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

• Published in: Nature Communications
• Main Authors: Mehrshad, Maliheh, Lopez-Fernandez, Margarita, Sundh, John, Bell, Emma Ecole Polytechnique Federale Lausanne . School of Architecture, Civil and Environmental Engineering. Environmental Engineering Inst. Environmental Microbiology Lab., Simone, Domenico Linnaeus Univ., Kalmar . Centre for Ecology and Evolution in Microbial Model Systems, Swedish Univ.y of Agricultural Sciences, Uppsala . SLU Bioinformatics Infrastructure, Buck, Moritz Swedish Univ. of Agricultural Sciences, Uppsala . Dept. of Aquatic Sciences and Assessment, Bernier-Latmani, Rizlan Ecole Polytechnique Federale Lausanne . School of Architecture, Civil and Environmental Engineering. Environmental Engineering Inst. Environmental Microbiology Lab., Bertilsson, Stefan Uppsala Univ. . Dept. of Ecology and Genetics. Limnology and Science for Life Lab.; Swedish Univ. of Agricultural Sciences, Uppsala . Dept. of Aquatic Sciences and Assessment, Dopson, Mark Linnaeus Univ., Kalmar . Centre for Ecology and Evolution in Microbial Model Systems
• Language: unknown
• Published: 2021
• Subjects: 54 ENVIRONMENTAL SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; Fennoscandian
• Online Access: http://www.osti.gov/servlets/purl/1816281; https://www.osti.gov/biblio/1816281; https://doi.org/10.1038/s41467-021-24549-z

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.