Amplicon Sequencing Reveals Microbial Community Structure and Its Relationships with Environmental Factors in Macrobrachium nipponense Aquaculture Ponds

Macrobrachium nipponense is one of the major economic species in freshwater aquaculture in China. As an important component of aquaculture ecosystem, microorganisms participate in key processes such as material cycling and water quality regulation, exerting significant impacts on the cultured organisms. In this study, high-throughput sequencing of the 16S rRNA, 18S rRNA, and ITS regions was employed to comparatively analyze the characteristics of microbial communities before and during the cultivation period, combined with correlation analysis of environmental factors. The results showed that the dominant microbial groups in the prawn pond water were Proteobacteria, Cyanobacteria, Ascomycota, Basidiomycota, Chlorophyta, and Arthropoda. The microbial community structure differed significantly between the pond water during the culture period and the pre-culture external river baseline: manifested as an increase in the relative abundances of Cyanobacteria, Chytridiomycota, and zooplankton, and a decrease in the abundances of Ascomycota, Basidiomycota, and Chlorophyta. Analysis of LEfSe revealed that the low-nitrogen pond was enriched with taxa such as Muribaculaceae; the high-nitrogen pond was enriched with taxa such as Cyanobium_PCC-6307; and the control pond was enriched with taxa such as CL500-29_marine_group. Functional prediction indicated that heterotrophic metabolism-related functions dominated the microbial communities. The abundance of fungal pathogens was significantly higher in the low-nitrogen group, while potential pathogenic bacteria were enriched in the high-nitrogen group. Ammonia nitrogen is a core environmental factor associated with differences in microbial community structure. The findings of this study can provide theoretical references and data support for water quality optimization and the construction of healthy aquaculture models in freshwater shrimp and crab farming waters.