Direct Assessment of Viral Diversity in Soils by Random PCR Amplification of Polymorphic DNA
ABSTRACT 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...
Published in: | Applied and Environmental Microbiology |
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Online Access: | http://dx.doi.org/10.1128/aem.00268-13 https://journals.asm.org/doi/pdf/10.1128/AEM.00268-13 |
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crasmicro:10.1128/aem.00268-13 2024-06-23T07:45:53+00:00 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 http://dx.doi.org/10.1128/aem.00268-13 https://journals.asm.org/doi/pdf/10.1128/AEM.00268-13 en eng American Society for Microbiology https://journals.asm.org/non-commercial-tdm-license Applied and Environmental Microbiology volume 79, issue 18, page 5450-5457 ISSN 0099-2240 1098-5336 journal-article 2013 crasmicro https://doi.org/10.1128/aem.00268-13 2024-06-03T08:10:55Z ABSTRACT 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. Article in Journal/Newspaper Antarc* Antarctic ASM Journals (American Society for Microbiology) Antarctic Applied and Environmental Microbiology 79 18 5450 5457 |
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Open Polar |
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ASM Journals (American Society for Microbiology) |
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crasmicro |
language |
English |
description |
ABSTRACT 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 |
Article in Journal/Newspaper |
author |
Srinivasiah, Sharath Lovett, Jacqueline Polson, Shawn Bhavsar, Jaysheel Ghosh, Dhritiman Roy, Krishnakali Fuhrmann, Jeffry J. Radosevich, Mark Wommack, K. Eric |
spellingShingle |
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 |
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://dx.doi.org/10.1128/aem.00268-13 https://journals.asm.org/doi/pdf/10.1128/AEM.00268-13 |
geographic |
Antarctic |
geographic_facet |
Antarctic |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_source |
Applied and Environmental Microbiology volume 79, issue 18, page 5450-5457 ISSN 0099-2240 1098-5336 |
op_rights |
https://journals.asm.org/non-commercial-tdm-license |
op_doi |
https://doi.org/10.1128/aem.00268-13 |
container_title |
Applied and Environmental Microbiology |
container_volume |
79 |
container_issue |
18 |
container_start_page |
5450 |
op_container_end_page |
5457 |
_version_ |
1802642827706892288 |