Temporal microbiome dynamics and fish health-associated dysbiosis in freshwater aquarium systems: a case study from River Wonders Singapore
Journal Publication ResearchOnline@JCUAbstract
Introduction: Aquarium systems are engineered yet biologically dynamic ecosystems where microbial communities underpin nutrient cycling, organic matter decomposition and water quality regulation. These processes directly affect aquatic animal health. Methods: This study conducted a two-month time series analysis of waterborne microbiomes across six freshwater exhibits at River Wonders, Singapore, using 16S rRNA gene sequencing. Exhibits were categorized as “Healthy” (LM, MJ, EE) or “Stressed” (P, MJR, RG) based on fish health, and as indoor or semi-indoor/outdoor by system design. Results and discussion: Temporal fluctuations in microbial composition and diversity were evident over time, with distinct profiles between indoor and semi-indoor/outdoor. Potential opportunistic or pathogenic genera, including Edwardsiella, Flavobacterium, Aeromonas, Pseudomonas and Mycobacterium, were consistently among the 30 most abundant taxa. The most severe dysbiosis occurred in exhibit P, characterized by a transient Pseudomonas bloom (51.4%), loss of nitrifiers (Nitrosomonas, Nitrospira) and concurrent fish health issues. MJR and RG harbored persistent polymicrobial risks, while “Healthy” exhibits maintained relatively more balanced microbial communities with lower pathogen loads. Routine husbandry interventions (e.g., partial water changes, substrate cleaning) coincided with improved microbial evenness and reductions in opportunistic taxa. These findings highlight diagnostic potential of microbiome profiling to detect early dysbiosis and support evidence-based husbandry in managed aquatic systems.
Journal
Frontiers in Microbiology
Publication Name
Frontiers In Microbiology
Volume
17
ISBN/ISSN
1664-302X
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Pages Count
11
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Publisher
Frontiers Research
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EISSN
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DOI
10.3389/fmicb.2026.1739391