Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla

Abstract

Research on geologic carbon sequestration raises questions about potential impacts of subsurface microbiota on carbon cycling and biogeochemistry. Subsurface, high-CO2 systems are poorly biologically characterized, partly because of difficulty accessing high-volume, uncontaminated samples. CO2 -driven Crystal Geyser (CG, Utah, USA), an established geologic carbon sequestration analogue, provides high volumes of deep (∼ 200-500 m) subsurface fluids. We explored microbial diversity and metabolic potential in this high-CO2 environment by assembly and analysis of metagenomes recovered from geyser water filtrate. The system is dominated by neutrophilic, iron-oxidizing bacteria, including 'marine' Mariprofundus (Zetaproteobacteria) and 'freshwater' Gallionellales, sulfur-oxidizing Thiomicrospira crunogena and Thiobacillus-like Hydrogenophilales. Near-complete genomes were reconstructed for these bacteria. CG is notably populated by a wide diversity of bacteria and archaea from phyla lacking isolated representatives (candidate phyla) and from as-yet undefined lineages. Many bacteria affiliate with OD1, OP3, OP9, PER, ACD58, WWE3, BD1-5, OP11, TM7 and ZB2. The recovery of nearly 100 genes encoding ribulose-1,5 bisphosphate carboxylase-oxygenase subunit proteins of the Calvin cycle and AMP salvage pathways suggests a strong biological role in high-CO2 subsurface carbon cycling. Overall, we predict microbial impacts on subsurface biogeochemistry via iron, sulfur, and complex carbon oxidation, carbon and nitrogen fixation, fermentation, hydrogen metabolism, and aerobic and anaerobic respiration.

New CRISPR–Cas systems from uncultivated microbes

“…For the Rifle data, DNA extraction, sequencing, assembly, and genome reconstruction were described by Anantharaman et al (2016) 26 and Brown et al (2015) 6 . For samples from Crystal Geyser, methods follow those described by Probst et al (2016) 38 and Emerson et al (2016) 39 . Rifle metatranscriptomic data was used from the data reported by Brown et al (2015) 6 .…”

Isolation and characterization of a CO2-tolerant Lactobacillus strain from Crystal Geyser, Utah, U.S.A.

“…Approximately 9.7 m of silicone tubing (Masterflex, Vernon Hills, IL) was lowered into the Crystal Geyser outlet and water pumped at a rate of 200 ml/min into a sterile container to allow for excess CO 2 to exsolve. We chose this method in comparison to Emerson et al (2015) in order to reduce the amount of oxidized Fe passing through filters so that clogging would not occur as quickly. Water was then filtered through a 90 mm, 0.1 µm sterile polycarbonate filter (Millipore, Billerica, MA) in a sterile stainless steel filter apparatus.…”

“…The source of water coming from Crystal Geyser is a combination of deeply sourced saline water as well as recharge from the nearby San Rafael swell (Baer and Rigby, 1978;Heath et al, 2009;McPherson and Heath, 2009;Burnside et al, 2013). Because recharge to Crystal Geyser may be seasonal, the microbial community of the site is likely dynamic and this could explain why CG-1 was not detected by Emerson et al (2015). Nevertheless, the detection and cultivation of CG-1 validates the findings of Morozova et al (2011), Mu et al (2014, Emerson et al (2015), Mu and Moreau (2015) showing that organisms present in CO 2 environments are viable and can potentially impact geochemistry.…”

“…It originated as an unsuccessful exploratory oil well 800 m deep and spudded in 1935 (Baer and Rigby, 1978;Heath et al, 2009;McPherson and Heath, 2009;Burnside et al, 2013). Previous work by Emerson et al (2015) have correlated the geochemistry of this field site to both the microbial community and the metagenomics profile from the sampled spring. This study reveals the presence of a microbial community within the geyser and reveals a metagenome with putative metabolisms that are consistent with iron biogeochemistry of the field site.…”

Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum

“…The Peregrinibacteria are a lineage within the bacterial CPR (Wrighton et al, 2012;Brown et al, 2015), a monophyletic radiation primarily of candidate phyla. Members of the Peregrinibacteria phylum have been genomically sampled from a contaminated sediment-hosted aquifer (Wrighton et al, 2012;Brown et al, 2015) and a deep subsurface high CO 2 environment (Emerson et al, 2015). However, ribosomal proteins and 16S rRNA gene sequences from this group have been detected in a variety of environments, including sediments and soil .…”