Application of molecular techniques to studies in Rhizobium ecology: a review

Abstract

The symbiosis between legumes and their specific root-nodule bacteria, rhizobia, has been employed to improve agricultural productivity for most of the 20th century. During this time, great advances have been made in our knowledge of both plant and bacterial genomes, the biochemistry of the symbiosis, plant and bacterial signaling and the measurement of nitrogen fixation. However, knowledge of the ecology of the bacterial symbiont has lagged behind, largely due to a lack of practical techniques that can be used to monitor and assess the performance of these bacteria in the field. Most techniques developed in the last few decades have relied on somehow ‘marking’ individual strains to allow us to follow their fate in the field environment. Such techniques, while providing knowledge of the success or failure of specific strains in a range of environments, have not allowed insight into the nature of the pre-existing rhizobial populations in these sites, nor the interaction between marked strains and the background population. The advent of molecular techniques has revolutionised the study of Rhizobium ecology by allowing us to follow the flux of a variety of ecotypes within a particular site and to examine how introduced rhizobia interact with a genetically diverse background. In addition, molecular techniques have increased our understanding of how individual strains and populations of root-nodule bacteria respond to changes in the environment and how genetic diversity evolves in field sites over time. This review focuses on recently developed molecular techniques that hold promise for continuing to develop our understanding of Rhizobium ecology and how these can be used to address a range of applied problems to yield new insights into rhizobial life in soil and as legume symbionts.