Subsurface Microbial Diversity in Deep-Granitic-Fracture Water in Colorado

Abstract

A microbial community analysis using 16S rRNA gene sequencing was performed on borehole water and a granite rock core from Henderson Mine, a >1,000-meter-deep molybdenum mine near Empire, CO. Chemical analysis of borehole water at two separate depths (1,044 m and 1,004 m below the mine entrance) suggests that a sharp chemical gradient exists, likely from the mixing of two distinct subsurface fluids, one metal rich and one relatively dilute; this has created unique niches for microorganisms. The microbial community analyzed from filtered, oxic borehole water indicated an abundance of sequences from iron-oxidizing bacteria (Gallionella spp.) and was compared to the community from the same borehole after 2 weeks of being plugged with an expandable packer. Statistical analyses with UniFrac revealed a significant shift in community structure following the addition of the packer. Phospholipid fatty acid (PLFA) analysis suggested that Nitrosomonadales dominated the oxic borehole, while PLFAs indicative of anaerobic bacteria were most abundant in the samples from the plugged borehole. Microbial sequences were represented primarily by Firmicutes, Proteobacteria, and a lineage of sequences which did not group with any identified bacterial division; phylogenetic analyses confirmed the presence of a novel candidate division. This "Henderson candidate division" dominated the clone libraries from the dilute anoxic fluids. Sequences obtained from the granitic rock core (1,740 m below the surface) were represented by the divisions Proteobacteria (primarily the family Ralstoniaceae) and Firmicutes. Sequences grouping within Ralstoniaceae were also found in the clone libraries from metal-rich fluids yet were absent in more dilute fluids. Lineage-specific comparisons, combined with phylogenetic statistical analyses, show that geochemical variance has an important effect on microbial community structure in deep, subsurface systems.

Taxonomically and functionally diverse microbial communities in deep crystalline rocks of the Fennoscandian shield

“…South Africa gold mine euryarchaeotic group 1 was detected at 200-1000 m and at 1300-1500 m. At 1900 and 2300 m, over 99% of the sequences were classified to Methanobacteriaceae family, causing a reduction in community evenness, diversity and richness (Supplementary Table S4). The prevalence of Proteobacteria, Firmicutes and methanogenic archaea in Outokumpu was consistent with the detection of these taxa in geographically distant continental crustal areas (Gihring et al, 2006;Sahl et al, 2008).…”

“…Previous studies using 16S rRNA gene cloning have reported up to 42 bacterial OTUs in continental crystalline rocks (Gihring et al, 2006;Sahl et al, 2008;Onstott et al, 2009), whereas analysis of rarefied pyrotag data obtained from Outokumpu in this study inferred 48-110 bacterial OTUs per sample (Supplementary Table S4). Archaeal OTU richness also greatly exceeded expectations based on earlier studies, with up to 112 OTUs detected in samples recovered above 1500 m (Takai et al, 2001;Sahl et al, 2008). Bacterial OTU richness peaked at 1300 m depth, which coincides with ophiolitic sequence of altered ultramafic rocks (that is, serpentinite, skarn and quartz).…”

“…Yet, studies conducted in mines and deep drill holes have documented that microbial life extends several kilometers into the Earth's crystalline crust with diverse microbial communities detected in a variety of continental areas (Havemann et al, 1999;Zhang et al, 2005;Gihring et al, 2006;Sahl et al, 2008;Onstott et al, 2009;Itävaara et al, 2011a;Nyyssö nen et al, 2012). Culture-based studies under laboratory conditions show that these microbial communities include both autotrophic and heterotrophic members with variable modes of metabolism including sulfate and iron reduction, methanogenesis and acetogenesis (Haveman et al, 1999;Haveman and Pedersen, 2002).…”

Comparison of the microbial community composition of pristine rock cores and technical influenced well fluids from the Ketzin pilot site for CO2 storage

“…Similar observations have been previously reported in other deep microbial ecosystems (Fry et al 1997;Sahl et al 2008). Basso and colleagues (2009) analyzed a deep subsurface gas storage aquifer and observed a microbial community primarily comprising Firmicutes and Deltaproteobacteria.…”

Sedimentological imprint on subseafloor microbial communities in Western Mediterranean Sea Quaternary sediments

“…Sequences belonging to the classes Alpha-and Gammaproteobacteria rarely occurred at this site (<3 %). Overall, sequences of this core were closely related to ubiquitous microorganisms previously recovered from marine or terrestrial environments contaminated with heavy metals (Selenska-Pobell et al, 2001;Akob et al, 2007;Bruun et al, 2010;Kampe et al, 2010), from soil (Phuong et al, 2008;Schouten et al, 2010), water, groundwater (Sahl et al, 2008) and petroleum crude oil samples (Yamane et al, 2008). Bacterial communities of the Ligurian Sea core KESC9-30 were composed of Proteobacteria (classes Alpha-, Beta-and Gammaproteobacteria), Chloroflexi, Bacteroidetes and candidate division OP8.…”