Genomic and Applied Microbiology

Research project:

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

-supported by the Deutsche Forschungsgemeinschaft (DA 374/6-1)

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.

Second funding period:
Assessment of structure and function of soil bacterial communities along land use and management gradients in the Biodiversity Exploratories
(DFG DA 374/6-1)

Bacteria are the most abundant and diverse group of microorganisms in soil. Bacteria are important for most nutrient transformations in soil and major drivers for biogeochemical cycles. The composition and function of soil bacterial communities along different land use types and management types will be analyzed in the framework of the three Biodiversity Exploratories. To identify changes in indigenous gene- and taxon-specific patterns and key metabolic functions accompanying different management types phylogenetic and functional profiling of soil bacterial communities are performed by using metagenomic and metatranscriptomic approaches. The changes in species richness, abundance, and distribution of phylogenetic groups and key functions are assessed and compared by bar-coded amplicon pyrosequenicng of bacterial 16S rRNA genes and pyrosequencing of mRNA (cDNA). To provide robust assessments of variability of soil bacterial community structures and the impact of management type comparison of large-effects and small-scale effects will be carried out by analysis of all 300 experimental plots and one individual plot, respectively. All data are correlated with soil attributes and management types. Another focus is to investigate the impact of tree species type on soil bacterial diversity, community structure, and function in selected pure forest stands (beech, oak, spruce) over time. In addition, the distribution of key functions will be monitored across all experimental plots by PCR-based approaches. The focus will be on genes involved in biogeochemical cycles (C and N).

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