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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 林立虹(Li-Hung Lin) | |
| dc.contributor.author | Yung-Hsin Chang | en |
| dc.contributor.author | 張永欣 | zh_TW |
| dc.date.accessioned | 2021-06-15T06:51:35Z | - |
| dc.date.available | 2013-02-20 | |
| dc.date.copyright | 2011-02-20 | |
| dc.date.issued | 2011 | |
| dc.date.submitted | 2011-02-14 | |
| dc.identifier.citation | Alain, K., Holler, T., Musat, F., Elvert, M., Treude, T., and Kruger, M. (2006) Microbiological investigation of methane- and hydrocarbon-discharging mud volcanoes in the Carpathian Mountains, Romania. Environmental Microbiology 8: 574-590.
Amann, R.I., Ludwig, W., and Schleifer, K.H. (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiological Reviews 59: 143-169. Amann, R.I., Binder, B.J., Olson, R.J., Chisholm, S.W., Devereux, R., and Stahl, D.A. (1990) Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Applied and Environmental Microbiology 56: 1919-1925. Ashelford, K.E., Chuzhanova, N.A., Fry, J.C., Jones, A.J., and Weightman, A.J. (2005) At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Applied and Environmental Microbiology 71: 7724-7736. Auman, A.J., Stolyar, S., Costello, A.M., and Lidstrom, M.E. (2000) Molecular characterization of methanotrophic isolates from freshwater lake sediment. Applied and Environmental Microbiology 66: 5259-5266. Bano, N., and Hollibaugh, J.T. (2002) Phylogenetic composition of bacterioplankton assemblages from the Arctic Ocean. Applied and Environmental Microbiology 68: 505-518. Barnes, R.O., and Goldberg, E.D. (1976) Methane production and consumption in anoxic marine sediments. Geology 4: 297-300. Beal, E.J., House, C.H., and Orphan, V.J. (2009) Manganese- and iron-dependent marine methane oxidation. Science 325: 184-187. Boden, R., Kelly, D.P., Murrell, J.C., and Schäfer, H. (2010) Oxidation of dimethylsulfide to tetrathionate by Methylophaga thiooxidans sp. nov.: a new link in the sulfur cycle. Environmental Microbiology 12: 2688-2699. Boetius, A., Ravenschlag, K., Schubert, C.J., Rickert, D., Widdel, F., Gieseke, A. et al. (2000) A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407: 623-626. Borowski, W.S., Paull, C.K., and Ussler, W. (1999) Global and local variations of interstitial sulfate gradients in deep-water, continental margin sediments: Sensitivity to underlying methane and gas hydrates. Marine Geology 159: 131-154. Botstein, D., White, R.L., Skolnick, M., and Davis, R.W. (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics 32: 314-331. Bowman, J. (2006) The Methanotrophs — The families Methylococcaceae and Methylocystaceae. In The Prokaryotes. Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K.-H., and Stackebrandt, E. (eds): Springer New York, pp. 266-289. Bréas, O., Guillou, C., Reniero, F., and Wada, E. (2001) The global methane cycle: isotopes and mixing ratios, sources and sinks. Isotopes in Environmental and Health Studies 37: 257-379. Brazelton, W.J., Schrenk, M.O., Kelley, D.S., and Baross, J.A. (2006) Methane- and sulfur-metabolizing microbial communities dominate the Lost City hydrothermal field ecosystem. Applied and Environmental Microbiology 72: 6257-6270. Capone, D.G., and Kiene, R.P. (1988) Comparison of microbial dynamics in marine and freshwater sediments: contrasts in anaerobic carbon catabolism. Limnology and Oceanography 33: 725-749. Carr, E.L., Eales, K., Soddell, J., and Seviour, R.J. (2005) Improved permeabilization protocols for fluorescence in situ hybridization (FISH) of mycolic-acid-containing bacteria found in foams. Journal of Microbiological Methods 61: 47-54. Chang, C.P., Angelier, J., and Huang, C.Y. (2000) Origin and evolution of a mélange: the active plate boundary and suture zone of the Longitudinal Valley, Taiwan. Tectonophysics 325: 43-62. Chang, C.P., Angelier, J., Huang, C.Y., and Liu, C.S. (2001) Structural evolution and significance of a melange in a collision belt: the Lichi Melange and the Taiwan arc-continent collision. Geological Magazine 138: 633-651. Chao, A. (1984) Nonparametric Estimation of the Number of Classes in a Population. Scandinavian Journal of Statistics 11: 265-270. Chao, H.-C., You, C.-F., and Sun, C.-H. (2010) Gases in Taiwan mud volcanoes: Chemical composition, methane carbon isotopes, and gas fluxes. Applied Geochemistry 25: 428-436. Colwell, R.K. (2009) EstimateS: Statistical estimation of species richness and shared species from samples. Version 8. (User's Guide and application.) Freeware published at http://viceroy.eeb.uconn.edu/estimates. Conrad, R. (1996) Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O, and NO). Microbiological Reviews 60: 609-640. Conrad, R. (1999) Contribution of hydrogen to methane production and control of hydrogen concentrations in methanogenic soils and sediments. FEMS Microbiology Ecology 28: 193-202. Conrad, R. (2009) The global methane cycle: recent advances in understanding the microbial processes involved. Environmental Microbiology Reports 1: 285-292. Costello, A.M., Auman, A.J., Macalady, J.L., Scow, K.M., and Lidstrom, M.E. (2002) Estimation of methanotroph abundance in a freshwater lake sediment. Environmental Microbiology 4: 443-450. Daims, H., Brühl, A., Amann, R., Schleifer, K.H., and Wagner, M. (1999) The domain-specific probe EUB338 is insufficient for the detection of all bacteria: Development and evaluation of a more comprehensive probe set. Systematic and Applied Microbiology 22: 434-444. Davenport, R.J., Curtis, T.P., Goodfellow, M., Stainsby, F.M., and Bingley, M. (2000) Quantitative use of fluorescent in situ hybridization to examine relationships between mycolic acid-containing Actinomycetes and foaming in activated sludge plants. Applied and Environmental Microbiology 66: 1158-1166. Dedysh, S.N., Knief, C., and Dunfield, P.F. (2005) Methylocella species are facultatively methanotrophic. The Journal of Bacteriology 187: 4665-4670. Dedysh, S.N., Khmelenina, V.N., Suzina, N., Trotsenko, Y.A., Semrau, J.D., Liesack, W., and Tiedje, J.M. (2002) Methylocapsa acidiphila gen. nov., sp. nov., a novel methane-oxidizing and dinitrogen-fixing acidophilic bacterium from Sphagnum bog. International Journal of Systematic and Evolutionary Microbiology 52: 251-261. DeLong, E.F. (1992) Archaea in coastal marine environments. Proceedings of the National Academy of Sciences of the United States of America 89: 5685-5689. Dimitrov, L.I. (2002) Mud volcanoes--the most important pathway for degassing deeply buried sediments. Earth-Science Reviews 59: 49-76. Dimitrov, L.I. (2003) Mud volcanoes—a significant source of atmospheric methane. Geo-Marine Letters 23: 155-161. Donachie, S.P., Hou, S., Lee, K.S., Riley, C.W., Pikina, A., Belisle, C. et al. (2004) The Hawaiian Archipelago: a microbial diversity hotspot. Microbial Ecology 48: 509-520. Dunfield, P.F., Yuryev, A., Senin, P., Smirnova, A.V., Stott, M.B., Hou, S. et al. (2007) Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. Nature 450: 879-882. Elizabeth W. A, Daniel B. Oerther, Niels Larsen, DAVID A. Stahl, and Raskin, L. (1996) The oligonucleotide probe database. Applied and Environmental Microbiology 62: 3557–3559. Eller, G., Kanel, L., and Kruger, M. (2005) Cooccurrence of aerobic and anaerobic methane oxidation in the water column of Lake Pluβsee. Appl Environ Microbiol 71: 8925-8928. Etiope, G., Lassey, K.R., Klusman, R.W., and Boschi, E. (2008) Reappraisal of the fossil methane budget and related emission from geologic sources. In Geophysical Research Letters: AGU, p. L09307. Ettwig, K.F., Butler, M.K., Le Paslier, D., Pelletier, E., Mangenot, S., Kuypers, M.M.M. et al. (2010) Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature 464: 543-548. Gotelli, N.J., and Entsminger, G.L. (2003) Swap algorithms in null model analysis. . Ecology 84: 532-535. Gu, J., Cai, H., Yu, S.-L., Qu, R., Yin, B., Guo, Y.-F. et al. (2007) Marinobacter gudaonensis sp. nov., isolated from an oil-polluted saline soil in a Chinese oilfield. International Journal of Systematic and Evolutionary Microbiology 57: 250-254. Hammer, Ø., Harper, D.A.T., and P. D. Ryan (2001) PAST: paleontological statistics software package for dducation and data analysis. Palaeontologia Electronica 4: 9. Hanson, R.S., and Hanson, T.E. (1996) Methanotrophic bacteria. Microbiological Reviews 60: 439-471. Hinrichs, K.U., Hayes, J.M., Sylva, S.P., Brewer, P.G., and DeLong, E.F. (1999) Methane-consuming archaebacteria in marine sediments. Nature 398: 802-805. Hoehler, T.M., Alperin, M.J., Albert, D.B., and Martens, C.S. (1994) Field and laboratory studies of methane oxidation in an anoxic marine sediment: evidence for a methanogen-sulfate reducer consortium. Global Biogeochemical Cycles 8: 451-463. Hoehler, T.M., Alperin, M.J., Albert, D.B., and Martens, C.S. (1998) Thermodynamic control on hydrogen concentrations in anoxic sediments. Geochimica et Cosmochimica Acta 62: 1745-1756. Hsu, T.L. (1976) The Lichi Mélange in the Coastal Range framework. Bulletin of the Geological Survey of Taiwan 25: 87-95. Hubert, C., Loy, A., Nickel, M., Arnosti, C., Baranyi, C., Brüchert, V. et al. (2009) A constant flux of diverse thermophilic bacteria into the cold Arctic seabed. Science 325: 1541-1544. Isenbarger, T.A., Finney, M., Rios-Velazquez, C., Handelsman, J., and Ruvkun, G. (2008) Miniprimer PCR, a new lens for viewing the microbial world. Applied and Environmental Microbiology 74: 840-849. Islam, T., Jensen, S., Reigstad, L.J., Larsen, Ø., and Birkeland, N.-K. (2008) Methane oxidation at 55°C and pH 2 by a thermoacidophilic bacterium belonging to the Verrucomicrobia phylum. Proceedings of the National Academy of Sciences 105: 300-304. Jagersma, G.C., Meulepas, R.J.W., Heikamp-de Jong, I., Gieteling, J., Klimiuk, A., Schouten, S. et al. (2009) Microbial diversity and community structure of a highly active anaerobic methane-oxidizing sulfate-reducing enrichment. Environmental Microbiology 11: 3223-3232. Kendall, M., and Boone, D. (2006) The order Methanosarcinales. In The Prokaryotes. Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K.-H., and Stackebrandt, E. (eds): Springer New York, pp. 244-256. Kendall, M.M., Wardlaw, G.D., Tang, C.F., Bonin, A.S., Liu, Y., and Valentine, D.L. (2007) Diversity of archaea in marine sediments from Skan Bay, Alaska, including cultivated methanogens, and description of Methanogenium boonei sp. nov. Applied and Environmental Microbiology 73: 407-414. Knight, V.K., Kerkhof, L.J., and Häggblom, M.M. (1999) Community analyses of sulfidogenic 2-bromophenol-dehalogenating and phenol-degrading microbial consortia. FEMS Microbiology Ecology 29: 137-147. Knittel, K., and Boetius, A. (2009) Anaerobic oxidation of methane: progress with an unknown process. Annual Review of Microbiology 63: 311-334. Knittel, K., Losekann, T., Boetius, A., Kort, R., and Amann, R. (2005) Diversity and distribution of methanotrophic archaea at cold seeps. Applied and Environmental Microbiology 71: 467-479. Knittel, K., Boetius, A., Lemke, A., Eilers, H., Lochte, K., Pfannkuche, O. et al. (2003) Activity, distribution, and diversity of sulfate reducers and other bacteria in sediments above gas hydrate (Cascadia Margin, Oregon). Geomicrobiology Journal 20: 269-294. Kopf, A.J. (2002) Significance of mud volcanism. Reviews of Geophysics 40. Lai, M.-C., Shu, C.-M., Chiou, M.-S., Hong, T.-Y., Chuang, M.-J., and Hua, J.J. (1999) Characterization of Methanosarcina mazei N2M9705 isolated from an aquaculture fishpond. Current Microbiology 39: 79-84. Lane, D.J. (1991) 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics. New York: Wiley, pp. 115-176. Liu, C., Wu, Y., Li, L., Ma, Y., and Shao, Z. (2007) Thalassospira xiamenensis sp. nov. and Thalassospira profundimaris sp. nov. International Journal of Systematic and Evolutionary Microbiology 57: 316-320. Liu, Y., and Whitman, W.B. (2008) Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea. Annals of the New York Academy of Sciences 1125: 171-189. Lloyd, K.G., Lapham, L., and Teske, A. (2006) Anaerobic methane-oxidizing community of ANME-1b archaea in hypersaline Gulf of Mexico sediments. Applied and Environmental Microbiology 72: 7218-7230. Lovley, D., Phillips, E., Lonergan, D., and Widman, P. (1995) Fe(III) and S0 reduction by Pelobacter carbinolicus. Applied and Environmental Microbiology 61: 2132-2138. Lozupone, C., and Knight, R. (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Applied and Environmental Microbiology 71: 8228 - 8235. Lu, Y.H., and Conrad, R. (2005) In situ stable isotope probing of methanogenic archaea in the rice rhizosphere. Science 309: 1088-1090. Lyimo, T., Pol, A., Op den Camp, H., Harhangi, H., and Vogels, G. (2000) Methanosarcina semesiae sp. nov., a dimethylsulfide-utilizing methanogen from mangrove sediment. International Journal of Systematic and Evolutionary Microbiology 50: 171-178. Madigan, M.T., Martinko, J. M., and Parker, J. (2006) Brock biology of microorganisms. In: Prentice-Hall, pp. 342-343. Martinez, R.J., Mills, H.J., Story, S., and Sobecky, P.A. (2006) Prokaryotic diversity and metabolically active microbial populations in sediments from an active mud volcano in the Gulf of Mexico. Environmental Microbiology 8: 1783-1796. McDonald, I.R., Bodrossy, L., Chen, Y., and Murrell, J.C. (2008) Molecular ecology techniques for the study of aerobic methanotrophs. Applied and Environmental Microbiology 74: 1305-1315. Melissa, M.K., and David, R.B. (2006) Cultivation of methanogens from shallow marine sediments at Hydrate Ridge, Oregon. Archaea 2: 31-38. Messing, J. (1993) M13 cloning vehicles. Their contribution to DNA sequencing. Methods in Molecular Biology 23: 9-22. Michaelis, W., Seifert, R., Nauhaus, K., Treude, T., Thiel, V., Blumenberg, M. et al. (2002a) Microbial reefs in the Black Sea fueled by anaerobic oxidation of methane. Science 297: 1013-1015. Michaelis, W., Seifert, R., Nauhaus, K., Treude, T., Thiel, V., Blumenberg, M. et al. (2002b) Microbial reefs in the Black Sea fueled by anaerobic oxidation of methane. Science 297: 1013-1015. Milkov, A.V., Sassen, R., Apanasovich, T.V., and Dadashev, F.G. (2003) Global gas flux from mud volcanoes: A significant source of fossil methane in the atmosphere and the ocean. Geophysical Research Letters 30. Miyashita, A., Mochimaru, H., Kazama, H., Ohashi, A., Yamaguchi, T., Nunoura, T. et al. (2009) Development of 16S rRNA gene-targeted primers for detection of archaeal anaerobic methanotrophs (ANMEs). FEMS Microbiology Letters 297: 31-37. Mori, K., Yamamoto, H., Kamagata, Y., Hatsu, M., and Takamizawa, K. (2000) Methanocalculus pumilus sp. nov., a heavy-metal-tolerant methanogen isolated from a waste-disposal site. International Journal of Systematic and Evolutionary Microbiology 50: 1723-1729. Morisita, M. (1959) Measuring of the dispersion of individuals and analysis of the distribution patterns. Memoirs of the Faculty of Science Kyushu University Series E Biology 2: 215-235. Mosier, A., Wassmann, R., Verchot, L., King, J., and Palm, C. (2004) Methane and nitrogen oxide fluxes in tropical agricultural soils: sources, sinks and mechanisms. Environment, Development and Sustainability 6: 11-49. Nakaya, T., Kobayashi, K., Akagi, T., Kimura, K., and Tai, H. (2000) Continuous monitoring of the methane concentration in the atmosphere by IR spectrometry with 1.66-μm diode laser. Analytical Sciences 16: 1211-1214. Nauhaus, K., Boetius, A., Krüger, M., and Widdel, F. (2002) In vitro demonstration of anaerobic oxidation of methane coupled to sulphate reduction in sediment from a marine gas hydrate area. Environmental Microbiology 4: 296-305. Nauhaus, K., Albrecht, M., Elvert, M., Boetius, A., and Widdel, F. (2007) In vitro cell growth of marine archaeal-bacterial consortia during anaerobic oxidation of methane with sulfate. Environmental Microbiology 9: 187-196. Niemann, H., Losekann, T., de Beer, D., Elvert, M., Nadalig, T., Knittel, K. et al. (2006) Novel microbial communities of the Haakon Mosby mud volcano and their role as a methane sink. Nature 443: 854-858. Nunoura, T., Hirayama, H., Takami, H., Oida, H., Nishi, S., Shimamura, S. et al. (2005) Genetic and functional properties of uncultivated thermophilic crenarchaeotes from a subsurface gold mine as revealed by analysis of genome fragments. Environmental Microbiology 7: 1967-1984. Omoregie, E.O., Mastalerz, V., de Lange, G., Straub, K.L., Kappler, A., Roy, H. et al. (2008) Biogeochemistry and community composition of iron- and sulfur-precipitating microbial mats at the Chefren mud volcano (Nile Deep Sea fan, Eastern Mediterranean). Applied and Environmental Microbiology 74: 3198-3215. Op den Camp, H.J.M., Islam, T., Stott, M.B., Harhangi, H.R., Hynes, A., Schouten, S. et al. (2009) Environmental, genomic and taxonomic perspectives on methanotrophic Verrucomicrobia. Environmental Microbiology Reports 1: 293-306. Orcutt, B., Boetius, A., Elvert, M., Samarkin, V., and Joye, S.B. (2005) Molecular biogeochemistry of sulfate reduction, methanogenesis and the anaerobic oxidation of methane at Gulf of Mexico cold seeps. Geochimica et Cosmochimica Acta 69: 4267-4281. Orcutt, B.N., Joye, S.B., Kleindienst, S., Knittel, K., Ramette, A., Reitz, A. et al. (2010) Impact of natural oil and higher hydrocarbons on microbial diversity, distribution, and activity in Gulf of Mexico cold-seep sediments. Deep Sea Research Part II: Topical Studies in Oceanography 57: 2008-2021. Oremland, R.S., Hoeft, S.E., Santini, J.M., Bano, N., Hollibaugh, R.A., and Hollibaugh, J.T. (2002) Anaerobic oxidation of arsenite in Mono Lake water and by a facultative, arsenite-oxidizing chemoautotroph, Strain MLHE-1. Applied and Environmental Microbiology 68: 4795-4802. Orita, M., Iwahana, H., Kanazawa, H., Hayashi, K., and Sekiya, T. (1989) Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proceedings of the National Academy of Sciences of the United States of America 86: 2766-2770. Orphan, V.J., House, C.H., Hinrichs, K.-U., McKeegan, K.D., and DeLong, E.F. (2001a) Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis. Science 293: 484-487. Orphan, V.J., Hinrichs, K.U., Ussler, W., Paull, C.K., Taylor, L.T., Sylva, S.P. et al. (2001b) Comparative analysis of methane-oxidizing archaea and sulfate-reducing bacteria in anoxic marine sediments. Applied and Environmental Microbiology 67: 1922-1934. Pachiadaki, M.G., Lykousis, V., Stefanou, E.G., and Kormas, K.A. (2010) Prokaryotic community structure and diversity in the sediments of an active submarine mud volcano (Kazan mud volcano, East Mediterranean Sea). FEMS Microbiology Ecology 72: 429-444. Pernthaler, A., Dekas, A.E., Brown, C.T., Goffredi, S.K., Embaye, T., and Orphan, V.J. (2008) Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics. Proceedings of the National Academy of Sciences 105: 7052-7057. Pernthaler, J., Glöckner, F.-O., Schönhuber, W., and Amann, R. (2001) Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes. In Methods in Microbiology. John, H.P. (ed): Academic Press, pp. 207-226. Pielou, E.C. (1966) The measurement of diversity in different types of biological collections. Journal of Theoretical Biology 13: 131-144. Pol, A., Heijmans, K., Harhangi, H.R., Tedesco, D., Jetten, M.S.M., and Op den Camp, H.J.M. (2007) Methanotrophy below pH 1 by a new Verrucomicrobia species. Nature 450: 874-878. Raghoebarsing, A.A., Pol, A., van de Pas-Schoonen, K.T., Smolders, A.J.P., Ettwig, K.F., Rijpstra, W.I.C. et al. (2006) A microbial consortium couples anaerobic methane oxidation to denitrification. Nature 440: 918-921. Ravenschlag, K., Sahm, K., Knoblauch, C., Jorgensen, B.B., and Amann, R. (2000) Community structure, cellular rRNA content, and activity of sulfate-reducing bacteria in marine Arctic sediments. Applied and Environmental Microbiology 66: 3592-3602. Reay, D., Smith, P., and Amstel, A.v. (2010) Methane and climate change. Washington, DC: Earthscan. Reeburgh, W.S. (1980) Anaerobic methane oxidation: Rate depth distributions in Skan Bay sediments. Earth and Planetary Science Letters 47: 345-352. Reeburgh, W.S. (1996) 'Soft Spots' in the global methane budget. In 8th International Symposium on Microbial Growth on C-1 Compounds. Tabita, M.E.L.a.F.R. (ed). Dordrecht: Kluwer pp. 334-342. Reeburgh, W.S. (2007a) Oceanic methane biogeochemistry. Chemical Reviews 107: 486-513. Reeburgh, W.S. (2007b) Global methane biogeochemistry. In Treatise on Geochemistry. Heinrich, D.H., and Karl, K.T. (eds). Oxford: Pergamon, pp. 1-32. Reitner, J., Peckmann, J., Blumenberg, M., Michaelis, W., Reimer, A., and Thiel, V. (2005a) Concretionary methane-seep carbonates and associated microbial communities in Black Sea sediments. Palaeogeography Palaeoclimatology Palaeoecology 227: 18-30. Reitner, J., Peckmann, J., Blumenberg, M., Michaelis, W., Reimer, A., and Thiel, V. (2005b) Concretionary methane-seep carbonates and associated microbial communities in Black Sea sediments. Palaeogeography, Palaeoclimatology, Palaeoecology 227: 18-30. Robertson, C.E., Spear, J.R., Harris, J.K., and Pace, N.R. (2009) Diversity and stratification of archaea in a hypersaline microbial mat. Applied and Environmental Microbiology 75: 1801-1810. Ronaghi, M., and Elahi, E. (2002) Pyrosequencing for microbial typing. Journal of Chromatography B 782: 67-72. Schafer, H. (2007) Isolation of Methylophaga spp. from marine dimethylsulfide-degrading enrichment cultures and identification of polypeptides induced during growth on dimethylsulfide. Applied and Environmental Microbiology 73: 2580-2591. Schink, B. (1985) Fermentation of acetylene by an obligate anaerobe, Pelobacter acetylenicus sp. nov. . Archives of Microbiology 142: 295-301. Sejian, V., Lal, R., Lakritz, J., and Ezeji, T. (2010) Measurement and prediction of enteric methane emission. International Journal of Biometeorology: 1-16. Shannon, C.E. (2001) A mathematical theory of communication. ACM SIGMOBILE Mobile Computing and Communications Review 5: 3-55. Shih, T.-T. (1967) A survey of the active mud volcanoes in Taiwan and a study of their types and the character of the mud. Petroleum Geology of Taiwan 5: 259-311. Simpson, E.H. (1949) Measurement of diversity. Nature 163: 688-688. Singh, S.K., Verma, P., Ramaiah, N., Chandrashekar, A.A., and Shouche, Y.S. (2010) Phylogenetic diversity of archaeal 16S rRNA and ammonia monooxygenase genes from tropical estuarine sediments on the central west coast of India. Research in Microbiology 161: 177-186. Sorokin, D., Tourova, T., Mußmann, M., and Muyzer, G. (2008) Dethiobacter alkaliphilus gen. nov. sp. nov., and Desulfurivibrio alkaliphilus gen. nov. sp. nov.: two novel representatives of reductive sulfur cycle from soda lakes. Extremophiles 12: 431-439-439. Sorokin, D.Y., Tourova, T.P., Lysenko, A.M., and Kuenen, J.G. (2001) Microbial thiocyanate utilization under highly alkaline conditions. Applied and Environmental Microbiology 67: 528-538. Sorokin, D.Y., Tourova, T.P., Lysenko, A.M., and Muyzer, G. (2006) Diversity of culturable halophilic sulfur-oxidizing bacteria in hypersaline habitats. Microbiology 152: 3013-3023. Stein, L.Y., La Duc, M.T., Grundl, T.J., and Nealson, K.H. (2001) Bacterial and archaeal populations associated with freshwater ferromanganous micronodules and sediments. Environmental Microbiology 3: 10-18. Stoecker, K., Bendinger, B., Schöning, B., Nielsen, P.H., Nielsen, J.L., Baranyi, C. et al. (2006) Cohn’s Crenothrix is a filamentous methane oxidizer with an unusual methane monooxygenase. Proceedings of the National Academy of Sciences of the United States of America 103: 2363-2367. Streit, W.R., and Schmitz, R.A. (2004) Metagenomics - the key to the uncultured microbes. Current Opinion in Microbiology 7: 492-498. Sun, C.-H., Chang, S.-C., Kuo, C.-L., Wu, J.-C., Shao, P.-H., and Oung, J.-N. (2010) Origins of Taiwan's mud volcanoes: Evidence from geochemistry. Journal of Asian Earth Sciences 37: 105-116. Sung, Y., Ritalahti, K.M., Sanford, R.A., Urbance, J.W., Flynn, S.J., Tiedje, J.M., and Loffler, F.E. (2003) Characterization of two tetrachloroethene-reducing, acetate-oxidizing anaerobic bacteria and their description as Desulfuromonas michiganensis sp. nov. Applied and Environmental Microbiology 69: 2964-2974. Suzuki, D., Ueki, A., Amaishi, A., and Ueki, K. (2007) Desulfopila aestuarii gen. nov., sp. nov., a Gram-negative, rod-like, sulfate-reducing bacterium isolated from an estuarine sediment in Japan. International Journal of Systematic and Evolutionary Microbiology 57: 520-526. Takai, K., and Horikoshi, K. (2000) Rapid detection and quantification of members of the archaeal community by quantitative PCR using fluorogenic probes. Applied and Environmental Microbiology 66: 5066-5072. Tamura, K., Dudley, J., Nei, M., and Kumar, S. (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 1596-1599. Tippmann, H.-F. (2004) Analysis for free: Comparing programs for sequence analysis. Briefings in Bioinformatics 5: 82-87. Trotsenko, Y.A., and Murrell, J.C. (2008) Metabolic aspects of aerobic obligate methanotrophy. In Advances in Applied Microbiology. Allen I. Laskin, S.S., and Geoffrey, M.G. (eds): Academic Press, pp. 183-229. Valentine, D. (2002) Biogeochemistry and microbial ecology of methane oxidation in anoxic environments: a review. Antonie van Leeuwenhoek 81: 271-282. Vigliotta, G., Nutricati, E., Carata, E., Tredici, S.M., De Stefano, M., Pontieri, P. et al. (2007) Clonothrix fusca Roze 1896, a filamentous, sheathed, methanotrophic gamma-Proteobacterium. Applied and Environmental Microbiology 73: 3556-3565. Waechter-Brulla, D., DiSpirito, A.A., Chistoserdova, L.V., and Lidstrom, M.E. (1993) Methanol oxidation genes in the marine methanotroph Methylomonas sp. strain A4. The Journal of Bacteriology 175: 3767-3775. Wang, J.S., Logan, J.A., McElroy, M.B., Duncan, B.N., Megretskaia, I.A., and Yantosca, R.M. (2004) A 3-D model analysis of the slowdown and interannual variability in the methane growth rate from 1988 to 1997. Global Biogeochemical Cycles 18. Ward, N., Larsen, Ø., Sakwa, J., Bruseth, L., Khouri, H., Durkin, A.S. et al. (2004) Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath). PLoS Biology 2: e303. Whiticar, M.J. (1999) Carbon and hydrogen isotope systematics of bacterial formation and oxidation of methane. Chemical Geology 161: 291-314. Whiticar, M.J., Faber, E., and Schoell, M. (1986) Biogenic methane formation in marine and freshwater environments: CO2 reduction vs. acetate fermentation--Isotope evidence. Geochimica et Cosmochimica Acta 50: 693-709. Whittenbury R, Dalton H, Eccleston M, and HL, R. (1975) The different types of methane-oxidizing bacteria and some of their more unusual properties. In Symposium on microbial production and utilization of gases (H2, CH4, CO). Schlegel HG, Gottschalk G, and N, P. (eds). Göttingen: Akademie der Wissenschaften, pp. 1-9. Williams, J.G.K., Kubelik, A.R., Livak, K.J., Rafalski, J.A., and Tingey, S.V. (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research 18: 6531-6535. Wuebbles, D.J., and Hayhoe, K. (2002) Atmospheric methane and global change. Earth-Science Reviews 57: 177-210. Yang, T.F., Yeh, G.-H., Fu, C.-C., Wang, C.-C., Lan, T.-F., Lee, H.-F. et al. (2004) Composition and exhalation flux of gases from mud volcanoes in Taiwan. Environmental Geology 46: 1003-1011. Zengler, K., Richnow, H.H., Rossello-Mora, R., Michaelis, W., and Widdel, F. (1999) Methane formation from long-chain alkanes by anaerobic microorganisms. Nature 401: 266-269. | |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/48294 | - |
| dc.description.abstract | 泥火山與冷泉系統皆是重要的甲烷逸散的地質構造，來自深部熱裂解源及微生物所產生的碳氫化合物，藉由裂隙等通道釋放至大氣與海洋中。其微生物族群在陸域泥火山中所扮演的角色，有助於了解碳循環在不同深度儲庫間的調控。本研究目的在於探討台灣東部雷公火泥火山中的微生物甲烷循環，藉由分析噴發泥與距離噴發口不同距離的岩芯樣本 (岩芯 A 距離噴發口 0.34 m，岩芯 B 距離噴發口 1.53 m)，嘗試了解深部的流體通量如何影響微生物族群結構。
分析結果顯示此地區主要的微生物族群多為厭氧、耐鹽或嗜鹽特性菌種。靠近噴發口的環境以厭氧型甲烷氧化作用為主，其中岩芯 A 中深度5-9 cm 及 29 cm，為鐵－甲烷過渡帶，主要優勢古菌為 ANME-2a，其族群數量在不同深度樣本間的分布與 Dusulfuromonas/Pelobacter 族群為正相關，顯示金屬還原伴隨甲烷氧化作用發生的可能性。甲烷生成作用主要為利用甲基類代謝的甲烷菌種，並活躍於岩芯 A 深度9-27 cm 及岩芯 B 的淺部區間。細菌族群相較於古菌族群則有較高的物種豐富度及多樣性，其主要優勢菌種在岩芯 A 為 Desulfuromonas、Pelobacter、Marinobacter及未培養的 Bacteroidetes 相關菌種，岩芯 B 則轉換成以 Thiohalophilus 及未培養的 Bacteroidetes 相關菌種為優勢菌種。 綜合分子生物證據與地化資料，顯示深部富含碳氫化合物的流體湧升和來自大氣的氧氣，為調控泥火山中微生物族群結構變化與功能表現的重要因子。本地區泥火山的甲烷逸散，微生物的調控扮演重要的角色，在靠近噴發口的位置，甲烷經金屬還原伴隨甲烷氧化作用被大量消耗。距離噴發口較遠的位置，源自甲烷菌生成的甲烷則直接逸散至大氣。 | zh_TW |
| dc.description.abstract | Mud volcanoes and cold seeps are important geological features that facilitate the export of microbial and/or thermogenic hydrocarbons from deep sources to the overlying seawater and/or atmosphere. Understanding how microbial communities are regulated in terrestrial mud volcanoes would facilitate to unravel the carbon cycles linking deep and shallow reservoirs. The objective of this study was to characterize microbial communities associated with bubbling fluid and sediments along depth in two sites of the Lei-Gong-Huo mud volcano in eastern Taiwan. These sites were chosen (BF: bubbling fluid; site A: 0.34 meter from venting center; site B: 1.53 meter from venting center) in order to investigate how fluid flux would shape the community structures.
Site comparisons revealed that anaerobic, halophillic, salt-tolerated microorganisms were prevalent in both sites. Iron to methane transition occurred at depths of 5-9 cm and 29 cm in site A where archaeal populations were dominated by ANME-2a. The abundances of ANME-2a were positively correlated with those of Desulfomonas/Pelobacter sp., suggesting that anaerobic methanotrophy is coupled to the metal reduction. Methanogenesis primarily catalyzed by methylotrophic methanogens were actived at 9-27 cm depths of site A and shallow intervals of site B. Bacterial communities were highly diverse and composed of different assemblages. Dominant bacterial members switched from Desulfuromonas, Pelobacter, Marinobacter and uncultured Bacteroidetes-related microorganisms in site A to Thiohalophilus and uncultured Bacteroidetes-related microorganisms in site B. The molecular evidence combined with geochemical characteristics revealed that the interplay between the upwelling, hydrocarbon-rich fluids, and downward atmospheric oxygen is essential to regulate community assemblages and functional expressions in mud volcanoes. Methane emission in the mud volcanoes was controlled by microbial processes. Near the venting site, methane is consumed by iron-dependent anaerobic oxidation of methane. Far from the venting site, methane produced from methanogen was directly realeased to atmosphere. | en |
| dc.description.provenance | Made available in DSpace on 2021-06-15T06:51:35Z (GMT). No. of bitstreams: 1 ntu-100-R97224106-1.pdf: 21392053 bytes, checksum: a40df1fbd4a1ad9b7c0cd0cf2d5fb4b4 (MD5) Previous issue date: 2011 | en |
| dc.description.tableofcontents | 目錄
誌謝................................................... I 中文摘要............................................... II 英文摘要............................................... III 目錄................................................... V 圖目錄................................................. VIII 表目錄................................................. IX 第一章 、引言......................................... 1 1.1. 全球甲烷循環...................................... 1 1.2. 微生物甲烷循環................................. 2 1.2.1. 微生物甲烷生成作用............................. 2 1.2.2. 微生物甲烷氧化作用............................. 4 1.3. 泥火山......................................... 8 1.4. 分子生物技術應用於環境微生物的研究............. 9 1.5. 研究目的....................................... 10 1.5.1. 動機........................................... 11 1.5.2. 目的........................................... 14 第二章、實驗材料與方法................................. 15 2.1. 採樣地點.......................................... 15 2.2. 採樣方法....................................... 15 2.3. 微生物族群結構分析............................. 15 2.3.1. 環境基因體 DNA 萃取............................ 15 2.3.2. 建立微生物 16S rDNA 選殖基因庫................. 17 2.3.3. 16S rDNA 選殖基因庫資料比對與分析.............. 20 2.4. 微生物生物多樣性分析........................... 20 2.4.1. 生物多樣性指標................................. 21 2.4.2. 物種累積曲線分析............................... 22 2.4.3. 群集分析....................................... 22 2.4.4. 物種間分佈相關性分析........................... 22 2.5. 微生物族群豐度測量：即時定量聚合酶連鎖反應..... 23 2.5.1. 樣本來源與引子選用............................. 23 2.5.2. 標準曲線的建立................................. 23 2.5.3. 即時定量聚合酶連鎖反應......................... 23 2.5.4. 沉積物中的微生物量計算......................... 25 2.6. 螢光原位雜交染色............................... 25 2.6.1. 樣本保存與前置處理............................. 25 2.6.2. 包埋、脫水、細胞通透性處理..................... 27 2.6.3. 雜交反應與清洗處理............................. 27 2.6.4. 細胞核染色..................................... 27 第三章、實驗結果....................................... 28 3.1. 微生物族群結構.................................... 28 3.1.1. Proteobacteria 菌門............................ 31 3.1.2. Bacteroidetes 及 Firmicutes 菌門............... 35 3.1.3. 其他分類菌門................................... 36 3.1.4. 古菌族群結構................................... 36 3.2. 微生物生物多樣性............................... 40 3.2.1. 生物多樣性指標................................. 40 3.2.2. 物種累積曲線分析............................... 42 3.2.3. 群集分析....................................... 42 3.2.4. 物種間分佈相關性分析........................... 47 3.3. 微生物菌群豐度................................. 47 3.4. 螢光原位雜交染色............................... 51 第四章、討論........................................... 54 4.1. LGH02 環境特徵與背景.............................. 54 4.2. 厭氧型甲烷氧化作用............................. 55 4.2.1. 分子生物分析證據............................... 55 4.2.2. 厭氧型甲烷氧化菌與鐵還原菌共生關係可能性探討... 57 4.2.3. AOM 作用速率與自由能大小....................... 58 4.3. 好氧型甲烷氧化作用............................. 59 4.4. 甲烷生成作用................................... 61 4.5. 硫循環......................................... 63 4.6. 微生物族群結構與多樣性探討..................... 64 4.7. LGH02 之生物地球化學循環....................... 65 第五章、結論........................................... 68 參考文獻............................................... 69 附錄................................................... 84 | |
| dc.language.iso | zh-TW | |
| dc.title | 台灣東部雷公火泥火山之微生物甲烷循環 | zh_TW |
| dc.title | Microbial methane cycling in the Lei-Gong-Huo mud volcano of eastern Taiwan. | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 99-1 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 王珮玲(Pei-Ling Wang),陳俊堯(Chun-Yao Chen),湯森林(Sen-Lin Tang) | |
| dc.subject.keyword | 泥火山,微生物甲烷循環, | zh_TW |
| dc.subject.keyword | mud volcano,microbial methane cycling, | en |
| dc.relation.page | 101 | |
| dc.rights.note | 有償授權 | |
| dc.date.accepted | 2011-02-15 | |
| dc.contributor.author-college | 理學院 | zh_TW |
| dc.contributor.author-dept | 地質科學研究所 | zh_TW |
| 顯示於系所單位： | 地質科學系 | |
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