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Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab. Swedish Univ Agr Sci, Dept Aquat Sci & Assessment, Uppsala, Sweden.ORCID iD: 0000-0002-1108-6888
Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Kalmar, Sweden; Univ Granada, Dept Microbiol, Granada, Spain.
Stockholm Univ, Sci Life Lab, Natl Bioinformat Infrastruct Sweden, Dept Biochem & Biophys, Solna, Sweden.ORCID iD: 0000-0003-3053-9392
Ecole Polytech Fed Lausanne, Sch Architecture Civil & Environm Engn, Environm Engn Inst, Environm Microbiol Lab, Lausanne, Switzerland; Univ Calgary, Dept Biol Sci, Calgary, AB, 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
Microbiology
Identifiers
URN: urn:nbn:se:uu:diva-453773DOI: 10.1038/s41467-021-24549-zISI: 000675329200009PubMedID: 34253732OAI: oai:DiVA.org:uu-453773DiVA, id: diva2:1602413
Funder
Swedish Research Council, 2018-04311Swedish Research Council, 2017-04422Swedish Research Council, 2014-4398Swedish Research CouncilSwedish National Infrastructure for Computing (SNIC), b2013127Swedish National Infrastructure for Computing (SNIC), SNIC 2019/3-22Swedish National Infrastructure for Computing (SNIC), SNIC 2020/5-19Knut and Alice Wallenberg FoundationSwedish Nuclear Fuel and Waste Management Company, SKBThe Crafoord Foundation, 20180599The Crafoord Foundation, 20130557Carl Tryggers foundation , KF16: 18Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

These authors contributed equally: Maliheh Mehrshad, Margarita Lopez-Fernandez

Available from: 2021-10-12 Created: 2021-10-12 Last updated: 2024-01-15Bibliographically approved

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Mehrshad, MalihehBertilsson, Stefan

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