Metabarcoding profiling of microbial diversity associated with trout fish farming

Mohamed A A Mahmoud,Mahmoud Magdy

doi:10.1038/s41598-020-80236-x

Abstract

Earthy and musty off-flavors are routinely observed in farmed trout worldwide. The microbial association to the production of those off-flavors was previously reported. The current manuscript aimed to catalog the microbial enrichment (eukaryotes and prokaryotes) in semi-intensive aquaculture freshwater sources that might influence the trout aquaculture quality production. The 16S rRNA and ITS metabarcoding analyses were applied on the inflow- and pond-water samples from trout farms previously recorded a malodor fish products and located alongside Moosach and Sempt Rivers in Bavaria province, Germany. The results showed that more than 99% of the detected prokaryotic OTUs (Operational Taxonomic Unit identification) were bacteria as of ~ 75.57% were Proteobacteria, and ~ 14.4% were Bacteroidetes. Meanwhile, 118 out of 233 of the eukaryotic OTUs were known species. Of these, ~ 45% were plant pathogens, and ~ 28% were mushroom/yeasts. Based on the comparative analysis between inflow- and pond-water samples, several pro- and eukaryotic microorganisms that affect the trout aquaculture water quality and industry have been detected, including the malodor-producing microorganisms, e.g., Cyanobacteria and Actinobacteria, along with fish infectious microorganisms, e.g., Chilodonella cyprinid, Metschnikowia bicuspidate. Additionally, the effect of the human- and industrial-related activities around the sampling area on the microbiota of the investigated farms were highlighted.

Highlights

Earthy and musty off-flavors are routinely observed in farmed trout worldwide
The advancements in statistical/computational software and databases with its ability to exploit a massive amount of data generated by next-generation sequencing have greatly improved species diversity d elimitation[14]
Based on the 16S rRNA dataset, prokaryotic OTU identification pipeline, > 99% of the detected OTUs belonged to the bacteria domain

Summary

Introduction

Earthy and musty off-flavors are routinely observed in farmed trout worldwide. The microbial association to the production of those off-flavors was previously reported. The high demand for fish meat has promoted rapid development in the supply chain to the point that about 47% of the world fish consumption originates from aquaculture farming[1] The downside of this development is the increasing amounts of waste (dissolved organic and inorganic waste and particulate waste) originated by aquaculture practices and its related adverse impacts on our environment, i.e., disrupting the homeostatic microbial community of aquaculture w ater[2,3]. The combined effect of nutrient leaching and the depletion of dissolved oxygen leads to a significant change in the composition of the ecosystem living c ommunities[4] Another negative consequence from the aquaculture industry point of view is the possible formation of malodors in aquaculture water due to the fluctuation of nutrients, which leads to the production of fish with poor sensorial q ualities[5,6]. The advancements in statistical/computational software and databases with its ability to exploit a massive amount of data generated by next-generation sequencing have greatly improved species diversity d elimitation[14]

Objectives

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Conclusion