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Funded PhD Opportunity

Antibiotic resistance in aquatic sediments: Persistence and proliferation

Subject: Geography, Environmental Studies and Archaeology


The reservoir function of aquatic sediments for environmental bacteria is now being utilised for pollution monitoring (Bragina, et al. 2017). Sediment sampling is also a potential strategy for monitoring antibiotic resistance in aquatic systems. Accumulation of antibiotic resistant bacteria and resistance genes has been substantiated in the vicinity of wastewater discharge sites (e.g. Czezalski et al, 2014) and there is evidence for impacts of antibiotics in therapeutic concentrations on ecosystem processes (Roose-Amsaleg & Laverman, 2016).

However, there are many unexplained questions regarding the role of aquatic sediments in persistence and proliferation of antibiotic resistance at subinhibitory concentrations typically encountered in natural settings. Even the conventional assumption that sediments are hotspots of antibiotic resistance and for horizontal resistance transfer cannot be universally applied (Hess et al 2018).

These knowledge gaps severely constrain the regulatory environment. Often government agencies still rely on published acute toxicity levels as their only reference for setting environmental limits for antibiotic substances. An advance in regulatory practice towards a more comprehensive reflection of the environmental impact of antibiotics requires the investigation of effects by particulate matter on antibiotic resistance and resistance transfer in aquatic systems.

Therefore this study aims to characterize model systems for benchscale investigations of bacterial antibiotic resistance in aquatic sediments. These systems will be applied to investigate the persistence and proliferation of antibiotic resistance in different regimes of nutrient provision, physical, chemical and biological disturbance and with different sediment characteristics.


1) Investigation of attachment and growth of target bacteria depending on characteristics of model sediments

2) Comparison of strain specific growth rates depending on disturbance amplitude and frequency

3) Monitoring of resistance gene frequency in bacterial communities depending on disturbance regime and ‘founder effects’

4) Assessment of antibiotic resistance transfer efficiency depending on sediment charcteristics and disturbance regimes

The study will involve the design of test systems, characterisation of sediments, application of phenotypic and genetic characterisation of bacteria and the cultivation of invertebrate test organisms.

Bragina, L, Sherlock, O, van Rossum, AJ and Jennings, E (2017) Cattle Exclusion using Fencing Reduces Escherichia coli (E. coli) Level in Stream Sediment Reservoirs in Northeast Ireland. Agriculture, Ecosystems and Environment, 239, 349-358

Czekalski, N, Gascon Diez, E & Burgmann, H (2014) Wastewater as a point source of antibioticresistance genes in the sediment of a freshwater lake. ISME J. 8, 1381–1390

Heß S, Berendonk TU, Kneis D (2018) Antibiotic resistant bacteria and resistance genes in the bottom sediment of a small stream and the potential impact of remobilization FEMS Microbiol Ecol. 94(9). doi: 10.1093/femsec/fiy128.

Roose-Amsaleg C, Laverman AM (2016) Do antibiotics have environmental side-effects? Impact of synthetic antibiotics on biogeochemical processes Environ. Sci. Pollut. Res., 23 (2016), pp. 4000-4012

Essential criteria

  • Upper Second Class Honours (2:1) Degree or equivalent from a UK institution (or overseas award deemed to be equivalent via UK NARIC)
  • A comprehensive and articulate personal statement

Desirable Criteria

If the University receives a large number of applicants for the project, the following desirable criteria may be applied to shortlist applicants for interview.

  • First Class Honours (1st) Degree
  • Masters at 65%
  • Research project completion within taught Masters degree or MRES
  • Experience using research methods or other approaches relevant to the subject domain
  • Work experience relevant to the proposed project
  • Experience of presentation of research findings


    Vice Chancellors Research Scholarships (VCRS)

    The scholarships will cover tuition fees and a maintenance award of £14,777 per annum for three years (subject to satisfactory academic performance). Applications are invited from UK, European Union and overseas students.


    The scholarship will cover tuition fees at the Home rate and a maintenance allowance of £ 14,777 per annum for three years. EU applicants will only be eligible for the fees component of the studentship (no maintenance award is provided).  For Non EU nationals the candidate must be "settled" in the UK.

Other information

The Doctoral College at Ulster University


Completing the MRes provided me with a lot of different skills, particularly in research methods and lab skills.

Michelle Clements Clements - MRes - Life and Health Sciences

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I would highly recommend Ulster University as you get so much support.  Coleraine is a beautiful town and the people are so friendly. It was a really positive experience.

Carin Cornwall - PhD Environmental Sciences

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Key dates

Submission deadline
Monday 18 February 2019

Interview Date
w/c 18 March 2019


Coleraine campus

Coleraine campus
Our coastal and riverside campus focussing on science and health

Contact supervisor

Dr Joerg Arnscheidt

Other supervisors


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