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Identification and quantification of soil borne root rot pathogens communities in smallholder agro-ecosystems of Kenya

Research Paper | January 1, 2020

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Samuel A. Were, Rama D Narla, Janice E. Thies, Eunice W. Mutitu, James W. Muthomi, Luiza. M. Munyua, Bernard Vanlauwe, Dries Robrooek.

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Int. J. Micro. Myco.11( 1), 1-17, January 2020


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The root rot disease complex has continued to be a major constraint in the production of common beans (Phaseolus vulgaris) resulting in losses of up to 70% in Kenya. The aim of this study was to establish (i) the occurrence and quantification of root rot fungal pathogens of common bean in Western Kenya and (ii) the effect of farming practices on the populations of the pathogens. A survey was conducted in Western Kenya’s LM1 LM2 UN1 and UM3 AEZ’s to obtain data on different farming practices and soil characteristics. Pathogens were isolated and identified using morphological and molecular techniques. Soil pH ranged from 4.59 to 6.01, Percent carbon and nitrogen ranged from 9.8g/Kg0 to 19g/Kg and 0.8 g/Kg to 1.5g/Kg. All farms were infected with root rot fungi, including Fusarium solani, Pythium ultimum, Rhizoctonia solani and Macrophomina phaseolina. Fusarium spp. was the most abundant with the highest populations of 62 X 103 cfu/g soil recorded in lower midland zone 2. The isolation frequency of Fusarium spp., Pythium spp. and Rhizoctonia spp. was high in upper midland zone 1. Quantification of genomic DNA from soil by qPCR was highest for Rhizoctonia solani (2.23X10º pg µL-1). Sand had a positive correlation with Pythium ultimum DNA and Rhizoctonia solani DNA while clay had a negative correlation with Fusarium spp. and Rhizoctonia solani DNA. In conclusion, soil properties, management practices and elevation affected root rot pathogen populations and should be considered when developing management strategies.


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Identification and quantification of soil borne root rot pathogens communities in smallholder agro-ecosystems of Kenya

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