The habitat differentiation, dynamics and functional potentials of bacterial and micro-eukaryotic communities in shrimp aquaculture systems with limited water exchange

Microbes are important in not only driving matter cycling, modulating water quality, but also serving as food for animals in intensive aquaculture systems, in which artificial substrates in combination of biofloc technology can be applied to strengthen microbial values and animal production. However, the influence of micro-habitats created by these practices on water quality and microbial diversity and dynamics remains poorly understood. In this study, samples of three micro-habitats, the biofilms formed on immersed meshes, the suspended macro-aggregates, and the pond water were collected from limited-water-exchange ponds for rearing Litopenaeus vannamei during a period of 80 days. Using high-throughput sequencing of 16S and 18S rRNA genes and statistical analyses, we found that the community structures of both bacteria and micro-eukaryotes were similar between biofilms and macro-aggregates (ANOVA, P > 0.05), but significantly different from those in the water (P 0.05). Functionally, microbes in both biofilms and macro-aggregates exhibited higher potentials of organic matter degradation and nitrogen removal, supporting the usefulness of application of biofloc technology and biofilms in recycling waste and nutrients in the shrimp ponds with limited water exchange. •Biofilm and biofloc had similar bacterial and micro-eukaryotic communities.•Biofilm and biofloc had high potentials of degrading organics and removing nitrogen.•Water bacteria held high potentials of biosynthesizing vitamins and antibiotics.•Bacteria and micro-eukaryotes had significant dynamics in a specific