gusA Derivatives for the Genetic Analysis of the Root Nodule Bacteria

Reeve, W.G.; Tiwari, Ravi; Rome, Sophie; Dilworth, M. J.; Glenn, A. R.; Howieson, John

doi:10.1007/978-94-011-5159-7_157

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“…To assess strain diversity and identify closely related isolates or clones, DNA fingerprinting was performed using a nif -directed RP01 primer [49] as per conditions indicated in Table S2. The PCR products were then separated on 2% (w/v) agarose gels and images captured [46] . The similarities among digitised profiles were calculated using the Pearson correlation in Bionumerics v5.1 (Applied Maths, Belgium) and an average linkage (UPGMA) dendrogram derived from the patterns.…”

Section: Methodsmentioning

confidence: 99%

Genetic diversity and symbiotic effectiveness of Phaseolus vulgaris-nodulating rhizobia in Kenya

Mwenda

O’Hara

Meyer

et al. 2018

Systematic and Applied Microbiology

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Phaseolus vulgaris (common bean) was introduced to Kenya several centuries ago but the rhizobia that nodulate it in the country remain poorly characterised. To address this gap in knowledge, 178 isolates recovered from the root nodules of P. vulgaris cultivated in Kenya were genotyped stepwise by the analysis of genomic DNA fingerprints, PCR-RFLP and 16S rRNA, atpD, recA and nodC gene sequences. Results indicated that P. vulgaris in Kenya is nodulated by at least six Rhizobium genospecies, with most of the isolates belonging to Rhizobium phaseoli and a possibly novel Rhizobium species. Infrequently, isolates belonged to Rhizobium paranaense, Rhizobium leucaenae, Rhizobium sophoriradicis and Rhizobium aegyptiacum. Despite considerable core-gene heterogeneity among the isolates, only four nodC gene alleles were observed indicating conservation within this gene. Testing of the capacity of the isolates to fix nitrogen (N2) in symbiosis with P. vulgaris revealed wide variations in effectiveness, with ten isolates comparable to Rhizobium tropici CIAT 899, a commercial inoculant strain for P. vulgaris. In addition to unveiling effective native rhizobial strains with potential as inoculants in Kenya, this study demonstrated that Kenyan soils harbour diverse P. vulgaris-nodulating rhizobia, some of which formed phylogenetic clusters distinct from known lineages. The native rhizobia differed by site, suggesting that field inoculation of P. vulgaris may need to be locally optimised.

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Section: Methodsmentioning

confidence: 99%