Effects of wheat flour and culture period on bacterial community composition in digestive tracts of Litopenaeus vannamei and rearing water in biofloc aquaculture system

Abstract In this study, we investigated the bacterial diversity in rearing water, shrimp (Litopenaeus vannamei) stomach and intestine based on temperature and exposure to wheat flour (carbon source) to determine the correlation between microbial community and surrounding environment in the zero-water exchange shrimp biofloc technology (BFT) system. Three temperature levels of 29 °C (optimal temperature for shrimp growth), 25 °C (rearing water temperature in winter) and 34 °C (summer) were used. Wheat flour was added to groups L (at late stage) and E (at early stage), and sodium bicarbonate was added to group N (wheat flour not added) to adjust the pH. During the operation of the system, the water quality was retained in groups E and N, while it seriously deteriorated in group L at all temperatures. After wheat flour addition in group L, all water quality parameters were recovered efficiently. Using next generation sequencing (NGS) analysis, a total of 26 phyla and 340 OTUs at the genus level were identified in rearing water (the number of samples, n = 31), shrimp stomach (n = 57), and intestine (n = 57). Five phyla, Proteobacteria, Planctomycetes, Actinobacteria, Verrucomicrobia, and Bacteroidetes and 13 bacterial groups related to Phaeobacter, Pirellulaceae, Verrucomicrobiaceae, Rhodobacteraceae, Flavobacteriaceae, Amaricoccus, Marinicellaceae, Acidimicrobiales, C111, Planctomyces, Nitrosomonadaceae, koll13, and Piscirickettsiaceae were found in all samples, representing the core microbiome. Alpha diversity and richness were higher in the shrimp digestive tract, in group E, and at 25 °C compared with the others under each condition. Based on Unifrac PCoA analysis, the samples were clearly classified according to habitat and culture period mostly. The correlation analysis showed that carbon source addition (wheat flour) had a positive correlation with alkalinity and pH, while it was negatively correlated with total ammonia nitrogen (TAN), and nitrate-N concentration in the rearing water (P