title: De novo sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, reveal a variable genomic landscape.
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.
authors.affiliation: Department of Biological Sciences, Dornsife College of Letters, Arts and Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089, USA.
authors.forename: Benjamin J
authors.initials: BJ
authors.lastname: Tully
authors.affiliation: Cooperative Institute for Research in Environmental Sciences, CIRES Building, Room 318, University of Colorado Boulder, Boulder, CO 80309, USA.
authors.forename: Joanne B
authors.initials: JB
authors.lastname: Emerson
authors.affiliation: Department of Environmental Science, Policy and Management, University of California, Berkeley, 54 Mulford Hall, Berkeley, CA 94720, USA.
authors.forename: Karen
authors.initials: K
authors.lastname: Andrade
authors.affiliation: Research School of Earth Sciences, The Australian National University, Canberra, ACT 0200, Australia.
authors.forename: Jochen J
authors.initials: JJ
authors.lastname: Brocks
authors.affiliation: Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0202, USA ; Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, CA 92093, USA.
authors.forename: Eric E
authors.initials: EE
authors.lastname: Allen
authors.affiliation: Cooperative Institute for Research in Environmental Sciences, CIRES Building, Room 318, University of Colorado Boulder, Boulder, CO 80309, USA.
authors.forename: Jillian F
authors.initials: JF
authors.lastname: Banfield
authors.affiliation: Department of Biological Sciences, Dornsife College of Letters, Arts and Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089, USA.
authors.forename: Karla B
authors.initials: KB
authors.lastname: Heidelberg
mesh_terms: D044822:Biodiversity; D019605:Euryarchaeota / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D023061:Gene Order; D019766:Genes, Archaeal; D060106:Lakes / Q000382:microbiology*; D053858:Metabolic Networks and Pathways / Q000235:genetics; D054892:Metagenome; D056186:Metagenomics; D017422:Sequence Analysis, DNA; D026801:Synteny; D014739:Victoria