PhD student in computational microbial ecology


Application deadline

July 22, 2024

PhD student in computational microbial ecology

Department of Forest Mycology and Plant Pathology

A PhD student position in computational microbial ecology is available at the Department of forest mycology and plant pathology, Swedish University of Agricultural Sciences in Uppsala. The department provides a dynamic and international research environment comprising experts who conduct fundamental and applied research on plant-microbe interactions, mycology, microbial ecology and evolution, as well as biodiversity. Central themes are forest and plant pathology, and nutrient and carbon cycling in terrestrial ecosystems. Resources within the department include a high-performance computing grid with in-house technical support, support for bioinformatic analyses through the SLU Bioinformatics Infrastructure, and a well-equipped molecular ecology research facility. This position is part of the PhD program within the SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS).

Data-driven life science (DDLS) uses data, computational methods and artificial intelligence to study biological systems and processes at all levels, from molecular structures and cellular processes to human health and global ecosystems. The SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS) aims to recruit and train the next-generation of data-driven life scientists and to create globally leading computational and data science capabilities in Sweden. The program is funded with a total of 3.1 billion SEK (about 290 MUSD) over 12 years from the Knut and Alice Wallenberg (KAW) Foundation.

During 2024 the DDLS Research School will be launched with the recruitment of 20 academic and 7 industrial PhD students. During the course of the DDLS program more than 260 PhD students and 200 postdocs will be part of the Research School. The DDLS program has four strategic areas: cell and molecular biology, evolution and biodiversity, precision medicine and diagnostics, epidemiology, and biology of infection. For more information, please see The future of life science is data driven. Will you be part of that change? Then join us in this unique program!

Data driven analyses of the nitrogen cycling microbiome for predictions of nitrous oxide emissions from soil


At SLU, we are looking to fill the position as PhD student within the area of data driven evolution and biodiversity. Data driven evolution and biodiversity concerns research that takes advantage of the massive data streams offered by techniques such as high-throughput sequencing of genomes and biomes, continuous recording of video and audio in the wild, high-throughput imaging of biological specimens, and large-scale remote monitoring of organisms or habitats.

The PhD project in computational microbial ecology will utilize a data-driven approach to reconstruct the nitrogen (N) cycle based on microbiome data from different terrestrial environments, and evaluate how to combine this information with soil chemical/physical and climatic data to predict the degree of a soil’s capacity as a source or a sink of nitrous oxide (N2O), a potent greenhouse gas. The PhD student will work within the Soil Microbiology group that works as a well-integrated team and is internationally recognized in the areas of evolution, ecology and genomics of nitrogen cycling microorganisms as well as how to apply this knowledge in sustainable agricultural and environmental engineering.

The project includes database management, bioinformatic work, predictive modelling, and writing of scientific articles. The student will carry out supervised research leading to a PhD thesis and take PhD courses corresponding to a minimum of 30 higher education credits.


You should have an MSc degree in microbiology, ecology, bioinformtics, or a subject relevant for the position. Skills in statistical, database management and scripting programming languages (e.g. python, SQL, bash, R) is desirable given the data-driven nature of the project. Formal training in bioinformatics, molecular evolution, and statistic are merits as well as documented knowledge in microbial ecology or ecology. You should show a keen interest in learning machine-learning and other AI methods. The working language is English and excellent communication skills in English orally and in writing are required. We are looking for a candidate that is highly motivated, organized and inquisitive, and interested in academic research. You should like to work in teams and contribute positively to the development of the research environment.

Place of work:           


Forms for employment:

Employment as PhD stduent (4 years of education)

Starting date:

According to agreement, but latest 2024-10-01.


Click the “Apply” button to submit your application. The deadline is 2024-07-22.

To qualify for third-cycle (Doctoral) courses and study programmes, you must have a second-cycle (Master’s) qualification. Alternatively, you must have conducted a minimum of four years of full-time study, of which a minimum of one year at second-cycle level.

Applicants will be selected based on their written application and CV, degree project, copies of their degree certificate and transcript of records from previous first and second-cycle studies at a university or higher education institution, two personal references, and knowledge of English. More information about the English language requirements can be found here:

Please note that applicants invited to interview must submit attested copies of their degree certificate, or equivalent, a transcript of records from previous first and second-cycle studies at a university or higher education institution. Applicants who are not Swedish citizens need to submit an attested copy of their passport’s information page containing their photograph and personal details.

Read about the PhD education at SLU at

Read about the benfits and what it is like to work at SLU:

The Swedish University of Agricultural Sciences (SLU) has a key role in the development for sustainable life, based on science and education. Through our focus on the interaction between humans, animals and ecosystems and the responsible use of natural resources, we contribute to sustainable societal development and good living conditions on our planet. Our main campuses are located in Alnarp, Umeå and Uppsala, however, the university also operates at research stations, experimental forests and teaching sites throughout Sweden.

SLU has around 3,000 employees, 5,000 students and doctoral students and a turnover of over SEK 3 billion. We are investing in attractive environments on all of our campuses. We strive to provide a work environment characterised by inclusivity and gender equality, where different experiences generate conversations between people and pave the way for science, creativity and development. Therefore, we welcome applications from people with diverse backgrounds and perspectives.

Last updated: 2024-05-08

Content Responsible: Hampus Persson(