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Title: Virus-Host and CRISPR Dynamics in Archaea-Dominated Hypersaline Lake Tyrrell, Victoria, Australia

Abstract

The study of natural archaeal assemblages requires community context, namely, a concurrent assessment of the dynamics of archaeal, bacterial, and viral populations. Here, we use filter size-resolved metagenomic analyses to report the dynamics of 101 archaeal and bacterial OTUs and 140 viral populations across 17 samples collected over different timescales from 2007–2010 from Australian hypersaline Lake Tyrrell (LT). All samples were dominated by Archaea (75–95%). Archaeal, bacterial, and viral populations were found to be dynamic on timescales of months to years, and different viral assemblages were present in planktonic, relative to host-associated (active and provirus) size fractions. Analyses of clustered regularly interspaced short palindromic repeat (CRISPR) regions indicate that both rare and abundant viruses were targeted, primarily by lower abundance hosts. Although very few spacers had hits to the NCBI nr database or to the 140 LT viral populations, 21% had hits to unassembled LT viral concentrate reads. This suggests local adaptation to LT-specific viruses and/or undersampling of haloviral assemblages in public databases, along with successful CRISPR-mediated maintenance of viral populations at abundances low enough to preclude genomic assembly. This is the first metagenomic report evaluating widespread archaeal dynamics at the population level on short timescales in a hypersaline system.

Authors:
 [1];  [2];  [3];  [4];  [5];  [6];  [7]
  1. Department of Earth and Planetary Science, University of California, Berkeley, 307 McCone Hall, Berkeley, CA 94720-4767, USA, Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA
  2. Department of Environmental Science, Policy, and Management, University of California, Berkeley, 54 Mulford Hall, Berkeley, CA 94720, USA
  3. Department of Earth and Planetary Science, University of California, Berkeley, 307 McCone Hall, Berkeley, CA 94720-4767, USA
  4. Department of Earth and Planetary Science, University of California, Berkeley, 307 McCone Hall, Berkeley, CA 94720-4767, USA, Department of Biology, University of Copenhagen, Copenhagen, Denmark
  5. Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, CA, USA, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0202, USA
  6. Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
  7. Department of Earth and Planetary Science, University of California, Berkeley, 307 McCone Hall, Berkeley, CA 94720-4767, USA, Department of Environmental Science, Policy, and Management, University of California, Berkeley, 54 Mulford Hall, Berkeley, CA 94720, USA
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1197872
Grant/Contract Number:  
FG02-07ER64505
Resource Type:
Published Article
Journal Name:
Archaea
Additional Journal Information:
Journal Name: Archaea Journal Volume: 2013; Journal ID: ISSN 1472-3646
Publisher:
Hindawi Publishing Corporation
Country of Publication:
United States
Language:
English

Citation Formats

Emerson, Joanne B., Andrade, Karen, Thomas, Brian C., Norman, Anders, Allen, Eric E., Heidelberg, Karla B., and Banfield, Jillian F. Virus-Host and CRISPR Dynamics in Archaea-Dominated Hypersaline Lake Tyrrell, Victoria, Australia. United States: N. p., 2013. Web. doi:10.1155/2013/370871.
Emerson, Joanne B., Andrade, Karen, Thomas, Brian C., Norman, Anders, Allen, Eric E., Heidelberg, Karla B., & Banfield, Jillian F. Virus-Host and CRISPR Dynamics in Archaea-Dominated Hypersaline Lake Tyrrell, Victoria, Australia. United States. doi:10.1155/2013/370871.
Emerson, Joanne B., Andrade, Karen, Thomas, Brian C., Norman, Anders, Allen, Eric E., Heidelberg, Karla B., and Banfield, Jillian F. Tue . "Virus-Host and CRISPR Dynamics in Archaea-Dominated Hypersaline Lake Tyrrell, Victoria, Australia". United States. doi:10.1155/2013/370871.
@article{osti_1197872,
title = {Virus-Host and CRISPR Dynamics in Archaea-Dominated Hypersaline Lake Tyrrell, Victoria, Australia},
author = {Emerson, Joanne B. and Andrade, Karen and Thomas, Brian C. and Norman, Anders and Allen, Eric E. and Heidelberg, Karla B. and Banfield, Jillian F.},
abstractNote = {The study of natural archaeal assemblages requires community context, namely, a concurrent assessment of the dynamics of archaeal, bacterial, and viral populations. Here, we use filter size-resolved metagenomic analyses to report the dynamics of 101 archaeal and bacterial OTUs and 140 viral populations across 17 samples collected over different timescales from 2007–2010 from Australian hypersaline Lake Tyrrell (LT). All samples were dominated by Archaea (75–95%). Archaeal, bacterial, and viral populations were found to be dynamic on timescales of months to years, and different viral assemblages were present in planktonic, relative to host-associated (active and provirus) size fractions. Analyses of clustered regularly interspaced short palindromic repeat (CRISPR) regions indicate that both rare and abundant viruses were targeted, primarily by lower abundance hosts. Although very few spacers had hits to the NCBI nr database or to the 140 LT viral populations, 21% had hits to unassembled LT viral concentrate reads. This suggests local adaptation to LT-specific viruses and/or undersampling of haloviral assemblages in public databases, along with successful CRISPR-mediated maintenance of viral populations at abundances low enough to preclude genomic assembly. This is the first metagenomic report evaluating widespread archaeal dynamics at the population level on short timescales in a hypersaline system.},
doi = {10.1155/2013/370871},
journal = {Archaea},
number = ,
volume = 2013,
place = {United States},
year = {2013},
month = {1}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1155/2013/370871

Citation Metrics:
Cited by: 6 works
Citation information provided by
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