Archaea in Yellowstone Lake

Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089-0740, USA.
The ISME Journal (Impact Factor: 9.3). 05/2011; 5(11):1784-95. DOI: 10.1038/ismej.2011.56
Source: PubMed


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.

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    • "The transcribed bacterial V1 – V3 and archaeal V1 – V2 16S rRNA regions were amplified from template cDNA and gDNA ( bacterial only ) with the 27F / 534R ( Wu et al . , 2010 ) and A2Fa / A571R ( Kan et al . , 2011 ) primer pairs respectively , with PCR ingredients and conditions per the cited studies for 30 amplification cycles in triplicate reactions . To enable multiplexed 454 pyrosequencing , barcode sequences were incorporated between the adaptors and forward primers ( Hamady et al . , 2008 ) . Amplicons were pooled and purified with the Agen"
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