Investigation of rhizobial competition

Investigation of rhizobial competition

Rhizobia are soil bacteria that engage in a nitrogen fixing symbiosis with legume plants. The largest part of biological nitrogen incorporation into the earth’s biosphere passes this fixation pathway. Additionally legumes represent important agricultural crop plants in wide parts of the world, because they produce protein rich seeds and are independent of nitrogen fertilization. The selection of rhizobial elite strains with maximum nitrogen fixation capacities is relatively easy, but their effective application in the field is unreliable. Competition of such elite strains with indigenous field populations for nodulation of the legume host plant is a major hindrance for the effective application of crop inoculants in agriculture and constitutes the so called „Rhizobium competition problem“. Genetic determinants that increase nodulation success are scarce and not well characterized. In our group we characterize and compare already isolated markers for their effectiveness. Increased rhizobial nod-gene expression and expression of gene products interfering with the plants ethylene signal transduction pathway have been shown to affect nodulation capacity. Their effectiveness is compared between each other and in competition with field populations.

Systematic screening for new competition determinants is a major aim of our group. Traditional mutational screens for genetic markers that aid competitiveness are limited to lab strains, which were selected for nitrogen fixing performance and not competitiveness. Those studies have produced very limited results so far. A new experimental approach is to characterise natural field populations of Rhizibia that nodulate their specific hosts under defined conditions alongside environmental gradients. Strains that are competitive „winners“ under specific conditions must carry the genetic traits responsible for their success in their genomes. Today, “2nd generation sequencing” allows the genetic analysis of such field isolates (Bailly et al. 2011). “Comparative genomics” with related non-competitive strains from the same selection experiment, will allow the identification of accessory genomic components. The accessory genome most likely contains the adaptive genetic traits responsible for competitive success. Traditional cosmid complementation studies will support the modern in-silico approach. We aim to establish a work pipeline for the systematic search for genetic traits that aid competitive rhizobial strains in the field. This is fundamental work to increase the use of effective crop inoculants in times of increasing energy cost for nitrogen fertilisation and increasing problems with eutrophication worldwide.

Bailly X, Giuntini E, Sexton MC, Lower RPJ, Harrison PW, Kumar N and Young JPW (2011) Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates. ISME Journal 5:1722–1734