Aquatic Microorganisms and Their Application in Aquaculture, 2nd Edition

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: 15 February 2026 | Viewed by 895

Special Issue Editor

South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
Interests: shrimp aquaculture; aquaculture microbiome; environmental control; biofloc technology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue, “Aquatic Microorganisms and Their Application in Aquaculture”, which features 16 publications.

Aquaculture is one of the world's fastest growing food production industries, which needs to meet the increasing global demand for fish, crustaceans, shellfish, seaweeds, and other aquatic species. These species are cultured in controlled aquatic ecosystems which harbor a wide variety of microbial communities. The microbiome of the hosts and their surroundings play a vital role in the growth and health of cultured species, as well as the steady state of their water environments. Currently, an increasing number of studies are seeking to use microbe-based technologies to support the sustainable development of modern aquaculture; the application and administration of microorganisms, including probiotic strains, has three main three targets: removing pollution and improving water quality, supplementing nutrients and promoting production performance, and improving health and preventing diseases in cultured species. This Special Issue will publish research on the role of aquatic microorganisms and their application in aquaculture to meet these aims. Both original research articles and reviews are welcome. Potential topics include, but are not limited to, the following: the diversity and function of microorganisms in aquaculture systems; the monitoring and management of microorganisms in aquaculture systems; microorganisms as aquafeed ingredients and functional additives for aquaculture; and probiotic bacteria and algae as biological control agents in aquaculture.

Dr. Wujie Xu
Guest Editor

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Keywords

  • aquatic microorganisms
  • aquaculture microbiome
  • microbial water management
  • microbial additives in feed
  • pathogenic microorganisms
  • microbial ecology
  • biofloc technology

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Published Papers (1 paper)

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Research

20 pages, 3607 KB  
Article
Oyster Aquaculture Impacts on Environment and Microbial Taxa in Dapeng Cove
by Fei Tong, Xue Feng, Huarong Yuan, Yuxiang Chen and Pimao Chen
Microorganisms 2025, 13(11), 2480; https://doi.org/10.3390/microorganisms13112480 - 30 Oct 2025
Viewed by 592
Abstract
Environmental physicochemical factors and microorganisms play critical roles in the health of oysters. However, the impact of high-density oyster farming—a highly efficient filter-feeding bivalve system—on environmental conditions and microbial community structure and function remains poorly understood. This study conducted four-season monitoring of the [...] Read more.
Environmental physicochemical factors and microorganisms play critical roles in the health of oysters. However, the impact of high-density oyster farming—a highly efficient filter-feeding bivalve system—on environmental conditions and microbial community structure and function remains poorly understood. This study conducted four-season monitoring of the water and sediment parameters in a semi-enclosed bay commercial oyster aquaculture (OA) system and a control area (CT), coupled with 16S rRNA amplicon sequencing of the environmental microbiota. Oyster aquaculture caused negligible disruption to water column parameters but significantly increased the concentrations of total organic carbon (TOC, annual mean OA vs. CT:1.15% vs. 0.56%), sulfides (annual mean OA vs. CT:67.72 vs. 24.99 mg·kg−1), and heavy metals (Cd, Pb, Cu, Zn, and Cr) in the sediment. α-diversity (Shannon and Chao indices) exhibited minimal overall perturbation, with significant inter-regional differences observed only in winter for both water and sediment. The bacterial community structure of the water column was significantly altered only in winter, whereas sediment communities showed structural shifts in spring, summer, and autumn. Water microbiota were primarily influenced by turbidity, dissolved oxygen, salinity, the Si/N ratio, and silicates. Sediment microbiota were correlated with Pb, Cu, Zn, TOC, Cr, and sediment particle size. Water bacterial functions displayed only four significantly divergent biogeochemical processes annually (sulfur compound respiration; OA vs. CT). In contrast, sediment bacteria exhibited 29 significantly disrupted functions annually, with the greatest seasonal divergence in winter (11/67 functions). Spring, summer, and autumn sediment functions showed distinct patterns. Understanding these environmental–microbial interactions is essential for sustainable oyster aquaculture and ecological optimization. Full article
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