Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils
Soils impact global carbon cycling and their resident microbes are critical to their biogeochemical processing and ecosystem outputs. Based on studies in marine systems, viruses infecting soil microbes likely modulate host activities via mortality, horizontal gene transfer, and metabolic control. Ho...
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crpeerj:10.7717/peerj.7265 2024-09-15T18:30:13+00:00 Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils Trubl, Gareth Roux, Simon Solonenko, Natalie Li, Yueh-Fen Bolduc, Benjamin Rodríguez-Ramos, Josué Eloe-Fadrosh, Emiley A. Rich, Virginia I. Sullivan, Matthew B. Genomic Science Program of the United States Department of Energy Office of Biological and Environmental Research The Office of Science, Office of Workforce Development for Teachers and Scientists, Office of Science Graduate Student Research Gordon and Betty Moore Foundation Investigator Award Oak Ridge Institute for Science and Education Office of Science of the US Department of Energy Ohio Supercomputer Center and by the National Science Foundation under Award Numbers 2019 http://dx.doi.org/10.7717/peerj.7265 https://peerj.com/articles/7265.pdf https://peerj.com/articles/7265.xml https://peerj.com/articles/7265.html en eng PeerJ http://creativecommons.org/licenses/by/4.0/ PeerJ volume 7, page e7265 ISSN 2167-8359 journal-article 2019 crpeerj https://doi.org/10.7717/peerj.7265 2024-08-26T04:20:28Z Soils impact global carbon cycling and their resident microbes are critical to their biogeochemical processing and ecosystem outputs. Based on studies in marine systems, viruses infecting soil microbes likely modulate host activities via mortality, horizontal gene transfer, and metabolic control. However, their roles remain largely unexplored due to technical challenges with separating, isolating, and extracting DNA from viruses in soils. Some of these challenges have been overcome by using whole genome amplification methods and while these have allowed insights into the identities of soil viruses and their genomes, their inherit biases have prevented meaningful ecological interpretations. Here we experimentally optimized steps for generating quantitatively-amplified viral metagenomes to better capture both ssDNA and dsDNA viruses across three distinct soil habitats along a permafrost thaw gradient. First, we assessed differing DNA extraction methods (PowerSoil, Wizard mini columns, and cetyl trimethylammonium bromide) for quantity and quality of viral DNA. This established PowerSoil as best for yield and quality of DNA from our samples, though ∼1/3 of the viral populations captured by each extraction kit were unique, suggesting appreciable differential biases among DNA extraction kits. Second, we evaluated the impact of purifying viral particles after resuspension (by cesium chloride gradients; CsCl) and of viral lysis method (heat vs bead-beating) on the resultant viromes. DNA yields after CsCl particle-purification were largely non-detectable, while unpurified samples yielded 1–2-fold more DNA after lysis by heat than by bead-beating. Virome quality was assessed by the number and size of metagenome-assembled viral contigs, which showed no increase after CsCl-purification, but did from heat lysis relative to bead-beating. We also evaluated sample preparation protocols for ssDNA virus recovery. In both CsCl-purified and non-purified samples, ssDNA viruses were successfully recovered by using the Accel-NGS 1S ... Article in Journal/Newspaper permafrost PeerJ Publishing PeerJ 7 e7265 |
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English |
description |
Soils impact global carbon cycling and their resident microbes are critical to their biogeochemical processing and ecosystem outputs. Based on studies in marine systems, viruses infecting soil microbes likely modulate host activities via mortality, horizontal gene transfer, and metabolic control. However, their roles remain largely unexplored due to technical challenges with separating, isolating, and extracting DNA from viruses in soils. Some of these challenges have been overcome by using whole genome amplification methods and while these have allowed insights into the identities of soil viruses and their genomes, their inherit biases have prevented meaningful ecological interpretations. Here we experimentally optimized steps for generating quantitatively-amplified viral metagenomes to better capture both ssDNA and dsDNA viruses across three distinct soil habitats along a permafrost thaw gradient. First, we assessed differing DNA extraction methods (PowerSoil, Wizard mini columns, and cetyl trimethylammonium bromide) for quantity and quality of viral DNA. This established PowerSoil as best for yield and quality of DNA from our samples, though ∼1/3 of the viral populations captured by each extraction kit were unique, suggesting appreciable differential biases among DNA extraction kits. Second, we evaluated the impact of purifying viral particles after resuspension (by cesium chloride gradients; CsCl) and of viral lysis method (heat vs bead-beating) on the resultant viromes. DNA yields after CsCl particle-purification were largely non-detectable, while unpurified samples yielded 1–2-fold more DNA after lysis by heat than by bead-beating. Virome quality was assessed by the number and size of metagenome-assembled viral contigs, which showed no increase after CsCl-purification, but did from heat lysis relative to bead-beating. We also evaluated sample preparation protocols for ssDNA virus recovery. In both CsCl-purified and non-purified samples, ssDNA viruses were successfully recovered by using the Accel-NGS 1S ... |
author2 |
Genomic Science Program of the United States Department of Energy Office of Biological and Environmental Research The Office of Science, Office of Workforce Development for Teachers and Scientists, Office of Science Graduate Student Research Gordon and Betty Moore Foundation Investigator Award Oak Ridge Institute for Science and Education Office of Science of the US Department of Energy Ohio Supercomputer Center and by the National Science Foundation under Award Numbers |
format |
Article in Journal/Newspaper |
author |
Trubl, Gareth Roux, Simon Solonenko, Natalie Li, Yueh-Fen Bolduc, Benjamin Rodríguez-Ramos, Josué Eloe-Fadrosh, Emiley A. Rich, Virginia I. Sullivan, Matthew B. |
spellingShingle |
Trubl, Gareth Roux, Simon Solonenko, Natalie Li, Yueh-Fen Bolduc, Benjamin Rodríguez-Ramos, Josué Eloe-Fadrosh, Emiley A. Rich, Virginia I. Sullivan, Matthew B. Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils |
author_facet |
Trubl, Gareth Roux, Simon Solonenko, Natalie Li, Yueh-Fen Bolduc, Benjamin Rodríguez-Ramos, Josué Eloe-Fadrosh, Emiley A. Rich, Virginia I. Sullivan, Matthew B. |
author_sort |
Trubl, Gareth |
title |
Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils |
title_short |
Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils |
title_full |
Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils |
title_fullStr |
Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils |
title_full_unstemmed |
Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils |
title_sort |
towards optimized viral metagenomes for double-stranded and single-stranded dna viruses from challenging soils |
publisher |
PeerJ |
publishDate |
2019 |
url |
http://dx.doi.org/10.7717/peerj.7265 https://peerj.com/articles/7265.pdf https://peerj.com/articles/7265.xml https://peerj.com/articles/7265.html |
genre |
permafrost |
genre_facet |
permafrost |
op_source |
PeerJ volume 7, page e7265 ISSN 2167-8359 |
op_rights |
http://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.7717/peerj.7265 |
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PeerJ |
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7 |
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e7265 |
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1810471688049000448 |