Research on the soil metagenome

Background

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:

  • To feed a growing world population while concomitantly experiencing a dramatic loss of fertile land by erosion and salinization. This forces us to increase agricultural productivity per acre while preserving and better exploiting its natural (microbial) potential.
  • because land conversion from natural ecosystems, e.g. forests, to crop land has enormous consequences for the living conditions of microorganisms. One of our current research priorities is to understand the implications of land conversion on microbial communities and their factions: what is lost and what is gained?
  • because cropping systems relyi on mono-cultures which may have immediate advantages for farmers, but bear the the risk that soil microbial pathogens may be enriched, threatening yield loss due to  plant diseases.
  • because increasing the intensity of soil tillage and management causes loss of soil organic matter and destroys soil structure, thus impairing the capacity of soil to store nutrients and sustain microbial activity. The addition of organic fertilizers, intended to compensate for that loss, is often inefficient, because significant amounts of added carbon are lost due to microbial activity as carbon dioxide.

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.