Abstract
The genetic diversity and identification of slow- and fast-growing soybean root nodule bacterial isolates from different agro-climatic regions in Mpumalanga, Limpopo and Gauteng Provinces of South Africa were evaluated. The 16S-rDNA-RFLP analysis of 100 rhizobial isolates and eight reference type strains placed the isolates into six major clusters, and revealed their site-dependent genomic diversity. Sequence analysis of single and concatenated housekeeping genes (atpD, glnII and gyrB), as well as the symbiotic gene nifH captured a considerably higher level of genetic diversity and indicated the dominance of Bradyrhizobium diazoefficiens and Bradyrhizobium japonicum in Mpumalanga, Limpopo and Gauteng Provinces. Gene sequence similarities of isolates with type strains of Bradyrhizobium ranged from 97.3 to 100% for the 16S rDNA, and 83.4 to 100% for the housekeeping genes. The glnII gene phylogeny showed discordance with the other genes, suggesting lateral gene transfer or recombination events. Concatenated gene sequence analysis showed that most of the isolates did not align with known type strains and might represent new species from South Africa. This underscores the high genetic variability associated with soybean Bradyrhizobium in South African soils, and the presence of an important reservoir of novel soybean-nodulating bradyrhizobia in the country. In this study, the grouping of isolates was influenced by site origin, with Group I isolates originating from Limpopo Province and Groups II and III from Mpumlanga Province in the 16S rDNA-RFLP analysis.
Highlights
Soybean (Glycine max [L.] Merrill) is a grain legume belonging to the family Leguminosae (Fabaceae) and sub-family Papilionoideae [16,23,65]
Pure single colony of each isolate was used for host-nodulation test with soybean variety PAN 1666, in fulfilment of Koch’s postulate. Reference strains such as Rhizobium leguminosarum USDA 2370T, B. japonicum USDA 6T, B. diazoefficiens USDA 110T, B. elkanii USDA 76T, Ensifer meliloti (Sinorhizobium meliloti) USDA 1002T and Ensifer medicae (S. medicae) USDA 103T used in this study, were obtained from the National Rhizobium Germplasm Resource Collection USDA-ARS-SGIL, Beltsvile, USA
Group II consisted of 22 rhizobial isolates that clustered with reference Bradyrhizobium strains USDA 6, H1, USDA 76 and USDA 110 with a similarity coefficient of 0.20
Summary
Soybean (Glycine max [L.] Merrill) is a grain legume belonging to the family Leguminosae (Fabaceae) and sub-family Papilionoideae [16,23,65]. It originated from North-eastern China and is currently cultivated worldwide under various climatic conditions [6,46]. About 109 980 000 ha of land are under soybean production worldwide [59]. Soybean production in Africa is constrained by several factors, including the lack of compatible rhizobia in many African soils [41]. Promiscuous soybean varieties, which nodulate with indigenous soil rhizobia, have been bred to overcome the nodulation problem [1,41]
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