Tracking seasonal microbial dynamics and potential pathogen exposure signals in coastal fish-farm waters using long-read metagenomics

초록

Coastal waters around open sea-cage aquaculture systems are continuously affected by residual feed inputs, fish fecal waste, and seasonal environmental changes. To investigate seasonal microbial dynamics in response to these environmental conditions, a Nanopore-based shotgun metagenomic approach was applied to seawater samples collected from rock bream sea-cage farms and adjacent coastal waters in Geoje Island across five seasonal periods: July, September, December, February, and May. During this time, water temperatures fluctuated by more than 15 degrees C. Seawater prokaryotes were concentrated by FeCl3-assisted flocculation and filtration, followed by species-level characterization using long-read metagenomic sequencing. The analysis revealed clear seasonal changes in microbial composition. Samples from the warmest period (September) exhibited significant enrichment of fast-growing heterotrophs, such as Alteromonas, and increased abundances of Vibrio harveyi, Shewanella algae, and fecal-associated bacteria (Shigella, Escherichia coli, Enterococcus faecalis). In contrast, colder periods (December and February) were dominated by nitrifying taxa, including Nitrosomarinus and Nitrosopelagicus, along with a higher prevalence of cold-water fish pathogens like Tenacibaculum dicentrarchi, T. finnmarkense, and Pseudomonas anguilliseptica. Antibiotic resistance genes were detected year-round, indicating a persistent anthropogenic influence on the microbial composition of coastal waters. Overall, long-read metagenomics effectively captured seasonal microbial shifts and revealed potential exposure signals of aquatic pathogens, fecal-associated bacteria, and ARGs in sea-cage aquaculture waters, supporting environmental monitoring and early microbial surveillance.

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