Aarhus University Seal

Environmental Microbiology

Section research areas

Our research in Microbial Ecology is internationally recognized and holds high merits within soil microbial ecology (fungi, bacteria, protists, and viruses), Arctic microbiology and biogeochemistry, pathogens in the environment, aero-microbiology, degradation of organic micro-pollutants, industry-related microbiology, effects of agricultural practices on the microbe-driven ecosystem services and biogeochemical processes. Consultancy includes environmental risk assessment of microorganisms (GMOs, production organisms, microbial control agents, bio-stimulants) as well as eDNA-based monitoring of non-indigenous species. Besides traditional microbiological techniques, molecular methodologies are pivotal to the research in the section, including sequencing of pure cultures and environmentally derived DNA and RNA using Illumina and Oxford Nanopore platforms.

The current specific areas of expertise form the platform for fulfilling the future ambitions of the section designed to meet society’s future requirements for research and for knowledge. The following research areas are in focus:

The role of microorganisms in sustainable soil practices:

Climate change mitigation by soil microorganisms with a focus on the possibilities of soil microorganisms to mitigate GHG emissions and how the soil quality is affected by agricultural climate change mitigation measures. There is a strong synergy with the research areas of eDNA, soil virus and soil protists.


Ecology of microbial communities (from microbial interactions to carbon and nutrient fluxes) on the Greenlandic ice sheet where microbes play a crucial role in ice melting. Phylogenetics of ice microorganisms to advance our level of understanding of microbial ecology, the nutritional background of the ice microbiota and hydrological processes that drive microbial communities in the Arctic.


Studies of low-level presence of nutrients and particles in Arctic environments, ice sheets, glacial runoff and studies on glacial hydrology. There is strong interaction with the cryo-microbiological research area.


Incidence, effect and dispersion of microorganisms in the atmosphere. Sampling methodologies of airborne microbes (viruses, bacteria, fungal propagules, pollen) and methodologies to identify and quantify them (eDNA, ddPCR) and understand their interactions with aerosols.

Industrial microbiology/biotechnology:

Discover and develop biotechnological approaches for sustainable usage of waste materials, optimize industrial processes (e.g. enzymatic) to improve sustainability. Research on cold adapted microorganisms.

Environmental virus ecology:

Research viruses that interact with microorganisms from soils to glaciers (e.g., how mycoviruses influence fungal ecology in relation to plants, soil and technical systems).

Pathogenic microorganisms in the environment:

This research is at the intersection between microbial ecology and medical microbiology. It examines the role of environment as a habitat for pathogenic microorganisms, and for their spread and exposure to humans.

eDNA and sequencing facilities

The section has several in-house approaches and develop further methodologies (e.g., SIP, total RNA, transcriptomics) to measure microbial occurrence and activity regarding plant pathogens, predator influence on population dynamics, presence of prokaryotes and invertebrates (e.g. protozoa, nematodes) as bio-indicators of soil quality to measure non-indigenous species, microbial processes involved in degradation of pollutants, indicators of soil health and microbial interactions and dynamics in icy environments.

EMBI offers advice to public and private sector in all research areas.