Genomic variation and biogeography of Antarctic haloarchaea
© 2018 The Author(s). 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 understan...
Published in: | Microbiome |
---|---|
Main Authors: | , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
eScholarship, University of California
2018
|
Subjects: | |
Online Access: | http://www.escholarship.org/uc/item/90s5b3d2 |
id |
ftcdlib:qt90s5b3d2 |
---|---|
record_format |
openpolar |
spelling |
ftcdlib:qt90s5b3d2 2023-05-15T13:43:56+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, AM Eloe-Fadrosh, EA Cavicchioli, R 113 2018-06-20 application/pdf http://www.escholarship.org/uc/item/90s5b3d2 english eng eScholarship, University of California qt90s5b3d2 http://www.escholarship.org/uc/item/90s5b3d2 public Tschitschko, B; Erdmann, S; DeMaere, MZ; Roux, S; Panwar, P; Allen, MA; et al.(2018). Genomic variation and biogeography of Antarctic haloarchaea. Microbiome, 6(1), 113. doi:10.1186/s40168-018-0495-3. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/90s5b3d2 article 2018 ftcdlib https://doi.org/10.1186/s40168-018-0495-3 2018-07-13T22:59:01Z © 2018 The Author(s). 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 University of California: eScholarship Antarctic Rauer Islands ENVELOPE(77.833,77.833,-68.850,-68.850) Vestfold Vestfold Hills Microbiome 6 1 |
institution |
Open Polar |
collection |
University of California: eScholarship |
op_collection_id |
ftcdlib |
language |
English |
description |
© 2018 The Author(s). 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, AM Eloe-Fadrosh, EA Cavicchioli, R |
spellingShingle |
Tschitschko, B Erdmann, S DeMaere, MZ Roux, S Panwar, P Allen, MA Williams, TJ Brazendale, S Hancock, AM Eloe-Fadrosh, EA Cavicchioli, R Genomic variation and biogeography of Antarctic haloarchaea |
author_facet |
Tschitschko, B Erdmann, S DeMaere, MZ Roux, S Panwar, P Allen, MA Williams, TJ Brazendale, S Hancock, AM 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 |
eScholarship, University of California |
publishDate |
2018 |
url |
http://www.escholarship.org/uc/item/90s5b3d2 |
op_coverage |
113 |
long_lat |
ENVELOPE(77.833,77.833,-68.850,-68.850) |
geographic |
Antarctic Rauer Islands Vestfold Vestfold Hills |
geographic_facet |
Antarctic Rauer Islands Vestfold Vestfold Hills |
genre |
Antarc* Antarctic Antarctica Rauer Islands |
genre_facet |
Antarc* Antarctic Antarctica Rauer Islands |
op_source |
Tschitschko, B; Erdmann, S; DeMaere, MZ; Roux, S; Panwar, P; Allen, MA; et al.(2018). Genomic variation and biogeography of Antarctic haloarchaea. Microbiome, 6(1), 113. doi:10.1186/s40168-018-0495-3. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/90s5b3d2 |
op_relation |
qt90s5b3d2 http://www.escholarship.org/uc/item/90s5b3d2 |
op_rights |
public |
op_doi |
https://doi.org/10.1186/s40168-018-0495-3 |
container_title |
Microbiome |
container_volume |
6 |
container_issue |
1 |
_version_ |
1766195198304452608 |