Determining Soil Microbial Communities and Their Influence on Ganoderma Disease Incidences in Oil Palm (Elaeis guineensis) via High-Throughput Sequencing

Abstract

Basal stem rot (BSR), caused by Ganoderma boninense, is the most devastating oil palm disease in South East Asia, costing US$500 million annually. Various soil physicochemical parameters have been associated with an increase in BSR incidences. However, very little attention has been directed to understanding the relationship between soil microbiome and BSR incidence in oil palm fields. The prokaryotic and eukaryotic microbial diversities of two coastal soils, Blenheim soil (Typic Quartzipsamment—calcareous shell deposits, light texture) with low disease incidence (1.9%) and Bernam soil (Typic Endoaquept—non-acid sulfate) with high disease incidence (33.1%), were determined using the 16S (V3–V4 region) and 18S (V9 region) rRNA amplicon sequencing. Soil physicochemical properties (pH, electrical conductivity, soil organic matter, nitrogen, phosphorus, cation exchange capacity, exchangeable cations, micronutrients, and soil physical parameters) were also analyzed for the two coastal soils. Results revealed that Blenheim soil comprises higher prokaryotic and eukaryotic diversities, accompanied by higher pH and calcium content. Blenheim soil was observed to have a higher relative abundance of bacterial taxa associated with disease suppression such as Calditrichaeota, Zixibacteria, GAL15, Omnitrophicaeota, Rokubacteria, AKYG587 (Planctomycetes), JdFR-76 (Calditrichaeota), and Rubrobacter (Actinobacteria). In contrast, Bernam soil had a higher proportion of other bacterial taxa, Chloroflexi and Acidothermus (Actinobacteria). Cercomonas (Cercozoa) and Calcarisporiella (Ascomycota) were eukaryotes that are abundant in Blenheim soil, while Uronema (Ciliophora) and mammals were present in higher abundance in Bernam soil. Some of the bacterial taxa have been reported previously in disease-suppressive and -conducive soils as potential disease-suppressive or disease-inducible bacteria. Furthermore, Cercomonas was reported previously as potential bacterivorous flagellates involved in the selection of highly toxic biocontrol bacteria, which might contribute to disease suppression indirectly. The results from this study may provide valuable information related to soil microbial community structures and their association with soil characteristics and soil susceptibility to Ganoderma.

Soil physicochemical properties in respect to plant health in Ganodermainfested oil palm plantation

“…Organic matter is a source of food for soil microorganisms, so if a soil has a low organic matter content, the abundance of health agents will also be low, while the population of G. boninense will continue to increase. This is also in line with what was explained by Susanto et al (2013) and Goh et al (2020), that the role of organic matter in suppressing the development of pathogens is not only by increasing soil microbial activity, but also by improving root health to make plants more resistant to disease.…”

“…Soil CEC describes the ability of the soil to hold or absorb plant nutrients in the form of cations available to plants, so the higher the CEC value, the more nutrients it can absorb (Nazari et al, 2020). However, soils that were severely exposed to basal stem rot disease had higher CECs than Ganoderma suppressive soils (Goh et al, 2020).…”

Effects of Liming on Soil Properties and Its Roles in Increasing the Productivity and Profitability of the Oil Palm Industry in Malaysia

“…These soil-dwelling microorganisms comprise different taxa, such as bacteria, arbuscular mycorrhizal fungi (AMF), actinomycetes, and cyanobacteria [30]. Important characteristics of these microbes include improving root systems, production of organic acids, phytohormones, antibiotics, siderophores, volatile bacterial compounds, solubilization of phosphorus, nitrogen-fixing, carbon cycling, and disease prevention [4,14]. The activities of these helpful microbes can be restricted by the soil's acidity, except for fungi, which may thrive in a broad range of soil pH [9].…”

“…The rising worldwide demand for palm oil has prompted an expansion in agricultural land dedicated to industrial oil palm cultivation [1,2]. This industrial expansion in the major palm oil-producing and exporting countries, such as Malaysia in Southeastern Asia, has resulted in massive conversion of existing agricultural lands and deforestation of tropical rainforests [3,4]; however, soil acidity and nutrient depletion are two major constraints in oil palm cultivation in tropical regions [5][6][7][8]. This is primarily because acidic soil increases the leaching of many essential plant nutrient elements and the availability of toxic elements by modifying various geochemical and biological reactions in the soil [9][10][11][12].…”

OIL PALM ECONOMIC PERFORMANCE IN MALAYSIA AND R&D PROGRESS IN 2020

“…Daza et al (2020) showed that with auxins, in particularly NAA and 2,4-D, it is feasible to produce good bunch of parthenocarpic fruits without having to rely on pollination. With its striking characteristics and the need to diversify the current guineensis-based planting materials, more efforts are being channelled to further unravel the oleifera and its hybrids for future applications (Ting et al, 2020b;Zulkifli et al, 2020).…”