Effects of Carassius auratus gibelio var. CAS Ⅲ cultured in the paddy fields on microbiota community structure of the rice-crab culture systems

Objective The study aimed to explore the differences in microbial community structures within the intestine of Eriocheir sinensis and their respective breeding environments under varying densities of Carassius auratus gibelio var. CAS Ⅲ.

Methods High-throughput sequencing method was used to analyze microbial community structure in the intestine of E. sinensis and breeding environment.

Results 1) There was no discernible impact of C. auratus gibelio var. CAS Ⅲ on the survival rates of E. sinensis. 2) When the stocking density of C. auratus gibelio var. CASⅢ was 100 ind/666.7 m², the final body mass, weight gain rate and specific growth rate of E. sinensis were significantly higher than those of other groups. 3) C. auratus gibelio var. CAS Ⅲ could increase the microbial diversity in the intestine of E. sinensis and breeding environment, the former had a significant effect, but the latter had no significant effect. 4) In different stocking densities of C. auratus gibelio var. CAS Ⅲ, the dominant phylum in water was Proteobacteria, Cyanobacteria and Actinobacteria; the dominant phylum in sediment was Proteobacteria, Actinobacteria and Chloroflexi; the dominant phylum in the intestine of E. sinensis was Firmicutes and Proteobacteria. 5) Phosphate (\rmPO_4^3- -P) and nitrite nitrogen (\rmNO_2^- -N) had a great effect on microbial community structure of water. The dominant genus norank_f_norank_o_Chloroplast and LD29 in water were positively correlated with pH, \rmNO_2^- -N, ammonia nitrogen (\rmNH_4^+ -N), dissolved oxygen (DO) and total nitrogen (TN). Cyanobium_PCC-6307 was positively correlated with \rmPO_4^3- -P, \rmNH_4^+ -N, DO and TN. Limnohabitans was positively correlated with the potassium permanganate index (COD_Mn). 6) \rmPO_4^3- -P and pH had a significant effect on microbial community structure of the intestine of E. sinensis. The dominant genus Candidatus_Bacilloplasma and Psychrobacter in the intestine of E. sinensis were positively correlated with pH and \rmNH_4^+ -N. Lactococcus was positively correlated with \rmPO_4^3- -P, TN, DO, COD_Mn and \rmNO_2^- -N. Acinetobacter was positively correlated with \rmPO_4^3- -P, TN, COD_Mn and \rmNH_4^+ -N. Citrobacter was positively correlated with pH and DO.

Conclusion Based on the experimental setup, an optimal stocking density for C. auratus gibelio var. CAS Ⅲ (48.53 ± 2.11) g/ind ranges between 100－200 ind/666.7 m². The rice-crab-fish farming system has been shown to positively affect the bacterial microbiota within the intestine of E. sinensis and the broader aquaculture ecosystem. This research contributes valuable insights into sustainable and healthful cultivation practices for E. sinensis.