A COMPARATIVE METAGENOMIC ANALYSIS OF SUPPRESSIVE AND CONDUCIVE SOIL TOWARDS GANODERMA BONINENSE INFECTIONS IN PALM OIL PLANTS (ELAEIS GUINEENSIS JACQ.) AT VARIOUS SOIL DEPTHS

• Main Author: Syafira, Dinda
• Format: Final Project
• Language: Indonesia
• Subjects: Ilmu hayati ; Biologi
• Online Access: https://digilib.itb.ac.id/gdl/view/55512
• Institution: Institut Teknologi Bandung

Oil palm (Elaeis guineensis Jacq.) is a plantation commodity with high economic value. One of the obstacles faced in the cultivation of oil palm in Indonesia is the Ganoderma boninense infection which can cause Basal Stem Rot Disease (BSR). G. boninense infection can be controlled by inducing suppressive soil formation through mediating biocontrol agents. To determine the types of microbes that have the potential to act as biocontrol agents, a comparison of the microbial profiles on suppressive and conducive soils can be carried out through a metagenomic approach based on the 16S rRNA gene marker, which is known to be able to overcome the limitations of conventional culture-dependent methods. In this study, an in-silico study was conducted on secondary data in 2016 consisting of 60 samples of data from 16S rRNA amplicon sequencing and edaphic data. The samples used came from the oil palm plantation soils in the islands of Sumatra and Sulawesi were grouped based on their ability to suppress pathogen infection (suppressive and conducive) and the depth of sampling (top soil and sub soil). The pipeline used includes the sequence quality control stage with the FastQC software, continued with diversity data processing and microbial classification with QIIME2 and functional prediction with PICRUSt2. Visualization of the main results from data processing was carried out using the GenePiper software. Principle Component Analysis (PCA) of edaphic factors was carried out using the XLSTAT software, while the Pearson correlation matrix between soil edaphic factors and bacteria was processed using RStudio. The results of the alpha diversity analysis showed that there were no significant differences in bacterial diversity in each soil type on the islands of Sumatra and Sulawesi. The results of the beta diversity analysis showed that the bacterial community structure between the soil samples from Sumatra and Sulawesi islands separated into two different groups. The results of the OTU Venn diagram analysis showed that on the Sumatra and Sulawesi islands, conducive subsoils had the highest number of unique OTUs compared to the other three types of soil. The results of the analysis of the relative abundance of genera in Sumatra showed that several bacteria have the potential to induce suppressive soil formation, such as Amycolaptopsis, Nitrospira, Rokubacteriales, and Vicinamibacteria which are found in suppressive soils (topsoil and subsoil). Alphaproteobacteria and Paraburkholderia was found in conducive soils (topsoil and subsoil). Sulawesi shows the same results that are the presence of Actinobacteria, Alphaproteobacteria, Rokubacteriales, and Vicinamibacteria bacteria in suppressive soils (topsoil and subsoil) and Paraburkholderia and Chromobacteria bacteria in conducive soils (topsoil and subsoil). The results of the functional prediction of bacterial genes related to suppressive soil formation can be observed in all types of soil in Sumatra and Sulawesi in the form of potential formation of anti-microbial compounds, siderophores, and quorum sensing mechanisms. However, the number of potential functions is more commonly found in suppressive soils than in conducive soils. The results of PCA analysis showed that suppressive soils are generally correlated with edaphic factors of organic carbon (OC), base saturation (BS), carbon exchange capacity (CEC), and pH, while conducive soils generally correlated with Al3+ and the percentage of sand and silt. The results of the correlation analysis between bacteria and edaphic factors showed that bacteria are positively correlated with edaphic factors that have a role in shaping the characteristics of the soil where the bacteria are found. Based on the results obtained, it can be concluded that in both Sumatra and Sulawesi soil samples, bacteria and functional predictions of genes that have the potential to suppress G. boninense infection in oil palm are more dominantly found in suppressive soil than conducive soil at both types of depth.The presence of these bacteria in a soil type is influenced by the edaphic conditions that shape the characteristics of the soil.