Microbial Ecology and Ecosystems

Bacteria colonising a mycorrhizal root tip of a beech tree.

Understanding biogeochemical cycles that enable life

Microorganisms are of critical importance for all global biogeochemical cycles and for food chains in terrestrial, aquatic and engineered ecosystems. At CeMESS, we study the structure and function of environmental microbiomes and the resulting flows of nutrient elements such as carbon, nitrogen, phosphorus and sulfur. These topics are investigated across scales, from the level of whole ecosystem processes, to the ecophysiology and biochemistry of single microbial species. We aim at a deeper understanding of how microorganisms contribute to ecosystem functions and how environmental microbiomes can be optimally utilised in engineered ecosystems, such as in wastewater treatment.

Selected topics, nitrogen and sulfur cycling:
Nitrogen fixation by free-living and plant-associated microbes
Ecophysiology, biochemistry, and evolution of nitrifying microorganisms in terrestrial, aquatic, and engineered ecosystems
Interactions of nitrifying microbes and plants in the rhizosphere
Utilisation of organic and inorganic nitrogen compounds by plants and microorganisms
Physiology and evolution of organic and inorganic sulfur-compound-utilising microorganisms in marine sediments and terrestrial wetlands
Development of isotope techniques to quantify nitrogen and sulfur cycle processes
Selected topics in soil microbiology:
Microbial C and N use efficiency
Microbial dormancy and resuscitation
Soil organic matter formation and soil carbon storage
Extracellular decomposition and microbial utilisation of soil organic C, N and P
Plant-soil-microbe interactions
Mathematical modelling of soil microbial communities

Microbial Nitrogen and Sulfur cycling

All living organisms need nitrogen (N) and sulfur (S) for the biosynthesis of nucleic acids, proteins, and other cellular components, and are thus directly dependent on the global N and S cycles. These cycles consist of multiple processes, many of which are catalysed exclusively by bacteria and archaea. Humans are transforming the global N cycle at a record pace, primarily through using artificial nitrogen fertilisers. We cannot feed a growing global population without these fertilisers, and yet, with fertilisation efficiency often below 50%, we are releasing unprecedented amounts of ammonium into the environment. Ecological consequences range from biodiversity loss, eutrophication and “dead zones” in water bodies, to increased emissions of the greenhouse gas nitrous oxide (N2O). Now more than ever, we urgently need science-backed strategies to ensure more efficient use of nitrogen fertilisers. The global S cycle is intimately intertwined with other elemental cycles, mainly through the activities of microbes. Microbial sulfate respiration is a critical step in the global carbon cycle – fuelling up to 50% of organic carbon mineralisation in marine sediments. Moreover, sulfur-cycling bacteria in terrestrial wetlands provide an important control function on methane emissions from these environments. CeMESS conducts internationally leading research that aims to illuminate the complex biology of the N and S cycles. This knowledge is indispensable for predicting and mitigating environmental threats caused by human activities and global change.

Probing nitrogen cycling in permafrost environments in the Canadian Arctic.

Microbiology of Soils

Soils play a pivotal role in the functioning of the Earth’s terrestrial ecosystems and harbour an almost inconceivable diversity of microorganisms. Our research addresses fundamental questions about what shapes this extensive microbial diversity, how microbial communities survive and thrive, and what functional roles they play in terrestrial ecosystems. Soil microorganisms are key players in the terrestrial carbon cycle. They decompose, transform and stabilise soil organic matter, the largest reservoir of organic carbon on Earth. To build a deeper understanding of soil organic matter dynamics and nutrient cycling, we explore questions about how microorganisms interact with each other, and with plants, animals, and the soil matrix. Finally, we explore the impact of climate and landuse change on the functioning of soil ecosystems and the potential repercussions on human wellbeing.