Genetic diversity and phylogeny of rhizobia and endophytic bacterial isolates and their symbiotic efficiency with promiscuous soybean varieties
| dc.contributor.author | Wambui, Simon Mburu | |
| dc.date.accessioned | 2025-08-21T08:36:45Z | |
| dc.date.available | 2025-08-21T08:36:45Z | |
| dc.date.issued | 2025-02 | |
| dc.description | A research thesis submitted in fulfillment of the requirements for the award of the degree of doctor of philosophy (microbiology) in the school of pure and applied sciences of Kenyatta University, February 2025 Supervisors: Prof. Ezekiel Mugendi Njeru Dr. John Maingi | |
| dc.description.abstract | In Sub-Saharan Africa (SSA), grain legumes such as soybeans play a key role in enriching soil fertility and improving food security in small-scale farming systems. Soybean’s symbiotic association with nitrogen fixing-rhizobia and other endophytic bacteria makes them valuable contributors to soil fertility. Despite the development and introduction of promiscuous varieties that readily form nodules with diverse native rhizobia, the full potential of biological nitrogen fixation has not yet been realized. The diverse agroecological conditions in SSA harbor a rich gene pool of native rhizobia and endophytic bacteria isolates that remain untapped. Therefore, this study aimed to determine soil microbial community, characterize and identify native rhizobia isolates and bacterial endophytes associated with soybean root nodules and assess the rhizobia symbiotic efficiency across different agroecological zones in Embu and Tharaka-Nithi counties. Standard morphological, biochemical and molecular methods were used for characterization. Rhizobia molecular characterization was performed using the 16S rRNA gene, while bacterial endophytes were analyzed through the V3-V4 region for nextgeneration sequencing. The isolates’ authentication and symbiotic effectiveness were carried out in the greenhouse using promiscuous soybean varieties and set in a complete randomized design with four replicates. This was followed by field experiments that was organized in a randomized complete block design (RCBD) and replicated four times. Based on the results, the identified rhizobia isolates included Rhizobium sp., Rhizobium pusense, Rhizobium wenxiniae, Rhizobium miluonense, Rhizobium tropici, Rhizobium gallicum, Rhizobium etli, and Burkholderia. This was also the first report of Rhizobium wenxiniae and Rhizobium gallicum strains being dominant in soybean plants in the Kenyan agroecological zones. Analysis of molecular variance (AMOVA) indicated significant genetic variations with 97% of the overall genetic variation attributed to diversity among populations. Remarkably, there was high diversity of endophytic bacteria distributed across 16 different genera, including Bacillus, Lysinibacillus, Enterobacter, Rahnella, Chrysobacterium, Anthrobacter Microbacterium, Ralstonia, Stenotrophomonas, Acinetobacter, Caballeronia, Citrobacter, Leclercia, Brevibacteria, Providencia and Pseudomonas. Nucleotide diversity (Pi) of endophytic bacterial populations was highest in Embu Lower Midland Zone (0.646) and lowest in TharakaNithi Lower Midland Zone (0.584). The symbiotic performance assessment identified isolates R11 (Rhizobium sp), R28b (Rhizobium miluonense) and R32 (Rhizobium etli) as the most effective rhizobial inoculants in N fixation with soybeans. Further investigation using next generation sequencing revealed that the dominant bacterial communities in the root nodules belonged to Proteobacteria (59.36-97.41%), Cyanobacteria (3.37-40.22%), Firmicutes (0.03-5.15%), and Actinobacteria (0.08-0.8%). Interestingly, despite the presence of other compatible soybean nodulating rhizobia, the Bradyrhizobium species were preferentially identified in high abundance (11.29-56.71%) across all the samples. The high diversity of soybean rhizobia isolates represents a valuable biological resource for identifying superior strains that can enhance sustainable crop production through symbiotic nitrogen fixation. | |
| dc.description.sponsorship | Kenyatta University | |
| dc.identifier.uri | https://ir-library.ku.ac.ke/handle/123456789/31271 | |
| dc.language.iso | en | |
| dc.publisher | Kenyatta University | |
| dc.title | Genetic diversity and phylogeny of rhizobia and endophytic bacterial isolates and their symbiotic efficiency with promiscuous soybean varieties | |
| dc.type | Thesis |