Soil microbiomes

Soil microbiomes are essential to ecosystem health, driving nutrient cycling, carbon storage, and plant productivity. At the ME2andA workgroup, our soil microbiome research focuses on uncovering how these microbial communities can be leveraged to enhance soil fertility and carbon storage in agricultural systems, while also addressing One Health challenges. Our overarching aim is to understand how soil microbes influence not only the productivity and resilience of agroecosystems, but also the spread of antimicrobial resistance (AMR) and pathogens from soil—the largest microbial reservoir—into food systems, urban areas, and hospitals. In the future, we plan to expand this research to explore additional processes and microbial players that impact these key areas.

Mapping Microbial Diversity for Sustainable Agriculture

We are excited to announce our newly funded project to create Slovenia's first comprehensive agricultural soil microbiome atlas. This groundbreaking initiative will provide unprecedented insights into the microbial communities that drive soil health and agricultural productivity across our diverse landscapes.

By systematically sampling and analyzing soil microbiomes from agricultural sites across Slovenia, we will generate the foundational knowledge needed to guide microbiomes toward optimized functional states in agricultural systems. 

Nitrification 

Nitrification, particularly ammonia oxidation, is a fundamental process in the nitrogen cycle that drives the conversion of ammonia to nitrate, influencing soil fertility and plant productivity. We have been working on ammonia oxidation for many years, with a recent focus on how soil aggregate sizes affect the distribution and activity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). By understanding the spatial organization of these microbial communities, we aim to uncover new insights into soil nitrogen cycling and its broader environmental impact.

Ecology and evolution of Clostridioides difficile - from the environmental perspective

Our second research focus explores the ecology and evolution of the pathogen Clostridioides difficile in soil environments. We are particularly interested in how soil ecosystems influence the activity and spread of this pathogen. This work is crucial to understanding how C. difficile evolves and spreads beyond its natural reservoirs, potentially reaching hospital and food systems. By integrating this research into the One Health concept, we aim to bridge the gap between environmental microbiology and public health, addressing the pathogen’s role in a broader ecological context.