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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Comparison of two DNA extraction methods widely used in aquatic microbial ecology

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Author(s):
Mateus-Barros, Erick [1, 2] ; Meneghine, Aylan K. [1] ; Bagatini, Inessa Lacativa [3] ; Fernandes, Camila C. [4, 5] ; Kishi, Luciano T. [4, 5] ; Vieira, Armando A. H. [3] ; Sarmento, Hugo [1]
Total Authors: 7
Affiliation:
[1] Univ Fed Sao Carlos, Dept Hydrobiol, Lab Microbial Proc & Biodivers, BR-13565905 Sao Carlos, SP - Brazil
[2] Univ Fed Sao Carlos, PPGERN, BR-13565905 Sao Carlos, SP - Brazil
[3] Univ Fed Sao Carlos, Dept Bot, Lab Phycol, BR-13565905 Sao Carlos, SP - Brazil
[4] Univ Estadual Paulista, Fac Ciencias Agr & Vet, Dept Tecnol, LBMP, BR-14884900 Jaboticabal, SP - Brazil
[5] UNESP, Fac Ciencias Agr & Vet, Dept Tecnol, Lab Multiusuario Centralizado Sequenciamento DNA, BR-14884900 Jaboticabal, SP - Brazil
Total Affiliations: 5
Document type: Journal article
Source: Journal of Microbiological Methods; v. 159, p. 12-17, APR 2019.
Web of Science Citations: 0
Abstract

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. (AU)

FAPESP's process: 11/50054-4 - Biodiversity of freshwater microalgae: germplasm bank and obtaining of molecular markers of cryopreserved species
Grantee:Armando Augusto Henriques Vieira
Support type: BIOTA-FAPESP Program - Thematic Grants
FAPESP's process: 14/14139-3 - Microbial processes and biodiversity in aquatic ecosystems
Grantee:Hugo Miguel Preto de Morais Sarmento
Support type: Research Grants - Young Investigators Grants
FAPESP's process: 16/07679-7 - Equipment acquisition for multi-user centralized labs - centralized multi-user lab sequencing and large scale gene expression (LMSeq)
Grantee:Eliana Gertrudes de Macedo Lemos
Support type: Multi-user Equipment Program