Metagenomic analysis of microbial communities in the sediments of a semi-intensive penaeid shrimp culture system

Abstract

The present study reports metagenomic sequencing and microbial diversity analysis of the sediment samples of a semi-intensive penaeid shrimp culture system. 16S rRNA gene-based high-throughput sequencing revealed distinct and diverse microbial communities in the analyzed sample. Analysis of the results showed a high abundance of Proteobacteria followed by Verrucomicrobia, Bacteroidetes, Planctomycetes, Firmicutes, Cyanobacteria, and Actinobacteria in the metagenome retrieved from the sediment sample. Unclassified bacteria also contributed a significant portion of the metagenome. Two potential shrimp pathogens viz Vibrio harveyi and Acinetobacter lwoffii detected in the sediment sample show the risk associated with the pond. Microbes that play essential roles in nutrient cycling and mineralization of organic compounds such as Bacteroidetes, Planctomycetes, Gammaproteobacteria, Firmicutes, Cyanobacteria, and Actinobacteria could also be identified. The present study provides preliminary data with respect to the microbial community present in the sediments of a shrimp culture system and emphasizes the application of metagenomics in exploring the microbial diversity of aquaculture systems, which might help in the early detection of pathogens within the system and helps to develop pathogen control strategies in semi-intensive aquaculture systems.