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Title: Genomic variation and biogeography of Antarctic haloarchaea

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 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 andmore » 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.« less

Authors:
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Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); Australian Research Council
OSTI Identifier:
1618939
Alternate Identifier(s):
OSTI ID: 1544022
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Published Article
Journal Name:
Microbiome
Additional Journal Information:
Journal Name: Microbiome Journal Volume: 6 Journal Issue: 1; Journal ID: ISSN 2049-2618
Publisher:
Springer Science + Business Media
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Haloarchaea; Halobacteria; Antarctica; Genome variation; Metagenomics; Pan-genome; Genomic islands; Replicons; Virus infection; Biogeography

Citation Formats

Tschitschko, Bernhard, Erdmann, Susanne, DeMaere, Matthew Z., Roux, Simon, Panwar, Pratibha, Allen, Michelle A., Williams, Timothy J., Brazendale, Sarah, Hancock, Alyce M., Eloe-Fadrosh, Emiley A., and Cavicchioli, Ricardo. Genomic variation and biogeography of Antarctic haloarchaea. United Kingdom: N. p., 2018. Web. doi:10.1186/s40168-018-0495-3.
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Tschitschko, Bernhard, Erdmann, Susanne, DeMaere, Matthew Z., Roux, Simon, Panwar, Pratibha, Allen, Michelle A., Williams, Timothy J., Brazendale, Sarah, Hancock, Alyce M., Eloe-Fadrosh, Emiley A., & Cavicchioli, Ricardo. Genomic variation and biogeography of Antarctic haloarchaea. United Kingdom. https://doi.org/10.1186/s40168-018-0495-3
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Tschitschko, Bernhard, Erdmann, Susanne, DeMaere, Matthew Z., Roux, Simon, Panwar, Pratibha, Allen, Michelle A., Williams, Timothy J., Brazendale, Sarah, Hancock, Alyce M., Eloe-Fadrosh, Emiley A., and Cavicchioli, Ricardo. Wed . "Genomic variation and biogeography of Antarctic haloarchaea". United Kingdom. https://doi.org/10.1186/s40168-018-0495-3.
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@article{osti_1618939,
title = {Genomic variation and biogeography of Antarctic haloarchaea},
author = {Tschitschko, Bernhard and Erdmann, Susanne and DeMaere, Matthew Z. and Roux, Simon and Panwar, Pratibha and Allen, Michelle A. and Williams, Timothy J. and Brazendale, Sarah and Hancock, Alyce M. and Eloe-Fadrosh, Emiley A. and Cavicchioli, Ricardo},
abstractNote = {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.},
doi = {10.1186/s40168-018-0495-3},
journal = {Microbiome},
number = 1,
volume = 6,
place = {United Kingdom},
year = {Wed Jun 20 00:00:00 EDT 2018},
month = {Wed Jun 20 00:00:00 EDT 2018}
}
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Publisher's Version of Record
https://doi.org/10.1186/s40168-018-0495-3
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Cited by: 20 works
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Figures / Tables:

Fig. 1 Fig. 1: Hypersaline lakes in the Vestfold Hills and Rauer Islands sampled for metagenomics. Photo credits: Alyce Hancock (Rauer 1 Lake, Rauer 3 Lake); Sarah Payne (Rauer 6 Lake, Rauer 13 Lake, Club Lake); Rick Cavicchioli (Deep Lake); Landsat Image Mosaic of Antarctica (LIMA) project for the satellite image. Hrr.more » lacusprofundi ACAM34 isolated from Deep Lake and R1S1 from Rauer 1 Lake« less
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    Works referencing / citing this record:

    Unexpected host dependency of Antarctic Nanohaloarchaeota
    journal, June 2019

    • Hamm, Joshua N.; Erdmann, Susanne; Eloe-Fadrosh, Emiley A.
    • Proceedings of the National Academy of Sciences, Vol. 116, Issue 29
    • DOI: 10.1073/pnas.1905179116

    Novel haloarchaeal viruses from Lake Retba infecting Haloferax and Halorubrum species
    journal, April 2019

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    • Environmental Microbiology, Vol. 21, Issue 6
    • DOI: 10.1111/1462-2920.14604

    Applying Genome-Resolved Metagenomics to Deconvolute the Halophilic Microbiome
    journal, March 2019

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