Sains Malaysiana 44(11)(2015): 1625-1633

Culture-independent-based Analyses Identified Site-specific Microbial in Two Oil-wells from Malaysia

(Analisis Bebas Kultur berasaskan Mikrob Khusus Tapak Dikenal Pasti di Dua Buah Telaga Minyak dari Malaysia)

CHENG-YEE FISH-LOW¹, AINON HAMZAH² & HUI-YEE CHEE¹*

¹Faculty of Medicine and Health Sciences, Department of Medical Microbiology and Parasitology, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan, Malaysia

²School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Darul Ehsan, Malaysia

Received: 6 February 2015/Accepted: 22 May 2015

ABSTRACT

Microbial communities of two oil reservoirs from Malaysia, denoted as Platform Bo and Platform Pe were studied using culture-independent approach. Environmental DNA was extracted and the universal amplified ribosomal region (UARR) was target amplified for both prokaryotes and eukaryotes. The amplified products were purified and cloned into pTZ57R/T vector to construct the 16S/18S rDNA library. Restriction endocucleasesHhaI and MspI were used to screen the library. From that, 125 and 253 recombinant plasmid representative clones from Platform Bo and Platform Pe, respectively, were sent for DNA sequencing. Twenty-six operational taxonomic units (OTUs) consist of 20 genera detected at Platform Bo and 17 OTUs consist of 13 genera detected at Platform Pe. Marinobacter and Acinetobacter species co-occurred in both platforms whereas the rest are site-specific. Gammaproteobacteria accounted for 86.0% of the microbial community in Platform Bo, where OTUs affiliated to Marinobacter, Pseudomonas and Marinobacterium that were the most abundant. The major OTUs in the Platform Pe were with affinities to Achromobacter, followed by Stenotrophomonas and Serratia. The only archaeal isolates were detected in Platform Pe, which affiliated to Thermocladium. The singletons and doubletons accounted for about 50.0% of the OTU abundance in both platforms, which considerably significant despite their rare occurrence.

Keywords: Microbial community; operational taxonomic unit; petroleum reservoir; 16S/18S rRNA

ABSTRAK

Komuniti mikrob di dua telaga minyak dari Malaysia, ditandakan sebagai Platform Bo dan Platform Pe telah dikaji menggunakan pendekatan bebas kultur. DNA alam sekitar diekstrak dan rantau ribosom umum teramplifikasi (UARR) adalah sasaran diperkuatkan untuk kedua-dua prokaryotes dan eukaryotes. Produk yang diperkuatkan telah ditulenkan dan diklon ke vektor pTZ57R/T untuk membina perpustakaan rDNA 16S/18S. Sekatan endocucleases HhaI dan MspI telah digunakan untuk menyaring perpustakaan tersebut. Daripada itu, 125 dan 253 wakil plasmid rekombinan klon masing-masing dari Platform Bo dan Platform Pe, telah dihantar untuk penjujukan DNA. Dua puluh enam unit taksonomi operasi (OTUs) terdiri daripada 20 genus dikesan di Platform Bo dan 17 OTUs terdiri daripada 13 genus dikesan di Platform Pe. SpesiesMarinobacter dan Acinetobacter hadir bersama-sama di kedua-dua platform manakala selebihnya adalah khusus tapak. Gammaproteobacteria menyumbang sebanyak 86.0% komuniti mikrob di Platform Bo, manakala gabungan OTUs Marinobacter, Pseudomonas dan Marinobacterium adalah yang paling banyak. OTUs utama di Platform Pe adalah gabungan Achromobacter, diikuti oleh Stenotrophomonas dan Serratia. Satu-satunya pencilan archaeal dikesan di Platform Pe iaitu bergabung dengan Thermocladium. Tunggalan dan duaan yang mewakili kira-kira 50.0% daripada kelimpahan OTU di kedua-dua platform agak ketara walaupun keadaan ini jarang berlaku.

Kata kunci: Komuniti mikrob; takungan petroleum; unit taksonomi operasi; 16/18S rRNA

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*Corresponding author; email: cheehy@upm.edu.my