Affiliation:
1. Universidade de Brasília, Brasil
2. Universidade Federal do Tocantins, Brasil
Abstract
Abstract Polymerase chain reaction (PCR) assays targeting 16S rRNA genes followed by DNA sequencing are still important tools to characterize microbial communities present in environmental samples. However, despite the crescent number of deposited archaeal DNA sequences in databases, until now we do not have a clear picture of the effectiveness and specificity of the universal primers widely used to describe archaeal communities from different natural habitats. Therefore, in this study, we compared the phylogenetic profile obtained when Cerrado lake sediment DNA samples were submitted to 16S rDNA PCR employing three Archaea-specific primer sets commonly used. Our findings reveal that specificity of primers differed depending on the source of the analyzed DNA. Furthermore, archaeal communities revealed by each primer pair varied greatly, indicating that 16S rRNA gene primer choice affects the community profile obtained, with differences in both taxon detection and operational taxonomic unit (OTU) estimates.
Subject
General Agricultural and Biological Sciences
Reference43 articles.
1. PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample;ACINAS S.G.;Applied and Environmental Microbiology,2005
2. Diversity of bacteria and archaea from two shallow marine hydrothermal vents from Vulcano Island;ANTRANIKIAN G.;Extremophiles,2017
3. Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment;BAHRAM M.;Environmental Microbiology Reports,2018
4. Review and re-analysis of domain-specific 16S primers;BAKER G.C.;Journal of Microbiological Methods,2003
5. Long-term effects of periodical fires on archaeal communities from Brazilian Cerrado soils;BELMOK A.;Archaea,2019
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