Unlocking the Toolbox of Soil Bacterial Biomarkers


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  Dr D Read, Dr J Bendle  No more applications being accepted  Funded PhD Project (European/UK Students Only)

About the Project

A wide range of environmental information from both terrestrial and marine realms is required from palaeoclimate archives to better understand the climate system and to provide a palaeoclimatic context for predictions of future rates of climate change. To address this, a range of organic biomarkers have become widely deployed tools in the reconstruction of past environmental conditions, especially in the marine realm. Most of these biomarker proxies are based on the physiological responses of bacterial or unicellular eukaryote cell membranes and lipids to the external environment. One such suite of proxies is the 3-hydroxy fatty acids (3-OH-FAs), which derive from lipopolysaccharide (LPS), the main component of the outer membrane of Gram-negative bacteria. However, the relationship between 3-OH-FAs, the species that produce them and environmental parameters has not been systematically investigated.

This project will take place in the context of a collaborative Leverhulme funded project between the University of Birmingham and the Centre for Ecology & Hydrology (CEH) in Oxfordshire, investigating the development of 3-OH-FAs as palaeoclimate biomarker proxies. Based at CEH, you will uniquely attempt to understand the ecological factors affecting the geographic distribution of lipid biomarkers (3-OH-FAs), by coupling biological assessments of microbial communities with geochemical data collected by the project. Specifically, you will attempt to identify which organisms are responsible for the strong relationship of 3-OH-FA distributions with climate, what drives their distribution and what is the underpinning ecological cause of these relationships? To our knowledge this is a global first and will give the PhD student a unique and marketable skills set.

Outcomes for will include a) constraining the influence of bacterial community diversity on 3-OH-FA distributions in both soils and lake settings; b) new landscape scale transects of bacterial distributions (and their first-order environmental controls) ; c) detailed molecular tracing of modern terrestrial biological material into lake sediments validating the fatty acid biomarker approaches; d) working with Bendle (University of Birmingham) a PDRA and a PhD student at Birmingham to deliver new paleoclimate data-sets that couple both geochemical and biological assessments of bacterial diversity. There will also be opportunities for the candidate to explore novel ancient eDNA approaches to date lake sediments complementing the fatty acid biomarker approaches and participation in related field campaigns for sample collection will be supported.

At the end of the Ph.D. you will have developed a strong skill set in the fields of molecular ecology, bioinformatics and paleoecology and will receive training in the methodologies for generating and interpreting community sequencing data, as well as statistical methods (including multivariate testing and source tracking of indicative taxa, spatial upscaling and mapping). These will be provided both in house at CEH and through links with the CENTA DTP PhD training cohort. At CEH, you will have access to modern molecular biology facilities, including in house sequencing, dedicated high performance computing facilities and bespoke bioinformatic platforms. You will be registered at the University of Birmingham (UoB), but will primarily based at the Centre for Ecology & Hydrology in Wallingford. Dr Daniel Read (CEH) will be lead supervisor with Bendle (Birmingham) the 2nd supervisor.

Applicants for a studentship must have obtained, or be about to obtain, a 2.1 degree or higher. If you have a 2.2 degree, but have also obtained a masters qualification, you are also eligible. Substantial relevant post-graduate experience may also be sufficient, please contact the supervisors for more information. We welcome applications from UK and EU students, students from outside of the EU are not eligible. An applicant needs to demonstrate that (a) from 1st September 2018 they are an EU national, (b) they have been ordinarily resident in the EEA for the three years prior to 1 September 2018, and (c) that the main purpose of such residency was not to receive full-time education.

To apply please send your CV and a covering letter to Daniel Read ([Email Address Removed]) and James Bendle ([Email Address Removed]) describing your academic background, experience and suitability for the project.

Funding Notes

This research project has funding attached. Applications for this project are welcome from suitably qualified candidates worldwide. Funding may only be available to a limited set of nationalities and you should read the project details for further information.