Patterns of in situ Mineral Colonization by Microorganisms in a ~60°C Deep Continental Subsurface Aquifer

Abstract

The microbial ecology of the deep biosphere is difficult to characterize, owing in part to sampling challenges and poorly understood response mechanisms to environmental change. Pre-drilled wells, including oil wells or boreholes, offer convenient access, but sampling is frequently limited to the water alone, which may provide only a partial view of the native diversity. Mineral heterogeneity demonstrably affects colonization by deep biosphere microorganisms, but the connections between the mineral-associated and planktonic communities remain unclear. To understand the substrate effects on microbial colonization and the community response to changes in organic carbon, we conducted an 18-month series of in situ experiments in a warm (57°C), anoxic, fractured carbonate aquifer at 752 m depth using replicate open, screened cartridges containing different solid substrates, with a proteinaceous organic matter perturbation halfway through this series. Samples from these cartridges were analyzed microscopically and by Illumina (iTag) 16S rRNA gene libraries to characterize changes in mineralogy and the diversity of the colonizing microbial community. The substrate-attached and planktonic communities were significantly different in our data, with some taxa (e.g., Candidate Division KB-1) rare or undetectable in the first fraction and abundant in the other. The substrate-attached community composition also varied significantly with mineralogy, such as with two Rhodocyclaceae OTUs, one of which was abundant on carbonate minerals and the other on silicic substrates. Secondary sulfide mineral formation, including iron sulfide framboids, was observed on two sets of incubated carbonates. Notably, microorganisms were attached to the framboids, which were correlated with abundant Sulfurovum and Desulfotomaculum sp. sequences in our analysis. Upon organic matter perturbation, mineral-associated microbial diversity differences were temporarily masked by the dominance of putative heterotrophic taxa in all samples, including OTUs identified as Caulobacter, Methyloversatilis, and Pseudomonas. Subsequent experimental deployments included a methanogen-dominated stage (Methanobacteriales and Methanomicrobiales) 6 months after the perturbation and a return to an assemblage similar to the pre-perturbation community after 9 months. Substrate-associated community differences were again significant within these subsequent phases, however, demonstrating the value of in situ time course experiments to capture a fraction of the microbial assemblage that is frequently difficult to observe in pre-drilled wells.

Depth wide distribution and metabolic potential of chemolithoautotrophic microorganisms reactivated from deep continental granitic crust underneath the Deccan Traps at Koyna, India

“…It was observed that microbial communities were clustered based on depth rather than the enrichment substrates (HC or BC). Stress was found to be ≤0.06 which indicated good fit of ordination ( Dexter et al, 2018 ; Mullin et al, 2020 ). The partitioning was observed clearly in between the two halves of the plot.…”

Evolutionary stasis of a deep subsurface microbial lineage

“…With the exception of several reads present in seafloor sediments near a methane seep off the coast of Oregon [ 66 ] and one read in Guaymas Basin sediment [ 67 ], all reads were found in samples from continental or island subsurface sites 400–1200 m deep (Table S 8 ). Most of the reads originated from a Pleistocene basaltic aquifer in Iceland [ 68 , 69 ]; an additional location in the same Paleozoic dolomite aquifer accessed by BLM1 and in the overlying Miocene volcanic units in Nevada [ 20 ]; in Neogene-Paleogene and Cretaceous gas reservoirs in Japan [ 70 , 71 ]; and in Upper Cretaceous coal bed gas reservoirs in Alberta, Canada [ 72 , 73 ]. A single CDA sequence read originated from a biofilm in an anaerobic geothermal reactor in Denmark; which could have originated from subsurface geothermal water that supplied the facility [ 74 ].…”

“…Physical parameters (temperature, dissolved O 2 , conductivity, and oxidation/reduction potential were obtained using an Idronaut Sonde (GeoVista, UK). The BLM1 water samples for chemistry and other measurements were collected and analyzed as described elsewhere [ 20 ]. Samples from Byelii Yar borehole 1-R (BY-1R) were collected on April 30, 2016 (Fig.…”

Microbial diversity and community dynamics in an active, high CO2subsurface rift ecosystem

“…We found this section of the subsurface to be particularly enriched in microaerophilic or facultative anaerobic heterotrophs of the genera Pseudomonas and Alshewanella. While both these taxa have been identified in various subsurface settings, including hydrocarbon environments, drill cores and deep groundwater [41,[64][65][66], closer phylogenetic evaluation suggested these taxa to be closely related to strains associated with surface water bodies. Elevated concentration of anion (sulfate) and cations (sodium and calcium) in these sediment layers further emphasize this area to diverge from the surrounding subsurface.…”