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Utilising Fourier-Transform Infrared (FTIR) Spectroscopy for the Characterisation of Intertidal Sediments

Postgraduate Training

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Dr J Robertson , Dr E Pagaling , Prof David Paterson No more applications being accepted Competition Funded PhD Project (European/UK Students Only)

About the Project

Intertidal sediments are physically and biologically dynamic, forming complex ecosystems that are historically attractive to human settlement (Boerema, 2017). Estuaries, for example, provide an extensive range of processes and functions known as ecosystem services. These can be regarded as beneficial, or even essential, to humans (Paterson, 2009). Ecosystem services provided by estuaries include flood mitigation, biodiversity provisioning, fisheries, aquaculture, agriculture, primary production, carbon storage, cultural heritage and recreation. Despite their value, historical and modern detrimental practices by humans have exposed these habitats to “multiple and escalating pressures” (Davis, 2012) resulting in estimated habitat loss faster than tropical rainforest decline (Duarte, 2008). The urgency in addressing estuarine ecosystem management has been renewed under global climate change scenarios. This goal can only be supported by the understanding of the ecosystem services delivered by depositional systems and their sediments. This project will develop techniques that can be used in research and industry alike to identify and quantify constituents of intertidal sediments that drive sediment characteristics and behavior that are key to coastal management practices. These include extracellular polymeric substance, mineralogy and organic matter, which can all be characterised using FTIR. Traditional bench-top characterisation of intertidal sediments is labour intensive and costly. The ability to rapidly characterise physical and biological properties of sediments, especially if this can be achieved in-situ, will be a significant contribution to all fields of estuarine and coastal science. The benefit of using spectroscopy for soil monitoring has been widely acknowledged (Nocita, 2015) and it has been used at the JHI to characterise chemical and physical properties and organic matter in soils and suspended sediments (Stutter, 2007; Artz, 2008; Robertson, 2015).

The primary aim of the project is to develop a novel monitoring tool for intertidal and coastal sediments. New techniques allowing for the rapid and reliable in-situ collection of spectra from sediments using portable FTIR technology will be developed. The ultimate aim of the project will be to develop and employ this new methodology to improve monitoring capabilities for one or more aspects of coastal management.

Previous collaboration between the James Hutton Institute and the Sediment Ecology Research Group has produced a large archive of sediments that have been characterized using traditional benchtop techniques (Wyness, 2017) that can be used for training, calibration and method development. The majority of the work will be undertaken at the Institute, where the benchtop FTIR is situated and the student can integrate with others in the IR section of the analytical group. The infrastructure and support is in place at the University of St Andrews for the sampling of intertidal sediments and performing traditional benchtop analyses. Initially, methods will be optimised on benchtop FTIR equipment, followed by calibration of predictive models for the characterisation and quantification of key sediment constituents using traditional analyses. In-situ techniques using the portable FTIR will be developed and used to explore their use in intertidal and coastal sediments.

Project Outline for 1-4 months: A literature search will be conducted to review the status of FTIR characterisation of soils and sediments. Recent developments in FTIR technology have resulted in an influx of research articles, where FTIR spectra have been unintentionally misinterpreted, and provides an opportunity for critical review. 5-12 months: Novel methodologies for the analysis of fresh and in-situ sediments using the Exoscan Portable FTIR (Agilent) will be developed. Initially, the suitability of the two approaches for FTIR analysis (Attenuated Total Reflectance and Diffuse Reflectance) will be compared for the characterisation of intertidal sediments. This will be followed by the optimisation of measurement parameters to overcome challenges of in-situ sediment analysis identified during preliminary work. These challenges include distortion of spectra by variation in particle size and water content of intertidal sediments. 12-18 months: Spectral analysis software will be used to calibrate predictive models for the measurement of key sediment constituents. The archive of intertidal sediments will be used for calibration and testing, in addition to the spiking of sediments with known material. 18+ months: With the development of the new techniques, large- scale, high-resolution sampling campaigns will be possible across one or several estuaries. Student Input: The student will be encouraged to direct their own research in order to explore the utility of rapid sediment characterisation in relation to ecosystem services. For example, the tracking of sediments prone to biological or chemical contaminants, or characterising organic matter and mineralogy with relation to sediment stability.

Funding Notes

The studentship is funded under the James Hutton Institute/University Joint PhD programme, in this case with the University of St Andrews. Applicants should have a first-class honours degree in a relevant subject or a 2.1 honours degree plus Masters (or equivalent).Shortlisted candidates will be interviewed in Jan/Feb 2018. A more detailed plan of the studentship is available to candidates upon application. Funding is available for European applications, but Worldwide applicants who possess suitable self-funding are also invited to apply


Artz, R. R. E. et al. (2008) FTIR spectroscopy can predict organic matter quality in regenerating cutover peatlands.. Soil Biology and Biochemistry, Elsevier, 2008, 40 (2), pp.515-527.

Boerema, A., Meire, P. (2017) Management for estuarine ecosystem services: A review, Ecological Engineering, Volume 98, Pages 172-182

Davis, J., Kidd, I. M. (2012). Identifying Major Stressors: The Essential Precursor to Restoring Cultural Ecosystem Services in a Degraded Estuary. Estuaries and Coasts 35:4, pages. 1007-1017

Duarte, C. M. et al. 2008) The Charisma of Coastal Ecosystems: Addressing the Imbalance. Estuaries and Coasts 31:2. P233-238

Nocita, M. et al. (2015) Soil spectroscopy: an alternative to wet chemistry for soil monitoring., Advances in Agronomy, 132, 139-159.
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