Microbiomes for biodegradation of environmental micropollutants

Applications are invited for a PhD fellowship/scholarship at Graduate School of Science and Technology, Aarhus University, Denmark, within the ‘Environmental Sciences’ programme. The position is located in Roskilde and is available from 1 May 2018 or later.

Microbiomes for biodegradation of environmental micropollutants

Research area and project description:

The Department of Environmental Science, Aarhus University (AU), Roskilde, Denmark is offering a 3 year PhD position in microbial biotechnology as a part of the MicroDegrade project. The project will be focused on discovery and study of pure cultures or consortia of microorganisms (bacteria and/fungi) with potential for biodegradation of micropollutants, for instance pesticide residues, pharmaceuticals, personal care products, hormones, or industrial chemicals. This will involve the combined approach of state-of-the art molecular tools, newest environmental analytical chemistry platforms and cutting-edge cultivation techniques.

The PhD project will explore and investigate the biodegradation potential of microbial communities of varying environmental origin where the microbes have been pre-exposed to micropollutants e.g. wastewater, agricultural soil, sand filters or groundwater. Work will be conducted partly in laboratory microcosms and degradation will be measured with mass spectrometry techniques and/or as total mineralization by use of 14C-labelled compounds.

Promising microbial communities will be characterized by amplicon sequencing on Illumina MiSeq and NextSeq platforms. This will further enable targeted enrichment and isolation of degrader strains or consortia. Isolated single strains will be sequenced for genomic and plasmid composition, and identification of degrader genes will be performed.

Further work will include the elucidation of downstream degradation pathway genes as well as the activity and mechanisms (transcriptomics and proteomics) of degrader consortia.

The research will be conducted individually and in collaboration with other researchers in the Environmental Microbial Genomics group (http://envs.au.dk/instituttet/sektioner/embi/emg/) amongst others mainly at AU (Roskilde).

Research questions/tasks may include but are not limited to:

  • Isolation of single microbial strains (bacteria or fungi) or consortia able to degrade selected environmental pollutants
  • Next-generation sequencing of degrader strains or consortia
  • Elucidation of degrader genes and degradation pathways
  • In field collection of environmental samples containing relevant microbial communities
  • Laboratory microcosms experiments where degradation potential will be measured by mass spectrometry techniques and/or as total mineralization by use of 14C-labelled compounds
  • Investigate environmental stability of isolated microorganisms
  • Study of the activity and mechanisms of degrader consortia by transcriptomics and proteomics.


Qualifications and specific competences:

Applicants must have a Master of Science (MSc) degree in biology, biochemistry, microbiology, environmental chemistry or similar from an internationally recognized University with a research thesis in one or more of the following areas: microbiology, genetics or biotechnology.

We expect the candidate to have the following qualifications:

  • Practical experience with experimental microbiology and microbial genetics
  • Knowledge about biotechnology and biodegradation of xenobiotics (preferred)
  • Experience with next-generation sequencing, qPCR and bioinformatics (preferred)
  • Good collaboratory skills and team spirit
  • An excellent level of both spoken and written English to accommodate scientific communication and dissemination

Please indicate in the application form: ‘2/3 financing is in place from supervisors projects, applying for 1/3 from GSST’.

Only candidates that are found qualified for this financing will be offered the position.

Place of Employment and Place of Work:

The PhD student will be enrolled in Graduate School of Science and Technology (GSST) at Aarhus University, and the place of work is Department of Environmental Science, Frederiksborgvej 399, 4000 Roskilde (near Copenhagen), Denmark.


Applicants seeking further information are invited to contact:

Professor Lars Hestbjerg Hansen, e-mail: lhha@envs.au.dk or Researcher Lea Ellegaard-Jensen, e-mail: leael@envs.au.dk


Application procedures

Before you apply

Information and attachments:

Please be aware that you must have all relevant appendices, attachments, addresses for referees, etc. ready when you apply, as the entire application must be uploaded to the system in one go.

Documentation of language skills:

The English language requirement at Graduates School of Science and Technology is comparable to an “English B level” in the Danish upper secondary school (“gymnasium”).

English language qualifications comparable to an “English B level” is documented by one of the following tests:

  • TOEFL test, minimum score: 560 (paper-based test) or 83 (internet-based test). The paper-based test must have a “total score”. From August call 2019, GSST no longer accepts the paper-based test.
    Aarhus University does not accept the TOEFL ITP test. Aarhus University’s TOEFL code is 8935. You must request that the test centre send your test results to Aarhus University, in order to enable verification of your test results.
  • IELTS (academic) test, minimum average score: 6.5 points
  • Cambridge English Language Assessment:
    Cambridge Certificate of Proficiency (CPE)
    Cambridge English: Certificate of Advanced English with grade A,B or C (CAE)
    Cambridge English: First Certificate  with grade A (FCE)

When to take the test and how to upload the documentation:
The test result must not be more than two years old at the time of application.

The English language test should be taken before applying for admission and uploaded under “language skills documentation” in the online application form.

It is possible to apply for admission before you have taken the test. In this case documentation stating that you have signed up for a test (please state expected submission date) must be uploaded. If the test result is not part of the original application the test result is to be sent to sphd@psys.au.dk no later than one month after the application deadline.

The following applicants are exempted from documenting their English qualifications/taking a test:

  • Applicants with citizenship from the following countries: Australia, Canada, Ireland, New Zealand, United Kingdom, United States, or one of the Nordic countries (Denmark, Finland, Iceland, Norway or Sweden).
  • Applicants with a Bachelor’s or Master’s programme completed in Australia, Canada, Ireland, New Zealand, United Kingdom, or United States. In this case, please upload your Bachelor’s or Master’s diploma under the section ”Language skills documentation”.
  • Applicants with a Bachelor’s or Master’s programme completed at Aarhus University for which the requirement was English B level at the time of admission. In this case, please upload your Bachelor’s or Master’s diploma under the section”Language skills documentation”.
  • Applicants able to document that English was the language of instruction during the whole period of their Bachelor’s and/or Master’s programme. This must be documented by uploading an official document from the institution stating this under “language skills documentation”. The onus is on the applicant to provide this information as GSST will not pursue information regarding language of instruction for any programmes or institutions.


The programme committee may request further information or invite the applicant to attend an interview.

How to apply:

1)      Find the application form:
Go to http://talent.au.dk/phd/scienceandtechnology/opencalls/
Choose February 2018 Call with deadline 1 February 2018 at 11.59 PM MET.
You will be directed to the call, and must choose the programme 'Environmental Science'  

2)      Fill in the following information:

  • Personal information
  • Academic background
  • Admission
  • Financing (if any)
  • Study: In the dropdown menu you must choose the project: "Microbiomes for biodegradation of environmental micropollutants"
  • Source (how you found out about the call)

Next to some of the information fields you will find a number. Click on the number to get further directions on how to fill in the information field/what information is needed.

3)      Application attachments:

Please be aware that you cannot submit the application if one or several of these documents have not been uploaded.

If you wish to upload more than one document under each section, you must scan/merge all documents into one large PDF file and upload this. Please note that we reserve the right to remove scientific papers, large reports, theses and the like. Instead you can indicate a URL where the information is available.

Please note that all information in the application must be in Danish or English.

As a minimum all applications must include (pdf-files only, max. 20 MB, no zip):

  • One reference (template for references)
  • Curriculum vitae,
  • Motivation (max. 1 page)
  • Transcripts and diploma(s)
  • Project description (½-4 pages). This document should describe your ideas and research plans for this specific project. If you wish to, you can indicate an URL where further information can be found. Please note that we reserve the right to remove scientific papers, large reports, theses and the like.
  • Documentation of language skills if required.

After submission of the application, you will receive a confirmation e-mail with an application ID, you should use for reference if needed. The e-mail will also include a link to the application – GSST urges you to check that all mandatory data, marked with an asterisk (*), is registered correctly and all attached files are readable. In case of significant errors, you should reply to the confirmation e-mail with the correct details before the application deadline.

GSST reserves the right to verify the authenticity of your educational diploma and transcripts:

  • Request additional information to verify an application.
  • Reject the application if it is proven, or if the University has reasonable belief, that the information provided is false or if the applicant refuses to provide the requested information, whether or not an offer has already been made. 
  • For further information on applying, assessment procedures, etc. please see the GSST application guide here  

Please note:

  • The programme committee may request further information or invite the applicant to attend an interview.
  • The project will only be initiated if final funding (from GSST/the faculty) is secured.

All interested candidates are encouraged to apply, regardless of their personal background.