Comparison of Intestinal Bacteria of Procambarus clarkii Farmed in Various Rice Paddy Regions

The aim of this study was to assess the regional differences of Procambarus clarkii through analyzing gut microbiota in specimens from different areas in China. The P. clarkii were collected from ten integrated rice-crayfish farming systems locating across ten major producing areas as follows: Feixi (FX), Suqian (SQ), Yangzhou (YZ), Xuyi (XY), Qianjiang (QJ), Jianli (JL), Honghu (HH), Yueyang (YY), Changsha (CS), and Nanxian (NX). The composition of gut microbiota was assessed by analyzing 16S rRNA sequences. The PCoA results indicated significant differences in microbial community composition among the ten areas (R = 0.999, p = 0.001). The intestinal microbial diversity in P. clarkii cultured in rice fields from YY and CS exceeded that of other regions, with NX displaying the least diversity. At the phylum level, Proteobacteria were most abundant in HH, while Firmicutes showed increased relative abundances in FX and SQ, contrasted by lower relative abundances of Bacteroidetes in these areas. At the genus level, Ralstonia, Amedibacillus, Bacteroides, Anaerorhabdus, and Dysgonomonas were the dominant bacteria. The bacterial co-occurrence networks analysis revealed that the community structures in locations FX, SQ, XY, HH, and NX were comparatively simplistic, whereas those in the YZ, QJ, JL, YY, and CS regions displayed as more complex. In summary, the diversity and relative abundance of intestinal bacteria exhibits regional variability. These findings can offer theoretical data for evaluating the quality of P. clarkii aquaculture.