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Marine Soundscapes and eDNA for Assessing Biodiversity and Functioning of Re-establishing European Flat Oyster Reefs, Ostrea edulis [SUPER Doctoral Training Partnership (DTP)]


School of Applied Sciences

Edinburgh United Kingdom Artificial Intelligence Biodiversity Bioinformatics Biotechnology Data Analysis Ecology Machine Learning Marine Biology Marine Sciences Molecular Biology

About the Project

European oyster reefs provide a habitat for ecologically and economically important species, improve water quality and contribute to blue carbon storage [1,2]. Due to extensive overfishing throughout Europe, by the early 1900’s few oyster beds survived, with those remaining now protected and classified as threatened and/or declining. As part of a Europe-wide effort, researchers, governments, NGOs and industry are collaborating to optimize, monitoring and restore these once abundant habitats.

This studentship is a fantastic and timely opportunity to contribute to global restoration efforts (UNdecadeonrestoration) by generating soundscape recordings of European native flat oyster reefs (ENFOR) and comparing their ecoacoustic reef expression [3,4] with environmental DNA (eDNA) expression [5]. The soundscape and eDNA data will be used as an indicator for (re-establishing) habitat complexity, biodiversity, ecosystem functioning [6] and inform restoration practice and conservation policy [5-8]. The focus of this PhD project is therefore of great interest to all partners and stakeholders (e.g. acoustics industry, regulators).

You will gain skills/expertise in

  • boat-based sampling joining the team in Loch Ryan and the Dornoch Firth, Scotland
  • developing an experimental design under consideration of available resources
  • generating the first soundscape recordings of ENFOR along a degradation gradient in Scotland, with potential opportunity of recording over old established reefs in Scandinavia
  • testing soundscape indices against biodiversity inventories for their performance [6,9]
  • developing machine learning methods to automate analyses of audio files to develop indicators for ecosystem health [8,10,11]
  • analysing water samples for eDNA; marker/primer selection, PCR-amplification, DNA library preparation; use of bioinformatic algorithms to extract information from the sequence-data [12]
  • comparing ecoacoustic and eDNA reef expression
  • using advanced coding and uni/multivariate statistics
  • conducting experiments to assess the role of ecoacoustics for larval settlement (depending on time) [13]
  • developing a tool for rapid assessment for ENFOR restoration projects

You will be based at Edinburgh Napier University, with frequent visits to neighbouring Heriot-Watt University, where Dr Sanderson is based, along with stays at Marine Scotland Science, Aberdeen, our CASE partner**. You will be part of a thriving PhD community and supportive environment. You will team up with two PhD students working on ENFOR and collaborate closely with the Dornoch Environmental Enhancement Project-DEEP.

As a SUPER DTP student, you will also benefit from inter-institutional support and shared training from 8 Scottish Universities, supported by our Graduate School and Postgraduate Professional Researcher Development Certificate (PG Cert.), to develop skills in communication, team-working and management. Training in coding/programming, data analyses and statistical modelling will be provided, as necessary. You will work with experts in soundscape analysis, DNA preparation/sequencing and bioinformatics. There will be numerous opportunities to present at conferences. With the national/international network built through the PhD partnership and the gained skill set, you will have an excellent employment potential across a range of different environments/disciplines and sectors (e.g. academic, industry, regulatory) following graduation.

Additional project advisors are:

  • Dr Marco Fusi (School of Applied Sciences, Edinburgh Napier University)
  • Samuel RP-J Ross (Trinity College Dublin)
  • Dr Marion Harrald or Dr Hannah Millar (Marine Scotland Science – MSS)

**MSS are very happy to consider UK citizens, Commonwealth citizens, and EU citizens with settled (or pre-settled) status and to work with them to achieve the necessary security clearance (known as BPSS) as a necessary precursor to them being permitted to work on MSS premises (including MSS vessels). Students with other backgrounds are unlikely to be able to achieve the BPSS.

English language requirements

IELTS score must be at least 6.5 (with no less than 6.0 in each of the four components). Other, equivalent qualifications will be accepted. Full details of the University's policy is available online.

Essential attributes:

  • Experience and interest in programming: This PhD will require a high degree of coding proficiency mainly in R
  • Interest in aquatic ecology, conservation or restoration ecology
  • Curiosity-driven, strong motivation and good time management skills
  • Willingness to undertake periods of field-sampling in Scotland, and potentially Scandinavia

Desirable attributes:

  • Basic knowledge/experience of machine-learning techniques, and ability to code in Python and Matlab (in addition to R)
  • Basic understanding of DNA sequencing and analysis
  • Experience in experimental design of lab/field studies
  • Providing required certifications, field-sampling can include scientific diving with the Heriot-Watt dive team

Funding Notes

This studentship forms part of the NERC-funded Doctoral training partnership SUPER View Website
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Start date: 27 September 2021
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The 3.5-year studentship covers:
• Tuition fees (UK fee rate only*)
• A stipend (around £15,000 p.a. for full-time study)
• Funding for research training/consumables
• Part-time study optional, a minimum of 50% of full-time effort being required.
APPLY HERE: View Website
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* for International students, there may be funding available to cover the full international tuition fee and this will be discussed at interview. If funds are not available, the candidate will be required to cover the difference in fees.

References

1. Fariñas-Franco JM, …, Sanderson WG (2018) Missing native oyster (Ostrea edulis L.) beds in a European Marine Protected Area: Should there be widespread restorative management? Biological Conservation; 221: 293-311.
2. Lee H…, Diele K, Sanderson WG (2020) Missing the full story: First estimates of carbon deposition rates for the European Flat Oyster Ostrea edulis. Aquatic Conservation: Marine and Freshwater Ecosystems. https://doi.org/10.1002/aqc.3402
3. Coquereau L et al. (2016) Acoustic behaviour of large crustaceans in NE Atlantic coastal habitats. PeerJ; 25: 151-163
4. Coquereau L et al. (2015) Sound production and associated behaviours of benthic invertebrates from a coastal habitat in the north east Atlantic. Marine Biology 163:127-136
5. Bani A et al. (2020) Informing marine spatial planning decisions with environmental DNA. Advances in Ecological Research; 62: 375-407 https://doi.org/10.1016/bs.aecr.2020.01.
6. Elise S et al. (2019) Assessing key ecosystem functions through soundscapes: A new perspective from coral reefs. Ecological Indicators; 107: 105623. https://doi.org/10.1016/j.ecolind.2019.105623
7. Dumyahn SL et al. (2011) Soundscape Conservation. Landscape Ecology 26:1327.
8. Ross SRP-J et al. (2018) Listening to ecosystems: data-rich acoustic monitoring through land-scape-scale sensor networks. Ecol. Res.; 33: 135-147.
9. Ross SRP-J et al. (2020) Utility of acoustic indices for ecological monitoring in complex sonic environments. Ecol. Indicat.; https://doi.org/10.1016/j.ecolind.2020.107114
10. Digby A et al. (2013) A practical comparison of manual, semi-automatic and automatic methods for acoustic monitoring. Methods Ecol. Evol.; 4: 675-683
11. Sethi et al. 2020. Characterizing soundscapes across diverse ecosystems using a universal acoustic feature set. PNAS; 117(29): 17049-17055
12. Aglieri G et al. (2020) Environmental DNA effectively captures functional diversity of coastal fish communities. Molecular Ecology; https://doi.org/10.1111/mec.15661
13. Lillis A et al. (2013) Oyster larvae settle in response to habitat-associated underwater sounds. PLoS ONE; 8(10): e79337 https://doi.org/10.1371/journal.pone.0079337
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ACADEMIC QUALIFICATIONS
Applicants should have, or be studying for:
• A postgraduate Master’s degree from a degree-awarding body recognised by the UK government, or equivalent,
or
• A first or upper second class honours degree from a degree awarding body recognised by the UK government
• A background in Computing, Marine Ecology, Molecular Biology, Ecology or equivalent is desirable
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APPLICATION CHECKLIST
- Completed application form
- CV
- 2 academic references, using the Postgraduate Educational Reference Form
- A personal research statement (this should include (a) why you are interested in this position and a brief description of your relevant experience and skills, (b) an indication of what you would uniquely bring to the project and (c) a statement of how this project fits with your future direction.)
- Evidence of proficiency in English (if appropriate)
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Application info and reference form can be found on https://www.napier.ac.uk/research-and-innovation/research-degrees/application-process)
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Interviews will be held late February/early March 2021.

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