Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater

Maliheh Mehrshad (), Margarita Lopez-Fernandez (), John Sundh, Emma Bell, Domenico Simone, Moritz Buck, Rizlan Bernier-Latmani, Stefan Bertilsson and Mark Dopson
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Maliheh Mehrshad: Uppsala University
Margarita Lopez-Fernandez: Linnaeus University
John Sundh: Stockholm University
Emma Bell: Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne
Domenico Simone: Linnaeus University
Moritz Buck: Swedish University of Agricultural Sciences
Rizlan Bernier-Latmani: Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne
Stefan Bertilsson: Uppsala University
Mark Dopson: Linnaeus University

Nature Communications, 2021, vol. 12, issue 1, 1-12

Abstract: Abstract 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.

Date: 2021
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DOI: 10.1038/s41467-021-24549-z

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