A new method of analyzing the sediments known as "DNA barcoding" has been developed by Swiss researchers that study impacts on micro-organisms found in the sediments and provides indicators for environmental changes that may be occurring as a result of salmon breeding. (Photo: Photo courtesy of Shutterstock)

Salmon farming has been found to be a serious environmental threat in the regions where it is practiced. For many years the harmful effects of this aquaculture production system were studied by visually analysing sediment samples collected at specific distances from spawning sites. But a new method of analyzing the sediments known as "DNA barcoding" has been developed by Swiss researchers that study impacts on micro-organisms found in the sediments and provides indicators for environmental changes that may be occurring as a result of salmon breeding.

Like Us on Facebook

The research published in the Molecular Ecology Resources journal was conducted by a team led by Jan Pawlowski, professor at the Faculty of Science of the University of Geneva (UNIGE), Switzerland. Salmon farming mainly threatens the environment in three ways. The waste feed and fish faeces released in the surrounding open waters, the toxicity caused by pesticides and chemicals that are used to clean salmon cages to prevent breeding of germs, and the excessive use of antibiotics on fish that have developed diseases.

The effects of these harmful practices can be gauged by monitoring different species of organisms living under the cages. But the traditional method of visually monitoring them under a microscope is both labor intensive and expensive. Further, only taxonomy specialists are qualified to accurately determine the species diversity. These reasons make the traditional method unsuitable for large scale examination. But the new research, says Pawlowski, eliminates this problem by "using sophisticated tools that analyse the DNA and RNA extracted from sediment samples."

The work was a collaboration with researchers from the Scottish Association of Marine Sciences (UK) and the University of Aarhus (Denmark). The team collected sediment samples at specific distances from two salmon farms in the heart of the Scottish fjords. "We used genetic barcodes that recognise specific fragments of DNA and RNA extracted from the sediment samples," explains researcher Franck Lejzerowicz, a PhD student in the team, "These 'genetic hooks' consist of DNA sequences that vary between species but remain stable within a given species."

The new tool works by recognizing the different foraminiferal species that are present in the sediments. These are amoeboid-single celled protists that show great diversity and live on or within the seafloor sediment. They are well known environmental bio-indicators of pollution in coastal areas since many species are sensitive to specific environment changes.

The geneticists were able to process a large number of samples using high-throughput DNA sequencing. The team says, "Our study revealed large variations between foraminiferal species collected near farms and those from remote sites. In addition, species diversity diminishes on sites affected by the farms."

This highly-accurate ecological analysis allowed to establish a correlation between species richness and distance from the cages, which is even more noticeable if the farm is situated in areas where there are weak sea currents. The species richness also depends on the availability of oxygen. As Jan Pawlowski says, "The vast amount of organic compounds on the farming sites can even sometimes generate anoxic sediments, which makes it impossible for most species to survive."

The biologists also discovered a new species of foraminifera, which could serve as a bioindicator of organic enrichment.

Metabarcoding technology is now rapidly gaining popularity as a fast and efficient method to characterize species biodiversity in mass samples. It offers several advantages over the traditional methods of sample testing, mainly speed and consistency. This study is one of the first to use the genome technology to assess the impact of industries such as aquaculture systems and offshore drilling on marine ecosystems.