Biogeochemical Gradients in a Serpentinization‐Influenced Aquifer: Implications for Gas Exchange Between the Subsurface and Atmosphere

Abstract

Serpentinization involves the hydration and alteration of ultramafic rocks, which produces hydrogen (H 2 ) and methane (CH 4 ) and results in distinctive groundwater chemistries. As reacted fluids mix with recharging surface water, gradients in chemistry and microbiology develop in the subsurface. We present a comprehensive analysis of biogeochemical gradients in the water column of a serpentinitehosted well, CSW1.1, at the Coast Range Ophiolite Microbial Observatory (CROMO) in California, USA. Samples for geochemistry, 16S rRNA gene sequencing, and metagenomics were collected at four discrete depths from the top of the well corresponding to 100%, 50%, 15%, and 0% of atmospheric oxygen (O 2 ) levels, and from the well base at 19.5 m depth. Gibbs energy calculations assessed the energy available for a suite of reactions coupled to O 2 , sulfate (SO 4 2− ), and nitrate (NO 3 − ). Metagenomic data from the profile was used to construct metagenome assembled genomes (MAGs) to evaluate the completeness of biochemical pathways and compare the relative abundance of key diagnostic genes. Bioenergetic data point to the favorability of CH 4 oxidation reactions despite little genetic evidence for this. Amplicon sequencing results highlight the abundance of key taxa affiliated with the genera Truepera, Serpentinomonas, and Dethiobacter. Although concentrations of NO 3 − and H 2 are low, genes for NO 3 − reduction and oxidation of H 2 and carbon monoxide (CO) were found in high abundance. Conceptual modeling results demonstrate the net depletion of H 2 and CO in the groundwater, the consumption of CO 2 and O 2 , and the potential for CH 4 emission into the atmosphere at this terrestrial site of serpentinization.Plain Language Summary Microorganisms living in extreme habitats on Earth generate energy by catalyzing chemical reactions using the compounds available. A water-rock interaction known as serpentinization creates high pH and low-oxygen waters, and a limited number of compounds for energy generation. Hydrogen, carbon monoxide, and methane are gases produced through serpentinization that may be used by microorganisms. To unravel small-scale subsurface processes, we studied a depth profile from a serpentinization-influenced groundwater well, and sampled the water at five depths. We measured chemical components of the groundwater (anions, dissolved gases), and calculated the energy available to organisms using a set of common metabolic reactions. We also assessed the microbial communities present, and determined their potential contributions to biogeochemical cycles. We found that three taxa, Serpentinomonas, Truepera, and Dethiobacter dominated. Despite high methane concentrations, genes for methane oxidation were absent throughout the profile. Rather, genes associated with the use of low abundance compounds, like carbon monoxide, hydrogen, and nitrate, were prevalent. This implies that carbon monoxide and hydrogen consumption can deplete these compounds before they reach the surface, and the lack of methane consumption ma...

Microbial Communities in a Serpentinizing Aquifer Are Assembled through Strong Concurrent Dispersal Limitation and Selection

“…Metagenomic and metatranscriptomic sequences were previously reported ( 15 , 20 , 22 , 88 ). Sample preparation and sequencing of metagenomes and metatranscriptomes were carried out as previously described ( 22 ).…”

“…There were no patterns in sample contamination by these two organisms when looking at sample collection or sample extraction logs. A similar approach to removing contaminant sequences from a deep subsurface data set was successfully used by Fullerton and colleagues ( 78 ) and Sabuda and colleauges ( 88 ). The final 16S rRNA data set used for analysis consisted of 13,444 OTUs and retained 96% of the original reads (5,974,056 reads).…”

“…Metagenome sequences previously published by Seyler and colleagues ( 20 ) are publicly available under the BioProject IDs: PRJNA410019 , PRJNA410020 , PRJNA410022 , PRJNA410035 , PRJNA410037 , PRJNA410553 , PRJNA410555 , PRJNA410036 , PRJNA410024 , PRJNA410028 , PRJNA410025 , PRJNA410023 , PRJNA410027 , and PRJNA410026 . Metagenomic sequences previously published by Sabuda and colleauges ( 88 ) are publicly available in the NCBI SRA database under the following accession IDs: SRX9385611 , SRX9385612 , and SRX9385613 . CROMO metatranscriptome sequences previously published by Sabuda and colleagues ( 22 ) are publicly available in the SRA under the following accession IDs: SRX3339504 , SRX3339503 , SRX3339089 , SRX3331179 , SRX3331177 , SRX3330963 , SRX3330943 , and SRX3330753 .…”

Aqueous Geochemical and Microbial Variation Across Discrete Depth Intervals in a Peridotite Aquifer Assessed Using a Packer System in the Samail Ophiolite, Oman

“…To date, gene sequences affiliated with Meiothermus have been detected at three other serpentinizing sites: Manleluag in the Zambales Ophiolite, Philippines (Woycheese et al, 2015), Prony Bay, New Caledonia (Mei et al, 2016), and La Crouen, New Caledonia (Quéméneur et al, 2021). Sequences related to another member of Deinococcota phlyum, the genus Truepera, have been detected somewhat more widely in serpentinizing environments including Cabeço de Vide, Portugal (Tiago & Veríssimo, 2013), Prony Bay, New Caledonia (Frouin et al, 2018;Mei et al, 2016), the Coast Range Ophiolite, USA (Sabuda et al, 2020(Sabuda et al, , 2021, Voltri, Italy (Quéméneur et al, 2015), and the Chimaera Seeps, Turkey (Neubeck et al, 2017). MAGs related to Truepera in DNA extracted from Coast Range Ophiolite groundwaters encoded homologs of proteins involved in a wide array of processes including oxygen tolerance, oxygen respiration, and nitrate respiration (Sabuda et al, 2021), and transcripts of genes encoding enzymes involved in sulfide oxidation, thiosulfate oxidation, and thiosulfate disproportionation were also affiliated with Truepera (Sabuda et al, 2020).…”

“…Downstream analyses of samples of potentially mixed origin therefore may obscure understanding of the subsurface peridotite-hosted biosphere. Sabuda et al (2021) began to address these issues by using peristaltic and bladder pumps to obtain fluid and biomass samples from five depths in a serpentinite-hosted well in the Coast Range Ophiolite, CA, USA across a range of dissolved 2 O concentrations from 100% to 0% air saturation.…”