Microbial diversity and functions within the Earth’s deep subsurface remain pivotal in the Earth’s major biogeochemical activities. Microbial communities of groundwater systems hosted by ~65-million-year-old Deccan basalts are investigated to delineate their characteristics, biogeochemical functions and environmental control. Quantitative PCR-based bacterial cell counts suggest 4.3 × 102–3.9 × 103 cells/mL. 16S rRNA gene sequence analysis shows considerable bacterial diversity and the existence of a core microbiome (16 amplicon sequence variants [ASVs] out of a total of 2020 ASVs) across the groundwater samples. Members of Burkholderiaceae and Moraxellaceae are predominant taxa within the groundwater. In comparison, the spring water and surface water microbiomes are significantly distinct. Non-metric multidimensional scaling highlights that the basaltic groundwater communities are influenced by local environmental parameters. Analysis of whole metagenomes indicates that the Calvin–Benson–Bassham cycle is a primary mode of carbon fixation in the subsurface water system of the Deccan traps. Metagenome-assembled genomes are affiliated to the genera Limnohabitans and Methylotenera, among others. Together with the presence of sulfate and nitrate in the groundwater environment, the presence of genes involved in dissimilatory nitrate and sulfate reduction indicates the prevalence of anaerobic/facultative anaerobic lifestyles among the microorganisms in this system. Amplicon and whole metagenome sequence-based analyses suggest the presence of microbial populations involved in local biogeochemical cycling. This study on the geomicrobiology of the water systems of Deccan traps elucidates microbial community composition and biogeochemical function in the igneous rock-hosted deep biosphere.

As the use of carbon dioxide (CO2)-enhanced oil recovery continues, understanding its impacts on the in situ oil well microbial communities is important. In this study, we update the already substantial investigation into five oil wells of the Olla and Nebo Hemphill fields in the southeastern United States with metagenomics. The Olla field has undergone CO2 injection, whereas the Nebo Hemphill field has not. Under anoxic conditions in Nebo Hemphill, our data suggest that methanogenic archaea are in competition with fermentative bacteria for shared substrates, leading to reduced biogenic methane production. However, in the Olla wells that had introduced CO2, we find genomic evidence for the growth and replication of bacteria able to respire oxygen. Based on the co-occurrence and potential replication of methanogens in these wells, we hypothesise that there are still anoxic niches for methanogens. Oxygen-utilising microbes may utilise phenolic substrates, creating a situation where more material is available for anaerobic growth, counterintuitively increasing the capacity for methane production in these wells. Our data suggest that this consortium may be the reason that greater methanogenesis is seen in these CO2-affected wells, and we hypothesise that the gas injection may have had contaminating air. Therefore, using existing wells for processes such as enhanced oil recovery or carbon capture and storage will not only depend on well history and in situ conditions, but also on the development of in situ microbial networks within modified wells.

The degradation of isoprene – a prevalent volatile organic compound (VOC) – in soil has primarily been attributed as a microbial process, but chemical degradation may also play a role. Separating simultaneous abiotic and biotic degradation pathways under representative conditions has been a technical challenge, leaving the fate of surface and subsurface isoprene inputs from the atmosphere, litter roots, and microbes to the soil uncertain. Here, we investigated the real-time dynamics of belowground isoprene degradation by introducing isoprene into the subsurface through an artificial root and tracking its fate along with primary gas-phase oxidation products via in situ soil gas probes and online high-resolution proton transfer reaction time-of-flight mass spectrometry. Isoprene additions generated oxidation products from known NO- and •OH-initiated pathways, revealing chemical degradation as an active loss pathway for isoprene in soil. Over time, isoprene concentrations plummeted relative to an inert tracer despite continuous and repeated isoprene addition, revealing a lasting up-regulation of microbial isoprene degradation that ultimately outcompeted the chemical sink. We verified the presence of putative bacterial isoprene-degrading genes in the soil by quantitative PCR of isoA and identified microbial groups that increased in abundance in response to isoprene availability using 16S amplicon sequencing. Overall, our results show for the first time the relevance of chemical degradation pathways to isoprene in soil and the capacity and dynamics of the soil microbiome to respond using community memory to increased isoprene availability. Soil is a dynamic oxidative and adaptive environment beneath our feet that may play additional roles in the biosphere–atmosphere exchange of isoprene, and by extension other VOCs, beyond what was previously expected.