Mutualism breakdown underpins evolutionary rescue in an obligate cross-feeding bacterial consortium

The full dataset used in this study is available on GitHub at https://github.com/ignamel/ER_mutualism.git and on Zenodo at https://doi.org/10.5281/zenodo.1499267063. All raw sequencing data is available on the US National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under...

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Detalhes bibliográficos
Autores: Melero-Jiménez, Ignacio J., Sorokin, Yael, Merlin, Ami, Li, Jiawei, Couce, Alejandro, Friedman, Jonathan
Formato: artículo
Estado:Versión publicada
Fecha de publicación:2025
País:España
Recursos:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/395007
Acesso em linha:http://hdl.handle.net/10261/395007
https://api.elsevier.com/content/abstract/scopus_id/105002967030
Access Level:acceso abierto
Palavra-chave:Bacterial evolution
Escherichia coli
Experimental evolution
Microbial ecology
Symbiosis
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dc.title.none.fl_str_mv Mutualism breakdown underpins evolutionary rescue in an obligate cross-feeding bacterial consortium
title Mutualism breakdown underpins evolutionary rescue in an obligate cross-feeding bacterial consortium
spellingShingle Mutualism breakdown underpins evolutionary rescue in an obligate cross-feeding bacterial consortium
Melero-Jiménez, Ignacio J.
Bacterial evolution
Escherichia coli
Experimental evolution
Microbial ecology
Symbiosis
title_short Mutualism breakdown underpins evolutionary rescue in an obligate cross-feeding bacterial consortium
title_full Mutualism breakdown underpins evolutionary rescue in an obligate cross-feeding bacterial consortium
title_fullStr Mutualism breakdown underpins evolutionary rescue in an obligate cross-feeding bacterial consortium
title_full_unstemmed Mutualism breakdown underpins evolutionary rescue in an obligate cross-feeding bacterial consortium
title_sort Mutualism breakdown underpins evolutionary rescue in an obligate cross-feeding bacterial consortium
dc.creator.none.fl_str_mv Melero-Jiménez, Ignacio J.
Sorokin, Yael
Merlin, Ami
Li, Jiawei
Couce, Alejandro
Friedman, Jonathan
author Melero-Jiménez, Ignacio J.
author_facet Melero-Jiménez, Ignacio J.
Sorokin, Yael
Merlin, Ami
Li, Jiawei
Couce, Alejandro
Friedman, Jonathan
author_role author
author2 Sorokin, Yael
Merlin, Ami
Li, Jiawei
Couce, Alejandro
Friedman, Jonathan
author2_role author
author
author
author
author
dc.contributor.none.fl_str_mv Israel Science Foundation
Agencia Estatal de Investigación (España)
Comunidad de Madrid
Universidad de Málaga
European Commission
Melero-Jiménez, Ignacio J. [0000-0003-1570-3828]
Couce, Alejandro [0000-0002-4153-6018]
Friedman, Jonathan [0000-0001-8476-8030]
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Bacterial evolution
Escherichia coli
Experimental evolution
Microbial ecology
Symbiosis
topic Bacterial evolution
Escherichia coli
Experimental evolution
Microbial ecology
Symbiosis
description The full dataset used in this study is available on GitHub at https://github.com/ignamel/ER_mutualism.git and on Zenodo at https://doi.org/10.5281/zenodo.1499267063. All raw sequencing data is available on the US National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under BioProject PRJNA1143481 (http://www.ncbi.nlm.nih.gov/bioproject/1143481). Source data are provided as a Source Data file. Source data are provided with this paper.
publishDate 2025
dc.date.none.fl_str_mv 2025
2025
2025
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url http://hdl.handle.net/10261/395007
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dc.language.none.fl_str_mv Inglés
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info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2022-142857NB-I00
2019-T1/BIO−12882
2023-5 A/BIO-28940
Melero-Jiménez, Ignacio J.; Sorokin, Yael; Merlin, Ami; Li, Jiawei; Couce, Alejandro; Friedman, Jonathan; 2025; Code and data for the article titled "Mutualism breakdown underpins evolutionary rescue in an obligate cross-feeding bacterial consortium" (v.1.0.0) [Dataset]; Zenodo; https://doi.org/10.5281/zenodo.14992670
https://github.com/ignamel/ER_mutualism.git
https://doi.org/10.1038/s41467-025-58742-1
Sí
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dc.publisher.none.fl_str_mv Nature Publishing Group
publisher.none.fl_str_mv Nature Publishing Group
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
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spelling Mutualism breakdown underpins evolutionary rescue in an obligate cross-feeding bacterial consortiumMelero-Jiménez, Ignacio J.Sorokin, YaelMerlin, AmiLi, JiaweiCouce, AlejandroFriedman, JonathanBacterial evolutionEscherichia coliExperimental evolutionMicrobial ecologySymbiosisThe full dataset used in this study is available on GitHub at https://github.com/ignamel/ER_mutualism.git and on Zenodo at https://doi.org/10.5281/zenodo.1499267063. All raw sequencing data is available on the US National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under BioProject PRJNA1143481 (http://www.ncbi.nlm.nih.gov/bioproject/1143481). Source data are provided as a Source Data file. Source data are provided with this paper.The Python 3.11.9 code used for analyzing, and creating figures is open-source and available on GitHub (https://github.com/ignamel/ER_mutualism.git) and stored at https://doi.org/10.5281/zenodo.1499267063.Populations facing lethal environmental change can escape extinction through rapid genetic adaptation, a process known as evolutionary rescue. Despite extensive study, evolutionary rescue is largely unexplored in mutualistic communities, where it is likely constrained by the less adaptable partner. Here, we explored empirically the likelihood, population dynamics, and genetic mechanisms underpinning evolutionary rescue in an obligate mutualism involving cross-feeding of amino acids between auxotrophic Escherichia coli strains. We found that over 80% of populations overcame a severe decline when exposed to two distinct types of abrupt, lethal stress. Of note, in all cases only one of the strains survived by metabolically bypassing the auxotrophy. Crucially, the mutualistic consortium exhibited greater sensitivity to both stressors than a prototrophic control strain, such that reversion to autonomy was sufficient to alleviate stress below lethal levels. This sensitivity was common across other stresses, suggesting it may be a general feature of amino acid–dependent obligate mutualisms. Our results reveal that evolutionary rescue may depend critically on the specific genetic and physiological details of the interacting partners, adding rich layers of complexity to the endeavor of predicting the fate of microbial communities facing intense environmental deterioration.We thank Valeria Tsvichenko and Rotem Shner for the laboratory assistance, and members of the Friedman lab and Couce lab for helpful discussions. JF was supported by the Israel Science Foundation (grant No. 883/22). AC supported by the Agencia Estatal de Investigación (Centros de Excelencia “Severo Ochoa”, SEV-2016-0672 and CEX2020-000999-S; Proyectos de I+D+i, PID2022-142857NB-I00), and a Comunidad de Madrid “Talento” Fellowship (2019-T1/BIO−12882, 2023-5 A/BIO-28940). IJMJ was supported by “Margarita Salas” post-doctoral Fellowship (MS2021_003, Universidad de Málaga, Unión Europea–NextGeneration EU, Ministerio de Universidades, Spain).With funding form the Spanish government through the "Severa Ochoa Centre of Excellence" accreditation (CEX2020-000999-S).Peer reviewedNature Publishing GroupIsrael Science FoundationAgencia Estatal de Investigación (España)Comunidad de MadridUniversidad de MálagaEuropean CommissionMelero-Jiménez, Ignacio J. [0000-0003-1570-3828]Couce, Alejandro [0000-0002-4153-6018]Friedman, Jonathan [0000-0001-8476-8030]Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202520252025info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10261/395007https://api.elsevier.com/content/abstract/scopus_id/105002967030reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/AEI//CEX2020-000999-Sinfo:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2022-142857NB-I002019-T1/BIO−128822023-5 A/BIO-28940Melero-Jiménez, Ignacio J.; Sorokin, Yael; Merlin, Ami; Li, Jiawei; Couce, Alejandro; Friedman, Jonathan; 2025; Code and data for the article titled "Mutualism breakdown underpins evolutionary rescue in an obligate cross-feeding bacterial consortium" (v.1.0.0) [Dataset]; Zenodo; https://doi.org/10.5281/zenodo.14992670https://github.com/ignamel/ER_mutualism.githttps://doi.org/10.1038/s41467-025-58742-1Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3950072026-05-22T06:33:51Z
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