Dr Thomas Wilding

        Image of Dr Tom Wilding on fieldwork

Benthic Ecologist

A benthic ecologist and statistical modeller specialising in assessing the impacts of man’s activities.  I am leading the development of novel imaging and eDNA-based approaches to monitoring change and am challenging current monitoring /assessment approaches.  I frequently work at the interface between research, policy, and regulation. 

Contact details:

Assessing changes occurring in our oceans is my main research interest.  My focus is on aquaculture, oil and gas decommissioning and marine renewables. 

In relation to aquaculture, I’m leading the development of eDNA-based alternatives to traditional macrobenthic monitoring (BactMetBar) and the application and training of deep-neural nets to help industry and regulators in assessing priority marine features in seabed survey imagery (SEA-AI). 

In relation to oil and gas and renewables:  I’m leading the North Sea 3D project, developing protocols to collect ROV footage which are optimised for machine-based auto-identification of key marine-growth taxa and 3D model construction.  We are linking the auto-identification and 3D models, from which biovolume and biomass can be estimated and informing ecosystem models and industry faced managing and understanding marine growth on their structures.  

I am an HSE Part IV qualified diver with >20 years’ experience of designing and conducting underwater experiments. 


Current research projects

North Sea 3D: Measuring and predicting marine growth on man-made structures by converting industry and bespoke ROV survey footage into 3D models with automatic faunal identification (2021 – 2024).

BactMetBar: Environmental DNA metabarcoding as an alternative to macrobenthic assessments in fish-farm compliance assessment  (2021 – 2024)

SEA-AI:  Streamlined and efficient artificial-intelligence assisted underwater video analysis (2022-24)

Selected past projects

Development of a strategic framework for the comparative assessment of pipeline decommissioning options: optimising environment and fishing interests: PI. Funded by NERC. Feb 2017 - Feb 2018.

Optimising decommissioning of oil and gas pipelines with respect to the commercial fishing sector on the UK continental shelf: PI. Funded by NERC. Apr 2017 - Mar 2018

Development of DNA-based metagenomics methodologies for seabed monitoring and aquaculture management (MeioMetBar): PI. Funded by the Scottish Aquaculture Innovation Centre. Jun 2017 - Dec 2018

Calcium in a changing environment: PI and Co-supervisor of PhD student. Funded by EU Marie-Curie Initial Training Network FP7. Nov 2013 - May 2018

Improving marine growth estimates using 3D photogrammetry. PI. Funded by NERC. Jan-Jun 2018

Impacts of chemotheraputants on the benthos (PAMP2): A 3 year project examining the association between chemicals used to treat sea lice in salmon farms on non-target crustacea living around those farms. Funded by the Scottish Aquaculture Research Forum. Nov 2013-Apr 2017

Developing monitoring protocols for the offshore renewables industry (TIDES): In depth assessment of the monitoring requirements in relation to developing offshore energy and recommendations for improvements. Funded by EU FP7. Apr 2013-Sep 2016

The Loch Linnhe Artificial Reef: a seven year project to design, licence and construct Europe’s largest artificial reef.  This project, with partners Foster Yeoman Limited (now Aggregate Industries Limited) was completed in 2005 and continues to support research into the interactions between marine structures and the sea and seabed.


Marine Science BSc: Module leader and lecturer for year 2 'Data Science'

Marine Science BSc: Lecturer year 3 'Marine Pollution'

Marine Science BSc: Lecturer year 4 'Aquaculture'


Aquaculture, Environment and Society MSc: Lecturer 

List of current research students

Victoria Ashley-Wheeler: Assessing benthic recovery following cessation of salmon farming using eDNA metabarcoding. PhD. UHI

Shraveena Venkatesh: Environmental DNA metabarcoding for assessing benthic ecological status associated with Salmon farming. PhD. UHI   


List of alumni research students

Kati Michalek: Levels of calcification and selection in naturally varying pH habitats in farmed vs wild Mytilus species. PhD 2014-2017. University of the Highlands and Islands

Michael Redford: Artificial reef creation using decommissioned mattresses – environmental performance and fisheries enhancement potential in the North Sea.  PhD 2017 – 2021.  UHI.  European Social Fund funding. 

Grace Russel: Using 3-D photogrammetry to quantify biofouling on artificial structures. MSc 2017. University of St Andrews

Sally Rouse: Understanding benthic productivity on artificial structures: maximising the benefits of marine renewable energy devices. PhD 2011-15. UHI/University of Aberdeen

Karen Alexander: Offshore power production and marine stakeholders: from understanding conflict to impact mitigation. PhD 2009-12. UHI/University of Aberdeen

Kyla Orr: Offshore power production and marine stakeholders: from understanding conflict to impact mitigation. PhD 2009-12. UHI/University of Aberdeen

Yassir Al-bouraee: Tidal hydrodynamics on the Loch Linnhe Artificial Reef. PhD 2008-12. University of Newcastle

Craig Rose: Modeling and measuring the habitat complexity of artifical reefs. PhD 2001-05. University of Newcastle

Aine Purcell-Milton. MRes 2014. University of St Andrews

Kirsty Wright. MRes 2014. University of St Andrews

Laura Tulip. MRes 2012. University of St Andrews

Tim Cross. MSc 2012. University of York

Fiona Mills. MSc 2009. Heriot-Watt University

Edwin Palmer. MSc 2008. University of Newcastle

Zoe Aston. MSc 2006. University of Newcastle

Craig Rose. MSc 2001. University of Newcastle

Consultancy and industry experience

I am a qualified statistician with 20 years of experience in applying a broad range of statistical modelling approaches. These approaches range from simple univariate modelling to developing more complex mixed- and multivariate-models and time-series analysis. I have applied these skills to both observational and manipulative studies and routinely advise colleagues and clients with respect to experimental design in order to optimize scientific research.

Accessing consultancy services from SAMS

SAMS consultancy work is delivered through its wholly owned commercial subsidiary, SAMS Enterprise, which operates a comprehensive Quality Management System (QMS) that is accredited to ISO9001:2008 standard, guaranteeing that all projects deliver the best possible service to our customers. All Enterprise projects are planned by a professional programme manager who oversees a team of dedicated project managers, all of whom are focussed specifically on client delivery, and have scientific experience and technical expertise in fields relevant to their assigned projects.

For further information concerning commercial enterprise opportunities at SAMS, please contact SAMS Enteprise by email (info@sams-enterprise.com) or phone +44 (0) 1631 559 470.

Peer-reviewed publications   

First author publications                                                        

Wilding, T.A., Stoeck, T., Morrissey, B.J., Carvalho, S.F., Coulson, M.W. (2022) Maximising signal-to-noise ratios in environmental DNA-based monitoring. Science of the Total Environment 858(1): 159735 https://doi.org/10.1016/j.scitotenv.2022.159735 

Wilding, T. A., A. B. Gill, A. Boon, E. V. Sheehan, J.-C. Dauvin, J.-P. Pezy, F. O'Beirn, U. Janas, L. Rostin and I. de Mesel (2017). Turning off the DRIP ('Data-rich, information-poor') -rationalising monitoring with a focus on marine renewable energy developments and the benthos. Renewable & Sustainable Energy Reviews 74: 848 – 859.

Wilding, T. A. (2014). "Effects of man-made structures on sedimentary oxygenation: Extent, seasonality and implications for offshore renewables." Marine Environmental Research 97: 39 - 47.

Wilding, T. A. and T. D. Nickell (2013). "Changes in Benthos Associated with Mussel (Mytilus edulis L.) Farms on the West-Coast of Scotland." Plos One 8(7): e68313.

Wilding, T. A. (2012). "Changes in Sedimentary Redox Associated with Mussel (Mytilus edulis L.) Farms on the West-Coast of Scotland." PLOS ONE 7 (9): e45159.

Wilding, T. A. (2011). "A characterization and sensitivity analysis of the benthic biotopes around Scottish salmon farms with a focus on the sea pen Pennatula phosphorea L." Aquaculture Research 42: 35-40.

Wilding, T. A., C. J. Cromey, T. D. Nickell and D. J. Hughes (2012). "Salmon farm impacts on muddy-sediment megabenthic assemblages on the west coast of Scotland." Aquaculture Environment Interactions 2(2): 145-156.

Wilding, T. A., E. J. L. Palmer and N. V. C. Polunin (2010). "Comparison of three methods for quantifying topographic complexity on rocky shores." Marine Environmental Research 69: 143 - 151.

Wilding, T. A., C. A. Rose and M. J. Downie (2007). "A novel approach to measuring subtidal habitat complexity." Journal of Experimental Marine Biology and Ecology 353(2): 279-286.

Wilding, T. A. (2006). "The benthic impacts of the Loch Linnhe artificial reef." Hydrobiologia 555: 345 - 353.

Wilding, T. A., M. D. J. Sayer and P. G. Provost (2003). "Factors affecting the performance of the acoustic ground discrimination system RoxAnn (TM)." ICES Journal of Marine Science 60(6): 1373-1380.

Wilding, T. A. and M. D. J. Sayer (2002). "Evaluating artificial reef performance: approaches to pre- and post-deployment research." ICES Journal of Marine Science 59: S222-S230.

Wilding, T. A. and M. D. J. Sayer (2002). "The physical and chemical performance of artificial reef blocks made using quarry by-products." ICES Journal of Marine Science 59: S250-S257.

Wilding, T. A. (2002). "Taxonomy and ecology and Toxisarcon alba, sp. nov. from Loch Linnhe, West coast of Scotland, UK." The Journal of Foraminiferal Research 32(4): 358-363.

Co-author publications

Frühe, L., V. Dully, D. Forster, N. B. Keeley, O. Laroche, X. Pochon, S. Robinson, T. A. Wilding and T. Stoeck (2021). "Global Trends of Benthic Bacterial Diversity and Community Composition Along Organic Enrichment Gradients of Salmon Farms." Frontiers in Microbiology 12(853).

Dully, V., G. Rech, T. A. Wilding, A. Lanzen, K. MacKichan, I. Berrill and T. Stoeck (2021). "Comparing sediment preservation methods for genomic biomonitoring of coastal marine ecosystems." Mar Pollut Bull 173(Pt B): 113129.

Frühe, L., T. Cordier, V. Dully, H.-W. Breiner, G. Lentendu, J. Pawlowski, C. Martins, T. A. Wilding and T. Stoeck (2020). "Supervised machine learning is superior to indicator value inference in monitoring the environmental impacts of salmon aquaculture using eDNA metabarcodes." Molecular Ecology https://doi.org/10.1111/mec.15434  

Dully, V., T. A. Wilding, T. Mühlhaus and T. Stoeck (2021). "Identifying the minimum amplicon sequence depth to adequately predict classes in eDNA-based marine biomonitoring using supervised machine learning." Computational and Structural Biotechnology Journal 19: 2256-2268.

Michalek, K., D. L. J. Vendrami, M. Bekaert, D. H. Green, K. S. Last, L. Telesca, T. A. Wilding and J. I. Hoffman (2021). "Mytilus trossulus introgression and consequences for shell traits in longline cultivated mussels." Evolutionary Applications.

Stewart‐Sinclair, P. J., K. S. Last, B. L. Payne and T. A. Wilding (2020). "A global assessment of the vulnerability of shellfish aquaculture to climate change and ocean acidification." Ecology and Evolution 10(7): 3518 - 3534.

Rouse, S., J. S. Porter and T. A. Wilding (2020). "Artificial reef design affects benthic secondary productivity and provision of functional habitat." Ecology and Evolution 10(4): 2122-2130.

Rouse, S., N. C. Lacey, P. Hayes and T. A. Wilding (2019). "Benthic Conservation Features and Species Associated With Subsea Pipelines: Considerations for Decommissioning." Frontiers in Marine Science 6.

Forster, D., G. Lentendu, S. Filker, E. Dubois, T. A. Wilding and T. Stoeck (2019). "Improving eDNA-based protist diversity assessments using networks of amplicon sequence variants." Environ Microbiol 21(11): 4109-4124.

Clark, M. S., … Wilding, T. A. et al (2020). "Deciphering mollusc shell production: the roles of genetic mechanisms through to ecology, aquaculture and biomimetics." Biol Rev Camb Philos Soc 95(6): 1812-1837.

Degraer, S., D. Wilhelmsson, T. A. Wilding, J. Vanaverbeke, L. Rostin, J. Reubens, A. Raoux, G. Martin, U. Janas, A. C. Jackson, Z. L. Hutchison, A. B. Gill, J. Derweduwen, I. De Mesel, J.-C. Dauvin, J. W. P. Coolen, A. R. Boon, R. Brzana, S. N. R. Birchenough, L. Bergström, J. Dannheim and J. Norkko (2020). "Benthic effects of offshore renewables: identification of knowledge gaps and urgently needed research." ICES Journal of Marine Science 77(3): 1092-1108.

Michalek K, Vendrami DLJ, Bekaert M, Green DH, Last KS, Telesca L, Wilding TA, Hoffman JI (2021) Mytilus trossulus introgression and consequences for shell traits in longline cultivated mussels. Evolutionary Applications 2021;00:1-14. https://doi.org/10.1111/eva.13245

Stewart-Sinclair PJ, Last KS, Payne BL, Wilding TA (2020) A global assessment of the vulnerability of shellfish aquaculture to climate change and ocean acidification. Ecology and Evolution 10(7): 3518–3534. https://doi.org/10.1002/ece3.6149 

Last, K. S., V. J. Hendrick, C. M. Beveridge, D. A. Roberts and T. A. Wilding (2016). "Lethal and sub-lethal responses of the biogenic reef forming polychaete Sabellaria alveolata to aqueous chlorine and temperature." Marine Environmental Research 117: 44-53.

Lejzerowicz, F., P. Esling, L. Pillet, T. A. Wilding, K. D. Black and J. Pawlowski (2015). "High-throughput sequencing and morphology perform equally well for benthic monitoring of marine ecosystems." Sci Rep 5: 13932.

Pawlowski, J., P. Esling, F. Lejzerowicz, T. Cedhagen and T. A. Wilding (2014). "Environmental monitoring through protist next-generation sequencing metabarcoding: assessing the impact of fish farming on benthic foraminifera communities." Molecular Ecology Resources 14(6): 1129 - 1140.

Orr, K. K., T. A. Wilding, L. Horstmeyer, S. Weigl and J. J. Heymans (2014). "Detached macroalgae: Its importance to inshore sandy beach fauna." Estuarine, Coastal and Shelf Science 150 (Part A): 125 - 135.

Alexander, K. A., J. J. Heymans, S. Magill, M. T. Tomczak, S. J. Holmes and T. A. Wilding (2014). "Investigating the recent decline in gadoid stocks in the west of Scotland shelf ecosystem using a foodweb model." ICES Journal of Marine Science: Journal du Conseil.

Alexander, K. A., T. A. Wilding and J. S. S. Heymans (2013). "Attitudes of Scottish fishers' towards marine renewable energy." Marine Policy 37: 239 - 244.

Alexander, K. A., T. Potts and T. A. Wilding (2013). "Marine renewable energy and Scottish west coast fishers: Exploring impacts, opportunities and potential mitigation." Ocean & Coastal Management 75(0): 1-10.

Alexander, K. A., R. Janssen, G. Arciniegas, T. G. O'Higgins, T. Eikelboom and T. A. Wilding (2012). "Interactive Marine Spatial Planning: Siting Tidal Energy Arrays around the Mull of Kintyre." Plos One 7(1): e30031.

Davidson, K., P. Miller, T. A. Wilding, J. Shutler, E. Bresnan, K. Kennington and S. Swan (2009). "A large and prolonged bloom of Karenia mikimotoi in Scottish waters in 2006." Harmful Algae 8(2): 349-361.

Day, J. G., M. Lorenz, T. A. Wilding, T. Friedl, K. Harding, T. Pröschold, D. Brennan, M. Julia, L. M. A. Santos, M. F. Santos, H. C. Osório, R. Amaral, A. Lukešová, P. Hrouzek, M. Lukeš, J. Elster, J. LukavskýIan, I. Probert, M. J. Ryan and E. E. Benson (2007). "The use of physical and virtual infrastructures fro the validation of algal cryopreservation methods in international culture collections." Cryobiology 28(5): 359 - 376.

Sayer, M. D. J. and T. A. Wilding (2002). "Planning, licensing, and stakeholder consultation in an artificial reef development: the Loch Linnhe reef, a case study." ICES Journal of Marine Science 59: S178-S185.

Other publications

Tett P, Benjamins S, Black KD, Coulson M, Davidson K, Fernandes T, Fox C, Hart M, Hicks N, Hughes A, Hunter D-C, Nickell T, Risch D, Tocher D, Vare L, Vespoor E, Wilding T, Wilson B, Wittich A (2018) Review of the environmental impacts of salmon farming in Scotland. Report for the Environment, Climate Change and Land Reform (ECCLR) Committee. The Scottish Parliament, 196 pp.

Wilding, T. A., D. J. Hughes and K. D. Black (2017). The association between emamectin benzoate use and crustacean assemblages around Scottish fish farms. SARF Report (submitted and in review)

Holtrop, G., B. Duff, S. Swan, T. A. Wilding, B. Narayanaswamy and K. Davidson (2016). Risk assessment of the Scottish monitoring programme for the marine biotoxins in shellfish harvested from classified production areas: review of the current sampling scheme to develop an improved programme based on evidence of risk. Food Standards Scotland: 218.

Wilding, T. A. and K. Black (2015). A statistical analysis of sea- lice medicine use and benthic monitoring at Scottish marine salmon farms (2002 – 2014).  Scottish Aquaculture Research Forum.  ISBN: 978-1-907266-75-1.

Davidson, K., P. I. Miller, J. Shutler, S. Gontarek, D. Aleynik, A. Kurekin and T. A. Wilding (2015). Synthesis and interpretation of data set relating to the harmful dinoflagellate Karenia mikimotoi in western Scottish waters. The Crown Estate.

Cook, E. J., C. M. Beveridge, P. Lamont, T. O’Higgins and T. A. Wilding (2014). Survey of Wild Pacific Oyster Crassostrea gigas in Scotland.  ISBN: 978-1-907266-65-2, SARF

Wilding, T. A., C. J. Cromey, J. Howe and P. Tett (2012). A systematic assessment of the environmental impact of Scottish shellfish farms, including benthos, water column and relevant special interactions, Scottish Aquaculture Research Forum.  ISBN: 978-1-907266-43-0.

Last, K., V. Hendrick, T. A. Wilding and C. Beveridge (2012). Tolerance of Sabellaria alveolata to aqueous chlorine.  Final Report to the BEEMS programme, Work Package 6, 17 February 2012, 44 pages. SAMS Commercial Report.

Wilding, T. A. and D. J. Hughes (2010). A review and assessment of the effects of marine fish farm discharges on Biodiversity Action Plan habitats.

Wilding, T. A. (2007). Krill as a source of aquafeed, The Crown Estate: 52.

Wilding, T. A., M. S. Kelly and K. D. Black (2006). Alternative marine sources of protein and oil for aquaculture feeds: State of the art and recommendation for further research, The Crown Estate: 60.

Wilding, T. A., J. Duncan, L. A. Nickell, T. P. Hughes, S. Gontarek, K. D. Black and M. D. J. Sayer (2005). Report for the Department of Trade and Industry - Synthesis of information on the Benthos of Area SEA6 - The Clyde Sea. Oban, Scottish Association for Marine Science: 41.

Wilding, T. A., D. J. Hughes, B. Wilson and K. D. Black (2005). The benthic environment of the North and West of Scotland and the Northern and Western Isles: sources of information and overview, Scottish Association for Marine Science: 27.

Professional activities

Sep 2016 - present: Member of the ScotMER Benthic Receptor Group (Marine Scotland Science)

Sep 2016 - 2020: Chair of MASTS Oil and Gas Environmental Research Forum: Chairing the forum, providing a contact point for industry and regulators in relation to environmental issues pertaining to Oil and Gas.

Sep 2015 - present: Invited member of SpORRAn: Provision of advice regards benthos to MSS (SpORRAn – Scottish Offshore Renewables Research Framework.

Mar 2015 - present: MASTS Oil and Gas Forum Steering Group Member: Developing a strategic vision for MASTS within the O&G sector, particularly in relation to decommissioning. 

Mar 2013 - present: ICES Working Group on Marine Benthal and Renewable Energy Developments (WGMBRED)

Employment history

Since 2017: Senior Lecturer in Benthic Ecology, SAMS

2016-17: Lecturer in Benthic Ecology. SAMS

2012-16: Lecturer in Hard Substratum and Megabenthos Ecology. SAMS

2009-12: Research Associate Hard Substratum and Megabenthos Ecology. SAMS

2007-09: Benthic Ecologist. SAMS

1996-2007: RA - numerous short fixed-term contracts. NERC

1994-95: Scientific Officer in Deep-Sea Ecology. NERC


2010. Diploma in Statistics. Open University

2003. PhD 'The prediction and assessment of the environmental impacts of the Loch Linnhe Artificial Reef. Heriot-Watt University

1993. HSE Part IV professional SCUBA in Commercial Diving. Heriot-Watt University

1993. MSc (with Distinction) in Marine Resource Development and Protection. Heriot-Watt University

1990. BSc (Hons) Biology. Exeter University