Substrate Independent Benthic Sampler (SIBS) for hard & mixed-bottom habitats: a proof of concept study

Sea cage fish farms are increasingly being situated over hard and mixed substrate habitats for production and waste-dispersion reasons; yet in many cases, these installations are not being effectively environmentally managed due to the lack of a practical benthic sampling method. This study presents the first set of results from a newly developed Substrate Independent Benthic Sampler (SIBS) device that captures the unconsolidated organic and inorganic matter that overlies almost all substrates. The contents of the samples were analyzed using extracted environmental DNA (eDNA) followed by metabarcoding of bacterial 16S rRNA gene and resulting microbial assemblages were shown to reliably change with proximity to farm. Other spatial differences, due to region and farm, were small in comparison and the effect of the underlying substrate type was minor. The samples contained sufficient previously encountered impact indicating bacterial taxa such that a meaningful biotic index could be calculated which enabled all samples to be placed on a well-established enrichment spectrum. This tool and associated analytical method provide very effective means for mapping spatial boundaries of farm effects irrespective of substrate type and typography. More importantly, this cost-effective method can be used to quantifiably assess benthic enrichment levels from almost any substrate in exposed and difficult-to-access (up to 120m depth) environments and give results in the context of soft-sediment ecology, for which there are well established environmental thresholds. It therefore has the potential to solve the hard-bottom problem that has until now prohibited effective environmental monitoring at mixed and hard bottom locations.