Aquatic Microorganisms and Their Application in Aquaculture

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

Deadline for manuscript submissions: 31 May 2025 | Viewed by 9013

Special Issue Editor

South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
Interests: shrimp aquaculture; environmental control; biofloc technology
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Special Issue Information

Dear Colleagues,

Aquaculture is one of the world's fastest growing food production industries, with a need to meet the increasing global demand for fish, crustaceans, shellfish, seaweeds, and other aquatic species. These species are widely 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 water environments. Currently, an increasing number of studies are seeking to research and apply microbe-based technologies to support the sustainable development of modern aquaculture; the application and administration of microorganisms, including probiotic strains, mainly includes three aspects: 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 cover research on the role of aquatic microorganisms and their application in aquaculture. 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
  • aquafeed

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Published Papers (9 papers)

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Research

21 pages, 4832 KiB  
Article
Development and Application of Lactobacillus plantarum PSCPL13 Probiotics in Olive Flounder (Paralichthys olivaceus) Farming
by Muhammad Aleem Abbas, Hae-Jung Kim, Ga-Yeong Lee, Hae-Yeon Cho, Syed Al Jawad Sayem, Eon-Bee Lee, Seung-Jin Lee and Seung-Chun Park
Microorganisms 2025, 13(1), 61; https://doi.org/10.3390/microorganisms13010061 - 2 Jan 2025
Viewed by 638
Abstract
Aquaculture has grown significantly, contributing to global food security and sustainability; however, intensified fish farming has increased disease susceptibility and antibiotic resistance. This study assessed the probiotic potential of Lactobacillus plantarum PSCPL13 (hereafter, PSCPL13), isolated from the intestines of Japanese eels, for enhancing [...] Read more.
Aquaculture has grown significantly, contributing to global food security and sustainability; however, intensified fish farming has increased disease susceptibility and antibiotic resistance. This study assessed the probiotic potential of Lactobacillus plantarum PSCPL13 (hereafter, PSCPL13), isolated from the intestines of Japanese eels, for enhancing the health of olive flounder. After screening 16 Lactobacillus isolates, PSCPL13 was selected because of its potential broad-spectrum antibacterial activity against many pathogens, such as Vibrio and Edwardsiella. This strain exhibited high acid and bile salt tolerance, which is crucial for intestinal survival. Molecular characterisation confirmed PSCPL13 to be L. plantarum. It was resistant to all tested antibiotics and exhibited significant enzyme activity. In vivo assays in olive flounder revealed that the body weight and length of the fish were significantly higher, while the prevalence of pathogens was lower in their gut microbiota. Regarding haematological parameters, the treated groups exhibited lower eosinophil counts and higher IgM levels, suggesting enhancement of the immune system. These findings indicate that PSCPL13 is a potential probiotic that can be used in aquaculture for naturally improving fish health, growth and immunity, in addition to combating antibiotic resistance and reducing environmental impacts. These findings not only highlight the potential of PSCPL13 in sustainable aquaculture but also provide a foundation for the development of future probiotics. Full article
(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture)
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19 pages, 7157 KiB  
Article
The Bile Acid Metabolism of Intestinal Microorganisms Mediates the Effect of Different Protein Sources on Muscle Protein Deposition in Procambarus clarkii
by Xiaodi Xu, Xiaochuan Zheng, Qunlan Zhou, Cunxin Sun, Aimin Wang, Aimin Zhu, Yuanyuan Zhang and Bo Liu
Microorganisms 2025, 13(1), 11; https://doi.org/10.3390/microorganisms13010011 - 24 Dec 2024
Viewed by 573
Abstract
The most economically important trait of the Procambarus clarkii is meat quality. Protein deposition is essential in muscle growth and nutritional quality formation. The effects and potential mechanisms of feed protein sources on crustaceans’ muscle protein deposition have not been elucidated. This study [...] Read more.
The most economically important trait of the Procambarus clarkii is meat quality. Protein deposition is essential in muscle growth and nutritional quality formation. The effects and potential mechanisms of feed protein sources on crustaceans’ muscle protein deposition have not been elucidated. This study established an all-animal protein source (AP) and an all-plant protein source group (PP), with a feeding period of 8 weeks (four replicates per group, 45 individuals per replicate). The results demonstrated that muscle protein deposition, muscle fiber diameter, and hardness were significantly higher in the PP group (p < 0.05). The transcript levels of genes involved in protein synthesis were notably upregulated, while those of protein hydrolysis and negative regulators of myogenesis notably downregulated in PP group (p < 0.05). Furthermore, protein sources shaped differential intestinal microbiota composition and microbial metabolites profiles, as evidenced by a significant decrease in g_Bacteroides (p = 0.030), and a significant increase in taurochenodeoxycholic acid (TCDCA) in PP group (p = 0.027). A significant correlation was further established by Pearson correlation analysis between the g_Bacteroides, TCDCA, and genes involved in the MSTN-mediated protein deposition pathway (p < 0.05). In vitro anaerobic fermentation confirmed the ability of the two groups of intestinal flora to metabolically produce differential TCDCA (p = 0.038). Our results demonstrated that the ‘Bacteroides-TCDCA-MSTN’ axis may mediate the effects of different protein sources on muscle development and protein deposition in P. clarkii, which was anticipated to represent a novel target for the muscle quality modulation in crustaceans. Full article
(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture)
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15 pages, 3448 KiB  
Article
Impact of Biochar Addition on Biofloc Nitrifying Bacteria and Inorganic Nitrogen Dynamics in an Intensive Aquaculture System of Shrimp
by Wujie Xu, Demin Zhang, Haochang Su, Yu Xu, Xiaojuan Hu, Guoliang Wen and Yucheng Cao
Microorganisms 2024, 12(12), 2581; https://doi.org/10.3390/microorganisms12122581 - 13 Dec 2024
Viewed by 618
Abstract
In this study, an eight-week culture trial of Penaeus vannamei juveniles was conducted in commercial intensive systems to compare the impacts of biochar and molasses addition on biofloc nitrifying bacteria and inorganic nitrogen dynamics under limited water exchange conditions. During the trial, the [...] Read more.
In this study, an eight-week culture trial of Penaeus vannamei juveniles was conducted in commercial intensive systems to compare the impacts of biochar and molasses addition on biofloc nitrifying bacteria and inorganic nitrogen dynamics under limited water exchange conditions. During the trial, the biofloc concentration (in terms of VSS and TSS), quantities of total bacteria (TB) and total Vibrio (TV), and ratio of TV/TB in the culture water were lower in the biochar group compared to the molasses group. Metagenomic sequencing analysis revealed that the bacterial community composition of bioflocs showed higher α-diversity and complexity in the biochar group compared to the molasses group. Moreover, the abundance of nitrifying bacterial genera and functional genes in bioflocs was higher in the biochar group compared to the molasses group. Inorganic nitrogen dynamics showed that NH4+-N and NO2-N were better controlled in the biochar group compared to the molasses group, as reflected by lower peaks of NH4+-N and NO2-N and higher NO3-N concentrations. Excellent production performance of shrimp was achieved, which in turn proved the reliable effect of biochar addition on the mediation of inorganic nitrogen transformation through nitrifying bacteria. These results showed that biochar addition could promote biofloc nitrifying bacteria and nitrification to more effectively control harmful nitrogen for shrimp efficient production. This study provides a practical example for the biochar application in biofloc-based systems for intensive aquaculture. Full article
(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture)
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23 pages, 3840 KiB  
Article
Longitudinal Microbiome Investigations Reveal Core and Growth-Associated Bacteria During Early Life Stages of Scylla paramamosain
by Yin Fu, Yongxu Cheng, Lingbo Ma and Qicun Zhou
Microorganisms 2024, 12(12), 2457; https://doi.org/10.3390/microorganisms12122457 - 29 Nov 2024
Viewed by 747
Abstract
In animals, growth and development are strongly correlated with the gut microbiota. The gut of the economically important marine crab (Scylla paramamosain) harbors a diverse microbial community, yet its associations with the surrounding environment, growth performance, and developmental stages remain obscure. [...] Read more.
In animals, growth and development are strongly correlated with the gut microbiota. The gut of the economically important marine crab (Scylla paramamosain) harbors a diverse microbial community, yet its associations with the surrounding environment, growth performance, and developmental stages remain obscure. In this study, we first characterized stage-specific microbiomes and shifts in the contributions of live feed and water via SourceTracker. We observed decreased microbial diversity and increased priority effects along zoea stages. Psychobacter was identified as the core genus, whereas Lactobacillus was the hub genus connecting different stages. Second, microbial correlations with various stage-specific growth traits were observed under interventions generating enhanced (probiotic mixture enrichment), normal (control), and reduced (antibiotic treatment) microbiomes. By combining machine learning regression and bioinformatics analysis, we identified four candidate growth performance-associated probiotics belonging to Rhodobacterales, Sulfitobacter, Confluentimicrobium, and Lactobacillus, respectively. Our study interpreted the dynamics and origins of the Scylla paramamosain zoea microbiome and underscored the importance of optimizing potential probiotics to increase growth performance during early life stages in marine invertebrates for effective larviculture. Full article
(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture)
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15 pages, 3734 KiB  
Article
Effect of Dietary Astragalus polysaccharides (APS) on the Growth Performance, Antioxidant Responses, Immunological Parameters, and Intestinal Microbiota of Coral Trout (Plectropomus leopardus)
by Xiaoqi Hao, Heizhao Lin, Ziyang Lin, Keng Yang, Jing Hu, Zhenhua Ma and Wei Yu
Microorganisms 2024, 12(10), 1980; https://doi.org/10.3390/microorganisms12101980 - 30 Sep 2024
Viewed by 993
Abstract
The potential effects of Astragalus polysaccharides (APS) were evaluated in coral trout (Plectropomus leopardus). Five APS levels (0%, 0.05%, 0.10%, 0.15%, and 0.20%) were added to the diet of coral trout, and a 56-day growth trial (initial weight 18.62 ± 0.05 [...] Read more.
The potential effects of Astragalus polysaccharides (APS) were evaluated in coral trout (Plectropomus leopardus). Five APS levels (0%, 0.05%, 0.10%, 0.15%, and 0.20%) were added to the diet of coral trout, and a 56-day growth trial (initial weight 18.62 ± 0.05 g) was conducted. Dietary APS enhanced growth performance, with the highest improvement observed in fish fed the 0.15% APS diet. This concentration also enhanced the antioxidant capacity and immunomodulation of the fish by regulating the expression of genes associated with antioxidant enzymes and immune responses. Intestinal microbiota analysis revealed that APS supplementation significantly increased the Chao1 index and relative abundance of beneficial bacteria (Firmicutes and Bacillus). A high level of APS (0.20%) did not provide additional benefits for growth and health compared to a moderate level (0.15%). These findings indicate that an optimal APS dose promotes growth, enhances antioxidant activity, supports immune function, and improves intestinal microbiota in coral trout. Based on a cubic regression analysis of the specific growth rate, the optimal APS level for the maximal growth of coral trout was determined to be 0.1455%. Full article
(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture)
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13 pages, 1388 KiB  
Article
Microeukaryotes Associated with Freshwater Mussels in Rivers of the Southeastern United States
by Akacia K. Halliday-Isaac and Colin R. Jackson
Microorganisms 2024, 12(9), 1835; https://doi.org/10.3390/microorganisms12091835 - 5 Sep 2024
Viewed by 750
Abstract
Microeukaryotes are a diverse and often overlooked group of microbes that are important in food webs and other ecological linkages. Little is known about microeukaryotes associated with aquatic invertebrates, although filter feeders such as mussels are likely to take in and potentially retain [...] Read more.
Microeukaryotes are a diverse and often overlooked group of microbes that are important in food webs and other ecological linkages. Little is known about microeukaryotes associated with aquatic invertebrates, although filter feeders such as mussels are likely to take in and potentially retain microeukaryotes in their gut while feeding. Microeukaryotes such as apicomplexans have been reported in marine mussel species, but no studies have examined the presence of these microorganisms in freshwater mussels or how they relate to mussel host species or environmental conditions. In this study, microbial community DNA was extracted from the gut tissue of over 300 freshwater mussels, representing 22 species collected from rivers in the southeastern USA. Microeukaryote DNA was detected using PCR amplification, followed by the sequencing of positive amplicons. Microeukaryotes were found in 167 individual mussels (53%) of those tested. Amplicons included dinoflagellates/algae that differed between mussel species and are likely food sources that were distinct from those found in water and sediment samples analyzed concurrently. A total of 5% of the positive amplicons were non-photosynthetic alveolates that could represent parasitic microeukaryotes. Understanding the distribution of microeukaryotes in the freshwater mussel gut microbiome could further our understanding of the ongoing decline of mussel populations. Full article
(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture)
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21 pages, 5963 KiB  
Article
Host Gut-Derived Probiotic, Exiguobacterium acetylicum G1-33, Improves Growth, Immunity, and Resistance to Vibrio harveyi in Hybrid Grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂)
by Mingqing Zhang, Yuwei Feng, Zhongxuan Zhong, Qianping Du, Wei Yu, Jinhui Wu, Xiaolin Huang, Zhong Huang, Guangting Xie and Hu Shu
Microorganisms 2024, 12(8), 1688; https://doi.org/10.3390/microorganisms12081688 - 16 Aug 2024
Cited by 2 | Viewed by 932
Abstract
Several exogenous probiotics are applicable in fish culture; however, challenges in isolation and verification have hindered the full utilization of numerous host probiotics. Therefore, this study aimed to apply the host probiotic Exiguobacterium acetylicum G1-33 to hybrid grouper (Epinephelus fuscoguttatus ♀ × [...] Read more.
Several exogenous probiotics are applicable in fish culture; however, challenges in isolation and verification have hindered the full utilization of numerous host probiotics. Therefore, this study aimed to apply the host probiotic Exiguobacterium acetylicum G1-33 to hybrid grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂) cultures and explore its mechanism of action. In total, 360 hybrid grouper were divided into four groups, which were fed the following for 60 days: three received commercial feed with varying concentrations of E. acetylicum G1-33 (106, 108, and 1010 CFU/g), while a control group received commercial feed. The results showed that supplementation with 106 and 108 CFU/g of E. acetylicum G1-33 enhanced gut morphology, upregulated growth-related genes (ghr1, igf-2, s6k1, tor), and promoted growth, with supplementation with 108 CFU/g resulting in the most notable enhancement. However, supplementation with 1010 CFU/g inhibited growth, possibly because of changes in intestinal morphology. Additionally, supplementation with E. acetylicum G1-33 upregulated the expression of immune-related genes (c3, myd88, Cu/Zn-sod, tlr3, and tnf2) in the liver and head kidney but led to an increase in malondialdehyde content, as well as a decrease in alkaline phosphatase and acid phosphatase activities, in the liver and serum, indicating increased oxidative stress. Moreover, supplementation with 106 and 108 CFU/g E. acetylicum G1-33 enhanced the widespread expression of immune-related genes in the head kidney and liver, respectively, and improved resistance to Vibrio harveyi, whereas supplementation with 1010 CFU/g weakened this resistance. In conclusion, E. acetylicum G1-33, particularly at 108 CFU/g, emerged as an effective probiotic, optimizing growth performance and immunity in hybrid grouper. This research is pioneering in its application of E. acetylicum in mariculture, potentially broadening the range of probiotic strategies in aquaculture. Full article
(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture)
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13 pages, 1720 KiB  
Article
Salmonirosea aquatica gen. nov., sp. nov., a Novel Genus within the Family Spirosomaceae, Was Isolated from Brackish Water in the Republic of Korea
by Kiwoon Baek, Sumin Jang, Jaeduk Goh and Ahyoung Choi
Microorganisms 2024, 12(8), 1671; https://doi.org/10.3390/microorganisms12081671 - 14 Aug 2024
Viewed by 1045
Abstract
A Gram-stain-negative, obligately aerobic, non-motile, rod-shaped bacterial strain designated SJW1-29T was isolated from brackish water samples collected from the Seomjin River, Republic of Korea. The purpose of this study was to characterize strain SJW1-29T and determine its taxonomic position as a [...] Read more.
A Gram-stain-negative, obligately aerobic, non-motile, rod-shaped bacterial strain designated SJW1-29T was isolated from brackish water samples collected from the Seomjin River, Republic of Korea. The purpose of this study was to characterize strain SJW1-29T and determine its taxonomic position as a potential new genus within the family Spirosomaceae. The strain grew within the range of 10–30 °C (optimum, 25 °C), pH 5.0–10.0 (optimum, 7.0), and 1–4% NaCl (optimum, 3%). Phylogenetic analysis based on the 16S rRNA gene revealed that strain SJW1-29T belongs to the family Spirosomaceae and is closely related to Persicitalea jodogahamensis Shu-9-SY12-35CT (91.3% similarity), Rhabdobacter roseus R491T (90.6%), and Arundinibacter roseus DMA-K-7aT (90.0%), while the similarities to strains within the order Cytophagales were lower than 90.0%. The genome is 7.1 Mbp with a G+C content of 50.7 mol%. The use of genome-relatedness indices confirmed that this strain belongs to a new genus. The major polar lipid profile consisted of phosphatidylethanolamine, and MK-7 was the predominant menaquinone. The predominant fatty acids were summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), iso-C15:0, iso-C17:0 3-OH, and C16:0, representing more than 80% of the total fatty acids. The phenotypic, chemotaxonomic, genetic, and phylogenetic properties suggest that strain SJW1-29T represents a novel species within a new genus in the family Spirosomaceae, for which the name Salmonirosea aquatica gen. nov., sp. nov., is proposed. The type strain of Salmonirosea aquatica is SJW1-29T (=KCTC 72493T = NBRC 114061T = FBCC-B16924T). Full article
(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture)
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22 pages, 7852 KiB  
Article
Effects of Dietary Multi-Strain Probiotics on Growth Performance, Antioxidant Status, Immune Response, and Intestinal Microbiota of Hybrid Groupers (Epinephelus fuscoguttatus× E. lanceolatus ♂)
by Guangting Xie, Xiaoying Chen, Yuwei Feng, Zhide Yu, Qiuqin Lu, Manfeng Li, Ziqi Ye, Heizhao Lin, Wei Yu and Hu Shu
Microorganisms 2024, 12(7), 1358; https://doi.org/10.3390/microorganisms12071358 - 2 Jul 2024
Cited by 3 | Viewed by 1653
Abstract
This study aims to examine the effects of the mixture of Bacillus cereus G1–11 and Exiguobacterium acetylicum G1–33, isolated from the gut of hybrid groupers (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂), on the host. The hybrid groupers were divided into a [...] Read more.
This study aims to examine the effects of the mixture of Bacillus cereus G1–11 and Exiguobacterium acetylicum G1–33, isolated from the gut of hybrid groupers (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂), on the host. The hybrid groupers were divided into a control (C, without any probiotics), B. cereus (BC, 1010 cfu/g), E. acetylicum (EA, 108 cfu/g), compound (mix, a 1:1 mixture of B. cereus and E. acetylicum), and positive reference group (P, Lactobacillus acidophilus, 5 × 108 cfu/L). Each group had four replicates, with 30 fish per replicate (53.30 ± 0.50 g), and were fed for 60 days. The results showed that adding probiotics to the feed significantly improved the weight gain, weight growth rate, specific growth rate, and digestive enzyme activities of hybrid groupers compared to the C group. The compound group was the most significant. In addition, composite probiotics added to feed significantly upregulated the expression levels of several growth-related genes in the liver and muscles. The activities of alkaline phosphatase, catalase, glutathione peroxidase, glutathione transferase, lysozyme, and total antioxidant capacity in the serum and liver were significantly influenced through mixed probiotic feeding. Moreover, the expression levels of several immune-related genes in the liver, spleen, and head kidney were significantly enhanced by adding single and mixed probiotics to feed, with the synergy of mixed probiotics being the best. An analysis of the gut microbiota showed that adding composite bacteria enhanced the richness and diversity of the gut microbiota, significantly increasing the relative abundance of potential probiotics (Cetobacterium and Microbacterium) while decreasing the presence of potential pathogens (Mycoplasma). Overall, our findings highlighted the efficacy of mixed probiotics (B. cereus and E. acetylicum) in enhancing growth performance, nutritional value of hybrid grouper feed, antioxidant capacity, immune response, and intestinal health, in finding the best combination of functional feed additives. Full article
(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture)
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