Local and Regional Diversity Reveals Dispersal Limitation and Drift as Drivers for Groundwater Bacterial Communities from a Fractured Granite Formation

Abstract

Microorganisms found in terrestrial subsurface environments make up a large proportion of the Earth’s biomass. Biogeochemical cycles catalyzed by subsurface microbes have the potential to influence the speciation and transport of radionuclides managed in geological repositories. To gain insight on factors that constrain microbial processes within a formation with restricted groundwater flow we performed a meta-community analysis on groundwater collected from multiple discrete fractures underlying the Chalk River Laboratories site (located in Ontario, Canada). Bacterial taxa were numerically dominant in the groundwater. Although these were mainly uncultured, the closest cultivated representatives were from the phenotypically diverse Betaproteobacteria, Deltaproteobacteria, Bacteroidetes, Actinobacteria, Nitrospirae, and Firmicutes. Hundreds of taxa were identified but only a few were found in abundance (>1%) across all assemblages. The remainder of the taxa were low abundance. Within an ecological framework of selection, dispersal and drift, the local and regional diversity revealed fewer taxa within each assemblage relative to the meta-community, but the taxa that were present were more related than predicted by chance. The combination of dispersion at one phylogenetic depth and clustering at another phylogenetic depth suggest both niche (dispersion) and filtering (clustering) as drivers of local assembly. Distance decay of similarity reveals apparent biogeography of 1.5 km. Beta diversity revealed greater influence of selection at shallow sampling locations while the influences of dispersal limitation and randomness were greater at deeper sampling locations. Although selection has shaped each assemblage, the spatial scale of groundwater sampling favored detection of neutral processes over selective processes. Dispersal limitation between assemblages combined with local selection means the meta-community is subject to drift, and therefore, likely reflects the differential historical events that have influenced the current bacterial composition. Categorizing the study site into smaller regions of interest of more closely spaced fractures, or of potentially hydraulically connected fractures, might improve the resolution of an analysis to reveal environmental influences that have shaped these bacterial communities.

Non‐random processes determine the colonization of groundwater sediments by microbial communities in a pristine porous aquifer

“…To date, most of the studies on ecological processes behind the assembly of microbial communities in groundwater environments have focused on planktonic communities suspended in the groundwater (Stegen et al, 2012;Beaton et al, 2016;Danczak et al, 2018), while studies on sediment-attached communities are scarce (Stegen et al, 2016b). In contrast, much insight has been gained over the past years into the assembly of sediment-attached communities in groundwater-surface water mixing zones (hyporheic zone).…”

Spatial Autocorrelation, Source Water and the Distribution of Total and Viable Microbial Abundances within a Crystalline Formation to a Depth of 800 m

“…The locations of these boreholes are shown in Figure 1 . Previous studies performed within this formation ( Stroes-Gascoyne et al, 2011 ; Beaton et al, 2016 ) showed that bacterial taxa were numerically dominant in the fracture water and that these bacteria displayed nitrogen metabolism with episodes of sulfur metabolism. This finding is akin to other crystalline subsurface environments hosting microbial communities that display metabolic activity such as nitrate, iron and sulfate reduction ( Kieft, 1990 ; Jain et al, 1997 ; Haveman et al, 1999 ; Sahl et al, 2008 ; Nyyssönen et al, 2012 ).…”

“…Hundreds of taxa were identified but only a few were found in abundance (>1%) across all 16S rRNA assemblages. A decay of phylogenetic similarity with distance up 1.5 km was evident within sampling locations separated by up to 5 km of rock ( Beaton et al, 2016 ). We propose that this decay distance is related to dispersal within vertical oriented fractures.…”

A Test in a High Altitude Lake of a Multi-Parametric Rapid Methodology for Assessing Life in Liquid Environments on Planetary Bodies: A Potential New Freshwater Polychaete Tubeworm Community

“…While groups commonly associated with sediments and soils were recovered (Bacteriodetes and Verrucomicrobia), the nitrite-oxidizing Bacteria Nitrospirae comprised >5% of the recovered sequences. These organisms are commonly associated with marine environments, though they have also been found in freshwaters (Beaton et al, 2016). The potential for sulfide oxidation in these sediments is indicated by the presence of sulfide-oxidizing Sulfurimonas and Sulfuricurvum species.…”