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Volume 2015 (2015), Article ID 875784, 12 pages
http://dx.doi.org/10.1155/2015/875784
Research Article

De Novo Sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, Reveal a Variable Genomic Landscape

1Department of Biological Sciences, Dornsife College of Letters, Arts and Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089, USA
2Cooperative Institute for Research in Environmental Sciences, CIRES Building, Room 318, University of Colorado Boulder, Boulder, CO 80309, USA
3Department of Environmental Science, Policy and Management, University of California, Berkeley, 54 Mulford Hall, Berkeley, CA 94720, USA
4Research School of Earth Sciences, The Australian National University, Canberra, ACT 0200, Australia
5Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0202, USA
6Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, CA 92093, USA

Received 19 June 2014; Revised 2 September 2014; Accepted 16 September 2014

Academic Editor: Timothy Williams

Copyright © 2015 Benjamin J. Tully 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

Hypersaline systems near salt saturation levels represent an extreme environment, in which organisms grow and survive near the limits of life. One of the abundant members of the microbial communities in hypersaline systems is the square archaeon, Haloquadratum walsbyi. Utilizing a short-read metagenome from Lake Tyrrell, a hypersaline ecosystem in Victoria, Australia, we performed a comparative genomic analysis of H. walsbyi to better understand the extent of variation between strains/subspecies. Results revealed that previously isolated strains/subspecies do not fully describe the complete repertoire of the genomic landscape present in H. walsbyi. Rearrangements, insertions, and deletions were observed for the Lake Tyrrell derived Haloquadratum genomes and were supported by environmental de novo sequences, including shifts in the dominant genomic landscape of the two most abundant strains. Analysis pertaining to halomucins indicated that homologs for this large protein are not a feature common for all species of Haloquadratum. Further, we analyzed ATP-binding cassette transporters (ABC-type transporters) for evidence of niche partitioning between different strains/subspecies. We were able to identify unique and variable transporter subunits from all five genomes analyzed and the de novo environmental sequences, suggesting that differences in nutrient and carbon source acquisition may play a role in maintaining distinct strains/subspecies.