home icon user icon
Welcome to International Network for Natural Sciences | INNS Pub.
Home My Account
Submit Manuscript
double_slash
breadcumb_bg

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

Paper Details

Research Paper 01/01/2020
Views (502) Download (56)
current_issue_feature_image
publication_file

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

Samuel A. Were, Rama D Narla, Janice E. Thies, Eunice W. Mutitu, James W. Muthomi, Luiza. M. Munyua, Bernard Vanlauwe, Dries Robrooek.
Int. J. Micro. Myco.11( 1), 1-17, January 2020.
Certificate: IJMM 2020 [Generate Certificate]
Key: Fusarium solaniPythium ultimumRhizoctonia solaniRoot rotSoil borne pathogens

Abstract

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.

VIEWS 70
Cover PDF

Abawi GS, Pastor-Corrales MA. 1990. Root Rots of Beans in Latin America and Africa. Diagnosis, Research Methodologies and Management Strategies. CIAT Publication No.35. Cali, Colombia 114 pp.

Abawi GS, Widmer TL. 2000. Impact of soil health management practices on soil borne pathogens, nematodes and root diseases of vegetable crops. Applied Soil Ecology 15, 37-47.

Bailey K, Lazarovits G. 2003. Suppressing soil-borne diseases with biomass management and organic amendments. Soil and Tillage Research 72, 169-180.

Birach EA, Ochieng J, Wozemba D, Ruraduma C, Niyuhire MC. 2011. Factors influencing smallholder farmers’ bean production and supply to market in Burundi 19(4), 335-342.

Blair ID. 1943. Behaviour of the fungus Rhizoctonia solani Kühn in the soil. Annals of Applied Biology 30, 118-127.

Bouyoucos GJ. 1962. Hydrometer method improved for making particle size analysis of soils. Agronomy Journal 54, 464-465.

Bremner JM. 1996. Nitrogen-Total. In Methods of Soil Analysis: Chemical Methods. Part 3. D.L. Sparks, editor. Soil Science Society of America. Madison WI.

Brenmer JM. 1965 Inorganic forms of Nitrogen p. 1179-1237. In CA Black et al., (ed.) Methods of soil analysis part 2. Agronomy Monograph. 9. ASA. Madison. WI.

Dick MW. 1990. Key to Pythium. College of Estate Management, Reading, p. 64.

Filion M, St-Arnaud M, Jabaji-Hare SH. 2003. Direct quantification of fungal DNA from soil substrate using real-time PCR. Journal of Microbiological Methods 53(1), 67-76.

Gardes M, Bruns TD. 1993. ITS primers with enhanced specificity for basidiomycetes – application to the identification of mycorrhizae and rusts. Molecular Ecology 2, 112-118.

Geiser DM, Jimenz Gasco MM, Kang S, Mkalowska I, Veeraraghavan N, Ward TJ, Zhang N, Kuldau GA, O’Donnell K. 2004. FUSARIUM-IDv.1.0: A DNA sequence database for identifying Fusarium. European Journal of Plant Pathology 110, 473-479.

Gill JS, Sivasithamparam K, Smettem KRJ. 2000. Soil types with different texture affects development of Rhizoctonia root rot of wheat seedlings. Plant and Soil 221(2), 113-120. https://doi.org/10.1023/A:1004606016745

Gonzalez HHL, Martinez EJ, Pacin A, Resnik SL. 1999. Relationship between Fusarium graminearum and Alternaria lternate contamination and deoxynivalenol occurrence on Argentinean durum wheat. Mycopathologia 144, 97-102.

González-Mendoza D, Argumedo-Delira R, Morales-Trejo A, Pulido-Herrera A, Cervantes-Díaz L, Grimaldo-Juarez O, Alarcon A. 2010. A rapid method for isolation of total DNA from pathogenic filamentous plant fungi. Genetics and Molecular Research 9(1), 162-166.

Jaetzold R, Schmidt H. 1983. Farm Management Handbook of Kenya. Vol. II. Natural Conditions and Farm Management Information Part A WEST KENYA (Nyanza and Western Provinces) 245-285. Kenya Ministry   of Agriculture.

Katungi E, Farrow A, Chianu J, Sperling L, Beebe S. 2009. Common bean in Eastern and Southern Africa: a situation and outlook analysis. International Centre for Tropical Agriculture 61.

Katungi E, Sperling L, Karanja D, Farrow A, Beebe S. 2011. Relative importance of common bean attributes and variety demand in the drought areas of Kenya. Journal of Development and Agricultural Economics 3(8), 411-422.

Kimiti JM, Odee DW, Vanlauwe B. 2009. “Area under grain legumes cultivation and problems faced by smallholder farmers in legume production in the semi-arid eastern Kenya”. Journal of Sustainable Development in Africa. 11(4), 305-315.

Leslie JF, Summerell BA. 2006. The Fusarium Laboratory Manual. Blackwell Publishing Professional, Ames, IA, USA

Lievens B, Brouwer M, Vanachter ACRC, Cammue BPA, Thomma BPHJ. 2006. Real-time PCR for detection and quantification of fungal and oomycete tomato pathogens in plant and soil samples. Plant Science 171, 155-165.

Lievens B, Brouwer M, Vanachter ACRC, Cammue BPA, Thomma BPHJ. 2005. Quantitative assessment of phytopathogenic fungi in various substrates using a DNA macroarray, Environmental Microbiology 7, 1698-1710.

Marzano SYL. 2012. Assessment of disease suppression in organic transitional cropping systems. Ph.D thesis, The University of Illinois, USA.

Medvecky B, Ketterings Q, Nelson E. 2007. Relationships among soil borne bean seedling diseases, Lablab purpureus L. and maize stover biomass management, bean insect pests and soil characteristics in Trans Nzoia district, Kenya. Applied Soil Ecology 35, 107-119.

Meenu B, Praveen K, Satish L. 2010. Effect of composts on microbial dynamics and activity, dry root rot severity and seed yield of cowpea in the Indian arid region. Phytopathologia Mediterranea 49, 381-392.

Mwang`ombe AW, Thiongo G, Olubayo FM, Kiprop EK. 2007. Occurrence of Root Rot Disease of Common Bean (Phaseolus vulgaris L.) In Association with Bean Stem Maggot (Ophyiomia sp.) In EMBU District, Kenya. Plant Pathology Journal 6, 141-146.

Mwang’ombe AW, Kipsumbai PK, Kiprop EK, Olubayo FM, Ochieng JW. 2008. Analysis of Kenyan isolates of Fusarium solani f. sp. phaseoli from common bean using colony characteristics, pathogenicity and microsatellite DNA. African Journal of Biotechnology 7(11), 1662-1671.

Naser B. 2015. Root rot pathogens in field soil, roots and seeds in relation to common bean (Phaseolus vulgaris), disease and seed production. International Journal of Pest Management, 61(1), 60-67.

Naseri B. 2014. Bean production and Fusarium root rot in diverse soil environments in Iran.Journal of soil science and plant nutrition14(1), 177-188.

Nelson DW, Sommers LE. 1996. Total carbon, organic carbon, and organic matter. In: Methods of Soil Analysis, Part 2, 2nd ed., Page AL. Ed. Agronomy. 9, American Society of Agronomy Inc. Madison, WI, 961-1010.

Nirenberg HI. 1981. A simplified method for identifying Fusarium spp occurring on wheat. Canadian Journal Botany 59,1599-1609.

Nzungize JR, Lyumugabe F, Busogoro J, Baudoin J. 2012. Pythium root rot of common bean: biology and control methods. A review Biotechnology, Agronomy, Society and Environment 16(3), 405-413.

Odendo M, Ojiem J, Okwosa E. 2004. Potential for adoption of legume green manure on smallholder farms in western Kenya. Managing nutrient cycles to sustain soil fertility in sub-Saharan Africa. Academy Science Publishers Nairobi, 557-570.

Okoth SA, Okoth P, Wachira PM, Roimen H. 2009;Spatial distribution of Trichoderma spp. in Embu and Taita regions, Kenya. Tropical and Subtropical Agroecosystems 11, 291-301.

Olsen S, Cole C, Watanabe F, Dean L. 1954 Estimation of available phosphorus in soils by extraction with sodium bicarbonate. USDA Circular Nr 939, US Gov. Print. Office, Washington, D.C.

Ongom PO, Nkalubo ST, Gibson PT, Mukankusi CM, Rubaihayo PR. 2012. Evaluating genetic association between Fusarium and Pythium root rots resistances in the bean genotype RWR 719. African Crop Science Journal 20(1), 31-39.

Otsyula R, Nderitu J, Buruchara R. 1999. Nutrient sources to enhance crop tolerance to root rot and stem maggot in Western Kenya. International Centre for Tropical Agriculture, Bean Project 1998 Annual Report, 159-160.

Otsyula RM, Ajanga SI, Buruchara RA, Wortmann CS. 1998. Development Of An Integrated Bean Root Rot Control Strategy For Western Kenya. African Crop Science Journal 6(1), 61-67.

Otsyula RM, Buruchara RA, Mahuku G, Rubaihayo P. 2003. Inheritance and transfer of root rot (Pythium) resistance to bean genotypes. African Crop Science Society 6, 295-298.

Paparu P, Acur A, Kato F, Acam C, Nakibuule J, Musoke S, Nkalubo S, Mukankusi C. 2017. Prevalence and Incidence of Four Common Bean Root Rots in Uganda. Experimental Agriculture, 1-13.

Plaats-Niterink AJ. 1981. Monograph of the genus Pythium. Studies in Mycology, 21, 1-244.

Rani VD, Sudini H. 2013. Review article: Management of soil borne diseases in crop plants : An overview Department of Plant Pathology, College of Agriculture, Acharya NG, Ranga Agricultural University, International Crops Research Institute for the Semi-Arid Tropics ( ICRISAT ), 156-164.

Sanchez P. 2002. Soil fertility and hunger in Africa. Science 295, 2019-2020.

Sun RY, Liu ZC, Fu K, Fan L, Chen J. 2012. Trichoderma biodiversity in China. Journal of applied genetics 53, 343-354.

Walkley A, Black IA. 1934. An examination of the Degtjareff method for determining organic carbon in soils: Effect of variations in digestion conditions and of inorganic soil constituents. Soil Science 63, 251-263.

White TJ, Bruns T, Lee S, Taylor J. 1999 Amplification and direct sequencing of fungal ribosomal genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ. eds. PCR Protocols: a Guide to Methods and Applications. New York Academic press, 315-322.

White TJ, Bruns T, Lee SJWT, Taylor JW. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR protocols: a guide to methods and applications 18(1), 315-322.

Wortmann CS, Kirkby RA, Elude CA, Allen DJ. 1998. Atlas of common bean (Phaseolus vulgaris L.) production in Africa 63. International Centre for Tropical Agriculture publication No. 297, Cali, Colombia.

Zaidi N, Singh U. 2004. Use of farm yard manure for mass multiplication and delivery of biocontrol agents, Trichoderma harzianum and Pseudomonas fluorescens. Asian Agri-History 8, 297-304.

Zhou X, Zhu H, Liu L, Lin J, Tang K, 2010. A review: recent advances and future prospects of taxol-producing endophytic fungi. Applied microbiology and biotechnology 86(6), 1707-1717.

Submit Manuscript