Geomicrobiology of sublacustrine thermal vents in Yellowstone Lake: geochemical controls on microbial community structure and function

Abstract

Yellowstone Lake (Yellowstone National Park, WY, USA) is a large high-altitude (2200 m), fresh-water lake, which straddles an extensive caldera and is the center of significant geothermal activity. The primary goal of this interdisciplinary study was to evaluate the microbial populations inhabiting thermal vent communities in Yellowstone Lake using 16S rRNA gene and random metagenome sequencing, and to determine how geochemical attributes of vent waters influence the distribution of specific microorganisms and their metabolic potential. Thermal vent waters and associated microbial biomass were sampled during two field seasons (2007-2008) using a remotely operated vehicle (ROV). Sublacustrine thermal vent waters (circa 50-90°C) contained elevated concentrations of numerous constituents associated with geothermal activity including dissolved hydrogen, sulfide, methane and carbon dioxide. Microorganisms associated with sulfur-rich filamentous "streamer" communities of Inflated Plain and West Thumb (pH range 5-6) were dominated by bacteria from the Aquificales, but also contained thermophilic archaea from the Crenarchaeota and Euryarchaeota. Novel groups of methanogens and members of the Korarchaeota were observed in vents from West Thumb and Elliot's Crater (pH 5-6). Conversely, metagenome sequence from Mary Bay vent sediments did not yield large assemblies, and contained diverse thermophilic and nonthermophilic bacterial relatives. Analysis of functional genes associated with the major vent populations indicated a direct linkage to high concentrations of carbon dioxide, reduced sulfur (sulfide and/or elemental S), hydrogen and methane in the deep thermal ecosystems. Our observations show that sublacustrine thermal vents in Yellowstone Lake support novel thermophilic communities, which contain microorganisms with functional attributes not found to date in terrestrial geothermal systems of YNP.

Keywords: Aquificales; Archaea; hydrogen; metagenome; methane; methanotrophs; sulfide; thermophiles.

Figure 1

Bathymetric map (Morgan and Shanks, 2005) of Yellowstone Lake showing heat flux iso-lines (mW/m²) (Morgan et al., 1977) and sampling locations of thermal vents (Table 1) discussed in the current study (IP, Inflated Plain; WT-DV, West Thumb Deep Vents; WT-OV, West Thumb Otter Vent; EC, Elliott's Crater; MB, Mary Bay; SA, Southeast Arm; see Table S1 for GPS coordinates).

Figure 2

(A) Scanning electron micrographs of thermal streamer communities obtained from 30 to 33 m vents in the Inflated Plain region, Yellowstone Lake (Sample ID). All scale bars = 1 μm. (B) Scanning electron micrographs of thermal vent biomass samples obtained from vent sites at West Thumb deep (Sample ID 339, 342; 2007), Elliot's Crater (351; 2008), and Mary Bay (349; 2008). Sediments associated with thermal vents show accumulation of diatom shells (e.g., Mary Bay, 349, lower right), which were also trapped in filamentous streamer communities (e.g., West Thumb, 369, lower left).

Figure 3

Phylogenetic tree (16S rRNA gene sequences) of the domain Archaea including long-fragment sequences observed in thermal vent microbial communities from Yellowstone Lake (neighbor-joining tree; bootstrap values reported based on 1000reps Log Det.). All long-fragment 16S rRNA gene sequences from Yellowstone Lake are deposited in GenBank (KT453543-KT453636).

Figure 4

Phylogenetic classification of short fragment bacterial 16S rRNA gene sequences from two different sulfur streamer communities from Inflated Plain (depth ~ 30–33 m; pH ~ 5.6) obtained using pyro-tag sequencing (sequences classified using RDP Naïve Bayesian rRNA Classifier version 2.5; also see Table 3).

Figure 5

Random shotgun sequence reads from four Yellowstone Lake thermal vent microbial communities plotted as a function of G + C content (%) and subjected to phylogenetic analysis using blast (90% identity). A significant number of sequence reads were not related to bacteria or archaea in current public databases.