Open AccessCombination of high throughput cultivation and dsr A sequencing for assessment of sulfate‐reducing bacteria diversity in sediments
Author(s) -
Colin Yannick,
GoñiUrriza Marisol,
Caumette Pierre,
Guyoneaud Rémy
Publication year - 2013
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.1574-6941.2012.01452.x
Subject(s) - biology , phylogenetic diversity , phylogenetic tree , 16s ribosomal rna , phylogenetics , desulfovibrio , phylotype , library , intertidal zone , genetic diversity , ribosomal rna , ecology , metagenomics , sulfate reducing bacteria , bacteria , botany , gene , genetics , population , demography , sociology
Improving the knowledge on sulfate‐reducing bacteria ( SRB ) diversity and ecophysiology will permit a better understanding on their key roles in aquatic ecosystems. Therefore, their diversity was evaluated in estuarine sediments by a polyphasic approach including dsr A gene cloning and sequencing (156 clones) and high‐throughput isolations in 384‐well microplates (177 strains). Using the related thresholds of 95% ( D sr A amino acid sequences) and 97% (16 S r RNA gene sequences) for sequence similarity, SRB were grouped into 60 and 22 operational taxonomic units, respectively. Both approaches poorly overlapped and rather complemented each other. The clone library was dominated by sequences related to the D esulfobacteraceae , while only one isolate belonged to this family. Most of the strains were affiliated to the genera D esulfopila and D esulfotalea within the D esulfobulbaceae . D esulfopila ‐related strains exhibited a high phylogenetic microdiversity and represented numerically significant populations. In contrast, D esulfovibrio isolates were less abundant but displayed a high phylogenetic diversity. Three hundred and eighty‐four‐well microplate isolations enhanced significantly the number of isolates handled. As a consequence, 15 new taxa sharing less than 98% sequence similarity (16 S r RNA gene) with their closest relatives were obtained. This polyphasic approach allowed to obtain a high phylogenetic diversity and thus a better view of sulfate‐reducing communities in intertidal sediments.