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Microorganisms
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Aquatic Microorganisms and Their Application in Aquaculture, 2nd Edition
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Aquatic Microorganisms and Their Application in Aquaculture, 2nd Edition

A Special Issue of Microorganisms (ISSN 2076-2607) belonging to the section "Environmental Microbiology".

Deadline for manuscript submissions: closed (31 August 2026) | Viewed by 5618

Editor

Dr. Wujie Xu

E-Mail Website
Guest 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”, to which features 18 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

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

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

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Related Special Issue

Published Papers (6 papers)

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Research

16 pages, 1853 KB  
Article
Source-Dependent Structuring of Hydrogen-Oxidising Bacterial Community Composition During Enrichment and Isolation from Freshwater Environments
by Emine Gozde Ozbayram and Marcell Nikolausz
Microorganisms 2026, 14(6), 1221; https://doi.org/10.3390/microorganisms14061221 - 28 May 2026
Viewed by 412
Abstract
This study set out to cultivate and isolate hydrogen-oxidising bacteria (HOB) for microbial protein production under a specific culture strategy with a particular focus on assessing the influence of different environmental sources on enrichment culture and strain diversity. Therefore, HOB were enriched from [...] Read more.
This study set out to cultivate and isolate hydrogen-oxidising bacteria (HOB) for microbial protein production under a specific culture strategy with a particular focus on assessing the influence of different environmental sources on enrichment culture and strain diversity. Therefore, HOB were enriched from samples collected from various freshwater lakes and streams, and novel strains were subsequently isolated from these cultures. The enrichment procedure revealed significant shifts in community compositions, which were mainly driven by changes in the relative abundance of genera affiliated to Pseudomonadota and Bacteroidota. Sample-specific variations were observed in the communities of the inocula, reflecting distinct community structures associated with distinct ecological functions. The most common autotrophic HOB, Hydrogenophaga, proliferated in some of the cultures. However, several genera, such as Acinetobacter and Klebsiella that have not been previously recognised with hydrogen-oxidation characteristics, were also enriched, suggesting potential novel contributors to HOB communities. Full article
(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture, 2nd Edition)
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19 pages, 4177 KB  
Article
Enhanced Nitrification in Yellow Clay Improves In Situ Water Purification for Eel Aquaculture: A Preliminary Assessment
by Lin Yuan, Liting Cheng, Guangnian Yuan, Chao Liu and Zhiwen Song
Microorganisms 2026, 14(5), 1126; https://doi.org/10.3390/microorganisms14051126 - 15 May 2026
Viewed by 458
Abstract
To address the issues of high water exchange rates and significant negative environmental impacts associated with eel aquaculture, this study explored the use of yellow clay as a carrier for nitrifying bacterial communities. By pre-enhancing the nitrification capacity of the yellow clay, we [...] Read more.
To address the issues of high water exchange rates and significant negative environmental impacts associated with eel aquaculture, this study explored the use of yellow clay as a carrier for nitrifying bacterial communities. By pre-enhancing the nitrification capacity of the yellow clay, we aimed to improve the control of inorganic nitrogen in the aquaculture water. Three experimental groups were established: NF-YCA (nitrifying-functional yellow clay-added eel aquaculture system); NN-YCA (non-nitrifying yellow clay-added eel aquaculture system); and YC-F (yellow clay-free eel aquaculture system, blank control). The NF-YCA group had zero water exchange, while the YC-F and NN-YCA groups underwent water exchange equivalent to 28.36 times the system volume. Nitrification was most pronounced in the NF-YCA group, where both mean and peak concentrations of total ammonia nitrogen and nitrite nitrogen were lower than in the YC-F and NN-YCA groups, whereas nitrate nitrogen concentrations in the NF-YCA group were significantly higher than in the other two groups. No significant differences were observed in the survival rate and specific growth rate of elvers among the three systems during the experiment. High-throughput sequencing results revealed that Pseudomonadota and Bacteroidota were the most dominant phyla across all systems. However, the bacterial community structure in NF-YCA was more abundant and stable, and nitrification-related genera, such as Nitrosomonas, were detected in high abundance in this system. The preliminary results demonstrate that the eel aquaculture system with enhanced yellow clay nitrification function, can effectively maintain water quality without water exchange, highlighting its potential for practical application. Full article
(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture, 2nd Edition)
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25 pages, 4497 KB  
Article
Amplicon Sequencing Reveals Microbial Community Structure and Its Relationships with Environmental Factors in Macrobrachium nipponense Aquaculture Ponds
by Wanqi Zhang, Xiaofan Fang, Yuefan Zhang, Yiwei Xiong, Wenyi Zhang, Shubo Jin, Hongtuo Fu, Sufei Jiang and Hui Qiao
Microorganisms 2026, 14(5), 982; https://doi.org/10.3390/microorganisms14050982 - 27 Apr 2026
Viewed by 744
Abstract
Macrobrachium nipponense is one of the major economic species in freshwater aquaculture in China. As an important component of aquaculture ecosystem, microorganisms participate in key processes such as material cycling and water quality regulation, exerting significant impacts on the cultured organisms. In this [...] Read more.
Macrobrachium nipponense is one of the major economic species in freshwater aquaculture in China. As an important component of aquaculture ecosystem, microorganisms participate in key processes such as material cycling and water quality regulation, exerting significant impacts on the cultured organisms. In this study, high-throughput sequencing of the 16S rRNA, 18S rRNA, and ITS regions was employed to comparatively analyze the characteristics of microbial communities before and during the cultivation period, combined with correlation analysis of environmental factors. The results showed that the dominant microbial groups in the prawn pond water were Proteobacteria, Cyanobacteria, Ascomycota, Basidiomycota, Chlorophyta, and Arthropoda. The microbial community structure differed significantly between the pond water during the culture period and the pre-culture external river baseline: manifested as an increase in the relative abundances of Cyanobacteria, Chytridiomycota, and zooplankton, and a decrease in the abundances of Ascomycota, Basidiomycota, and Chlorophyta. Analysis of LEfSe revealed that the low-nitrogen pond was enriched with taxa such as Muribaculaceae; the high-nitrogen pond was enriched with taxa such as Cyanobium_PCC-6307; and the control pond was enriched with taxa such as CL500-29_marine_group. Functional prediction indicated that heterotrophic metabolism-related functions dominated the microbial communities. The abundance of fungal pathogens was significantly higher in the low-nitrogen group, while potential pathogenic bacteria were enriched in the high-nitrogen group. Ammonia nitrogen is a core environmental factor associated with differences in microbial community structure. The findings of this study can provide theoretical references and data support for water quality optimization and the construction of healthy aquaculture models in freshwater shrimp and crab farming waters. Full article
(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture, 2nd Edition)
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32 pages, 15468 KB  
Article
Highly Efficient Nitrogen Removal by Stutzerimonas stutzeri Strain MJ20: Metabolic Pathways and Potential for Biofloc Systems and Low C/N Ratio Aquaculture Wastewater
by Miao Xie, Yongkui Liu, Chongqing Wen, Jiayi Zhong, Huanying Pang, Jia Cai, Yishan Lu, Jichang Jian and Yu Huang
Microorganisms 2026, 14(5), 975; https://doi.org/10.3390/microorganisms14050975 - 26 Apr 2026
Cited by 1 | Viewed by 617
Abstract
Although numerous studies have focused on the potential application of heterotrophic nitrification–aerobic denitrification (HNAD) bacteria in wastewater treatment, research exploring their potential in aquaculture biofloc systems remains limited. In this study, a promising HNAD strain, identified as Stutzerimonas stutzeri MJ20, was isolated from [...] Read more.
Although numerous studies have focused on the potential application of heterotrophic nitrification–aerobic denitrification (HNAD) bacteria in wastewater treatment, research exploring their potential in aquaculture biofloc systems remains limited. In this study, a promising HNAD strain, identified as Stutzerimonas stutzeri MJ20, was isolated from mature biofloc. This strain efficiently utilized low-cost carbon sources (e.g., glucose) and small-molecule carbon sources (e.g., sodium acetate and sodium succinate). Under conditions with glucose as the carbon source, a carbon-to-nitrogen (C/N) ratio of 15, pH 6–9, temperature 25–35 °C, salinity 0–35‰, and shaker speed of 0–150 rpm, it achieved removal rates of 95–100% for NH4+-N, NO2−-N, and NO3−-N at initial concentrations of 100 mg/L each. Even at higher concentrations (up to 200 mg/L NH4+-N and 500 mg/L for both NO2−-N and NO3−-N), removal rates exceeded 99%. Under mixed nitrogen sources, strain MJ20 demonstrated efficient nitrogen removal, preferentially utilizing NH4+-N, with only minimal and transient accumulation of nitrite and nitrate. Genomic analysis revealed that MJ20 carries key denitrification genes, including napA, nirS, norB and nosZ, and possesses complete pathways for nitrate reduction to nitrogen gas and ammonia assimilation, although typical autotrophic nitrification genes were not detected. Combined genomic data and autotrophic culture experiments indicated that, in addition to utilizing various organic carbon sources, the strain also exhibited certain autotrophic growth capabilities. Furthermore, MJ20 showed strong flocculation ability (flocculation rate > 96% within 16 h), sensitivity to multiple common antibiotics, and no toxicity to zebrafish, demonstrating favorable biosafety. In simulated seawater aquaculture wastewater with a C/N ratio of 5, it achieved a total nitrogen removal rate exceeding 94% within 72 h. These results indicate that strain MJ20 possesses comprehensive advantages, including efficient nitrogen removal, broad carbon source adaptability, strong environmental resilience, minimal accumulation of intermediate nitrogen products, excellent flocculation ability, and high biosafety. These traits highlight its potential for application in biofloc systems and in treating aquaculture tail water with a low C/N ratio. This study provides theoretical insights and practical guidance for screening HNAD bacteria suitable for biofloc systems. Full article
(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture, 2nd Edition)
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23 pages, 3500 KB  
Article
Algicidal Characteristics of Bacillus cereus Strain PT1 Against Microcystis aeruginosa in Sulfate-Type Saline–Alkaline Environments
by Qing Wang, Yucheng Cao, Yunna Xu, Keng Yang, Chuangwen Xu, Guoliang Wen, Jinfan Liu, Jianshe Zhang and Xiaojuan Hu
Microorganisms 2026, 14(3), 647; https://doi.org/10.3390/microorganisms14030647 - 13 Mar 2026
Viewed by 810
Abstract
Biologically controlling Microcystis aeruginosa blooms in saline–alkaline environments remains a major challenge in aquatic ecosystem management. Here, the algicidal performance of an indigenous algicidal bacterium, Bacillus cereus strain PT1 isolated from a sulfate-type saline–alkaline pond, against M. aeruginosa was evaluated, and the underlying [...] Read more.
Biologically controlling Microcystis aeruginosa blooms in saline–alkaline environments remains a major challenge in aquatic ecosystem management. Here, the algicidal performance of an indigenous algicidal bacterium, Bacillus cereus strain PT1 isolated from a sulfate-type saline–alkaline pond, against M. aeruginosa was evaluated, and the underlying metabolic mechanisms were elucidated using non-targeted metabolomics. PT1 exhibited pronounced, stable algicidal activity under saline–alkaline conditions, decreasing the algal cell density from 2 × 106 to 1.25 ± 0.5 × 105 cells mL−1 within 4 days at a rate of 93.75 ± 2.5% (p < 0.05). The above results demonstrate that strain PT1 has a significant lytic effect on M. aeruginosa. Non-targeted liquid chromatography–mass spectrometry analysis identified 298 PT1-induced accumulated metabolic features, and the top 30 candidates comprised organic acids and aromatic compounds, including benzoic acid, coumarin, malonic acid, and signaling-related molecules, including indoleacetaldehyde and nitroprusside. These differential metabolites were associated with algicidal-related pathways, including quorum sensing, two-component systems, ABC transporters, and tryptophan metabolism, outlining a coordinated “regulation–transport–metabolic remodeling” framework. Our findings demonstrate the potential of the indigenous algicidal strain PT1 from saline–alkali ponds to control M. aeruginosa blooms. They also provide an important theoretical basis and data foundation for further elucidating the molecular characteristics of algae solubilizing activity under saline–alkali conditions and developing microbial agents for preventing and controlling Microcystis blooms in saline–alkali ponds. Full article
(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture, 2nd Edition)
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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
Cited by 1 | Viewed by 1569
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
(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture, 2nd Edition)
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