Dynamic changes in bacterial communities and potential health risks of pathogenic bacteria in a rice–crayfish coculture system in spring

ABSTRACT Objective This study was designed to explore the relationship between bacterial communities in different habitats and analyze how water quality affects the structure of bacterial communities and the distribution of pathogenic bacteria. The findings support healthy cultivation of red swamp crayfish Procambarus clarkii in rice–crayfish coculture systems and assist in assessing the health risks to the ecological environment. Methods The researchers used 16S ribosomal RNA gene sequencing to investigate the composition and diversity of the bacterial community in the crayfish gut and environment (water and sediment) in rice–crayfish coculture systems across various growth stages (larvae, juvenile, and adult). The water quality parameters were measured at different stages, and the duration of the investigation was 3 months. Results The bacterial communities in sediment showed higher α-diversity values than those in water and the crayfish gut microbiota. Proteobacteria dominated in all environments, particularly in the gut, whereas Acidobacteria and Chloroflexi were prevalent in sediment and Cyanobacteria and Verrucomicrobia in water. Gut microbiota exhibited significant shifts over the developmental stages, with increased prevalence of pathogens like Aeromonas and Acinetobacter. The SourceTracker analysis revealed a minimal contribution of sediment to gut microbiota, with water contributing significantly to gut microbiota at the juvenile stage. Environmental factors including dissolved oxygen, total phosphorus, orthophosphate, chemical oxygen demand (CODMn), and chlorophyll a have the greatest influence on bacterial communities. Notably, a pathogenic bacterium, Acinetobacter lwoffii, which was detected both in the gut (9.79–36.83%) and in the water (0.00–12.47%), showed a significant correlation with CODMn levels (P < 0.05). Conclusions The contribution to gut bacteria of the bacterial community in water was greater than that of the bacterial community in sediment. Environmental dissolved oxygen, total phosphorus, orthophosphate, CODMn, and chlorophyll a molded the bacterial community, especially the increase of CODMn, which can promote the distribution of intestinal pathogens. These results provide scientific reference for healthy crayfish culture, prevention of bacterial disease transmission, and health risk assessments of the ecological environment.