FUNCTIONAL METAGENOMICS SUPPRESSIVE AND CONDUCIVE SOILS AGAINST FUSARIUM OXYSPORUM F.SP. CUBENSE CAUSED FUSARIUM WILT DISEASE IN BANANA

• Main Author: Nisrina, Lulu'
• Format: Theses
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/49416
• Institution: Institut Teknologi Bandung

Fusarium wilt disease caused by soil pathogen Fusarium oxysporum f.sp. cubense (Foc) is a major obstacle for the banana plantation industry. This disease threatens the sustainability of the banana industry in Indonesia. Fumigation and fungicide have been used to control Foc but have not solved the problem. Therefore, another approach is needed to suppress Foc with the concept of suppressive soil that utilized the ability of soil microbes. This study aimed to obtain the profile and function of microbes in suppressive soil through metagenomic functional analysis. Shotgun sequencing was carried out to read DNA from suppressive and conducive soil samples. Quality control (FASTQC ver.0.11.5), de-novo assembly (MEGAHIT ver.1.2.9), de-novo assembly evaluation (MetaQUAST ver.5.02 and BBMap), alignment (DIAMOND ver.0.9.24.125), gene prediction (Prokka ver.1.14.6), microbial abundance and diversity, co-occurrence network, gene ontology, and functional analysis (MEGAN6-LR ver.6.19.9) was performed. This study found a Phred score quality of sequences was above 30. Analysis of microbial abundance showed Actinobacteria, Betaproteobacteria, Rhizobiales, Burkholderiales, Bradyrhizobiaceae, Methylobacteriaceae, Rhodopseudomonas palustris and Methylobacterium nodulans were higher in the suppressive than conducive soils. Many species belongs those bacteria groups are members of Plant Growth Promoting Rhizobacteria (PGPR). Analysis of microbial diversity showed the higher value of alpha diversity in suppressive than conducive soils. The co-occurrence analysis found the presence of Pseudomonas, Burkholderia, and Streptomyces in the suppressive soils. Additionally, the relative abundance of Pseudomonas and Burkholderia was higher in the suppressive than conducive soils. Therefore, it is assumed Pseudomonas and Burkholderia play a role to suppress Foc based on co-occurrence and abundance analysis. Analysis of gene ontology showed an abundance of responses to stress, response to chemical, signal transduction, transport, coenzyme binding, and peroxidase activity were consistently higher in conducive soil. It assumed these ontology genes is the response of soil microbes to the presence of Foc in the soil. KEGG functional analysis showed the abundance of cellular community-prokaryotes consisted of the quorum-sensing pathway and biofilm formation was consistently higher in the suppressive than conducive soils. Furthermore, PCA and PCoA analysis showed quorum sensing consistently higher in suppressive than conducive soils. Thus, it assumed quorum sensing performed by PGPR bacteria quorum sensing to produce various sensing proteins such as anti- fungi, antimicrobials, nematicidal compounds, biofilms, and degradative enzymes contribute to the formation of suppressive soils.