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Salme Timmusk

Salme Timmusk
Associate Professor



Understanding how woody and herbaceous plants as  holobionts function in wild and harsh habitats and how microbiome mediates vegetation dynamics and carbon allocation   as well as plant and ecosystem biodiversity, enables us to identify key factors for plant fitness and develop strategies for sustainable production systems.

Just as we think it is highly  important to  characterise indigenous rhizosphere microbiome genomic and metabolomic features influencing plant biotic- and abiotic stress tolerance in native environments,  we also pay attention to our activities regarding communication and dissemination of  results.   Our cross disciplinary collaboration team involves scientists ranging from community- and systems ecology to analytical chemistry and social science. 

Plant root microbiome interactions are studied by observation using gradually increasing resolution  LM (A and B),  ESEM (C), SEM-EDS(D), AFM (E) and cryo-EM (F). 

Keywords *Deciphering plant–microbe interactions, construction of genome-scale metabolic models of microorganisms and plants. *Habitat re-creation *Extremophilic microorganisms and their biochemical adaptation and biotechnological application. *Bioremediation: decontamination of soil and water pollution generated by manmade chemicals


Ongoing research projects:

Development of native rhizosphere community-based microbial consortia (CBC) for crop stress tolerance improvement and habitat re-creation


Integrating rhizosphere microbiomes in Africa, Israel, South America and in the Baltic Sea Region   we analyze the role of  crop plant microbiome in crop plant adaptation to selected  stress habitats. These studies illustrate the importance of method for selection of CBC (also known as PGPR) and  nanoparticles for the CBC formulation. These results explain the generally observed inconsistent behaviour of PGPRs in field application. The nanoparticle effect is soil specific and is related to the particles’ ability to modulate the surface formation of complexes with important types of biomolecules such as phospholipids and proteins. Understanding the pathways improves the effectiveness of formulation and optimize the mutually complex interactions, as it allows their regulated delivery and release, focusing on specific tissues and cells at specific times. In this innovative transdisciplinary approach experimental studies with breeding lines and rhizosphere microbiomes are combined with cultivation-independent bioinformatic analysis to identify putative microbial consortia. 


Reveal the CBC effect on plant vegetation characteristics and C N dynamics. Validation of the CBC performance in model systems (i) and at  the stations for measuring ecosystem atmosphere relations (SMEAR) (ii)


Goal: Identification of crop plant genomic sequences associated with the stress factor of the study. Identification of genomic markers for CBC interaction to be employed in breeding programs

i. CBC from project 1 with improved plant performance are characterized using MULTIOMICs techniques. The beneficial microbiome is selected through construction of an interaction network and potential key microbes are identified based on structural properties and/or functional modules.

ii. SMEAR,  a high end ecosystem interaction study platform, there long-term life history datasets are created, is established in Estonia in collaboration to the Estonian University of Life Sciences . At the station comprehensive, long-term, real-time measurements of meteorological characteristics and atmospheric trace gases, and atmospheric particulate matter, are conducted together with eco-physiological measurements at soil and plant level. The measurements are combined with continuous monitoring of ecosystem net primary productivity. In the station a comprehensive large-scale scientific infrastructure provides continuous high-quality data of a large set of environmental parameters. 


Bioremediation of pollution generated by manmade chemicals in the form of industrial activity, agricultural chemicals, or the improper disposal of waste

Goal: Replacement of conventional methods routinely used for the remediation of contaminated environmental soil and water such as excavation, transport to specialized landfills, incineration, stabilization, and vitrification. Bioremediation technologies using native microbial consortia offer many advantages over traditional remediation technologies as they can be applied in situ without the need for removal and transport of contaminated soil/water, are economical, less labour-intensive and have a lower carbon footprint.


Dissemination and communication: Crop plant microbiome is an  essential tool for future production systems

Goal: To maximize the impact of project 1, 2 and 3 derived information  While human microbiome research is increasingly applied in practical medicine, plant-microbial interaction research has a relatively weak link to practical agriculture. The future production  systems will be based on carefully designed crops and crop specific microbiome focusing on ecological restoration, habitat creation and crop production profitability. The link to public education, practical agriculture/industry  and civil society  will  be strengthened via product and method communication. In collaboration to social scientists, we establish trans-national collaboration between researchers and stakeholders and carry out dissemination and communication activities addressed to district audiences by using  our projects concepts and results.


Industrial application of microbial consortia :Grapes under Climate Change (Grapes CC)

In order to develop climate change mitigation strategies, researchers from different climate zones  will necessitate  working together. For these strategies to be as efficient and comprehensive as possible, a multi-actor approach, involving academic and agricultural stakeholders at an international level, is fundamental. 

Our approach is seeing the issues in the local ecosystem, production system and in  the  global scale context. Hence, soil C and N dynamics are focused. Our two main objectives are internationalisation of research (i) and internationalisation of education (ii) in the field of wine-making under climate change.

(i) Internationalisation of research - aims at facilitating exchanges of knowledge and experience as well as co-creation of common strategies between researchers from Sweden, Armenia, Georgia and Chile.

(ii) Internationalisation of education - focuses on the strategies of education students. In order to adapt wine grapes to extreme, unpredictable conditions, future wine producers will have to be able to share expertise and best practices with colleagues from other geographical zones. As international collaboration is crucial, students need to acquire the skills to engage in it.



Prof. Eviatar Nevo Institute of Evolution, Haifa University, Israel: Evolutionary Biology; four natural laboratories of “Evolution Canyons" in Israel

Dr. Diriba Muleta, Addis Ababa University, Ethiopian small-grain cereals and their wild progenitors

Prof. Jill Farrant University of Cape Town, ZA  Myrothamnus flabellifolia,  and  Xerophyta schlechteri rhizosphere metatranscriptomics

Prof. Bernhard Glick University of Waterloo, Canada: Mechanisms of microbe-mediated abiotic and biotic stress mitigation  

Prof. Jonas Bergquist Uppsala University (UU), Chemistry BMC, Sweden: Temporal dynamics of plant-soil metabolome 

Prof. Anna Strålenhielm- Martensson SLU: Viticulture, Soil chemistry

Dr. Ilmar Tamm Estonian Crop Research Institute (ECRI), Estonia: Plant breeding, circular bioeconomy, NordGen genebank

Prof. Ylo Niinemets and Steffen Noe Estonian University of Life Sciences: Station for Measuring Ecosystems Atmospheric Relations (SMEAR Estonia)

Dr. Julian Conrad Swedish National Cryo-EM facility, SciLifeLab, Stockholm, Sweden:  Super-resolution microscopy


Prof. Erik Rudloff-Bongcam SLU-Global Bioinformatics Centre

Taavi Pall University of Tartu, Faculty of Medicine, Institute of Biomedicine and Translational Medicine

Dissemination and communication activities

Dr. Paul Fuehrer Södertörn University, School of Social Sciences 

Dr. Lawrence Behers Novawest Technology and Communications, USA



Researcher at the Department of Forest Mycology and Plant Pathology; Division of Forest Microbiology
Telephone: +4618-672727
Postal address:
Skoglig mykologi och växtpatologi , Box 7026
750 07 UPPSALA
Visiting address: Almas Allé 5, Uppsala