Genetic Diversity of Rhizobia and Non-Rhizobial Endophytes Associated with Desmodium Species in Push-Pull Cropping Systems in Western Kenya
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Date
2025-01
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Kenyatta University
Abstract
Desmodium species used as companion crops in push-pull technology (PPT) are known to preserve soil biodiversity, deter pests and suppress Striga sp. weed. While the above-ground aspects of PPT have been well investigated and documented, Desmodium root nodule microorganisms remain unexplored. This study investigated the shifts in root nodule microbiome and the effect associated with soil physico-chemical properties of Desmodium incanum (AID), Desmodium intortum (GLD) and Desmodium uncinatum (SLD) used in PPT. Soil and Desmodium-root nodule samples were collected from selected PPT farms in Homabay, Siaya, Vihiga and Kisumu counties in Western Kenya. Healthy and unbroken root nodules were selected and crushed. Afterwards, gDNA was extracted, and sequenced for bacterial and fungal diversity. Soil characteristics, including micro and macronutrients, as well as soil texture, were also analysed. The study revealed that AID exhibited better physico-chemical properties as compared to GLD and SLD, particularly in pH, nitrogen, phosphorous, potassium, and organic carbon. Each Desmodium species exhibited a unique microbe composition, with a major shift in fungi communities as opposed to bacteria. Over 98% of the sequences identified belonged to Bradyrhizobium genus across all Desmodium species and locations. Within the Bradyrhizobium genus, several species were detected, namely Bradyrhizobium liaoningense, Bradyrhizobium japonicum and Phenylobacterium spp., which were more enriched in AID as compared to SLD and GLD. Enterobacter kobei, Variovorax paradoxus, Mycobacterium neoaurum and Streptomyces griseorubiginosus, were only associated with SLD, while Labrys neptuniae was only associated with GLD. Analysis of root nodule mycobiome revealed Fusarium as the most abundant fungal genus although with varying abundances across the treatments. Fusarium spp. was more enriched in both AID and SLD as compared to GLD whereas Clonostachys spp. and Fusarium sacchari were more enriched in GLD as compared to AID and SLD. Fusarium solani was more enriched in AID whereas Sistotrema spp. and Poaceascoma spp. were more enriched in SLD. Additionally, the study also identified three arbuscular mycorrhiza fungi in Desmodium root nodules namely Funneliformis geosporum, Scutellospora reticulata and Racocetra crispa which are recognized for various plant growth-promoting abilities. While a more pronounced shift was observed for fungal community compositions compared to bacteria, no significant differences were detected in alpha diversity of fungal and bacterial communities among the three Desmodium species. Similarly, beta diversity was not significantly different among the three Desmodium species (P > 0.05). Despite the shifts in metabolic pathways among the three Desmodium species, significant differences were only observed in the sequences responsible for energy biosynthesis (GLYCOLYSIS-E-D, PWY-3001 and GLUCONEO-PWY). However, energy and amino acid biosynthesis pathways were significantly higher in SLD compared to AID and GLD (P < 0.05). Therefore, it is likely that the root nodules of the three Desmodium species host comparable microbes reflecting shared symbiotic partner selection and adaptability among the three Desmodium species to the local environment. Their abundance may be useful in generating effective inocula for use in different habitats. Subsequent experiments are warranted to evaluate the impact of the microbes on general plant growth, paving the way for sustainable agricultural practices.
Description
A Thesis Submitted in Partial Fulfillment of the Requirements for the Award of the Degree of Master of Science in Biotechnology in the School of Pure and Applied Sciences of Kenyatta University, January 2025.
Supervisor
1. George Ochieng’ Asudi
2. Daniel Munyao Mutyambai
3. Saliou Niassy