Functional redundancy and metabolic flexibility of microbial communities in two Mid-Atlantic bays

13 pages, 7 figures, 1 table, supplementary material https://doi.org/10.1093/ismeco/ycag021.-- Data availability: The metagenomes, metatranscriptomes, and MAGs are available in NCBI under the umbrella project PRJNA432171. All the detailed codes and calculations are available on our GitHub page: http...

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Detalles Bibliográficos
Autores: John, Jojy, Ortiz, Maximiliano, Ramond, Pierre, Campbell, Barbara J.
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2026
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:dnet:digitalcsic_::b31fea67226bf5b7c04500cf274833b3
Acceso en línea:http://hdl.handle.net/10261/430653
Access Level:acceso abierto
Palabra clave:Estuarine microbiome
Metabolic flexibility
Metagenome assembled genomes
Metatranscriptomics
Microbial functional redundancy
http://metadata.un.org/sdg/14
Conserve and sustainably use the oceans, seas and marine resources for sustainable development
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spelling Functional redundancy and metabolic flexibility of microbial communities in two Mid-Atlantic baysJohn, JojyOrtiz, MaximilianoRamond, PierreCampbell, Barbara J.Estuarine microbiomeMetabolic flexibilityMetagenome assembled genomesMetatranscriptomicsMicrobial functional redundancyhttp://metadata.un.org/sdg/14Conserve and sustainably use the oceans, seas and marine resources for sustainable development13 pages, 7 figures, 1 table, supplementary material https://doi.org/10.1093/ismeco/ycag021.-- Data availability: The metagenomes, metatranscriptomes, and MAGs are available in NCBI under the umbrella project PRJNA432171. All the detailed codes and calculations are available on our GitHub page: https://github.com/Campbelllab-bioinfo under FRed-and-metabolic-flexibility-of-estuarine-microbiomeFunctional redundancy (FRed) is expected to buffer ecosystems against change, yet it has rarely been characterized in natural systems. How changes in microbial metabolisms, activity, and FRed in ecosystems are influenced by temporal, spatial, and environmental patterns is especially unclear. Here, we analyzed paired metagenomic and metatranscriptomic datasets from surface water samples collected in the Chesapeake and Delaware Bays, USA. These adjacent estuaries experience similar climatic conditions but differ in nutrient availability, salinity, and other environmental factors. We reconstructed 345 high quality metagenome assembled genomes and assessed their metabolic flexibility, and the extent of gene encoded (potential) and expressed (realized) FRed as a function of environmental drivers, microbial lifestyle (free living vs. particle attached), and gene function. The microbiomes exhibited high metabolic flexibility, reflecting their potential, and in many cases, realized gene expression, to exploit diverse energy sources, ranging from organic carbon substrates to trace gases. Potential and expressed FRed varied across seasons, lifestyles, and gene functions, and was structured within each bay by environmental factors such as temperature, salinity, and concentrations of phosphate, silicate, and chlorophyll a. These findings highlight variability in community-level metabolism, and FRed across estuarine microbiomes, shaped by environmental conditions, seasonality, and lifestyle, and provide insights into how these communities may respond to future perturbationsThe research cruises were supported by a National Science Foundation grant (OCE-082546) to B.J.C. Metagenomic, and metatranscriptomic sequencing was supported by a DOE/JGI grant (CSP-1621) to B.J.C. A National Science Foundation grant (EF-2025541) to B.J.C. supported data processingThis work contributes to the Institut de Ciències del Mar "Severo Ochoa Centre of Excellence" accreditation CEX2024-001494-S funded by AEI 10.13039/501100011033 of the Spanish Ministry of Science and InnovationPeer reviewedOxford University PressAgencia Estatal de Investigación (España)National Science Foundation (US)Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202620262026info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/430653reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Ingléshttps://doi.org/10.1093/ismeco/ycag021Síinfo:eu-repo/semantics/openAccessoai:dnet:digitalcsic_::b31fea67226bf5b7c04500cf274833b32026-05-22T06:33:51Z
dc.title.none.fl_str_mv Functional redundancy and metabolic flexibility of microbial communities in two Mid-Atlantic bays
title Functional redundancy and metabolic flexibility of microbial communities in two Mid-Atlantic bays
spellingShingle Functional redundancy and metabolic flexibility of microbial communities in two Mid-Atlantic bays
John, Jojy
Estuarine microbiome
Metabolic flexibility
Metagenome assembled genomes
Metatranscriptomics
Microbial functional redundancy
http://metadata.un.org/sdg/14
Conserve and sustainably use the oceans, seas and marine resources for sustainable development
title_short Functional redundancy and metabolic flexibility of microbial communities in two Mid-Atlantic bays
title_full Functional redundancy and metabolic flexibility of microbial communities in two Mid-Atlantic bays
title_fullStr Functional redundancy and metabolic flexibility of microbial communities in two Mid-Atlantic bays
title_full_unstemmed Functional redundancy and metabolic flexibility of microbial communities in two Mid-Atlantic bays
title_sort Functional redundancy and metabolic flexibility of microbial communities in two Mid-Atlantic bays
dc.creator.none.fl_str_mv John, Jojy
Ortiz, Maximiliano
Ramond, Pierre
Campbell, Barbara J.
author John, Jojy
author_facet John, Jojy
Ortiz, Maximiliano
Ramond, Pierre
Campbell, Barbara J.
author_role author
author2 Ortiz, Maximiliano
Ramond, Pierre
Campbell, Barbara J.
author2_role author
author
author
dc.contributor.none.fl_str_mv Agencia Estatal de Investigación (España)
National Science Foundation (US)
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Estuarine microbiome
Metabolic flexibility
Metagenome assembled genomes
Metatranscriptomics
Microbial functional redundancy
http://metadata.un.org/sdg/14
Conserve and sustainably use the oceans, seas and marine resources for sustainable development
topic Estuarine microbiome
Metabolic flexibility
Metagenome assembled genomes
Metatranscriptomics
Microbial functional redundancy
http://metadata.un.org/sdg/14
Conserve and sustainably use the oceans, seas and marine resources for sustainable development
description 13 pages, 7 figures, 1 table, supplementary material https://doi.org/10.1093/ismeco/ycag021.-- Data availability: The metagenomes, metatranscriptomes, and MAGs are available in NCBI under the umbrella project PRJNA432171. All the detailed codes and calculations are available on our GitHub page: https://github.com/Campbelllab-bioinfo under FRed-and-metabolic-flexibility-of-estuarine-microbiome
publishDate 2026
dc.date.none.fl_str_mv 2026
2026
2026
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/430653
url http://hdl.handle.net/10261/430653
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv https://doi.org/10.1093/ismeco/ycag021
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
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repository.mail.fl_str_mv
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