Functional integration of nitrogen-fixation in Australian indigenous rhizobia to improve soil fertility

The use of chemical nitrogen fertilizers in agricultural and pasture systems causes pollution of soil, air and water, lethal effects on soil microorganisms, disturbs soil fertility and affects human health. Additionally, with the increase of human population, solutions for sustainable food production are becoming increasingly important. Soil bacteria able to establish nitrogen fixing symbioses with legumes (rhizobia) are an eco-friendly alternative to the use of chemical nitrogen fertilizer. During legume-rhizobia symbiosis, rhizobia induce the formation of root nodules within which they fix atmospheric nitrogen and provide the plant with ammonia for growth. Rhizobia eliminate nitrogen chemical fertilization in legume cultivation and ameliorate soil with biological nitrogen which is released into the soil following plant decay, or deposition from grazing livestock. Legume cultivation increases soil organic carbon sequestration and yield of subsequent crop rotations.
In Australia, all cultivated legumes are inoculated with rhizobial inoculants sourced from overseas because introduced legumes lack their rhizobial partner in soil. However, in rhizobia, genes for the establishment of a nitrogen fixing symbiosis are located on elements capable of moving between bacteria via horizontal gene transfer (HGT), and in farmers’ fields, symbiosis genes transfer from the commercial inoculants to indigenous rhizobia. Indigenous rhizobia then outcompete the commercial inoculants for nodule occupancy because are adapted to local soils, but once inside the nodules, they often fix nitrogen poorly. This extensively documented phenomenon results in the loss of effectiveness of biological nitrogen inoculant strains.
The transition from a soil-dwelling bacterium to a symbiotic lifestyle is complex and, in addition to symbiosis genes, a specific genetic background is required for the integration of the novel metabolic functions into the cellular metabolism. However, the factors allowing symbiosis genes to effectively convert soil bacteria into nitrogen fixers are currently unknown.
The aim of this project is to identify the metabolic processes required for the functional integration of nitrogen fixation in the cell metabolism. My previous work on Australian-indigenous Mesorhizobium highlighted instances where variations in the bacterial genetic background did not support the transition into symbionts. Strains of the same species were either able to fix (fix+) or unable to fix (fix-) nitrogen. This collection represents a unique opportunity to identify genes enabling efficient nitrogen fixation.