Analysis of Functional Microbial Diversity against Ganoderma boninense in Oil Palm Rhizosphere Soils

Abstract

Oil palm (Elaeis guineensis Jacq.) is one of the most important crops in the world which particularly susceptible to Ganoderma boninense attack. The uses of chemical control has brought some disadvantages mainly due to their nature that can harm our environment and health. Thus, the uses of microbes as biocontrol agent might be the answer to the problems. Soil microbes have been known for their diverse and major roles in the plant growth and health. However, little is known about the differences in soil microbes between the healthy and Ganoderma-infected rhizosphere soils in oil palm plantation, also their potential to be the biocontrol agent. This study aim to profile microbial community diversity and their potential as biocontrol agents using several approaches: Next Generation Sequencing, culture dependent isolation, EcoplateTM, and PCR detection of functional genes. High microbial diversity were found in the oil palm plantation from both healthy and infected samples. Healthy samples had higher microbial diversity than infected rhizosphere soils. Dominant bacteria found were: Clostridium cluster XI, Lysinibacillus, Buttiauxella, and Bacillus. Mezerozyma and Talaromyces were the dominant fungi in this study. Several successfully isolated microbes were: Serratia marcescens, Enterobacter sp., Klebsiella varicolla, Geotrichum candidum, Burkholderia cenocepacia, Lactococcus lactis, and several Bacillus sp. EcoplateTM screening and antagonistic test against Ganoderma demonstrate low percentage of growth inhibition. Additionally, only phenazine, pyrrolnitrin, and chitinase related genes were detected from rhizosphere soil samples. Pyrrolnitrin and chitinase were further confirmed by sequencing. In contrast, no genes were detected from pure isolates.