Metabarcoding profiling of microbial diversity associated with trout fish farming

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.

Composition and functionality of bacterioplankton communities in marine coastal zones adjacent to finfish aquaculture

“…ASVs assigned to the chemoheterotrophs Hyphomonadaceae and Spirosomaceae were enriched at the surface waters of the Lease 2 sample area, similar to a previous study conducted in a trout aquaculture farm, where these two aerobic bacteria were abundant in the pond-water (Mahmoud and Magdy, 2021). Finally, oligotrophic chemoheterotroph Flavobacteriaceae (NS3a marine group) and the predatory Bacteriovoracaceae were already observed in other microbial aquaculture studies in the sediments (Frühe et al, 2021) and in a zero-discharge system (Kandel et al, 2014), respectively.…”

“…These include members of the taxa Psychromonadaceae ( Psychromonas ), Fusobacteriales (Fusobacteriaceae), Vibrionaceae, Desulfovibrionaceae (Desulfovibrio), Sulfurimonadaceae (Sulfurimonas), Sulfurovaceae (Sulfurovum), Fusibacteraceae (Fusibacter), Rhizobiales , and Sphingomonadaceae . Various microbial groups have been associated with marine environments receiving high level of nutrients and some have been reported as potential aquaculture impact biomarkers in the past (Blancheton et al, 2013; Kandel et al, 2014; Rasigraf et al, 2017; Verhoeven et al, 2018; Yang et al, 2019; Haro-Moreno et al, 2020; Zhang et al, 2020; Aalto et al, 2021; Dully et al, 2021; Frühe et al, 2021; Mahmoud and Magdy, 2021; Pan et al, 2021). According to these studies, such taxa are usually found in high abundance in near-cages sites, including Sulfurovum, Vibrionaceae, Desulfovibrionaceae, Methylotenera, Hyphomonadaceae, Spirosomaceae and Fusibacter, Flavobacteriaceae (NS3a marine group) and Bacteriovoracaceae .…”

“…Aquaculture activities are known to increase nutrient loading and change trophic status near the fish cages from waste, by-products, fish feces or feed products inputs (Belias et al, 2003, Buschmann et al, 2006, Amirkolaie, 2011). Various microbial groups have been associated with high level of nutrient inputs in the water column (Haro-Moreno et al, 2020, Yang et al, 2019), sediments (Verhoeven et al, 2018, Fruhe et al, 2021, Zhang et al, 2020, Asami et al, 2005, Dully et al, 2021) and land-based aquaculture operations (Mahmoud and Magdy, 2021, Kandel et al, 2014, Aalto et al, 2021, Blancheton et al, 2013) and some have been reported as potential aquaculture impact biomarkers. (Haro-Moreno et al, 2020, Mahmoud and Magdy, 2021, Kandel et al, 2014, Verhoeven et al, 2018, Frühe et al, 2021, Zhang et al, 2020, Aalto et al, 2021, Blancheton et al, 2013, Yang et al, 2019, Rasigraf et al, 2017, Dully et al, 2021).…”

“…Various microbial groups have been associated with high level of nutrient inputs in the water column (Haro-Moreno et al, 2020, Yang et al, 2019), sediments (Verhoeven et al, 2018, Fruhe et al, 2021, Zhang et al, 2020, Asami et al, 2005, Dully et al, 2021) and land-based aquaculture operations (Mahmoud and Magdy, 2021, Kandel et al, 2014, Aalto et al, 2021, Blancheton et al, 2013) and some have been reported as potential aquaculture impact biomarkers. (Haro-Moreno et al, 2020, Mahmoud and Magdy, 2021, Kandel et al, 2014, Verhoeven et al, 2018, Frühe et al, 2021, Zhang et al, 2020, Aalto et al, 2021, Blancheton et al, 2013, Yang et al, 2019, Rasigraf et al, 2017, Dully et al, 2021). In accordance with these studies, we found differentially abundant ASVs in lease areas that could be related to higher levels of organic matter and the presence of farmed fish.…”

Early Neonatal Meconium Does Not Have a Demonstrable Microbiota Determined through Use of Robust Negative Controls with cpn 60-Based Microbiome Profiling

“…In this context, no confident distinction can be made between contaminants and taxa truly present in such environments. When controls are included, contamination becomes evident; one meconium study detected thousands of reads aligning to Pelomonas puraquae , a species isolated from industrial water and associated with environmental pollutants in marine studies ( 37 , 38 ), in 38/43 samples and within negative controls. Previous work has identified Pelomonas spp.…”