ISME Journal最新文献

Model cyanobacterial consortia reveal a consistent core microbiome independent of inoculation source or cyanobacterial host species. 蓝藻菌群模型揭示了一个一致的核心微生物组独立于接种源或蓝藻宿主物种。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2025-07-08 DOI: 10.1093/ismejo/wraf142

Andreja Kust, Jackie Zorz, Catalina Cruañas Paniker, Keith Bouma-Gregson, Netravathi Krishnappa, Wendy Liu, Jillian F Banfield, Spencer Diamond

{"title":"Model cyanobacterial consortia reveal a consistent core microbiome independent of inoculation source or cyanobacterial host species.","authors":"Andreja Kust, Jackie Zorz, Catalina Cruañas Paniker, Keith Bouma-Gregson, Netravathi Krishnappa, Wendy Liu, Jillian F Banfield, Spencer Diamond","doi":"10.1093/ismejo/wraf142","DOIUrl":"https://doi.org/10.1093/ismejo/wraf142","url":null,"abstract":"Cyanobacteria are integral to biogeochemical cycles, influence climate processes, and hold promise for commercial applications. In natural habitats, they form complex consortia with other microorganisms, where interspecies interactions shape their ecological roles. Although in vitro studies of these consortia have significantly advanced our understanding, they often lack the biological replication needed for robust statistical analysis of shared microbiome features and functions. Moreover, the microbiomes of many model cyanobacterial strains, which are central to our understanding of cyanobacterial biology, remain poorly characterized. Here, we expanded on existing in vitro approaches by co-culturing five well-characterized model cyanobacterial strains with microorganisms filtered from three distinct freshwater sources, generating 108 stable consortia. Metagenomic analyses revealed that, despite host and inoculum diversity, these consortia converged on a similar set of non-cyanobacterial taxa, forming a 25-species core microbiome. The large number of stable consortia in this study enabled statistical validation of both previously observed and newly identified core microbiome functionalities in micronutrient biosynthesis, metabolite transport, and anoxygenic photosynthesis. Furthermore, core species showed significant enrichment of plasmids, and functions encoded on plasmids suggested plasmid-mediated roles in symbiotic interactions. Overall, our findings uncover the potential microbiomes recruited by key model cyanobacteria, demonstrate that laboratory-enriched consortia retain many taxonomic and functional traits observed more broadly in phototroph-heterotroph assemblages, and show that model cyanobacteria can serve as robust hosts for uncovering functional roles underlying cyanobacterial community dynamics.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144585526","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

"Paraxenoviridae", a putative family of globally distributed marine bacteriophages with double-stranded RNA genomes. “副鼻病毒科”，一个假定的全球分布的具有双链RNA基因组的海洋噬菌体家族。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2025-07-04 DOI: 10.1093/ismejo/wraf139

Mitsuhiro Yoshida, Sofia Medvedeva, Akihito Fukudome, Yuri I Wolf, Syun-Ichi Urayama, Yosuke Nishimura, Yoshihiro Takaki, Eugene V Koonin, Mart Krupovic, Takuro Nunoura

{"title":"\"Paraxenoviridae\", a putative family of globally distributed marine bacteriophages with double-stranded RNA genomes.","authors":"Mitsuhiro Yoshida, Sofia Medvedeva, Akihito Fukudome, Yuri I Wolf, Syun-Ichi Urayama, Yosuke Nishimura, Yoshihiro Takaki, Eugene V Koonin, Mart Krupovic, Takuro Nunoura","doi":"10.1093/ismejo/wraf139","DOIUrl":"10.1093/ismejo/wraf139","url":null,"abstract":"Metatranscriptome sequencing dramatically expanded the known diversity of the global RNA virome and, in particular, suggested several new candidate phyla in riboviruses. Using a double-stranded RNA (dsRNA) sequencing, here we report five complete, bisegmented RNA genomes of a putative phylum group, paraxenoviruses, identified from marine environments. Phylogenetic analysis of the RNA-directed RNA polymerases of paraxenoviruses demonstrated their affinity with the ribovirus order Durnavirales within the class Duplopiviricetes of the phylum Pisuviricota. The order Durnavirales includes families Cystoviridae that consists of well-characterized dsRNA bacteriophages and less thoroughly studied Picobirnaviridae that are also suspected to infect bacteria. Consistently, modeling and analysis of the structure of the predicted capsid protein (CP) of several paraxenoviruses revealed similarity to picobirnavirus CP although the paraxenovirus CP is much larger and contains unique structural elaborations. Taken together, these affinities suggest that paraxenoviruses represent a distinct family within Durnavirales, which we provisionally name \"Paraxenoviridae\". Both genomic segments in Picobirnaviridae and \"Paraxenoviridae\" encompass multiple open reading frames, each preceded by a typical bacterial ribosome-binding site, strongly suggesting that these families consist of bacterial viruses. Search for homologs of paraxenovirus genes shows widespread distribution of this virus group in the global ocean, suggesting a potential important contribution to marine microbial ecosystems. Our findings further expand the diversity and ecological role of the bacterial RNA virome, reveal extensive structural variability of RNA viral capsid proteins, and demonstrate the common ancestry of several distinct families of bacterial viruses with dsRNA genomes.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144561818","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

Niche creation improves bioaugmentation of an organic micropollutant degrader in oligotrophic waters. 生态位的建立提高了有机微污染物降解剂在低营养水体中的生物增强作用。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2025-07-04 DOI: 10.1093/ismejo/wraf140

Jinsong Wang, Bart Raes, Cato Debrabandere, Veerle van Aken, Sebastián Jaramillo-Toro, Steffen Waldherr, Benjamin Horemans, Dirk Springael

{"title":"Niche creation improves bioaugmentation of an organic micropollutant degrader in oligotrophic waters.","authors":"Jinsong Wang, Bart Raes, Cato Debrabandere, Veerle van Aken, Sebastián Jaramillo-Toro, Steffen Waldherr, Benjamin Horemans, Dirk Springael","doi":"10.1093/ismejo/wraf140","DOIUrl":"https://doi.org/10.1093/ismejo/wraf140","url":null,"abstract":"Bioaugmentation of sand filters is an alternative process for eliminating organic micropollutants in drinking water treatment. Bioaugmentation resembles an invasion process and niche availability is a prime determinant for successful invasion. This is particularly relevant for oligotrophic environments where organic micropollutants hardly provide a selective C-source and exploitative competition for the scarce intrinsic organic carbon exists between inoculated organic micropollutant-degraders and resident microbiota. Building on microbial invasion theories, we tested the hypothesis that the success of bioaugmentation and associated organic micropollutant degradation can be enhanced through niche creation by supplying a selective carbon source for the introduced degrader. Sand filter microbiota reduced growth of the 2,6-dichlorobenzamide degrading strain Aminobacter niigataensis MSH1 and 2,6-dichlorobenzamide degradation in different natural waters. This was counteracted by adding benzamide as a selective C-source for MSH1 resulting in a 3-fold faster 2,6-dichlorobenzamide biodegradation and a 6-fold increase in MSH1 growth. An additive biokinetic model underpredicted growth of MSH1 in the presence of sand filter microbiota suggesting that the community, despite its overall negative effect, supported MSH1 growth. Moreover, benzamide retarded 2,6-dichlorobenzamide degradation likely due to enzyme competitive inhibition. The results demonstrate the use of deliberately creating dedicated niches selective for the inoculum and the successful translation of ecological invasion theories into microbial community management, for improved bioaugmentation of complex communities.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144561828","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

Climate Warming Enhances Biodiversity and Stability of Grassland Soil Phosphorus-Cycling Microbial Communities. 气候变暖对草地土壤磷循环微生物群落多样性和稳定性的影响

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2025-06-18 DOI: 10.1093/ismejo/wraf118

Zijian Wang, I L Han, Jangho Lee, Guangyu Li, Peisheng He, Mathew T Baldwin, Jenny Kao-Kniffin, Liyou Wu, Jizhong Zhou, April Z Gu

{"title":"Climate Warming Enhances Biodiversity and Stability of Grassland Soil Phosphorus-Cycling Microbial Communities.","authors":"Zijian Wang, I L Han, Jangho Lee, Guangyu Li, Peisheng He, Mathew T Baldwin, Jenny Kao-Kniffin, Liyou Wu, Jizhong Zhou, April Z Gu","doi":"10.1093/ismejo/wraf118","DOIUrl":"https://doi.org/10.1093/ismejo/wraf118","url":null,"abstract":"Climate warming poses significant challenges to global phosphorus sustainability, an essential component of Earth biogeochemistry cycling and water-food-energy nexus. Despite the crucial role of polyphosphate-accumulating organism as key functional microbial agents in phosphorus cycling, the impacts of global climate warming on polyphosphate accumulating organism communities remain largely enigmatic. This study investigates the effects of climate warming on the taxonomic, network, and functional profiles of soil bacterial polyphosphate-accumulating organisms, leveraging fluorescence-activated cell sorting and single-cell Raman spectroscopy. Climate warming enhances both taxonomic and functional biodiversity of polyphosphate-accumulating organisms via biotic interactions and environmental filtering, with observed functionality-biodiversity relationships supporting the functional redundancy theory. Furthermore, polyphosphate-accumulating organism network complexity and stability rise under warming with strengthened positive relationships, supporting stress gradient hypothesis and the belief that complexity begets stability. Finally, polyphosphate-accumulating organisms are significantly correlated to key ecosystem functioning in carbon and phosphorus cycling under warming. Our study suggests that preserving polyphosphate-accumulating organism communities is crucial for maintaining soil ecosystem functioning and sustainable phosphorus management in a warming world and opens avenues for predicting the responses of other functional microbial groups to climate change, beneficially or maliciously.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144509221","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 patterns of Endozoicomonas within tissues of the coral Acropora loripes. 珊瑚组织内内生单胞菌的不同聚集模式。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2025-03-28 DOI: 10.1093/ismejo/wraf059

Cecilie R Gotze, Ashley M Dungan, Allison M L van de Meene, Katarina Damjanovic, Gayle K Philip, Justin Maire, Lone Høj, Linda L Blackall, Madeleine J H van Oppen

{"title":"Differential aggregation patterns of Endozoicomonas within tissues of the coral Acropora loripes.","authors":"Cecilie R Gotze, Ashley M Dungan, Allison M L van de Meene, Katarina Damjanovic, Gayle K Philip, Justin Maire, Lone Høj, Linda L Blackall, Madeleine J H van Oppen","doi":"10.1093/ismejo/wraf059","DOIUrl":"https://doi.org/10.1093/ismejo/wraf059","url":null,"abstract":"Bacteria in the genus Endozoicomonas are well-known coral symbionts commonly found as clusters within tissues of several coral species. Mapping the spatial distribution of these microbial communities is critical to gaining a holistic understanding of the potential role they may play within the coral host. This study focuses on characterizing bacterial aggregates associated with the common reef-building coral, Acropora loripes, from the central Great Barrier Reef, Australia. A conventional cultivation-based method was employed to establish a pure culture collection of 11 undescribed Endozoicomonas strains isolated from A. loripes. Subsequent 16S rRNA gene amplicon sequencing revealed their classification into two distinct phylogenetic clades. To resolve their spatial distribution in hospite, clade-specific fluorescence in situ hybridization probes were designed. Aggregates were consistently observed in the gastrodermal tissue layers surrounding the upper and lower gastrovascular cavity and were predominantly formed by cells from the same phylogenetic clade, with a minor proportion of aggregates formed by Endozoicomonas from both targeted clades. Furthermore, a clear distinction in aggregation pattern was observed; one clade exhibited clusters with regular and contained growth patterns, whereas the other formed clusters lacking clear boundaries and having irregular shapes. Scanning electron microscopy revealed the presence of a membrane of unknown origin associated with bacterial aggregates in two instances, suggesting potential structural or functional differences in these aggregates. These morphological differences highlight the importance of further investigations into the mechanisms governing bacterial aggregate formation in corals.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143744253","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

Uncertain fate of pelagic calcifying protists: a cellular perspective on a changing ocean. 远洋钙化原生生物的不确定命运：变化中的海洋的细胞视角。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2025-02-21 DOI: 10.1093/ismejo/wraf007

Adva Shemi, Assaf Gal, Assaf Vardi

{"title":"Uncertain fate of pelagic calcifying protists: a cellular perspective on a changing ocean.","authors":"Adva Shemi, Assaf Gal, Assaf Vardi","doi":"10.1093/ismejo/wraf007","DOIUrl":"https://doi.org/10.1093/ismejo/wraf007","url":null,"abstract":"Pelagic calcifying protists such as coccolithophores and foraminifera represent an important microbial component of the marine carbon cycle. Although their calcitic shells are preserved in oceanic sediments over millennia, their resilience in the future decades is uncertain. We review current literature describing the response of calcifying protists to ocean acidification and temperature warming. We examine these key ecological and biogeochemical processes through the cellular perspective, exploring the physiological, metabolic, and molecular responses of calcifying protists. Ocean acidification is a chemical process that takes place in the seawater outside the cell, whereas protists calcify inside a modified cellular microenvironment. The function of these calcification compartments depends on cellular response to ocean acidification, such as maintaining pH homeostasis. The response of calcifying protists to ocean acidification and temperature warming is species-specific, with no unifying trends but rather a range of sensitivity levels. Coccolithophores and foraminifera display physiological sensitivity that may hamper their ecological success in comparison to non-calcifying species. Yet, certain species may be more adaptable, especially when comparing to highly vulnerable calcifying molluscs as pteropods. As the molecular machinery mediating cellular calcification is not fully resolved, as well as the functional role of the calcitic shell, our ability to predict the fate of calcifying microorganisms in a warmer, more acidic ocean is limited. We propose the urgent need to expand the study of these model systems by advancing cell biology approaches, to better understand the impact of climate change on microbial food webs in the ocean.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143469740","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

Selection for toxin production in spatially structured environments increases with growth rate. 在空间结构环境中产生毒素的选择随着生长速度的增加而增加。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2025-01-02 DOI: 10.1093/ismejo/wraf061

Ave T Bisesi, Jeremy M Chacón, Michael J Smanski, Linda Kinkel, William R Harcombe

{"title":"Selection for toxin production in spatially structured environments increases with growth rate.","authors":"Ave T Bisesi, Jeremy M Chacón, Michael J Smanski, Linda Kinkel, William R Harcombe","doi":"10.1093/ismejo/wraf061","DOIUrl":"10.1093/ismejo/wraf061","url":null,"abstract":"Microbes adopt diverse strategies to successfully compete with coexisting strains for space and resources. One common strategy is the production of toxic compounds to inhibit competitors, but the strength and direction of selection for this strategy vary depending on the environment. Existing theoretical and experimental evidence suggests that growth in spatially structured environments makes toxin production more beneficial because competitive interactions are localized. Because higher growth rates reduce the length scale of interactions in structured environments, theory predicts that toxin production should be especially beneficial under these conditions. We tested this hypothesis by developing a genome-scale metabolic modeling approach and complementing it with comparative genomics to investigate the impact of growth rate on selection for costly toxin production. Our modeling approach expands the current abilities of the dynamic flux balance analysis platform Computation Of Microbial Ecosystems in Time and Space (COMETS) to incorporate signaling and toxin production. Using this capability, we find that our modeling framework predicts that the strength of selection for toxin production increases as growth rate increases. This finding is supported by comparative genomics analyses that include diverse microbial species. Our work emphasizes that toxin production is more likely to be maintained in rapidly growing, spatially structured communities, thus improving our ability to manage microbial communities and informing natural product discovery.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12041421/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143804535","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Surfactin facilitates establishment of Bacillus subtilis in synthetic communities. 表面素促进枯草芽孢杆菌在合成群落中的建立。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2025-01-02 DOI: 10.1093/ismejo/wraf013

Carlos N Lozano-Andrade, Caja Dinesen, Mario Wibowo, Nil Arenos Bach, Viktor Hesselberg-Thomsen, Scott A Jarmusch, Mikael Lenz Strube, Ákos T Kovács

{"title":"Surfactin facilitates establishment of Bacillus subtilis in synthetic communities.","authors":"Carlos N Lozano-Andrade, Caja Dinesen, Mario Wibowo, Nil Arenos Bach, Viktor Hesselberg-Thomsen, Scott A Jarmusch, Mikael Lenz Strube, Ákos T Kovács","doi":"10.1093/ismejo/wraf013","DOIUrl":"10.1093/ismejo/wraf013","url":null,"abstract":"Soil bacteria are prolific producers of a myriad of biologically active secondary metabolites. These natural products play key roles in modern society, finding use as anti-cancer agents, as food additives, and as alternatives to chemical pesticides. As for their original role in interbacterial communication, secondary metabolites have been extensively studied under in vitro conditions, revealing many roles including antagonism, effects on motility, niche colonization, signaling, and cellular differentiation. Despite the growing body of knowledge on their mode of action, biosynthesis, and regulation, we still do not fully understand the role of secondary metabolites on the ecology of the producers and resident communities in situ. Here, we specifically examine the influence of Bacillus subtilis-produced cyclic lipopeptides during the assembly of a bacterial synthetic community, and simultaneously, explore the impact of cyclic lipopeptides on B. subtilis establishment success in a synthetic community propagated in an artificial soil microcosm. We found that surfactin production facilitates B. subtilis establishment success within multiple synthetic communities. Although neither a wild type nor a cyclic lipopeptide non-producer mutant had a major impact on the synthetic community composition over time, both the B. subtilis and the synthetic community metabolomes were altered during co-cultivation. Overall, our work demonstrates the importance of surfactin production in microbial communities, suggesting a broad spectrum of action of this natural product.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11833321/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143025722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Phylogenomic resolution of marine to freshwater dinoflagellate transitions. 海洋到淡水鞭毛虫转变的系统发育分析。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2025-01-02 DOI: 10.1093/ismejo/wraf031

Mahara Mtawali, Elizabeth C Cooney, Jayd Adams, Joshua Jin, Corey C Holt, Patrick J Keeling

{"title":"Phylogenomic resolution of marine to freshwater dinoflagellate transitions.","authors":"Mahara Mtawali, Elizabeth C Cooney, Jayd Adams, Joshua Jin, Corey C Holt, Patrick J Keeling","doi":"10.1093/ismejo/wraf031","DOIUrl":"10.1093/ismejo/wraf031","url":null,"abstract":"Dinoflagellates are an abundant and diverse group of protists that inhabit aquatic environments worldwide. They are characterized by numerous unique cellular and molecular traits, and have adapted to an unusually broad range of life strategies, including phototrophy, heterotrophy, parasitism, and all combinations of these. For most microbial groups, transitions from marine to freshwater environments are relatively rare, as changes in salinity are thought to lead to significant osmotic challenges that are difficult for the cell to overcome. Recent work has shown that dinoflagellates have overcome these challenges relatively often in evolutionary time, but because this is mostly based on single gene trees with low overall support, many of the relationships between freshwater and marine groups remain unresolved. Normally, phylogenomics could clarify such conclusions, but despite the recent surge in data, virtually no freshwater dinoflagellates have been characterized at the genome-wide level. Here, we generated 30 transcriptomes from cultures and single cells collected from freshwater environments to infer a robustly supported phylogenomic tree from 217 conserved genes, resolving at least seven transitions to freshwater in dinoflagellates. Mapping the distribution of ASVs from freshwater environmental samples onto this tree confirms these groups and identifies additional lineages where freshwater dinoflagellates likely remain unsampled. We also sampled two species of Durinskia, a genus of \"dinotoms\" with both marine and freshwater lineages containing Nitzschia-derived tertiary plastids. Ribosomal RNA phylogenies show that the host cells are closely related, but their endosymbionts are likely descended from two distantly-related freshwater Nitzschia species that were acquired in parallel and relatively recently.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11937819/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143469739","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Widespread distribution of bacteria containing PETases with a functional motif across global oceans. 含有具有功能基序的petase的细菌在全球海洋中的广泛分布。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2025-01-02 DOI: 10.1093/ismejo/wraf121

Intikhab Alam, Ramona Marasco, Afaque A Momin, Nojood Aalismail, Elisa Laiolo, Cecilia Martin, Isabel Sanz-Sáez, Begoña Baltá Foix, Elisabet L Sá, Allan Kamau, Francisco J Guzmán-Vega, Tahira Jamil, Silvia G Acinas, Josep M Gasol, Takashi Gojobori, Susana Agusti, Daniele Daffonchio, Stefan T Arold, Carlos M Duarte

{"title":"Widespread distribution of bacteria containing PETases with a functional motif across global oceans.","authors":"Intikhab Alam, Ramona Marasco, Afaque A Momin, Nojood Aalismail, Elisa Laiolo, Cecilia Martin, Isabel Sanz-Sáez, Begoña Baltá Foix, Elisabet L Sá, Allan Kamau, Francisco J Guzmán-Vega, Tahira Jamil, Silvia G Acinas, Josep M Gasol, Takashi Gojobori, Susana Agusti, Daniele Daffonchio, Stefan T Arold, Carlos M Duarte","doi":"10.1093/ismejo/wraf121","DOIUrl":"10.1093/ismejo/wraf121","url":null,"abstract":"Accumulating evidence indicates that microorganisms respond to the ubiquitous plastic pollution by evolving plastic-degrading enzymes. However, the functional diversity of these enzymes and their distribution across the ocean, including the deep sea, remain poorly understood. By integrating bioinformatics and artificial intelligence-based structure prediction, we developed a structure- and function-informed algorithm to computationally distinguish functional polyethylene terephthalate-degrading enzymes (PETases) from variants lacking PETase activity (pseudo-PETase), either due to alternative substrate specificity or pseudogene origin. Through in vitro functional screening and in vivo microcosm experiments, we verified that this algorithm identified a high-confidence, searchable sequence motif for functional PETases capable of degrading PET. Metagenomic analysis of 415 ocean samples revealed 23 PETase variants, detected in nearly 80% of the samples. These PETases mainly occur between 1,000 and 2,000 m deep and at the surface in regions with high plastic pollution. Metatranscriptomic analysis further identified PETase variants that were actively transcribed by marine microorganisms. In contrast to their terrestrial counterparts-where PETases are taxonomically diverse-those in marine ecosystems were predominantly encoded and transcribed by members of the Pseudomonadales order. Our study underscores the widespread distribution of PETase-containing bacteria across carbon-limited marine ecosystems, identifying and distinguishing the PETase motif that underpins the functionality of these specialized cutinases.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12224614/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144259262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0