Adapted rhizobia to boost chickpea performance

Chickpea is an introduced crop and the specific group of rhizobia that fix nitrogen with it are not naturally present in Australian soils. This means chickpeas need to be inoculated with the Group N inoculant rhizobia strain Mesorhizobium ciceri CC1192. This strain, originally sourced from Israel, has been used since 1977 as the inoculant for chickpeas across Australia.

Starting in the mid-1990s, work in New Zealand and Australia on introduced Mesorhizobium inoculant strains for pasture legumes showed this group of rhizobia carry symbiosis genes on a mobile piece of DNA that can transfer between bacteria in the soil.

Analysis of the chickpea inoculant strain by Murdoch University’s Legume Rhizobium Sciences (LRS) centre showed that it similarly carries its symbiosis genes on a mobile region of DNA called an Integrative and Conjugative Element, or ICE.  The ICE carrying the symbiosis genes can move from CC1192 to a recipient strain that normally is unable to nodulate and fix nitrogen with chickpeas.

More recent work has shown that in Australian soils, strains receiving the symbiosis ICE appear to be groups of indigenous bacteria genetically similar to CC1192, but which lack their own symbiosis genes. When they pick up the symbiosis genes, they are converted into a symbiotic strain. The problem is that although these newly evolved strains have acquired the ability to nodulate chickpeas, they don’t always fix nitrogen effectively.

It is not clear whether suboptimally effective novel strains are more competitive at nodulating chickpeas than CC1192. If they are, this could potentially reduce the efficacy of legume nitrogen fixation.

Dr Yvette Hill investigating newly evolved rhizobia species.    Photo: Evan Collis

Jumping rhizobium genes

To get a handle on how widespread symbiosis ICE transfer is and its impact on nitrogen fixation, work at LRS has examined the genetic diversity and effectiveness of chickpea rhizobia isolated from soils sampled from farms across all of Western Australia’s agro-ecological zones.

Using a rhizobia-specific genome sequencing pipeline developed at LRS, this has shown that 28 per cent of strains isolated were not the inoculant strain. The distribution of CC1192 versus novel ICE recipients isolated varied considerably across the zones, with the Ord River irrigation area and Western Australian central agro-ecological zones having 81 per cent and 51 per cent novel strains, with decreasing proportions through the eastern, northern and sandplain zones at 22, 12 and 4 per cent of the strains isolated respectively.

Additionally, the diversity of the ICE recipients collected from across the state that are capable of nodulating chickpeas is considerable, with more than 31 different novel strains detected based on molecular fingerprints. All the novel strains have the CC1192 symbiosis genes, meaning they have evolved recently by acquiring these genes from the inoculant strain.

The study so far has found some novel strains are suboptimally effective, with work to understand their prevalence and impact on nitrogen fixation ongoing. Current work is also extending this survey to chickpea growing areas in NSW and Queensland to better understand symbiosis ICE transfer in areas of sustained and intensive chickpea production.

Adapted to Australian soils

Several novel strains have been identified from the WA study that fix nitrogen on par with CC1192, but with potential for greater tolerance to acid soils and desiccation than the inoculant strain.

These strains are currently being evaluated through a national program which tests their performance throughout chickpea regions across the country, in comparison to the current commercial inoculant strain. If they prove superior to CC1192, they could ultimately become a new inoculant for chickpeas, but this will take up to 10 years depending on future research outcomes and extensive field trials and inoculum stability tests.

Selecting nodules to assess nodule occupancy by rhizobia and nodule morphology. Photo: Evan Collis

Importantly, although the novel strains isolated from Australian soils are genetically very diverse, their symbiosis genes are not – they are in fact all derived from CC1192.

This means the likelihood of finding a strain that is more effective than CC1192 from isolations made in Australia is very low. CC1192 has been the commercial inoculant for chickpeas in Australia for 45 years, yet this strain was originally selected from a very small cohort of five strains.

In contrast, modern strain selection programs for other agricultural legumes have delivered new elite inoculant strains after screening many hundreds, if not thousands, of potential strains. Therefore, more rhizobia germplasm needs to be sourced from international locations with long histories of chickpea cultivation, and which are climatically and edaphically matched to Australian growing conditions.

These collections will have a much better chance of identifying symbiotically diverse chickpea rhizobia that could well provide Australian growers with a more-effective and robust inoculant strain for this grain legume.