Genomic and Applied Microbiology

Research project:

Assessment of the functional diversity of soil microbial communities in the German Biodiversity Exploratories by metagenomics

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-supported by the Deutsche Forschungsgemeinschaft

The microbial diversity in soils exceeds that of other environments and analyzing the diversity of soil microbial communities is still a great challenge. The project is part of an initiative that aims to explore the diversity of soil microorganisms with respect to vegetation type and land use intensity and relate it to ecological gradients at different scales by employing metagenomic technologies. The research is carried out at grassland and forest sampling sites within the framework of the three German Biodiversity Exploratories. An approach will be developed and exemplarily applied that copes with the enormous microbial diversity of soil. The approach is based on identifying and selecting (filtering) targets such as groups of organisms or genes encoding key microbial functions (here cellulolytic and lipolytic enzymes) before analyzing their distribution at different spatiotemporal scales in relation to vegetation type and use intensity. This strategy relies on three steps: (i) Construction of complex metagenomic libraries from microbial DNA extracted from soil samples covering different vegetation types and use intensities. (ii) Comparative screening of the libraries for exemplary groups of organisms and functions and metabolic profiling via snapshot sequencing are performed to identify (filter) targets that display differences and present distinct profiles between the sampling plots. (iii) Construction and use of microarrays and primers for monitoring the filtered targets in the Exploratories in relation to vegetation type, use intensity, and spatiotemporal variation.


Subproject: Exploring a cradle of multi-resistant bacteria – antibiotic resistance in soil and its link to different land use types and intensities

Human pathogenic bacteria resistant to multiple classes of antibiotics pose risks to public health and are considered as one of the major global challenges within the 21st century. Some of the antibiotic resistance genes carried by these bacteria have been traced to soil origins and can potentially spread via e.g., groundwater or wildlife. In this project, the dynamics of soil’s antibiotic resistance pool will be analyzed along a wide array of land use types and intensities within the three Biodiversity Exploratories.

Goals:

  • To explore changes in antibiotic resistance gene abundance level associated with different land use practices and intensities.
  • To investigate land use-induced changes in community profiles of antibiotic-resistant soil bacteria.
  • Identification of land use-specific shifts in quantity and diversity of plasmids potentially allowing spread of antibiotic resistance.
  • To discover antibiotic resistance genes and mechanisms in soils derived from hardly as well as intensively managed forest and grassland.


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