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INPLAMINT Subproject C

Christoph Schmid, Peter Schröder und Michael Schloter
Research Unit for Comparative Microbiome Analysis
Helmholtz Zentrum München

Helmholtz Zentrum München

Comparative Microbiome Analysis

Our subproject aims to improve our understanding on the consequences of different amendments to soil for the soil microbiome and its functional traits. Focus is given on processes linked to carbon turnover and nutrient mobilization (mainly N and P). However also other microbial traits liked to an improved plant performance including biocontrol of phytopathogens, plant growth promotion by phytohormones etc. as influenced by the amendments are in the focus of this subproject. Our research is closely linked to the work of FU Berlin, where mainly transportation of nutrients by mycorrhizal fungi are studied, another important function of the soil microbiome in terms of plant growth.
The experimental platforms include the long term field trials in Kiel and Speyer as well as the chronosequence of soils provided by RWE, which differ in their history of agricultural management (0–50 years). Furthermore we contribute to the mesocosm experiments of INPLAMINT and plan an experiment, where microbial diversity will be manipulated in the climate chambers of the Helmholtz Zentrum München. We study both microbiomes of the bulk soil, as they provide the maximal diversity present at a site, and plant associated microbiomes (mostly in the rhizosphere or the root interior). Like in the other subprojects, barley (summer and winter varieties) has been selected as a model plant

Main project aims:

  • To reconstruct of carbon and nutrient cycles in soils where amendments changing the stoichiometry of C:N:P have been applied. Therefore metagenomic tools are used for the characterization of the potential traits provided by microbiomes of different soil- and plant compartments, which are complemented with metatranscritpomic studies, which indicate activation of genes.
  • To identify spatial and temporal dynamics of the microbiomes and to characterize core microbiomes in soil and their interaction pattern (Figure 1). In this respect, we want to understand the role of diversity for resilience and process stability
  • To visualize important microbial groups at the plant soil interface and link these groups to specific activity pattern related to nutrient acquisition (Figure 2)

Overview of Experiments:
The role of microbial diversity for resilience and process stability and the effects of amendments

We are performing an experiment where we artificially reduce diversity in soil. Therefore the original microbiome from a soil will be applied in different dilutions (reducing diversity but not total biomass) to the same soil, which has been sterilized. After an equilibration phase mesocosm experiments will be performed using barley as model plants. We will investigate consequences of resuced diversity for nutrient mobilization as well as carbon sequestration. Further we will analyse plant performance and microbial traits related to plant growth promotion, including biocontrol and production of phytohormones. The plant experiments include the application of different amendments which are typical used at the field sites. Samples will be analyzed in addition by the project partners for root morphology, mycorrhization and nutrient fluxes.

Microbial Network StructuresFigure 1: Microbial network structures and definition of core microbiomes

Microbes in the rhizosphere of barleyFigure 2: Microbes in the rhizosphere of barley (different colors indicate different microbial groups)