Comparison of two DNA extraction methods widely used in aquatic microbial ecology
Autor(a) principal: | |
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Data de Publicação: | 2019 |
Outros Autores: | , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1016/j.mimet.2019.02.005 http://hdl.handle.net/11449/188735 |
Resumo: | In recent years, the rapid advances of culture-independent methods and new molecular tools have revolutionized our understanding of microbial biodiversity and ecological functions. DNA extraction from microbial communities is a critical step in this process and several methods have been proposed and used, but the influence of the extraction method on the outcome and ultimately on ecological inferences from the results is not yet precisely determined. Here, we compared two of the most commonly used extraction methods in aquatic microbial ecology, and investigated whether the two methods yielded comparable results for community ecology analyses. We extracted DNA from 15 different shallow lakes with phenol:chloroform, a classical and widely used extraction method, and with the PowerSoil DNA isolation Kit, often suggested as the standard DNA extraction method, with some adaptations for aquatic environments. We found that although only 5% of all OTUs showed significant differences in pairwise comparisons (using the 15 lakes as replicates), these OTUs accounted for >35% (on average) of the relative abundance. Diversity and richness did not differ significantly between the two extraction methods, but the beta-dispersion of the communities indicated that the organic extraction yielded more homogeneous communities, while the kit extraction generated variability. Consequently, we conclude that despite the small number of OTUs with significant differences, their impact on the community composition obtained was not negligible, and therefore the results from these two extraction methods were not comparable. |
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Comparison of two DNA extraction methods widely used in aquatic microbial ecologyAquatic microbial ecologyHigh-throughput sequencingNext-generation sequencingPhenol:chloroform extractionPowerSoil extraction kitIn recent years, the rapid advances of culture-independent methods and new molecular tools have revolutionized our understanding of microbial biodiversity and ecological functions. DNA extraction from microbial communities is a critical step in this process and several methods have been proposed and used, but the influence of the extraction method on the outcome and ultimately on ecological inferences from the results is not yet precisely determined. Here, we compared two of the most commonly used extraction methods in aquatic microbial ecology, and investigated whether the two methods yielded comparable results for community ecology analyses. We extracted DNA from 15 different shallow lakes with phenol:chloroform, a classical and widely used extraction method, and with the PowerSoil DNA isolation Kit, often suggested as the standard DNA extraction method, with some adaptations for aquatic environments. We found that although only 5% of all OTUs showed significant differences in pairwise comparisons (using the 15 lakes as replicates), these OTUs accounted for >35% (on average) of the relative abundance. Diversity and richness did not differ significantly between the two extraction methods, but the beta-dispersion of the communities indicated that the organic extraction yielded more homogeneous communities, while the kit extraction generated variability. Consequently, we conclude that despite the small number of OTUs with significant differences, their impact on the community composition obtained was not negligible, and therefore the results from these two extraction methods were not comparable.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Universidade Estadual PaulistaFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Universidade Federal de São Carlos (UFSCar) Department of Hydrobiology Laboratory of Microbial Processes and BiodiversityPost Graduate Program in Ecology and Natural Resources (PPGERN) UFSCarUFSCar Department of Botany Laboratory of PhycologyUniversidade Estadual Paulista (UNESP) Faculdade de Ciências Agrárias e Veterinárias Departamento de Tecnologia Laboratório de Bioquímica de Microrganismos e Plantas – LBMPUNESP Faculdade de Ciências Agrárias e Veterinárias Departamento de Tecnologia Laboratório Multiusuário Centralizado para Sequenciamento de DNA em Larga Escala e Análise de Expressão Gênica – LMSeqUniversidade Estadual Paulista (UNESP) Faculdade de Ciências Agrárias e Veterinárias Departamento de Tecnologia Laboratório de Bioquímica de Microrganismos e Plantas – LBMPUNESP Faculdade de Ciências Agrárias e Veterinárias Departamento de Tecnologia Laboratório Multiusuário Centralizado para Sequenciamento de DNA em Larga Escala e Análise de Expressão Gênica – LMSeqUniversidade Estadual Paulista: 2009/53984-2FAPESP: 2011/50054-4FAPESP: 2013/18083-0FAPESP: 2014/14139-3Universidade Estadual Paulista: 2016/07679-7CNPq: 309514/2017-7Universidade Federal de São Carlos (UFSCar)Universidade Estadual Paulista (Unesp)Mateus-Barros, ErickMeneghine, Aylan K.Bagatini, Inessa LacativaFernandes, Camila C. [UNESP]Kishi, Luciano T. [UNESP]Vieira, Armando A.H.Sarmento, Hugo2019-10-06T16:17:35Z2019-10-06T16:17:35Z2019-04-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article12-17http://dx.doi.org/10.1016/j.mimet.2019.02.005Journal of Microbiological Methods, v. 159, p. 12-17.1872-83590167-7012http://hdl.handle.net/11449/18873510.1016/j.mimet.2019.02.0052-s2.0-85061643788Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengJournal of Microbiological Methodsinfo:eu-repo/semantics/openAccess2021-10-22T19:03:31Zoai:repositorio.unesp.br:11449/188735Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462021-10-22T19:03:31Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Comparison of two DNA extraction methods widely used in aquatic microbial ecology |
title |
Comparison of two DNA extraction methods widely used in aquatic microbial ecology |
spellingShingle |
Comparison of two DNA extraction methods widely used in aquatic microbial ecology Mateus-Barros, Erick Aquatic microbial ecology High-throughput sequencing Next-generation sequencing Phenol:chloroform extraction PowerSoil extraction kit |
title_short |
Comparison of two DNA extraction methods widely used in aquatic microbial ecology |
title_full |
Comparison of two DNA extraction methods widely used in aquatic microbial ecology |
title_fullStr |
Comparison of two DNA extraction methods widely used in aquatic microbial ecology |
title_full_unstemmed |
Comparison of two DNA extraction methods widely used in aquatic microbial ecology |
title_sort |
Comparison of two DNA extraction methods widely used in aquatic microbial ecology |
author |
Mateus-Barros, Erick |
author_facet |
Mateus-Barros, Erick Meneghine, Aylan K. Bagatini, Inessa Lacativa Fernandes, Camila C. [UNESP] Kishi, Luciano T. [UNESP] Vieira, Armando A.H. Sarmento, Hugo |
author_role |
author |
author2 |
Meneghine, Aylan K. Bagatini, Inessa Lacativa Fernandes, Camila C. [UNESP] Kishi, Luciano T. [UNESP] Vieira, Armando A.H. Sarmento, Hugo |
author2_role |
author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Federal de São Carlos (UFSCar) Universidade Estadual Paulista (Unesp) |
dc.contributor.author.fl_str_mv |
Mateus-Barros, Erick Meneghine, Aylan K. Bagatini, Inessa Lacativa Fernandes, Camila C. [UNESP] Kishi, Luciano T. [UNESP] Vieira, Armando A.H. Sarmento, Hugo |
dc.subject.por.fl_str_mv |
Aquatic microbial ecology High-throughput sequencing Next-generation sequencing Phenol:chloroform extraction PowerSoil extraction kit |
topic |
Aquatic microbial ecology High-throughput sequencing Next-generation sequencing Phenol:chloroform extraction PowerSoil extraction kit |
description |
In recent years, the rapid advances of culture-independent methods and new molecular tools have revolutionized our understanding of microbial biodiversity and ecological functions. DNA extraction from microbial communities is a critical step in this process and several methods have been proposed and used, but the influence of the extraction method on the outcome and ultimately on ecological inferences from the results is not yet precisely determined. Here, we compared two of the most commonly used extraction methods in aquatic microbial ecology, and investigated whether the two methods yielded comparable results for community ecology analyses. We extracted DNA from 15 different shallow lakes with phenol:chloroform, a classical and widely used extraction method, and with the PowerSoil DNA isolation Kit, often suggested as the standard DNA extraction method, with some adaptations for aquatic environments. We found that although only 5% of all OTUs showed significant differences in pairwise comparisons (using the 15 lakes as replicates), these OTUs accounted for >35% (on average) of the relative abundance. Diversity and richness did not differ significantly between the two extraction methods, but the beta-dispersion of the communities indicated that the organic extraction yielded more homogeneous communities, while the kit extraction generated variability. Consequently, we conclude that despite the small number of OTUs with significant differences, their impact on the community composition obtained was not negligible, and therefore the results from these two extraction methods were not comparable. |
publishDate |
2019 |
dc.date.none.fl_str_mv |
2019-10-06T16:17:35Z 2019-10-06T16:17:35Z 2019-04-01 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1016/j.mimet.2019.02.005 Journal of Microbiological Methods, v. 159, p. 12-17. 1872-8359 0167-7012 http://hdl.handle.net/11449/188735 10.1016/j.mimet.2019.02.005 2-s2.0-85061643788 |
url |
http://dx.doi.org/10.1016/j.mimet.2019.02.005 http://hdl.handle.net/11449/188735 |
identifier_str_mv |
Journal of Microbiological Methods, v. 159, p. 12-17. 1872-8359 0167-7012 10.1016/j.mimet.2019.02.005 2-s2.0-85061643788 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Journal of Microbiological Methods |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
12-17 |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
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1799965352568815616 |