Unusual metabolic diversity of hyperalkaliphilic microbial communities associated with subterranean serpentinization at The Cedars

Abstract

Water from The Cedars springs that discharge from serpentinized ultramafic rocks feature highly basic (pH=~12), highly reducing (E<-550 mV) conditions with low ionic concentrations. These conditions make the springs exceptionally challenging for life. Here, we report the metagenomic data and recovered draft genomes from two different springs, GPS1 and BS5. GPS1, which was fed solely by a deep groundwater source within the serpentinizing system, was dominated by several bacterial taxa from the phyla OD1 ('Parcubacteria') and Chloroflexi. Members of the GPS1 community had, for the most part, the smallest genomes reported for their respective taxa, and encoded only archaeal (A-type) ATP synthases or no ATP synthases at all. Furthermore, none of the members encoded respiration-related genes and some of the members also did not encode key biosynthesis-related genes. In contrast, BS5, fed by shallow water, appears to have a community driven by hydrogen metabolism and was dominated by a diverse group of Proteobacteria similar to those seen in many terrestrial serpentinization sites. Our findings indicated that the harsh ultrabasic geological setting supported unexpectedly diverse microbial metabolic strategies and that the deep-water-fed springs supported a community that was remarkable in its unusual metagenomic and genomic constitution.

FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies

“…Metagenomes from the Cedars (Suzuki et al, 2017), a hyperalkaline terrestrial serpentinite-hosted site, encodes a diversity of iron acquisition genes, similar to that observed in the open ocean, suggesting potential iron-limiting conditions. Accordingly, we did not detect any genes associated with iron reduction or oxidation.…”

“…All NCBI accessions are listed in Supplementary Table S2, as well as Supplementary Data Sheets S2, S3, S10, S11. Metagenome assemblies were downloaded from the NCBI GenBank database (BioProject Accession ID: PRJDB2971): GCA_002581605.1 (GPS1 2012), GCA_002581705.1 (GPS1 2011), GCA_002581825.1 (BS5 2012), and GCA_002583255.1 (BS5 2011) (Suzuki et al, 2017). GPS1 (Grotto Pool Springs) is sourced by deep groundwater while BS5 (Barnes Springs 5) is sourced by ∼15% deep groundwater and ∼85% shallow groundwater.…”

“…Two samples were collected from each spring and represent temporal duplicates taken approximately 1 year apart. These metagenomes were processed as described in Suzuki et al (2017). • Amazon River plume estuary: Raw metagenome reads were downloaded from NCBI's Sequence Read Archive (SRA) corresponding to BioSamples SAMN02628402 (Station 3), SAMN02628424 (Station 27), and SAMN02628416 (Station 10); these correspond to samples taken along a salinity gradient formed as the Amazon River flows into the Atlantic Ocean (Satinsky et al, 2017).…”

Formation and loss of metastable brucite: does Fe(II)-bearing brucite support microbial activity in serpentinizing ecosystems?

“…Therefore, one of the guiding strategies for seeking life in serpentinizing systems is to identify fluid mixing zones, such as where H 2 -rich hydrothermal fluids are discharged from ultramafic rocks into lower pH, more oxidizing fluids. Excellent modern examples include locales such as Lost City hydrothermal field near the Mid-Atlantic Ridge, the Prony Bay Hydrothermal Field, New Caledonia, and springs in Samail Ophiolite, Oman and the Cedars, California, to name just a few locales [66][67][68][69][70][71]. It has also been proposed to seek chemical disequilibria [51]), or at contact zones between crust and mantle rocks, such as zones where gabbro and peridotite are juxtaposed [64].…”

Lipid analysis of CO2-rich subsurface aquifers suggests an autotrophy-based deep biosphere with lysolipids enriched in CPR bacteria

“…However, the diversity of subsurface ecosystems is manifold. Physicochemical characteristics as well as the availability of electron donors and acceptors shape different microbial communities within these ecosystems (e.g., [1, 2]). Serpentinizing systems can harbor large amounts of abiotically-produced methane that can serve as the primary electron donor and as a carbon substrate entering biosynthesis via methanotrophy [3–5].…”