How is microbial diversity connected to ecosystem functions? To address this question, we analyse the genetic information stored in soil, i.e., the soil metagenome. Since the end of the 1980’s it has been clear that classical microbiological cultivation techniques provide inadequate access to total microbial diversity: Only 0.1 % of all soil microorganisms are able to grow on common laboratory media and under lab conditions. Alternatively, we therefore analyse total DNA, which we extract directly from soil samples.
Thanks to technological progress, the speed of DNA sequencing has increased by 4 to 5 orders of magnitude since the year 2000. This is a revolution for the way we do soil microbiology. Until a few years ago, a whole research project was required to detect and differentiate a couple of hundred bacteria from a soil sample, but today, we can get the collect genes from several million bacteria in a few days with a single analysis and. To understand this huge body of genetic information, however, requires specific new expertise, especially from the field of bioinformatics. At the Thünen Institute, we integrate the expertise from biodiversity research, ecology, microbiology and bioinformatics. Thereby we are in the position to utilize and exploit the new methodological potentials of the next generation DNA sequencing. And this is important for soil protection, because we only protect what we know. Soil protection becomes more and more important:
Can we develop smarter soil tillage and management practices to prevent the fast microbial degradation of organic fertilizer? Can we increase soil microbial diversity and supress soil microbial pathogens by crop rotations? What happens to microorganisms, e.g., spore-forming clostridia or faecal bacteria, which are introduced with organic fertilizers into soil? How long can they survive in soil and do they actively interfere with soil microbial functions?
In order to evaluate the ecological risks associated with the cultivation of genetically modified (GM) plants, we analyse the diversity of their microbial communities in the rhizosphere. Until a few years ago, we could only detect the dominant community members and typically found no differences with conventional cultivars, but with the new high-throughput DNA sequencing technologies, we find differences. However, the differences between a GM and its parental cultivar is commonly smaller than the differences between two conventionally bread cultivars. Each plant enriches its own microbial community in the rhizosphere, differences between them are natural. But we would like to learn more about the identity of microorganisms and how their functions are stimulated or inhibited by genetically modified crops. Controlled field studies are inevitable to get meaningful data, because soil microorganisms respond differently under field conditions than they do in potting experiments in the laboratory or greenhouse.