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Genomic variation and biogeography of Antarctic haloarchaea

Citation

Tschitschko, B and Erdmann, S and DeMaere, MZ and Roux, S and Panwar, P and Allen, MA and Williams, TJ and Brazendale, S and Hancock, A and Eloe-Fadrosh, EA and Cavicchioli, R, Genomic variation and biogeography of Antarctic haloarchaea, Microbiome, 6, (1) Article 113. ISSN 2049-2618 (2018) [Refereed Article]


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Copyright Statement

Copyright 2018 The Authors. Licensed under Creative Commons Attribution 4.0 International (CC BY 4.0) https://creativecommons.org/licenses/by/4.0/

DOI: doi:10.1186/s40168-018-0495-3

Abstract

Background

The genomes of halophilic archaea (haloarchaea) often comprise multiple replicons. Genomic variation in haloarchaea has been linked to viral infection pressure and, in the case of Antarctic communities, can be caused by intergenera gene exchange. To expand understanding of genome variation and biogeography of Antarctic haloarchaea, here we assessed genomic variation between two strains of Halorubrum lacusprofundi that were isolated from Antarctic hypersaline lakes from different regions (Vestfold Hills and Rauer Islands). To assess variation in haloarchaeal populations, including the presence of genomic islands, metagenomes from six hypersaline Antarctic lakes were characterised.

Results

The sequence of the largest replicon of each Hrr. lacusprofundi strain (primary replicon) was highly conserved, while each of the strainsí two smaller replicons (secondary replicons) were highly variable. Intergenera gene exchange was identified, including the sharing of a type I-B CRISPR system. Evaluation of infectivity of an Antarctic halovirus provided experimental evidence for the differential susceptibility of the strains, bolstering inferences that strain variation is important for modulating interactions with viruses. A relationship was found between genomic structuring and the location of variation within replicons and genomic islands, demonstrating that the way in which haloarchaea accommodate genomic variability relates to replicon structuring. Metagenome read and contig mapping and clustering and scaling analyses demonstrated biogeographical patterning of variation consistent with environment and distance effects. The metagenome data also demonstrated that specific haloarchaeal species dominated the hypersaline systems indicating they are endemic to Antarctica.

Conclusion

The study describes how genomic variation manifests in Antarctic-lake haloarchaeal communities and provides the basis for future assessments of Antarctic regional and global biogeography of haloarchaea.

Item Details

Item Type:Refereed Article
Keywords:Antarctica, holoarchaea, genomic variation
Research Division:Biological Sciences
Research Group:Genetics
Research Field:Genomics
Objective Division:Environmental Management
Objective Group:Management of Antarctic and Southern Ocean environments
Objective Field:Biodiversity in Antarctic and Southern Ocean environments
UTAS Author:Hancock, A (Miss Alyce Hancock)
ID Code:131866
Year Published:2018
Web of Science® Times Cited:9
Deposited By:CRC-Antarctic Climate & Ecosystems
Deposited On:2019-04-10
Last Modified:2021-05-27
Downloads:11 View Download Statistics

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