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Investigating the Impact of Storage Conditions on Microbial Community Composition in Soil Samples

Recent advances in DNA sequencing technologies have allowed scientists to probe increasingly complex biological systems, including the diversity of bacteria in the environment. However, despite a multitude of recent studies incorporating these methods, many questions regarding how environmental samp...

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Autores principales: Rubin, Benjamin E. R., Gibbons, Sean M., Kennedy, Suzanne, Hampton-Marcell, Jarrad, Owens, Sarah, Gilbert, Jack A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3729949/
https://www.ncbi.nlm.nih.gov/pubmed/23936206
http://dx.doi.org/10.1371/journal.pone.0070460
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author Rubin, Benjamin E. R.
Gibbons, Sean M.
Kennedy, Suzanne
Hampton-Marcell, Jarrad
Owens, Sarah
Gilbert, Jack A.
author_facet Rubin, Benjamin E. R.
Gibbons, Sean M.
Kennedy, Suzanne
Hampton-Marcell, Jarrad
Owens, Sarah
Gilbert, Jack A.
author_sort Rubin, Benjamin E. R.
collection PubMed
description Recent advances in DNA sequencing technologies have allowed scientists to probe increasingly complex biological systems, including the diversity of bacteria in the environment. However, despite a multitude of recent studies incorporating these methods, many questions regarding how environmental samples should be collected and stored still persist. Here, we assess the impact of different soil storage conditions on microbial community composition using Illumina-based 16S rRNA V4 amplicon sequencing. Both storage time and temperature affected bacterial community composition and structure. Frozen samples maintained the highest alpha diversity and differed least in beta diversity, suggesting the utility of cold storage for maintaining consistent communities. Samples stored for intermediate times (three and seven days) had both the highest alpha diversity and the largest differences in overall beta diversity, showing the degree of community change after sample collection. These divergences notwithstanding, differences in neither storage time nor storage temperature substantially altered overall communities relative to more than 500 previously examined soil samples. These results systematically support previous studies and stress the importance of methodological consistency for accurate characterization and comparison of soil microbiological assemblages.
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spelling pubmed-37299492013-08-09 Investigating the Impact of Storage Conditions on Microbial Community Composition in Soil Samples Rubin, Benjamin E. R. Gibbons, Sean M. Kennedy, Suzanne Hampton-Marcell, Jarrad Owens, Sarah Gilbert, Jack A. PLoS One Research Article Recent advances in DNA sequencing technologies have allowed scientists to probe increasingly complex biological systems, including the diversity of bacteria in the environment. However, despite a multitude of recent studies incorporating these methods, many questions regarding how environmental samples should be collected and stored still persist. Here, we assess the impact of different soil storage conditions on microbial community composition using Illumina-based 16S rRNA V4 amplicon sequencing. Both storage time and temperature affected bacterial community composition and structure. Frozen samples maintained the highest alpha diversity and differed least in beta diversity, suggesting the utility of cold storage for maintaining consistent communities. Samples stored for intermediate times (three and seven days) had both the highest alpha diversity and the largest differences in overall beta diversity, showing the degree of community change after sample collection. These divergences notwithstanding, differences in neither storage time nor storage temperature substantially altered overall communities relative to more than 500 previously examined soil samples. These results systematically support previous studies and stress the importance of methodological consistency for accurate characterization and comparison of soil microbiological assemblages. Public Library of Science 2013-07-31 /pmc/articles/PMC3729949/ /pubmed/23936206 http://dx.doi.org/10.1371/journal.pone.0070460 Text en © 2013 Rubin et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Rubin, Benjamin E. R.
Gibbons, Sean M.
Kennedy, Suzanne
Hampton-Marcell, Jarrad
Owens, Sarah
Gilbert, Jack A.
Investigating the Impact of Storage Conditions on Microbial Community Composition in Soil Samples
title Investigating the Impact of Storage Conditions on Microbial Community Composition in Soil Samples
title_full Investigating the Impact of Storage Conditions on Microbial Community Composition in Soil Samples
title_fullStr Investigating the Impact of Storage Conditions on Microbial Community Composition in Soil Samples
title_full_unstemmed Investigating the Impact of Storage Conditions on Microbial Community Composition in Soil Samples
title_short Investigating the Impact of Storage Conditions on Microbial Community Composition in Soil Samples
title_sort investigating the impact of storage conditions on microbial community composition in soil samples
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3729949/
https://www.ncbi.nlm.nih.gov/pubmed/23936206
http://dx.doi.org/10.1371/journal.pone.0070460
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