THE ROLE OF ROKUBACTERIA AS A KEYSTONE TAXA CANDIDATE IN THE FORMATION OF SUPRESSIVE SOILS ON FUSARIUM WILT DISEASE IN BANANA PLANTS BASED ON METAGENOMIC APPROACHES

• Main Author: Trihartomo, Didit
• Format: Theses
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/52166
• Institution: Institut Teknologi Bandung

Fusarium wilt disease in bananas is caused by Fusarium oxysporum f.sp. cubense (Foc), which infects through the roots of banana plants. This disease is still a major obstacle to the banana industry in the world and also in Indonesia. Currently, efforts to control the disease have been carried out but they have had negative effects such as fumigant contamination and fungicide resistance, so that better alternative solutions are needed, one of which is the formation of suppressive soil. Suppressive soil naturally suppresses pathogens. In its development, apart from using the culture dependent approach, the metagenomic approach is an alternative to suppressive soil studies. Network analysis and functional prediction using 16S rRNA gene markers to determine bacterial interactions and their role in more depth in the formation of suppressive soils are also challenges in suppressive soil studies. This study aims to obtain information on community structure, co-occurrence network patterns, prediction of keystone taxa, and prediction of the function of rhizosphere bacteria that affect the formation of suppressive soil for Fusarium wilt disease in banana plants through the metagenomic 16S rRNA approach. Two suppressive soil samples were taken from the soil around the banana plant roots with healthy condition, while two conducive soil samples were taken from the soil around the banana plant roots which had been infected with Foc. DNA isolation was performed using the ZymoBIOMICS ™ DNA Miniprep Kit and then sequenced using the Illumina HiSeq 2500 System. The bioinformatics analysis of sequenced data was carried out using QIIME2 2019.10 as the main pipeline with the SILVA 138 taxonomic database. Cytoscape 3.7.2 was used for network inference analysis and PICRUSt2 was used for functional prediction analysis based on the 16S rRNA gene marker. Based on the bioinformatics analysis, alpha diversity in suppressive soils was lower but not significantly different (p> 0.05) compared to conducive soils, while beta diversity showed suppressive soil samples formed one cluster together while on conducive soils did not form clusters. The Rokubacteria group gave a relatively higher abundance value and significantly different (P ? 0,05) from the phylum level (Methylomirabilota) to the genus level (Rokubacteriales) on all suppressive soils (3% - 4%) compared to conducive soils (0.6% - 1%). Cooccurrence network pattern on suppressive soils show higher positive interactions (1238) than negative interactions (1150). In suppressive soils, a separate network module which only has positive interactions, is formed with Rokubacteria as one of the nodes. Based on network analysis, Rokubacteriales was predicted to be one of the keystone taxa on suppressive soils with a value of degree = 16, closeness centrality = 1 and beetweness centrality = 0.077, along with 3 other genera (Collinsella, IMCC26256 and TK10). Functional predictions show that pathways related to the biosynthesis of terpenoids and other secondary metabolites as well as pathways associated with salicylic acid and O-antigen biosynthesis have higher abundance (P > 0.05) in suppressive soils, whereas the abundance of pathways associated with antibiotic biosynthesis is higher (P ? 0.05). in suppressive soils and pathway abundance associated with terpenes degradation was higher (P ? 0.05) in conducive soils. Rokubacteria has the NRPS/PKS gene which is thought to act as an antibiotic agent that correlates in the formation of Foc suppressive soils. However, the mechanism that occurs is not clear.