About the Project
The vast microbial diversity in natural environments underpins the global ecosystem functioning on earth. The central aim of this project is to understand the largely underexplored physiological and ecological processes that generate high microbial functional diversity in nature, with a special focus on a functionally important group of archaea, the Thaumarchaeota, that play a key role in the nitrogen cycle. Their high diversity and abundance, together with our recent demonstration of the influence of pH on both niche specialisation (Gubry-Rangin et al., 2011; Vico-Oton et al., 2016) and lineage formation through deep evolutionary time (Gubry-Rangin et al., 2015), provide an excellent system to address this aim. The paucity of cultivated representatives has severely limited their investigation, but this restriction can now be alleviated by major recent technical innovations in single cell genome sequencing and cultivation techniques (informed by genomic data) enabling physiological studies. Better knowledge about an abundant, globally distributed but unexplored and uncultivated group of Thaumarchaeota that dominate ammonia oxidiser communities in many agricultural neutral and alkaline soils seems crucial to unravel their ecophysiology and contribution to soil nitrification and greenhouse gas emission. By using a single-cell genomics-driven cultivation approach, the physiological mechanisms implicated in thaumarchaeotal alkaline adaptation will be determined, and novel isolates will in turn allow further experimental physiological studies. The suggested mechanisms allowing growth, activity and preferential selection over the other nitrifying communities will finally be tested in many alkaline soils. This ambitious project will strongly impact on our fundamental knowledge of the general integrated ecological-functional mechanisms of adaptation that generate high microbial diversity in nature, using Thaumarchaeota as a model.
The University of Aberdeen Nitrification Group, headed by Prof. James Prosser (https://www.abdn.ac.uk/ibes/people/profiles/j.prosser) and Dr Cécile Gubry-Rangin (https://www.abdn.ac.uk/ibes/people/profiles/c.rangin), is a well-established group with world-wide recognised reputation in microbial ecology and a high-impact track record.
The PhD student will join a dynamic team of researchers within the Institute of Biological and Environmental Sciences (https://www.abdn.ac.uk/ibes/) and the School of Biological Sciences (http://www.abdn.ac.uk/sbs/). The University of Aberdeen (UoA) was ranked 1st in the UK by the ‘Agriculture, Veterinary and Food Science’ REF2014 exercise and provides an excellent scientific environment. In addition, the University of Aberdeen provides state-of-the-art technological support facilities with a unique single-cell genomics platform, highly-specialised cytometry and genomic platforms, an exclusive thaumarchaeotal culture collection, molecular and environmental facilities and a High Performance Computing system. The University of Aberdeen also provides diverse training opportunities for all aspects of research and for transferable academic and generic skills. The academic requirement for entry is a first or upper second class degree or equivalent.
For any inquiry, please send an email describing your research interests directly to the principal investigator Dr Cécile Gubry-Rangin ([Email Address Removed]).
Application Process:
Please apply for admission to the ’Degree of Doctor of Philosophy in Biological Science’ to ensure that your application is passed to the correct college for processing.
Please provide a copy of the degree certificate and transcript for each previous degree undertaken, a copy of your English language proficiency certificate (if relevant), and contact details of two referees who can comment on your previous academic performance (at least one should be from your current degree programme). References will be requested if you are selected for interview. Incomplete applications will not be considered.
Funding Notes
These studentships are available to UK and other EU nationals and provides funding for tuition fees and stipend, subject to eligibility.
Candidates should have (or expect to achieve) a minimum of a 2.1 Honours degree in a relevant subject. Applicants with a minimum of a 2.2 Honours degree may be considered provided they have a Distinction at Masters level.
References
Gubry-Rangin C, Hai B, Quince C, Engel M, Thompson BC, James P, Schloter M, Griffiths RI, Prosser JI, Nicol GW. (2011) Niche specialization of terrestrial archaeal ammonia oxidizers. Proc Natl Acad Sci USA 108(52):21206-21211.
Gubry-Rangin C, Kratsch C, Williams TA, McHardy AC, Embley TM, Prosser JI, Macqueen DJ. (2015) Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota. Proc Natl Acad Sci USA 112(30):9370-9375.
Lehtovirta-Morley LE, Ross J, Hink L, Weber E, Gubry-Rangin C, Thion C, Prosser JI, Nicol GW. (2016) Isolation of ‘Candidatus Nitrosocosmicus franklandus’, a novel ureolytic soil archaeal ammonia oxidiser with tolerance to high ammonia concentration. FEMS Microbiol Ecol 92(5):fiw057.
Lehtovirta-Morley LE, Stoecker K, Vilcinskas A, Prosser JI, Nicol GW. (2011) Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil. Proc Natl Acad Sci U S A 108(38):15892-7.
Vico Oton E, Quince C, Nicol GW, Prosser JI, Gubry-Rangin C. (2016) Ecological coherence and phylogenetic congruence in Thaumarchaeota. ISME J 10(1):85-96.