Archaeal Diversity in Tidal Flat Sediment as Revealed by 16S rDNA Analysis |
Kim Bong Soo
(School of Biological Sciences, Seoul National University)
Oh Huyn Myung (School of Biological Sciences, Seoul National University) Kan Ho Jeong (Department of Environmental Science and Engineering, School of Engineering, Ewha Womans University) Chun Jong Sik (School of Biological Sciences, Seoul National University) |
1 | Borneman, J. and E.W. Triplett. 1997. Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation. Appl. Environ. Microbiol. 63, 2647-2653 PUBMED |
2 | Buckley, D.H., J.R. Graber, and T.M. Schmidt. 1998. Phylogenetic analysis of nonthermophilic members of the kingdom crenarchaeota and their diversity and abundance in soils. Appl. Environ. Microbiol. 64, 4333-4339 PUBMED |
3 | Eder, W., M. Schmidt, M. Koch, D. Garbe-Schonberg, and R. Huber. 2002. Prokaryotic phylogenetic diversity and corresponding geochemical data of the brine-seawater interface of the Shaban deep, Red Sea. Environ. Microbiol. 4, 758-763 DOI ScienceOn |
4 | Huber, H., M.J. Hohn, R. Rachel, T. Fuchs, V.C. Wimmer, and K.O. Stetter. 2002. A new phylum of archaea represented by a nanosized hyperthermophilic symbiont. Nature 417, 63-67 DOI ScienceOn |
5 | Hugenholtz, P., B.M. Goebel, and N.R. Pace. 1998. Impact of culture- independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180, 4765-4774 PUBMED |
6 | Jurgens, G., F. Glockner, R. Amann, A. Saano, L. Montonen, M. Likolammi, and U. Munster. 2000. Identification of novel archaea in bacterioplankton of a boreal forest lake by phylogenetic analysis and fluorescent in situ hybridization(1). FEMS Microbial. Ecol. 34, 45-56 |
7 | Klute, A 1986. Part 1: Physical and mineralogical methods, p. 383-409. In A. Klute (ed.), Methods of soil analysis, 2nd ed. American Society of Agronomy, Madison, Wisconsin |
8 | Massana, R., A.E. Murray, C.M. Preston, and E.E DeLong. 1997. Vertical distribution and phylogenetic characterization of marine planktonic archaea in the Santa Barbara channel. Appl. Environ. Microbiol. 63, 50-56 PUBMED |
9 | Massana, R., E.F. DeLong, and C. Pedros-Alio. 2000. A few cosmopolitan phylotypes dominate planktonic archaeal assemblages in widely different oceanic provinces. Appl. Environ. Microbiol. 66, 1777-1787 DOI ScienceOn |
10 | Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4,406-425 PUBMED |
11 | Takai, K. and K Horikoshi. 1999a. Genetic diversity of archaea in deep-sea hydrothermal vent environments. Genetics 152, 1285-1297 PUBMED |
12 | Preston, C.M., K.Y. Wu, T.F Molinski, and E.F. Delong. 1996. A psychrophilic crenarchaeon inhabits a marine sponge: Crenarchaeum symbiosum gen. nov., sp. nov. Proc. Natl. Acad. Sci. 93, 6241-6246 |
13 | Sessitsch, A., A. Weilharter, M.H. Gerzabek, H. Kirchmann, and E. Kandeler. 2001. Microbial population structures in soil particle size fractions of a long-term fertilizer field experiment. Appl. Environ. Microbiol. 67,4215-4224 DOI ScienceOn |
14 | Carling, P.A. 1982. Temporal and spatial variation in intertidal sedimentation rates. Sedimentol. 29, 17-23 DOI |
15 | Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791 DOI ScienceOn |
16 | Maidak, B.L., G.J. Olsen, N. Larsen, R. Overbeek, M.J. McCaughey, and C.R. Woese. 1997. The RDP (Ribosomal Database Project). Nucleic Acids Res. 25, 109-111 DOI ScienceOn |
17 | Jurgens, G., K. Lindstrom, and A. Saano, 1997. Novel group within the kingdom crenarchaeota from boreal forest soil. Appl. Environ. Microbiol. 63, 803-805 PUBMED |
18 | Stein, L.Y., G Jones, B. Alexander, K Elmund, C. Wright-Jones, and K.H. Nealson. 2002. Intriguing microbial diversity associated with metal-rich particles from a freshwater reservoir. FEMS Microbiol. Ecol. 42,431-440 DOI ScienceOn |
19 | Vetriani, C., A.L. Reysenbach, and J. Dore. 1998. Recovery and phylogenetic analysis of archaeal rRNA sequences from continental shelf sediments. FEMS Microbiol. Lett. 161, 83-88 DOI ScienceOn |
20 | Chin, K.J., T. Lukow, and R. Conrad. 1999. Effect of temperature on structure and function of the methanogenic archaeal community in an anoxic rice field soil. Appl. Environ. Microbiol. 65, 2341-2349 |
21 | Reed, D.W., Y. Fujita, M.E. Delwiche, D.B. Blackwelder, P.P. Sheridan, T. Uchida, and F.S. Colwell. 2002. Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin. Appl. Environ. Microbiol. 68, 3759-3770 DOI ScienceOn |
22 | Nedwell, D.B. 1984. The input and mineralization of organic carbon in anaerobic aquatic sediments. Adv. Microb. Ecol. 7, 93-130 |
23 | Bintrim, S.B., T.J. Donohue, J. Handelsman, G.P. Roberts, and R.M. Goodman. 1997. Molecular phylogeny of archaea from soil. Proc. Natl. Acad. Sci. 94, 277-282 |
24 | Inagaki, F., M. Suzuki, K. Takai, and K. Horikoshi. 2003. Microbial communtiy structure in subseafloor sediments from the sea of Okhotsk. Appl. Environ. Microbiol. 69, 7224-7235 DOI ScienceOn |
25 | Barns, S.M., C.F. Delwiche, J.D. Palmer, and N.R. Pace. 1996. Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc. Natl. Acad Sci. 93, 9188-9193 |
26 | von Wintzingerode, F., U.B. Gobel, and E. Stackebrandt. 1997. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21,213-229 DOI ScienceOn |
27 | Reysenbach, A.L., K. Longnecker, and J. Kirshtein. 2000. Novel bacterial and archaeal lineages from an in situ growth chamber deployed at a Mid-Atlantic Ridge hydrothermal vent. Appl. Environ. Microbiol. 66, 3798-3806 DOI ScienceOn |
28 | Bano, N., S. Ruffin, B. Ransom, and J.T. Hollibaugh. 2004. Phylogenetic composition of Arctic Ocean archaeal assemblages and comparison with Antarctic assemblages. Appl. Environ. Microbiol. 70,781-789 DOI ScienceOn |
29 | Hur, I. and J. Chun. 2004. A method for comparing multiple bacterial community structures from 16S rDNA clone library sequences. J. Microbiol. 42, 9-13 |
30 | Hurst, C.J. 1997. Recovery of bacterial community DNA from soil, p. 433-434. In CJ. Hurst, R.L. Crawford, G.R. Knudsen, M.J. McInerney, and L.D. Stetzenbach (eds.), Manual of Environmental Microbiology, 2nd ed. American Society for Microbiology, Washington D.C |
31 | Barns, S.M., R.E. Fundyga, M. W. Jeffries, and N.R. Pace. 1994. Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc. Natl. Acad Sci. 91, 1609-1613 |
32 | Vetriani, C., H.W. Jannasch, B.J. MacGregor, D.A. Stahl, and A.L. Reysenbach. 1999. Population structure and phylogenetic characterization of marine benthic archaea in deep-sea sediments. Appl. Environ. Microbiol. 65, 4375-4384 PUBMED |
33 | Orphan, V.J., L.T. Taylor, D. Hafenbradl, and E.F. Delong. 2000. Culture-dependent and culture-independent characterization of microbial assemblages associated with high-temperature petroleum reservoirs. Appl. Environ. Microbiol. 66, 700-711 DOI ScienceOn |
34 | Munson, M.A., D.B. Nedwell, and T.M. Embley. 1997. Phylogenetic diversity of Archaea in sediment samples from a coastal salt marsh. Appl. Environ. Microbiol. 63, 4729-4733 PUBMED |
35 | Watts, J.E.M. 1999. Ph. D. thesis. University of Warwick, Warwick, United Kingdom |
36 | Chun, J., A. Huq, and R.R. Colwell. 1999. Analysis of 16S-23S rRNA intergenic spacer regions of Vibrio cholerae and Vibrio mimicus. Appl. Environ. Microbiol. 65, 2202-2208 PUBMED |
37 | Torsvik, V., R. Sorheim, and J. Goksoyr. 1996. Total bacterial diversity in soil and sediment communities - a review. J. Ind Microbiol. 17, 170-178 DOI ScienceOn |
38 | Kim, B.S., H.-M. OH, H. Kang, S.-S. Pack, and J. Chun. 2004. Remarkable bacterial diversity in the tidal flat sediment as revealed by 16S rDNA analysis. J. Microbiol. Biotechnol. 14, 205-211 |
39 | Takai, K., D.P. Moser, M. DeFlaun, T.C. Onstott, and J.K Fredrickson. 2001. Archaeal diversity in waters from deep South African gold mines. Appl. Environ. Microbiol. 67, 5750-5760 DOI ScienceOn |
40 | McInerney, J.O., M. Wilkinson, J.W. Patching, T.M. Embley, and R. Powell. 1995. Recovery and phylogenetic analysis of novel archaeal rRNA sequences from a deep-sea deposit feeder. Appl. Environ. Microbiol. 61, 1646-1648 PUBMED |
41 | Teske, A, KU. Hinrichs, V. Edgcomb, A de Vera Gomez, D. Kysela, S.P. Sylva, M.L. Sogin, and H.W. Jannasch. 2002. Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities. Appl. Environ. Microbiol. 68, 1994-2007 DOI ScienceOn |
42 | Lovely, D.R., D.F. Dwyer, and M.J. Klug. 1982. Kinetic analysis of competition between sulfate reducers and methanogens for hydrogen in sediments. Appl. Environ. Microbiol. 43, 1373-1379 PUBMED |
43 | Hinrichs, K.U., J.M. Hayes, S.P. Sylva, P.G. Brewer, and E.F. DeLong. 1999. Methane-consuming archaebacteria in marine sediments. Nature 398, 802-805 DOI PUBMED ScienceOn |
44 | Cho, H.-B., J.-K. Lee, and Y.-K. Choi. 2003. The genetic diversity analysis of the bacterial community in groundwater by denaturing gradient gel electrophoresis (DGGE). J. Microbiol. 41, 327-334 |
45 | Fuhrman, J.A., K. McCallum, and A.A. Davis. 1992. Novel major archaebacterial group from marine plankton. Nature 356, 148-149 DOI ScienceOn |
46 | Oremland, R.S. and S. Polcin. 1982. Methanogenesis and sulfate reduction: competitive and non-competitive substrates in estuarine sediments. Appl. Environ. Microbiol. 44, 1270-1276 PUBMED |
47 | DeLong, E.F. 1992. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. 89, 5685-5689 |
48 | Gro kopf, R., S. Stubner, and W. Liesack. 1998. Novel euryarchaeotal lineages detected on rice roots and in the anoxic bulk soil of flooded rice microcosms. Appl. Environ. Microbiol. 64, 4983-4989 PUBMED |
49 | Takai, K and K. Horikoshi. 1999b. Molecular phylogenetic analysis of archaeal intron-containing genes coding for rRNA obtained from a deep-subsurface geothermal water pool. Appl. Environ. Microbiol. 65, 5586-5589 PUBMED |
50 | Holben, W.E., J.K. Jansso, B.K. Chelm, and J.M. Tiedje. 1988. DNA probe method for the detection of specific microorganisms in the soil bacterial community. Appl. Environ. Microbiol. 54, 703-711 PUBMED |
51 | Jukes, T.H. and C.R. Cantor. 1969. Evolution of protein molecules, p. 21-132. In H.N. Munro (ed.), Mammalian protein metabolism. Academic Press, New York |
52 | Sandaa, R.A., O. Enger, and V. Torsvik. 1999. Abundance and diversity of Archaea in heavy-metal-contaminated soils. Appl. Environ. Microbiol. 65, 3293-3297 PUBMED |
53 | van der Maarel, M.J., W. Sprenger, R. Haanstra, and L.J. Forney. 1999. Detection of methanogenic archaea in seawater particles and the digestive tract of a marine fish species. FEMS Microbiol. Lett. 173, 189-194 PUBMED |
54 | Hershberger, K.L., S.M. Barns, A.L. Reysenbach, S.C. Dawson, and N.R. Pace. 1996. Crenarchaeota in low-temperature terrestrial environments. Nature 384, 420 |
55 | Lee, J.-H., H.-H. Shin, D.-S. Lee, K.K. Kwon, S.-J. Kim, and H.K. Lee. 1999. Bacterial diversity of culturable isolates from seawater and a marine coral, Plexauridae sp., near Mun-Sum, Cheju-Islnd. J. Microbiol. 37, 193-199 |