Genetic and symbiotic characterization of rhizobia isolated from tree and herbaceous legumes grown in soils from ecologically diverse sites in Kenya

Abstract

Natural genetic diversity and symbiotic status were studied among 41 root nodule bacteria from ecologically diverse sites in Kenya having no history of growing domesticated legumes, but where species of Acacia and Sesbania sesban grow naturally. Isolates originated either from nodules of field plants (trees and shrubs) or from trap host plants grown in field-collected soil. The host plants were Acacia mellifera, Acacia nilotica, Acacia nubica, Acacia polyacantha, Acacia seyal, Acacia tortilis, Acacia xanthophloea, and Faidherbia (Syn. Acacia) albida, Prosopis juliflora, S. sesban, Macroptilium atropurpureum, Phaseolus vulgaris and Vigna unguiculata. Two molecular methods were used to characterize these strains; PCR–RFLP of the 16S rRNA gene (12 distinct genotypes) and sequence analysis of a 230bp fragment of this gene (10 genotypes) with the former showing better discriminatory power. The two methods were in good agreement in delineating five bacterial genera: Agrobacterium, Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium. Bradyrhizobium strains were all alkali-producing, exhibiting very slow to intermediate growth; Mesorhizobium strains were acid-producing with intermediate to fast growth; Rhizobium and Sinorhizobium were acid-producing with fast to very fast growth, and Agrobacterium strains were acid-producing and showed very fast growth. PCR–RFLP analysis further revealed strains corresponding to the species Bradyrhizobium elkanii, Bradyrhizobium japonicum, Rhizobium leguminosarum and Rhizobium tropici IIB, as well as others characterized to genus level only. Apparent diversity varied from site to site and was greatly influenced by host of isolation. For example, five rhizobial genotypes (four genera) were found using five different trap host species in a single Acacia tortilis woodland site, thus reaffirming occurrence of a heterogeneous population regardless of their nodulating ability with the native legume species. Bradyrhizobium spp. (F. albida), known for their preference of F. albida in tropical African soils, were abundant and widespread mainly because F. albida was the most frequently used trap host. Twenty Kenyan and eight reference strains were tested on tree species that are a priority for Kenyan use; these showed considerable diversity in symbiotic characters. Whereas Acacia species and F. albida showed variation in symbiotic effectiveness with test strains, S. sesban nodulated most effectively only with its homologous strains. Agrobacterium-allied strains failed to nodulate any of the host species tested. The high diversity (rhizobial genotypes, host affinities and their symbiotic effectiveness) found in the Kenyan sites will require rigorous selection for host×strain×site combinations in order to obtain effective and competitive inoculants for legume trees and crops in rehabilitation and agroforestry programmes.