Analysis of bacterial community functional diversity in late-stage shrimp (Litopenaeus vannamei) ponds using Biolog EcoPlates and PICRUSt2

Abstract

The role of microorganisms in the environment is reflective of the function of the community; however, our understanding of the functional diversity of the bacterial microbiome found in water and sediment from shrimp ponds is currently fragmentary. This study utilized high-throughput sequencing techniques and community level physiological profiling (CLPP) methods to study the structural and functional diversity of the bacterial communities found in water samples and sediment from three intensive Litopenaeus vannamei culture ponds at late stage. The correlation between the presumptive functions using PICRUSt2 and the actual metabolic profiles via Biolog EcoPlates was evaluated. Results revealed that the genetic and functional diversity of the microbial community in the sediment of the aquaculture ponds was significantly higher than that of the water samples. In the water samples, the most dominant carbon sources utilized by the microbial community included carboxylic acids (35.08%), polymers (24.91%), and carbohydrates (23.16%); while polymers (25.61%) and amino acids (21.31%) were utilized most often in the sediment samples. Proteobacteria (38.67%), Cyanobacteria (15.96%), and Actinobacteria (16.48%) were the most dominant bacteria phyla found in the water samples. Proteobacteria (40.96%), Chloroflexi (11.79%), Bacteroidetes (9.66%) were the most dominant bacteria phyla in the sediment. Importantly, our results demonstrated that Actinobacteria, Verrucomicrobia, and Firmicutes were significantly positively correlated with the carbon source uses of the microbial community in the Biolog EcoPlates in the water samples, Proteobacteria were significantly positively correlated in the sediment. Besides, Linear discriminant analyses of predicted function of the microbial community showed that the metabolism and the cellular processes were significantly enriched in the water samples and sediment, the difference was that environmental information processing were significantly enriched in the water samples, genetic information processing were significantly enriched in the sediment. Moreover, there was a significant correlation between the predicted function and the actual metabolic profiles of the microbial community in the water samples and sediment. These findings facilitate an understanding of the relationship between the microbial community structure and the function in shrimp ponds and also provide a reference for water purification and the future commercial development of novel aquatic probiotics.