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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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Autores principales: Emerson, Joanne B., Andrade, Karen, Thomas, Brian C., Norman, Anders, Allen, Eric E., Heidelberg, Karla B., Banfield, Jillian F.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3703381/
https://www.ncbi.nlm.nih.gov/pubmed/23853523
http://dx.doi.org/10.1155/2013/370871
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author Emerson, Joanne B.
Andrade, Karen
Thomas, Brian C.
Norman, Anders
Allen, Eric E.
Heidelberg, Karla B.
Banfield, Jillian F.
author_facet Emerson, Joanne B.
Andrade, Karen
Thomas, Brian C.
Norman, Anders
Allen, Eric E.
Heidelberg, Karla B.
Banfield, Jillian F.
author_sort Emerson, Joanne B.
collection PubMed
description 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.
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spelling pubmed-37033812013-07-12 Virus-Host and CRISPR Dynamics in Archaea-Dominated Hypersaline Lake Tyrrell, Victoria, Australia Emerson, Joanne B. Andrade, Karen Thomas, Brian C. Norman, Anders Allen, Eric E. Heidelberg, Karla B. Banfield, Jillian F. Archaea Research Article 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. Hindawi Publishing Corporation 2013-06-18 /pmc/articles/PMC3703381/ /pubmed/23853523 http://dx.doi.org/10.1155/2013/370871 Text en Copyright © 2013 Joanne B. Emerson et al. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
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
title Virus-Host and CRISPR Dynamics in Archaea-Dominated Hypersaline Lake Tyrrell, Victoria, Australia
title_full Virus-Host and CRISPR Dynamics in Archaea-Dominated Hypersaline Lake Tyrrell, Victoria, Australia
title_fullStr Virus-Host and CRISPR Dynamics in Archaea-Dominated Hypersaline Lake Tyrrell, Victoria, Australia
title_full_unstemmed Virus-Host and CRISPR Dynamics in Archaea-Dominated Hypersaline Lake Tyrrell, Victoria, Australia
title_short Virus-Host and CRISPR Dynamics in Archaea-Dominated Hypersaline Lake Tyrrell, Victoria, Australia
title_sort virus-host and crispr dynamics in archaea-dominated hypersaline lake tyrrell, victoria, australia
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3703381/
https://www.ncbi.nlm.nih.gov/pubmed/23853523
http://dx.doi.org/10.1155/2013/370871
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