Bacterial community structure and bacterial isolates having antimicrobial potential in shrimp pond aquaculture

Diseases outbreaks in pond aquaculture have resulted in huge losses to the aquaculture industry. The emergence of non-antimicrobial and environment friendly agents (probiotics) is the potential consideration for the healthy shrimp aquaculture. The present study was aimed to compare the bacterial community compositions in shrimp ponds and surrounding seawater, as well as isolate probiotic bacteria from the shrimp ponds. Based on the high-throughput of 16S rRNA gene sequencing, all sequences were assigned to 3584 unique operational taxonomic units (OTUs) at 97% similarity levels, which were affiliated with 24 phyla, 54 classes, 235 families, and 367 genera. The 10 most abundant phyla were Bacteroidota, Proteobacteria, Actinobacteriota, Planctomycetota, Cyanobacteria, Chloroflexi, Firmicutes, Desulfobacterota, Patescibacteria and Verrucomicrobiota. Notably, the alpha diversity (Shannon diversity) of shrimp ponds was significantly differences (P < 0.05) with that of surrounding seawater. There were 2498 and 791 unique OTUs in shrimp ponds and surrounding seawater, respectively. A total of 15 isolates were obtained in the culturable bacterial diversity, and the antibacterial activities were recorded for potential probiotic bacterial isolates against different tested bacterial isolates including pathogenic bacteria. An isolate Hallobacillus marinus HMALI004 showed strong inhibitory effects against three pathogenic bacteria, Vibrio cholerae CECT 514, non AHPND V. parahaemolyticus BCRC12959 and AHPND V. parahaemolyticus PD-2. The isolates Algophigus sanaruensis AGALI005, Algoriphagus taiwanensis ATALI009 and Bacillus aequororis BAALI008 were also identified as potential probiotics strains. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13568-022-01423-9.