3. eDNA

3.1. Benefits and Challenges

  1. Whilst eDNA analysis using Polymerase Chain Reaction (PCR) amplification and sequencing is a rapidly developing technique, it is acknowledged that species libraries (such as Illumina MiSeq) are currently a work in progress and these can be highly subject to errors. This also leads to a high proportion of results being identified to higher taxonomic levels due to low confidence in genus and species categories. In line with this, some more cryptic or rare species may not yet be recognised using Deoxyribonucleic Acid (DNA) techniques due to low confidence in genus or species assignment.
  2. eDNA can however be a useful tool to detect the presence of cryptic or rare species or invasive and non-native species (INNS), where such species’ DNA are already mapped and available within their respective libraries. The majority of research applications for eDNA have been associated with fish species in support of stock assessment and similar applications, however, mor recently the North Sea has been subject to a reasonable degree of sampling for eDNA for invertebrates (e.g. BP Exploration Operating Company Limited, 2023, for the Northern Endurance Partnership) therefore whilst species libraries cannot be considered complete and will be continually evolving, key species or PMFs such as horse mussel Modiolus modiolus may be detected if present.
  3. DNA samples can be obtained through both sediment sampling and seawater sampling, and the most appropriate method is dependent upon the overall objectives of the campaign.
  4. Sediment eDNA sampling can present challenges due to the increased longevity of shed or residual DNA within the sediment, as opposed to free-floating in the water column with seawater sampling. For example, presence records in sediment samples can be indicative of species which have occurred in the location over a long period of time (potentially years) and may not be reflective of the current environment and associated communities. Distribution of sediment bound DNA can also be subject to resuspension and hydrodynamic transport away from the location where the DNA material was shed, meaning spatial results should be interpreted with caution (Turner et al., 2015).
  5. Seawater DNA samples are considered more reflective of the contemporary environment, and are typically considered to represent a single tidal cycle, although free-floating DNA material can last up to a few days before becoming degraded (the rate of degradation is based upon multiple variables, such as temperature, salinity, weather, hydrodynamics etc.). Based on this degradation time, water samples are considered to reflect the local area, assuming a non-extreme hydrodynamic regime (Cristescu and Herbert, 2018). However, it is worth noting that eDNA in offshore environments is reported to degrade at a slower pace than inshore environments, with seasonality having a minor effect on degradation rates, showing slightly higher rates of DNA degradation in winter as opposed to summer (Collins et al., 2018). Port et al. (2016) analysed a series of seawater samples for DNA collected in a highly dynamic environment from 2 m to 70 m water depth in an area of kelp forest and deeper rocky reef. This study found that spatial resolution of vertebrate community results compared favourably to visual surveys, within a range of 60 m to 100 m, showing relatively accurate and reliable spatial data relating to the distribution of those communities identified.
  6. Due to eDNA within the marine water column being relatively dilute (when compared to freshwater systems), larger water samples tend to be required to obtain sufficient material for analysis (Cristescu and Herbert, 2018). Seawater samples typically require a minimum volume of 5 litres of seawater to be collected per depth sampled, whereas for sediments, only a small sample of <100 g is typically required. The use of eDNA can also introduce occurrences of false positives, where the species is not actually present (DNA material may have been released into the water column following mortality (including within predator faecal deposits), or have been transported from elsewhere; Roussel et al., 2015). Conversely, the absence of a detection does not necessarily mean that the organism is not present, however this caveat can also be applied to standard macrofaunal sampling (Roussel et al., 2015).
  7. Quantitative analysis is not possible using DNA techniques due the number of Operational Taxonomic Units (OTU) being linked to the number of positive detections of a particular DNA sequence, rather than the number of individual organisms within a species group. Organisms can contain huge amounts of DNA, with many replicates of the same sequence present, although, high level comparisons of the amount of DNA present (relative abundance) can be made, however this may reflect the presence of different sized specimens, or behavioural anomalies where organisms shed higher amounts of DNA during particular events. The technique is therefore applicable only as a presence-absence tool at the current stage of development and should always be used alongside standard macrofaunal techniques for benthic ecology, for example, to enable quantitative analysis.
  8. The benefits and challenges associated with eDNA are summarised in Table 3.3   Open ▸ .

 

Table 3.3:
Summary of the Benefits and Challenges Associated with eDNA Analysis

Table 3.3: Summary of the Benefits and Challenges Associated with eDNA Analysis

 

  1. Based on the above, eDNA analysis can provide information to support biodiversity assessment, but should be conducted alongside other techniques, particularly for marine benthos to allow for quantification of results.
  2. eDNA analysis can be a useful tool for identifying the presence of multiple species within a defined assay (or assays), although results should be interpreted with caution surrounding false positives and the potential for identification to higher taxonomic levels only, due to low confidence in genus and species data based upon the available reference library. The absence of sequenced data for some cryptic or rare species may lead to false negatives, where species are present, but are not detected due to the absence of sufficient data within the library to provide species level identification. Where used, eDNA results should be interpreted with consideration of the caveats outlined earlier within the section.

4. Proposed Approach

  1. For the Ossian Array subtidal benthic ecology characterisation, standard macrofaunal sampling, along with drop-down camera and epifaunal trawling was undertaken. The laboratory processing of macrofaunal and epifaunal samples allowed identification of specimens to the lowest taxonomic level possible, with most organisms identified to genus and species level. This approach, combined with substrate determination using both physical sampling and geophysical data allowed for the exact species within a sample at an exact location to be identified and used to inform the habitat description at that specific location. The geophysical data, combined with results from multiple sediment sampling stations then allowed for this information to be extrapolated in line with the seabed textural data to provide a detailed habitat chart of the Array. eDNA sampling from sediment samples may lead to false positives, in terms of identifying the presence of DNA from historic occurrences which are not representative of the current environment. eDNA is therefore considered more supportive of broadscale characterisation than targeted site-specific characterisation to inform habitat mapping. The approach undertaken for the Ossian Array is considered sufficient to produce a detailed habitat map, and to support robust characterisation of the benthic communities present in combination with available desktop data sources, allowing for confident identification of Important Ecological Features to carry through to assessment.
  2. The baseline characterisation developed for fish for the Ossian Array is based on varied data sources, collated over a long time period and at a regional spatial scale. As such, the species that may interact with the Ossian Array is fully captured in this data, encompassing seasonality and annual variation. The list of species scoped in is therefore considered precautionary, and extensive, and it's considered unlikely that eDNA samples would identify additional species. The approach undertaken for the Ossian Array is considered sufficient to provide a robust characterisation of the fish and shellfish assemblages likely to occur within the regional fish and shellfish study area, and within the Ossian Array.
  3. In summary, whilst eDNA is a useful tool alongside more standard sampling practices, it is important to note that the baseline characterisation provided for the Array benthic subtidal ecology and fish and shellfish ecology study areas have not been contested by MD-LOT or other stakeholders. Further, the site-specific survey data collection methodology to inform the baseline characterisation was developed in consultation with MD-LOT, and all advisory responses to such consultation were taken forwards into the final subtidal benthic ecology survey design.
  4. Based on the accepted baseline presented within the Ossian Array EIA Scoping Report (Ossian OWFL, 2023), the Scoping Opinion received (MD-LOT, 2023), expert judgement and understanding of the baseline environment within the region and the application timelines, it is not considered necessary to supplement the baseline with additional eDNA data for the Array, as sufficient information has been drawn together to allow for robust characterisation and understanding of the baseline environment.
  5. For the Proposed offshore export cable corridor subtidal benthic ecology survey, collection of seawater and sediment samples will be considered for eDNA analysis at a representative number of stations to enhance the baseline characterisation for fish and shellfish ecology and benthic subtidal ecology, alongside standard drop-down camera and grab sampling operations. Due to the anticipated length of the offshore export cable corridor it is anticipated that this area is likely to reflect a wider range of subtidal habitats than the Array, based upon broadscale habitat mapping (EMODnet, 2021). Further consultation on future benthic surveys will be undertaken following identification of the proposed offshore export cable corridor.

4.1. References

BP Exploration Operating Company Limited (2023) Offshore Environmental Statement for the Northern Endurance Partnership. Reference: D/4271/2021. Document: NS051-EV-REP-000-00021. 684pp.

Collins, R. A, Wangensteen, O. S., O’Gorman, E. J., Mariani, S., Sims, D. W. and Genner, M. J. (2018). Persistence of environmental DNA in marine systems. Communications Biology. 1: 185.

Cristescu, M. E. and Herbert, P. D. N. (2018). Uses and Misuses of Environmental DNA in Biodiversity Science and Conservation. The Annual Review of Ecology, Evolution, and Systematics. 49: 209-230.

MD-LOT (2023). Ossian Array Scoping Opinion (14th June 2023). Report adopted by Scottish Ministers under The Electricity Works (Environmental Impact Assessment) (Scotland) Regulations 2017 and The Marine Works (Environmental Impact Assessment) Regulations 2007. 39pp.

Ossian OWFL (2023). Ossian Array EIA Scoping Report. Available online: https://marine.gov.scot/sites/default/files/ossian_wind_-_array_eia_scoping_report_-_eor0811a.pdf. Accessed: 22 October 2023.

Port, J. A., O’Donnell, J. L., Romera-Maraccini, O. C., Leary, P. R., Litvin, S. Y., Nickols, K. J., Yamahara, K. M. and Kelly, R. P. (2016). Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA. Molecular Ecology. 25: 527-541.

Roussel, J. M., Paillisson, J. M., Tréguier, A. and Petit, E. (2015). The downside of eDNA as a survey tool in water bodies. Journal of Applied Ecology. 52: 823-826.

Shu, L., Ludwig, A. and Peng, Z. (2020) Standards for Methods Utilizing Environmental DNA for Detection of Fish Species. Genes. 11 (3): 296.

Turner, C. R., Uy, K. L. and Everhart, R. C. (2015). Fish environmental DNA is more concentrated in aquatic sediments than surface water. Conservation Biology. 183: 93-102.