Soil Microbiology

Last changed: 05 February 2024
A man in a cap is sitting on the ground with soil in his hand, photo.

Microorganisms are at the center of all major biogeochemical processes on Earth, providing valuable ecosystem services such as nutrient cycling, climate regulation and degradation of organic matter and pollutants. Proper stewardship of these services requires a scientific understanding of the ecological processes that govern the diversity and functioning of microbial communities.

The Nitrogen Cycle – Functional microbial ecology

Nitrogen (N) is a primary nutrient for all living organisms, and the cycling of N is critical for sustaining life on Earth. However, the anthropogenic discharge of reactive N into the biosphere has led to an imbalance in the global N cycle, causing eutrophication and emission of the greenhouse gas nitrous oxide (N2O). Microbial communities that mediate different N-cycle processes ultimately determine whether N is gained or lost in an ecosystem. Understanding how abiotic or biotic factors shape the diversity, structure, and functioning of these communities is critical for predicting the fate of N in Earth’s ecosystems.


Sara Hallin (Professor) is interested in functional ecology of microbial communities in biogeochemical cycles, and in particular the nitrogen cycle. Also applied research of relevance for agricultural, the environment and climate are in focus.

Karina Clemmensen (Assoc. Senior lecturer) focuses on understanding drivers of below-ground fungal community composition and how fungal communities interact with other biota and contribute to ecosystem level properties, such as carbon sequestration and vegetation successions, particularly in the Arctic, Boreal and Temperate biomes.

Christopher Jones (Researcher) is interested in the underlying processes that drive the diversification and assembly of nitrifying and denitrifying communities in terrestrial ecosystems. A key research aim is to better understand the link between diversity and ecosystem functioning.

Jaanis Juhansson (Researcher) studies the microbial communities across arctic tundra soils to find effects of climate warming induced changes in vegetation on the diversity and activity of mycorrhizal fungi and N-metabolizing prokaryotes.

Maria Hellman (Research engineer and PhD student) works in the projects “miNing” and NITREM, both focusing biological removal of nitrogen from mine waters in cold climates. Wetlands, bioreactors and pond systems are investigated.

Valerie Hubalek (Postdoc) works in on artificial recharge of aquifers. She is specifically looking at the microbial N-cycling processes and communities in barriers constructed to prevent nutrients, contaminates, pathogens etc entering the aquifers, all within the JPI Water project ACWAPUR.

Mathilde Jeanbille (postdoc) investigates the interactions within prokaryotic and fungal communities in arctic tundra soils and litters from the long-term warming experiments of the ITEX network, in relation to climate-related vegetation changes and nitrogen cycling.

Aurélien Saghaï (Postdoc) works in a project investigating how soil microbial diversity affects plant performance and how crop diversification affects the functioning of soil microbiota in agro-ecosystems. We aim at unraveling whether practices that increase plant diversity promote the simultaneous delivery of multiple beneficial soil ecosystem services in the EU ERA-NET (Biodiversa) project Digging Deeper.

Lea Wittorf (Postdoc) studies the microbial communities in soils from long-term field experiments subjected to different nitrogen and carbon regimes. The aim is to determine when and how the denitrification pathway is divided between different organisms within a community and how this might impact nitrogen loss and N2O emissions.

Yvonne Bösch (PhD student) focuses on the ecology of fungal denitrifiers and their importance for nitrous oxide emissions. By also analyzing fungal denitrifiers on a genetic and evolutionary level, we will gain a fundamental understanding of their ecology.

Arpita Maheshwari (PhD Student) studies ecological processes that drive assembly of N2O reducing communities in soils along environmental gradients. The underlying ecophysiology is determined through enrichment experiments and studies of pure cultures.

Martina Putz (PhD Student) investigates microbial N transformations in agricultural soils within the NORA project. The focus is on the identification of factors influencing the activity and assembly of microbial communities affecting nitrous oxide emissions.


Germán Bonilla Rosso
Daniel Graf
Robert Almstrand
Enid Ming Zhao
Maren Emmerich
Allana Welsh
Rosalia Trías
Ella Wessén
Janet Andert
Karin Enwall
Karin Nyberg
Ingela Throbäck


Our aim is to address fundamental questions on the causes and consequences of biodiversity within microbial functional guilds. We also apply this knowledge to solve specific problems relating to sustainable agriculture and bioremediation of N-polluted soils and water. 

Our approach is to implement a functional ecology framework, where microbial communities are defined by the functions they perform. We use nitrifying and denitrifying microbial communities as model systems to study the link between microbial community dynamics and ecosystem processes, as well as identify key organisms and factors that control N-transformation processes.

Our expertise is in the implementation of molecular tools and bioinformatics of functional genes in combination with activity measurements and statistical modeling to study microbial functional guilds that drive N cycle processes in various ecosystems.


Portrait photo of a woman with dark hair, photo.Professor Sara Hallin

Department of Forest Mycology and Plant Pathology, 018-673209