Direct Assessment of Viral Diversity in Soils by Random PCR Amplification of Polymorphic DNA
Viruses are the most abundant and diverse biological entities within soils, yet their ecological impact is largely unknown. Defining how soil viral communities change with perturbation or across environments will contribute to understanding the larger ecological significance of soil viruses. A new a...
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ftpubmed:oai:pubmedcentral.nih.gov:3754152 2023-05-15T13:52:38+02:00 Direct Assessment of Viral Diversity in Soils by Random PCR Amplification of Polymorphic DNA Srinivasiah, Sharath Lovett, Jacqueline Polson, Shawn Bhavsar, Jaysheel Ghosh, Dhritiman Roy, Krishnakali Fuhrmann, Jeffry J. Radosevich, Mark Wommack, K. Eric 2013-09 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3754152 http://www.ncbi.nlm.nih.gov/pubmed/23793630 https://doi.org/10.1128/AEM.00268-13 en eng American Society for Microbiology http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3754152 http://www.ncbi.nlm.nih.gov/pubmed/23793630 http://dx.doi.org/10.1128/AEM.00268-13 Copyright © 2013, American Society for Microbiology. All Rights Reserved. Methods Text 2013 ftpubmed https://doi.org/10.1128/AEM.00268-13 2014-03-02T01:51:32Z Viruses are the most abundant and diverse biological entities within soils, yet their ecological impact is largely unknown. Defining how soil viral communities change with perturbation or across environments will contribute to understanding the larger ecological significance of soil viruses. A new approach to examining the composition of soil viral communities based on random PCR amplification of polymorphic DNA (RAPD-PCR) was developed. A key methodological improvement was the use of viral metagenomic sequence data for the design of RAPD-PCR primers. This metagenomically informed approach to primer design enabled the optimization of RAPD-PCR sensitivity for examining changes in soil viral communities. Initial application of RAPD-PCR viral fingerprinting to soil viral communities demonstrated that the composition of autochthonous soil viral assemblages noticeably changed over a distance of meters along a transect of Antarctic soils and across soils subjected to different land uses. For Antarctic soils, viral assemblages segregated upslope from the edge of dry valley lakes. In the case of temperate soils at the Kellogg Biological Station, viral communities clustered according to land use treatment. In both environments, soil viral communities changed along with environmental factors known to shape the composition of bacterial host communities. Overall, this work demonstrates that RAPD-PCR fingerprinting is an inexpensive, high-throughput means for addressing first-order questions of viral community dynamics within environmental samples and thus fills a methodological gap between narrow single-gene approaches and comprehensive shotgun metagenomic sequencing for the analysis of viral community diversity. Text Antarc* Antarctic PubMed Central (PMC) Antarctic Applied and Environmental Microbiology 79 18 5450 5457 |
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Methods Srinivasiah, Sharath Lovett, Jacqueline Polson, Shawn Bhavsar, Jaysheel Ghosh, Dhritiman Roy, Krishnakali Fuhrmann, Jeffry J. Radosevich, Mark Wommack, K. Eric Direct Assessment of Viral Diversity in Soils by Random PCR Amplification of Polymorphic DNA |
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Methods |
description |
Viruses are the most abundant and diverse biological entities within soils, yet their ecological impact is largely unknown. Defining how soil viral communities change with perturbation or across environments will contribute to understanding the larger ecological significance of soil viruses. A new approach to examining the composition of soil viral communities based on random PCR amplification of polymorphic DNA (RAPD-PCR) was developed. A key methodological improvement was the use of viral metagenomic sequence data for the design of RAPD-PCR primers. This metagenomically informed approach to primer design enabled the optimization of RAPD-PCR sensitivity for examining changes in soil viral communities. Initial application of RAPD-PCR viral fingerprinting to soil viral communities demonstrated that the composition of autochthonous soil viral assemblages noticeably changed over a distance of meters along a transect of Antarctic soils and across soils subjected to different land uses. For Antarctic soils, viral assemblages segregated upslope from the edge of dry valley lakes. In the case of temperate soils at the Kellogg Biological Station, viral communities clustered according to land use treatment. In both environments, soil viral communities changed along with environmental factors known to shape the composition of bacterial host communities. Overall, this work demonstrates that RAPD-PCR fingerprinting is an inexpensive, high-throughput means for addressing first-order questions of viral community dynamics within environmental samples and thus fills a methodological gap between narrow single-gene approaches and comprehensive shotgun metagenomic sequencing for the analysis of viral community diversity. |
format |
Text |
author |
Srinivasiah, Sharath Lovett, Jacqueline Polson, Shawn Bhavsar, Jaysheel Ghosh, Dhritiman Roy, Krishnakali Fuhrmann, Jeffry J. Radosevich, Mark Wommack, K. Eric |
author_facet |
Srinivasiah, Sharath Lovett, Jacqueline Polson, Shawn Bhavsar, Jaysheel Ghosh, Dhritiman Roy, Krishnakali Fuhrmann, Jeffry J. Radosevich, Mark Wommack, K. Eric |
author_sort |
Srinivasiah, Sharath |
title |
Direct Assessment of Viral Diversity in Soils by Random PCR Amplification of Polymorphic DNA |
title_short |
Direct Assessment of Viral Diversity in Soils by Random PCR Amplification of Polymorphic DNA |
title_full |
Direct Assessment of Viral Diversity in Soils by Random PCR Amplification of Polymorphic DNA |
title_fullStr |
Direct Assessment of Viral Diversity in Soils by Random PCR Amplification of Polymorphic DNA |
title_full_unstemmed |
Direct Assessment of Viral Diversity in Soils by Random PCR Amplification of Polymorphic DNA |
title_sort |
direct assessment of viral diversity in soils by random pcr amplification of polymorphic dna |
publisher |
American Society for Microbiology |
publishDate |
2013 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3754152 http://www.ncbi.nlm.nih.gov/pubmed/23793630 https://doi.org/10.1128/AEM.00268-13 |
geographic |
Antarctic |
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Antarctic |
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Antarc* Antarctic |
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Antarc* Antarctic |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3754152 http://www.ncbi.nlm.nih.gov/pubmed/23793630 http://dx.doi.org/10.1128/AEM.00268-13 |
op_rights |
Copyright © 2013, American Society for Microbiology. All Rights Reserved. |
op_doi |
https://doi.org/10.1128/AEM.00268-13 |
container_title |
Applied and Environmental Microbiology |
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79 |
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18 |
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5450 |
op_container_end_page |
5457 |
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1766257061435277312 |