Community metagenomic assembly reveals microbes that contribute to the vertical stratification of nitrogen cycling in an aquaculture pond

The identities and functional capacities of the microbial populations within surface water (SW), bottom water (BW), surface sediment (SS) and deep sediment (DS) samples from a typical grass carp (Ctenopharyngodon idellus) culturing pond in central China were explored using metagenomics. In total, the community structure and microbial processes of the water columns was distinct from that of the SS and DS layers. Alphaproteobacteria, Actinobacteria, Cyanobacteria and Planctomycetes were abundant in the water, while Deltaproteobacteria, Gammaproteobacteria, Euryarchaeota (Archaea) and Nitrospirae were more abundant in the sediment (P < .05). The functional potential and microorganisms responsible for the N nutrient cycles were also reconstructed in silico. The high functional potential for N assimilation, protein synthesis and cell proliferation in pond water should be responsible for low ammonia concentration detected. Ammonia oxidation functional genes were present in very low abundances, and were mostly detected in the water columns and related to Nitrosomonas (100%). Denitrification were observed mostly in SS and the main taxon involved was Rhodocyclales. The potential for N fixation (nif genes) and dissimilatory nitrate reduction to ammonium was also observed mostly in sediment, which is a disadvantage for ammonia reduction in the pond ecosystem. Overall, these results offer a more detailed perspective on the microbial functional ecology of the aquaculture pond.