Microbial and Antimicrobial Resistance Profiles of Microbiota in Common Carps (Cyprinus carpio) from Aquacultured and Wild Fish Populations.

Modestas Ruzauskas,Elena Bartkienė,Julija Armalytė,Eglė Lastauskienė,Irena Klimienė,Raimundas Mockeliūnas,Rita Šiugždinienė

doi:10.3390/ani11040929

Modestas Ruzauskas, Elena Bartkienė + Show 5 more

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https://doi.org/10.3390/ani11040929

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Abstract

Simple SummaryThis study was focused on differences in microbial varieties in common carp living in two different environments: open fish ponds and in nature. The results demonstrated that wild fish carry more than 2.5 times the bacterial species in their gut compared with aquacultured fish. More than 400 species of bacteria were identified, the majority of which are considered beneficial microbiota. Besides bacterial variety, it was determined that aquacultured fish harbored more bacteria that are treated as pathogens in animals and humans. The frequency of antimicrobial resistance in bacterial indicators was more common in aquacultured fish compared with bacteria from a wild population, therefore fish farming can be treated as a potential source of environmental contamination with antimicrobial resistant bacteria.In this study we analyzed differences in microbial composition and antimicrobial resistance profiles in common carp living in two different environments: fish ponds, where carp have been kept under the same growing conditions over the last 50 years, and from the wild. The results demonstrated that wild fish carry a great variety of bacterial species (448 species with a prevalence of at least 0.01% from the total number of reads). Aquacultured individuals harbored 2.56 times fewer species in their gut. Significant microbial differences were observed in all taxonomic ranks, including bacterial classes and phyla. Besides bacterial variety, it was determined that aquacultured fish harbored more bacteria that are considered pathogens or opportunistic pathogens, such as Moraxellaceae, Flavobacteriaceae, and Staphylococcaceae. The frequency of antimicrobial resistance in bacterial indicators was more common in aquacultured fish than in wild fish, therefore fish farming may be a potential source of environmental contamination with antimicrobial resistant bacteria.

Highlights

Aquaculture is the farming of fish and other aquatic organisms for food and other purposes
A good quality of DNA was obtained from both samples the number of reads differed significantly: 33,782 and 67,093 reads were obtained from C. carpio from fish ponds and from C. carpio from a lake, respectively
The main differences were observed among Tenericutes and Bacteroidetes, which were more prevalent in carp from fish ponds, as well as among Firmicutes which were more obvious in fish living in the lake

Summary

Introduction

Aquaculture is the farming of fish and other aquatic organisms for food and other purposes. Aquaculture systems mirror agriculture, in that some aquaculture operations convert land into ponds to grow aquatic organisms, just as land is converted 4.0/). Fish farm effluent affects the area immediately surrounding the farm, but can alter different ecosystems [3]. Aquaculture systems are classified according their location (water-based systems, land-based systems, and integrated farming systems), methods of confinement (closed systems with or without connection to the environment, open ponds), and feed/fertilizer input. During recent years aquaculture knowledge has advanced in areas such as water quality, disease control, and generated stock improvements by selective breeding, hybridization, and molecular genetic technologies [4], some technologies have not changed much in decades

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