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PhD projects

If you are interested in carrying out PhD research in my group, I would be pleased to hear from you before you submit an application.

For enquiries regarding two project outlines given below, or to discuss other potential projects in my group, please feel free to email me at H.Schaefer@warwick.ac.uk.


Competitive funding available from NERC Central England Training Alliance (NERC-CENTA)
APPLICATION DEADLINE 22 January 2018

PROJECT 1: Can urban air quality be improved through the use of plant associated bacteria?

Supervisors: Hendrik Schäfer (Warwick), Gary Bending (Warwick) & Tijiana Blanusa (Royal Horticultural Society)

Over 90% of the UK population is urban and thus facing a range of urban-specific environmental challenges (higher temperatures, increased flooding risks, reduced air quality). Green infrastructure can help mitigate some of these challenges, but the choice of planting can have significant impact on the extent of benefits. Plants with certain structural and functional properties (hairy leaves, large leaf areas, high transpiration rate) tend to provide higher level of services. Of particular interest are ecosystem services related to the mitigation of air pollution. Air pollution causes millions of premature deaths and is an important issue in metropolitan areas worldwide. Air pollutants include a number of volatile species, such as NOx, SO2, carbon monoxide and a range of volatile organic compounds. In addition, particulate matter (PM) is a major concern for air quality and public health. PM are produced from natural and anthropogenic processes, the latter including transport emissions.

The role of vegetation in maintaining and improving air quality is undisputed, but the underlying mechanisms are not fully understood at present. One such mechanism involves the trapping and removal of pollutants from the atmosphere, such as PM, but also in providing a habitat for plant associated microbial communities in the phyllosphere (above ground parts of plants); these bacteria too can act to remove and metabolise some of these gaseous pollutants. Building on previous research at RHS and Warwick, we are keen to test the potential of plants and bacteria to contribute to air quality improvement. The ability of plants to trap particulate matter is enhanced by properties such as having hairy leaves. Trapped PM may remain bound to the leaf structure or can be transferred into soil by being washed off by rain water. Research at RHS has highlighted hairy-leaved plants like Stachys and Salvia species to be beneficial for PM trapping.

Bacteria inhabiting the above ground parts of plants, the so-called phyllosphere, have the potential to degrade atmospheric volatile compounds and may contribute to degradation of volatile pollutants and chemicals bound to PM. Ongoing research at Warwick has shown microbial communities associated with tree leaves to degrade para-nitrophenol (PNP; Palmer, Bending, Schäfer, unpublished), a dominant atmospheric nitrophenol, which is a component of particulate matter from diesel engines. We have also observed phyllosphere microbiota to be capable of carbon monoxide degradation.
In this PhD project you will address fundamental aspects of plant-bacterial partnerships and their potential to mitigate air pollutants. Key questions to be addressed are how the presence of leaf hairs affects microbial colonisation of the phyllosphere and how the microbiota interacts with the plant and atmospherically derived pollutants. This will be carried out with plants previously identified as providing a high level of ecosystem services within green infrastructure (Stachys and Salvia spp.). Interestingly, these plants also have high content of phenolic compounds, which may affect colonisation of the phyllosphere, but may also prime the microbiota to degrade plant and atmosphere derived phenolic compounds. Suitable comparisons will be done with ‘control’ plants lacking hairy leaves/phenolic content. Overall, you will assess whether the extent of ecosystem services delivery by these plants can be enhanced through the air pollutant degradation via partnership with specific microorganisms.

Download full project description here.


PROJECT 2: Is there a cryptic organosulfur cycle in benthic marine environments?

Supervisors: Hendrik Schäfer and Yin Chen (School of Life Sciences, Warwick)

Coastal saltmarshes are important environments for the cycling of organic matter. They are a source and sink for a number of atmospheric trace gases including volatile organic sulphur compounds such as dimethylsulfide (DMS) and methanethiol (MT), methyl halides and methane important as climate active gases or ozone depleting compounds.

stiffkey_saltmarsh_wide.jpg

Saltmarsh environment of the lower marsh at Stiffkey (at low tide) with tidal creeks and pools,
illustrating a hotspot for organic sulfur cycling

Previous work in the Schäfer group has identified methylotrophic bacterial populations in the Stiffkey saltmarsh (Norfolk, UK) that utilise DMS as a carbon and energy source (Schäfer, personal communication). Another fate of DMS degradation is its oxidation to dimethylsulfoxide. Bacterial groups that have been shown capable of DMS to DMSO oxidation including anoxygenic phototrophs such as Rhodovulum sulfidophilum (using DMS dehydrogenase ddhA) heterotrophs that utilise DMS as an energy source (eg Sagittula stellata) and aerobic heterotrophs like Ruegeria pomeroyi which co-oxidatively convert DMS to DMSO using the enzyme trimethylamine monooxygenase (Tmm) dependent on the presence of methylated amines.

DMSO produced as described above is then available to act as a terminal electron acceptor for anaerobic respiration through the action of DMSO reductases which reduce DMSO to DMS. Despite many years of study of DMSO reductases and closely related (and functionally equivalent) trimethylamine N-oxide (TMAO) reductases, very little is known about the role of DMSO reduction as a terminal pathway of carbon turnover in anoxic sediments.
Although the potential for DMSO (and TMAO) reduction in anoxic habitats is widely distributed, neither the populations responsible for DMSO/TMAO reduction nor the relative importance of this pathway to overall anaerobic respiration in sediments has been determined previously, constituting another area of fundamental lack of understanding related to DMSO reduction.

Given that DMSO reduction under anaerobic conditions produces DMS, it is conceivable that the DMS thus formed may undergo re-oxidation to DMSO in the surface sediment constituting a full cycle of DMS to DMSO oxidation and DMSO to DMS reduction.


The aim of this project is to investigate how taxonomically and functionally diverse bacteria contribute to DMS/DMSO cycling in saltmarsh sediments, and how they contribute to organic carbon degradation under anaerobic conditions.

Download full project description here.


Applying for projects?

More information about how to apply is available on our Warwick NERC studentships website, if so, please also contact me prior to submitting an application (H.Schaefer@warwick.ac.uk) . Enquiries and applications are also welcome from candidates holding their own funding.