Abstract
Natural microbial communities consist of a limited number of abundant species and an extraordinarily diverse population of rare species referred to as the rare biosphere. Recent studies have revealed that the rare biosphere is not merely an inactive dormant population but may play substantial functional roles in the ecosystem. However, structure, activity and community assembly processes of the rare biosphere are poorly understood. In this study, we evaluated the present and living microbial community structures including rare populations in an aquifer ecosystem, the Mahomet Aquifer, USA, by both 16S rDNA and rRNA amplicon deep sequencing. The 13 groundwater samples formed three distinct groups based on the “entire” community structure, and the same grouping was obtained when focusing on the “rare” subcommunities (<0.1% of total abundance), while the “abundant” subcommunities (>1.0%) gave a different grouping. In the correlation analyses, the observed grouping pattern is associated with several geochemical factors, and structures of not only the entire community but also the rare subcommunity are correlated with geochemical profiles in the aquifer ecosystem. Our findings first indicate that the living rare biosphere in the aquifer system has the metabolic potential to adapt to local geochemical factors which dictate the community assembly processes.
Highlights
Enormous species diversity is a key feature of natural microbial communities and the origin of diversity and its contribution to community function have been central issues of microbial ecology
The objective of this study was to gain insights into the community assembly processes of the rare biosphere as well as the abundant biosphere by (1) clarifying the living microbial community structure including taxa having less than 0.1% of total abundance, (2) obtaining the habitat geochemical information, and (3) evaluating the contribution of various geochemical variables to the community differentiation by correlation analyses
Proteobacterial classes, Nitrospira and Clostridia were observed to dominate as was seen for the rare subcommunity (Fig. 2B; Betaproteobacteria [20%; abundance in total bacterial population], Deltaproteobacteria [16%], Nitrospira [11%], Gammaproteobacteria [10%], Alphaproteobacteria [6%], and Clostridia [6%])
Summary
Enormous species diversity is a key feature of natural microbial communities and the origin of diversity and its contribution to community function have been central issues of microbial ecology. The objective of this study was to gain insights into the community assembly processes of the rare biosphere as well as the abundant biosphere by (1) clarifying the living microbial community structure (rRNA-based amplicon sequencing) including taxa having less than 0.1% of total abundance, (2) obtaining the habitat geochemical information, and (3) evaluating the contribution of various geochemical variables to the community differentiation by correlation analyses. To this end we investigated the bacterial and archaeal community diversity and geochemistry of a subsurface groundwater ecosystem. The relationship between groundwater geochemical profiles and microbial community compositions was evaluated to identify key parameters involving the community assembly process for both the entire community and the rare subcommunity
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