This study investigated the effect of different carbon sources on water quality, ammonia removal pathways, the bacterial community, and the production of Litopenaeus vannamei in outdoor culture tanks. Three systems were established: a clear water system (CW) and biofloc technology (BFT) systems with added molasses (M-BF) or poly (3-hydroxybutyric acid-co-3-hydrovaleric acid) (PHBV) (P-BF). The average pH, total alkalinity, total organic carbon, biofloc volume, chlorophyll a, nitrite, nitrate, total nitrogen, and nitrification rate were significantly different among the treatments. Microbial composition varied and different dominant taxa were identified in the treatments by linear discriminant analysis effect size. Redundancy analysis indicated that the water quality parameters affected the distribution of the microbial community. Moreover, the genus Leucothrix was closely related to the M-BF treatment. Chemoheterotrophy and aerobic chemoheterotrophy were the most abundant functions in all treatments. A comparison of functions using BugBase indicated that the relative abundance of several functions such as biofilm formation, stress tolerance and functions related to anaerobic processes increased in the M-BF treatment. The specific growth rate, growth rate, and survival rate of shrimp were significantly higher in the P-BF system than in the CW system and the feed conversion ratio in the BFT treatments was significantly lower than that in the CW system. Overall, adding carbon sources affected water quality, microbial community, and shrimp performance. The results show that PHBV is a good alternative to carbon sources.

Understanding how habitat bacteria affect animal development, reproduction, and aging is essential for deciphering animal biology. Our recent study showed that Shewanella algae impaired Litoditis marina development and lifespan, compared with Escherichia coli OP50 feeding; however, the underlying mechanisms remain unclear. Here, multi-omics approaches, including the transcriptome of both L. marina and bacteria, as well as the comparative bacterial metabolome, were utilized to investigate how bacterial food affects animal fitness and physiology. We found that genes related to iron ion binding and oxidoreductase activity pathways, such as agmo-1, cdo-1, haao-1, and tdo-2, were significantly upregulated in L. marina grown on S. algae, while extracellular structural components-related genes were significantly downregulated. Next, we observed that bacterial genes belonging to amino acid metabolism and ubiquinol-8 biosynthesis were repressed, while virulence genes were significantly elevated in S. algae. Furthermore, metabolomic analysis revealed that several toxic metabolites, such as puromycin, were enriched in S. algae, while many nucleotides were significantly enriched in OP50. Moreover, we found that the “two-component system” was enriched in S. algae, whereas “purine metabolism” and “one-carbon pool by folate” were significantly enriched in E. coli OP50. Collectively, our data provide new insights to decipher how diet modulates animal fitness and biology.