Thomas A. Wilding

Environmental monitoring through protist next-generation sequencing metabarcoding: assessing the impact of fish farming on benthic foraminifera communities

The measurement of species diversity represents a powerful tool for assessing the impacts of human activities on marine ecosystems. Traditionally, the impact of fish farming on the coastal environment is evaluated by monitoring the dynamics of macrobenthic infaunal populations. However, taxonomic sorting and morphology‐based identification of the macrobenthos demand highly trained specialists and are extremely time‐consuming and costly, making it unsuitable for large‐scale biomonitoring efforts involving numerous samples. Here, we propose to alleviate this laborious task by developing protist metabarcoding tools based on next‐generation sequencing (NGS) of environmental DNA and RNA extracted from sediment samples. In this study, we analysed the response of benthic foraminiferal communities to the variation of environmental gradients associated with salmon farms in Scotland. We investigated the foraminiferal diversity based on ribosomal minibarcode sequences generated by the Illumina NGS technology. We compared the molecular data with morphospecies counts and with environmental gradients, including distance to cages and redox used as a proxy for sediment oxygenation. Our study revealed high variations between foraminiferal communities collected in the vicinity of fish farms and at distant locations. We found evidence for species richness decrease in impacted sites, especially visible in the RNA data. We also detected some candidate bioindicator foraminiferal species. Based on this proof‐of‐concept study, we conclude that NGS metabarcoding using foraminifera and other protists has potential to become a new tool for surveying the impact of aquaculture and other industrial activities in the marine environment.

High-throughput sequencing and morphology perform equally well for benthic monitoring of marine ecosystems

Environmental diversity surveys are crucial for the bioassessment of anthropogenic impacts on marine ecosystems. Traditional benthic monitoring relying on morphotaxonomic inventories of macrofaunal communities is expensive, time-consuming and expertise-demanding. High-throughput sequencing of environmental DNA barcodes (metabarcoding) offers an alternative to describe biological communities. However, whether the metabarcoding approach meets the quality standards of benthic monitoring remains to be tested. Here, we compared morphological and eDNA/RNA-based inventories of metazoans from samples collected at 10 stations around a fish farm in Scotland, including near-cage and distant zones. For each of 5 replicate samples per station, we sequenced the V4 region of the 18S rRNA gene using the Illumina technology. After filtering, we obtained 841,766 metazoan sequences clustered in 163 Operational Taxonomic Units (OTUs). We assigned the OTUs by combining local BLAST searches with phylogenetic analyses. We calculated two commonly used indices: the Infaunal Trophic Index and the AZTI Marine Biotic Index. We found that the molecular data faithfully reflect the morphology-based indices and provides an equivalent assessment of the impact associated with fish farms activities. We advocate that future benthic monitoring should integrate metabarcoding as a rapid and accurate tool for the evaluation of the quality of marine benthic ecosystems.

Interactive Marine Spatial Planning: Siting Tidal Energy Arrays around the Mull of Kintyre

The rapid development of the offshore renewable energy sector has led to an increased requirement for Marine Spatial Planning (MSP) and, increasingly, this is carried out in the context of the ‘ecosystem approach’ (EA) to management. We demonstrate a novel method to facilitate implementation of the EA. Using a real-time interactive mapping device (touch-table) and stakeholder workshops we gathered data and facilitated negotiation of spatial trade-offs at a potential site for tidal renewable energy off the Mull of Kintyre (Scotland). Conflicts between the interests of tidal energy developers and commercial and recreational users of the area were identified, and use preferences and concerns of stakeholders were highlighted. Social, cultural and spatial issues associated with conversion of common pool to private resource were also revealed. The method identified important gaps in existing spatial data and helped to fill these through interactive user inputs. The workshops developed a degree of consensus between conflicting users on the best areas for potential development suggesting that this approach should be adopted during MSP.

Factors affecting the performance of the acoustic ground discrimination system RoxAnn

Wilding, T. A., Sayer, M. D. J., and Provost, P. G. 2003. Factors affecting the performance of the acoustic ground discrimination system RoxAnn. e ICES Journal of Marine Science, 60: 1373e1380. The resolution, temporal variability and survey vessel speed dependence of the acoustic ground discrimination system RoxAnn was assessed over a 1 km 2 area in Loch Linnhe on the west coast of Scotland. The resolution of the system was relatively poor and of the sediment parameters quantified (stone cover and sediment texture), only stone cover was consistently and significantly related to the RoxAnn output. The output showed considerable variability over the same ground when sampled within the same day and between days and months. The effect of survey vessel speed on the output was also significant but highly variable during all surveys. The apparent magnitude and unpredictable nature of the variation in the RoxAnn output have implications for the use of such systems in habitat mapping, particularly when surveying biological communities where there are only small differences in the physical properties of the seabed and also where monitoring temporal change. These aspects are discussed.

Changes in benthos associated with mussel (Mytilus edulis L.) farms on the west-coast of Scotland.

Aquaculture, as a means of food production, is growing rapidly in response to an increasing demand for protein and the over-exploitation of wild fisheries. This expansion includes mussels (family Mytilidae) where production currently stands at 1.5 million tonnes per annum. Mussel culture is frequently perceived as having little environmental impact yet mussel biodeposits and shell debris accumulate around the production site and are linked to changes in the benthos. To assess the extent and nature of changes in benthos associated with mussel farming grab and video sampling around seven mussel farms was conducted. Grab samples were analysed for macrofauna and shell-hash content whilst starfish were counted and the shell-hash cover estimated from video imaging. Shell-hash was patchily distributed and occasionally dominated sediments (maximum of 2116 g per 0.1 m2 grab). Mean shell-hash content decreased rapidly at distances >5 m from the line and, over the distance 1–64 m, decreased by three orders of magnitude. The presence of shell-hash and the distance-from-line influenced macrofaunal assemblages but this effect differed between sites. There was no evidence that mussel farming was associated with changes in macrobenthic diversity, species count or feeding strategy. However, total macrofaunal count was estimated to be 2.5 times higher in close proximity to the lines, compared with 64 m distance, and there was evidence that this effect was conditional on the presence of shell-hash. Starfish density varied considerably between sites but, overall, they were approximately 10 times as abundant close to the mussel-lines compared with 64 m distance. There was no evidence that starfish were more abundant in the presence of shell-hash visible on the sediment surface. In terms of farm-scale benthic impacts these data suggest that mussel farming is a relatively benign way of producing food, compared with intensive fish-farming, in similar environments.

Changes in sedimentary redox associated with mussel (Mytilus edulis L.) farms on the west-coast of Scotland.

Aquaculture is growing rapidly in response to an increasing demand for protein and the over-exploitation of wild fisheries. Mussel (family Mytilidae) production has doubled over the last decade and currently stands at 1.5 million tonnes production per annum. Mussels produce organic biodeposits which are dispersed around the production site and, potentially, impact the receiving environment in a number of inter-linked ways. The reported benthic impacts that occur, primarily through the accumulation of these biodeposits and associated organic enrichment, vary widely between studies. The objectives of this research were to determine the nature of the relationship between sediment redox (a proxy for oxygenation) and farm-proximity and covariables whilst accounting for, and quantifying, differences in redox between sites. Sediment cores (N = 159) were taken remotely around a random sample of mussel farms, redox was measured at 10 mm sediment depth and linked to farm-distance and sediment organic/shell content and particle size, using an additive, mixed, weighted regression model. Redox varied considerably between sites and there was a highly significant reduction (50 mV) in redox adjacent to the mussel lines. Redox increased non-linearly with distance, rising rapidly at >7 m from the farm edge. The modest reduction in sediment oxygenation in close proximity to mussel farms reported here suggests that farms located over sediments characterised by pre-existing oxygen stress are likely to exacerbate benthic species impoverishment associated with reducing sedimentary conditions whilst those located over highly oxygenated sediments are likely to increase benthic productivity.

Comparison of three methods for quantifying topographic complexity on rocky shores

Topographic complexity (TC) is an important factor in determining community structure in aquatic habitats and there are numerous methods for its estimation. Here we assess and compare three (chain, divider and distance-wheel) methods across different users and substrata over scales of 78-1030 mm. All three techniques showed the same basic trend in TC over different substrata. However, the chain took approximately 1.5x as long to use, at larger-scales (>271 mm), as the other techniques and resulted in highly variable TC estimates. The chain and divider techniques both have the potential to miss relevantly scaled TC depending on the survey starting point, a disadvantage not suffered by the distance-wheel. TC measured using the distance-wheel was approximately 1.8x that recorded by the divider technique and significantly (P<0.05) less variable compared with the chain technique. The distance-wheel was rapid and easy to use, superior in accessing awkward topographies and has considerable potential for improvement. It is recommended as a technique for estimating the TC of rock-surfaces at scales >50 mm.

Offshore pipeline decommissioning: Scale and context

The spatial extent of human activities must be understood for consistent and proportionate regulation, and effective marine planning. Redundant offshore pipelines can be removed or left in situ, but data on the footprint of these options are not readily available. The extents of three North Sea in situ decommissioning scenarios are presented. Leaving pipelines in situ would occupy <0.01% (12.3 km2) of UK waters, and this was similar to, or smaller than, other regulated activities (e.g. aggregate extraction). Adding armouring to large pipelines occupied up to 95 km2, while creating fisheries exclusion zones occupied up to 1119 km2. Removal of pipelines >30″ would be required to regain 50% or more of the seabed currently occupied. At present, the technology to remove pipelines >16″ safely and cost-efficiently is untested for large-scale decommissioning projects. The summaries presented inform the debate over the significance of decommissioning, and the regional consequences of different options.