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.
Highlights
Fungal communities are an essential constituent of soil microbial biomass that is involved, and/or linked to processes of carbon and nitrogen cycles, organic matter decomposition, as well as nitrogen mineralization and immobilization (Bloem et al, 1995; Bååth and Anderson, 2003; Wall et al, 2012; Berthrong et al, 2013; Milner, 2014; Fierer, 2017)
In this study we assessed the fungal community composition in 32 soil samples collected from long-term farming system comparison trials at Chuka and Thika in Kenya
This study revealed that farming systems have a profound impact on soil fungal communities
Summary
Fungal communities are an essential constituent of soil microbial biomass that is involved, and/or linked to processes of carbon and nitrogen cycles, organic matter decomposition, as well as nitrogen mineralization and immobilization (Bloem et al, 1995; Bååth and Anderson, 2003; Wall et al, 2012; Berthrong et al, 2013; Milner, 2014; Fierer, 2017). Mutualistic root endophytic fungi induce systemic resistance in host plants thereby increasing crops tolerance levels to biotic and abiotic stress factors (Lahlali et al, 2014). They are a key component of sustainable soil-plant systems that govern major plant nutrient cycles sustaining the vegetation cover and ecosystem services (Schreiner and Bethlenfalvay, 1997; Dighton, 2003; Johansson et al, 2004). Soil fungal community composition is influenced by soil physicochemical properties, plant populations and geoclimatic conditions (Tkacz et al, 2015) In agroecosystems, they are exposed to added influencing factors associated with soil and crop agronomic management practices. Since many fungi are unculturable and rarely produce visible sexual structures, molecular techniques have become widely used for taxonomic detection of species to understand shifts in their richness and composition along environmental gradients (Persoh, 2015; Balint et al, 2016; Tedersoo and Nilsson, 2016; Tedersoo et al, 2018)
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