The Impact of Intensive Fish Farming on Pond Sediment Microbiome and Antibiotic Resistance Gene Composition

Abstract

Aquaculture is a fast-growing animal food sector, and freshwater fish farming is particularly common in Central and Eastern Europe. As the biodiversity of fishery ponds is changed toward fulfilling the industrial needs, precautions should be taken to keep the system sustainable and protect the adjacent environment from possible damage. Due to risk of infectious diseases, antibiotics are used in aquaculture production systems. The constant exposure to antimicrobials can contribute to the rise of antibiotic resistance in aquaculture products and the adjacent ecosystems, with possibility of dissemination to the wider environment as well as between animals and humans. Even though previous studies have found antibiotic resistance genes in the sediments and water of farming ponds, the tendency and direction of spreading is not clear yet. The objective of this project was to evaluate the influence of intensive fish farming on the condition of water bodies used for the aquaculture and the environment, concentrating on the impact of the aquaculture on the surrounding water ecosystems as well as the possibility of transferring the pollutants and antibiotic resistance genes to both environment and the human hosts. Combined measurement of antibiotic and heavy metal contamination, toxicity assessment, microorganism diversity, and the detection of common antibiotic resistance genes was performed in the sediments of one fishery farm ponds as well as sampling points upstream and downstream. All the tested sediment samples did not show significantly elevated heavy metal concentrations and no substantial veterinary antibiotic pollution. From the antibiotic resistance genes tested, the presence of aminoglycoside and β-lactam resistance determinants as well as the presence of integrons could be of concern for the possibility of transfer to humans. However, despite the lack of heavy metal and antibiotic pollution, the sediments showed toxicity, the cause of which should be explored more.

From microbes to mammals: Pond biodiversity homogenization across different land‐use types in an agricultural landscape

“…Comparative studies on the land use effect on aquatic microbial communities have mostly been conducted on running water (rivers and streams) (Chen et al, 2018; Fasching et al, 2020; Le et al, 2018) or lakes (Marmen et al, 2020), revealing cases in which local land use has a stronger influence on community composition than upstream land use (Le et al, 2018). Microbiome studies on ponds in agricultural landscapes (e.g., Chopyk et al, 2018, 2020) or aquaculture (e.g., Lastauskienė et al, 2021) have been mostly focused on individual ponds.…”

Interaction of Microbiota between Fish and the Environment of an In-Pond Raceway System in a Lake

“…The microbiota in aquaculture systems is an essential aspect of affecting the health status of farmed animals and evaluating system safety, which can reflect the health status of aquaculture systems to a certain extent [19,20]. A limited number of studies on microbiota in the IPRS have provided preliminary insights.…”

Functional and Seasonal Changes in the Structure of Microbiome Inhabiting Bottom Sediments of a Pond Intended for Ecological King Carp Farming

“…Bottom sediments are composed of sedimentary material deposited on the bottom of rivers and water bodies. Fish ponds are rich in dissolved organic matter due to intensive feeding and fecal waste [ 10 ]. Ponds accumulate bottom sediments after their basins are formed under the influence of the water regime (emptying and filling).…”

“…Ponds accumulate bottom sediments after their basins are formed under the influence of the water regime (emptying and filling). These sediments are formed from biological debris originating from the ponds and their catchments, as well as soil particles and other non-biological materials that have entered the water body [ 10 ]. Cellulolytic bacteria, numerous anaerobic chemoautotrophs, and anaerobic microbiota typically thrive in bottom sediments [ 10 ].…”

“…These sediments are formed from biological debris originating from the ponds and their catchments, as well as soil particles and other non-biological materials that have entered the water body [ 10 ]. Cellulolytic bacteria, numerous anaerobic chemoautotrophs, and anaerobic microbiota typically thrive in bottom sediments [ 10 ]. In the Arctic sediments in Baffin Bay, Cramm, et al [ 11 ] noted the presence of putative methane-oxidizing Methyloprofundus , sulfate-reducing Desulfobulbaceae , and sulfide-oxidizing Sulfurovum .…”