Crotalarieae and Genisteae of the South African Great Escarpment are nodulated by novel Bradyrhizobium species with unique and diverse symbiotic loci

Beukes, Chrizelle W.; Stępkowski, Tomasz; Venter, Stephanus N.; Cłapa, Tomasz; Phalane, Francina L.; Roux, M.M. Le; Steenkamp, Emma Theodora

doi:10.1016/j.ympev.2016.04.011

Cited by 37 publications

(47 citation statements)

References 99 publications

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“…Furthermore, a recent study of the symbionts of legumes found in the sub-Himalayan region of India showed that they are nodulated by distinct Bradyrhizobium strains that represent new species to science [ 19 ]. Likewise, legumes of the Core Cape Subregion (CCR) of Southern Africa are predominantly nodulated by unique Burkholderia and Mesorhizobium strains [ 20 , 21 , 22 ], whereas those from the Grassland and Savannah biomes of the region are largely nodulated by unique strains of Bradyrhizobium [ 23 ]. Therefore, the distribution of rhizobia is as prone to biogeographic limitations as other living organisms.…”

Section: Introductionmentioning

confidence: 99%

Differential Preference of Burkholderia and Mesorhizobium to pH and Soil Types in the Core Cape Subregion, South Africa

Dludlu

Chimphango

Stirton

et al. 2017

Genes

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Over 760 legume species occur in the ecologically-heterogeneous Core Cape Subregion (CCR) of South Africa. This study tested whether the main symbionts of CCR legumes (Burkholderia and Mesorhizobium) are phylogenetically structured by altitude, pH and soil types. Rhizobial strains were isolated from field nodules of diverse CCR legumes and sequenced for 16S ribosomic RNA (rRNA), recombinase A (recA) and N-acyltransferase (nodA). Phylogenetic analyses were performed using Bayesian and maximum likelihood techniques. Phylogenetic signals were determined using the D statistic for soil types and Pagel’s λ for altitude and pH. Phylogenetic relationships between symbionts of the narrowly-distributed Indigofera superba and those of some widespread CCR legumes were also determined. Results showed that Burkholderia is restricted to acidic soils, while Mesorhizobium occurs in both acidic and alkaline soils. Both genera showed significant phylogenetic clustering for pH and most soil types, but not for altitude. Therefore, pH and soil types influence the distribution of Burkholderia and Mesorhizobium in the CCR. All strains of Indigofera superba were identified as Burkholderia, and they were nested within various clades containing strains from outside its distribution range. It is, therefore, hypothesized that I. superba does not exhibit rhizobial specificity at the intragenic level. Implications for CCR legume distributions are discussed.

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Section: Introductionmentioning

confidence: 99%

Differential Preference of Burkholderia and Mesorhizobium to pH and Soil Types in the Core Cape Subregion, South Africa

Dludlu

Chimphango

Stirton

et al. 2017

Genes

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“…The strength of ecological drift is indeed assumed to be stronger in functionally redundant taxa such as the case of Mesorhizobium in rooibos (Hassen et al, 2012;Zhou and Ning, 2017). The fact that we find a number of endemic Bradyrhizobium taxa in Skimmelberg is also suggestive that rhizobia in rooibos can become isolated, particularly in such a heterogeneous landscape (Cowling et al, 2009;Beukes et al, 2016;Dudlu et al, 2018;Stepkowski et al, 2018). However, even in Skimmelberg or the Cederberg mountain ranges we identified all rhizobial community types, indicating that soil rhizobial populations still underpin soil legacies from historical events of dispersal and changing habitat conditions (Stepkowski et al, 2018).…”

Section: Discussionmentioning

confidence: 62%

Ecological patterns of root nodule diversity in cultivated and wild rooibos populations: a community prediction approach

Ramoneda

Roux

Frossard

et al. 2020

Preprint

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There is interest in understanding the factors behind the biogeography of root-associated bacteria due to the joint effects that plant host, climate, and soil conditions can have on bacterial diversity. For legume crops with remaining wild populations, this is of even more importance, because the effects of cropping on undisturbed root-associated bacterial communities can be addressed. Here, we used a community prediction approach to describe the diversity of the root nodule bacterial communities of rooibos (Aspalathus linearis), an endemic legume crop from South Africa. The goal was to reveal whether patterns of root nodule community composition in paired cultivated and wild rooibos populations could be related to geographical distance, plant traits, and plant population type (i.e. cultivated or uncultivated). We identified a core of dominant and widespread Mesorhizobium ZOTUs that each defined one of 4 different root nodule community classes. Rooibos cultivation impacted root nodule bacterial diversity at regional and local scales, while the geographical origin of the root nodule communities was the strongest predictor of root nodule community structure. Beyond impacts of cultivation on root nodule bacterial diversity, this study suggests a mixture of dispersal limitation and ecological drift regionally, and selection by different plant populations locally, define the biogeography of rooibos root nodule bacterial communities.

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“…It has been reported that sequence analysis of nodA and nifH genes can be useful to examine the symbiotic diversity of Bradyrhizobium strains and elucidate the role of LGT in inheritance of the symbiotic loci (Degefu et al 2018). The phylogenetic studies of nodA and nifH symbiotic genes, which revealed 16 major clades in the genus Bradyrhizobium, have facilitated the development of the phylogeographic framework for this group of bacteria (Beukes et al 2016;Stępkowski et al 2018). In our study the clustering results of the nodA sequences of the tested isolates were essentially similar to those obtained from the nifH gene sequence analysis (Figs.…”

Section: Discussionmentioning

confidence: 99%

“…4). Following the classification scheme described for symbiotic genes of Bradyrhizobium symbionts, the strains nodulating L. anagyroides in Poland, like all other B. jicamae supergroup strains, appear to belong to a group referred to as Clade IV (Beukes et al 2016).…”

Section: Discussionmentioning

confidence: 99%

Bradyrhizobia associated with Laburnum anagyroides, an exotic legume grown in Poland

Sajnaga

Jach

2020

Symbiosis

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We isolated 18 rhizobial strains from root nodules of a leguminous shrub Laburnum anagyroides (common laburnum) grown in Southeast Poland as an exotic plant. With the use of BOX-PCR fingerprinting, the isolates were clustered into 2 main groups and one separate lineage, which was congruent with the ITS-RFLP results. The phylogenetic trees constructed based on 16S rRNA and combined atpD, dnaK, glnA, and recA gene sequence data separated the representative strains into three evolutionary lineages within the Bradyrhizobium jicamae supergroup, with Bradyrhizobium algeriense and Bradyrhizobium valentinum as the closest relatives. The nodA and nifH gene phylogenies proved that the L. anagyroides symbionts carry a symbiotic gene variant known as Clade IV, representing the symbiovar retamae. Phenotypic characteristics of the isolates and reference strains are also reported. Our study of the rhizobia nodulating L. anagyroides growing in Poland complements earlier few findings on the symbiotic associations of this Genisteae species.

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Crotalarieae and Genisteae of the South African Great Escarpment are nodulated by novel Bradyrhizobium species with unique and diverse symbiotic loci

Cited by 37 publications

References 99 publications

Differential Preference of Burkholderia and Mesorhizobium to pH and Soil Types in the Core Cape Subregion, South Africa

Differential Preference of Burkholderia and Mesorhizobium to pH and Soil Types in the Core Cape Subregion, South Africa

Ecological patterns of root nodule diversity in cultivated and wild rooibos populations: a community prediction approach

Bradyrhizobia associated with Laburnum anagyroides, an exotic legume grown in Poland

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