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Microorganisms
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Microbes in Aquaculture
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Microbes in Aquaculture

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

Deadline for manuscript submissions: 31 December 2025 | Viewed by 1337

Special Issue Editor

Dr. Jiasong Zhang

E-Mail Website
Guest Editor
South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences. No. 231 West Xinggang Road, Haizhu District, Guangzhou 510300, China
Interests: aquaculture; disease; stress; gut microbiota; gut microbiome
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Aquaculture is among the fastest-growing sectors in global food production, playing a pivotal role in addressing the increasing demand for sustainable protein sources. However, the industry is confronted with numerous challenges, including disease outbreaks, environmental degradation, and the need for more efficient feed utilization. In this context, microorganisms serve critical and multifaceted functions in aquaculture systems. Microbes not only support the health and growth of aquatic species but also enhance the sustainability and resilience of aquaculture ecosystems.

Microbial communities are essential in maintaining water quality, participating in nutrient cycling, biofiltration, and the degradation of waste products such as ammonia and organic matter. The gut microbiota of aquatic organisms significantly influences digestion, nutrient absorption, immune responses, and overall health. Probiotics, prebiotics, and other microbial-based strategies are increasingly recognized for their ability to improve growth performance, boost disease resistance, and reduce dependence on antibiotics, thus mitigating negative environmental impacts. Additionally, beneficial microbes can outcompete pathogens, decreasing the risk of disease outbreaks and enhancing biosecurity.

The integration of microbial technologies presents vast potential for advancing the sustainability, efficiency, and health of aquaculture systems. Innovations such as probiotics, biofloc systems, and biotechnological approaches are driving more sustainable and environmentally friendly practices. These microbial interventions are crucial for improving feed conversion ratios, reducing environmental footprints, and strengthening the resilience of aquaculture systems.

This Special Issue welcomes contributions that explore the diverse roles of microbes in aquaculture. We encourage research on how microbial communities contribute to pathogen management, nutrient cycling, water quality, and overall system health. Submissions focusing on microbial interventions, including probiotics and biofloc technology, and their applications in disease control, environmental sustainability, and feed efficiency, are especially welcome. By gathering innovative research, this Special Issue aims to address critical challenges in aquaculture and highlight the potential of microbial innovations for securing sustainable global food production.

Dr. Jiasong Zhang
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 100 words) can be sent to the Editorial Office for announcement on this website.

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-blind 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

  • aquaculture microbiomes
  • probiotics in aquaculture
  • gut microbiota
  • disease management
  • pathogen and host interaction
  • water quality

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Published Papers (4 papers)

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Research

18 pages, 3395 KiB  
Article
Characterization, Microbial Community Structure, and Pathogen Occurrence in Two Typical Eel Farms
by Jing-Ying Lai, Hui-Rong Lin, Xiao-Hui Sun, Gong-Ren Hu, Rui-Lian Yu and Jia-Qi Li
Microorganisms 2025, 13(7), 1624; https://doi.org/10.3390/microorganisms13071624 - 10 Jul 2025
Abstract
Pollutants and pathogens in aquaculture systems may cause economic losses and threaten public health. Yet, the risks associated with microbiological contaminants and their relationship with environmental factors remain largely unknown. In this study, two typical eel farms in southeast China were chosen for [...] Read more.
Pollutants and pathogens in aquaculture systems may cause economic losses and threaten public health. Yet, the risks associated with microbiological contaminants and their relationship with environmental factors remain largely unknown. In this study, two typical eel farms in southeast China were chosen for investigation of water quality and microbial community in the treatment processes. It was found that flocculant addition can only effectively reduce total phosphorus (TP) in both farms. However, excessive total nitrogen (TN) was found (6.16 mg/L and 6.74 mg/L, respectively). NH4+ (3.98 mg/L) was the main nitrogen pollutant in QR farm, while NO3− (3.81 mg/L) and NO2− (1.22 mg/L) were the main nitrogen pollutants in ZJ farm. The treatment processes could not effectively remove nitrogen pollution, and the abundance of nitrogen functional bacteria was low. NO2− was positively correlated with Verrucomicrobiota (p < 0.05). NH4+ and TN were significantly negatively correlated with Nitrospirota and unclassified_f_Anaerolineaceae, respectively (p < 0.05). Some typical pathogens associated with aquaculture (e.g., Lactococcus) and human beings (e.g., Escherichia-Shigella,) were found in the systems. This study proposes suggestions for aquaculture tailwater by analyzing the shortcomings of the existing treatment processes. Meanwhile, it offers certain support for the prevention of pathogen risks in aquaculture systems. Full article
(This article belongs to the Special Issue Microbes in Aquaculture)
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20 pages, 3681 KiB  
Article
Regime Shifts in Microbial and Water Quality Dynamics in Red Tilapia Ponds
by Ziyan Liu, Jiaqi Li, Lei Luo, Yang Yu, Jianing Yan, Caiyun Sun, Xiangjun Miao and Wensheng Li
Microorganisms 2025, 13(7), 1553; https://doi.org/10.3390/microorganisms13071553 - 2 Jul 2025
Viewed by 208
Abstract
Changes in the aquatic ecological environment have a significant impact on aquaculture efficiency. In order to understand the changes in water quality and the dynamics of microalgae and bacteria in the process of aquaculture, 16S rRNA and 18S rRNA high-throughput sequencing technologies were [...] Read more.
Changes in the aquatic ecological environment have a significant impact on aquaculture efficiency. In order to understand the changes in water quality and the dynamics of microalgae and bacteria in the process of aquaculture, 16S rRNA and 18S rRNA high-throughput sequencing technologies were used to determine the microorganisms in a red tilapia (Oreochromis sp.) aquaculture pond. During the breeding period (from 6 July 2023 to 13 November 2023), water samples were collected from three ponds, on average once every 20 days. The results of water quality analysis showed that at the end of culture (13 November 2023), the concentrations of NH4+-N and NO2−-N increased significantly, and both the air temperature (36.00 ± 0.00 to 21 ± 0.00 °C) and water temperature (32.83 ± 0.29 to 22.75 ± 0.42 °C) decreased significantly. The NH4+-N and NO2−-N concentrations increased by 597% (0.67 ± 0.17 to 4.67 ± 0.33 mg/L) and 782% (0.34 ± 0.16 to 3.00 ± 1.15 mg/L), respectively, from T1 to T6. Bacterial diversity decreased to T3 and then increased. The relative abundance of hgcI_clade (from 14.91% to 7.18%) and CL500-29_marine_group (from 3.35% to 1.39%) in aquaculture water generally decreased with the extension of aquaculture time. The abundance of Komma increased from T1 (1.44%) to T3 (13.90%) and decreased from T3 to T6 (4.21%). The pH, dissolved oxygen concentration, and temperature were main factors affecting the dynamics of bacteria, while dissolved oxygen, NH4+-N, and NO2−-N concentrations affected that of microalgae. In conclusion, this study revealed regime shift in the water quality and microalgal–bacterial community with increasing culture time in red tilapia aquaculture ponds. Full article
(This article belongs to the Special Issue Microbes in Aquaculture)
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18 pages, 1659 KiB  
Article
The Impact of Tank Disinfectants on the Development of Microbiota in Gilthead Seabream (Sparus aurata) Larviculture Systems
by Georgia Apostolopoulou, Naima Bel Mokhtar, Elias Asimakis, Eva Dionyssopoulou, Kosmas Toskas, George Koumoundouros, George Tsiamis and Panagiota Stathopoulou
Microorganisms 2025, 13(6), 1359; https://doi.org/10.3390/microorganisms13061359 - 11 Jun 2025
Viewed by 292
Abstract
Aquaculture play a vital role in enhancing human nutrition by producing commercially valuable fish, with gilthead seabream (Sparus aurata) being a key species in the Mediterranean region. In seabream larviculture, disinfection is commonly used to control pathogens and prevent microbial imbalances. [...] Read more.
Aquaculture play a vital role in enhancing human nutrition by producing commercially valuable fish, with gilthead seabream (Sparus aurata) being a key species in the Mediterranean region. In seabream larviculture, disinfection is commonly used to control pathogens and prevent microbial imbalances. However, this process may also remove beneficial microbiota that contribute to ecosystem stability. This study aims to investigate the impact of tank disinfection operations on the bacterial communities associated with seabream larvae and their rearing water in a commercial hatchery using 16S rRNA amplicon sequencing. For further comparison, the bacterial communities present in eggs and feed were also analyzed for comparison. Results showed that the use of different disinfectants significantly altered the bacterial composition of the larvae, while the duration of the dry period had no measurable effect. Across all larval samples, the phylum Pseudomonadota dominated, with members of the genus Psychrobacter consistently detected regardless of disinfection treatment. This suggests that Psychrobacter may be transmitted from eggs or acquired through the feed, mainly rotifers and Artemia nauplii. In contrast, the bacterial communities in the rearing water were more diverse and showed only minor differences in relative abundance across disinfection methods. Full article
(This article belongs to the Special Issue Microbes in Aquaculture)
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22 pages, 3157 KiB  
Article
Effects of Dietary Supplementation with Three Different Probiotics on Growth Performance, Antioxidant Capacity, and Intestinal Microbiota in Grass Carp (Ctenopharyngodon idella)
by Wanjia Zhu, Yi Yi, Zhiwei Zou, Haipeng Li, Ting Liang, Qianhe Shi, Liwei Liu and Jianmei Su
Microorganisms 2025, 13(6), 1222; https://doi.org/10.3390/microorganisms13061222 - 27 May 2025
Cited by 1 | Viewed by 386
Abstract
The growing demand for sustainable aquaculture has intensified research on probiotics as antibiotic alternatives. This study aims to evaluate the effects of three probiotic supplements—1 × 1010 CFU/g of Bacillus subtilis (BS), Clostridium butyricum (CB), or Enterococcus faecalis (EF)—on growth performance, antioxidant [...] Read more.
The growing demand for sustainable aquaculture has intensified research on probiotics as antibiotic alternatives. This study aims to evaluate the effects of three probiotic supplements—1 × 1010 CFU/g of Bacillus subtilis (BS), Clostridium butyricum (CB), or Enterococcus faecalis (EF)—on growth performance, antioxidant capacity, intestinal structure, and gut microbiota in grass carp (Ctenopharyngodon idella; initial body weight: 42.52 ± 4.17 g) for 28 d. Compared to the non-supplemented (NC) control group, all probiotic-supplemented groups significantly enhanced final body weight, weight gain rate, specific growth rate, and crude protein content, and reduced feed conversion ratio (p < 0.05). Probiotic supplementation upregulated the intestinal ctrb1 gene expression and increased villus length. Serum superoxide dismutase (SOD) and catalase activity were elevated in the BS group, whereas only SOD was increased in the CB group (p < 0.05). Gut microbiota analysis revealed reduced Proteobacteria abundance in all probiotic-supplemented groups. Compared with the NC group, the BS group enriched Bacteroidetes and Prevotella_7, while the CB group promoted the abundance of Actinobacteria, Lactobacillus, and Clostridium_sensu_stricto_1. The EF group increased the abundance of Fusobacteria, Cetobacterium, and Bacteroides (p < 0.05). These findings demonstrate that dietary supplementation with probiotics enhances growth performance by modulating antioxidant responses, intestinal morphology, and microbial community balance. Full article
(This article belongs to the Special Issue Microbes in Aquaculture)
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