Advanced molecular tools for analysis of bacterial communities and their interactions in the rhizosphere

The analysis of microbial communities of the plant rhizosphere has recently been spurred by the greatly advanced DNA- or RNA-based molecular techniques that have become available. The application of these tools has allowed us to understand, at the phylogenetic level, which organisms occur together at the plant root. We can further infer, from the nucleic-acid-based data, which organisms may be positively or negatively selected by the plant root. In that respect, the traditional fingerprinting methods such as PCR-DGGE have, in recent years, been overwhelmed by direct pyrosequencing approaches. The outcomes of both types of studies have yielded rather similar conclusions with respect to effects of plant cultivar type and growth stage on the plant-associated bacteria. On the other hand, using these very advanced tools, it has been difficult to discern the interactions that are key to determining the intricacies of the life of root-associated microorganisms. We examine here the existing state of the art in this area, making use of case studies that illustrate the key achievements that have been made. Major points discussed are the intricacies of the use of environmental nucleic acids for the analyses, as well as the effects of plant physiology and plant type in shaping the plant-associated microbiota. In addition, we critically examine how to move forward in our examination of microbial interactions in the rhizosphere. It is vital that the emerging tools are now applied to dissect the interactions between microorganisms at the micrometer level, which is the scale at which interorganism signals are perceived and obeyed