The productivity of agricultural systems is usually nitrogen dependent. As oil prices rise, so does the price of nitrogen fertilizer, which impacts strongly on global farming economics. The only substitute for fertilizer nitrogen is the use of symbiotic legumes and their nitrogen-fixing rhizobia. This market is worth in excess of US$13 billion globally. The clover rhizobia are amongst the most utilized species of root-nodule bacteria in world agriculture, yet no clover microsymbiont genome has been sequenced. It is thus the goal of this project to completely sequence Rhizobium leguminosarum bv. trifolii (hereafter R. trifolii) using the well characterized, yet dissimilar strains, WSM1325 and WSM2304. Strain WSM1325 is compatible with many perennial clovers of Mediterranean origin used in farming, such as T. pratense, and is therefore one of the most important clover inoculants. However, WSM1325 is incompatible with American and African perennial clovers, such as those nodulated by WSM2304, and it is essential we understand this incompatibility. Progress in this pursuit will be greatly enhanced by genome sequence information.

One of the critical challenges faced by farmers growing clovers is to produce highly effective nitrogen-fixing symbioses in both annual and perennial species using current inoculum-quality strains of rhizobia. Although, historically, annual and perennial species have rarely been used simultaneously, the development of secondary salinity from rising water tables has necessitated a redesign of water use systems in agriculture. This is particularly so in Australia, but also in both North and South America as well as in the Indian subcontinent. It is likely that perennial species will be grown alongside annual species to achieve hydrological stability.

Most inoculants form nitrogen-fixing symbioses with either annual or perennial species; very few form nitrogen-fixing symbioses with both, and those that do tend to have a restricted host range. This nexus presents severe problems for the management of symbiotic interactions in agricultural soils where there are background populations that may nodulate, but ineffectively fix nitrogen. Competition for legume nodulation, such as that between annual and perennial, or indigenous and introduced inoculants, is a recurring and widespread issue that compromises nitrogen fixation, and hence legume productivity in many farming systems.