During the call for 2012 proposals for the DOE JGI’s Community Sequencing Program, one of the areas of focus researchers were asked to consider was that of plant-microbe interactions. Microbes that live in plants or in the rhizosphere where plant roots and soil interact can play crucial roles in plant health. This is of particular interest to bioenergy researchers who want to develop feedstock crops for cellulosic biofuels production.
With this in mind, an international team of researchers including DOE JGI Microbial Genomics Program Lead Tanja Woyke conducted the first metagenomic analysis of a microbial community of endophytes found inside rice plant roots. The study was published online October 4, 2011 in Molecular Plant-Microbe Interactions.
“Roots are the primary site of interaction between plants and microorganisms,” wrote the researchers. “To meet food demands in changing climates, improved yields and stress resistance are increasingly important, stimulating efforts to identify factors that affect plant productivity.” Learning more about the roles of bacterial endophytes, they added, has been challenging because of the difficulties in cultivating microbes outside of their native environments.
The metagenome was sequenced and assembled at the DOE JGI using the Sanger platform and then gene predictions and annotation were conducted using the IMG/M-ER pipelines. “Our data suggest a high potential of the endophyte community for plant-growth promotion, improvement of plant stress resistance, biocontrol against pathogens and bioremediation, irrespective of their culturability,” the team noted.