Metagenomics for the analysis of microbial soil functions

Wien

2007

S. 12

Artikel aus einer ZeitschriftUnselbständiges Werk

200140632

The vast majority of soil microorganisms cannot be studied in pure culture and therefore are poorly characterized regarding their functional roles. Introducing cultivation-independent, molecular methods based on phylogenetic markers such as 16S rRNA genes has opened new perspectives on microbial communities and their phylogenetic relationships, but gives only limited clues about their ecological roles. Functional gene based analysis, conversely, gives information on the metabolic capabilities of microbial communities in their natural settings, but in many cases fails to relate these qualities to specific organisms. Metagenomics provides a novel, powerful tool for linking phylogeny and function of uncultured microorganisms within microbial ecology studies. This technology targets the collective genomes of a given microbial community, i.e. the metagenome, and makes them accessible by direct cloning into a cultivable host, typically E. coli. The resulting metagenomic libraries can then be screened for physiological functions as well as for "phylogenetic anchors", which enable to phylogenetically assign the respective metagenomic clones. Metagenomic libraries were constructed from soil of the Rothwald forest, which is extraordinarily rich in nutrients and microbial biomass and shows rapid nutrient turnover. These libaries, which comprise 23.500 fosmid clones with average insert sizes of 30 kb, are valuable resources for multiple microbial functions relevant not only for ecological studies but also for biotechnological applications. In the present study, which is centered on nitrogen cycling in the Rothwald forest soil, the fosmid libaries are used to explore the denitrifying bacteria in this forest soil. A sequence-driven screening technique is employed which uses magnetic beads to capture fosmid clones harboring nitrite reductase genes and the genetic context of these genes is successively analyzed. Complementary to the metagenomics studies, the denitrifying communities in the Rothwald forest are described through functional gene analysis and process measurements.