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.

The subsurface sediment collected from Integrated Ocean Drilling Program Site U1385 of the Iberian Margin was examined via metagenomics. Examination of the assembled metagenomes across different depths showed abundant signatures of Aerophobia and Bacteroidia, with additional lineages in lower abundance. We found that predicted functions, such as formaldehyde oxidation and the reverse tricarboxylic acid cycle, decrease with depth, whereas acetogenesis and hemicellulose debranching increase with depth. Genomic signatures of iron reduction and nitrate reduction were widespread in the sediment column. Once binned into metagenome-assembled genomes (MAGs) across all depths, six MAGs were of sufficient quality for characterisation and taxonomically assigned to the classes Promethearchaeia, Thorarchaeia, Atribacterota, Aerophobia, Bacteroidia and SM23-21. We examined how these MAGs varied in relative abundance across sediment depths and how predicted function varied among MAGs and compared to geochemistry. Coverage signatures of Promethearchaeia decreased with depth, whereas signatures for other lineages, particularly the Atribacterota and Bacteroidia, increased with depth. Functions like beta oxidation and glycolysis were well represented across MAGs. Very few genomic signatures of methane and sulfate metabolic cycling were observed in MAGs. This analysis indicates that while the Iberian Margin sediment is a well-preserved site for paleoclimate, which suggests limited microbial or chemical diagenesis, it also contains signatures of subsurface microbes that suggest activity in situ as a result of depth-dependent abundance trends.

Biogenic iron-manganese (Fe-Mn) mixed oxides are thought to be of significant environmental importance because of their strong reactivity and frequent occurrence in natural settings. Despite their critical role in elemental biogeochemical cycling, their formation pathways in different environmental conditions and detailed characterisation remain underexplored. This research presents an in-depth investigation into the synthesis of biogenic Fe-Mn mixed oxides, mediated by the aerobic Mn(II)-oxidising bacterium Pseudomonas putida MnB1, under conditions mimicking the oxic–anoxic interface of a water column, a potential pathway described here for the first time. Synthesis of biogenic Fe-Mn mixed oxides was performed in laboratory experiments consisting of two successive steps: (1) bio-oxidation of Mn(II) to produce biogenic Mn oxide; and (2) oxidation of Fe(II) by the biogenic Mn oxides. A series of analytical techniques, including X-ray diffraction, scanning electron microscopy, scanning transmission electron microscopy, scanning transmission electron microscopy-energy dispersive X-ray spectroscopy, transmission electron microscopy selected area electron diffraction, and inductively coupled plasma mass spectrometry, revealed the formation of heterogeneously distributed distinct phases of Fe and Mn oxide minerals, subsequently identified as poorly crystalline birnessite and Fe(III) oxyhydroxide nanocrystals closely associated with bacterial cells and extracellular polymeric substances. The synthesised biogenic Fe-Mn mixed oxides showed diverse morphologies, including large granules, long chains and ultrathin sheets, produced extracellularly on the bacterial cell surfaces. The synthesis process described in this study provides a better understanding of one of the possible pathways of Mn and Fe cycling at the oxic-anoxic interface of the water column. Potential environmental implications of the formation of these phases are also discussed, including trace metals transport dynamics in aquatic environments.

Iron-metabolising bacteria play a key role in the biogeochemical Fe cycle, linking it to the bioavailability and transformation of other bioessential elements such as carbon, nitrogen and phosphorus. Fe(III)-reducing bacteria use Fe(III) as an electron acceptor and Fe(II)-oxidising bacteria oxidise Fe(II) to gain energy, forming biogenic iron(III) oxyhydroxides (BIOS). Little is known about the bioavailability of the Fe(III) associated to BIOS (BIOSFe(III)), limiting predictions of its role in the mobility of other bioessential elements. Here we tested the bioavailability of BIOSFe(III) as a function of: (1) BIOS origin (phototrophic and mixotrophic/autotrophic nitrate-reduction coupled to Fe(II) oxidation), resulting in a gradient of cell-mineral associations from encrustation to loose attachments; (2) two model Fe(III)-reducing microorganisms, Shewanella oneidensis MR-1 and Geobacter sulfurreducens PCA; (3) the presence or absence of added organic carbon (lactate or acetate); and (4) before and after freeze-thawing, simulating conditions relevant to temperate environments. Statistical redundancy analysis showed that despite variations in the properties of the BIOS (e.g. particle size, surface areas, organic content) due to its origin and freeze-thaw treatment, organic carbon availability was the main factor controlling BIOSFe(III) reduction rates and extents. With added organic carbon, BIOSFe(III) were reduced completely, with faster rates observed for G. sulfurreducens, suggesting limited availability of BIOS-associated organic carbon (BIOSOC) to these microorganisms. BIOSFe(III) was also more bioavailable than synthetic 2-line ferrihydrite, attributed to increased redox reactivity originating from BIOSOC (e.g. residual cells and extracellular polymeric substances). Freeze-thawing, a process relevant in high-latitude zones, mountain glaciers and other temperate climate regions across Earth, mostly decreased the rate and extent of BIOSFe(III) reduction, although the magnitude and direction of the effect depend on the specific variable combination. Thus, we conclude that environmental organic carbon availability is the primary factor controlling the bioavailability of BIOSFe(III), with subsequent effects on the transformation of other bioessential elements.

Ancient Fe(II)-oxidising photoautotrophic bacteria may have facilitated the precipitation of iron- and silica-rich chemical sediments known as Banded Iron Formations (BIFs). BIFs contain a diverse assemblage of iron oxides, carbonates and silicates, which are thought to have originated from the diagenesis of one or more primary seawater precipitates. While the identity and Fe redox state of these mineral precursors remain poorly understood, a compelling hypothesis suggests that the precipitation and transformation of mixed-valence phases such as green rust might have been a key component of BIF deposition. However, it remains unknown whether photoferrotrophy in an anoxic and Fe(II)aq-rich environment can produce such mixed-valence minerals. To test whether green rust can be produced by iron-oxidising phototrophs (photoferrotrophs) thought to play a role in BIF deposition, we cultured photoferrotrophs in an environment constantly buffered by Fe(II) from the dissolution of the Fe(II)-mineral siderite (FeCO3). Here we show that the photoferrotroph Rhodopseudomonas palustris TIE-1 produces Fe(III) oxyhydroxides dominated by goethite (α-FeO(OH)) even when provided with a constant excess of Fe(II)aq. Fe(III)aq was formed extracellularly and rapidly hydrolysed, probably precipitating as metastable ferrihydrite, which then transformed into goethite following Fe(II)aq-catalysed recrystallisation. Given the prevailing circumneutral pH levels, we speculate that high [Fe(III)aq] around microbial cells prevented the formation of mixed-valence phases. Our results showing that Fe(III) minerals precipitated from solutions even with an excess of Fe(II)aq indicate that an oxidative mechanism influences the identity of primary precipitates by dictating local chemical conditions at the site of Fe(II) oxidation. Further investigation is needed to understand conditions promoting the formation of Fe(II,III) phases in conditions representative of Earth’s ancient oceans.