Assay and comparison the impact of primer in evaluation of bacterial community structure in semiarid area by Illumina Miseq

The aim of this study was to compare the effect of primers in evaluating soil bacterial community structure. For this purpose, soil samples were taken from cold and warm area which grazed (disturbed) or not grazed (undisturbed) in spring and autumn. Microbial DNA was extracted and sequenced after amplification by two primers which amplify V1-V3 and V4-V5 area of 16S rRNA. Next generation sequencing data were analyzed by QIME to determine bacterial community structure. Results showed the effect of area, grazing and season on bacterial community structure. NGS data analysis showed that primers which amplified V4-V5 area identified more bacteria (97.9%) in compared to V1-V3 primers (90.4%). V1-V3 primers had better efficiency to identify Proteobacteria (37.85%) in compared to V4-V5 which identified more Actinobacteria (33.6%). In addition, V4-V5 primers identified more bacteria in class, family and genus taxonomic groups in compared to V1-V3 primer. Although V4-V5 primer had better efficiency in bacteria identification, it is recommended to use both primers to evaluate precisely bacterial community structure.