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

Karanja, Edward N.; Fliessbach, Andreas; Adamtey, Noah; Kambura, Anne Kelly; Musyoka, Martha; Fiaboe, Komi and Mwirichia, Romano (2020) Fungal diversity within organic and conventional farming systems in Central Highlands of Kenya. African Journal of Microbiology Research, 14 (6), pp. 242-258.

[thumbnail of Karanja-etal-2020-AJMR-Vol14-Issue6-p242-258.pdf] PDF - English
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Document available online at: https://academicjournals.org/journal/AJMR/article-abstract/619642063963


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.

EPrint Type:Journal paper
Keywords:Long-term farming systems, fungi, internal transcribed spacer (ITS), diversity, Illumina sequencing, Abacus, FiBL10119, FiBL6516601
Agrovoc keywords:
farming systems
Subjects: Soil > Soil quality
Crop husbandry
"Organics" in general > Countries and regions > Africa
Research affiliation: Switzerland > FiBL - Research Institute of Organic Agriculture Switzerland > International > Regions > Africa
Switzerland > FiBL - Research Institute of Organic Agriculture Switzerland > Soil > Soil quality
DOI:DOI: 10.5897/AJMR2020.9294
Deposited By: Forschungsinstitut für biologischen Landbau, FiBL
ID Code:39129
Deposited On:02 Feb 2021 14:36
Last Modified:03 Feb 2021 10:26
Document Language:English
Refereed:Peer-reviewed and accepted

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