Open AccessComparison of 16 S r RNA and protein‐coding genes as molecular markers for assessing microbial diversity ( B acteria and A rchaea ) in ecosystems
Author(s) -
Roux Simon,
Enault François,
Bronner Gisè,
Debroas Didier
Publication year - 2011
Publication title -
fems microbiology ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.377
H-Index - 155
eISSN - 1574-6941
pISSN - 0168-6496
DOI - 10.1111/j.1574-6941.2011.01190.x
Subject(s) - biology , 16s ribosomal rna , metagenomics , ribosomal rna , genetics , proteobacteria , archaea , gene , actinobacteria , rpob , housekeeping gene , computational biology , gene expression
Abstract PCR amplification of the r RNA gene is the most popular method for assessing microbial diversity. However, this molecular marker is often present in multiple copies in cells presenting, in addition, an intragenomic heterogeneity. In this context, housekeeping genes may be used as taxonomic markers for ecological studies. However, the efficiency of these protein‐coding genes compared to 16 S r RNA genes has not been tested on environmental data. For this purpose, five protein marker genes for which primer sets are available, were selected ( rplB , pyrG , fusA , leuS and rpoB ) and compared with 16 S r RNA gene results from PCR amplification or metagenomic data from aquatic ecosystems. Analysis of the major groups found in these ecosystems, such as A ctinobacteria , B acteroides , P roteobacteria and C yanobacteria , showed good agreement between the protein markers and the results given by 16 S r RNA genes from metagenomic reads. However, with the markers it was possible to detect minor groups among the microbial assemblages, providing more details compared to 16 S r RNA results from PCR amplification. In addition, the use of a set of protein markers made it possible to deduce a mean copy number of r RNA operons. This average estimate is essentially lower than the one estimated in sequenced genomes.