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Archaea
Volume 2013 (2013), Article ID 370871, 12 pages
http://dx.doi.org/10.1155/2013/370871
Research Article

Virus-Host and CRISPR Dynamics in Archaea-Dominated Hypersaline Lake Tyrrell, Victoria, Australia

1Department of Earth and Planetary Science, University of California, Berkeley, 307 McCone Hall, Berkeley, CA 94720-4767, USA
2Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA
3Department of Environmental Science, Policy, and Management, University of California, Berkeley, 54 Mulford Hall, Berkeley, CA 94720, USA
4Department of Biology, University of Copenhagen, Copenhagen, Denmark
5Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, CA, USA
6Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0202, USA
7Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA

Received 7 December 2012; Revised 17 May 2013; Accepted 27 May 2013

Academic Editor: Yoshizumi Ishino

Copyright © 2013 Joanne B. Emerson et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

The study of natural archaeal assemblages requires community context, namely, a concurrent assessment of the dynamics of archaeal, bacterial, and viral populations. Here, we use filter size-resolved metagenomic analyses to report the dynamics of 101 archaeal and bacterial OTUs and 140 viral populations across 17 samples collected over different timescales from 2007–2010 from Australian hypersaline Lake Tyrrell (LT). All samples were dominated by Archaea (75–95%). Archaeal, bacterial, and viral populations were found to be dynamic on timescales of months to years, and different viral assemblages were present in planktonic, relative to host-associated (active and provirus) size fractions. Analyses of clustered regularly interspaced short palindromic repeat (CRISPR) regions indicate that both rare and abundant viruses were targeted, primarily by lower abundance hosts. Although very few spacers had hits to the NCBI nr database or to the 140 LT viral populations, 21% had hits to unassembled LT viral concentrate reads. This suggests local adaptation to LT-specific viruses and/or undersampling of haloviral assemblages in public databases, along with successful CRISPR-mediated maintenance of viral populations at abundances low enough to preclude genomic assembly. This is the first metagenomic report evaluating widespread archaeal dynamics at the population level on short timescales in a hypersaline system.