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

Zahidah Ayob, . and Nor Azizah Kusai, . A comparative study of bacterial communities determined by culture dependent and-independent approaches in oil palm planted on tropical peatland. pp. 588-606. ISSN 2811-4701

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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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.

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Item Type:	Article
AGROVOC Term:	Oil palm
AGROVOC Term:	Peatlands
AGROVOC Term:	Microbial ecology
AGROVOC Term:	Soil sciences
AGROVOC Term:	Ecosystems
AGROVOC Term:	analysis
AGROVOC Term:	Field experimentation
AGROVOC Term:	Laboratory experimentation
AGROVOC Term:	Data collection
AGROVOC Term:	Biodiversity
Depositing User:	Mr. AFANDI ABDUL MALEK
Last Modified:	24 Apr 2025 00:55
URI:	http://webagris.upm.edu.my/id/eprint/10267

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