Rhizobia compatible with crop and pasture legumes aren’t naturally present in Australian soils, which has led to the introduction of many highly effective nitrogen-fixing bacteria from other parts of the world as commercial inoculant strains. Rhizobial symbiosis genes (nod/nif/fix) are encoded from mobile genetic elements, such as plasmids or integrative and conjugative elements (ICEs). As a result they are highly mobile and able to transfer between strains (Poole, Ramachandran et al. 2018).
Recently, it has become increasingly clear that the genetic diversity of strains nodulating legumes far exceeds the diversity of strains introduced as inoculants (Demezas, Reardon et al. 1995, Hebb, Richardson et al. 1998, Ballard, Charman et al. 2004, Stepkowski, Moulin et al. 2005). This could partly be explained by horizontal transfer of symbiosis genes between inoculants and pre-existing soil bacteria, creating novel hybrid rhizobia (Nandasena, O'Hara et al. 2006, Nandasena, O'Hara et al. 2007, Hill, Colombi et al. 2021). It could also be due to the accumulation of mutations giving rise to newly evolved rhizobia.
Given this genetic instability, a blueprint for inoculant genomes is important to maintain the integrity of this crucial national resource. However, we lack the genomic data on the commercial legume inoculants needed to track changes in genome structure and content as well as the technology to easily identify strains within nodules. In this project, we describe the complete genome sequencing of the Australian commercial rhizobial inoculants, with special attention paid to the symbiosis genes, and examine their relationship to each other, as well as to the broader set of publicly available genome sequences. This critical baseline data can be used to address fundamental issues surrounding inoculant usage including the identity of the bacterium within a nodule and how the inoculants change over time.