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De novo sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, reveal a variable genomic landscape. | LitMetric

De novo sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, reveal a variable genomic landscape.

Archaea

Department of Biological Sciences, Dornsife College of Letters, Arts and Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089, USA.

Published: November 2015

AI Article Synopsis

  • Hypersaline systems, like Lake Tyrrell in Australia, harbor organisms such as the square archaeon Haloquadratum walsbyi that thrive in extreme conditions near salt saturation.
  • A comparative genomic analysis of H. walsbyi revealed significant genomic variation among its strains, indicating that previous classifications do not encompass its full genetic diversity.
  • Research on ATP-binding cassette transporters showed unique transport subunits in different strains, hinting that variations in nutrient and carbon source acquisition contribute to the maintenance of distinct strains within the Haloquadratum community.

Article 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.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4330952PMC
http://dx.doi.org/10.1155/2015/875784DOI Listing

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