title: 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.
authors.affiliation: Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089-0740, USA.
authors.forename: Jinjun
authors.initials: J
authors.lastname: Kan
authors.forename: Scott
authors.initials: S
authors.lastname: Clingenpeel
authors.forename: Richard E
authors.initials: RE
authors.lastname: Macur
authors.forename: William P
authors.initials: WP
authors.lastname: Inskeep
authors.forename: Dave
authors.initials: D
authors.lastname: Lovalvo
authors.forename: John
authors.initials: J
authors.lastname: Varley
authors.forename: Yuri
authors.initials: Y
authors.lastname: Gorby
authors.forename: Timothy R
authors.initials: TR
authors.lastname: McDermott
authors.forename: Kenneth
authors.initials: K
authors.lastname: Nealson
mesh_terms: D001105:Archaea / Q000145:classification* / Q000235:genetics; D019641:DNA, Archaeal / Q000032:analysis / Q000235:genetics; D060086:Hydrothermal Vents; D060106:Lakes / Q000382:microbiology*; D015205:Northwestern United States; D010802:Phylogeny; D016133:Polymerase Chain Reaction
chemical_list: D019641:DNA, Archaeal