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

Doris K Puozaa,Sanjay K Jaiswal,Felix D Dakora

doi:10.1016/j.syapm.2019.02.004

Doris K Puozaa, Sanjay K Jaiswal + Show 1 more

Open Access

https://doi.org/10.1016/j.syapm.2019.02.004

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Abstract

In the N2-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 (573–1298bp) 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.

Highlights

Cowpea was first domesticated in West Africa and has since spread throughout the tropical and semi-arid regions of the world [10]
The analysis revealed 30 unique inter-transcribed spacer (ITS)-restriction fragment length polymorphism (RFLP) patterns which grouped in five major clusters (Cluster I–V) at a low cut-off point of approx 0.1 Jaccard’s similarity coefficient (Fig. S2)
The results showed high similarity with reference type strains belonging to the Bradyrhizobium genus

Summary

Introduction

Cowpea was first domesticated in West Africa and has since spread throughout the tropical and semi-arid regions of the world [10]. Studies done across Africa on cowpea have shown significantly high but varying levels of symbiotic dependency on N2 fixation for its N nutrition, e.g. 59–93% in South Africa, 99% in Ghana, 70–87% in Mozambique and 66% in Botswana [33,40,41]. This N2-fixing trait underpins the ability of cowpea and other legumes to thrive under low-nutrient conditions in the soils of Sub-Saharan Africa. Within Africa, Chidebe et al Mohammed et al and Pulemeulenberg et al [9,32,40] have found differences in the diversity of rhizobia nodulating different cowpea varieties in different geographic locations

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