Archaea in Yellowstone Lake

Abstract

The Yellowstone geothermal complex has yielded foundational discoveries that have significantly enhanced our understanding of the Archaea. This study continues on this theme, examining Yellowstone Lake and its lake floor hydrothermal vents. Significant Archaea novelty and diversity were found associated with two near-surface photic zone environments and two vents that varied in their depth, temperature and geochemical profile. Phylogenetic diversity was assessed using 454-FLX sequencing (~51,000 pyrosequencing reads; V1 and V2 regions) and Sanger sequencing of 200 near-full-length polymerase chain reaction (PCR) clones. Automated classifiers (Ribosomal Database Project (RDP) and Greengenes) were problematic for the 454-FLX reads (wrong domain or phylum), although BLAST analysis of the 454-FLX reads against the phylogenetically placed full-length Sanger sequenced PCR clones proved reliable. Most of the archaeal diversity was associated with vents, and as expected there were differences between the vents and the near-surface photic zone samples. Thaumarchaeota dominated all samples: vent-associated organisms corresponded to the largely uncharacterized Marine Group I, and in surface waters, ~69-84% of the 454-FLX reads matched archaeal clones representing organisms that are Nitrosopumilus maritimus-like (96-97% identity). Importance of the lake nitrogen cycling was also suggested by >5% of the alkaline vent phylotypes being closely related to the nitrifier Candidatus Nitrosocaldus yellowstonii. The Euryarchaeota were primarily related to the uncharacterized environmental clones that make up the Deep Sea Euryarchaeal Group or Deep Sea Hydrothermal Vent Group-6. The phylogenetic parallels of Yellowstone Lake archaea to marine microorganisms provide opportunities to examine interesting evolutionary tracks between freshwater and marine lineages.

Figure 1

Collector's curves estimating numbers of Archaea OTUs identified for all samples, and as a function of sequence identity set at 97% and quality screened as described by Kunin et al. (2010).

Figure 2

Proportional occurrence of 454-FLX Archaea OTUs unique to each of the designated lake locations. OTUs were assigned based on 97% identity match. DV, West Thumb Deep Vent; OV, Otter Vent; IP, Inflated Plain Photic Zone; SEA, Southeast Arm Photic Zone.

Figure 3

Phylogenetic associations of the near-full-length PCR clones of Yellowstone Lake Crenarchaeal Groups (YLCGs). Approximate % representation of 454-FLX sequences for West Thumb Deep Vent, Otter Vent, Inflated Plain Photic and Southeast Arm Photic are shown within parentheses. Clones lacking parenthetical data were not found in the pyrosequencing data set. Clones highlighted in gray boxes represent phylotypes that represented at least 10% of the pyrosequencing reads from at least one location.

Figure 4

Phylogenetic associations of the near-full-length PCR clones of Yellowstone Lake Euryarchaeal Groups (YLEGs). Approximate % representation of 454-FLX sequences represented for West Thumb Deep Vent, Otter Vent, Inflated Plain Photic and Southeast Arm Photic are shown within parentheses. Clones lacking parenthetical data were not found in the pyrosequencing data set. Clones highlighted in gray boxes represent phylotypes that represented at least 10% of the pyrosequencing reads from at least one location.