Comparison of 16S rRNA Gene Primers on Studying Microbial Community Composition in Bottom Water and Sediment of Artificial Reefs in Laoshan Bay, China

Marine microorganisms are indispensable regulators of nutrient cycling and energy flow, which are crucial for artificial reefs (ARs) ecosystems. However, little is known about the microbial communities in the bottom water and sediment of ARs. Studies of microbial diversities have greatly advanced due to the development of high-throughput sequencing technologies, whereas the results may vary significantly due to the primers’ choice. This study investigated the influences of two 16S ribosomal RNA gene primer choices (V4 and V3–V4) on microbial community compositions and structures. The results showed that the taxonomic assignment detected by primer V3–V4 was higher compared with that obtained by primer V4, whereas microbial community compositions had strong correlations between the two primers. Microbial beta diversities of ARs can be uncovered by both primers, but the relationships between communities and environmental parameters were inconsistent. The performances of the two primers for water samples were highly consistent, but the inconformity was evident for sediment samples. Given the relatively lower taxonomic classification of primer V4 for sediment samples, primer V3–V4 was recommended for later studies. With the development and advancement of ARs in China, our findings provide a meaningful reference for ecologists focusing on the microbial diversities and ecological functions of these artificial habitats in the future.