PCR-based DGGE and FISH analysis of methanogens in an anaerobic closed digester tank for treating palm oil mill effluent
16S ribosomal RNA (rRNA)-targeted fluorescent in situ hybridization combined with polymerase chain reaction (PCR)-cloning, light microscopy using Gram stains, scanning electron microscopy and denatured gradient gel electrophoresis were used to reveal the distribution of methanogens within an anaerob...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English English |
| Published: |
Pontificia Universidad Católica de Valparaíso
2009
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| Online Access: | http://psasir.upm.edu.my/id/eprint/16061/ http://psasir.upm.edu.my/id/eprint/16061/1/16061.pdf |
| _version_ | 1848842855150256128 |
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| author | Tabatabaei, Meisam Zakaria @ Mamat, Mohd Rafein Abdul Rahim, Raha Wright, Andre-Denis G. Shirai, Yoshihito Abdullah, Norhani Sakai, Kenji Ikeno, Shinya Mori, Masatsugu Kazunori, Nakamura Sulaiman, Alawi Hassan, Mohd Ali |
| author_facet | Tabatabaei, Meisam Zakaria @ Mamat, Mohd Rafein Abdul Rahim, Raha Wright, Andre-Denis G. Shirai, Yoshihito Abdullah, Norhani Sakai, Kenji Ikeno, Shinya Mori, Masatsugu Kazunori, Nakamura Sulaiman, Alawi Hassan, Mohd Ali |
| author_sort | Tabatabaei, Meisam |
| building | UPM Institutional Repository |
| collection | Online Access |
| description | 16S ribosomal RNA (rRNA)-targeted fluorescent in situ hybridization combined with polymerase chain reaction (PCR)-cloning, light microscopy using Gram stains, scanning electron microscopy and denatured gradient gel electrophoresis were used to reveal the distribution of methanogens within an anaerobic closed digester tank fed with palm oil mill effluent. For specific detection of methanogens, 16S rRNA-cloning analysis was conducted followed by restriction fragment length polymorphism (RFLP) for presumptive identification of methanogens. To cover the drawbacks of the PCR-cloning study, the organization of the microorganisms was visualized in the activated sludge sample by using fluorescent oligonucleotide probes specific to several different methanogens, and a probe for bacteria. In situ hybridization with methanogens and bacterial probes and denatured gradient gel electrophoresis within activated sludge clearly confirmed the presence of Methanosaeta sp. and Methanosarcina sp. cells. Methanosaeta concilii was found to be the dominant species in the bioreactor. These results revealed the presence of possibly new strain of Methanosaeta in the bioreactor for treating palm oil mill effluent called Methanosaeta concilii SamaliEB (Gene bank accession number: EU580025). In addition, fluorescent hybridization pictured the close association between the methanogens and bacteria and that the number of methanogens was greater than the number of bacteria. |
| first_indexed | 2025-11-15T08:05:45Z |
| format | Article |
| id | upm-16061 |
| institution | Universiti Putra Malaysia |
| institution_category | Local University |
| language | English English |
| last_indexed | 2025-11-15T08:05:45Z |
| publishDate | 2009 |
| publisher | Pontificia Universidad Católica de Valparaíso |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | upm-160612019-10-24T06:47:13Z http://psasir.upm.edu.my/id/eprint/16061/ PCR-based DGGE and FISH analysis of methanogens in an anaerobic closed digester tank for treating palm oil mill effluent Tabatabaei, Meisam Zakaria @ Mamat, Mohd Rafein Abdul Rahim, Raha Wright, Andre-Denis G. Shirai, Yoshihito Abdullah, Norhani Sakai, Kenji Ikeno, Shinya Mori, Masatsugu Kazunori, Nakamura Sulaiman, Alawi Hassan, Mohd Ali 16S ribosomal RNA (rRNA)-targeted fluorescent in situ hybridization combined with polymerase chain reaction (PCR)-cloning, light microscopy using Gram stains, scanning electron microscopy and denatured gradient gel electrophoresis were used to reveal the distribution of methanogens within an anaerobic closed digester tank fed with palm oil mill effluent. For specific detection of methanogens, 16S rRNA-cloning analysis was conducted followed by restriction fragment length polymorphism (RFLP) for presumptive identification of methanogens. To cover the drawbacks of the PCR-cloning study, the organization of the microorganisms was visualized in the activated sludge sample by using fluorescent oligonucleotide probes specific to several different methanogens, and a probe for bacteria. In situ hybridization with methanogens and bacterial probes and denatured gradient gel electrophoresis within activated sludge clearly confirmed the presence of Methanosaeta sp. and Methanosarcina sp. cells. Methanosaeta concilii was found to be the dominant species in the bioreactor. These results revealed the presence of possibly new strain of Methanosaeta in the bioreactor for treating palm oil mill effluent called Methanosaeta concilii SamaliEB (Gene bank accession number: EU580025). In addition, fluorescent hybridization pictured the close association between the methanogens and bacteria and that the number of methanogens was greater than the number of bacteria. Pontificia Universidad Católica de Valparaíso 2009 Article PeerReviewed text en http://psasir.upm.edu.my/id/eprint/16061/1/16061.pdf Tabatabaei, Meisam and Zakaria @ Mamat, Mohd Rafein and Abdul Rahim, Raha and Wright, Andre-Denis G. and Shirai, Yoshihito and Abdullah, Norhani and Sakai, Kenji and Ikeno, Shinya and Mori, Masatsugu and Kazunori, Nakamura and Sulaiman, Alawi and Hassan, Mohd Ali (2009) PCR-based DGGE and FISH analysis of methanogens in an anaerobic closed digester tank for treating palm oil mill effluent. Electronic Journal of Biotechnology, 12 (3). pp. 1-12. ISSN 0717-3458 http://www.ejbiotechnology.info/index.php/ejbiotechnology/article/view/v12n3-4 10.2225/vol12-issue3-fulltext-4 English |
| spellingShingle | Tabatabaei, Meisam Zakaria @ Mamat, Mohd Rafein Abdul Rahim, Raha Wright, Andre-Denis G. Shirai, Yoshihito Abdullah, Norhani Sakai, Kenji Ikeno, Shinya Mori, Masatsugu Kazunori, Nakamura Sulaiman, Alawi Hassan, Mohd Ali PCR-based DGGE and FISH analysis of methanogens in an anaerobic closed digester tank for treating palm oil mill effluent |
| title | PCR-based DGGE and FISH analysis of methanogens in an anaerobic closed digester tank for treating palm oil mill effluent |
| title_full | PCR-based DGGE and FISH analysis of methanogens in an anaerobic closed digester tank for treating palm oil mill effluent |
| title_fullStr | PCR-based DGGE and FISH analysis of methanogens in an anaerobic closed digester tank for treating palm oil mill effluent |
| title_full_unstemmed | PCR-based DGGE and FISH analysis of methanogens in an anaerobic closed digester tank for treating palm oil mill effluent |
| title_short | PCR-based DGGE and FISH analysis of methanogens in an anaerobic closed digester tank for treating palm oil mill effluent |
| title_sort | pcr-based dgge and fish analysis of methanogens in an anaerobic closed digester tank for treating palm oil mill effluent |
| url | http://psasir.upm.edu.my/id/eprint/16061/ http://psasir.upm.edu.my/id/eprint/16061/ http://psasir.upm.edu.my/id/eprint/16061/ http://psasir.upm.edu.my/id/eprint/16061/1/16061.pdf |