Postdoctoral position in Ecology of arctic aquatic fungal communities

Swedish University of Agricultural Sciences


June 30, 2022


Department of Aquatic Sciences and Assessment The Department of Aquatic Sciences and Assessment (www.

sciences) 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 department has some 130 employees. The research focuses on geochemical and hydrological processes, aquatic ecology and biodiversity, as well as on aquatic ecotoxicology and environmental chemistry. The department is part of a Soil- Water-Environment cluster, a recently established competence centre for landscape-level processes that also includes the Departments of ‘Soil and Environment' and ‘Energy and Technology'. The breadth of expertise among the 300 members in combination with a well-equipped infrastructure creates a unique platform for high quality research as well as environmental monitoring and assessment.

Read more about our benefits and what it is like to work at SLU at www.


The position will be embedded in a dynamic and new research group in aquatic microbial ecology and biogeochemistry. We study microorganisms and their processes in lakes and other aquatic ecosystems using a combination of molecular, cellular and isotope tracer methods. Tools such as large-scale metagenome sequencing and single cell analyses are frequently used and the research include both field work and controlled laboratory experiments. The postdoc will engage and lead a research project to study the ecological role of arctic aquatic fungal communities. Permafrost thaw is changing the Arctic landscape, leading to the emergence of thaw ponds which receive a large input of organic matter form the thawing peat, making them hotspots for the carbon cycling. It is still an open question what the contribution of aquatic fungal communities in the degradation of the dissolved organic matter in those ponds is, and we look for a highly motivated candidate to study their functional role.

The work will consist of analyzing a large set of metagenomic data using a variety of bioinformatic tools to evaluate the carbon degradation potential of fungal communities across a thaw gradient. The successful candidate will also conduct a sampling campaign in Abisko, Sweden during summer to sample emerging thaw ponds. We will use single cell genomics, metagenome sequencing, and carbon assimilation assays to learn more about the ability of aquatic fungi in degrading the dissolved organic matter. As a postdoc you will engage in independent research, but do so as part of a local and internationally distributed team of expert scientists. This work is part of an international collaborative research project and will take place in Sweden and Germany, in a collaboration with the Technical University of Munich. You will be able to influence the study design and will get to report the work in scientific publications. There will also be opportunities to train and learn new techniques and to supervise student projects.


We look for a candidate with availability to conduct a 3-year project, where part of the research must be conducted in Germany from July 2023 to August 2025. The successful candidate must have a solid training and PhD degree in biology, bioengineering or related subjects, with strong merits in environmental microbiology/genomics. Preference will be given to the candidate with previous experience and publications on aquatic fungal communities and arctic freshwater ecosystems affected by thawing. The candidate further needs to demonstrate documented experience and knowledge sufficient for using modern DNA/RNA-based methods to analyze complex microbial communities, as well as bioinformatic skills to analyze fungal sequences from metagenomes. The job includes bioinformatic processing and statistical analyses of fungal sequences, ribosomal RNA sequences and metagenomes retrieved from aquatic habitats. The bioinformatic analyses will involve quality control, assembly and functional annotation of shotgun metagenomes using tools such as Trimmomatic, Megahit, Spades, IDBA-UD, BBMap, Kaiju, EukRep, MetaEuk, eggNOG and HTSeq. Statistical analyses and visualization of the results are expected to be done using R. We expect the holder of the position to independently handle these tasks without any further training. Proficiency in English (both written and spoken) is required, as is demonstrated ability to effectively and clearly communicate research results in scientific publications. Finally, it is a merit to demonstrate grant writing skills by having received a longer (> 2 years) research grant as applying PI.

As postdoctoral appointments are career-developing positions for junior researchers, we are primarily looking for candidates with a doctoral degree that is three years old at most.

Place of work:

Uppsala, Sweden, and Munich, Germany

Form of employment:

Temporary employment, 36 months



Starting date:



We welcome your application no later than 2022-06-30, use the button below.

Academic union representatives:

https: // vid-rekrytering/

The Swedish University of Agricultural Sciences (SLU) is a world-class international university with research, education and environmental assessment within the sciences for sustainable life. Its principal sites are in Alnarp, Umeå and Uppsala, but activities are also conducted at research stations, experimental parks and educational establishments throughout Sweden. We bring together people who have different perspectives, but they all have one and the same goal: to create the best conditions for a sustainable, thriving and better world.

SLU has just over 3,000 employees, 5,000 students and a turnover of SEK 3 billion. The university has invested heavily in a modern, attractive environment on its campuses.


Contact person

Stefan Bertilsson



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