Jens Kallmeyer

Microbial communities influence key processes in oil reservoirs, including souring, corrosion, and hydrocarbon degradation, so characterizing them is important for reservoir management. Reliable characterization depends on obtaining a sample that represents the community living in the subsurface. As nucleic acids are difficult to recover from oil, produced water, the aqueous phase separated from reservoir fluids, is widely used as a convenient proxy for analyzing the reservoir microbiome. However, whether produced water faithfully represents that community, to our knowledge, has never been tested with paired samples. We addressed this question using 16S rRNA gene amplicon and metagenomic sequencing of reservoir fluids and produced water collected from the same production wells across four North Sea oil fields. The two sample types harbored markedly different microbial communities and functional profiles. This difference persisted after accounting for reservoir identity, and it was larger than the differences between reservoirs. Produced water was less diverse, more uniform across fields, and dominated by aerobic genera associated with seawater and aquifers. Reservoir fluids, in contrast, retained the thermophilic, halophilic, and anaerobic taxa characteristic of the deep subsurface. Only 41% of reservoir-fluid genera and 21% of their amplicon sequence variants were also detected in the paired produced water, indicating overlapping broad taxa but largely distinct populations. Notably, the putatively native reservoir community remained detectable in reservoir fluids even after decades of production, while produced water offered only an incomplete, directionally biased view. Reservoir fluids should therefore be sampled wherever feasible to characterize the in-situ microbiome.

Archean cratons may provide stable microbial habitats in the deep subsurface, as evidenced by the discovery of billion-year-old crustal fluids ^1,2 . However, the long-term habitability of these cratonic environments is uncertain, as polymetamorphic evolution in most cratons typically destroys microbial habitats through mineral reactions and porosity loss ^3,4 . Preservation of deep microbial habitats is more likely where mantle-derived magma intruded the craton after metamorphic overprinting ⁴ . Here we report the discovery of dense microbial colonization at 814 m depth within the 2.05-billion-year-old, unmetamorphosed Bushveld Igneous Complex intrusion, South Africa ⁵ . Using advanced contamination-control protocols ^6,7 and synchrotron-based X-ray spectroscopy, we identified indigenous microbial cells localized at the rims of phlogopite, a hydrous phyllosilicate mineral. Our study reveals that microbial colonization is associated with Fe(III) derived from the structure of phlogopite, where the dehydrogenation likely oxidizes Fe(II) to Fe(III) coupled to H ₂ generation ⁸ . Despite the absence of fracture-driven fluid ingress in the unfractured rock matrix, aqueous alteration evidenced at the rims by potassium removal indicates a self-sustaining habitat driven by an internal redox gradient ⁹ . These findings demonstrate that aqueous alteration of ultramafic rocks can sustain isolated microbial life over geological timescales, significantly expanding the potential for long-term habitability on both Earth and Mars ^4,10 .

In marine environments, small hydrocarbon (HC) fluxes through organic-poor sediments are often fully degraded by microorganisms before reaching the seabed. Yet, these fluxes influence sediment geochemistry by stimulating microbial activity. We analyzed 50 gravity cores from the southwestern Barents Sea, covering zones affected by inconspicuous HC seepage and unaffected reference zones. Using various organic and inorganic geochemical analyses of the sediment along with pore water geochemistry, we assess the effects of low-intensity seepage and identify potential geochemical signatures. While analysis of the organic geochemical analyses provided limited insights, inorganic geochemical analyses revealed formation of minerals such as carbonates and sulfides, linked to microbial reductive processes. Element concentrations suggested that HC degradation leaves distinct signatures, particularly in redox-sensitive minerals. Pore water profiles in HC-affected zones showed significant variation, indicating carbonate precipitation. In contrast, sediments not affected by HC seepage displayed more uniform pore water profiles. Estimated fluxes of sulfate, calcium, and alkalinity varied notably between cores, particularly in HC-affected zones, suggesting local and potentially transient differences in seepage intensity. While microbial HC degradation likely occurs deeper than our sampling interval, high-resolution geochemical analysis of both sediment fractions and pore water revealed a clear imprint of HC seepage. This imprint, reflected in authigenic minerals and pore water gradients, allows identification of past and present seepage activity, with authigenic minerals providing evidence for past seepage, and pore water profiles informing about ongoing seepage.

Sandy sediments of the coastal ocean are generally not considered a habitat for highly active sulfate-reducing microorganisms (SRM) due to fluctuations in oxygen concentrations and carbon availability. This study investigated the taxonomic composition and gene expression patterns of sulfate-reducing communities in both sandy, organic-poor sediments and muddy, organic-rich sediments in the mesohaline southern Baltic Sea. Our results revealed that a novel order-level lineage within the class Thermodesulfovibrionia (phylum Nitrospirota), named Arenidesulfomonadales, contributed significantly to sulfate reduction in the sandy sediments and supported sulfate reduction rates similar to those in the organic-rich, muddy sediments. In the sands, Thermodesulfovibrionia effectively competed with Desulfobacterales, which strongly dominated the sulfate-reducing communities in the organic-rich sediments. Metatranscriptomic data revealed that Desulfobacterales functioned as typical secondary fermenters in both sediment types and expressed nearly complete sets of genes for the catabolism of fermentation products such as lactate, propionate, and butyrate. In contrast, the gene expression profile of Thermodesulfovibrionia suggests that hydrogenotrophic sulfate reduction, coupled with carbon fixation via the Wood–Ljungdahl pathway and a reduced capacity to oxidize organic compounds, was a competitive metabolic strategy enabling sulfate reduction to proceed independently of fermentation-derived carbon. Overall, our results suggest that overlooked lineages of SRM may contribute to higher levels of sulfate reduction than previously assumed in the extensive areas of permeable sediments of coastal and shelf seas.

In marine environments, small hydrocarbon (HC) fluxes through organic-poor sediments are often fully degraded by microorganisms before reaching the seabed. Yet, these fluxes influence sediment geochemistry by stimulating microbial activity. We analyzed 50 gravity cores from the southwestern Barents Sea, covering zones affected by inconspicuous HC seepage and unaffected reference zones. Using various organic and inorganic geochemical analyses of the sediment along with pore water geochemistry, we assess the effects of low-intensity seepage and identify potential geochemical signatures. While analysis of the organic geochemical analyses provided limited insights, inorganic geochemical analyses revealed formation of minerals such as carbonates and sulfides, linked to microbial reductive processes. Element concentrations suggested that HC degradation leaves distinct signatures, particularly in redox-sensitive minerals. Pore water profiles in HC-affected zones showed significant variation, indicating carbonate precipitation. In contrast, sediments not affected by HC seepage displayed more uniform pore water profiles. Estimated fluxes of sulfate, calcium, and alkalinity varied notably between cores, particularly in HC-affected zones, suggesting local and potentially transient differences in seepage intensity. While microbial HC degradation likely occurs deeper than our sampling interval, high-resolution geochemical analysis of both sediment fractions and pore water revealed a clear imprint of HC seepage. This imprint, reflected in authigenic minerals and pore water gradients, allows identification of past and present seepage activity, with authigenic minerals providing evidence for past seepage, and pore water profiles informing about ongoing seepage.

In marine environments, small hydrocarbon (HC) fluxes through organic-poor sediments are often fully degraded by microorganisms before reaching the seabed. Yet, these fluxes influence sediment geochemistry by stimulating microbial activity. We analyzed 50 gravity cores from the southwestern Barents Sea, covering zones affected by inconspicuous HC seepage and unaffected reference zones. Using various organic and inorganic geochemical analyses of the sediment along with pore water geochemistry, we assess the effects of low-intensity seepage and identify potential geochemical signatures. While analysis of the organic geochemical analyses provided limited insights, inorganic geochemical analyses revealed formation of minerals such as carbonates and sulfides, linked to microbial reductive processes. Element concentrations suggested that HC degradation leaves distinct signatures, particularly in redox-sensitive minerals. Pore water profiles in HC-affected zones showed significant variation, indicating carbonate precipitation. In contrast, sediments not affected by HC seepage displayed more uniform pore water profiles. Estimated fluxes of sulfate, calcium, and alkalinity varied notably between cores, particularly in HC-affected zones, suggesting local and potentially transient differences in seepage intensity. While microbial HC degradation likely occurs deeper than our sampling interval, high-resolution geochemical analysis of both sediment fractions and pore water revealed a clear imprint of HC seepage. This imprint, reflected in authigenic minerals and pore water gradients, allows identification of past and present seepage activity, with authigenic minerals providing evidence for past seepage, and pore water profiles informing about ongoing seepage.

In marine environments, small hydrocarbon (HC) fluxes through organic-poor sediments are often fully degraded by microorganisms before reaching the seabed. Yet, these fluxes influence sediment geochemistry by stimulating microbial activity. We analyzed 50 gravity cores from the southwestern Barents Sea, covering zones affected by inconspicuous HC seepage and unaffected reference zones. Using various organic and inorganic geochemical analyses of the sediment along with pore water geochemistry, we assess the effects of low-intensity seepage and identify potential geochemical signatures. While analysis of the organic geochemical analyses provided limited insights, inorganic geochemical analyses revealed formation of minerals such as carbonates and sulfides, linked to microbial reductive processes. Element concentrations suggested that HC degradation leaves distinct signatures, particularly in redox-sensitive minerals. Pore water profiles in HC-affected zones showed significant variation, indicating carbonate precipitation. In contrast, sediments not affected by HC seepage displayed more uniform pore water profiles. Estimated fluxes of sulfate, calcium, and alkalinity varied notably between cores, particularly in HC-affected zones, suggesting local and potentially transient differences in seepage intensity. While microbial HC degradation likely occurs deeper than our sampling interval, high-resolution geochemical analysis of both sediment fractions and pore water revealed a clear imprint of HC seepage. This imprint, reflected in authigenic minerals and pore water gradients, allows identification of past and present seepage activity, with authigenic minerals providing evidence for past seepage, and pore water profiles informing about ongoing seepage.

In marine environments, small hydrocarbon (HC) fluxes through organic-poor sediments are often fully degraded by microorganisms before reaching the seabed. Yet, these fluxes influence sediment geochemistry by stimulating microbial activity. We analyzed 50 gravity cores from the southwestern Barents Sea, covering zones affected by inconspicuous HC seepage and unaffected reference zones. Using various organic and inorganic geochemical analyses of the sediment along with pore water geochemistry, we assess the effects of low-intensity seepage and identify potential geochemical signatures. While analysis of the organic geochemical analyses provided limited insights, inorganic geochemical analyses revealed formation of minerals such as carbonates and sulfides, linked to microbial reductive processes. Element concentrations suggested that HC degradation leaves distinct signatures, particularly in redox-sensitive minerals. Pore water profiles in HC-affected zones showed significant variation, indicating carbonate precipitation. In contrast, sediments not affected by HC seepage displayed more uniform pore water profiles. Estimated fluxes of sulfate, calcium, and alkalinity varied notably between cores, particularly in HC-affected zones, suggesting local and potentially transient differences in seepage intensity. While microbial HC degradation likely occurs deeper than our sampling interval, high-resolution geochemical analysis of both sediment fractions and pore water revealed a clear imprint of HC seepage. This imprint, reflected in authigenic minerals and pore water gradients, allows identification of past and present seepage activity, with authigenic minerals providing evidence for past seepage, and pore water profiles informing about ongoing seepage.

In marine environments, small hydrocarbon (HC) fluxes through organic-poor sediments are often fully degraded by microorganisms before reaching the seabed. Yet, these fluxes influence sediment geochemistry by stimulating microbial activity. We analyzed 50 gravity cores from the southwestern Barents Sea, covering zones affected by inconspicuous HC seepage and unaffected reference zones. Using various organic and inorganic geochemical analyses of the sediment along with pore water geochemistry, we assess the effects of low-intensity seepage and identify potential geochemical signatures. While analysis of the organic geochemical analyses provided limited insights, inorganic geochemical analyses revealed formation of minerals such as carbonates and sulfides, linked to microbial reductive processes. Element concentrations suggested that HC degradation leaves distinct signatures, particularly in redox-sensitive minerals. Pore water profiles in HC-affected zones showed significant variation, indicating carbonate precipitation. In contrast, sediments not affected by HC seepage displayed more uniform pore water profiles. Estimated fluxes of sulfate, calcium, and alkalinity varied notably between cores, particularly in HC-affected zones, suggesting local and potentially transient differences in seepage intensity. While microbial HC degradation likely occurs deeper than our sampling interval, high-resolution geochemical analysis of both sediment fractions and pore water revealed a clear imprint of HC seepage. This imprint, reflected in authigenic minerals and pore water gradients, allows identification of past and present seepage activity, with authigenic minerals providing evidence for past seepage, and pore water profiles informing about ongoing seepage.

In marine environments, small hydrocarbon (HC) fluxes through organic-poor sediments are often fully degraded by microorganisms before reaching the seabed. Yet, these fluxes influence sediment geochemistry by stimulating microbial activity. We analyzed 50 gravity cores from the southwestern Barents Sea, covering zones affected by inconspicuous HC seepage and unaffected reference zones. Using various organic and inorganic geochemical analyses of the sediment along with pore water geochemistry, we assess the effects of low-intensity seepage and identify potential geochemical signatures. While analysis of the organic geochemical analyses provided limited insights, inorganic geochemical analyses revealed formation of minerals such as carbonates and sulfides, linked to microbial reductive processes. Element concentrations suggested that HC degradation leaves distinct signatures, particularly in redox-sensitive minerals. Pore water profiles in HC-affected zones showed significant variation, indicating carbonate precipitation. In contrast, sediments not affected by HC seepage displayed more uniform pore water profiles. Estimated fluxes of sulfate, calcium, and alkalinity varied notably between cores, particularly in HC-affected zones, suggesting local and potentially transient differences in seepage intensity. While microbial HC degradation likely occurs deeper than our sampling interval, high-resolution geochemical analysis of both sediment fractions and pore water revealed a clear imprint of HC seepage. This imprint, reflected in authigenic minerals and pore water gradients, allows identification of past and present seepage activity, with authigenic minerals providing evidence for past seepage, and pore water profiles informing about ongoing seepage.