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]
Copyright 2018 The Authors. Licensed under Creative Commons Attribution 4.0 International (CC BY 4.0) https://creativecommons.org/licenses/by/4.0/
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.
The sequence of the largest replicon of each Hrr. lacusprofundi strain (primary replicon) was highly conserved, while each of the strains’ 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.
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 Type:||Refereed Article|
|Keywords:||Antarctica, holoarchaea, genomic variation|
|Research Division:||Biological Sciences|
|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)|
|Web of Science® Times Cited:||16|
|Deposited By:||CRC-Antarctic Climate & Ecosystems|
|Downloads:||17 View Download Statistics|
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