Abstract: Recirculating aquaculture system (RAS) has gradually replaced the traditional earthen pond (Earth) for shrimp cultivation because of its less pollution and higher economical benefit. A comprehensive knowledge on bacterial community structure is necessary for disease control and process improvement. In this paper amplicon pyrosequencing of 16S rRNA gene was used to compare the bacterial community structure among recirculating aquaculture system (water and biofilm) and earthen pond (water). The results showed that the bacterial communities were distinct among Earth water, RAS water and biofilm, with the highest alpha-diversity in RAS water. Cyanobacteria and Actinobacteria were the predominant phyla in earthen pond. In contrast, Alphaproteobacteria was the highest in the RAS water, while Betaproteobacteria and Bacteroidetes were the dominant phyla in the RAS biofilm. Similarity percentage (SIMPER) analysis identified 11 OTUs that cumulatively contributed to 35.14% dissimilarity of the bacterial community. These taxa were affiliated with Saprospiraceae, Rhodobacteraceae, ACK-M1 and Synechococcaceae, Caldilineaceae, Betaproteobacteria, Sphingomonadales, Flavobacteria. At a finer resolution, the members of family Nitrosomonadaceae and Nitrospiraceae, which contribute to denitrification and nitrification, were dramatically higher in RAS biofilm than in waters. Overall, this work provides microbial ecological evidences for the advantages of recirculating aquaculture system over earthen pond.

Key words: Litopenaeus vannamei－recirculating aquaculture system－ biofilm, bacterial community structure－high-throughput sequencing