MOLECULAR APPROACHES IN ASSESSING THE SOIL MICROBIAL DIVERSITY OF MALAYSIAN OIL PALM PLANTATIONS: A REVIEW

Abstract

Soil microorganisms are vital to the overall function, stability and sustainability of the ecosystem. Microbial communities are key bio-indicators for sustainable agro-ecosystem management and for evaluating oil palm soil health in Malaysia. The development of effective methods for studying the diversity, distribution and behaviour of soil microorganisms is essential for a broader understanding of soil quality and fertility. In the past, culture-dependent, Denaturing Gradient Gel Electrophoresis (DGGE) and Terminal-Restriction Fragment Length Polymorphism (T-RFLP) were used to assess soil microbial community, abundance and diversity in the oil palm soils. However, these methods have significant shortcomings and limitations in microbial ecology monitoring. In recent years, high-throughput next-generation sequencing has dramatically increased the resolution and detectable spectrum of microbial from environmental samples, and has played a significant role in microbial ecology studies. Next-generation sequencing using 454-pyrosequencing, Ion Torrent, Illumina and PacBio platforms are rapid and flexible. These sequencing platforms are powerful metagenomic tools for analysing microbial communities, including their structure, metabolic potential, diversity and their impact on ecosystem functions. In this review, the major development of molecular approaches used in the characterisation of soil microbial community dynamics and their functions in Malaysian oil palm plantations are also discussed.