Abstract: To explore the temporal and spatial variations of the intestinal microbiota of benthic community in Anhui section of Huai River, 16S rDNA amplicon sequencing technology was used to compare the intestinal microbiota characteristics of Exopalaemon modestus, one dominant shrimp species of the region. A total of 37 phylum and 855 genera of microbes were detected from E. modestus intestines, with Pseudomonas, Brevundimonas, Ralstonia, Caulobacter, Lactococcus and Sphingomonas as the dominant genera. There were significant differences in the intestinal microbiota richness of E. modestus (P<0.05) among low-water period (March), mean-flow period (June) and high-flow period (September). The β diversity index showed the intestinal microbiota composition in all sub-sections tended to be similar from March to September. The common ASVs in intestines of E. modestus increased gradually from low-water period to high-flow period. There were significant divergences of intestinal microbiota both in the low-water and mean-flow period (P<0.05), but not in the high-flow period. Due to the different habitats and hydrological regimes of different water bodies, the intestinal microbiota of E. modestus in Anhui section of Huai River (main stream) generally exhibited temporal and spatial variations. The intestinal microbiota composition of E. modestus in each sub-section showed the maximum divergence in low-water period, followed by mean-flow period, but no significant divergence in high-flow period.

Key words: Exopalaemon modestus, river water phase, intestinal microbiota, differential marker bacteria.