Metabarcoding profiling of microbial diversity associated with trout fish farming
Mohamed A A Mahmoud1,2,3, Mahmoud Magdy4
1Chair of Aroma and Smell Research, Department of Chemistry and Pharmacy, Emil Fischer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestraße 9, 91054, Erlangen, Germany.
Scientific Reports
|January 12, 2021
Summary
Microbial analysis of German trout farms revealed bacteria like Proteobacteria and Bacteroidetes, alongside eukaryotic plant pathogens and yeasts. These microbes, including malodor-producing Cyanobacteria and infectious Chilodonella, impact aquaculture quality.
Area of Science:
- Aquaculture microbiology
- Environmental microbiology
- Fish health
Background:
- Earthy and musty off-flavors are common issues in farmed trout globally.
- Previous research has linked microbial activity to the production of these undesirable flavors.
- Understanding the microbial communities in aquaculture water is crucial for maintaining fish quality.
Purpose of the Study:
- To identify and catalog the enrichment of prokaryotic and eukaryotic microorganisms in freshwater sources used for semi-intensive trout aquaculture.
- To investigate the microbial communities in water from trout farms in Bavaria, Germany, known for malodor fish products.
- To assess the influence of these microbial communities on trout aquaculture production quality.
Main Methods:
- 16S rRNA and ITS metabarcoding analyses were performed on inflow and pond water samples.
- Samples were collected from trout farms located along the Moosach and Sempt Rivers in Bavaria, Germany.
- Comparative analysis was conducted between inflow and pond water samples to identify microbial shifts.
Main Results:
- Over 99% of detected prokaryotic Operational Taxonomic Units (OTUs) were bacteria, primarily Proteobacteria (~75.57%) and Bacteroidetes (~14.4%).
- Among 233 eukaryotic OTUs, 118 were known species, with ~45% identified as plant pathogens and ~28% as mushroom/yeasts.
- Malodor-producing microorganisms (Cyanobacteria, Actinobacteria) and fish infectious agents (Chilodonella cyprinid, Metschnikowia bicuspidate) were detected.
- Human and industrial activities near the farms were found to influence the local microbiota.
Conclusions:
- The study identified specific prokaryotic and eukaryotic microorganisms impacting trout aquaculture water quality and industry.
- Key microbial contributors to malodor and fish infections in farmed trout were cataloged.
- Environmental factors, including anthropogenic influences, play a significant role in shaping the microbial landscape of aquaculture systems.
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