African Journal of
Microbiology Research

  • Abbreviation: Afr. J. Microbiol. Res.
  • Language: English
  • ISSN: 1996-0808
  • DOI: 10.5897/AJMR
  • Start Year: 2007
  • Published Articles: 5058

Full Length Research Paper

Fungal diversity within organic and conventional farming systems in Central Highlands of Kenya

Edward Nderitu Karanja
  • Edward Nderitu Karanja
  • Department of Biological Sciences, School of Pure and Applied Sciences, University of Embu, P. O. Box 6-60100, Embu, Kenya.
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Andreas Fliessbach
  • Andreas Fliessbach
  • Research Institute of Organic Agriculture, Ackerstrasse 113, 5070 Frick, Switzerland.
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Noah Adamtey
  • Noah Adamtey
  • Research Institute of Organic Agriculture, Ackerstrasse 113, 5070 Frick, Switzerland.
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Anne Kelly Kambura
  • Anne Kelly Kambura
  • School of Agriculture, Earth and Environmental Sciences, Taita Taveta University, P. O. Box 635-80300, Voi, Kenya.
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Martha Musyoka
  • Martha Musyoka
  • International Centre for Insect Physiology and Ecology (icipe). P. O. Box 30772-00100, Nairobi, Kenya.
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Komi Fiaboe
  • Komi Fiaboe
  • International Centre for Insect Physiology and Ecology (icipe). P. O. Box 30772-00100, Nairobi, Kenya.
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Romano Mwirichia
  • Romano Mwirichia
  • Department of Biological Sciences, School of Pure and Applied Sciences, University of Embu, P. O. Box 6-60100, Embu, Kenya.
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  •  Received: 25 January 2020
  •  Accepted: 26 May 2020
  •  Published: 30 June 2020

Abstract

Fungal diversity in agro-ecosystems is influenced by various factors related to soil and crop management practices. However, due to the complexity in fungal cultivation, only a limited number has been extensively studied. In this study, amplicon sequencing of the Internal Transcribed Spacer (ITS) region was used to explore their diversity and composition within long-term farming system comparison trials at Chuka and Thika in Kenya. Sequences were grouped into operational taxonomic units (OTUs) at 97% similarity and taxonomy assigned via BLASTn against UNITE ITS database and a curated database derived from GreenGenes, RDPII and NCBI. Statistical analyses were done using Vegan package in R. A total of 1,002,188 high quality sequences were obtained and assigned to 1,128 OTUs; they were further classified into eight phyla including Ascomycota, Basidiomycota, Chytridiomycota, Glomeromycota, Calcarisporiellomycota, Kickxellomycota, Mortierellomycota and unassigned fungal phyla. Ascomycota was abundant in conventional systems at Chuka site while Basidiomycota and Chytridiomycota were dominant in conventional systems in both sites. Kickxellomycota and Calcarisporiellomycota phyla were present in all organic systems in both sites. Conventional farming systems showed a higher species abundance and diversity compared to organic farming systems due to integration of organic and inorganic inputs.

 

Key words: Long-term farming systems, fungi, internal transcribed spacer (ITS), diversity, Illumina sequencing.