Isolation and rice plants response to bio-fertilizing and bio-enhancing isolates from Kenyan Coastal, Central and Western regions

Abstract

Plant growth promoting microorganisms (PGPMs) are beneficial microbes with the ability to improve growth of plants through a broad range of mechanisms. The PGPMs use in agriculture is suddenly rising as it provides a substitute to inorganic fertilizers. This study was undertaken to establish the microorganisms present in the rice ecosystem and to evaluate their contribution on rice production as indigenous bio-fertilizers and bio-enhancers. Microorganisms were isolated and characterized from the rhizosphere, rhizoplane and phyllosphere of Kenyan rice ecosystems for the enhancement of growth of rice plants. A total of 250 isolates, out of which 130 were bacterial and 120 fungal were identified and characterized according to their morphological, microscopic, staining, biochemical and molecular characteristics. These isolates were screened for their physiological properties as PGPMs. Selected isolates were further investigated to show the PGPR traits in rice plants. To study the effects of microbial concentration and different microbial inoculants on growth performance and yield of rice, field experiments were conducted at Jomo Kenyatta University of Agriculture and Technology (JKUAT). The design of the experiment was split – plot with the treatments replicated four times. Three different inoculant concentrations (main plots) and 16 microbial inoculants and two control treatments; C – where nothing was applied and C2 – farmers practice (sub-plots) were used during the study. Three destructive harvests were undertaken during the production period and data were collected on growth and yield attribute parameters. The data was subjected to analysis of variance (ANOVA) and where there were significant differences among treatment means, Duncan multiple range test (DMRT) was used to separate the means. Plant tissue nutrient contents were assessed to determine nitrate-nitrogen (NO3- - N), total phosphorus (P) and indole acetic acid (IAA). Out of the 130 bacterial isolates, 76.2% were able to solubilize phosphate, over 80% fixed nitrogen and 38.5% produced IAA. Out of the 120 fungi isolates, 17.5% solubilized phosphate and 5% produced IAA. The morphological characteristics of the bacterial isolates did not vary widely except in colour as opposed to that of the fungal isolates. The microscopic identification of the fungal isolates at genus level placed them xix into eight groups. High diversity of bacterial community majority belonging to the genus Bacillus was revealed by analysis of 16S rRNA sequence whereas the 18S rRNA sequence analysis was dominated by the genera Penicillium and Aspergillus. Effect of inoculation on growth, dry matter and yield of rice plants at all the three harvests (45, 75 and 105 days after planting) for the main plots were significantly different (p<0.05) in height, root length, tillers numbers, shoot and root dry weights, panicle numbers and length as well as 100 seed weight. Plants inoculated with species of Pseudomonas, Staphylococcus, Enterobacter, Micrococcus, Brevudimonas, Bacillus, Trichoderma, Penicillium, Aspergillus and mixed bacteria performed better than the uninoculated controls in all parameters tested. Despite the non-significant differences in all treatments for the N content, during the 3rd harvest significant differences were observed for P content. High levels of IAA content were observed in microbial inoculated plants as compared to the C2 treated plants. The present study suggests that there exist diverse microorganisms in the Kenyan rice ecosystem, some of which could fix nitrogen, solubilize phosphates and produce IAA. Also the application of PGPMs as bio-fertilizers and bio-enhancers improved growth and yield of the rice plants and therefore studies should be conducted to identify the most effective PGPM groups for further development of bio-fertilizers and bio-enhancers for rice production.