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Mobile symbiotic elements in inoculant rhizobia

MacLean G Kohlmeier 1, Graham W O’Hara 1, Joshua P Ramsay 2, and Jason J Terpolilli 1 

1 Legume Rhizobium Sciences, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia 

2 Curtin Medical School and Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia,

Australia Rhizobia are nitrogen-fixing bacteria that form symbiotic relationships with legumes and are widely used as inoculants in Australian agriculture. However, the agricultural legumes grown in Australia are exotic species, meaning the rhizobia naturally found in Australian soils are not compatible and cannot establish symbiosis with them. As a result, compatible rhizobia have been imported from other parts of the world for use as inoculants. In rhizobia, the genes required for establishing and maintaining symbiosis are located on mobile genetic elements, such as plasmids (pSyms), integrative and conjugative elements (ICEs), and symbiosis islands (SIs). These mobile elements can transfer between strains via horizontal gene transfer (HGT). Following inoculation, the transfer of symbiosis-related genes from inoculant rhizobia to non-symbiotic soil bacteria can generate novel symbionts with varying nitrogen fixation efficiencies. This can potentially lead to competition with the original inoculant strains, reducing the efficacy of the inoculation. However, there is limited genomic information available for most inoculant strains, complicating the study of HGT. To address this gap, 37 novel genomes were generated, and 42 total sequences were analysed, with particular focus on mobile symbiosis-related regions. The inoculants analysed were diverse, representing five genera— Bradyrhizobium, Mesorhizobium, Methylobacterium, Rhizobium, and Sinorhizobium— and at least 19 different species. Symbiotic genetic elements were identified in every strain, including 17 pSyms, four symbiosis ICEs, and 20 SIs. Importantly, these genome sequences will enable accurate strain identification and monitoring of inoculants in the environment. They will also facilitate the detection of HGT events involving native rhizobia, helping to ensure the continued efficacy and integrity of Australia's legume inoculation program.

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