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University of Khartoum (2022)

DNA Metabarcoding of Soil Fungal Communities in Four Agricultural Sites in Khartoum State, Sudan

Marwa Hatim Eltahir Elnaiem

Titre : DNA Metabarcoding of Soil Fungal Communities in Four Agricultural Sites in Khartoum State, Sudan

Auteur : Marwa Hatim Eltahir Elnaiem

Université de soutenance : University of Khartoum

Grade : PhD in Agriculture (Agricultural Biotechnology) 2022

Résumé partiel
Fungi are one of the most diverse groups of organisms on earth, and are considered as one of the least-explored biodiversity resources of our planet. Therefore, this research attempted to investigate soil fungal communities (Mycobiome), their taxonomic and functional composition, diversity and biomass in four in Khartoum State, Sudan. Six land-use types (Soils cultivated with onion, salad rocket, mango, citrus, forage sorghum and bare land) were selected. A total of 87 soil samples were taken randomly from the top 20 cm of the surface soil collected from Shambat (27), Elgref (24), Omdurman (30) and Elseleit (6). The sampling was done during two successive seasons (Winter and summer) of the entire region of 2019. Total DNA was extracted from soil samples using Qiagen Dneasy® PowrSoil® DNA extraction kit. The extracted DNA was used in qPCR to determine the quantity of the soil fungi based on fungal rRNA gene. Also, it was used to amplify the internal transcribed spacer 1 (ITS1) region which was then sequenced using the Ion Torrent sequencing technique. The ITS1 raw sequencing data was processed and analyzed using QIIME2 and DADA2 R package pipeline with the default parameters. All other analyses were performed in R software version 3.6.3 using various packages. Alpha diversity was checked using observed number of taxa and Shannon indices, whereas beta diversity was studied using Bray-Curtis dissimilarity distance and visualized by non-metric multidimensional scaling (NMDS). Fungal functional composition was predicted using FUNGuild tool. Results indicated that fungal biomass in the soil communities varied between 1.86x109 to 3.31x106 copy number per one-gram wet soil with an average of 4.24x108 copy number per sample. Statistical analysis revealed that the fungal biomasses were not significant in the four sites and the two seasons (P-value 0.404), but it was significantly different in the different land-use types. The taxonomic composition of all soil samples, after filtering, revealed 12 fungal phyla encompassing 29 classes, 60 orders, 104 families, 169 genera and 250 species. Ascomycota was the most abundant phylum (86.51%) followed by Basidiomycota (8.06%). Mortierellomycota, Glomeromycota, Chytridiomycota, Rozellomycota, Mucoromycota, Blastocladiomycota, Calcarisporiellomycota, Aphelidiomycota, Zoopagomycota and Oidiomycosis were also recorded and collectively represented 5.42% of the total abundance. The taxonomic units Sordariomycetes (41.02%), Sordariales (23.64%), Cheatomiaceae (15.31%) and Aspergillus (8.42%) were the most abundant class, order, family and genus, respectively. Fusarium kyushuense was the most abundant species which accounted for 2.54% followed by Fusarium solani (2.39%) and Curvularia lunata (2.11%). The observed number of taxa (richness) ranged from 69 to 362 taxa, whereas Shannon index ranged from 2.79 to 5.23. NMDS indicates that fungal communities of Omdurman, Elgerf and Elseleit sites tended to cluster together irrespective of the land-use type.

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Page publiée le 10 février 2023