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.
Empty fruit bunch (EFB) and palm oil mill effluent (POME) are the major wastes generated by the oil palm industry in Malaysia. The practice of EFB and POME digester sludge co-composting has shown positive results, both in mitigating otherwise environmentally damaging waste streams and producing a useful product (compost) from these streams. In this study, the bacterial ecosystems of 12-week-old EFB-POME co-compost and POME biogas sludge from Felda Maokil, Johor were analysed using 16S metagenome sequencing. Over ten phyla were detected, with Chloroflexi being the predominant phylum, representing approximately 53% of compost and 23% of the POME microbiome reads. The main bacterial lineage found in the compost and POME was Anaerolinaceae (Chloroflexi) with 30% and 18% of the total gene fragments, respectively. The significant differences between compost and POME communities were abundances of Syntrophobacter, Sulfuricurvum and Coprococcus. No methanogens were identified due to the bias in general 16S primers to eubacteria. The preponderance of anaerobic species in the compost and high abundance of secondary metabolite fermenting bacteria is due to an extended composting time, with anaerobic collapse of the pile due to the tropical heat. Predictive functional profiles of the metagenomes using 16S rRNA marker genes suggest that the presence of enzymes involved in degradation of polysaccharides such as glucoamylase, endoglucanase and arabinofuranosidase, all of which were strongly active in POME. Eubacterial species associated with cellulytic methanogenesis were present in both samples.
Bacteria play an important roles in the soil ecosystem and in the rhizosphere, they are intricately linked to nutrient content
and its accessibility to plants, plant protection and sometimes pathogenicity. Banana grows well in the tropics and it is
popularly grown in Orang Asli (OA) (indigenous people) settlements. Banana is also grown in commercial plantations.
In traditional planting practices, the OA do not add pesticide nor fertilizer to their crops which are planted for selfsustenance
mainly. On the other hand, fertilizer and pesticide are added to commercial banana plantations to maximise
yield. Rhizosphere bacteria from the banana plant, Pisang Nipah, grown in OA fields and commercial plantations were
identified by clone library construction of the 16S rRNA gene. This was to determine whether farming practices influenced
the bacterial community in the banana plant rhizosphere. Acidobacteria, Proteobacteria and Actinobacteria were found in
all the soil. Other common phyla found in some soil (but not all) were Nitrospirae, Firmicutes, Bacteroidetes, Chloroflexi,
Verrumicrobia, Gemmatimonadetes and Cyanobacteria. The bacterial diversity was a little more diverse in the OA fields
than the commercial plantations. The latter had higher contents of nitrogen, phosphorus and potassium. These could
have exerted selective pressure to reduce the bacterial diversity in the commercial plantations.