A global perspective on microbial diversity in the terrestrial deep subsurface

Abstract

SummaryWhile recent efforts to catalogue Earth’s microbial diversity have focused upon surface and marine habitats, 12% to 20% of Earth’s bacterial and archaeal biomass is suggested to inhabit the terrestrial deep subsurface, compared to ∼1.8% in the deep subseafloor1–3. Metagenomic studies of the terrestrial deep subsurface have yielded a trove of divergent and functionally important microbiomes from a range of localities4–6. However, a wider perspective of microbial diversity and its relationship to environmental conditions within the terrestrial deep subsurface is still required. Here, we show the diversity of bacterial communities in deep subsurface groundwater is controlled by aquifer lithology globally, by using 16S rRNA gene datasets collected across five countries on two continents and from fifteen rock types over the past decade. Furthermore, our meta-analysis reveals that terrestrial deep subsurface microbiota are dominated by Betaproteobacteria, Gammaproteobacteria and Firmicutes, likely as a function of the diverse metabolic strategies of these taxa. Despite this similarity, evidence was found not only for aquifer-specific microbial communities, but also for a common small consortium of prevalent Betaproteobacteria and Gammaproteobacterial OTUs across the localities. This finding implies a core terrestrial deep subsurface community, irrespective of aquifer lithology, that may play an important role in colonising and sustaining microbial habitats in the deep terrestrial subsurface. Anin-silicocontamination-aware approach to analysing this dataset underscores the importance of downstream methods for assuring that robust conclusions can be reached from deep subsurface-derived sequencing data. Understanding the global panorama of microbial diversity and ecological dynamics in the deep terrestrial subsurface provides a first step towards understanding the role of microbes in global subsurface element and nutrient cycling.

Microbial Diversity Under the Influence of Natural Gas Storage in a Deep Aquifer

“…Almost half of the cultivable sulfate reducers (0.9·10 1 cells.ml −1 ) could be related to Peptococcaceae because of their capacity to sporulate and develop in sulfate-reducing conditions ( Table 2 ). The presence of the microorganisms identified during this study is consistent with other studies relating to various deep continental environments, in particular deep aquifers ( Basso et al, 2009 ; Mu et al, 2014 ; Frank et al, 2016 ; Kadnikov et al, 2017 ; Gulliver et al, 2019 ; Karnachuk et al, 2019 ; Soares et al, 2019 ; Stemple et al, 2021 ). However, the discovery of several taxa of bacteria associated with aerobic or nitrate-reducing metabolism identified here does not seem to be compatible with what we currently know about the physicochemical conditions of deep aquifers.…”

Microbial diversity of drilling fluids from 3000 m deep Koyna pilot borehole provides insights into the deep biosphere of continental earth crust

“…Unique OTUs (top 10) of sample DF6 exhibited close lineage with Marinilactibacillus piezotollerans, which is a known peizotolerant bacterium, and other representatives from hydraulic fracture fluids, deep bedrock aquifer and subsurface aquifer sediments (Toffin et al, 2005). Subsequently most of the top 10 unique OTUs of DF7 were similar to Thermincola (anaerobic, thermophilic, chemolithotrophic organism), Thermosinus (anaerobic, thermophilic and carbon monoxide oxidizing bacterium), extremotolerant Paenibacillus and other representatives from geothermal deep aquifers (Zavarina et al, 2007;Sokolova et al, 2004). Based on these observations we hypothesized that due to the prolonged interaction of DF with the subsurface granitic crust these organisms might have become infused in the DF.…”

Innovating carbon-capture biotechnologies through ecosystem-inspired solutions

“…The deep subsurface biomass is estimated to exceed that of the earth's surface by ca. 45%, and the bacterial and archaeal biomass may contain up to 31 Pg C. 26,27 The microbial communities of the deep subsurface rely on metabolic approaches using varying chemical redox reactions and are able to utilize carbon in diverse ways. The microbial environment is also able to quickly respond to biotic and abiotic environmental changes.…”

“…[47][48][49] Complex microbial communities dominate these environments and have a high functional capacity (Box 1) for the turnover of CO 2 and CH 4 . 26,27,[47][48][49][50] The deep subsurface is spatially heterogeneous, and microbial functions change depending on location, which also affects long-term geological storage of carbon. This has implications for engineering efforts aiming to control the geological storage of CO 2 , which is the major direction for contemporary CCS.…”