Characterization of Fungal Microbiome Structure in Leaf Litter Compost through Metagenomic Profiling of the Nuclear Ribosomal Internal Transcribed Spacer Region

Abstract

Abstract This study addressed the significant but understudied role of fungal communities in leaf litter and organic waste compost ecosystems, using advanced ITS metagenomic profiling. The research aims to comprehensively characterize these fungal communities to better understand their diversity, composition, and potential functions, with practical implications for optimizing composting processes and promoting sustainable waste management practices. Various compost samples were collected, including leaf litter composts and other matured organic waste composts, from different sources in Delhi-National Capital Region, India. DNA was extracted from these samples and amplified using PCR to obtain the DNA sequence of the fungal internal transcribed spacer (ITS) region. It was followed by sequencing and bioinformatics analysis to characterize the fungal microbiome and assess diversity within the compost ecosystems. Results revealed that leaf litter composts and cow dung manure had the highest fungal read counts, while kitchen waste compost had the lowest. Alpha diversity indices, including Chao1 and Shannon, exhibited differences in species richness and diversity among composts, though statistical significance was limited. The study also identified dominant fungal phyla such as Ascomycota, Basidiomycota, Mucoromycota, and Zoopagomycota, across the composts. The presence of beneficial fungal genera like Pichia, Trichoderma, Mortierella, Basidiobolus, as well as pathogenic viz. Alternaria, Fusarium, and Acremonium, in these composts underscored the need for proper composting practices and source selection to optimize soil fertility and minimize disease risks in agriculture. Overall, these findings contribute to optimizing composting processes, advancing waste management practices, and enhancing the use of compost as a bio-organic fertilizer. The results also highlighted the significance of monitoring compost quality and its impact on soil health for sustainable agricultural practices.