Wahome, Caroline Nyawira2024-10-012024-10-012024-05https://ir-library.ku.ac.ke/handle/123456789/29007A 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, May 2024 Supervisors 1. John Maingi 2. Omwoyo Ombori 3. Ezekiel Mugendi NjeruBanana production in Kenya predominantly involves smallholder farmers, yet current yields fall short of meeting local and international market demands due to constraints faced by these farmers among them being soil health and lack of clean planting materials. To address this issue, the study assessed banana cultivation practices in Kisii, Nyamira, and Embu counties, aiming to understand strengths and challenges within these regions. In this study, rhizospheric soil physicochemical properties and the diversity of microbial communities was assessed, shedding light on soil health status. Furthermore, the efficacy of a cost-effective micro-propagation technique for local banana cultivars was determined, considering contamination susceptibility and acclimatization efficacy of arbuscular mycorrhizal fungi on micropropagated banana plantlets. The study revealed a reliance on ineffective traditional propagation methods, with over 30% of the smallholder farmers facing a banana seedlings shortage. The soil physic-chemical parameters indicated signs of degradation, with low pH and nutrient deficiencies raising concerns with Embu County having the lowest pH measured (4.43). Soil metagenomic studies by NGS showed that proteobacteria and basidiomycota were the two most prevalent bacterial and fungus divisions, respectively. Based on the Shannon diversity indices, the highest bacterial and fungal community diversity was in soil samples obtained from Embu County and Kisii County respectively. To evaluate efficacy using low cost tissue culture technology, selected banana cultivars were utilized and results indicated the highest survival rate of 100 % in Kiganda, Muraru and Kienyeji banana cultivars established in BAP and IAA. Ng’ombe cultivar best responded to low cost micropropagation with the highest shoot establishment (80.5 %) and shoot emergence rates (75.5 %) producing the highest number of shoots per culture (10.61). To investigate clonal fidelity of the tissue culture plantlets Inter Simpler Sequence Repeats (ISSR) and the research demonstrated genetic homogeneity in banana seedlings generated via low cost tissue culture to the mother plant. During the micropropagation process the presence of bacterial and fungal contaminants in the tissue culture laboratory was noted with the most predominant bacterial and fungal contaminants being Microccoccus luteus and Cladosporium sp respectively. Additionally, broad-spectrum antimicrobial agents nalidixic acid (30 µg) and carbendazim+ triadimefom (0.3 µg and 0.6 µg) exhibited 100% inhibition rates against these contaminants. To determine the response of the micropropagated plantlets to AMF acclimatization, it was observed that Kiganda cultivar responded best to Rhizophagus irregularis which showed the highest recorded biomass at 0.97. There is need to emphasize collaborative efforts among various stakeholders in establishing sustainable practices. Additionally, low-cost TC is a viable tool for producing disease-free seedlings and intergrating antimicrobial agents is recommended to minimize contamination risks. Finally, the use of AMF treatment in acclimatization with further research needed for validation across different agroecological conditions. These recommendations aim to enhance productivity, sustainability, and resilience in banana farming systems.enThesis