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All Journal HAYATI Journal of Biosciences MEDIA PETERNAKAN - Journal of Animal Science and Technology Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Jurnal Ilmu Pertanian Indonesia Jurnal Fitopatologi Indonesia Jurnal Akuakultur Indonesia Jurnal Pengolahan Hasil Perikanan Indonesia Jurnal Ilmu dan Teknologi Kelautan Tropis Jurnal Akuatika Microbiology Indonesia BIOTROPIA - The Southeast Asian Journal of Tropical Biology Biota: Jurnal Ilmiah Ilmu-Ilmu Hayati Biogenesis: Jurnal Ilmiah Biologi Jurnal AgroBiogen Current Biochemistry Jurnal Pengelolaan Sumberdaya Alam dan Lingkungan (Journal of Natural Resources and Environmental Management) Jurnal Sumberdaya Hayati Elkawnie Journal of Tropical Biodiversity and Biotechnology JURNAL BIOLOGI INDONESIA Jurnal Biodjati Omni-Akuatika Jurnal Penelitian Pendidikan IPA (JPPIPA) Jurnal Biologi Tropis ANNALES BOGORIENSES LIMNOTEK - Perairan Darat Tropis di Indonesia Biosaintifika: Journal of Biology & Biology Education Jurnal Teknik Pertanian Lampung (Journal of Agricultural Engineering) Jurnal Riset Akuakultur Menara Perkebunan Jurnal Mangifera Edu Grouper: Jurnal Ilmiah Perikanan Konservasi Hayati Makara Journal of Science Jurnal Ilmu Kehutanan Jurnal Ilmu Kehutanan Annales Bogorienses
Iman Rusmana
Departmen Biologi, Fakultas Matematika Dan Ilmu Pengetahuan Alam, Institut Pertanian Bogor, Kampus IPB Darmaga, Bogor 16680, Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Decision Sciences, Operations Research & Management Earth & Planetary Sciences Economics, Econometrics & Finance Education Engineering Environmental Science Immunology & microbiology Library & Information Science Materials Science & Nanotechnology Medicine & Pharmacology Physics Veterinary

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Journal : ANNALES BOGORIENSES

 1 
Identification of nifD and nifH Genes of Methanotrophic Bacteria from Rice Field Bintarti, Ari Fina; Rusmana, Iman; Wahyudi, Aris Tri
ANNALES BOGORIENSES Vol 18, No 2 (2014): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (879.425 KB) | DOI: 10.1234/97

Abstract

Metanotrophic bacteria have ability to oxidize methane and fix atmospheric nitrogen, hence the bacteria has an important role as a nitrogen source provider on wetland area like rice fields. Nitrogen fixation process is catalyzed by the nitrogenase enzyme complex, encoded by nifD and nifH genes. However, characteristic of these genes from indigenous-methanotrophic bacteria still poorly understood. Hence, nifD and nifH genes of methanotrophic bacteria isolated from rice fields in Indonesia (BGM3, BGM9, SS1, SS3, SS10, ST18, SP3 and INP4) were identified and characterized. Detection of nifH and nifD genes was conducted by polymerase chain reaction (PCR) amplification. nifH and nifD gene sequences were analyzed using BLAST-X and phylogenetic trees were constructed using Neighbour Joining method. Based on nifH sequences analysis, SS1 closely related to Beijerinckia mobilis and SS3, SS10, ST 18 closely related to Beijerinckia indica subsp. indica ATCC 9039, while, BGM3, INP4, and BGM9 related to nifH of uncultured nitrogen-fixing bacterium. In other hand, sequence analysis of nifD gene showed that SS1, SS3, SS10, ST 18 closely related to B. indica subsp. indica ATCC 9039 and BGM3, BGM9, INP4 closely related to Xanthobacter autotrophicus Py2. Identification by 16 SrRNA indicated that SS1, SS3, SS10, and ST18 had closeness to Beijerinckia sp. P310-1, while INP4 closely related to Xanthobacter sp. M5C24.
Identification of nifD and nifH Genes of Methanotrophic Bacteria from Rice Field Ari Fina Bintarti; Iman Rusmana; Aris Tri Wahyudi
ANNALES BOGORIENSES Vol 18, No 2 (2014): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (879.425 KB) | DOI: 10.14203/ann.bogor.2014.v18.n2.13-25

Abstract

Metanotrophic bacteria have ability to oxidize methane and fix atmospheric nitrogen, hence the bacteria has an important role as a nitrogen source provider on wetland area like rice fields. Nitrogen fixation process is catalyzed by the nitrogenase enzyme complex, encoded by nifD and nifH genes. However, characteristic of these genes from indigenous-methanotrophic bacteria still poorly understood. Hence, nifD and nifH genes of methanotrophic bacteria isolated from rice fields in Indonesia (BGM3, BGM9, SS1, SS3, SS10, ST18, SP3 and INP4) were identified and characterized. Detection of nifH and nifD genes was conducted by polymerase chain reaction (PCR) amplification. nifH and nifD gene sequences were analyzed using BLAST-X and phylogenetic trees were constructed using Neighbour Joining method. Based on nifH sequences analysis, SS1 closely related to Beijerinckia mobilis and SS3, SS10, ST 18 closely related to Beijerinckia indica subsp. indica ATCC 9039, while, BGM3, INP4, and BGM9 related to nifH of uncultured nitrogen-fixing bacterium. In other hand, sequence analysis of nifD gene showed that SS1, SS3, SS10, ST 18 closely related to B. indica subsp. indica ATCC 9039 and BGM3, BGM9, INP4 closely related to Xanthobacter autotrophicus Py2. Identification by 16 SrRNA indicated that SS1, SS3, SS10, and ST18 had closeness to Beijerinckia sp. P310-1, while INP4 closely related to Xanthobacter sp. M5C24.
Co-Authors Abdjad Asih Nawangsih ACENG RUYANI Achmad Dinoto Aderiana Masthura AKHADIYA, ALINA Alfan Cahyadi Alfisah, Rizal Khoirun Aliati Iswantari Alina Akhdiya Alina Akhdiya ALINA AKHDIYA Amanda, Nisa Widya Angela Mariana Lusiastuti Angela Mariana Lusiastuti Ani Suryani Ani Suryani Ani Widiyati ANIK KUSMIATUN Anja Meryandini Anja Meryandini Antonius Suwanto Apon Zaenal Mustopa Ari Fina Bintarti Ari Fina Bintarti, Ari Fina Aris Tri Wahyudi Armanisa, Khafifah Baskoro S Wibowo Cahyadi, Alfan Cecep Kusmana CECILIA ANNA SEUMAHU CECILIA ANNA SEUMAHU Ciptadi Achmad YUSUP Daniel Djokosetiyanto Darmono Taniwiryono Desniar - - Dewi Puspaningsih DIAH ISKANDRIATI Dian Hendrayanti Dinamella Wahjuningrum Dondin Sajuthi DWI ANDREAS SANTOSA Dwi Ningsih Susilowati Eddy Supriyono Emei Widiyastuti Fachriyan Hasmi Pasaribu Fachriyan Hasmi Pasaribu Faturrahman Faturrahman Ferbiyanto, Andri Fredinan Yulianda Frijona Fabiola Lokollo GALUH WENING PERMATASARI Gunawan Djajakirana Hamim Hamim Happy Widiastuti Hefni Effendi Hessy Novita Hessy Novita I Komang Gede Wiryawan I MADE ARTIKA I Made Samudra Ifa Manzila Ika Roostika Tambunan, Ika Roostika Ika Setianingsih, Ika Indriyani, Yohanna Anisa Irwan Cahyadi It Jamilah KATHARINA JESSICA Khairul Syahputra Kukuh Nirmala Kuntari, Wahyu Budi Lena Novita Lingga, Rahmad Lizawati . Maggy Thenawidjaya Suhartono Maggy Thenawidjaya Suhartono Mahdani, Wilda Mahyarudin, Mahyarudin Manguntungi, Baso Masrukhin Masrukhin Masthura, Aderiana Miftahudin . Mukti Ali MUNTI YUHANA MUTTAQIN, MAFRIKHUL Nedwell, David B. Niken T.M Pratiwi, Niken T.M NISA RACHMANIA MUBARIK Nisa Widya Amanda Novita, Lena Nurfahmi, Riziq Ilham Nurhakiki Nurjanah PRIHASTO SETYANTO Prihasto Setyanto Priyo Handoyo Wicaksono Rahman Rahman Rahman Rahman Rahminovita Herlis RATNA SETYANINGSIH RATNA SETYANINGSIH RATNANINGTYAS, SUSI RIDWAN AFFANDI Rika Indri Astuti RIKA RAFFIUDIN Rina Hesti Utami Risky Hadi Wibowo Risky Hadi wibowo Roedhy Poerwanto Rosadela, Fitri Sipriyadi Sipriyadi Sipriyadi Siti Nur Jannah Sobir Sobir Solly Aryza Sri Budiarti Poerwanto Suhartono Suhartono SUSAN SOKA Syaiful Anwar T. Widiyanto Taruna D. Satwika TARUNI SRI PRAWAST MIEN KAOMINI ANY ARYANI DEDY DURYADI SOLIHIN Thenawidjaya, Maggy Tri Eko WAHYONO Tri Handayani Kurniati Tri Handayani Kurniati Tri Muji Ermayanti Tri P. Priyatno Tri Panji Tri Puji Priyatno Tri Widiyanto Tridesianti, Siska Tuasalamony, Mutia Musdalifah Utut Widyastuti Wahyuni, Reza Wibowo, Risky Hadi WIDANARNI WIDANARNI Widiyanto, Tri Wilda Mahdani Wildan Nurusallam Wiraswati, Sri Martina Yadi Suryadi Yani Aryati Yohana A Dahliani Yohanna Anisa Indriyani Yuli Siti Fatma Yuli Siti Fatma YULIN LESTARI Yuni Puji Hastuti Yusli Wardiatno Zaenal Arifin, Sukarya Zulfarina Zulfarina Zulfarina,