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Stefan Bertilsson

Stefan Bertilsson
Professor in ´Functional Ecology of Freshwatersand Director of the Swedish Infrastructure for Ecosystem Science (SITES). Field of research: (i) Aquatic Microbial Ecology, (ii) Biogeochemistry, (iii) Environmental Genomics and single cell methodology. Ongoing research projects on microbial transformation and cycling of Carbon, Nitrogen, Mercury and associated elements in freshwaters, oceans, and the deep terrestrial biosphere.


My research focus on the role of microorganisms in nature and foremost their ability to transform and redistribute central elements (e.g. carbon, nitrogen, mercury). In my research group we rely on a combination of molecular (DNA and RNA-based) methods, isotope tracers and analytical chemical tools to understand processes such as nitrogen fixation, autotrophic carbon fixation, mercury methylation (and demethylation) and degradation of biopolymers and organic pollutants. We also study predation, symbiosis and other interactions between microorganisms (microbial ecology) and their evolution. We work both exprimentally in the laboratory and in the field (lakes, oceans) and study microorganisms in more exotic environments such as polar ecosystems and the deep terrestrial biosphere.

Environmental analysis

For information about the scope and mission of SITES follow this link


Coordinator of the Research Community Program AMRI (Aquatic Microbiome Research Initiative for research coordination and outreach 

For information about the scope and mission of the SciLifeLab  Single Cell Genomics facility, follow this link


Brief BiO:

1994: Master of Science in Biology, Uppsala University

1999: PhD in Water and Environmental Studies, Linköping University

1999-2002: Postdoctoral Fellow, Massachusetts Institute of Technology, USA

2002-2005: Wallenberg Fellow in Environment and Sustainability, Uppsala University

2005-2011: VR Researcher (Rådsforskare), Uppsala University

2009: Guest Researcher, University of Georgia-Athens, USA

2011-2019: Professor, Uppsala University

2013-2015: Scientific Director, Science for Life Laboratory

2012-present: Director SciLifeLab Microbial Single Cell Genomics Facility

2018-present: Director for the Swedish Infrastructure for Ecosystem Science.

2019-present: Professor in Functional Ecology of Freshwaters


As main advisor: Alexander Eiler (PhD 2007), Sara Beier (PhD 2010), Friederike Heinrich (PhD 2015), Valerie Hubalek (PhD 2015), Torsten Jeske (PhD 2015), Monica Ricao (PhD 2016), Jingying Xu (PhD 2018). As assistant advisor: Paraskevi Polymenakou (PhD 2005), Karin Enwall (PhD 2008), Anna Lundqvist (PhD 2011), Erik Pelve (PhD 2012), Katarzyna.Zaremba (PhD 2013), Inga Richert (PhD 2014), Alexandra Linz (UW-Madison, PhD 2018). Current main supervisor for 5 PhD students: Lorena Grubisic, Leyden Fernandez-Vidal, Rhiannon Mondav, Javier Florenza-Garcia, Pilar Lopez Hernandez.
Jan Olsson, 2003; Mona Johansson 2003-2004 + 2006; Carlos Gonzalez-Rey, Xinmei Feng, 2007-2008; Laura Alonso-Saez, 2007-2010; Anders Andersson, 2008-2009; Ramiro Logares, 2008-2010; Stephan Gantner, 2008-2010; Henry Holmstrand, 2008-2009; Jay De, 2009-2011; Claudia Bergin, 2012-2014; Martha Schattenhofer, 2013-2016; Omneya Ahmed, 2011-2016; Andrea Garcia-Bravo, 2012-2016; Hayian Hu, 2016-2019, Moritz Buck, 2016-present, Sarahi Garcia, 2017-2019, Javier Segura, 2018-present, Maliheh Mehrshad, 2019-present

Selected publications

(1) Bravo, A.G., Peura, S., Buck, M., Ahmed, O., Mateos-Rivera, A., Herrero Ortega, S., Schaefer, J.K., Bouchet, S., Tolu, J., Björn, E., Bertilsson, S. 2018. Methanogens and iron-reducing bacteria: the overlooked members of mercury methylating microbial communities in boreal lakes. Appl. Environ. Microbiol. 84:e01774-18.
(2) Bravo, A.G., Bouchet, S., Tolu, J., Björn, E, Mateos-Rivera, A., Bertilsson, S. 2017. Molecular composition of organic matter controls methylmercury formation in boreal lakes. Nature Communications. 8:e14255.
(3) Eiler, A., Mondav, R., Sinclair, L., Fernandez-Vidal, L., Scofield, D.G., Schwientek, P., Martinez-Garcia, M., Torrents, D., McMahon, K.D., Andersson, S.G.E., Stepanauskas, R., Woyke, T., Bertilsson, S., 2016. Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria. The ISME Journal 10:1902-1914.
(4) Logares, R, Lindström, ES, Langenheder, S, Logue, JB, Paterson, HP, Laybourn-Parry, J, Rengefors, K, Tranvik, L, Bertilsson, S. 2013. Biogeography of bacterial communities exposed to long-term environmental change. The ISME Journal 7:937-948.
(5) Alonso-Saez, L, Waller, A, Mend, D, Bakker, K, Farnelid, H, Yager, P, Lovejoy, C, Tremblay, JE, Potvin M, Heinrich, F, Estrada, M, Riemann, L, Bork, P, Pedros-Alio, C, Bertilsson, S. 2012. Role for urea in nitrification by polar marine archaea. Proceedings of the National Academy of Sciences 109:17989-17994.


This is a temporary (incomplete) version of my personal page. For more information you can visit my "old" webpage at Uppsala University here.


Professor at the Department of Aquatic Sciences and Assessment; Division of Microbial Ecology
Telephone: +4618673153
Postal address:
Institutionen för vatten och miljö
Box 7050
750 07 UPPSALA
Visiting address: Lennart Hjelms väg 9, Uppsala

Publications list: