The symbiosis is initiated by nitrogen starvation within the plant, this leads to an exchange of signal molecules between the pant and the rhizobium spp leading to extended rooting and root nodule formation expressing the genes for nitrogen fixation in the bacteria. This allows atmospheric nitrogen (N₂) to be converted into ammonium (NH₄+).

The Rhizobia provide ammonia or amino acids whilst the plant provides organic acids as a carbon and energy source.

There are two hypothesis that are not exclusive as to how the relationship is managed.

The Sanction Choice – the plant limits oxygen, carbon dioxide supply to the parasitic rhizobia resulting in smaller nodules, earlier nodule death.

The plant may not be able to recognise the other more parasitic or less nitrogen fixing rhizobia that can drain the plant. The second hypothesis – Partner Choice – proposes the plant only accepts specific rhizobia not the parasitic spp, and only supports them with nutrients.

Neither is exclusive and both mechanism can contribute to the rhizobia population management.

Thus inoculation is a way of putting the odds in the plants favour of a positive association and maximising the symbiotic relationship.