Genomic variation and biogeography of Antarctic haloarchaea
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 variatio...
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Online Access: | https://doi.org/10.1186/s40168-018-0495-3 http://www.ncbi.nlm.nih.gov/pubmed/29925429 http://ecite.utas.edu.au/131866 |
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ftunivtasecite:oai:ecite.utas.edu.au:131866 2023-05-15T13:59:46+02:00 Genomic variation and biogeography of Antarctic haloarchaea Tschitschko, B Erdmann, S DeMaere, MZ Roux, S Panwar, P Allen, MA Williams, TJ Brazendale, S Hancock, A Eloe-Fadrosh, EA Cavicchioli, R 2018 application/pdf https://doi.org/10.1186/s40168-018-0495-3 http://www.ncbi.nlm.nih.gov/pubmed/29925429 http://ecite.utas.edu.au/131866 en eng BioMed Central Ltd. http://ecite.utas.edu.au/131866/1/131866 - Genomic variation and biogeography of Antarctic haloarchaea.pdf http://dx.doi.org/10.1186/s40168-018-0495-3 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] http://www.ncbi.nlm.nih.gov/pubmed/29925429 http://ecite.utas.edu.au/131866 Biological Sciences Genetics Genomics Refereed Article PeerReviewed 2018 ftunivtasecite https://doi.org/10.1186/s40168-018-0495-3 2021-05-31T22:16:36Z 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 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. 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. Article in Journal/Newspaper Antarc* Antarctic Antarctica Rauer Islands eCite UTAS (University of Tasmania) Antarctic Vestfold Hills Vestfold Rauer Islands ENVELOPE(77.833,77.833,-68.850,-68.850) Microbiome 6 1 |
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Open Polar |
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eCite UTAS (University of Tasmania) |
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ftunivtasecite |
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English |
topic |
Biological Sciences Genetics Genomics |
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Biological Sciences Genetics Genomics Tschitschko, B Erdmann, S DeMaere, MZ Roux, S Panwar, P Allen, MA Williams, TJ Brazendale, S Hancock, A Eloe-Fadrosh, EA Cavicchioli, R Genomic variation and biogeography of Antarctic haloarchaea |
topic_facet |
Biological Sciences Genetics Genomics |
description |
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 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. 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. |
format |
Article in Journal/Newspaper |
author |
Tschitschko, B Erdmann, S DeMaere, MZ Roux, S Panwar, P Allen, MA Williams, TJ Brazendale, S Hancock, A Eloe-Fadrosh, EA Cavicchioli, R |
author_facet |
Tschitschko, B Erdmann, S DeMaere, MZ Roux, S Panwar, P Allen, MA Williams, TJ Brazendale, S Hancock, A Eloe-Fadrosh, EA Cavicchioli, R |
author_sort |
Tschitschko, B |
title |
Genomic variation and biogeography of Antarctic haloarchaea |
title_short |
Genomic variation and biogeography of Antarctic haloarchaea |
title_full |
Genomic variation and biogeography of Antarctic haloarchaea |
title_fullStr |
Genomic variation and biogeography of Antarctic haloarchaea |
title_full_unstemmed |
Genomic variation and biogeography of Antarctic haloarchaea |
title_sort |
genomic variation and biogeography of antarctic haloarchaea |
publisher |
BioMed Central Ltd. |
publishDate |
2018 |
url |
https://doi.org/10.1186/s40168-018-0495-3 http://www.ncbi.nlm.nih.gov/pubmed/29925429 http://ecite.utas.edu.au/131866 |
long_lat |
ENVELOPE(77.833,77.833,-68.850,-68.850) |
geographic |
Antarctic Vestfold Hills Vestfold Rauer Islands |
geographic_facet |
Antarctic Vestfold Hills Vestfold Rauer Islands |
genre |
Antarc* Antarctic Antarctica Rauer Islands |
genre_facet |
Antarc* Antarctic Antarctica Rauer Islands |
op_relation |
http://ecite.utas.edu.au/131866/1/131866 - Genomic variation and biogeography of Antarctic haloarchaea.pdf http://dx.doi.org/10.1186/s40168-018-0495-3 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] http://www.ncbi.nlm.nih.gov/pubmed/29925429 http://ecite.utas.edu.au/131866 |
op_doi |
https://doi.org/10.1186/s40168-018-0495-3 |
container_title |
Microbiome |
container_volume |
6 |
container_issue |
1 |
_version_ |
1766268557493010432 |