Bacterial community characterization of water and sediment in different culture systems of prawn Macrobrachium rosenbergii

As one of the main models for prawn Macrobrachium rosenbergii aquaculture, polyculture systems enhance production by optimizing prawn growth and improving the culture environment. This study aimed to evaluate the ecological effects of different polyculture systems, with the goal of identifying the most sustainable and low-risk aquaculture practice. Nine ponds (0.6 ha) of prawn with an initial density of 600,000 individuals ha−1 were divided into the following three culture groups according to polyculture species: Prawn monoculture (PM), prawn+shrimp Litopenaeus vannamei (PS), and prawn+crucian Carassius auratus (PC) groups, 3 replicates per group. Three traditional crucian ponds (CM) were also examined for comparison. The water qualities (TN, TP, NO2––N, NH4+–N and CODMn) were analyzed at days 15, 30, 60, and 120 of the experiment. Microbial community composition in water and sediment was analyzed using Illumina MiSeq high-throughput sequencing at day 120 of the experiment. The results revealed that PC group significantly enhanced water parameters compared with the PM group at the mid-late period of the experiment, while the PS group was in accordance with the PM group. Moreover, polyculture groups (PS and PC) showed an increase of alpha diversity (ACE, Chao1, and Shannon) in water. Bacterial community structure showed that the culture groups shared similar bacterial communities at the phylum level. Proteobacteria, Bacteroidetes, Verrucomicrobia, Actinobacteria, Planctomycetes, and Chloroflexi were the dominant phyla in different culture groups in water and sediment. At the genus level, Spartobacteria_genera_incertae_sedis, Phycisphaera, Ilumatobacter, Thermogutta, and Rhodobacter were the main common abundant species in the water of different culture groups, whereas Desulfuromonas, Povalibacter, and Thermogutta were abundant in the sediment of different culture groups. PS group and PM group shared dominant genera Roseomonas, Phaeodactylibacter, and Pirellula in water, Sulfuricurvum, Longilinea, Ornatilinea, and Thiobacillus in sediment. The hierarchical cluster tree based on the Bray–Curtis results revealed the clustering of PM with PS and PC with CM, suggesting that bacterial community shifts correlate with cultured species’ genetic relationships. Notably, potential pathogens persisted at negligible levels across all culture systems. However, the PC group recorded the highest levels of total potential pathogens both in water and sediment. These results demonstrate that the prawn-shrimp polyculture system maintains not only stable water quality but also minimizes pathogenic risks, supporting its feasibility as an ecologically balanced aquaculture strategy.