Subsurface microbial diversity in deep-granitic-fracture water in Colorado - PubMed (original) (raw)

Subsurface microbial diversity in deep-granitic-fracture water in Colorado

Jason W Sahl et al. Appl Environ Microbiol. 2008 Jan.

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.

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Figures

FIG. 1.

FIG. 1.

Schematic diagram of the Henderson Mine, showing the two levels where water samples were taken (7150 and 7025) as well as the location of the rock core sample.

FIG. 2.

FIG. 2.

Concentrations of manganese, fluoride, and sulfate in water sampled from boreholes at the 7150 and 7025 levels in the Henderson mine.

FIG. 3.

FIG. 3.

Phylogenetic tree showing representative bacterial divisions constructed with Bayesian inference. Sequences that form the Henderson group 1 are shown in bold. Numbers at bifurcations indicate posterior probabilities calculated by MrBayes v3.1. The rooting archaeal outgroup (a sequence from Halobacteria) has been removed for clarity.

FIG. 4.

FIG. 4.

Pie charts showing microbial community compositions of drill hole 1 (pre- and postpacker) and drill hole 4 (postpacker), all at the 7025 level. “Others” refers to pooled divisions representing <1% of each respective library.

FIG. 5.

FIG. 5.

Phylogenetic tree of the division Proteobacteria. Numbers at nodes represent posterior probabilities. Numbers following accession numbers indicate how many sequences grouped with each phylotype.

FIG. 6.

FIG. 6.

Phylogenetic trees of the division Firmicutes (A) and the domain Archaea (B). Sequences obtained in this study are in bold. Numbers at branching nodes indicate posterior probabilities. The rooting outgroup for the Firmicutes has been removed for clarity.

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