Bacterial diversity determination using culture-dependent and culture-independent methods
Mud volcanoes are taken into consideration by geologists and oil industry experts have given their association with oil and gas reserves and methane greenhouse gas production in hydrosphere and atmosphere. Gomishan mud volcano phenomenon in the southeastern edge of the Caspian Sea, given its oil and...
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2017-04-01
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| Series: | Global Journal of Environmental Science and Management |
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| author | M. Ghiasian A. Akhavan Sepahy M.A. Amoozegar S. Saadatmand M. Shavandi |
| author_facet | M. Ghiasian A. Akhavan Sepahy M.A. Amoozegar S. Saadatmand M. Shavandi |
| author_sort | M. Ghiasian |
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| description | Mud volcanoes are taken into consideration by geologists and oil industry experts have given their association with oil and gas reserves and methane greenhouse gas production in hydrosphere and atmosphere. Gomishan mud volcano phenomenon in the southeastern edge of the Caspian Sea, given its oil and gas resources, has been studied by some geologists in terms of geology and tectonics but not in terms of microbiology. Accordingly, it seems necessary to study this phenomenon from the perspective of microbiology in order to identify prokaryotes living in this area. Prokaryotes diversity in Mud volcano has been studied by cultivation techniques, fluorescence in situ hybridization, and denaturing gradient gel electrophoresis of PCR-amplified fragments of 16S rRNA genes. Total cell abundance in the mud volcano from 1×101-6×101per milliliter was determined by 4', 6-diamidino-2-phenylindole direct count. The detectable proportion of Archaea to Bacteria in the community by FISH was one to five. High viable counts (1 – 3 × 106) were obtained in culture media. A total of 122 isolates were obtained, 46 colonies were selected based on primarily morphological and physiological traits, and their 16S rRNA sequences were determined. The isolated genera included Halomonas (20%), Arthrobacter (5%), Kocuria (5%), Thalassobacillus (5%), Marinobacter (20%), Paracoccus (5%), Roseovarius (5%), Jeotgalicoccus (5%), Bacillus (15%), and Staphylococcus (15%). Regarding DGGE analysis, selected bands were obtained from the gels, reamplified and sequenced. Overall, 75% of the bacterial sequences were related to Rahnella and 25% related to Serratia. |
| format | Article |
| id | doaj-art-66c5f34b36d845079c96b9d294e560ba |
| institution | Kabale University |
| issn | 2383-3572 2383-3866 |
| language | English |
| publishDate | 2017-04-01 |
| publisher | GJESM Publisher |
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| series | Global Journal of Environmental Science and Management |
| spelling | doaj-art-66c5f34b36d845079c96b9d294e560ba2025-02-02T12:33:34ZengGJESM PublisherGlobal Journal of Environmental Science and Management2383-35722383-38662017-04-013215316410.22034/gjesm.2017.03.02.00423306Bacterial diversity determination using culture-dependent and culture-independent methodsM. Ghiasian0A. Akhavan Sepahy1M.A. Amoozegar2S. Saadatmand3M. Shavandi4Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, IranDepartment of Microbiology, Faculty of Biological Science, North Tehran Branch, Islamic Azad University, Tehran, IranExtremophiles Laboratory, Department of Microbiology, Faculty of Biology, College of Sciences, University of Tehran, Tehran, IranDepartment of Biology, Science and Research Branch, Islamic Azad University, Tehran, IranMicrobiology and Biotechnology Group, Research Institute of Petroleum Industry, Tehran, IranMud volcanoes are taken into consideration by geologists and oil industry experts have given their association with oil and gas reserves and methane greenhouse gas production in hydrosphere and atmosphere. Gomishan mud volcano phenomenon in the southeastern edge of the Caspian Sea, given its oil and gas resources, has been studied by some geologists in terms of geology and tectonics but not in terms of microbiology. Accordingly, it seems necessary to study this phenomenon from the perspective of microbiology in order to identify prokaryotes living in this area. Prokaryotes diversity in Mud volcano has been studied by cultivation techniques, fluorescence in situ hybridization, and denaturing gradient gel electrophoresis of PCR-amplified fragments of 16S rRNA genes. Total cell abundance in the mud volcano from 1×101-6×101per milliliter was determined by 4', 6-diamidino-2-phenylindole direct count. The detectable proportion of Archaea to Bacteria in the community by FISH was one to five. High viable counts (1 – 3 × 106) were obtained in culture media. A total of 122 isolates were obtained, 46 colonies were selected based on primarily morphological and physiological traits, and their 16S rRNA sequences were determined. The isolated genera included Halomonas (20%), Arthrobacter (5%), Kocuria (5%), Thalassobacillus (5%), Marinobacter (20%), Paracoccus (5%), Roseovarius (5%), Jeotgalicoccus (5%), Bacillus (15%), and Staphylococcus (15%). Regarding DGGE analysis, selected bands were obtained from the gels, reamplified and sequenced. Overall, 75% of the bacterial sequences were related to Rahnella and 25% related to Serratia.http://www.gjesm.net/article_23306_efe9d91658b6ba9698aa3f8553275d14.pdfDenaturing gradient gel electrophoresis (DGGE)Deoxyribonucleic acid (DNA)4, 6-diamidino-2-phenylindole (DAPI)ExtractionFluorescence in situ hybridization (FISH)Mud volcanoPhylogenetic treePolymerase chain reaction (PCR) |
| spellingShingle | M. Ghiasian A. Akhavan Sepahy M.A. Amoozegar S. Saadatmand M. Shavandi Bacterial diversity determination using culture-dependent and culture-independent methods Global Journal of Environmental Science and Management Denaturing gradient gel electrophoresis (DGGE) Deoxyribonucleic acid (DNA) 4, 6-diamidino-2-phenylindole (DAPI) Extraction Fluorescence in situ hybridization (FISH) Mud volcano Phylogenetic tree Polymerase chain reaction (PCR) |
| title | Bacterial diversity determination using culture-dependent and culture-independent methods |
| title_full | Bacterial diversity determination using culture-dependent and culture-independent methods |
| title_fullStr | Bacterial diversity determination using culture-dependent and culture-independent methods |
| title_full_unstemmed | Bacterial diversity determination using culture-dependent and culture-independent methods |
| title_short | Bacterial diversity determination using culture-dependent and culture-independent methods |
| title_sort | bacterial diversity determination using culture dependent and culture independent methods |
| topic | Denaturing gradient gel electrophoresis (DGGE) Deoxyribonucleic acid (DNA) 4, 6-diamidino-2-phenylindole (DAPI) Extraction Fluorescence in situ hybridization (FISH) Mud volcano Phylogenetic tree Polymerase chain reaction (PCR) |
| url | http://www.gjesm.net/article_23306_efe9d91658b6ba9698aa3f8553275d14.pdf |
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