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Volumn 26, Issue 2, 2009, Pages 104-118

Bacterial and archaeal 16S rRNA genes in late pleistocene to holocene muddy sediments from the kanto plain of Japan

Author keywords

16S rRNA gene; Extra cellular DNA; Holocene sediments; Microbial community; Muddy sediments

Indexed keywords

HOLOCENE; MARINE SEDIMENT; MICROBIAL COMMUNITY; PHYLOGENETICS; PLEISTOCENE; RNA; TAXONOMY;

EID: 61349193192     PISSN: 01490451     EISSN: 15210529     Source Type: Journal    
DOI: 10.1080/01490450802662355     Document Type: Article
Times cited : (18)

References (60)
  • 2
    • 33644869355 scopus 로고    scopus 로고
    • Microbiological investigation of methane- and hydrocarbon-discharging mud volcanoes in the Carpathian Mountains, Romania
    • Alain, K., Holler, T., Musat, F., Elvert, M., Treude, T. and Kreuger, M. (2006) Microbiological investigation of methane- and hydrocarbon-discharging mud volcanoes in the Carpathian Mountains, Romania. Environ Microbiol, 8, pp. 574-590.
    • (2006) Environ Microbiol , vol.8 , pp. 574-590
    • Alain, K.1    Holler, T.2    Musat, F.3    Elvert, M.4    Treude, T.5    Kreuger, M.6
  • 4
    • 29144504177 scopus 로고    scopus 로고
    • At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies
    • 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. Appl Environ Microbiol, 71, pp. 7724-7736.
    • (2005) Appl Environ Microbiol , vol.71 , pp. 7724-7736
    • Ashelford, K.E.1    Chuzhanova, N.A.2    Fry, J.C.3    Jones, A.J.4    Weightman, A.J.5
  • 5
    • 0003121848 scopus 로고
    • Distribution and activity of microorganisms in subsurface sediments of a pristine study site in Oklahoma
    • Beloin, R. M., Sinclair, J. L. and Ghiorse, W. C. (1988) Distribution and activity of microorganisms in subsurface sediments of a pristine study site in Oklahoma. Microb Ecol, 16, pp. 85-97.
    • (1988) Microb Ecol , vol.16 , pp. 85-97
    • Beloin, R.M.1    Sinclair, J.L.2    Ghiorse, W.C.3
  • 9
    • 0031811165 scopus 로고    scopus 로고
    • Phylogenetic diversity of Archaea Bacteria in a deep subsurface paleosol
    • Chandler, D. P., Brockman, F. J., Bailey, T. J. and Fredrickson, J. K. (1998) Phylogenetic diversity of Archaea Bacteria in a deep subsurface paleosol. Microb Ecol, 36, pp. 37-50.
    • (1998) Microb Ecol , vol.36 , pp. 37-50
    • Chandler, D.P.1    Brockman, F.J.2    Bailey, T.J.3    Fredrickson, J.K.4
  • 10
    • 0031763993 scopus 로고    scopus 로고
    • Analysis of subfossil molecular remains of purple sulfur bacteria in a lake sediment
    • Coolen, M JL and Overmann, J. (1998) Analysis of subfossil molecular remains of purple sulfur bacteria in a lake sediment. Appl Environ Microbiol, 64, pp. 4513-4521.
    • (1998) Appl Environ Microbiol , vol.64 , pp. 4513-4521
    • Coolen, M.J.L.1    Overmann, J.2
  • 11
    • 12244258230 scopus 로고    scopus 로고
    • Simultaneous recovery of extracellular and intracellular DNA suitable for molecular studies from marine sediments
    • Corinaldesi, C., Danovaro, R. and Dell'Anno, A. (2005) Simultaneous recovery of extracellular and intracellular DNA suitable for molecular studies from marine sediments. Appl Environ Microbiol, 71, pp. 46-50.
    • (2005) Appl Environ Microbiol , vol.71 , pp. 46-50
    • Corinaldesi, C.1    Danovaro, R.2    Dell'Anno, A.3
  • 12
    • 0013258174 scopus 로고    scopus 로고
    • Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin
    • Dhillon, A., Teske, A., Dillon, J., Stahl, D. A. and Sogin, M. L. (2003) Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin. Appl Environ Microbiol, 69, pp. 2765-2772.
    • (2003) Appl Environ Microbiol , vol.69 , pp. 2765-2772
    • Dhillon, A.1    Teske, A.2    Dillon, J.3    Stahl, D.A.4    Sogin, M.L.5
  • 13
    • 0024849887 scopus 로고
    • Lithotrophic and heterotrophic bacteria in deep subsurface sediments and their relation to sediment properties
    • Fredrickson, J. K., Garland, T. R., Hicks, R. J., Thomas, J. M., Li, S. W. and McFadden, K. M. (1989) Lithotrophic and heterotrophic bacteria in deep subsurface sediments and their relation to sediment properties. Geomicrobiol J, 7, pp. 53-66.
    • (1989) Geomicrobiol J , vol.7 , pp. 53-66
    • Fredrickson, J.K.1    Garland, T.R.2    Hicks, R.J.3    Thomas, J.M.4    Li, S.W.5    McFadden, K.M.6
  • 15
    • 85040138714 scopus 로고
    • Prentice Hall, Inc., Englewood Cliffs, NJ
    • Freeze, A. and Cherry, H. (1979) Groundwater, Prentice Hall, Inc., Englewood Cliffs, NJ
    • (1979) Groundwater
    • Freeze, A.1    Cherry, H.2
  • 16
    • 0030613343 scopus 로고    scopus 로고
    • Population structure of microbial communities associated with two deep, anaerobic, alkaline aquifers
    • Fry, N. K., Fredrickson, J. K., Fishbain, S., Wagner, M. and Stahl, D. (1997) Population structure of microbial communities associated with two deep, anaerobic, alkaline aquifers. Appl Environ Microbiol, 63, pp. 1498-1504.
    • (1997) Appl Environ Microbiol , vol.63 , pp. 1498-1504
    • Fry, N.K.1    Fredrickson, J.K.2    Fishbain, S.3    Wagner, M.4    Stahl, D.5
  • 17
    • 53749085723 scopus 로고    scopus 로고
    • The distribution of microbial taxa in the subsurface water of the Kalahari Shield, South Africa
    • Gihring, T., Moser, D. P. and Onstott, T. C. (2006) The distribution of microbial taxa in the subsurface water of the Kalahari Shield, South Africa. Geomicrobiol J, 23, pp. 415-430.
    • (2006) Geomicrobiol J , vol.23 , pp. 415-430
    • Gihring, T.1    Moser, D.P.2    Onstott, T.C.3
  • 18
    • 6944246004 scopus 로고    scopus 로고
    • Methanogenic pathway and archaeal community structure in the sediment of eutrophic Lake Dagow: Effect of temperature
    • Glissman, K., Chin, K. J., Casper, P. and Conrad, R. (2004) Methanogenic pathway and archaeal community structure in the sediment of eutrophic Lake Dagow: Effect of temperature. Microb Ecol, 48, pp. 389-399.
    • (2004) Microb Ecol , vol.48 , pp. 389-399
    • Glissman, K.1    Chin, K.J.2    Casper, P.3    Conrad, R.4
  • 19
  • 21
    • 0242285526 scopus 로고    scopus 로고
    • Characterization of methanogenic Archaea in the leachate of a closed municipal solid waste landfill
    • Huang, L. N., Chen, Y. Q., Zhou, H., Luo, S., Lan, C. Y. and Qu, L. H. (2003) Characterization of methanogenic Archaea in the leachate of a closed municipal solid waste landfill. FEMS Microbiol Ecol, 46, pp. 171-177.
    • (2003) FEMS Microbiol Ecol , vol.46 , pp. 171-177
    • Huang, L.N.1    Chen, Y.Q.2    Zhou, H.3    Luo, S.4    Lan, C.Y.5    Qu, L.H.6
  • 24
    • 18144401354 scopus 로고    scopus 로고
    • The paleome: A sedimentary genetic record of past microbial communities
    • Inagaki, F., Okada, H., Tsapin, A. I. and Nealson, K. H. (2005) The paleome: A sedimentary genetic record of past microbial communities. Astrobiology, 5, pp. 141-153.
    • (2005) Astrobiology , vol.5 , pp. 141-153
    • Inagaki, F.1    Okada, H.2    Tsapin, A.I.3    Nealson, K.H.4
  • 27
    • 33747622474 scopus 로고    scopus 로고
    • Sedimentary facies, physical properties, and radiocarbon dates of the GS-SK-1 core obtained from Kakinoki district, Nakagawa lowland, central Japan
    • Ishihara, Y., Kimura, K., Tanabe, S., Nakashima, R., Miyachi, Y., Hori, K., Inazaki, T. and Hachinohe, S. (2004) Sedimentary facies, physical properties, and radiocarbon dates of the GS-SK-1 core obtained from Kakinoki district, Nakagawa lowland, central Japan. Bull Geol Surv Japan, 55, pp. 183-200.
    • (2004) Bull Geol Surv Japan , vol.55 , pp. 183-200
    • Ishihara, Y.1    Kimura, K.2    Tanabe, S.3    Nakashima, R.4    Miyachi, Y.5    Hori, K.6    Inazaki, T.7    Hachinohe, S.8
  • 28
    • 0030619458 scopus 로고    scopus 로고
    • Characterization of microbial communities in deep groundwater from granitic rock
    • Jain, D. K., Stroes-Gascoyne, S., Providenti, M., Tanner, C. and Cord, I. (1997) Characterization of microbial communities in deep groundwater from granitic rock. Can J Microbiol, 43, pp. 272-283.
    • (1997) Can J Microbiol , vol.43 , pp. 272-283
    • Jain, D.K.1    Stroes-Gascoyne, S.2    Providenti, M.3    Tanner, C.4    Cord, I.5
  • 29
    • 34548418027 scopus 로고    scopus 로고
    • Microbial response to salinity change in Lake Chaka, a hypersaline lake on Tibetan plateau
    • Jiang, H., Dong, H., Yu, B., Liu, X., Li, Y., Ji, S. and Zhang, C. L. (2007) Microbial response to salinity change in Lake Chaka, a hypersaline lake on Tibetan plateau. Environ Microbiol, 9, pp. 2603-2621.
    • (2007) Environ Microbiol , vol.9 , pp. 2603-2621
    • Jiang, H.1    Dong, H.2    Yu, B.3    Liu, X.4    Li, Y.5    Ji, S.6    Zhang, C.L.7
  • 31
    • 0002947936 scopus 로고
    • Microbial communities in the saturated groundwater environment II: Diversity of bacterial communities in a Pleistocene sand aquifer and their in vitro activities
    • Kolbel-Boelke, J., Anders, E-M and Nehrkorn, A. (1988) Microbial communities in the saturated groundwater environment II: Diversity of bacterial communities in a Pleistocene sand aquifer and their in vitro activities. Microb Ecol, 16, pp. 31-48.
    • (1988) Microb Ecol , vol.16 , pp. 31-48
    • Kolbel-Boelke, J.1    Anders, E.-M.2    Nehrkorn, A.3
  • 33
    • 61349110165 scopus 로고    scopus 로고
    • Bacterial and archaeal diversity in surface sediments from the south slope of the South China Sea
    • Li, T., Wang, P. and Wang, P-X (2008) Bacterial and archaeal diversity in surface sediments from the south slope of the South China Sea. Acta Microbiol Sin, 48, pp. 323-329.
    • (2008) Acta Microbiol Sin , vol.48 , pp. 323-329
    • Li, T.1    Wang, P.2    Wang, P.-X.3
  • 35
    • 33747623681 scopus 로고    scopus 로고
    • Sedimentary facies, physical properties, and radiocarbon dates of the GS-KM-1 cores from Komatsugawa district, Tokyo Lowland, central Japan
    • Miyachi, Y., Kimura, K., Ishihara, Y., Tanabe, S., Nakashima, R., Hori, K., Nakayama, T. and Saito, Y. (2004) Sedimentary facies, physical properties, and radiocarbon dates of the GS-KM-1 cores from Komatsugawa district, Tokyo Lowland, central Japan. Bull Geol Surv Japan, 55, pp. 201-219.
    • (2004) Bull Geol Surv Japan , vol.55 , pp. 201-219
    • Miyachi, Y.1    Kimura, K.2    Ishihara, Y.3    Tanabe, S.4    Nakashima, R.5    Hori, K.6    Nakayama, T.7    Saito, Y.8
  • 37
    • 61349150055 scopus 로고    scopus 로고
    • Sequence stratigraphy of the Pleistocene Kioroshi Formation, Shimousa Group beneath the Omiya Upland, central Kanto Plain, central Japan
    • Nakazawa, T., Nakashima, R., Ueki, T., Tanabe, S., Oshima, H. and Horiuchi, S. (2006) Sequence stratigraphy of the Pleistocene Kioroshi Formation, Shimousa Group beneath the Omiya Upland, central Kanto Plain, central Japan. J Geol Soc Japan, 112, pp. 349-368.
    • (2006) J Geol Soc Japan , vol.112 , pp. 349-368
    • Nakazawa, T.1    Nakashima, R.2    Ueki, T.3    Tanabe, S.4    Oshima, H.5    Horiuchi, S.6
  • 38
    • 0025178066 scopus 로고
    • Distribution and activity of bacteria in deep granitic groundwaters of southeastern Sweden
    • Pedersen, K. and Ekendahl, S. (1990) Distribution and activity of bacteria in deep granitic groundwaters of southeastern Sweden. Microb Ecol, 20, pp. 37-52.
    • (1990) Microb Ecol , vol.20 , pp. 37-52
    • Pedersen, K.1    Ekendahl, S.2
  • 42
    • 0002708478 scopus 로고
    • Three-dimensional observation of soil bacteria in organic debris with a confocal laser scanning microscope
    • Someya, T. (1995) Three-dimensional observation of soil bacteria in organic debris with a confocal laser scanning microscope. Soil Microorg, 46, pp. 61-69.
    • (1995) Soil Microorg , vol.46 , pp. 61-69
    • Someya, T.1
  • 43
    • 35748979124 scopus 로고    scopus 로고
    • Spatial structure of the microbial community in sandy carbonate sediment
    • Sørensen, K. B., Glazer, B., Hannides, A. and Gaidos, E. (2007) Spatial structure of the microbial community in sandy carbonate sediment. Mar Ecol Prog Ser, 346, pp. 61-74.
    • (2007) Mar Ecol Prog Ser , vol.346 , pp. 61-74
    • Sørensen, K.B.1    Glazer, B.2    Hannides, A.3    Gaidos, E.4
  • 48
    • 17444372781 scopus 로고    scopus 로고
    • Comparative analysis of bacterial diversity in freshwater sediment of a shallow eutrophic lake by molecular and improved cultivation-based techniques
    • Tamaki, H., Sekiguchi, Y., Hanada, S., Nakamura, K., Nomura, N., Matsumura, M. and Kamagata, Y. (2005) Comparative analysis of bacterial diversity in freshwater sediment of a shallow eutrophic lake by molecular and improved cultivation-based techniques. Appl Environ Microbiol, 71, pp. 2162-2169.
    • (2005) Appl Environ Microbiol , vol.71 , pp. 2162-2169
    • Tamaki, H.1    Sekiguchi, Y.2    Hanada, S.3    Nakamura, K.4    Nomura, N.5    Matsumura, M.6    Kamagata, Y.7
  • 49
    • 61349185209 scopus 로고    scopus 로고
    • Sedimentary facies, radiocarbon dates and physical properties of the GS-AMG-1 core from Motogi district, Adachi-ku, western area of the Tokyo Lowland, central Japan
    • Tanabe, S., Nakashima, R., Nakanishi, T., Kimura, K. and Shibata, Y. (2006) Sedimentary facies, radiocarbon dates and physical properties of the GS-AMG-1 core from Motogi district, Adachi-ku, western area of the Tokyo Lowland, central Japan. Bull Geol Surv Japan, 57, pp. 289-307.
    • (2006) Bull Geol Surv Japan , vol.57 , pp. 289-307
    • Tanabe, S.1    Nakashima, R.2    Nakanishi, T.3    Kimura, K.4    Shibata, Y.5
  • 50
    • 24744454397 scopus 로고    scopus 로고
    • Pore size distribution of clayey soils measured by mercury intrusion porosimetry and its relation to hydraulic conductivity
    • Tanaka, H., Shiwakoti, D. R., Omukai, N., Rito, F., Locat, J. and Tanaka, M. (2003) Pore size distribution of clayey soils measured by mercury intrusion porosimetry and its relation to hydraulic conductivity. Soils Found, 43, pp. 63-73.
    • (2003) Soils Found , vol.43 , pp. 63-73
    • Tanaka, H.1    Shiwakoti, D.R.2    Omukai, N.3    Rito, F.4    Locat, J.5    Tanaka, M.6
  • 51
    • 40549089938 scopus 로고    scopus 로고
    • Microbial community succession and bacterial diversity in soils during 77 000 years of ecosystem development
    • Tarlera, S., Jangid, K., Ivester, A. H., Whitman, W. B. and Williams, M. A. (2008) Microbial community succession and bacterial diversity in soils during 77 000 years of ecosystem development. FEMS Microbiol Ecol, 64, pp. 129-140.
    • (2008) FEMS Microbiol Ecol , vol.64 , pp. 129-140
    • Tarlera, S.1    Jangid, K.2    Ivester, A.H.3    Whitman, W.B.4    Williams, M.A.5
  • 53
    • 0029161178 scopus 로고
    • A new fluorescence staining assay for visualizing living microorganisms in soil
    • Tsuji, T., Kawasaki, Y., Takeshima, S., Sekiya, T. and Tanaka, S. (1995) A new fluorescence staining assay for visualizing living microorganisms in soil. Appl Environ Microbiol, 61, pp. 3415-3421.
    • (1995) Appl Environ Microbiol , vol.61 , pp. 3415-3421
    • Tsuji, T.1    Kawasaki, Y.2    Takeshima, S.3    Sekiya, T.4    Tanaka, S.5
  • 54
    • 0032868072 scopus 로고    scopus 로고
    • Population structure and phylogenetic characterization of marine benthic archaea in deep-sea sediments
    • Vetriani, C., Jannasch, H. W., MacGregor, B. J., Stahl, D. A. and Reysenbach, A-L (1999) Population structure and phylogenetic characterization of marine benthic archaea in deep-sea sediments. Appl Environ Microbiol, 65, pp. 4375-4384.
    • (1999) Appl Environ Microbiol , vol.65 , pp. 4375-4384
    • Vetriani, C.1    Jannasch, H.W.2    MacGregor, B.J.3    Stahl, D.A.4    Reysenbach, A.-L.5
  • 55
    • 4644305740 scopus 로고    scopus 로고
    • Widespread occurrence of a novel division of bacteria identified by 16S rRNA gene sequences originally found in deep marine sediments
    • Webster, G., Parkes, R. J., Fry, J. C. and Weightman, A. J. (2004) Widespread occurrence of a novel division of bacteria identified by 16S rRNA gene sequences originally found in deep marine sediments. Appl Environ Microbiol, 70, pp. 5708-5713.
    • (2004) Appl Environ Microbiol , vol.70 , pp. 5708-5713
    • Webster, G.1    Parkes, R.J.2    Fry, J.C.3    Weightman, A.J.4
  • 56
    • 0026067797 scopus 로고
    • 16S ribosomal DNA amplification for phylogenetic study
    • Weisburg, W. G., Barns, S. M., Pelletier, D. A. and Lane, D. J. (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol, 173, pp. 697-703.
    • (1991) J Bacteriol , vol.173 , pp. 697-703
    • Weisburg, W.G.1    Barns, S.M.2    Pelletier, D.A.3    Lane, D.J.4
  • 59
    • 33947182125 scopus 로고    scopus 로고
    • Archaeal communities in mangrove soil characterized by 16S rRNA gene clones
    • Yan, B., Hong, K. and Yu, Z. M. (2006) Archaeal communities in mangrove soil characterized by 16S rRNA gene clones. J Microbiol, 44, pp. 566-571.
    • (2006) J Microbiol , vol.44 , pp. 566-571
    • Yan, B.1    Hong, K.2    Yu, Z.M.3
  • 60
    • 0037031127 scopus 로고    scopus 로고
    • Molecular analysis of ancient microbial infections
    • Zink, A. R., Reischl, U., Wolf, H. and Nerlich, A. G. (2002) Molecular analysis of ancient microbial infections. FEMS Microbiol Lett, 213, pp. 141-147.
    • (2002) FEMS Microbiol Lett , vol.213 , pp. 141-147
    • Zink, A.R.1    Reischl, U.2    Wolf, H.3    Nerlich, A.G.4


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