Core microbiome involved in nitrite removal in shrimp culture ponds

Abstract

Microorganisms play an important role in aquaculture systems; however, we know a little about their contributions to nitrogen cycling and balancing nitrite conversion. Both 16S rRNA pyrosequencing-based analysis and quantifying functional genes related to nitrite conversion were performed to study the niche function of microbial flora in a marine aquaculture system. During the whole aquaculture period, bacterial abundance was maintained at a high level (1010−11 copies/L), which was 105 times larger than that of archaea. Proteobacteria and Bacteroidetes dominated the bacterial communities, and the core species mainly belonged to the families Rhodobacteraceae and Flavobacteriaceae. Bacterial denitrifiers and dissimilatory nitrate reduction to ammonium (DNRA) bacteria were highly abundant and played key roles in the conversion and removal of nitrite, and the narG and nirK genes were highly correlated with the variation in nitrate and nitrite contents. Ammonia- and nitrite-oxidizing microorganisms might contribute little to the conversion of nitrite during the whole aquaculture, although high abundance of bacterial amoA gene was detected at Day 131. The nitrite conversion-related microbial community consisted dominantly of diverse microorganisms, and Flavobacteriaceae, Rhodobacteraceae and Alteromonadaceae were the main groups. Temperature and NH4+ had the largest impact on the microbial community. These results indicated that in eutrophic water of shrimp aquaculture, the core microbiome, including Flavobacteriaceae and Rhodobacteraceae, and other denitrifiers, plays an important role in nitrite cycling and maintaining the health of the aquaculture system.