Original Research ARTICLE

Front. Microbiol., 10 September 2013 | doi: 10.3389/fmicb.2013.00274

Yellowstone Lake Nanoarchaeota

Scott Clingenpeel1†, Jinjun Kan2†, Richard E. Macur3†, Tanja Woyke1, Dave Lovalvo4, John Varley5, William P. Inskeep6,7*, Kenneth Nealson8,9 and Timothy R. McDermott5,6*
  • 1DOE Joint Genome Institute, Walnut Creek, CA, USA
  • 2Stroud Water Research Center, Avondale, PA, USA
  • 3Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
  • 4Eastern Oceanics, West Redding, CT, USA
  • 5Montana Institute on Ecosystems, Montana State University, Bozeman, MT, USA
  • 6Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
  • 7Thermal Biology Institute, Montana State University, Bozeman, MT, USA
  • 8Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
  • 9J. Craig Venter Institute, San Diego, CA, USA

Considerable Nanoarchaeota novelty and diversity were encountered in Yellowstone Lake, Yellowstone National Park (YNP), where sampling targeted lake floor hydrothermal vent fluids, streamers and sediments associated with these vents, and in planktonic photic zones in three different regions of the lake. Significant homonucleotide repeats (HR) were observed in pyrosequence reads and in near full-length Sanger sequences, averaging 112 HR per 1349 bp clone and could confound diversity estimates derived from pyrosequencing, resulting in false nucleotide insertions or deletions (indels). However, Sanger sequencing of two different sets of PCR clones (110 bp, 1349 bp) demonstrated that at least some of these indels are real. The majority of the Nanoarchaeota PCR amplicons were vent associated; however, curiously, one relatively small Nanoarchaeota OTU (71 pyrosequencing reads) was only found in photic zone water samples obtained from a region of the lake furthest removed from the hydrothermal regions of the lake. Extensive pyrosequencing failed to demonstrate the presence of an Ignicoccus lineage in this lake, suggesting the Nanoarchaeota in this environment are associated with novel Archaea hosts. Defined phylogroups based on near full-length PCR clones document the significant Nanoarchaeota 16S rRNA gene diversity in this lake and firmly establish a terrestrial clade distinct from the marine Nanoarcheota as well as from other geographical locations.

Keywords: Nanoarchaeota, Yellowstone Lake, pyrosequencing

Citation: Clingenpeel S, Kan J, Macur RE, Woyke T, Lovalvo D, Varley J, Inskeep WP, Nealson K and McDermott TR (2013) Yellowstone Lake Nanoarchaeota. Front. Microbiol. 4:274. doi: 10.3389/fmicb.2013.00274

Received: 21 June 2013; Accepted: 22 August 2013;
Published online: 11 September 2013.

Edited by:

Hongyue Dang, Xiamen University, China

Reviewed by:

Jennifer F. Biddle, University of Delaware, USA
Craig E. Nelson, University of Hawaii at Manoa, USA

Copyright © 2013 Clingenpeel, Kan, Macur, Woyke, Lovalvo, Varley, Inskeep WP, Nealson K and McDermott. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

*Correspondence: William P. Inskeep and Timothy R. McDermott, Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA e-mail: binskeep@montana.edu; timmcder@montana.edu

These authors have contributed equally to this work and listed alphabetically.

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