https://jopr.mpob.gov.my Fri, 06 Sep 2024 08:33:15 +0000 en-US hourly 1 https://wordpress.org/?v=7.0 https://jopr.mpob.gov.my/molecular-approaches-in-assessing-the-soil-microbial-diversity-of-malaysian-oil-palm-plantations-a-review/ Tue, 15 Aug 2023 07:09:46 +0000 https://jopr.mpob.gov.my/?p=13025 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.

]]> https://jopr.mpob.gov.my/a-comparative-study-of-bacterial-communities-determined-by-culturedependent-and-independent-approaches-in-oil-palm-planted-on-tropical-peatland/ Wed, 17 Nov 2021 01:07:47 +0000 https://jopr.mpob.gov.my/V2/?p=622 A combination of deoxyribonucleic acid (DNA)-based method and sequencing technologies have initiated a new era of soil microbial ecology to examine the patterns of bacterial communities in tropical peatland. The aims of the study are to verify and compare the bacterial communities in a 12-year-old oil palm plantation on peat of Sibu, Sarawak, Malaysia using culture-dependent and culture-independent approaches. The bacterial diversity identified from both approaches were amplified using 16S ribosomal deoxyribonucleic acid (rDNA) (341/907) primer, sequenced and analysed. This resulted in recovering a total of 227 bacterial isolates belonging to four major phyla accumulated from 22 genera. Meanwhile, about 216 denaturing gradient gel electrophoresis (DGGE) bands were excised, which corresponded to 195 different bacterial species from 20 different phyla by culture-independent method. Although both approaches detected a total of four predominant bacterial phyla (Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes), in general, different taxonomic sequences were targeted by each method. In comparison to culture-dependent, polymerase chain reaction-(PCR) DGGE method identified a higher rate of bacterial diversity and richness and also detected non-culturable bacteria. Thus, this suggests that culture-independent method was showed to be more efficient on the bacterial diversity identification that will lead towards unravelling the hidden bacterial species associated with agricultural practices carried out in Southeast Asia peatland.

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