Sediment microbial communities contribute to shrimp intestine microbiota in cultural pond ecosystems

Abstract Background Microorganisms in a shrimp cultural pond ecosystem (SCPE) play important roles for animal and environmental health. While the microbial diversity and assembly mechanism, and how communities of multiple habitats contribute to the SCPE metacommunity are poorly understood. Here, we analyzed phylogenetic structure of 792 samples of three habitats (water, shrimp intestine and sediment) from 88 shrimp cultural ponds across six regional sites in China. Results We show that the microbial communities of three habitats in the SCPE contained 15,197 operational taxonomic units (OTUs), and the microbial community of sediment had the highest OTUs (14,857). Despite the high microbial diversity, the SCPE has small core taxa (13 OTUs) among three habitats, and 30, 15, 53 core OTUs in water, shrimp intestine, and sediment, respectively. Especially, some opportunistic pathogens or functional microbes were core taxa in shrimp intestine or water and sediment. Of the SCPE metacommunity, the microbial diversity of the SCPE was mainly contributed by‾αLocalCommunities (66.0%), and followed by βInterHabitats (29.0%). The sediment microbial communities had a larger contribution (56.8%) to shrimp intestine microbiota compared to water communities (18.1%), which was also corroborated by the Sloan neutral community model analysis. Further, microbial assembly of three habitats appeared to be largely driven by stochastic processes (over 78%) in the SCPE. Conclusions Our results demonstrate that those core microbial taxa of three habitats were distinct with each other, that sediment communities mainly contributed to shrimp intestine communities, and that the microbial assembly was largely driven by stochastic processes. Our study enhances the mechanistic understanding of the microbial diversity and assembly in the SCPE for further analyzing metacommunities, and has important implications for microbial ecology and shrimp culture strategies.