What is the microbiome?
Microorganisms can be found everywhere in the environment, where they colonize soils, plants and animals. Microbes interact with each other and with their host. In addition, they form stable communities which are essential for the proper functioning and health of soil, plants and animals. The microorganisms that inhabit a particular habitat are called "microbiota", and the "microbiome" refers to all of the microbiota and their genomes.
Why is studying the microbiome important for organic agriculture?
Microbial communities play important roles in key agricultural processes. In soils, for example, microbes catalyze essential steps in nutrient cycling that contribute to soil fertility and plant nutrition. Microbes also decompose dead plants and animals thereby contributing to humus formation. The microbiota associated with plants includes pathogens such as Pythium ultimum and Rhizoctonia solani which causes diseases in various crops and symbionts, for example nitrogen-fixing bacteria and arbuscular mycorrhiza fungi, which provide nutritional elements necessary for plant growth. In ruminants, microbes in the guts are essential for the digestion of the plant polymer cellulose. Understanding the interactions of microbiota and their host/habitat and how agricultural management affects the health of the microbiome are crucial objectives for the development of a more sustainable agriculture.
Why did we choose an interdisciplinary approach for this topic?
With the recent development of new DNA sequencing technologies, microbiome research has advanced dramatically. For example, DNA can be extracted from an environmental sample and directly sequenced, a technique called "metagenomics". The methods to compare microbial communities across different habitats are similar. This interdisciplinary theme coordination provides a platform for the exchange of laboratory protocols and bioinformatic tools across FiBL. In addition, we will identify funding opportunities to research and understand the benefits of microbial communities for plants and animals, thus increasing the sustainability of agriculture. Finally, we will help our colleagues at FiBL identify strategies to use microbial communities in organic agriculture.