Naturalised populations of mesorhizobia in chickpea (Cicer arietinum L.) cropping soils: effects on nodule occupancy and productivity of commercial chickpea

Background and aims: Chickpea rhizobia did not occur naturally in Australian cropping soils, necessitating inoculation at sowing. Now, after more than 30 years of chickpea cultivation using a single inoculant strain, CC1192, it is likely that chickpea rhizobia are established in 1.0-1.5 Mha cropping land. The aims of this study were to examine effects of the naturalised chickpea rhizobia on nodulation and productivity (total crop N, crop N fixed and grain yield) of commercial chickpea. Methods: Soil was sampled from 26 fields to estimate chickpea rhizobial numbers, relate numbers to edaphic factors and years since previous chickpea crop, determine the proportions of CC1192 and novel strains using RAPD-PCR and subject a subset of novel strains from one site to 16S rRNA analysis. Nodules were harvested from 15 inoculated, commercial chickpea crops to determine occupancy by CC1192. The symbiotic effectiveness of a second subset of novel strains was assessed. Results: The mean number of rhizobia in the soils varied from log 0.08 to log 5.16 rhizobia g soil⁻¹ with population size positively correlated with soil moisture content and negatively correlated with salt concentration (ECe). RAPD-PCR analysis of 570 strains of chickpea rhizobia isolated from the soils indicated only 14 % with molecular fingerprints similar to CC1192. Occupancy by CC1192 of nodules harvested from commercial crops ranged 0-100 %, with an average of 53 %. Occupancy by CC1192 declined by an average 17 % with each log unit increase in numbers of novel chickpea rhizobia. Conclusions: We found no evidence that the novel mesorhizobia in the chickpea soils compromised N₂ fixation or productivity of commercial chickpea crops, even though individual strains had generally reduced symbiotic effectiveness relative to CC1192

Dynamic genomic architecture of mutualistic cooperation in a wild population of Mesorhizobium

Research on mutualism seeks to explain how cooperation can be maintained when uncooperative mutants co-occur with cooperative kin. Gains and losses of the gene modules required for cooperation punctuate symbiont phylogenies and drive lifestyle transitions between cooperative symbionts and uncooperative free-living lineages over evolutionary time. Yet whether uncooperative symbionts commonly evolve from within cooperative symbiont populations or from within distantly related lineages with antagonistic or free-living lifestyles (i.e., third-party mutualism exploiters or parasites), remains controversial. We use genomic data to show that genotypes that differ in the presence or absence of large islands of symbiosis genes are common within a single wild recombining population of Mesorhizobium symbionts isolated from host tissues and are an important source of standing heritable variation in cooperation in this population. In a focal population of Mesorhizobium , uncooperative variants that lack a symbiosis island segregate at 16% frequency in nodules, and genome size and symbiosis gene number are positively correlated with cooperation. This finding contrasts with the genomic architecture of variation in cooperation in other symbiont populations isolated from host tissues in which the islands of genes underlying cooperation are ubiquitous and variation in cooperation is primarily driven by allelic substitution and individual gene gain and loss events. Our study demonstrates that uncooperative mutants within mutualist populations can comprise a significant component of genetic variation in nature, providing biological rationale for models and experiments that seek to explain the maintenance of mutualism in the face of non-cooperators

Diverse Mesorhizobium spp. with unique nodA nodulating the South African legume species of the genus Lessertia

Background and aims: Legumes of the genus Lessertia have recently been introduced to Australia in an attempt to increase the range of forage species available in Australian farming systems capable of dealing with a changing climate. This study assessed the diversity and the nodulation ability of a collection of Lessertia root nodule bacteria isolated from different agro-climatic areas of the Eastern and Western Capes of South Africa. Methods: The diversity and phylogeny of 43 strains was determined via the partial sequencing of the dnaK, 16srRNA and nodA genes. A glasshouse experiment was undertaken to evaluate symbiotic relationships between six Lessertia species and 17 rhizobia strains. Results: The dnaK and 16S rRNA genes of the majority of the strains clustered with the genus Mesorhizobium. The position of the strains at the intra-genus level was incongruent between phylogenies with few exceptions. The nodA genes from Lessertia spp. formed a cluster on their own, separate from the previously known Mesorhizobium nodA sequences. Strains showed differences in their nodulation and nitrogen fixation patterns that could be correlated with nodA gene phylogeny. L. diffusa, L. herbacea and L. excisa nodulated with nearly all the strains examined while L. capitata, L. incana and L. pauciflora were more stringent. Conclusion: Root nodule bacteria from Lessertia spp. were identified mainly as Mesorhizobium spp. Their nodA genes were unique and correlated with the nodulation and nitrogen fixation patterns of the strains. There were marked differences in promiscuity within Lessertia spp. and within strains of root nodule bacteria