Colonization by bacteria of the rhizosphere is crucial to plant productivity, with plants secreting 10-30% of total photosynthate to the rhizosphere. While rhizosphere colonization is poorly understood, recent advances in genome sequencing and analysis makes it possible to address this in exciting new ways. Microarray and metabolic analysis has been used to dissect the composition of the pea root secretome and map the transcriptional response of bacterial to secreted metabolites. Most recently this work has led to identification of the master regulator of attachment of Rhizobium leguminosarum to pea roots.
We are now developing a suite of lux biosensors to the presence of specific metabolites that are being used for spatial and temporal mapping of root secretion. In addition they are excellent biosensors to enable identification of plant mutants altered in metabolite secretion. Plants are also excellent models to develop systems of experimental selection to examine how specific microbes are selected. Fingerprinting techniques such as ARISA and high through put sequencing are being used to map community level changes in the rhizosphere microbial community (microbiome). Coming full circle these techniques allow us to examine how natural variation and mutation of key regulatory systems in plants control the rhizosphere microbiome.