Analysis of microbial community structure in rice-shrimp integrated culture system of three different areas

Environmental microbiota plays important roles in the intestinal microbiota of aquatic animals. Procambarus clarkii has become the most important commercial species of shrimp in China with high commercial value, and the main culture mode of P. clarkii is rice-crayfish co-existing. P. clarkii culture is an important economic mainstay in Hubei province, China. However, information on the gut microbiota of P. clarkii is limited. To study the difference of bacterial community structure in the intestinal tract of P. clarkii and the environment of rice- crayfish comprehensive culture system in different areas, and to provide some basis for improving the comprehensive culture strategy of rice in different areas, Illumina MiSeq high-throughput sequencing method was used to sequence and analyze the two high-variation regions (V3-V4) of 16S rRNA gene of microbia of the water, sediment and intestine of P. clarkii in different regions (Wuhan, Yongzhou and Shaoguan). Redundancy analysis (RDA)was used to analyze the relationship among water, intestinal microorganisms and environmental factors. The results showed that the diversity of the bacterial community in the water, sediment and crawfish gut of rice shrimp integrated culture system in Wuhan area was higher than those in Yongzhou area and Shaoguan area. The bacterial community structure in the water and sediment of the rice shrimp integrated breeding system in Wuhan area was similar to those in Yongzhou area and Shaoguan area. Actinobacteria, Cyanobacteria, Proteobacteria and Bacteroidetes were the dominant phylum in water, Proteobacteria was the dominant phylum in sediments. The dominant bacteria in the intestin of P. clarkii in Wuhan area were Proteobacteria, Firmicutes and Bacteroidetes at the phylum level, and Citrobacter (10.85%), Aeromonas (9.88%) and Anaerorhabdus_furcosa_group (8.43%) at the genus level. The dominant bacteria in the intestin of P. clarkii in Yongzhou area were Firmicutes and Actinomycetes at the phylum level, and ZOR0006(9.78%), Bacteroides (5.41%) and Anaerorhabdus_furcosa_group (3.98%) at the genus level. The dominant bacteria in the intestine of P. clarkii in Shaoguan area were Firmicutes and Proteobacteria at the phylum level, and Citrobacter (9.31%) , bacteroidetes (4.29%) and Anaerorhabdus_furcosa_group (4.58%) at the genus level. The results of correlation analysis between environmental factors and bacterial communities showed that TSS and TP had significant effect on the bacterial community structure of water, and PO₄³⁻-P and CODcr had significant effect on the intestinal microbial community structure. The results show that there are some differences among the gut of P. clarkii, water and sediment of different regions, and the microbial structure of water bodies and sediment is more similar. The microbial diversity in the water body of rice shrimp integrated culture system in Wuhan area is the highest, which is beneficial to the stability of the breeding system.The culture environment in different regions did not affect the core phyla of microorganisms in the culture system, but changed the relative abundance of dominant phyla and genera. The nutrient content of culture environment will affect the microbial community structure to a certain extent.