Analysis of the bacterial diversity in schirmacher oasis, antarctica

Teo, Jenny Kim Chee (2013) Analysis of the bacterial diversity in schirmacher oasis, antarctica. UNSPECIFIED thesis, Universiti Malaysia Sabah.

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Abstract

Schirmacher Oasis (34 km²) is situated at about 100km from the Princes Astrid coast of Queen Maud Land, east of Antarctica. It is isolated and only housed a few research stations there. There are relatively few data on the diversity of the bacteria of this region. Hence, this work was set out to analyze the bacterial diversity of the Schirmacher Oasis. Ten soil samples (IS1, IS2, IS3, M4, M5, W2, W5, W6, W7 and W8) were collected within the Schirmacher Oasis. PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) targeting for the 16S rRNA gene was used to generate a community fingerprint of the soil. Between 1.52 and 9 ;g of the total DNA was extracted from one gram of soil, followed by partial 16S rDNA amplification using the GC357F and 907R primer set. The PCR reaction required ten to 100- fold dilution of the template to successfully reduce the inhibitory effect of the contaminants on the Taq polymerase. The amplicons were resolved using the Denaturing Gradient Gel Electrophoresis (DGGE). The DGGE results revealed that each soil samples had unique DNA fingerprint for dominant bacterial species. According to the similarity matrix generated via GelCompar II software, sample IS2 had the highest similarity (72.7%) with sample W5 and 71.4% likeness with sample W7, while the others have less than 70% similarity among them. The predominant bands were excised for sequence determination and bacterial identification. A total of 79 DNA fragments excised from the DGGE gel had been sequenced and 63 different OTUs representing bacteria from seven different phyla were identified. The most dominant phylum was Acidobacteria (39.2%), followed by Proteobacteria (25.7%), Bacteroidetes (14.8%), Actinobacteria (6.8%), Plantomycetes, Cyanobacteria and BRC1 (2.7%). There were 5.4% of unclassified bacteria. 87% of the OTUs have closest relative with uncultured bacterium from the NCBI GenBank database. 32% of the OTUs had been retrieved in regions from the Antarctica, 46% from Arctic and cold regions. To conclude, the soil bacterial diversity in Schirmacher Oasis found in this work was different from other regions in Antarctica.

Item Type:	Thesis (UNSPECIFIED)
Keyword:	Schirmacher Oasis, Bacterial diversity, Antarctica, Soil samples, PCR-DGGE, 16S rRNA gene, DNA fingerprinting
Subjects:	Q Science > QH Natural history > QH301-705.5 Biology (General) > QH540-549.5 Ecology
Department:	INSTITUTE > Biotechnology Research Institute (BRI)
Depositing User:	DG MASNIAH AHMAD -
Date Deposited:	11 Mar 2025 09:57
Last Modified:	11 Mar 2025 09:57
URI:	https://eprints.ums.edu.my/id/eprint/43079

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