Carbon assimilation strategies in ultrabasic groundwater: clues from the integrated study of a serpentinization-influenced aquifer

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Seyler, L. M., Brazelton, W. J., McLean, C., Putman, L. I., Hyer, A., Kubo, M. D. Y., Hoehler, T., Cardace, D., & Schrenk, M. O. . Carbon assimilation strategies in ultrabasic groundwater: clues from the integrated study of a serpentinization-influenced aquifer. mSystems, 5(2), (2020): e00607-00619, doi: 10.1128/mSystems.00607-19.Serpentinization is a low-temperature metamorphic process by which ultramafic rock chemically reacts with water. Such reactions provide energy and materials that may be harnessed by chemosynthetic microbial communities at hydrothermal springs and in the subsurface. However, the biogeochemistry mediated by microbial populations that inhabit these environments is understudied and complicated by overlapping biotic and abiotic processes. We applied metagenomics, metatranscriptomics, and untargeted metabolomics techniques to environmental samples taken from the Coast Range Ophiolite Microbial Observatory (CROMO), a subsurface observatory consisting of 12 wells drilled into the ultramafic and serpentinite mélange of the Coast Range Ophiolite in California. Using a combination of DNA and RNA sequence data and mass spectrometry data, we found evidence for several carbon fixation and assimilation strategies, including the Calvin-Benson-Bassham cycle, the reverse tricarboxylic acid cycle, the reductive acetyl coenzyme A (acetyl-CoA) pathway, and methylotrophy, in the microbial communities inhabiting the serpentinite-hosted aquifer. Our data also suggest that the microbial inhabitants of CROMO use products of the serpentinization process, including methane and formate, as carbon sources in a hyperalkaline environment where dissolved inorganic carbon is unavailable.We thank McLaughlin Reserve, in particular Paul Aigner and Cathy Koehler, for hosting sampling at CROMO and providing access to the wells, A. Daniel Jones and Anthony Schilmiller for their advice regarding metabolite extraction and mass spectrometry, Elizabeth Kujawinski for her guidance in metabolomics data analysis and interpretation, and Julia McGonigle, Christopher Thornton, and Katrina Twing for assistance with metagenomic and computational analyses

Establishment of the Coast Range ophiolite microbial observatory (CROMO): Drilling objectives and preliminary outcomes

Abstract. This project aimed to establish a subsurface microbial observatory in ultramafic rocks, by drilling into an actively serpentinizing peridotite body, characterizing cored rocks, and outfitting the boreholes for a program of long-term observation and experimentation to resolve the serpentinite-hosted subsurface biosphere. We completed drilling in August 2011, drilling two boreholes with core recovery and possibility for down-hole experimentation, and six smaller-diameter monitoring wells arrayed around the two primary holes, in the Coast Range ophiolite (CRO) locality in the UC-Davis McLaughlin Natural Reserve, Lower Lake, CA. Every effort was made during drilling to keep the cores and wells as free of drilling-induced contamination as possible: clean, purified water was used as drilling fluid, fluorescent microbead tracers were suspended in that water for quantification of drilling fluid penetration into the cores, and high resolution next generation sequencing approaches were used to characterize the microbial populations in the drill fluids and core materials. In December 2011, we completed installation of well pumps (slow flow bladder pumps) in the monitoring wells, and have deployed a set of in situ incubation experiments in the two uncased boreholes. Preliminary findings illustrate natural variability in actively serpentinizing strata, and confirm distinct groundwater flow regimes and microbial ecosystems in (a) shallow, surface-impacted soil water horizons and (b) deeper, ultramafic bedrock-sourced formation fluids

Feasible Metabolisms in High pH Springs of the Philippines

A field campaign targeting high pH, H2-, and CH4-emitting serpentinite-associated springs in the Zambales and Palawan Ophiolites of the Philippines was conducted in 2012-2013, and enabled description of several springs sourced in altered pillow basalts, gabbros, and peridotites. We combine field observations of pH, temperature, conductivity, dissolved oxygen, and oxidation-reduction potential with analyses of major ions, dissolved inorganic carbon, dissolved organic carbon, and dissolved gas phases in order to model the activities of selected phases important to microbial metabolism, and to rank feasible metabolic reactions based on energy yield. We document changing geochemical inventories in these springs between sampling years, and examine how the environment supports or prevents the function of certain microbial metabolisms. In all, this geochemistry-based assessment of feasible metabolisms indicates methane cycling, hydrogen oxidation, some iron and sulfur metabolisms, and ammonia oxidation are feasible reactions in this continental site of serpentinization

High pH Microbial Ecosystems in a Newly Discovered, Ephemeral, Serpentinizing Fluid Seep at Yanartaş (Chimera), Turkey

Gas seeps emanating from Yanartaş (Chimera), Turkey, have been documented for thousands of years. Active serpentinization produces hydrogen and a range of carbon gases that may provide fuel for life. Here we report a newly discovered, ephemeral fluid seep emanating from a small gas vent at Yanartaş. Fluids and biofilms were sampled at the source and points downstream. We describe site conditions, and provide microbiological data in the form of enrichment cultures, Scanning electron microscopy (SEM), carbon and nitrogen isotopic composition of solids, and PCR screens of nitrogen cycle genes. Source fluids are pH 11.95, with a Ca:Mg of ~200, and sediments under the ignited gas seep measure 60°C. Collectively, these data suggest the fluid is the product of active serpentinization at depth. Source sediments are primarily calcite and alteration products (chlorite and montmorillonite). Downstream, biofilms are mixed with montmorillonite. SEM shows biofilms distributed homogeneously with carbonates. Organic carbon accounts for 60% of the total carbon at the source, decreasing downstream to \u3c15% as inorganic carbon precipitates. δ13C ratios of the organic carbon fraction of solids are depleted (−25 to −28‰) relative to the carbonates (−11 to −20‰). We conclude that heterotrophic processes are dominant throughout the surface ecosystem, and carbon fixation may be key down channel. δ15N ratios ~3‰, and absence of nifH in extracted DNA suggest that nitrogen fixation is not occurring in sediments. However, the presence of narG and nirS at most locations and in enrichments indicates genomic potential for nitrate and nitrite reduction. This small seep with shallow run-off is likely ephemeral, but abundant preserved microterracettes in the outflow and the surrounding area suggest it has been present for some time. This site and others like it present an opportunity for investigations of preserved deep biosphere signatures, and subsurface-surface interactions

Out of the Dark: Transitional Subsurface-to-Surface Microbial Diversity in a Terrestrial Serpentinizing Seep (Manleluag, Pangasinan, the Philippines)

In the Zambales ophiolite range, terrestrial serpentinizing fluid seeps host diverse microbial assemblages. The fluids fall within the profile of Ca2+-OH−-type waters, indicative of active serpentinization, and are low in dissolved inorganic carbon (DIC) (\u3c0.5 ppm). Influx of atmospheric carbon dioxide (CO2) affects the solubility of calcium carbonate as distance from the source increases, triggering the formation of meter-scale travertine terraces. Samples were collected at the source and along the outflow channel to determine subsurface microbial community response to surface exposure. DNA was extracted and submitted for high-throughput 16S rRNA gene sequencing on the Illumina MiSeq platform. Taxonomic assignment of the sequence data indicates that 8.1% of the total sequence reads at the source of the seep affiliate with the genus Methanobacterium. Other major classes detected at the source include anaerobic taxa such as Bacteroidetes (40.7% of total sequence reads) and Firmicutes (19.1% of total reads). Hydrogenophaga spp. increase in relative abundance as redox potential increases. At the carbonate terrace, 45% of sequence reads affiliate with Meiothermus spp. Taxonomic observations and geochemical data suggest that several putative metabolisms may be favorable, including hydrogen oxidation, H2-associated sulfur cycling, methanogenesis, methanotrophy, nitrogen fixation, ammonia oxidation, denitrification, nitrate respiration, methylotrophy, carbon monoxide respiration, and ferrous iron oxidation, based on capabilities of nearest known neighbors. Scanning electron microscopy and energy dispersive X-ray spectroscopy suggest that microbial activity produces chemical and physical traces in the precipitated carbonates forming downstream of the seep\u27s source. These data provide context for future serpentinizing seep ecosystem studies, particularly with regards to tropical biomes

Nonequilibrium clumped isotope signals in microbial methane

Methane is a key component in the global carbon cycle with a wide range of anthropogenic and natural sources. Although isotopic compositions of methane have traditionally aided source identification, the abundance of its multiply-substituted “clumped” isotopologues, e.g., 13CH3D, has recently emerged as a proxy for determining methane-formation temperatures; however, the impact of biological processes on methane’s clumped isotopologue signature is poorly constrained. We show that methanogenesis proceeding at relatively high rates in cattle, surface environments, and laboratory cultures exerts kinetic control on 13CH3D abundances and results in anomalously elevated formation temperature estimates. We demonstrate quantitatively that H2 availability accounts for this effect. Clumped methane thermometry can therefore provide constraints on the generation of methane in diverse settings, including continental serpentinization sites and ancient, deep groundwaters.National Science Foundation (U.S.) (EAR-1250394)National Science Foundation (U.S.) (EAR-1322805)Deep Carbon Observatory (Program)Natural Sciences and Engineering Research Council of CanadaDeutsche Forschungsgemeinschaft (Gottfried Wilhelm Leibniz Program)United States. Dept. of Defense (National Defense Science and Engineering Graduate Fellowship)Neil & Anna Rasmussen FoundationGrayce B. Kerr Fund, Inc. (Fellowship)MIT Energy Initiative (Shell-MITEI Graduate Fellowship)Shell International Exploration and Production B.V. (N. Braunsdorf and D. Smit of Shell PTI/EG grant

Structure and serpentinization of the subducting Cocos plate offshore Nicaragua and Costa Rica

Author Posting. © American Geophysical Union, 2011. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 12 (2011): Q06009, doi:10.1029/2011GC003592.The Cocos plate experiences extensional faulting as it bends into the Middle American Trench (MAT) west of Nicaragua, which may lead to hydration of the subducting mantle. To estimate the along strike variations of volatile input from the Cocos plate into the subduction zone, we gathered marine seismic refraction data with the R/V Marcus Langseth along a 396 km long trench parallel transect offshore of Nicaragua and Costa Rica. Our inversion of crustal and mantle seismic phases shows two notable features in the deep structure of the Cocos plate: (1) Normal oceanic crust of 6 km thickness from the East Pacific Rise (EPR) lies offshore Nicaragua, but offshore central Costa Rica we find oceanic crust from the northern flank of the Cocos Nazca (CN) spreading center with more complex seismic velocity structure and a thickness of 10 km. We attribute the unusual seismic structure offshore Costa Rica to the midplate volcanism in the vicinity of the Galápagos hot spot. (2) A decrease in Cocos plate mantle seismic velocities from ∼7.9 km/s offshore Nicoya Peninsula to ∼6.9 km/s offshore central Nicaragua correlates well with the northward increase in the degree of crustal faulting outboard of the MAT. The negative seismic velocity anomaly reaches a depth of ∼12 km beneath the Moho offshore Nicaragua, which suggests that larger amounts of water are stored deep in the subducting mantle lithosphere than previously thought. If most of the mantle low velocity zone can be interpreted as serpentinization, the amount of water stored in the Cocos plate offshore central Nicaragua may be about 2.5 times larger than offshore Nicoya Peninsula. Hydration of oceanic lithosphere at deep sea trenches may be the most important mechanism for the transfer of aqueous fluids to volcanic arcs and the deeper mantle.This work was funded by the U.S. National Science Foundation MARGINS program under grants OCE0405556, OCE 0405654, and OCE 0625178

Phospholipid fatty acid and quinone composition of sediments from ODP Leg 205 sites

Assessing the habitability of deep-sea sediments undergoing compaction, compression, and subduction at convergent margins adds to our understanding of the limits of the terrestrial biosphere. In this work, we report exploratory biomarker data on sediments obtained at Ocean Drilling Program (ODP) Sites 1253, 1254, and 1255 during drilling at the Costa Rica subduction trench and forearc sedimentary wedge. The samples selected for postcruise biomarker analyses were located within intervals of potentially enhanced fluid flow within the décollement and sedimentary wedge fault zones (Sites 1254 and 1255) and within basal carbonates at the reference site (Site 1253). The passage of fluids that are geochemically distinct from ambient interstitial water provides a disequilibrium setting that may enhance habitability. Biomarker data show low levels of microbial biomass in subseafloor sediments sampled at the Costa Rica convergent margin as deep as ~370 meters below seafloor