Microbial communities in the rhizosphere analyzed by cultivation-independent dna-based methods

Abstract

The development of methods to extract nucleic acids directly from the rhizosphere or from microbial cells detached by a mechanical treatment from roots opened new dimensions to study the rhizosphere microbiome and to overcome limitations of cultivation-dependent methods. This chapter summarizes the potentials and limitations of cultivation-independent methods used by our group in the last 15 years to investigate microbial communities in the rhizosphere and their response to changing environmental conditions. We showed that rhizosphere microbial communities are highly dynamic, and that their composition is mainly shaped by the plant and the soil type and factors influencing these drivers of microbial diversity in the rhizosphere.