Subsurface Microbial Ecosystems and The Origin of Methane In Serpentinites of The Samail Ophiolite, Oman

Serpentinization of ultramafic rocks can produce hydrogen (H2), a strong electron donor that microbes can react with electron acceptors such as carbon dioxide (CO2) to produce methane (CH4) and yield energy. This type of chemosynthetic process is relevant to life on Earth and potentially on other silicate bodies of the Solar System. However, serpentinization results in high-pH (&gt; 11), low-CO2&nbsp;conditions that can be challenging to life. This dissertation assesses relationships between hydrogeochemical parameters and subsurface microbial communities at a site of low-temperature serpentinization in the Samail Ophiolite, Oman. We pumped groundwaters from deep wells, determined fluid chemical compositions, analyzed taxonomic profiles of microbial communities, and measured isotopic compositions of hydrocarbon gases. For some work, we used a packer system to pump discrete intervals as deep as 108 m to 132 m from two 400 m-deep wells, isolating multiple aquifers ranging in pH from 8 to 11. 16S rRNA gene sequencing of deep groundwaters revealed the presence of an ecosystem dominated by microbial sulfate reduction coupled to oxidation of H2&nbsp;and small organic acids. In shallower, oxidized groundwaters, heterotrophic aerobes or denitrifiers were more prevalent. However, the majority of this dissertation focused on the origin of CH4 in hyperalkaline fluids. Although it has been argued that CH4&nbsp;in the ophiolite is abiotic due to its 13C-enriched composition (&delta;13C commonly &minus;10&permil; to +5&permil;&nbsp;VPDB), we found that 16S rRNA gene sequences affiliated with methanogens were widespread and in high relative abundance in some samples. Further, we measured clumped isotopologue (13CH3D and 12C&nbsp;H2D2) relative abundances less than equilibrium, consistent with microbial CH4&nbsp;production. Relationships between CO2&nbsp;concentrations and &delta;13CCH4&nbsp;suggest that the C isotope effect of microbial CH4&nbsp;production is modulated by C availability, and strongly suppressed at pH &gt; 11. CH4&nbsp;samples from two wells had 14C contents significantly above analytical blanks, and one well had CH4&nbsp;of up to 0.304 fraction modern. This is the first proof of active (&lt; 10 ka) conversion of atmospheric CO2&nbsp;to CH4&nbsp;in a serpentinizing setting. Although we do infer a second abiotic source of CH4&nbsp;from high &delta;13C values of co-occurring ethane and propane, we attribute substantial CH4&nbsp;production to microbial activity despite high pH and C limitation.</p

Geologic map of the Samail Ophiolite, Oman and United Arab Emirates

A geologic map of the Samail Ophiolite in Oman and the United Arab Emirates has been georeferenced and digitized. The data are provided in GeoPackage (.gpkg) format that can be imported into GIS software such as QGIS and Arc. The GeoPackage contains vector layers for lithologies and faults. Five lithologies are represented: Dunite/Wehrlite, Harzburgite, Mafic, Metamorphic Sole, and Plagiogranite. Further, a QGIS project file is provided, which should allow for layer styles to be preserved if opened in QGIS. The map data (not georeferenced) were originally published as &nbsp; Nicolas, A., Boudier, F., Ildefonse, B., Ball, E., 2000. Accretion of Oman and United Arab Emirates ophiolite - Discussion of a new structural map. Mar Geophys Res 21, 147&ndash;179. doi:10.1023/A:1026769727917 &nbsp; Please cite both works if you use the georeferenced data. A GeoTIFF of the original Nicolas et al. map subdivided into greater lithological detail is also provided in the GeoPackage.</div

Parapatric speciation of Meiothermus in serpentinite-hosted aquifers in Oman

The factors that control the distribution and evolution of microbial life in subsurface environments remain enigmatic due to challenges associated with sampling fluids from discrete depth intervals via boreholes while avoiding mixing of fluids. Here, using an inflatable packer system, fracture waters were isolated and collected from three discrete depth intervals spanning &gt;130 m in a borehole intersecting an ultramafic rock formation undergoing serpentinization in the Samail Ophiolite, Sultanate of Oman. Near surface aquifer waters were moderately reducing and had alkaline pH while deeper aquifer waters were reduced and had hyperalkaline pH, indicating extensive influence by serpentinization. Metagenomic sequencing and analysis of DNA from filtered biomass collected from discrete depth intervals revealed an abundance of aerobes in near surface waters and a greater proportion of anaerobes at depth. Yet the abundance of the putatively obligate aerobe, Meiothermus, increased with depth, providing an opportunity to evaluate the influence of chemical and spatial variation on its distribution and speciation. Two clades of Meiothermus metagenome assembled genomes (MAGs) were identified that correspond to surface and deep populations termed Types I (S) and II (D), respectively; both clades comprised an apparently Oman-specific lineage indicating a common ancestor. Type II (D) clade MAGs encoded fewer genes and were undergoing slower genome replication as inferred from read mapping. Further, single nucleotide variants (SNVs) and mobile genetic elements identified among MAGs revealed detectable, albeit limited, evidence for gene flow/recombination between spatially segregated Type I (S) and Type II (D) populations. Together, these observations indicate that chemical variation generated by serpentinization, combined with physical barriers that reduce/limit dispersal and gene flow, allowed for the parapatric speciation of Meiothermus in the Samail Ophiolite or a geologic precursor. Further, Meiothermus genomic data suggest that deep and shallow aquifer fluids in the Samail Ophiolite may mix over shorter time scales than has been previously estimated from geochemical data

Geological and Geochemical Controls on Subsurface Microbial Life in the Samail Ophiolite, Oman.

Microbial abundance and diversity in deep subsurface environments is dependent upon the availability of energy and carbon. However, supplies of oxidants and reductants capable of sustaining life within mafic and ultramafic continental aquifers undergoing low-temperature water-rock reaction are relatively unknown. We conducted an extensive analysis of the geochemistry and microbial communities recovered from fluids sampled from boreholes hosted in peridotite and gabbro in the Tayin block of the Samail Ophiolite in the Sultanate of Oman. The geochemical compositions of subsurface fluids in the ophiolite are highly variable, reflecting differences in host rock composition and the extent of fluid-rock interaction. Principal component analysis of fluid geochemistry and geologic context indicate the presence of at least four fluid types in the Samail Ophiolite ("gabbro," "alkaline peridotite," "hyperalkaline peridotite," and "gabbro/peridotite contact") that vary strongly in pH and the concentrations of

Intact polar lipidome and membrane adaptations of microbial communities inhabiting serpentinite-hosted fluids

The generation of hydrogen and reduced carbon compounds during serpentinization provides sustained energy for microorganisms on Earth, and possibly on other extraterrestrial bodies (e.g., Mars, icy satellites). However, the geochemical conditions that arise from water-rock reaction also challenge the known limits of microbial physiology, such as hyperalkaline pH, limited electron acceptors and inorganic carbon. Because cell membranes act as a primary barrier between a cell and its environment, lipids are a vital component in microbial acclimation to challenging physicochemical conditions. To probe the diversity of cell membrane lipids produced in serpentinizing settings and identify membrane adaptations to this environment, we conducted the first comprehensive intact polar lipid (IPL) biomarker survey of microbial communities inhabiting the subsurface at a terrestrial site of serpentinization. We used an expansive, custom environmental lipid database that expands the application of targeted and untargeted lipodomics in the study of microbial and biogeochemical processes. IPLs extracted from serpentinite-hosted fluid communities were comprised of &gt;90% isoprenoidal and non-isoprenoidal diether glycolipids likely produced by archaeal methanogens and sulfate-reducing bacteria. Phospholipids only constituted ~1% of the intact polar lipidome. In addition to abundant diether glycolipids, betaine and trimethylated-ornithine aminolipids and glycosphingolipids were also detected, indicating pervasive membrane modifications in response to phosphate limitation. The carbon oxidation state of IPL backbones was positively correlated with the reduction potential of fluids, which may signify an energy conservation strategy for lipid synthesis. Together, these data suggest microorganisms inhabiting serpentinites possess a unique combination of membrane adaptations that allow for their survival in polyextreme environments. The persistence of IPLs in fluids beyond the presence of their source organisms, as indicated by 16S rRNA genes and transcripts, is promising for the detection of extinct life in serpentinizing settings through lipid biomarker signatures. These data contribute new insights into the complexity of lipid structures generated in actively serpentinizing environments and provide valuable context to aid in the reconstruction of past microbial activity from fossil lipid records of terrestrial serpentinites and the search for biosignatures elsewhere in our solar system

An international intercomparison of stable carbon isotope composition measurements of dissolved inorganic carbon in seawater

We report results of an intercomparison of stable carbon isotope ratio measurements in seawater dissolved inorganic carbon (δ 13C‐DIC) which involved 16 participating laboratories from various parts of the world. The intercomparison involved distribution of samples of a Certified Reference Material for seawater DIC concentration and alkalinity and a preserved sample of deep seawater collected at 4000 m in the northeastern Atlantic Ocean. The between‐lab standard deviation of reported uncorrected values measured with diverse analytical, detection, and calibration methods was 0.11‰ (1σ ). The multi‐lab average δ 13C‐DIC value reported for the deep seawater sample was consistent within 0.1‰ with historical measured values for the same water mass. Application of a correction procedure based on a consensus value for the distributed reference material, improved the between‐lab standard deviation to 0.06‰. The magnitude of the corrections were similar to those used to correct independent data sets using crossover comparisons, where deep water analyses from different cruises are compared at nearby locations. Our results demonstrate that the accuracy/uncertainty target proposed by the Global Ocean Observing System (±0.05‰) is attainable, but only if an aqueous phase reference material for δ 13C‐DIC is made available and used by the measurement community. Our results imply that existing Certified Reference Materials used for seawater DIC and alkalinity quality control are suitable for this purpose, if a “Certified” or internally consistent “consensus” value for δ 13C‐DIC can be assigned to various batches.publishedVersio

Parapatric speciation of <i>Meiothermus</i> in serpentinite-hosted aquifers in Oman

The factors that control the distribution and evolution of microbial life in subsurface environments remain enigmatic due to challenges associated with sampling fluids from discrete depth intervals via boreholes while avoiding mixing of fluids. Here, using an inflatable packer system, fracture waters were isolated and collected from three discrete depth intervals spanning &gt;130 m in a borehole intersecting an ultramafic rock formation undergoing serpentinization in the Samail Ophiolite, Sultanate of Oman. Near surface aquifer waters were moderately reducing and had alkaline pH while deeper aquifer waters were reduced and had hyperalkaline pH, indicating extensive influence by serpentinization. Metagenomic sequencing and analysis of DNA from filtered biomass collected from discrete depth intervals revealed an abundance of aerobes in near surface waters and a greater proportion of anaerobes at depth. Yet the abundance of the putatively obligate aerobe, Meiothermus, increased with depth, providing an opportunity to evaluate the influence of chemical and spatial variation on its distribution and speciation. Two clades of Meiothermus metagenome assembled genomes (MAGs) were identified that correspond to surface and deep populations termed Types I (S) and II (D), respectively; both clades comprised an apparently Oman-specific lineage indicating a common ancestor. Type II (D) clade MAGs encoded fewer genes and were undergoing slower genome replication as inferred from read mapping. Further, single nucleotide variants (SNVs) and mobile genetic elements identified among MAGs revealed detectable, albeit limited, evidence for gene flow/recombination between spatially segregated Type I (S) and Type II (D) populations. Together, these observations indicate that chemical variation generated by serpentinization, combined with physical barriers that reduce/limit dispersal and gene flow, allowed for the parapatric speciation of Meiothermus in the Samail Ophiolite or a geologic precursor. Further, Meiothermus genomic data suggest that deep and shallow aquifer fluids in the Samail Ophiolite may mix over shorter time scales than has been previously estimated from geochemical data