Functional microbial ecology

Last changed: 12 January 2024
Cyanobacteria Dolichospermum sp.,  short corkscrews. Microscope image.

Microorganisms are diverse and can have multifaceted and unexpected impacts on ecosystems and the cycling of carbon and other bioactive elements. Understanding the functional ecology and diversity of microorganisms aid efficient and sustainable management of ecosystems and natural resources.

At the Department of Aquatic Sciences and Assessment, researchers with a shared passion for understanding the diversity, metabolism, and ecology of these ecosystem engineers have formed the Functional Microbial Ecology Lab (FUME). The group use methods such as environmental genomics, biogeochemical assays for field studies and experiments to address an array of interlinked questions on functional ecology, diversity, and microbial evolution. Our focus is on aquatic ecosystems, but the research also covers bacteria, archaea, microeukaryotes, and viruses in a wide range of ecosystems.

Ongoing research projects

The FUME is involved in around 20 research projects. Examples of some of these projects:


Lecture about FUME

This video is the inauguration lecture of Stefan Bertilsson, describing FUME

FUME lab members

  • Stefan Bertilsson (Professor)
  • Jennifer Anderson (Researcher)
  • Moritz Buck (Researcher-Bioinformatics)
  • Lauren Davies (Research Assistant)
  • Matthias Hoetzinger (Researcher)
  • Mariana Kluge (Postdoc)
  • Marcus Korvela (Chemist)
  • Prune Leroy (Research Engineer)
  • Pilar López-Hernandez (PhD student)
  • Mahwash Jamy (Postdoc)
  • Maliheh Mehrshad (Researcher) 
  • Malin Olofsson (Researcher) 
  • Fernando Puente-Sanchéz (MSCA-Researcher) 
  • Attila Szábo (Postdoc) 
  • Anna Székely (Researcher) 
  • Klas Udekwu (Researcher)
  • Javier Vargas Calle (Research Engineer)

Guests, students, and short term employees

  • Tong Liu (Guest postdoc, SLU Umeå)
  • Eric Capo (Guest Postdoc, CSIC) 
  • Javier Florenza Garcia (Guest PhD student, Uppsala University)
  • Carlos Palazin Lizarbe (Guest postdoc, University of Eastern Finland)
  • Asmus Olesen (Guest PhD student, University of Copenhagen)
  • Aliecha van’t Spijker (Erasmus internship student)
  • Nhat Ton Nguyen (Erasmus MSc student)

Read more

Collaborative centres and research infrastructures

SLU Knowledge bank

SLU news articles within the FUME area


The FUME microbiology lab

A fully equipped laboratory for environmental microbiology and molecular analyses. The labs of 130 m2 are located on floor 3 in Biocentrum at SLU Uppsala campus. Work is documented in the LabCollector electronic lab notebook and LIMS system. We keep Synology servers for local computing and storage.

Instrumentation in the lab

Semi automated Olympus IX73 inverted epifluorescence microscope, Illumina MiSeq sequencer, Beckman Coulter Cytoflex flow cytometer with multiwell capability and blue/violet lasers, BioRad CFX Touch 96 well 4-color QPCR system, Standard gradient 96-well PCR systems (x2), Hidex sense plate reader for absorbance, fluorescence and chemiluminescence, Perkin-Elmer Labchip GX-HT fragment analyzer, Gel documentation, DNA/RNA extraction robot, Hamilton liquid handling robot, Bead beater, Anaerobic glove box, Laminar flow and UV hoods (x4), Autoclave, Barcode reader, ULT freezers (x4), Bioscreen growth monitoring system, Filtration setups, Pumps (Vacuum, peristaltic, membrane), Ice machine, Q-grade water, Incubators, Bioreactors, Centrifuges, Vacuum manifolds and more.  

The FUME chemical lab

Agilent 1200 HPLC systems with diode array, fluorescence and electrochemical detectors (x4), Thermo Fisher Delta Ray Stable Isotope analysis system, Ocean Optics JAZ spectrometer, Ocean Optics USB2000 Fluorometer, Unisense OX10 oxygen microsensor with a microcontroller, Metrohm 881 Ion chromatograph, Waltz Phyto-PAM.