PhD Studentship: Eat in or eat out? The role of plant communities for microbial metabolic activity

United Kingdom
Dec 04, 2017
Jan 05, 2018
Organization Type
University and College
Full Time

Dr Marc Dumont (Biological Sciences, UoS), Dr Vincent EJ Jassey (University of Toulouse, France)


Application Deadline:

5 January 2018


PhD Description:

Plant community composition has a large influence on microbial community composition 

  1. Recently, we have shown that peatland plant functional groups are associated to specific microbial communities 
  2. What is not understood is if plants create a selective environment select for microbial communities that specialize on plant–specific resources (i.e. exudates or plant litter). As a first step, this project will study the link between plant species composition and the microbial community. A close plant–microbe link could entail microbial specialisation (i.e. adaptation) on plant–specific resources, causing negative priming 
  3. ultimately increasing the robustness of the peatland carbon sink capacity.


The absence of specific plant-microbe links could indicate the microbes are generalists, suggesting the plant community to not impact the carbon sink-strength. This PhD project is structured to first determine the link between plant community (functional) composition and the microbiome at a molecular level. Next, the project aims to assess the functional identity of peatland microbial communities, and will address the question as to whether the latter are functionally adapted to the local, plant–specific, conditions, irrespective of environmental context. This project will highlight how the presence or absence of specific plant-microbe linkages affects ecosystem processes, guiding peatland conservation strategies



Taking a multidisciplinary approach – combining community ecology, molecular microbiology and molecular biochemistry – this project will provide deeper understanding on the role of plant community assembly in defining microbial community structure and function (e.g. carbon and nitrogen cycling, organic chemistry). The primary resource for this work will be a long-term plant removal experiment in the Store Mosse peatland in Southern Sweden, to study the presence/absence of specific plant-microbe links. Further, a series of lab/mesocosm experiments will allow to test if peatland microbiomes are adapted to plant exudates or if they are generalists. 

The student will use molecular and microscope techniques to detail the microbial community associated to distinct plant communities, and it relation to soil properties (e.g. organic chemistry, nutrient stoichiometry). Stable isotopes (13C, 15N) will be used to elucidate mechanistic links between plants and microbes. The functionality and structure of the microbial communities will be further studied using in- and ex-situ physiological profiling techniques (e.g MicroRespTM), gas flux measurements, and food-web modeling. Controlled mesocosm, re-assembly experiments, and lab-incubation experiments (using leachates from different plant communities) will be necessary to establish if microbial communities are functionally adapted to local environments, and will later constitute the thesis chapters. 



The SPITFIRE DTP programme provides comprehensive personal and professional development training alongside extensive opportunities for students to expand their multi-disciplinary outlook through interactions with a wide network of academic, research and industrial/policy partners. The student will be registered at the University of Southampton and hosted at the University of Southampton, Biological Sciences. Specific training will include: 

  • an initial literature review/meta-analysis. 
  • a visit to the University of Toulouse, EcoLab, to get training in microbial food–web modeling and techniques to determine microbial functional diversity.
  • setting-up experiments and analyzing results in the R statistical environment.
  • molecular techniques to study microbial diversity.
  • measuring and analyzing plant functional traits.
  • training in isotopic tracer techniques, GHG measurements, ecophysiological profiling, and enzymatic activity to study the functionality of microbial communities.


We expect the student to maintain existing collaborations with the staff of the Store Mosse National Park, and to exchange results and translate them to conservation practice. 


  1. Grigulis K et al. (2012) Journal of Ecology, 101, 47–57.
  2. Robroek BJM, et al. (2015) Journal of Ecology, 103, 925–934.
  3. Kuzyakov Y, Friedel JK and Stahr K (2000) Soil Biology and Biochemistry, 32, 1485–1498.


For more information:


Funding Notes:

The project is funded for 3.5 years and welcomes applicants from the UK and EU (EU applicants need to have been residents in the UK for at least 3 years prior to application), who have or expect to obtain at least an upper second class degree (BSc or MSc) in Biological Sciences or allied subjects. Funding will cover fees and a stipend at current research council rates of £14,553 per annum for 2017-18, subject to rise for 2018-19 entrants.

Due to funding restrictions, this position is only open to UK/EU applicants who have been resident in the UK for at least 3 years prior to application. 


Please place Bjorn Robroek’s name in the field for proposed supervisor. 

General enquiries should be made to Bjorn Robroek at or Marc Dumont at Any queries on the application process should be made to 

The University of Southampton and Biological Sciences both hold an Athena Swan Silver Award demonstrating their commitment to provide equal opportunities and to advance the representation of women in STEM/M subjects: science, technology, engineering, mathematics and medicine. Due consideration will be given to applicants who have taken a career break. University benefits include onsite childcare facilities, state-of-the-art on-campus sports, arts and culture facilities, a full programme of events and a range of staff discounts.

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