Bacterial Community Composition and Prevalence of <i>Aeromonas dhakensis</i> in Four Tilapia Freshwater Aquaculture Systems in Malaysia
The tilapia (<i>Oreochromis</i>) aquaculture industry in Malaysia has expanded rapidly to meet the increasing demand for animal protein. However, this growth is challenged by microbial infections, particularly those caused by the emerging pathogen <i>Aeromonas dhakensis</i>....
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MDPI AG
2025-05-01
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| author | Sook Ling Lim Suat Moi Puah Siti Nursyuhada Baharudin Nur Insyirah Mohd Razalan Kieng Soon Hii Wei Ching Khor Yen Ching Lim Kyaw Thu Aung Kek Heng Chua Po Teen Lim Chui Pin Leaw |
| author_facet | Sook Ling Lim Suat Moi Puah Siti Nursyuhada Baharudin Nur Insyirah Mohd Razalan Kieng Soon Hii Wei Ching Khor Yen Ching Lim Kyaw Thu Aung Kek Heng Chua Po Teen Lim Chui Pin Leaw |
| author_sort | Sook Ling Lim |
| collection | DOAJ |
| description | The tilapia (<i>Oreochromis</i>) aquaculture industry in Malaysia has expanded rapidly to meet the increasing demand for animal protein. However, this growth is challenged by microbial infections, particularly those caused by the emerging pathogen <i>Aeromonas dhakensis</i>. This study aimed to investigate the microbial community composition across four distinct tilapia farming systems and assess associated water physicochemical parameters, with a focus on detecting the presence of <i>A. dhakensis</i> and elucidating its environmental associations. Water physicochemical parameters were measured to evaluate environmental conditions, microbial communities were characterized through 16S rDNA metabarcoding, and <i>A. dhakensis</i> was detected using both microbiological and molecular approaches. Principal component analysis (PCA) and canonical correspondence analysis (CCA) were employed to explore the influence of environmental variables and microbial community dynamics on pathogen occurrence. Our results indicated that floating cages exhibited higher levels of temperature, ammonium, and fecal coliform, while cement tanks showed signs of nutrient accumulation. PCA revealed that both systems were associated with degraded water quality. A total of 45 <i>A. dhakensis</i> strains with distinct fingerprints were isolated. The 16S metabarcoding revealed Proteobacteria, Actinobacteria, and Planctomycetota as the dominant phyla. Alpha diversity did not differ significantly among pond systems, while beta diversity revealed variations in microbial assemblages across aquaculture systems. CCA identified dissolved oxygen, temperature, macronutrients (phosphate, ammonium, nitrate, and nitrite), and turbidity as significant environmental drivers shaping the microbial community structure across the pond systems. In conclusion, this study highlights the importance of environmental factors, particularly dissolved oxygen, temperature, and nutrient levels, in shaping microbial community composition and potentially influencing the presence of pathogenic bacteria such as <i>A. dhakensis</i>. These findings underscore the need for improved environmental management in tilapia aquaculture to mitigate disease risks and support fish health. |
| format | Article |
| id | doaj-art-7ad08a0c75c845ee9f84cc6474b22520 |
| institution | DOAJ |
| issn | 2410-3888 |
| language | English |
| publishDate | 2025-05-01 |
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| spelling | doaj-art-7ad08a0c75c845ee9f84cc6474b225202025-08-20T03:14:41ZengMDPI AGFishes2410-38882025-05-0110520410.3390/fishes10050204Bacterial Community Composition and Prevalence of <i>Aeromonas dhakensis</i> in Four Tilapia Freshwater Aquaculture Systems in MalaysiaSook Ling Lim0Suat Moi Puah1Siti Nursyuhada Baharudin2Nur Insyirah Mohd Razalan3Kieng Soon Hii4Wei Ching Khor5Yen Ching Lim6Kyaw Thu Aung7Kek Heng Chua8Po Teen Lim9Chui Pin Leaw10Department of Biomedical Science, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, MalaysiaDepartment of Biomedical Science, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, MalaysiaBachok Marine Research Station, Institute of Ocean and Earth Sciences, Universiti Malaya, Bachok 16310, Kelantan, MalaysiaDepartment of Biomedical Science, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, MalaysiaBachok Marine Research Station, Institute of Ocean and Earth Sciences, Universiti Malaya, Bachok 16310, Kelantan, MalaysiaNational Centre for Food Science, Singapore Food Agency, 7 International Business Park, Singapore 609919, SingaporeNational Centre for Food Science, Singapore Food Agency, 7 International Business Park, Singapore 609919, SingaporeNational Centre for Food Science, Singapore Food Agency, 7 International Business Park, Singapore 609919, SingaporeDepartment of Biomedical Science, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, MalaysiaBachok Marine Research Station, Institute of Ocean and Earth Sciences, Universiti Malaya, Bachok 16310, Kelantan, MalaysiaBachok Marine Research Station, Institute of Ocean and Earth Sciences, Universiti Malaya, Bachok 16310, Kelantan, MalaysiaThe tilapia (<i>Oreochromis</i>) aquaculture industry in Malaysia has expanded rapidly to meet the increasing demand for animal protein. However, this growth is challenged by microbial infections, particularly those caused by the emerging pathogen <i>Aeromonas dhakensis</i>. This study aimed to investigate the microbial community composition across four distinct tilapia farming systems and assess associated water physicochemical parameters, with a focus on detecting the presence of <i>A. dhakensis</i> and elucidating its environmental associations. Water physicochemical parameters were measured to evaluate environmental conditions, microbial communities were characterized through 16S rDNA metabarcoding, and <i>A. dhakensis</i> was detected using both microbiological and molecular approaches. Principal component analysis (PCA) and canonical correspondence analysis (CCA) were employed to explore the influence of environmental variables and microbial community dynamics on pathogen occurrence. Our results indicated that floating cages exhibited higher levels of temperature, ammonium, and fecal coliform, while cement tanks showed signs of nutrient accumulation. PCA revealed that both systems were associated with degraded water quality. A total of 45 <i>A. dhakensis</i> strains with distinct fingerprints were isolated. The 16S metabarcoding revealed Proteobacteria, Actinobacteria, and Planctomycetota as the dominant phyla. Alpha diversity did not differ significantly among pond systems, while beta diversity revealed variations in microbial assemblages across aquaculture systems. CCA identified dissolved oxygen, temperature, macronutrients (phosphate, ammonium, nitrate, and nitrite), and turbidity as significant environmental drivers shaping the microbial community structure across the pond systems. In conclusion, this study highlights the importance of environmental factors, particularly dissolved oxygen, temperature, and nutrient levels, in shaping microbial community composition and potentially influencing the presence of pathogenic bacteria such as <i>A. dhakensis</i>. These findings underscore the need for improved environmental management in tilapia aquaculture to mitigate disease risks and support fish health.https://www.mdpi.com/2410-3888/10/5/204<i>Aeromonas dhakensis</i>alpha diversitybeta diversitycanonical correlation analysiseDNA metabarcodingfreshwater aquaculture |
| spellingShingle | Sook Ling Lim Suat Moi Puah Siti Nursyuhada Baharudin Nur Insyirah Mohd Razalan Kieng Soon Hii Wei Ching Khor Yen Ching Lim Kyaw Thu Aung Kek Heng Chua Po Teen Lim Chui Pin Leaw Bacterial Community Composition and Prevalence of <i>Aeromonas dhakensis</i> in Four Tilapia Freshwater Aquaculture Systems in Malaysia Fishes <i>Aeromonas dhakensis</i> alpha diversity beta diversity canonical correlation analysis eDNA metabarcoding freshwater aquaculture |
| title | Bacterial Community Composition and Prevalence of <i>Aeromonas dhakensis</i> in Four Tilapia Freshwater Aquaculture Systems in Malaysia |
| title_full | Bacterial Community Composition and Prevalence of <i>Aeromonas dhakensis</i> in Four Tilapia Freshwater Aquaculture Systems in Malaysia |
| title_fullStr | Bacterial Community Composition and Prevalence of <i>Aeromonas dhakensis</i> in Four Tilapia Freshwater Aquaculture Systems in Malaysia |
| title_full_unstemmed | Bacterial Community Composition and Prevalence of <i>Aeromonas dhakensis</i> in Four Tilapia Freshwater Aquaculture Systems in Malaysia |
| title_short | Bacterial Community Composition and Prevalence of <i>Aeromonas dhakensis</i> in Four Tilapia Freshwater Aquaculture Systems in Malaysia |
| title_sort | bacterial community composition and prevalence of i aeromonas dhakensis i in four tilapia freshwater aquaculture systems in malaysia |
| topic | <i>Aeromonas dhakensis</i> alpha diversity beta diversity canonical correlation analysis eDNA metabarcoding freshwater aquaculture |
| url | https://www.mdpi.com/2410-3888/10/5/204 |
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