An approach for quantifying the influence of fish farm waste on hard-bottom habitats

Sea-based fish farms release significant quantities of fish feaces, waste feed and associated contaminants into the surrounding environment, necessitating ecological effects-based monitoring. Traditionally, this has been achieved by measuring geochemical and biological properties of sediments obtained by a benthic grab. However, many modern high-capacity farms are situated over hard substrates, rendering conventional sampling methods ineffective and hindering environmental management. Fortunately, new possibilities have emerged with the advent of high-throughput sequencing, and in-particular, the use of microbial eDNA as an indicator of benthic enrichment, and new methods have been developed for obtaining the source material irrespective of substrate. Here, we first demonstrate how applying the default approach used by the world's largest salmon farming industry to hard substrates is essentially qualitative and can lead to inappropriate conclusions. We then show the results from a substrate independent benthic sampling (SIBS) method coupled with a structured quantitative visual assessment of seabed images. The approach utilizes three novel indicators that quantify the degree of visual organic loading (VOL) and ecological effects (VEE) and elucidate the magnitude and spatial extent of the waste influence field via an index (bMBI) derived from 16S eDNA. VOL and VEE were useful for quantifying and classifying effects beneath farms, but were of limited use further away, whereas the bMBI was both highly quantitative and sensitive in the immediate and more distant receiving environments. This dual approach provides a basis for the development of a quantitative hard-bottom monitoring system and should therefore permit effective environment management in the future.