Arbetsbeskrivning

Department of Aquatic Sciences and Assessment

Third-cycle subject area

Biology

Description of the doctoral project

Antimicrobial resistance (AMR) is one of the most pressing global health challenges of our time. A key driver of AMR spread is the horizontal transfer of antibiotic resistance genes via conjugative plasmids — mobile genetic elements that move between bacteria. Plasmid-dependent phages (PDPs) are viruses that specifically infect bacteria carrying these plasmids, making them a potentially powerful but largely overlooked tool in controlling resistance gene transmission.

This PhD project is part of ECOPHARM, a research project funded by the Knut and Alice Wallenberg Foundation (Wallenberg Academy Fellows 2025) and is based at the Department of Aquatic Sciences and Assessment, SLU Uppsala. The overarching aim of ECOPHARM is to decipher the mechanisms driving PDP interactions with conjugative plasmids and bacterial hosts, and to understand their impact on antibiotic resistance gene transmission in aquatic environments.

As a PhD student, you will investigate the diversity, ecology, and functional interactions of plasmid-dependent phages in aquatic ecosystems. The work will combine environmental sampling, cultivation-based approaches, metagenomics, genome analysis, and experimental infection assays. You will work in a dynamic and internationally connected research environment at the intersection of microbial ecology, virus-host coevolution, and AMR research. To learn more about our research you can check out our webpage https://www.bionomics-mmlab.com/

About the position

The PhD student will be expected to:

• Design and carry out field sampling of aquatic environments to characterize PDP communities
• Perform laboratory experiments to study PDP–plasmid–host interactions under controlled conditions
• Apply metagenomic and bioinformatic tools to analyze microbial and viral community data
• Contribute to experimental work on phage isolation, cultivation, and infection assays
• Present findings at lab meetings, national and international conferences, and contribute to scientific publications
• Adhere to lab policies on data management practices
• Communicate progress and bottlenecks timely and clearly
• Collaborate with national and international project partners within the ECOPHARM network

Requirements

To meet the general entry requirements you must have been awarded a second-cycle (Master's) qualification, satisfied the requirements for courses comprising at least 240 credits of which at least 60 credits were awarded in the second-cycle, or acquired substantially equivalent knowledge in some other way in Sweden or abroad ( Higher Education Ordinance 1993:100, Chapter 7, Section 39).

Specific entry requirements for the third-cycle courses and study programme in biology. To meet the specific entry requirements, you must have at least 90 HEC in biology-related subjects. This must include a degree project and at least 30 HEC must be at second-cycle level.

You must also meet the equivalent English language requirements as those necessary for the Swedish upper-secondary qualification Engelska B/6.

Your profile

Required:

• A Master's degree in microbiology, biology, molecular biology, environmental science, or a closely related field
• Solid background in microbiology or molecular biology
• Experience with laboratory techniques relevant to microbial or environmental research
• Proficiency in written and spoken English

Highly desirable:

• Experience with bioinformatics or computational analysis of sequencing data
• Familiarity with phage biology, plasmid biology, or antimicrobial resistance research
• Experience with aquatic or environmental sampling

Personal qualities we are looking for:

• High agency — you take initiative, define problems independently, and push work forward engaging your supervisor
• Collaborative mindset — you contribute actively to a team environment and support those around you
• Clear communicator — you can convey complex ideas in writing and in person, to both specialist and non-specialist audiences
• Curiosity, rigor, and resilience in the face of scientific uncertainty

About us

The Department of Aquatic Sciences and Assessment is working with applied environmental science, with a national responsibility for assessing the condition of Swedish surface waters with respect to water chemistry, pollution and aquatic biota. The research focuses on geochemical and hydrological processes, aquatic ecology and biodiversity, microbial ecology as well as on environmental chemistry and aquatic ecotoxicology. The department has about 150 employees, of which approximately half are researchers/doctoral students and the other half are technical and administrative staff.

For more information about the department visit: http://www.slu.se/aquatic-sciences

Read more about staff benefits and life as an SLU employee on https://www.slu.se/om-slu/jobba-pa-slu/

Read more about third-cycle courses and study programmes on http://www.slu.se/utbildning/program-kurser/forskarutbildning/

Form of employment / Funding

Employment as a doctoral student (4-year programme)

Doctoral student's salaries are set following the local collective agreement. Salary progression is fixed.

Location:

Uppsala

Scope:

100%

Start date:

1st of October 2026

Application and selection:

Please submit your application using the link below. The deadline is 30th of August 2026.

Your application should include:

• A one-page reflection including (1) why you plan to pursue a PhD education (2) why specifically you think our group is a good target for you and (3) why this project interests you
• Send 2 publications related to the topic of "plasmid dependent phages" that you find most interesting
• All application documents should be prepared in English

Read more about the other attachments that your application should include at https://www.slu.se/en/study/programmes-courses/doctoral-education/how-can-i-become-a-doctoral-student/application/

Selection among eligible applicants is based on the documents attached to the application, and is carried out with regard to the applicant's ability to complete the programme within the allotted time.

Academic union representatives:

https://internt.slu.se/en/my-employment/employee-associations/kontaktpersoner-vid-rekrytering/