Serpentinization-Influenced Groundwater Harbors Extremely
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fmicb-08-00308 February 27, 2017 Time: 16:48 # 1 ORIGINAL RESEARCH published: 01 March 2017 doi: 10.3389/fmicb.2017.00308 Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH Katrina I. Twing1,2*, William J. Brazelton2, Michael D. Y. Kubo3, Alex J. Hyer2, Dawn Cardace4, Tori M. Hoehler5, Tom M. McCollom6 and Matthew O. Schrenk1 1 Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA, 2 Department of Biology, University of Utah, Salt Lake City, UT, USA, 3 SETI Institute, Mountain View, CA, USA, 4 Department of Geosciences, University of Rhode Island, Kingston, RI, USA, 5 Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA, 6 Laboratory for Atmospheric and Space Physics, University of Colorado, Boulder, CO, USA Serpentinization is a widespread geochemical process associated with aqueous Edited by: alteration of ultramafic rocks that produces abundant reductants (H2 and CH4) for Cody Sheik, life to exploit, but also potentially challenging conditions, including high pH, limited University of Minnesota Duluth, USA availability of terminal electron acceptors, and low concentrations of inorganic carbon. Reviewed by: Thomas L. Kieft, As a consequence, past studies of serpentinites have reported low cellular abundances New Mexico Institute of Mining and limited microbial diversity. Establishment of the Coast Range Ophiolite Microbial and Technology, USA Wesley Douglas Swingley, Observatory (California, U.S.A.) allowed a comparison of microbial communities Northern Illinois University, USA and physicochemical parameters directly within serpentinization-influenced subsurface *Correspondence: aquifers. Samples collected from seven wells were subjected to a range of Katrina I. Twing analyses, including solute and gas chemistry, microbial diversity by 16S rRNA gene [email protected] sequencing, and metabolic potential by shotgun metagenomics, in an attempt to Specialty section: elucidate what factors drive microbial activities in serpentinite habitats. This study This article was submitted to describes the first comprehensive interdisciplinary analysis of microbial communities Microbiological Chemistry and Geomicrobiology, in hyperalkaline groundwater directly accessed by boreholes into serpentinite rocks. a section of the journal Several environmental factors, including pH, methane, and carbon monoxide, were Frontiers in Microbiology strongly associated with the predominant subsurface microbial communities. A single Received: 14 January 2017 Accepted: 14 February 2017 operational taxonomic unit (OTU) of Betaproteobacteria and a few OTUs of Clostridia Published: 01 March 2017 were the almost exclusive inhabitants of fluids exhibiting the most serpentinized Citation: character. Metagenomes from these extreme samples contained abundant sequences Twing KI, Brazelton WJ, Kubo MDY, encoding proteins associated with hydrogen metabolism, carbon monoxide oxidation, Hyer AJ, Cardace D, Hoehler TM, McCollom TM and Schrenk MO carbon fixation, and acetogenesis. Metabolic pathways encoded by Clostridia and (2017) Serpentinization-Influenced Betaproteobacteria, in particular, are likely to play important roles in the ecosystems Groundwater Harbors Extremely Low Diversity Microbial Communities of serpentinizing groundwater. These data provide a basis for further biogeochemical Adapted to High pH. studies of key processes in serpentinite subsurface environments. Front. Microbiol. 8:308. doi: 10.3389/fmicb.2017.00308 Keywords: serpentinization, alkaliphile, extremophile, groundwater, borehole Frontiers in Microbiology| www.frontiersin.org 1 March 2017| Volume 8| Article 308 fmicb-08-00308 February 27, 2017 Time: 16:48 # 2 Twing et al. Microbial Communities in Serpentinizing Groundwater INTRODUCTION et al., 2013, 2014), or previously established wells, such as at the Cabeço de Vide Aquifer (CVA) in Portugal (Tiago and Veríssimo, The Earth’s subsurface is predicted to be an expansive habitat 2013). In these studies of continental serpentinite sites, microbial for microorganisms (Whitman et al., 1998; Edwards et al., communities were dominated by clades of Betaproteobacteria 2012; Kallmeyer et al., 2012). Unlike surface biomes, the and Firmicutes (Schrenk et al., 2013). subsurface is largely decoupled from photosynthetic primary Surveys of the Tablelands Ophiolite suggest that subsurface production; instead, many subsurface ecosystems are influenced serpentinite communities are dominated by Erysipelotrichia, a by carbon and energy liberated from the Earth’s mantle and class within the phylum Firmicutes, in the deep, anoxic source- crust. However, given the inherent lack of accessibility, direct waters and microaerophilic H2-oxidizing Betaproteobacteria sampling of subsurface, rock-hosted environments has been at the shallow, oxic/anoxic interface (Brazelton et al., 2013). limited. In continental settings, researchers have used caves Microcosm experiments from the Coast Range Ophiolite (Northrup and Lavoie, 2001; Engel et al., 2004), mines (Onstott Microbial Observatory (CROMO), the location of this study, et al., 2003; Chivian et al., 2008), springs (Brazelton et al., 2012, have indicated that Betaproteobacteria closely related to 2013; Suzuki et al., 2013; Cardace et al., 2015), and isolated Hydrogenophaga pseudoflava and Clostridia (phylum Firmicutes) boreholes (Stevens and McKinley, 1995; Itävaara et al., 2011) closely related to Dethiobacter alkaliphilus, are stimulated by as windows into the subsurface environment. These features small organic molecules that are expected to be available in grant access to an otherwise inaccessible environment, but they the serpentinite environment (Crespo-Medina et al., 2014). represent opportunistic sampling locations. In the present study, Furthermore, recently published genomes of cultivated isolates a series of wells were drilled directly into serpentinization- of the proposed genus Serpentinomonas, which are most closely influenced aquifers of the Coast Range Ophiolite, a portion related to the genus Hydrogenophaga, are consistent with a role of ancient seafloor in northern California, USA, to sample for these organisms at oxic/anoxic interfaces in serpentinizing microbial communities in serpentinizing rocks and groundwater. systems (Suzuki et al., 2014). This observatory represents the first opportunity to investigate While these previous studies suggest that distinct microbial microbial communities with direct access to the range of communities inhabit different physico-chemical regimes in conditions in the serpentinizing subsurface (Cardace et al., serpentinizing groundwater, these relationships have not 2013). yet been studied directly. Furthermore, little genomic or Serpentinization is a widespread geochemical process metagenomic data for organisms other than Serpentinomonas involving the aqueous alteration of peridotite to serpentine are available from serpentinizing environments. This study minerals, resulting in an abundance of potential reductants, in combines environmental 16S rRNA gene sequencing, shotgun the form of hydrogen, methane, and small organic molecules metagenomic analyses, and geochemical monitoring across a (McCollom and Seewald, 2007; Proskurowski et al., 2008; range of conditions in order to relate patterns in microbial Schrenk et al., 2013). Serpentinization also releases hydroxyl diversity and metabolic potential to underlying geochemical ions, which creates extremely high pH fluids (pH > 10). At processes in serpentinite subsurface environments. This work high pH, bicarbonate and carbonate are the dominant species of improves our understanding of the physiology and ecology of dissolved inorganic carbon (DIC), and the latter can precipitate the dominant bacteria in these ubiquitous ecosystems, and it will out of solution as carbonate minerals when in the presence of facilitate our integration of these systems into models of carbon divalent cations, such as Ca2C and Mg2C commonly found in cycling. serpentinite fluids. Thus, fluids associated with serpentinization are characteristically low in DIC, particularly dissolved CO2. Compared to the abundance of reductants in these systems, MATERIALS AND METHODS there is a lack of corresponding oxidants, which likely limits the range of potential microbial metabolisms. Thus subsurface Site Description and Sample Collection serpentinite environments are characterized by unusual The Coast Range Ophiolite is a 155–170 million year old ophiolite challenges to life, such as extreme pH (>10), limited availability located in northern California, containing numerous calcium- of dissolved carbon, and a lack of potential terminal electron hydroxide rich springs, indicating serpentinizing activity below acceptors. the surface (Barnes and O’Neil, 1971). The CROMO, which The best-characterized serpentinite-hosted microbial is located at the UC-Davis McLaughlin Natural Reserve in ecosystem to date is the Lost City Hydrothermal Field, located Lower Lake, CA and was established in August 2011 and using 15 km from the Mid-Atlantic Ridge (Kelley et al., 2005). The clean drilling techniques to enable subsequent monitoring of the tall carbonate chimneys at Lost City are dominated by methane- microbial communities and associated geochemistry within the cycling archaea in the anoxic chimney interiors (Schrenk et al., serpentinite subsurface (Cardace et al., 2013). CROMO consists 2004) and by methanotrophic and sulfur-oxidizing bacteria in of two sets