Abstract
Sediment environments harbor a repertoire of microorganisms that contribute to animal health and the microecosystem in aquaculture ecosystems, but their community diversity and the potential factors that control it remain unclear. Here, we applied 16S rRNA gene amplicon sequencing to investigate bacterial diversity and assembly mechanisms in the sediments of shrimp cultural ponds at the mesoscale. Our results showed that sediment bacterial communities contained 10,333 operational taxonomic units (OTUs) but had only 34 core OTUs and that the relative abundances of these core OTUs were significantly correlated with the physicochemical properties of the sediments. Proteobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Acidobacteria, Firmicutes, Actinobacteria, Ignavibacteriae, Spirochaetae and Planctomycetes were the ten most abundant bacterial phyla. Notably, some opportunistic pathogens (e.g. Vibrio and Photobacterium) and potential functional microbes (e.g. Nitrospira, Nitrosomonas, Desulfobulbus and Desulfuromusa) were widely distributed in shrimp cultural pond sediments. More importantly, we found that there was a significant negative but weak distance-decay relationship among bacterial communities in shrimp culture pond sediments at the mesoscale, and that the spatial turnover of these bacterial communities appeared to be largely driven by stochastic processes. Additionally, environmental factors, such as pH and total nitrogen, also played important roles in influencing the sediment bacterial structure. Our findings enhance our understanding of microbial ecology in aquatic ecosystems and facilitate sediment microbiota management in aquaculture.
Key points
• Core bacterial taxa in cultural pond sediments contributed to the shrimp health and element cycling.
• There was a significant negative distance-decay relationship among bacterial communities in shrimp culture pond sediments at the mesoscale, and its spatial turnover appeared to be largely driven by stochastic processes.
• Environmental factors (e.g. pH and total nitrogen) played important roles in influencing bacterial structure in shrimp cultural pond sediments.
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Data availability
All the raw reads in the current study have been deposited at the Sequence Read Archive of the NCBI under the accession number PRJNA545396.
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Funding
This work was financially supported by National Natural Science Foundation of China (31902392); China Agriculture Research System of MOF and MARA; the China Agriculture Research System (CARS-48); China- ASEAN Maritime Cooperation Fund, China-ASEAN Center for Joint Research and Promotion of Marine Aquaculture Technology; Natural Science Foundation of Guangdong Province, China (2019A1515011557); Fundamental Research Funds for the Central Universities (19lgpy103); and Key Research and Development Projects in Guangdong Province (2020B0202010009).
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DW Hou, RJ Zhou, SZ Zeng, DD Wei, XS Deng and CG Xing performed the sample collections and experiments. DW Hou and RJ Zhou analysed the data. DW Hou, ZJ Huang SP Weng and JG He contributed the conception of this work and wrote the paper. ZJ Huang was primarily responsible for the final content.
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Hou, D., Zhou, R., Zeng, S. et al. Stochastic processes shape the bacterial community assembly in shrimp cultural pond sediments. Appl Microbiol Biotechnol 105, 5013–5022 (2021). https://doi.org/10.1007/s00253-021-11378-9
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DOI: https://doi.org/10.1007/s00253-021-11378-9