A comparative study of bacterial communities determined by culture-dependent and independent approaches in oil palm planted on tropical peatland

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.