As is the case in most countries, the Norwegian standard for monitoring of organic impacts of salmon farming is centered
around the analysis of chemical and biological parameters of soft-sediments habitats . However, m any fish farms are situated in areas with hard or mixed substrates and this is likely to increase given the anticipated
shift to more physically dynamic sites.
Although a nalogous changes are probably occurring on these mixed-bottoms
habitats , our knowledge of
any
potential interactions is severely lacking , and more critically,
are going largely unmonitored due to the absence of a suitable sampling method.
There are however emerging alternative biological indicators that may provide a solution. Recently, several studies have demonstrated
the potential of using genetic material from micro-organisms (e.g. bacteria, foraminifera etc.), assessed
through rapid, high-throughput sequencing techniques, to discern benthic enrichment. To date, these have been necessarily restricted
to sampleable soft-sediment habitats. The small, ubiquitous, highly abundant and diverse nature of these
organisms means that they are likely to be present in the biofilms and/or flocculent layers that
overly most hard- and mixed-bottom substrates.
Here we present the first set of results using eDNA to describe the microbial communities of samples collected using a newly developed ‘Substrate Independent Benthic Sampler’ device. Samples were obtained from sand, shellsand , gravel, and bedrock using a low-cost surface operated suction device and are compared to more conventional microbial eDNA samples from soft-sediments and to macrofauna samples, where feasible. Minor differences were observed between sample types and farms, but in general, very g ood congruence wa s observed between the datasets with respect to distance from farm and anticipated benthic effects. Sampling of flocculent material overlying all substrates provides a potentially vital monitoring tool for the management of fish farm effects in the future.