Phylogeny and distribution of Bradyrhizobium symbionts nodulating cowpea (Vigna unguiculata L. Walp) and their association with the physicochemical properties of acidic African soils

Abstract

In the N 2 -fixing symbiosis, the choice of a symbiotic partner is largely influenced by the host plant, the rhizobial symbiont, as well as soil factors. Understanding the soil environment conducive for the survival and multiplication of root-nodule bacteria is critical for microbial ecology. In this study, we collected cowpea-nodules from acidic soils in Ghana and South Africa, and nodule DNA isolates were characterized using 16S–23S rRNA-RFLP, phylogenetic analysis of housekeeping and symbiotic genes, and bradyrhizobial community structure through canonical correspondence analysis (CCA). The CCA ordination plot results showed that arrow of soil pH was overlapping on CCA2 axis and was the most important to the ordination. The test nodule DNA isolates from Ghana were positively influenced by soil Zn, Na and K while nodule DNA isolates from South Africa were influenced by P. The amplified 16S–23S rRNA region yielded single polymorphic bands of varying lengths (573–1298 bp) that were grouped into 28 ITS types. The constructed ITS-dendrogram placed all the nodule DNA isolates in five major clusters at low cut-off of approx. 0.1 Jaccard’s similarity coefficient. The phylogenetic analysis of 16S rRNA and housekeeping genes ( glnII, gyrB, and atpD ) formed distinct Bradyrhizobium groups in the phylogenetic trees. It revealed the presence of highly diverse bradyrhizobia (i.e. Bradyrhizobium vignae , Bradyrhizobium elkanii , Bradyrhizobium iriomotense , Bradyrhizobium pachyrhizi , and Bradyrhizobium yuanmingense ) together with novel/unidentified bradyrhizobia in the acidic soils from Ghana and South Africa. Discrepancies noted in the phylogenies of some nodule DNA isolates could be attributed to horizontal gene transfer or recombination.

Phylogenetic evidence of allopatric speciation of bradyrhizobia nodulating cowpea (Vigna unguiculata L. walp) in South African and Mozambican soils

“…(Mohammed, Jaiswal and Dakora 2018) and Puozaa et al . (Puozaa, Jaiswal and Dakora 2019) also reported that soil pH and mineral nutrients can influence the diversity of bradyrhizobial populations in South African and Ghanaian soils, and found that N, P and Na concentrations could specifically influence South African isolates. The results of this study also suggested that bradyrhizobial distribution in soil was strongly controlled by soil physico-chemical properties such as pH, and mineral nutrients.…”

“…Cowpea is one of the most important indigenous legume crops in Africa, with both wild and cultivated forms growing across the continent (Mohammed, Jaiswal and Dakora 2018). West Africa is the centre of origin of this crop (Jaiswal and Dakora 2019; Puozaa, Jaiswal and Dakora 2019). Cowpea can meet 66% to 96% of its N nutrition from symbiotic fixation (Jaiswal and Dakora 2019).…”

“…2017; Tampakaki et al . 2017; Chidebe, Jaiswal and Dakora 2018; Mohammed, Jaiswal and Dakora 2018; Jaiswal and Dakora 2019; Puozaa, Jaiswal and Dakora 2019). However, knowledge gaps still exist in the genetic diversity and biogeographic distribution of indigenous N 2 -fixing rhizobia in Southern Africa.…”

Symbiotic effectiveness and ecologically adaptive traits of native rhizobial symbionts of Bambara groundnut (Vigna subterranea L. Verdc.) in Africa and their relationship with phylogeny

“…Puozaa et al . 3,19 and Ndungu et al . 29 also recently reported a significant influence of soil mineral nutrients on the bradyrhizobial distribution in some African soils, which all indicate the roles of these soil factors on the occurrence and persistence of rhizobial types in different geographic areas.…”

A Genomotaxonomy View of the Bradyrhizobium Genus

“…Novel markers such as ftsA gene provide congruent phylogenies to those derived from recA and glnII gene sequences (Kalita and Malek, 2019). Bradyrhizobium diversity knowledge has expanded recently with studies from native legumes in Africa (Gronemeyer et al, 2017; Jaiswal and Dakora, 2019; Puozaa et al, 2019), from Brazilian and Indian Chamaecrista (Santos et al, 2017; Rathi et al, 2018), from threatened native species in Brazil (Fonseca et al, 2012), from Genisteae plants in Poland (Kalita and Malek, 2017), indigenous trees in China (Yao et al, 2015) as examples. In addition, new bradyrhizobial species have been reported as well (Yao et al, 2015; Araujo et al, 2017; Gronemeyer et al, 2017; Helene et al, 2017; Ahnia et al, 2018; Bunger et al, 2018).…”