This suggests the high utility of primer pair 341f/785r for soil and plant-associated bacterial microbiome studies. In silico, primer pair 341f/785r showed the highest coverage of the domain Bacteria (96.1%) with no obvious bias toward the majority of bacterial species. Primer pair 68f/518r showed overall low coverage and a bias toward Alphaproteobacteria. Primer pair 341f/785r produced the highest number of bacterial OTUs, phylogenetic richness, Shannon diversity, low non-specificity and most reproducible results, followed by 967f/1391r and 799f/1193r. Here we evaluated the performance of four bacterial primers for characterizing complex microbial communities in explosives contaminated and non-contaminated forest soil and by in silico evaluation against the current SILVA123 database.
However, primers specific for the domain Bacteria were often developed some time ago against database versions that are now out of date. To reliably detect the members, or operational taxonomic units (OTUs), that make up bacterial communities, taxonomic surveys rely on the use of the most informative PCR primers to amplify the broad range of phylotypes present in up-to-date reference databases. 3Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, Canadaīacterial taxonomic community analyses using PCR-amplification of the 16S rRNA gene and high-throughput sequencing has become a cornerstone in microbiology research.2Department of Biology, Lund University, Lund, Sweden.1Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium.
Van Hamme 3, Nele Weyens 1 and Jaco Vangronsveld 1 Sofie Thijs 1 * †, Michiel Op De Beeck 2, Bram Beckers 1, Sascha Truyens 1, Vincent Stevens 1, Jonathan D.
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