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

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 populati...

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Bibliographic Details
Published in:Archaea 2013-01, Vol.2013 (2013), p.143-154
Main Authors: Emerson, Joanne B., Andrade, Karen, Thomas, Brian C., Norman, Anders, Allen, Eric E., Heidelberg, Karla B., Banfield, Jillian F.
Format: Article
Language:English
Subjects:
Analysis
Archaea - genetics
Archaea - metabolism
Archaeabacteria
Bacteria - genetics
Bacteria - metabolism
BASIC BIOLOGICAL SCIENCES
DNA, Archaeal - analysis
DNA, Archaeal - genetics
DNA, Bacterial - analysis
DNA, Bacterial - genetics
DNA, Intergenic - analysis
DNA, Intergenic - genetics
DNA, Viral - analysis
DNA, Viral - genetics
Host-virus relationships
Inverted Repeat Sequences
Lakes - microbiology
Metagenomics
Microbial Consortia - genetics
Microbiology
Plankton
RNA, Ribosomal, 16S - genetics
Salinity
Victoria
Viruses - genetics
Viruses - metabolism
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Summary: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.
ISSN:1472-3646
1472-3654
DOI:10.1155/2013/370871