Diversity and interactions of plasmid dependent phages in aquatic ecosystems

Department of Water and Environment

Research education subject:

Biology

Description of the doctoral project:

Antibiotic resistance (AMR) is one of the most pressing global health challenges of our time. A key driver behind the spread of AMR is the horizontal transfer of antibiotic resistance genes via conjugative plasmids, i.e., 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 hitherto overlooked tool for controlling the spread of resistance genes.

This doctoral project is part of ECOPHARM, a research project funded by the Knut and Alice Wallenberg Foundation (Wallenberg Academy Fellows 2025). The overall goal of ECOPHARM is to map the mechanisms governing PDPs' interactions with conjugative plasmids and bacterial hosts, as well as to understand their impact on the transfer of antibiotic resistance genes in aquatic environments.

As a doctoral student, you will investigate the diversity, ecology, and functional interactions of PDPs in aquatic ecosystems. The work will combine environmental sampling, culture-based methods, metagenomics, genome analysis, and infection analyses. 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 are welcome to visit our website https://www.bionomics-mmlab.com/

Tasks:

As a doctoral student, you are expected to:

Design and conduct field sampling in aquatic environments to map PDP communities Perform laboratory experiments to study PDP–plasmid–host interactions under controlled conditions Apply metagenomic and bioinformatic tools to analyze data from microbial and viral communities Contribute to experimental work involving phage isolation, cultivation, and infection analyses Present results at lab meetings, national and international conferences, and contribute to scientific publications Follow laboratory guidelines for data management Communicate progress and obstacles in a timely and clear manner Collaborate with national and international project partners within the ECOPHARM network

Eligibility:

Basic eligibility is granted to those who have completed a degree at an advanced level, fulfilled course requirements of at least 240 credits, of which at least 60 credits are at an advanced level, or who have otherwise acquired substantially equivalent knowledge within or outside the country (the Higher Education Ordinance, Chapter 7, Section 39).

Special eligibility for admission to doctoral studies in the subject of biology is granted to those who have knowledge equivalent to at least 90 higher education credits (hp) in biological subjects. These must include an independent project, and at least 30 hp must be at an advanced level.

Additionally, you are required to have knowledge of English equivalent to a passing grade in English B/6 from a Swedish upper secondary school.

Your background:

Requirements:

A master's degree in microbiology, biology, molecular biology, environmental science, or a closely related field Background in microbiology or molecular biology Experience with laboratory techniques relevant to microbial or environmental research Good knowledge of English, both written and spoken

Merit:

Experience in bioinformatics or computational analysis of sequence data Knowledge of phage biology, plasmid biology, or antibiotic resistance research Experience in sampling in aquatic or other natural environments

Personal qualities we are looking for:

High degree of independence - you take initiative, define problems on your own, and drive the work forward in dialogue with your supervisor Collaborative - you actively contribute to a good team environment and support your colleagues Clear communicator - you can convey complex ideas both in writing and orally, to both specialists and non-specialists Curiosity, precision, and the ability to handle scientific uncertainty

About us:

The Department of Water and Environment is a competence center for applied environmental research with a national responsibility for monitoring the environmental status of Swedish lakes and watercourses regarding water chemistry, environmental pollution, and aquatic biota. Research at the department focuses on geochemical and hydrological processes, aquatic ecology and biodiversity, microbial ecology, as well as environmental chemistry and aquatic ecotoxicology. The department has over 150 employees, of which approximately half are researchers/doctoral students and the other half is technical and administrative staff.

More information about the department: http://www.slu.se/vatten-miljo

Read more about our benefits and what it is like to work at SLU at https://www.slu.se/om-slu/jobba-pa-slu/

Read more about SLU's doctoral education at http://www.slu.se/utbildning/program-kurser/forskarutbildning/.

Terms of employment and salary:

Employment as a doctoral student (4 years of education).

The salary for the doctoral position follows the local collective agreement with fixed salary steps.

Extent:

100%

Location:

Uppsala

Start date:

2026-10-01

Application and selection:

Welcome with your application via the application button below no later than 2026-08-30.

Your application should include:

One page where you reflect on (1) why you want to pursue a doctorate, (2) why you specifically see our research group as a good match for you, and (3) why this project interests you Two publications related to the subject "plasmid dependent phages" that you find most interesting All application documents must be written in English

Read more about the attachments that your application must also include at https://www.slu.se/utbildning/studera/forskarutbildning/hur-kan-jag-bli-doktorand/ansokan-och-bilagor/

Selection among eligible applicants is based on the attachments included in the application and shall be made with consideration to the ability to complete the education within the allotted time.

Union contact persons

https://internt.slu.se/min-anstallning/facket/kontaktpersoner/