Multi-kingdom microbial community dynamics in freshwater aquaculture systems: Microbial-scale support for the advantages of rice-crayfish co-culture model.

Authors

Lu Zhang, Yujie Mao, Zhi Wang

Published in

Journal of environmental sciences (China). Volume 170. Pages 595-607. Epub May 01, 2026.

Abstract

This study investigated multi-kingdom microbial dynamics in freshwater aquaculture systems to address remaining issues regarding multi-kingdom community variation and microbial evidence for the ecological benefits of the rice-crayfish co-culture model (RCCM). Bacteria, archaea, fungi, and viruses in three typical aquaculture models in the Jianghan Plain, including RCCM, fish pond (FP), and crab-crayfish co-culture pond (CCFP), were analyzed. Bacteria dominated the freshwater aquaculture environment (97.86 %). The structure of microbial communities differed significantly across habitats (water vs. sediment), aquaculture stages and models. Compared with July (mid-aquaculture stage), the diversity of multi-kingdom microbes in water decreased significantly in October (late-aquaculture stage) across three aquaculture models, whereas only bacterial diversity in sediment decreased. Bacterial diversity in sediment was significantly higher than that in water across all models and stages. Notably, regardless of stages or habitats, RCCM demonstrated clear microbial advantages over non-RCCM (FPs and CCFPs), including lower pathogenic bacterial abundance and more stable communities. Cohesion indices (RCCM: 0.98 for water and 0.97 for sediment; non-RCCM: 0.83 for water and 0.63 for sediment) and small-world coefficients (RCCM: 5.03 for water and 6.65 for sediment; non-RCCM: 3.52 for water and 6.36 for sediment) confirmed this stability. Deterministic processes predominated in multi-kingdom community assembly, and the influence of antibiotics on assembly was stronger when antibiotic concentrations in water (mid-aquaculture stage) or sediment (late-aquaculture stage) were higher. Overall, this study provides insights into multi-kingdom microbial communities in freshwater aquaculture systems and microbial-scale evidence supporting the ecological advantages of RCCM, contributing to the promotion of sustainable freshwater aquaculture.

PMID:
43014941
Bibliographic data and abstract were imported from PubMed on 12 Nov 2026.

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