The research group Microbial ecology aims to resolve the ecological and molecular mechanisms that give rise to biogeochemical transformations in soil and organic matter. We work in environments ranging from the Arctic to the Tropics, and engage both with pristine and managed ecosystems. Our work builds on environmental surveys, field experiments, and laboratory experiments.

The microbial world represents the largest reservoir of biodiversity that also is fundamental to sustaining key ecosystem processes, including the terrestrial carbon and nutrient cycles and the maintenance of plant fertility, across the breadth of the Earth’s ecosystems. In order to understand the role of microbial communities in ecosystem processes and to solve the major problems associated with human impact on the environment, a comprehensive and fundamental knowledge of microbial ecology is essential. The focus of the Microbial Ecology Group is to understand the ecology, diversity and functions of microorganisms in natural and engineered ecosystems, and the research is organized into several groups led by individual PI:s, as described below.

Dimitrios Floudas Lab

We study the biochemical and molecular mechanisms that fungi use to cause organic matter transformation and decomposition focusing both on intact tissues such as wood, but also processed molecules such as soil organic matter. A fundamental part of our studies also includes a deeper understanding of the evolutionary processes that have shaped and keep shaping these mechanisms. Finally, we are also interested in harnessing metabolic processes of fungi for use in biomaterial applications. Our experimental methods include wet lab experiments, sequencing, spectroscopy and X-ray scattering.

Read more about Dimitrios Floudas

Edith Hammer Lab

Soils store more carbon than the atmosphere and living biomass together, therefore are carbon compounds entering or leaving the soil C storage system of large importance for greenhouse effect mitigation. Soil organisms, and especially mycorrhizal fungi, channel large proportions of fresh carbon compounds entering the soil ecosystem, and we want to better understand their role in sequestering and stabilizing or decomposing soil organic matter.

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Lettice C. Hicks Lab

We want to understand how microorganisms regulate the mineralization of carbon and nutrients from soil organic matter, both under steady-state conditions and during dynamic perturbations (for example drying-rewetting). To do so, we typically employ a range of isotope-based approaches which allow us to examine the microbial use and transformations of carbon and nitrogen in soil systems. We study soils from across the globe, but have been particularly interested in subarctic ecosystems which are undergoing rapid environmental change, leading to pronounced changes in microbial resource use and biogeochemistry.

Read more about Lettice C. Hicks

Per Persson Lab

The main objective of my research is to provide fundamental understanding of chemical speciation, mechanisms and rate of reactions in the inherently heterogeneous aquatic and terrestrial environments. This is accomplished by a combination of techniques including Infrared and Raman spectroscopy, synchrotron-based X-ray absorption spectroscopy, X-ray photoelectron spectroscopy, Infrared microspectroscopy and imaging, and wet-chemical and theoretical methods.

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Milda Pucetaite Lab

Studying single-cell physiology and responses to environmental triggers is crucial for increased understanding of how microbes in soil function and contribute to larger scale biogeochemical cycles. My research is thus aimed at disentangling the microscale chemistry of complex biotic and abiotic microbial interactions by taking use of advanced microspectroscopy methods at home laboratories and at synchrotron facilities.

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Johannes Rousk Lab

We study the ecology of microorganisms in natural and engineered soil systems. We are interested in the factors that influence the spatial and temporal variability in microbial communities and how the microorganisms, in turn, control biogeochemistry in soil. We firmly believe that the secret to unlocking the ecology of microorganisms is to study how microbial growth rates respond to change, and we have a particular interest in comparing the roles of fungi and bacteria in their contribution to biogeochemical cycles.

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Anders Tunlid Lab

My present research focuses on examining the molecular mechanisms underlying the decomposition of organic matter by ectomycorrhizal and saprotrophic fungi and how this activity affect the cycling of nutrients and carbon in forest soils. We are studying how the functional activities encoded in the genomes of fungi are linked to biogeochemical processes operating at different spatial scales – from nanoscale minerals to forest sites using methods from genomics, molecular geochemistry, physical chemistry and computational biology.

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Håkan Wallander Lab

I work with ectomycorrhizal fungi that form symbiotic relationships with trees. They produce several hundreds of kilogram of mycelia per hectare every year in most forest ecosystems. This is important for nutrient uptake of the trees, but also for carbon sequestration and N retention in the soil. My main research interest is to understand how this flux of carbon below ground is regulated, and how important the composition of the ectomycorrhizal community is for carbon sequestration and nutrient uptake.

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Head of Microbial Ecology Group

Johannes Rousk

Associated PI’s

• David Wårlind
• Ulf Olsson
• Luigi Gentile

Research engineer

Anna Sterngren, PhD, responsible for the sequencing facility.

Postdocs and researchers (host)

• Albert C. Brangarí (Johannes Rousk)
• Carla Cruz-Paredes  (Johannes Rousk)
• Francois Maillard (Anders, Tunlid, Dimitrios Floudas)
• Guoxiang Niu (Johannes Rousk)
• Vanesa Santás Miguel (Johannes Rousk)
• Tao Zhang (Johannes Rousk)

PhD-students (supervisor)

• Ashish Ashish (Dimitrios Floudas)
• Agnieszka Rzepczynska (Lettice Hicks)
• Daniel Tajmel (Johannes Rousk)
• Sara Winterstedt (Johannes Rousk)
• Mingyue Yuan (Johannes Rousk) 
• Siyuan Zhou (Lettice Hicks)

Emeriti

• Erland Bååth
• Bengt Söderström

Masters-/internship students (supervisor / host)

• Franklin Harris (Johannes Rousk, Lettice Hicks, Daniel Tajmel)
• Styliani Alexandropoulou (Johannes Rousk, Vanesa Santas Miguel)
• Charlotte Hopf (Johannes Rousk, Carla Cruz-Paredes, Daniel Tajmel)
• Honorine Dumontel (Lettice Hicks, Agnieszka Rzepczynska)

Alumni

• Kristin Rath, PhD student 2013–2018, Data Scientist, King.
• Margarida Soares, PhD student 2014–2019, Researcher CEC, Lund University.
• Ainara Leizeaga, PhD student 2015–2020, Postdoc Manchester University, United Kingdom.
• Meng Na, CSC PhD student 2019–2021. Assistant Professor, China
• Qinmei Zhong, CSC PhD student 2019–2020. Assistant professor, China.
• Jintao Li, CSC PhD student 2020­–2021.
• Huimin Xu, CSC PhD student 2020–2021.
• Annelein Meisner, Postdoc 2013–2015. Wageningen University & Research, Netherlands.
• David Fernandez-Calvino, Postdoc 2012–2014. Professor University of Vigo, Spain.
• Yuqien Tang, Visiting researcher, 2019–2020. Assistant professor, China.
• Per Bengtson, Researcher 2010–2022. Safety Medical Writer, Ferring Pharmaceuticals, Denmark.