PhD Study : Antibiotic resistance in aquatic sediments: Persistence and proliferation

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Summary

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.

Objectives:

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

Applicants should hold, or expect to obtain, a First or Upper Second Class Honours Degree in a subject relevant to the proposed area of study.

We may also consider applications from those who hold equivalent qualifications, for example, a Lower Second Class Honours Degree plus a Master’s Degree with Distinction.

In exceptional circumstances, the University may consider a portfolio of evidence from applicants who have appropriate professional experience which is equivalent to the learning outcomes of an Honours degree in lieu of academic qualifications.

  • 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

Funding and eligibility

The University offers the following levels of support:

Vice Chancellors Research Studentship (VCRS)

The following scholarship options are available to applicants worldwide:

  • Full Award: (full-time tuition fees + £19,000 (tbc))
  • Part Award: (full-time tuition fees + £9,500)
  • Fees Only Award: (full-time tuition fees)

These scholarships will cover full-time PhD tuition fees for three years (subject to satisfactory academic performance) and will provide a £900 per annum research training support grant (RTSG) to help support the PhD researcher.

Applicants who already hold a doctoral degree or who have been registered on a programme of research leading to the award of a doctoral degree on a full-time basis for more than one year (or part-time equivalent) are NOT eligible to apply for an award.

Please note: you will automatically be entered into the competition for the Full Award, unless you state otherwise in your application.

Department for the Economy (DFE)

The scholarship will cover tuition fees at the Home rate and a maintenance allowance of £19,000 (tbc) per annum for three years (subject to satisfactory academic performance).

This scholarship also comes with £900 per annum for three years as a research training support grant (RTSG) allocation to help support the PhD researcher.

  • Candidates with pre-settled or settled status under the EU Settlement Scheme, who also satisfy a three year residency requirement in the UK prior to the start of the course for which a Studentship is held MAY receive a Studentship covering fees and maintenance.
  • Republic of Ireland (ROI) nationals who satisfy three years’ residency in the UK prior to the start of the course MAY receive a Studentship covering fees and maintenance (ROI nationals don’t need to have pre-settled or settled status under the EU Settlement Scheme to qualify).
  • Other non-ROI EU applicants are ‘International’ are not eligible for this source of funding.
  • Applicants who already hold a doctoral degree or who have been registered on a programme of research leading to the award of a doctoral degree on a full-time basis for more than one year (or part-time equivalent) are NOT eligible to apply for an award.

Due consideration should be given to financing your studies. Further information on cost of living

The Doctoral College at Ulster University

Key dates

Submission deadline
Monday 18 February 2019
12:00AM

Interview Date
w/c 18 March 2019

Preferred student start date
September 2019

Applying

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Contact supervisor

Dr Joerg Arnscheidt

Other supervisors