A Comparative Study of Bacterial Communities Determined by Culture-Dependent and-Independent Approaches in Oil Palm Planted on Tropical Peatland

Abstract

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.

Molecular Approaches in Assessing the Soil Microbial Diversity of Malaysian Oil Palm Plantations: A Review

“…Moreover, this method provides limited information on microbial communities because more than 99% soil microorganisms remain 'unculturable' in the laboratory as they require specific growth conditions. As a result, a large proportion of microbial communities remains unexplored, and organisms such as Acidobacteria are underrepresented in isolated cultures (Ayob and Kusai, 2021;Liu et al, 2006) when compared to the molecular methods. The molecular methods that describe communities dominated by predominantly uncultivated microorganisms' groups that are not detected by culture, provide a more rapid result, less time-consuming, and been shown to have great flexibility in terms of gene target and target region (Montalvo et al, 2014;Rudkjøbing et al, 2016).…”

“…On the other hand, Trichoderma harzianum (Figure 2h) has biocontrol properties against devastating oil palm disease; basal stem rot caused by Ganoderma boninense, and has widely been used as a biofertiliser to reduce disease incidence in oil palm plantations (Naher et al, 2012;Sundram et al, 2008). Meanwhile, the most isolated bacteria in the oil palm plantations of Sarawak are Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes (Ayob and Kusai, 2021;Kusai and Ayob, 2020). Isolated bacteria Burkholderia cepacia (class Betaproteobacteria) has been used as a biocontrol agent to reduce incidene of basal stem rot in oil palm by 42%.…”

“…These PCR-based genetic fingerprinting techniques provide microbial profiling based on the variation of targeted genes amplified from the soil (Anderson and Cairney, 2004). These techniques are reproducible and effective at characterising the dynamics of microbial diversity, including uncultivated microbes (Ayob and Kusai, 2021;Gryta and Frąc, 2020). Nevertheless, these methods have limitations as they are very laborious, expensive with low throughput (Nkongolo and Narendrula-Kotha, 2020).…”

“…Furthermore, the analysis of diversity can be conducted by considering factors that influence the biodiversity of soil microbial communities and its impact on oil palm management practices, and predicting ecosystem responses to a changing environment (Ayob and Kusai, 2021;Tripathi et al, 2012). There have been several studies that investigated the effects of land use change on the microbial community in the Malaysian oil palm plantation ecosystem using traditional and advance molecular methods, as listed in Table 1.…”

OIL PALM ECONOMIC PERFORMANCE IN MALAYSIA AND R&D PROGRESS IN 2021

“…Amit et al (2021) concluded that bird species diversity, abundance and their feeding guild can be improved by letting ground layer vegetation grow naturally and maintaining the water quality of the drainage system in the early stage of oil palm development to attract birds which prefer this habitat. Ayob et al (2021) recovered 227 bacterial isolates belonging to four major phyla (22 genera) from culturedependent and -independent approaches in oil palms planted on tropical peatland.…”