Microbiomes inhabiting rearing ponds have been frequently associated with the survival rate of cultured animals. However, specific studies reporting on the structure, composition, and functional genes of bacteria in commercial ponds with different survival rates are still scarce. Thus, using high-throughput sequencing, the present study addressed this gap by investigating microbiomes in commercial ponds with different survival rates of Pacific white shrimp, Litopenaeus vannamei. Water samples were collected from ponds with low survival rates (LSR) and ponds with high survival rates (HSR) and profiled by high-throughput sequencing of the 16S rRNA gene. Then, functional genes of microbiomes were predicted using PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) software. The results showed that ponds with different survival rates had distinct bacterial communities. At the genus level, 20 genera had different relative abundance in the two pond groups (LDA > 3), of which 11 genera were in HSR ponds and nine genera were in LSR ponds. The top five most abundant bacterial genera found in LSR ponds were Vibrio, Kocuria, Tepidiphilus, unidentified_Alphaproteobacteria, and Pseudoalteromonas, while the five most abundant found in the HSR ponds were Candidatus_Aquiluna, unidentified_Acinobacteria, Ilumatobacter, unidentified_Deltaproteobacteria, and Marivita. PICRUSt analysis revealed that nine metabolic pathways were higher in HSR grow-out ponds and associated with carbohydrate metabolism, chlorophyll biosynthesis, lignin degradation, arginine and glucosamine biosynthesis, and vitamin K2 synthesis, while nine metabolic pathways were found to be significantly higher in LSR grow-out ponds including lipid IVA biosynthesis (conserved structure in diverse Gram-negative pathogens), and L-tryptophan degradation activity (proteolytic agents). To the authors' knowledge, this is the first study to report the diversity, composition, and metabolic activity of microbiomes in commercial shrimp grow-out ponds and their effect on the survival rate of Pacific white shrimp. Overall, these findings suggest that the specific microbiomes in rearing water may be linked to the impact on improved survival of Pacific white shrimp.

Introduction Probiotics have been commonly practiced in commercial shrimp farms to increase pond production. However, these possibilities were based on the results of in vitro studies or laboratory in vivo trials. While studies on probiotic applications in commercial-scale farms are still rarely investigated, this study addresses the fate of probiotic species in ponds and the intestinal tract of white shrimps reared in an intensive aquaculture system. Material and methods Four commercial probiotic species (Lactobacillus plantarum, Lactobacillus fermentum, Bacillus subtilis, and Pseudomonas putida) were applied to the commercial shrimp ponds (@800 m2 area of high-density polyethene ponds) in the morning at a dose of 5 ppm once every 2 days in the first month, and once a week from second month onward. Then, the presence of the probiotic species was traced by collecting the rearing water and shrimp’s intestines on day 47 of culture to monitor their composition and abundance using high-throughput sequencing. Results None of the commercial probiotic species could be detected from both rearing water and shrimp intestinal tracts. These results suggest that the probiotic species had low viability and adaptability in the rearing pond as well as the shrimp intestines when applied on commercial-scale farms. These facts may explain the high variation in the yield among shrimp ponds in spite of having similar treatments. Conclusion Probiotic strains had low viability and adaptability in commercial farms. Thus, methods and strategies in probiotic application to commercial-scale shrimp farms should be evaluated and further developed to increase probiotic efficacy.