Rhizobia Indigenous to the Okavango Region in Sub-Saharan Africa: Diversity, Adaptations, and Host Specificity

Abstract

The rhizobial community indigenous to the Okavango region has not yet been characterized. The isolation of indigenous rhizobia can provide a basis for the formulation of a rhizobial inoculant. Moreover, their identification and characterization contribute to the general understanding of species distribution and ecology. Isolates were obtained from nodules of local varieties of the pulses cowpea, Bambara groundnut, peanut, hyacinth bean, and common bean. Ninety-one of them were identified by BOX repetitive element PCR (BOX-PCR) and sequence analyses of the 16S-23S rRNA internally transcribed spacer (ITS) and the recA, glnII, rpoB, and nifH genes. A striking geographical distribution was observed. Bradyrhizobium pachyrhizi dominated at sampling sites in Angola which were characterized by acid soils and a semihumid climate. Isolates from the semiarid sampling sites in Namibia were more diverse, with most of them being related to Bradyrhizobium yuanmingense and Bradyrhizobium daqingense. Host plant specificity was observed only for hyacinth bean, which was nodulated by rhizobia presumably representing yet-undescribed species. Furthermore, the isolates were characterized with respect to their adaptation to high temperatures, drought, and local host plants. The adaptation experiments revealed that the Namibian isolates shared an exceptionally high temperature tolerance, but none of the isolates showed considerable adaptation to drought. Moreover, the isolates' performance on different local hosts showed variable results, with most Namibian isolates inducing better nodulation on peanut and hyacinth bean than the Angolan strains. The local predominance of distinct genotypes implies that indigenous strains may exhibit a better performance in inoculant formulations.T he catchment area of the Okavango River extends across parts of the three sub-Saharan African countries of Angola, Namibia, and Botswana and is mainly characterized by smallholder and subsistence farming. Since cultivation techniques remain underdeveloped, e.g., in terms of irrigation and the application of agrochemicals or rhizobial inoculants, local farmers are confronted with low yields and decreasing soil fertilities (1). Pulses like cowpea (Vigna unguiculata), Bambara groundnut (Vigna subterranea), peanut (Arachis hypogaea), hyacinth bean (Lablab purpureus), and common bean (Phaseolus vulgaris) are cultivated and occasionally intercropped, but natural nodulation rates are often low (2), presumably due to a seasonal reduction of the rhizobial population caused by drought and heat. Thus, nitrogen input via symbiotic N 2 fixation might be very limited.Field-grown cowpea plants in Ghana have been reported to fix more than 200 kg N/ha (89% of plant N) (3). In contrast, values of only 4 to 29 kg N-fixed/ha (15 to 56% of plant N) were observed in semiarid southwestern Zimbabwe (4). In such areas, the application of a rhizobial inoculant may thus hold the potential to increase plant nutrition and soil fertility. Many effective rhizobial strains have been identif...

Isolation, characterization and selection of indigenous Bradyrhizobium strains with outstanding symbiotic performance to increase soybean yields in Mozambique

“…Very often, inoculant strains must compete with populations of indigenous or naturalized rhizobia, frequently not effective, but highly competitive and already adapted to the environment (Streeter, 1994; Al-Falih, 2002; Grönemeyer et al, 2014). It is broadly believed that inoculation responses are more likely to occur when there are less than 10 cells of indigenous or naturalized rhizobia per gram of soil (Thies et al, 1991, Thies et al, 1992, Sanginga et al, 1996, Sessitsch et al, 2002, Okogun and Sanginga, 2003), or when a substantial component of the population is not effective (Brockwell et al, 1995, Osunde et al, 2003).…”

Bradyrhizobium kavangense sp. nov., a symbiotic nitrogen-fixing bacterium from root nodules of traditional Namibian pulses

“…In a previous survey on root-nodule symbiotic bacteria (Grönemeyer et al , 2014), populations from nodules of pulses collected in the Kavango region of Namibia were analysed, and pure cultures of Bradyrhizobium characterized. On the basis of multi-locus sequence analysis (MLSA) of concatemers of three protein-coding genes ( glnII-recA-rpoB ) and intergenic spacer (ITS) sequences, our analyses identified several novel lineages within the genus Bradyrhizobium (Grönemeyer et al , 2014). A group of eight strains clustered in one of the novel lineages.…”

“…Strains 14-3 T , 34 1-1, 34 3-1, 35 3-3 and 35 3-4 originated from cowpea, while three other strains, 37 1-1, 37 2-1 and 1BT 1-1, were isolated from Bambara groundnut nodules, the latter in a trapping experiment from soil. All strains were grouped according to BOX-PCR fingerprints (Grönemeyer et al , 2014, strain 1BT 1-1 not shown). BOX-PCR patterns revealed at least four similar genotypes, with the pattern of strain 37 1-1 being very similar to 37 2-1, and patterns of strains 34 1-1, 35 3-3 and 35 3-4 being almost identical.…”

“…This group was further analysed. The following sequences were amplified from test or reference strains and aligned for sequence analyses: 16S rRNA gene amplified with primers Bac8uf and Univ1492r (1339 nt for strain 14-3 T ) according to Grönemeyer et al (2012), 1285 aligned positions were used to calculate sequence similarities, with 1259 positions used for phylogenetic analysis; ITS (ungapped), 656 bp amplified with primers FGPS1490 and FGPS132 (Laguerre et al , 1996), with 641 positions used for phylogenetic analysis according to Willems et al (2003); glnII , 504 bp amplified with primers glnII 12F and glnII 689R (Vinuesa et al , 2005); recA , 381 bp amplified with primers recA 41F and recA 640R (Vinuesa et al , 2005); rpoB , 416 bp amplified with primers rpoB -454F and rpoB -1364R (Vinuesa et al , 2008); dnaK , 239 bp amplified with primers TSdnaK2 and TSdnaK4 (Stepkowski et al , 2005, 2007) under conditions described previously (Grönemeyer et al , 2014); and nodC , 441 bp amplified with primers NodCfor540 and NodCrev1160 (Sarita et al 2005). Concatemers of glnII-recA-rpoB-dnaK contained 1540 positions.…”

Native Bradyrhizobium Strains From Ghana Can Enhance Grain Yields of Field-Grown Cowpea and Groundnut

“…As many strains used in inoculant formulations originated from indigenous pools of their country of origin, isolation and characterization to identify local elite strains present a strategy to improve BNF. Studies that focused on the characterization of indigenous rhizobium have revealed them as important sources of inoculant strains that are able to improve nodulation and BNF in grain legumes (Fening and Danso, 2002;Bogino et al, 2006;Ampomah et al, 2008;Grönemeyer et al, 2014). Furthermore, effective native strains, when identified, will serve as an important source of local inoculants to enhance BNF and subsequently yields of target legumes due to inherent adaptability to local conditions.…”