Aquatic microorganisms in the sediment and water column are closely related; however, their distribution patterns between these two habitats still remain largely unknown. In this study, we compared sediment and water microeukaryotic and bacterial microorganisms in aquaculture ponds from different areas in China, and analyzed the influencing environmental factors as well as the inter-taxa relationships. We found that bacteria were significantly more abundant than fungi in both sediment and water, and the bacterial richness and diversity in sediment were higher than in water in all the sampling areas, but no significant differences were found between the two habitats for microeukaryotes. Bacterial taxa could be clearly separated through cluster analysis between the sediment and water, while eukaryotic taxa at all classification levels could not. Spirochaetea, Deltaproteobacteria, Nitrospirae, Ignavibacteriae, Firmicutes, Chloroflexi, and Lentimicrobiaceae were more abundantly distributed in sediment, while Betaproteobacteria, Alphaproteobacter, Cyanobacteria, Roseiflexaceae, Dinghuibacter, Cryomorphaceae, and Actinobacteria were more abundant in water samples. For eukaryotes, only Cryptomonadales were found to be distributed differently between the two habitats. Microorganisms in sediment were mainly correlated with enzymes related to organic matter decomposition, while water temperature, pH, dissolved oxygen, and nutrient levels all showed significant correlation with the microbial communities in pond water. Intensive interspecific relationships were also found among eukaryotes and bacteria. Together, our results indicated that eukaryotic microorganisms are distributed less differently between sediment and water in aquaculture ponds compared to bacteria. This study provides valuable data for evaluating microbial distributions in aquatic environments, which may also be of practical use in aquaculture pond management.
Keywords: aquaculture pond; bacterial community; eukaryotic microorganisms; sediment; water.