间捕食中肽聚糖水解酶驱动的两步定位
The ISME Journal Pub Date : 2025-09-16 DOI: 10.1093/ismejo/wraf208
Huihui Song, Yuxiang Zhu, Zhelin Qu, Meixue Zhu, Xindong Li, Lijia Zhao, Kunpeng Wang, Ruizhen Zhang, Lei Cui, Yuying Li, Zeran Bian, Weijia Zhang, Yiliang Chen, Liangcheng Du, Jun-Lei Wang, Xian Zhao, Lu Deng, Yan Wang
{"title":"Two-step localization driven by peptidoglycan hydrolase in interbacterial predation","authors":"Huihui Song, Yuxiang Zhu, Zhelin Qu, Meixue Zhu, Xindong Li, Lijia Zhao, Kunpeng Wang, Ruizhen Zhang, Lei Cui, Yuying Li, Zeran Bian, Weijia Zhang, Yiliang Chen, Liangcheng Du, Jun-Lei Wang, Xian Zhao, Lu Deng, Yan Wang","doi":"10.1093/ismejo/wraf208","DOIUrl":"https://doi.org/10.1093/ismejo/wraf208","url":null,"abstract":"Mechanisms of bacterial predation are crucial for revealing microbial adaptation strategies and interaction behaviors in the environment, yet they remain poorly understood. Previously, predators were reported to localize prey via specific cues. However, the process and mechanisms by which these cues, including signaling molecules, mediate predator localization remain unclear. Herein, we investigate the dynamic interaction between the predatory bacteria Lysobacter enzymogenes and its prey bacteria. By integrating genetic manipulation, transcriptomic analysis, biochemical assays, and live-cell tracking microscopy at the single-cell level, we present a novel predation strategy mediated by peptidoglycan hydrolase LssL, named peptidoglycan hydrolase-driven Prey Localization and Utilization System (phPLUS). In phPLUS, predators secrete LssL to initiate the Step I of the localization process. LssL then hydrolyzes prey and releases small molecules of glycine, which serve as signaling cues to guide the predator's directional movement and promote the Step II of localization. In turn, prey signals upregulate the expression of LssL, which synergize with type VI secretion system to ultimately mediate prey killing through a novel regulatory pathway. This study reveals a new two-step localization strategy in bacterial predation, highlighting a previously unrecognized predation process and signal regulation mechanism, and expanding our understanding of predator-prey interactions and microbial ecological dynamics.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"54 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145089631","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}
引用次数: 0
Widespread distribution of BpfA-mediated bisphenol F degradation among members of the Pseudomonadota and Actinomycetota. 双酚a介导的双酚F降解在假单胞菌和放线菌中的广泛分布。
The ISME Journal Pub Date : 2025-09-15 DOI: 10.1093/ismejo/wraf206
Mingliang Zhang,Changchang Wang,Yanni Huang,Qian Li,Junqiang Hu,Kaihua Pan,Qian Zhu,Wankui Jiang,Jiguo Qiu,Xin Yan,Qing Hong
{"title":"Widespread distribution of BpfA-mediated bisphenol F degradation among members of the Pseudomonadota and Actinomycetota.","authors":"Mingliang Zhang,Changchang Wang,Yanni Huang,Qian Li,Junqiang Hu,Kaihua Pan,Qian Zhu,Wankui Jiang,Jiguo Qiu,Xin Yan,Qing Hong","doi":"10.1093/ismejo/wraf206","DOIUrl":"https://doi.org/10.1093/ismejo/wraf206","url":null,"abstract":"Bisphenol F, a widely used primary raw material in the production of polycarbonate and epoxy resins, is frequently detected in the environment and poses significant risks to ecosystems and human health. Microorganisms play an important role in bisphenol F degradation in the natural environment; however, the genetic determinants involved remain unknown. A flavoprotein oxidase BpfA from Microbacterium sp. strain F2 was identified in this study, which is responsible for the crucial steps of bisphenol F degradation involving its conversion to 4,4'-dihydroxybenzophenone through three consecutive reactions. BpfA phylogenetically clusters within the 4-phenol oxidizing subfamily of the vanillyl alcohol oxidase/para-cresol methylhydroxylase flavoprotein family. Three homologs in this subfamily-vanillyl alcohol oxidase, eugenol oxidase, and flavoprotein oxidase-shared over 35.0% identity with BpfA and demonstrated bisphenol F-degrading activity, yet the catalytic efficiency of BpfA against bisphenol F (508.1 mM-1 s-1) was significantly higher than that of vanillyl alcohol oxidase (0.2 mM-1 s-1), eugenol oxidase (0.2 mM-1 s-1), and flavoprotein oxidase (0.3 mM-1 s-1). Structural analysis indicated that strong active site hydrophobicity was likely the reason for this high catalytic efficiency. Bioinformatics-based taxonomic profiling revealed that candidate bisphenol F degraders carrying bpfA mainly belonged to the Pseudomonadota and Actinomycetota phyla, and were predominantly found in metagenomes from cultivated land and forests. This study elucidated the function and distribution pattern of bpfA, enhancing our understanding of microbial bisphenol F degradation in the environment.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145089787","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}
引用次数: 0
Pore-Scale Mass Transfer Heterogeneity Shapes Nutrient Accessibility and Functional Assembly in Porous Microbial Ecosystems. 多孔微生物生态系统中孔隙尺度传质不均一性影响养分可及性和功能组装。
The ISME Journal Pub Date : 2025-09-12 DOI: 10.1093/ismejo/wraf205
Liming Wu,Daixiu Bao,Hui Liao,Meiyu Yan,Yitong Ge,Zinuan Han,Xiaole Xia
{"title":"Pore-Scale Mass Transfer Heterogeneity Shapes Nutrient Accessibility and Functional Assembly in Porous Microbial Ecosystems.","authors":"Liming Wu,Daixiu Bao,Hui Liao,Meiyu Yan,Yitong Ge,Zinuan Han,Xiaole Xia","doi":"10.1093/ismejo/wraf205","DOIUrl":"https://doi.org/10.1093/ismejo/wraf205","url":null,"abstract":"Porous ecosystems represent ubiquitous microbial habitats across natural settings including soil, gut tract, and food matrices, where microscale spatial architecture critically shapes microbial colonization and interactions. Yet, the mechanisms of how pore-scale physical constraints influence microbial community assembly and metabolic performance remain poorly understood. Here, we employed a microfluidic platform with tunable inter-pillar spacings, coupled with a multi-omics approach including in situ imaging, exometabolomics, metagenomics, and metatranscriptomics, to investigate how pore-size modulates microbial community dynamics. Comparing representative small (50 μm) and large (150 μm) pore-sizes, we found that larger pore-sizes promoted greater biomass accumulation and significantly enhanced exometabolite production, particularly of amino acids. Microscopy and quantitative assays revealed that 150 μm pores facilitated more efficient substrate degradation, especially of carbohydrates. Taxonomic profiling showed that increasing pore-size reduced community evenness while enhancing richness, selectively enriching carbohydrate-degrading and amino acid-producing taxa, and promoting more complex, positively correlated co-occurrence networks. Metatranscriptomic analysis further demonstrated that larger pore-size significantly upregulated key functional genes involved in substrate degradation, amino acid biosynthesis, and stress response pathways. Fluorescent tracer assays revealed pronounced mass transfer heterogeneity, where smaller pores exhibited prolonged solute persistence and steeper chemical gradients, ultimately restricting substrate availability and microbial activity. Collectively, our results reveal that alleviation of microscale spatial constraints enhances nutrient accessibility, metabolic function, and community organization in porous ecosystems, underscoring the pivotal role of physical microstructure in regulating both the taxonomic composition and functional capacity of microbial ecosystems.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"126 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145083443","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}
引用次数: 0
Biofilm lifestyle across different lineages of ammonia-oxidizing archaea. 氨氧化古菌不同谱系的生物膜生活方式。
The ISME Journal Pub Date : 2025-09-09 DOI: 10.1093/ismejo/wraf182
Maximilian Dreer,Thomas Pribasnig,Logan H Hodgskiss,Zhen-Hao Luo,Fran Pozaric,Christa Schleper
{"title":"Biofilm lifestyle across different lineages of ammonia-oxidizing archaea.","authors":"Maximilian Dreer,Thomas Pribasnig,Logan H Hodgskiss,Zhen-Hao Luo,Fran Pozaric,Christa Schleper","doi":"10.1093/ismejo/wraf182","DOIUrl":"https://doi.org/10.1093/ismejo/wraf182","url":null,"abstract":"Although ammonia-oxidizing archaea (AOA) are globally distributed in nature, growth in biofilms has been relatively little explored. Here we investigated six representatives of three different terrestrial and marine clades of AOA in a longitudinal and quantitative study for their ability to form biofilm, and studied gene expression patterns of three representatives. Although all strains grew on a solid surface, soil strains of the genera Nitrosocosmicus and Nitrososphaera exhibited the highest capacity for biofilm formation. Based on microscopic and gene expression data, two different colonization strategies could be distinguished. S-layer containing AOA (from both soil and marine habitats) initialized attachment as single cells, subsequently forming denser layers, whereas the S-layer free species of the Nitrosocosmicus clade attached as suspended aggregates to the surface and henceforth showed fastest establishment of biofilm. Transcription profiles were significantly different between planktonic and biofilm growth in all strains, and revealed individual transcriptomic responses, albeit fulfilling shared functions. In particular, the strong expression of different types of multicopper oxidases was observed in all strains suggesting modifications of their cell coats. S-layer carrying AOA each additionally expressed a set of adhesion proteins supporting attachment. Detoxification of nitrous compounds, copper acquisition as well as the expression of transcription factor B were also shared responses among biofilm producing strains. However, the majority of differentially expressed protein families was distinct among the three strains, illustrating that individual solutions have evolved for the shared growth mode of biofilm formation in AOA, probably driven by the different ecological niches.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"103 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145018214","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}
引用次数: 0
Environment-dependent mutualism–parasitism transitions in the incipient symbiosis between Tetrahymena utriculariae and Micractinium tetrahymenae 四膜虫与微膜虫共生初期的环境依赖性互寄生过渡
The ISME Journal Pub Date : 2025-09-06 DOI: 10.1093/ismejo/wraf203
Kamal Md Mostafa, Yu-Hsuan Cheng, Li-Wen Chu, Phuong-Thao Nguyen, Chien-Fu Jeff Liu, Chia-Wei Liao, Thomas Posch, Jun-Yi Leu
{"title":"Environment-dependent mutualism–parasitism transitions in the incipient symbiosis between Tetrahymena utriculariae and Micractinium tetrahymenae","authors":"Kamal Md Mostafa, Yu-Hsuan Cheng, Li-Wen Chu, Phuong-Thao Nguyen, Chien-Fu Jeff Liu, Chia-Wei Liao, Thomas Posch, Jun-Yi Leu","doi":"10.1093/ismejo/wraf203","DOIUrl":"https://doi.org/10.1093/ismejo/wraf203","url":null,"abstract":"Mutualistic endosymbiosis is a cornerstone of evolutionary innovation, enabling organisms to exploit diverse niches unavailable to individual species. However, our knowledge about the early evolutionary stage of this relationship remains limited. The association between the ciliate Tetrahymena utriculariae and its algal endosymbiont Micractinium tetrahymenae indicates an incipient stage of photoendosymbiosis. Although T. utriculariae cells rely on endosymbiotic algae to grow in low-oxygen conditions, they gradually lose the endosymbionts in oxic conditions. In this study, comparative phylogenomics revealed accelerated evolution in mitochondrial DNA and nucleus-encoded mitochondrial genes in T. utriculariae. Symbiotic cells displayed elongated mitochondria that interacted intimately with endosymbionts. Inhibition of mitochondrial fatty acid oxidation reduced host fitness but increased the endosymbiont population. Time-series transcriptomics revealed physiological fine-tuning of the host across day-night cycles, highlighting symbiosis-associated regulatory adjustments. Endosymbiotic algae downregulated photosynthesis-related genes compared with free-living cells, which correlated with reduced chlorophyll content, suggesting a shift toward host resource exploitation to compensate for diminished photosynthetic capacity. Under oxic conditions, symbiotic T. utriculariae cells exhibited lower fitness than aposymbiotic cells. Our results demonstrate that incipient endosymbioses employ mitochondrial remodeling and endosymbiont metabolic reprogramming to actively regulate transitions between mutualistic and parasitic states, revealing how symbiotic partnerships navigate environmental pressures during their incipient stage of evolutionary establishment.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"64 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145002957","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}
引用次数: 0
Net rate of lateral gene transfer in marine prokaryoplankton. 海洋原核浮游生物中基因横向转移的净速率。
The ISME Journal Pub Date : 2025-09-05 DOI: 10.1093/ismejo/wraf159
Ramunas Stepanauskas,Julia M Brown,Shayesteh Arasti,Uyen Mai,Gregory Gavelis,Maria Pachiadaki,Oliver Bezuidt,Jacob H Munson-McGee,Tianyi Chang,Steven J Biller,Paul M Berube,Siavash Mirarab
{"title":"Net rate of lateral gene transfer in marine prokaryoplankton.","authors":"Ramunas Stepanauskas,Julia M Brown,Shayesteh Arasti,Uyen Mai,Gregory Gavelis,Maria Pachiadaki,Oliver Bezuidt,Jacob H Munson-McGee,Tianyi Chang,Steven J Biller,Paul M Berube,Siavash Mirarab","doi":"10.1093/ismejo/wraf159","DOIUrl":"https://doi.org/10.1093/ismejo/wraf159","url":null,"abstract":"Lateral gene transfer is a major evolutionary process in Bacteria and Archaea. Despite its importance, lateral gene transfer quantification in nature using traditional phylogenetic methods has been hampered by the rarity of most genes within the enormous microbial pangenomes. Here, we estimated lateral gene transfer rates within the epipelagic tropical and subtropical ocean using a global, randomized collection of single amplified genomes and a non-phylogenetic computational approach. By comparing the fraction of shared genes between pairs of genomes against a lateral gene transfer-free model, we show that an average cell line laterally acquires and retains ~13% of its genes every 1 million years. This translates to a net lateral gene transfer rate of ~250 genes L-1 seawater day-1 and involves both \"flexible\" and \"core\" genes. Our study indicates that whereas most genes are exchanged among closely related cells, the range of lateral gene transfer exceeds the contemporary definition of bacterial species, thus providing prokaryoplankton with extensive genetic resources for lateral gene transfer-based adaptation to environmental stressors. This offers an important starting point for the quantitative analysis of lateral gene transfer in natural settings and its incorporation into evolutionary and ecosystem studies and modeling.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"24 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144995771","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}
引用次数: 0
Colonization history of snow algae on Hawai'i Island. 雪藻在夏威夷岛上的殖民历史。
The ISME Journal Pub Date : 2025-09-05 DOI: 10.1093/ismejo/wraf197
Takahiro Segawa,Nozomu Takeuchi,Ryo Matsuzaki,Takahiro Yonezawa,Kenji Yoshikawa
{"title":"Colonization history of snow algae on Hawai'i Island.","authors":"Takahiro Segawa,Nozomu Takeuchi,Ryo Matsuzaki,Takahiro Yonezawa,Kenji Yoshikawa","doi":"10.1093/ismejo/wraf197","DOIUrl":"https://doi.org/10.1093/ismejo/wraf197","url":null,"abstract":"Red-pigmented snow algae are cold-adapted (including cryophilic) photosynthetic microbes commonly found in polar and alpine snowpacks worldwide, but their dispersal across isolated cryospheres remains poorly understood. We report the occurrence of snow algae on Maunakea, Hawai'i, the most isolated cryosphere in the world, during an unusually prolonged summer snow retention event in 2023 associated with La Niña conditions. Red-pigmented algal cells were observed in snow samples collected during this event. ITS2 amplicon sequencing identified two major Chlorophyta groups: the cosmopolitan Sanguina group and the endemic Chloromonadinia snow group. The cosmopolitan Sanguina group disperses into Hawai'i from other cryospheres under present climate conditions, whereas the endemic Chloromonadinia assemblage shows multiple arrivals, with the largest Hawaiian clade indicating colonization between approximately 253 and 130 ka, overlapping the Pohakuloa glaciation (MIS 6) when Maunakea's summit was ice-capped. This study shows how specific climate conditions, such as glaciation, provided long-term habitats that enabled the establishment of distinct snow algae lineages, highlighting the timing and processes of their dispersal as shaped by glaciation and climate change.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"33 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144995769","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}
引用次数: 0
Retention of a SulP-family bicarbonate transporter in a periplasmic N2-fixing cyanobacterial endosymbiont of an open ocean diatom. sulp家族碳酸氢盐转运体在开放海洋硅藻的质周固定n2的蓝藻内共生体中的保留。
The ISME Journal Pub Date : 2025-09-04 DOI: 10.1093/ismejo/wraf202
Mercedes Nieves-Morión,Rubén Romero-García,Sepehr Bardi,Luis López-Maury,Martin Hagemann,Enrique Flores,Rachel A Foster
{"title":"Retention of a SulP-family bicarbonate transporter in a periplasmic N2-fixing cyanobacterial endosymbiont of an open ocean diatom.","authors":"Mercedes Nieves-Morión,Rubén Romero-García,Sepehr Bardi,Luis López-Maury,Martin Hagemann,Enrique Flores,Rachel A Foster","doi":"10.1093/ismejo/wraf202","DOIUrl":"https://doi.org/10.1093/ismejo/wraf202","url":null,"abstract":"Symbioses between diatoms and the N2-fixing, heterocyst-forming cyanobacterium Richelia spp. are widespread and contribute to primary production. Unique to these symbioses is a variation in the symbiont location: one lives in the host cytoplasm (endobiont) vs. residing between the host frustule and plasmalemma (periplasmic endobiont). Both partners are photosynthetic, yet how the partners acquire, share, or compete for bicarbonate necessary for their photosynthesis is unknown. The genomes of both endobionts (ReuHH01 and RintRC01, respectively) contain genes encoding SulP-family proteins, which are oxyanion transporters. To study the possible involvement of these transporters in bicarbonate uptake, we used complementation in a Synechocystis sp. PCC 6803 mutant that is unable to grow at air levels of CO2 because all five of its inorganic carbon uptake systems have been inactivated. Of the five genes tested, only one (RintRC_3892) from the periplasmic endobiont complemented the mutant to grow with air levels of CO2 or at low bicarbonate concentrations. The complemented strain showed strong sodium-dependent and low-affinity bicarbonate uptake that was consistent with bicarbonate concentrations expected in the diatom periplasm. Additionally, all the amino acids involved in the bicarbonate binding site of BicA from Synechocystis sp. PCC 6803 are conserved in RintRC_3892. Finally, the importance of the RintRC_3892 protein was confirmed by the consistent detection of its transcripts in wild Richelia populations from three different oceans. Combined our results showed no evidence for a bicarbonate transporter in the cytoplasmic endobiont, whereas the periplasmic endobiont has retained a SulP-type bicarbonate transporter for its own photosynthesis.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"59 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144962774","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}
引用次数: 0
Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda 趋同的肠道微生物功能策略推动了熊科物种的能量代谢适应,挑战了大熊猫的独特性
The ISME Journal Pub Date : 2025-09-03 DOI: 10.1093/ismejo/wraf201
Tingbei Bo, Xiaoming Xu, He Liu, Liqiu Tang, Haihong Xu, Siqi Zhao, Jinzhen Lv, Dehua Wang
{"title":"Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda","authors":"Tingbei Bo, Xiaoming Xu, He Liu, Liqiu Tang, Haihong Xu, Siqi Zhao, Jinzhen Lv, Dehua Wang","doi":"10.1093/ismejo/wraf201","DOIUrl":"https://doi.org/10.1093/ismejo/wraf201","url":null,"abstract":"The gut microbiota is a key regulator of host energy metabolism, but its role in seasonal adaptation and evolution of bears is still unclear. Although giant pandas are considered an extraordinary member of the Ursidae family due to their specialized herbivory and low metabolic rate, there is still controversy over whether the metabolic regulation mechanism of their gut microbiota is unique. This study analyzed the seasonal dynamics of gut microbiota in giant pandas (Ailuropoda melanoleuca), Asian black bears (Ursus thibetanus), brown bears (Ursus arctos), and polar bears (Ursus maritimus), and combined with fecal microbiota transplantation (FMT) experiments, revealed the following findings. The microbial composition of the four bear species is similar, with both Firmicutes and Proteobacteria dominating. The enrichment of Firmicutes in winter enhances lipid metabolism, and adapts to dietary differences, indicating the existence of convergent microbial functional strategies in the Ursidae family. Our results demonstrate that bear gut microbiota promoted seasonal adaptation. In FMT experiments, bear gut microbiota in winter may had stronger functional capabilities on regulating host energy metabolism in mice, and regulate host appetite to increase energy intake. Finally, despite feeding on bamboo, giant pandas microbiota driven energy metabolism pathways (such as SCFAs) are highly conserved compared to other bears, suggesting a deep commonality in the adaptability of bear microbiota in evolution. Therefore, this study challenges the traditional view of microbial uniqueness of giant pandas, and emphasizes the co-evolutionary mechanism of energy metabolism adaptation in bear animals through microbial plasticity. In the future, it is necessary to integrate wild samples to eliminate the interference of captive diet and further analyze the genetic basis of host gut microbiota interactions.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144930772","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}
引用次数: 0
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