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Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater
Uppsala University, Sweden;Swedish University of Agricultural Science, Sweden.ORCID iD: 0000-0002-1108-6888
Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Granada, Spain. (Ctr Ecol & Evolut Microbial Model Syst EEMiS)ORCID iD: 0000-0003-3588-6676
Stockholm University, Sweden.ORCID iD: 0000-0003-3053-9392
Ecole Polytech Fed Lausanne, Switzerland;Univ Calgary, Canada.ORCID iD: 0000-0002-2064-6496
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2021 (English)In: Nature Communications, E-ISSN 2041-1723, Vol. 12, no 1, article id 4253Article in journal (Refereed) Published
Abstract [en]

While oligotrophic deep groundwaters host active microbes attuned to the low-end of the bioenergetics spectrum, the ecological constraints on microbial niches in these ecosystems and their consequences for microbiome convergence are unknown. Here, we provide a genome-resolved, integrated omics analysis comparing archaeal and bacterial communities in disconnected fracture fluids of the Fennoscandian Shield in Europe. Leveraging a dataset that combines metagenomes, single cell genomes, and metatranscriptomes, we show that groundwaters flowing in similar lithologies offer fixed niches that are occupied by a common core microbiome. Functional expression analysis highlights that these deep groundwater ecosystems foster diverse, yet cooperative communities adapted to this setting. We suggest that these communities stimulate cooperation by expression of functions related to ecological traits, such as aggregate or biofilm formation, while alleviating the burden on microorganisms producing compounds or functions that provide a collective benefit by facilitating reciprocal promiscuous metabolic partnerships with other members of the community. We hypothesize that an episodic lifestyle enabled by reversible bacteriostatic functions ensures the subsistence of the oligotrophic deep groundwater microbiome. Ecological constraints on microbial niches in oligotrophic deep groundwaters remain elusive. This study provides support for the existence of a common core microbiome in two deep groundwater biomes of the Fennoscandian Shield using a genome-resolved, integrated omics analysis.

Place, publisher, year, edition, pages
Springer Nature, 2021. Vol. 12, no 1, article id 4253
National Category
Ecology Microbiology
Research subject
Ecology, Microbiology
Identifiers
URN: urn:nbn:se:lnu:diva-106676DOI: 10.1038/s41467-021-24549-zISI: 000675329200009PubMedID: 34253732Scopus ID: 2-s2.0-85110622948Local ID: 2021OAI: oai:DiVA.org:lnu-106676DiVA, id: diva2:1590111
Available from: 2021-09-01 Created: 2021-09-01 Last updated: 2023-03-28Bibliographically approved

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Lopez-Fernandez, MargaritaSimone, DomenicoDopson, Mark

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Mehrshad, MalihehLopez-Fernandez, MargaritaSundh, JohnBell, EmmaSimone, DomenicoDopson, Mark
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