Project title: The role of Arabidopsis MAP kinase MPK1, MPK2 signalling in biotic and abiotic stress
Project abstract: The conserved eukaryotic MAP kinase signal transduction pathways have essential roles in plants to relay information from the environment to the nucleus of the cell and to ensure appropriate remedial responses to biotic (bacteria, fungi) and abiotic (heat, salt) stresses. This project will focus on the analysis of MAP kinase pathway T-DNA insertion mutants in Arabidopsis thaliana (in particular, MPK1, MPK2, and also double mutants of these lines), with respect to basal resistance to microbial pathogens (e.g. Pseudomonas syringae), and to drought and salt stress. Physiological and biochemical responses (changes in gene expression using q-PCR) will be determined. The plant hormones ethylene, salicylic acid, abscisic acid and jasmonic acid play key roles in stress responses and endogenous levels of these compounds in response to stress will be determined by GC or HPLC. The molecular interactions of MAP kinase signalling pathway proteins with putative osmosensing receptors will be explored using genetic and molecular biological techniques.
Supervisor: Dr Peter Morris
Al-Ghanem, Mai Mohammed
Project title: Characterization of antibacterial activity of a novel environmental isolate of Serratia plymuthica
Project abstract: Over the years Serratia species have become an important source of bioactive compounds with numerous studies concerning their production of secondary metabolites with applications in medicine, pharmaceutics and biotechnology. My project investigates the secreted antibacterial activity present in the cell-free culture supernatant (CFCS) of a marine bacterial isolate of S. plymuthica. Different cultivation parameters such as culture medium, aeration and temperature have a clear impact on the production of the secreted antibacterial activity which might help in future large-scale production of the antimicrobial compounds. The secreted activity is thermo-stable and remains active even after sterilization (121°C/15mins) and is insensitive to methanol and Tween. These characteristics of the antibacterial activity hold promising potentials in industrial and environmental biotechnology, food industry and bioremediation. Structural characterization of the antibacterial compounds was confirmed via NMR and COSY spectrometry. Antibacterial compounds produced by this novel isolate of S. plymuthica have highly promising potential as antibacterial agents.
Supervisor: Dr Derek Jamieson
Almoghayer, Mohammed Alaa
Project title: Contribution Of Tidal Energy To An Integrated Island Energy System
Project abstract: The practical use of tidal stream energy requires extraction that is efficient and appropriate, both in engineering design and environmentally, socially and economically. The study will design a tidal array for Orkney waters, testing it against a wide range of constraints from engineering efficiency to market suitability.
Supervisor: Dr David K Woolf
Cecchetto, Marta Maria
Project title: Ecosystem wide survey across the deep seafloor biome of the Clarion Clipperton Zone to help assess and manage the impacts of polymetallic nodule mining and climate change
Project abstract: A benthic lander with 3 benthic respirometers will be used to assess and quantify benthic ecosystem functioning, sediment oxygen demand, CO2 production, nutrient fluxes and C-uptake rates. Oxygen, CO2 and nutrient fluxes will allow to assess the contribution of organism respiration vs oxidation processes and benthic nutrient cycling process at the seafloor. Furthermore, pulse chase experiment will be carried out with isotopically labeled algae to quantify the uptake and turnover of specific elements (i.e C-13) and assign the organisms and pathways responsible. Linear inverse modelling framework will be used for the quantification of carbon flows and ecosystem budgets. Experimental data sets will be used to form the foundation of food web models focusing on transfer of carbon through the benthic ecosystem.
Supervisors: Dr. Andrew Sweetman
Project title: Ecological, conservation and societal consequences of shellfish restoration in Marine Protected Areas
Project abstract: The project aims to investigate scenarios for shellfish restoration using the Dornoch Firth as a case study site. The project seeks to do this by understanding carrying-capacity and populations of different shellfish and dependent bird species within the system then manipulating the system in environmental models that reflect potential restoration scenarios and thereby explore potential consequences for biodiversity and livelihoods. The project will also interpret the findings within the context of at least two other MPAs in Scotland using extant data.
Supervisors: Dr. William Sanderson (Heriot-Watt University), Dr. Richard Bates (St Andrews University) & Dr. David Donnan (Scottish Natural Heritage).
De Clippele, Laurence
Project title: An integrated ecological and geophysical study of cold-water coral habitats
Project abstract: Cold-water coral reefs are listed by the United Nations as Vulnerable Marine Ecosystems and are in need of protection. These long-living, slow growing reefs are hotspots of biodiversity threatened by fishing activities and climate change. To be able to protect these ecosystems efficiently, there is a need to improve our understanding of the distribution of these cold-water corals, their habitats and the diversity and distribution of their associated fauna. In this project high-definition video material, acoustic data (e.g. bathymetry, backscatter), predictive models and maps were used in this project to help fill gaps. These helps us to enhance our knowledge on the function of cold-water corals in the deep sea and on the factors that control the distribution of these organisms.
Supervisor(s): Professor Murray Roberts, Dr Veerle Huvenne & Professor Hamish Mair
Project title: The Blue Carbon of Shellfish Beds: Understanding the vaults of biogenic reefs (O. edulis, M. modiolus and M. edulis)
Project abstract: Bivalve molluscs provide a wealth of ecosystem goods and services from water quality management to the reduction of turbidity and storage of carbon (‘Blue Carbon’). Historically, overfishing and disease has led to the depletion of bivalve stocks globally. Consequently, biogenic reefs formed by shellfish have recently become the focus of a series of restoration projects across an international scale. In recent years the value of blue carbon stocks has been recognised with extensive focus on mangroves, saltmarshes and seagrass meadows.
This project aims to quantify the potential of shellfish beds to be more widely considered as blue carbon sinks. Quantification will be achieved by focusing on 1) carbon budgeting of shellfish; quantification of annual carbon storage versus annual output, 2) the role of biogenic reefs in carbon sequestration under controlled and natural conditions and 3) to apply knowledge to other shellfish species and format a large-scale carbon storage assessment.
Supervisor(s): Dr William Sanderson (Heriot Watt), Dr Karen Diele (Edinburgh Napier), Dr Ian Davies (Marine Scotland), Professor John Baxter (Scottish Natural Heritage) & Professor Ted Henry.
Project title: Future vulnerability of Modiolus modiolus reefs to climate change: From mechanisms to management
Project abstract: The main project aim is to investigate the sensitivity of M. modiolus to future climate change conditions (warming and hypoxia). The project will assess acclimatory capacities (examination of climate change sensitivities as determined by oxidative stress biomarkers and energetics) under aquarium-based future climate conditions. Examination will include species- and population-level investigation of sensitivities of a number of key reef populations from across the UK (including the southern limit of the species range) and Isle of Man. Additionally, the project will carry out analyses of population genetics (via microsatellite screening) to determine genetic connectivity of populations and to provide preliminary indication of a potential genetic basis for particular sensitivities. Such outcomes will then inform management strategies in order to conserve these important marine ecosystems.
Supervisors: Dr Joanne Porter, Dr Bill Sanderson & Dr Mark Hartl
Project title: Role of the world's deepest living marine algae in the global carbon cycle
Project abstract: Crustose coralline algae are important marine photosynthesizers and carbonate builders found throughout the euphotic zone of the world’s oceans. Calcareous nodules of these algae (called rhodoliths) form large reef ecosystems from the intertidal to 300+ m depth in the ocean. As well as providing habitat, rhodolith beds are also major carbon sinks. As photosynthesizers, they take up carbon from the environment, perhaps helping to mitigate rising CO2 levels. However, most of our knowledge of coastal / benthic carbon cycling is based on shallow water systems. It is not yet known how coralline algae are able to photosynthesize in the low light levels of the deeper photic zone (known as the mesophotic) as so their role in carbon biogeochemistry remains unclear. The aim of this research is to elucidate the photosynthetic mechanisms of mesophotic algae in an effort to better understand its role in the global carbon cycle.
Supervisors: Dr Heidi Burdett & Dr Andrew Sweetman
Project title: High-sulphur source rock systems – expanding the potential of unconventional resources
Project abstract: Sulphur- and organic-rich deposits are becoming increasingly relevant as energy production from unconventional resources is rising globally. The phase association of sulphur is critical for the kinetic and conversion behaviour of organic matter in source rocks, with profound effects all the way from oil quality in reservoirs to production and final refining of crude, including risk assessment (e.g. H2S).
This project aims to improve our understanding of the conditions during and after deposition of different source rocks, their internal variability, and the effects these have on the phase association of sulphur up to the present day. All major sulphur phases will be characterised by the application of advanced (bulk and molecular) organic and inorganic techniques, including sulphur isotopes, bulk and molecular composition of organo-sulphur compounds, and advanced imaging.
Supervisors: Professor Thomas Wagner & Dr Ryan Pereira
Project title: Evaluation of Toxicity of New Generation Nanomaterials in Zebrafish
Project abstract: Engineered nanomaterials (NMs) are widely used in a variety of products that include electronics, medicine, and environmental applications. As a result of their small size, NMs have many unique and useful properties. Investigating the toxicity of NMs in the aqueous phase is dependent on establishing the physicochemical properties of the NMs and relating these properties to toxicological responses.
Future Nano Needs project “Framework to respond to regulatory needs of future nanomaterials and markets”, an EU FP7 supported investigation aimed at assessment of nanomaterial hazard and environmental impact assessment for next generation ENMs.
My thesis will address several hypothesis-driven objectives including the following: 1) evaluate relations between NP physicochemistry and acute toxicity of NMs in zebrafish with development of enhanced exposure methods; 2) investigate effects of associations between co-contaminants and NMs in aqueous phase and co-contaminant bioavailability; 3) evaluate effects of NM dietary exposure on tissue toxicity and changes in zebrafish gut microbiota.
Supervisors: Dr Ted Henry & Professor Teresa Fernandes
Project title: Ecotoxicity of Copper Nanomaterials on the benthic freshwater ecosystem
Project abstract: This research project is funded by the European FP7 project SUN “Sustainable Nanotechnologies” which aims to address the entire lifecycle of nanotechnologies to ensure ample nanosafety evaluation and incorporate the results into tools and guidelines for sustainable manufacturing, easily accessible by industries, regulators and other stakeholders.
Nanotechnology is a rapidly developing field and the commercial use of nanomaterials for novel applications continues to increase. Despite nanotechnology still being a developing area, today nanomaterials can be found in products used in our daily lives. Nanotechnology is recognised as a discipline in itself, because at the nanometre scale (between 1 and 100 nm) material can express novel properties totally different from their macroscopic counterparts; leading to greater interaction with molecules, cells and tissues and raising safety concerns. For this reason, many studies have started to address the potential risks to human health, ecosystems and organisms due to the intentional and unintentional release of nanomaterials (NMs) into the environment.
Copper oxide nanomaterials (CuO NM) are frequently employed for their antimicrobial properties in antifouling paints and other applications. Their extensive use can lead to contamination of aquatic ecosystems.
This PhD focus on the assessment of NM contamination of aquatic benthic systems by studying the effects of CuO NMs on a model test organisms, the snail Lymnaea stagnalis.
Based on an array of individual test systems using repeated dose exposures scenarios to CuO NM, multiple endpoints such mortality, behaviour and reproduction, and biomarkers such as metallothionein and heat shock proteins gene expression will be investigated.
The results will help inform the development of a cost-effective environmental service solution for low carbon management and improved occupant wellbeing in Scottish care homes.
Supervisor: Professor Teresa Fernandes
Rodriguez Perez, Ana
Project title: European oyster (Ostrea edulis) restoration: Marine Protected Areas and built structures
Project abstract: The European native flat oyster Ostrea edulis once formed vast beds along European coastlines that constituted a central ecological and socio-economic resource. These beds were biodiversity hotspots that mediated effective coastal ecosystem functioning, while harvesting of O. edulis contributed to food security and spurred local economies. Yet, centuries of overfishing, combined with more recent stressors such as coastal development, have led to the functional extinction of this habitat throughout most of its distribution range.
This project seeks to guide restoration efforts of this habitat by 1) finding suitable restoration sites in areas protected from the principal fishing pressure, such as MPAs and marine renewable energy development sites, 2) studying larval dispersal and settlement behaviour, in order to incorporate this knowledge into hydrodynamic models, and select restoration sites which can promote larval recruitment and connectivity between restored beds, and 3) studying the community development and biodiversity associated with O. edulis beds.
Supervisors: Dr William Sanderson, Dr Mark James (St. Andrews University) & Dr David Donnan (Scottish Natural Heritage)
Project title: Investigation of effects of the toxic cyanbacteria (Microcystis aeruginosa) on zebrafish reproductive system physiology at molecular, tissue, and whole organism levels of biological organization.
Project abstract: Cyanobacteria (blue-green algae) are photosynthetic organisms that can be present in freshwaters in extremely high numbers (blooms) and cause major environmental problems. Among cyanobacteria are Microcystis sp. which can produce and release hepatotoxins known as microcystins (MCs) along with other biologically active substances including endo/exotoxins [e.g., lipopolysaccharides (LPS)].
This project will investigate the effects of microcystin (MC) and Microcystis aeruginosa on zebrafish reproductive system physiology at molecular, tissue, and whole organism levels of biological organization.
Microcystis aeruginosa will be cultured in the laboratory and lyophilized in preparation for zebrafish exposure via diet and aqueous routes. Zebrafish will be exposed at different life stages to lyophilized cells of Microcystis aeruginosa in fish water. Then, the zebrafish embryos, larva, and adults male and female will be exposed to pure MC-LR in different doses, and to pure LPS. Concentrations of microcystin that accumulate in tissues of zebrafish will be assessed, and toxicological endpoints from gene expression, enzyme activity, and tissue histopathology will be assessed in male and female fish, and reproductive success will be evaluated for groups of exposed fish.
Supervisors: Dr Ted Henry and Dr Tony Gutierrez
Project title: Understanding the Biology of Cancer pagurus in relation to human and fisheries impacts.
Project abstract: Cancer pagurus is an important crustacean to the global fishing industry and is one of the most important commercial species in the UK. Despite their importance there are still large gaps in our understanding of their biology and ecology.
Recent studies have shown that mature female edible crabs have specific chosen sites for egg laying and undergo annual migrations along specific routes for larval dispersal. This information will be used with behavioural ecology work to determine if these areas could be at risk from future offshore and inshore developments and to try to obtain a better understanding of the larval stage of this species to aid in management schemes and fisheries data.
Information on the effect of both fisheries and other human impacts on this species are scarce. This work hopes to provide a clearer picture on what effect these different factors are having on a behavioural and physiological level to this important species and its life-cycle.
Supervisors: Dr Alastair Lyndon & Dr Dan Harris
Project title: The molluscan shell secretome: Unlocking Ca2+ pathways in a changing world
Project abstract: I'm interested in how life works. I aim to develop a mechanistic understanding of how biological molecules fit together into pathways, from genes to proteins, and then try to build-up the picture to the whole organism level. My research aims to understand how Antarctic and temperate clams build their shells using a multidisciplinary approach (transcriptomics, qPCR, in situ hybridisation, immunology, physiology, field work and experimentation).
Supervisors: Dr Melody S Clark, Professor Lloyd S Peck, Dr Liz A Dyrynda & Professor Val J Smith
Project title: Ecotoxicology of sunscreen on tropical corals in a changing ocean
Project abstract: Titanium dioxide nanoparticles (nTiO2) are common UV-filter ingredients in sunscreen. Between 4000 and 6000 tons of sunscreen are estimated to be released into coral reef areas annually thus posing a potential major threat to tropical corals.
Corals are known to be vulnerable to ocean acidification and increased seawater temperature driven by climate change, with mass coral bleaching becoming more frequent. Nevertheless, the combined effect of nTiO2 toxicity and climate change is unknown.
The aim of this project is to investigate the impact of TiO2 nanoparticles found in sunscreen on tropical corals, both host coral and isolated and in hospite algal symbiont (Symbiodinium sp.). The response of diverse Symbiodinium strains and coral species will be compared following exposures to different sunscreen formulations, nanoparticles coatings and different environmental conditions. Studies will address whether sunscreen toxicity change in interaction with projected future ocean conditions. Multiple endpoints to be investigated include symbiont density, photosynthetic activity, calcification, respiration, reactive oxygen species (ROS) production and heat shock proteins (HSP) expression.
Supervisors: Professor Teresa Fernandes & Dr Sebastian Hennige
Project title: The role of dissolved organic matter in Atmosphere-Land-Ocean interactions
Project abstract: Understanding how carbon is stored and transported along the land-ocean continuum is one of society's greatest challenges and an integral component of the global climate system. The advent of the industrial age has changed the way carbon is transported between the major stores on land and in the ocean by disturbing natural fluxes, creating new pathways and feedback mechanisms. Carbon cycling is intimately linked with the hydrological cycle through various chemical and physical processes across temporal and spatial scales, directly influencing the structure, composition and adaptation of ecosystems. Understanding these relationships between carbon and the water cycle and their effects on the environment and ecosystems is of central importance to improve our ability to better predict the consequences of global warming.
Supervisors: Dr Ryan Pereira and Dr Thomas Wagner
Project title: Ecological status of Scottish biogenic reefs. A case study of habitat degradation in Loch Creran (Argyll)
Project abstract: Loch Creran is designated as a Special Area of Conservation (SAC) for its bedrock reefs and biogenic reefs of the tube worm Serpula vermicularis and the horse mussel Modiolus modiolus. In 2005 HWU conducted an intensive study of the distribution and status of the serpulid reefs in Loch Creran (Moore et al. 2006). In 2014 we conducted a follow-up survey and documented a catastrophic decline in the extent and condition of these reefs (Tulbure 2015).
This PhD project will investigate the causes, consequences and significance of the observed changes to the reefs through (but not limited to) the following approaches:
- Surveys of reef areas to document the current condition of the habitats in comparison to those indicated in historical records.
- Focused studies seeking to establish the causes of reef decline.
- Studies of factors influencing the regeneration capacity of the reefs.
Supervisors: Dr Daniel Harries & Dr Alastair Lyndon
Project title: Environmental assessment of deep-water sponge fields in relation to oil and gas activities: a west of Shetland case of study
Project abstract: Constituting the phylum Porifera, sponges are filter-feeding organisms that perform a number of ecological functions. Widely distributed and diverse, they can form high density fields, supporting complex macrofaunal communities and can host an array of microorganisms.
Deep-water sponge fields are now considered Vulnerable Marine Ecosystems and Ecologically and Biologically Significant Areas. Their sensitivity to oil extraction activities in the Faroe-Shetland Channel Marine Protected Area (FSC MPA) where sponges are present close to offshore operations consequently needs to be investigated.
1. Complete visual surveys of sponge density and occurrence in the FSC MPA
2. Conduct experimental exposures to determine sponge response to oil/oil dispersant mixtures;
3. Analyse microbial community of deep-water sponges in the FSC MPA
This project is part of the NERC CDT in Oil and Gas and is funded by Heriot-Watt University, the British Geological Survey as well as Oil & Gas UK and is supported by BP.
Supervisors: Dr Ted Henry, Professor Murray Roberts & Sophie Green (BGS)
Project Title: Evaluating the application of commercially available regional-scale hydrodynamic modelling software to predict the effects of tidal stream energy extraction
Project abstract: Tidal stream power is a promising form of marine renewable energy that is under development in Scotland and elsewhere. There has been a great deal of research on the available energy resource, and a lesser amount on the environmental effects of extracting energy. This work has often used academic modelling codes that are not used in industry. This project examines how effects of tidal energy extraction can best be predicted using unaltered commercial software packages which are known and trusted by industry and investors.
It has three primary components:
1. A trial of simulating the Orkney area using MIKE 3 and Delft3D, two well-known commercial model codes.
2. An original improvement to the representation of tidal turbines in MIKE 3.
3. A case study of Lashy Sound, a channel in the Orkney Isles in which a tidal energy development is planned but which has been studied little in academic literature.
Supervisors: Dr David Woolf, Professor Jonathan Side & Dr Susana Baston
Project title: Who owns the sea?: Investigating trends and perceptions of enclosure and privatisation at sea
Project abstract: My research focuses on the need for enclosure and privatisation of ocean space/resources as a means of sustainable ‘blue' growth. I am investigating how current governance schemes, on both spatial (MSP and zoning) and non-spatial (ITQs and licences) levels, attempt to solve ongoing conflicts between environmental protection and economic development by way of redistributing property rights. Furthermore, I will look at how stakeholders and the public understand these changing rights, and whether these redistributions of rights are considered ‘fair' and ‘just'.
Supervisor(s): Dr Sandy Kerr and Dr Kate Johnson