This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Inagaki, F.
Right arrow Articles by Horikoshi, K.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Inagaki, F.
Right arrow Articles by Horikoshi, K.
Agricola
Right arrow Articles by Inagaki, F.
Right arrow Articles by Horikoshi, K.

 Previous Article  |  Next Article 

Applied and Environmental Microbiology, December 2003, p. 7224-7235, Vol. 69, No. 12
0099-2240/03/$08.00+0     DOI: 10.1128/AEM.69.12.7224-7235.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.

Microbial Communities Associated with Geological Horizons in Coastal Subseafloor Sediments from the Sea of Okhotsk

Fumio Inagaki,1* Masae Suzuki,1 Ken Takai,1 Hanako Oida,1 Tatsuhiko Sakamoto,2 Kaori Aoki,3 Kenneth H. Nealson,1,4 and Koki Horikoshi1

Subground Animalcule Retrieval (SUGAR) Project, Frontier Research System for Extremophiles,1 Research Program for Paleoenvironment, Institute for Frontier Research on Earth Evolution (IFREE), Japan Marine Science and Technology Center (JAMSTEC), Yokosuka 237-0061,2 Geological Survey of Japan, AIST, Tsukuba 305-8567, Japan,3 Department of Earth Sciences, University of Southern California, Los Angeles, California 90089-07404

Received 16 June 2003/ Accepted 29 September 2003

Microbial communities from a subseafloor sediment core from the southwestern Sea of Okhotsk were evaluated by performing both cultivation-dependent and cultivation-independent (molecular) analyses. The core, which extended 58.1 m below the seafloor, was composed of pelagic clays with several volcanic ash layers containing fine pumice grains. Direct cell counting and quantitative PCR analysis of archaeal and bacterial 16S rRNA gene fragments indicated that the bacterial populations in the ash layers were approximately 2 to 10 times larger than those in the clays. Partial sequences of 1,210 rRNA gene clones revealed that there were qualitative differences in the microbial communities from the two different types of layers. Two phylogenetically distinct archaeal assemblages in the Crenarchaeota, the miscellaneous crenarchaeotic group and the deep-sea archaeal group, were the most predominant archaeal 16S rRNA gene components in the ash layers and the pelagic clays, respectively. Clones of 16S rRNA gene sequences from members of the gamma subclass of the class Proteobacteria dominated the ash layers, whereas sequences from members of the candidate division OP9 and the green nonsulfur bacteria dominated the pelagic clay environments. Molecular (16S rRNA gene sequence) analysis of 181 isolated colonies revealed that there was regional proliferation of viable heterotrophic mesophiles in the volcanic ash layers, along with some gram-positive bacteria and actinobacteria. The porous ash layers, which ranged in age from tens of thousands of years to hundreds of thousands of years, thus appear to be discrete microbial habitats within the coastal subseafloor clay sediment, which are capable of harboring microbial communities that are very distinct from the communities in the more abundant pelagic clays.

* Corresponding author. Mailing address: Subground Animalcule Retrieval (SUGAR) Project, Frontier Research System for Extremophiles, Japan Marine Science & Technology Center (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan. Phone: 81-468-67-9687. Fax: 81-468-67-9715. E-mail: inagaki{at}jamstec.go.jp.

Applied and Environmental Microbiology, December 2003, p. 7224-7235, Vol. 69, No. 12
0099-2240/03/$08.00+0     DOI: 10.1128/AEM.69.12.7224-7235.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Miyazaki, J., Higa, R., Toki, T., Ashi, J., Tsunogai, U., Nunoura, T., Imachi, H., Takai, K. (2009). Molecular Characterization of Potential Nitrogen Fixation by Anaerobic Methane-Oxidizing Archaea in the Methane Seep Sediments at the Number 8 Kumano Knoll in the Kumano Basin, Offshore of Japan. Appl. Environ. Microbiol. 75: 7153-7162 [Abstract] [Full Text]  
  • Futagami, T., Morono, Y., Terada, T., Kaksonen, A. H., Inagaki, F. (2009). Dehalogenation Activities and Distribution of Reductive Dehalogenase Homologous Genes in Marine Subsurface Sediments. Appl. Environ. Microbiol. 75: 6905-6909 [Abstract] [Full Text]  
  • Vandecandelaere, I., Nercessian, O., Segaert, E., Achouak, W., Mollica, A., Faimali, M., Vandamme, P. (2009). Nautella italica gen. nov., sp. nov., isolated from a marine electroactive biofilm. Int. J. Syst. Evol. Microbiol. 59: 811-817 [Abstract] [Full Text]  
  • Harrison, B. K., Zhang, H., Berelson, W., Orphan, V. J. (2009). Variations in Archaeal and Bacterial Diversity Associated with the Sulfate-Methane Transition Zone in Continental Margin Sediments (Santa Barbara Basin, California). Appl. Environ. Microbiol. 75: 1487-1499 [Abstract] [Full Text]  
  • Elkins, J. G., Podar, M., Graham, D. E., Makarova, K. S., Wolf, Y., Randau, L., Hedlund, B. P., Brochier-Armanet, C., Kunin, V., Anderson, I., Lapidus, A., Goltsman, E., Barry, K., Koonin, E. V., Hugenholtz, P., Kyrpides, N., Wanner, G., Richardson, P., Keller, M., Stetter, K. O. (2008). A korarchaeal genome reveals insights into the evolution of the Archaea. Proc. Natl. Acad. Sci. USA 105: 8102-8107 [Abstract] [Full Text]  
  • Mikucki, J. A., Priscu, J. C. (2007). Bacterial Diversity Associated with Blood Falls, a Subglacial Outflow from the Taylor Glacier, Antarctica. Appl. Environ. Microbiol. 73: 4029-4039 [Abstract] [Full Text]  
  • Katayama, T., Tanaka, M., Moriizumi, J., Nakamura, T., Brouchkov, A., Douglas, T. A., Fukuda, M., Tomita, F., Asano, K. (2007). Phylogenetic Analysis of Bacteria Preserved in a Permafrost Ice Wedge for 25,000 Years. Appl. Environ. Microbiol. 73: 2360-2363 [Abstract] [Full Text]  
  • Lloyd, K. G., Lapham, L., Teske, A. (2006). An Anaerobic Methane-Oxidizing Community of ANME-1b Archaea in Hypersaline Gulf of Mexico Sediments. Appl. Environ. Microbiol. 72: 7218-7230 [Abstract] [Full Text]  
  • Nakagawa, S., Inagaki, F., Suzuki, Y., Steinsbu, B. O., Lever, M. A., Takai, K., Engelen, B., Sako, Y., Wheat, C. G., Horikoshi, K., Integrated Ocean Drilling Program Expedition 301 S, (2006). Microbial Community in Black Rust Exposed to Hot Ridge Flank Crustal Fluids. Appl. Environ. Microbiol. 72: 6789-6799 [Abstract] [Full Text]  
  • Brazelton, W. J., Schrenk, M. O., Kelley, D. S., Baross, J. A. (2006). Methane- and Sulfur-Metabolizing Microbial Communities Dominate the Lost City Hydrothermal Field Ecosystem. Appl. Environ. Microbiol. 72: 6257-6270 [Abstract] [Full Text]  
  • Sorensen, K. B., Teske, A. (2006). Stratified communities of active archaea in deep marine subsurface sediments.. Appl. Environ. Microbiol. 72: 4596-4603 [Abstract] [Full Text]  
  • Wilms, R., Sass, H., Kopke, B., Koster, J., Cypionka, H., Engelen, B. (2006). Specific Bacterial, Archaeal, and Eukaryotic Communities in Tidal-Flat Sediments along a Vertical Profile of Several Meters. Appl. Environ. Microbiol. 72: 2756-2764 [Abstract] [Full Text]  
  • Biddle, J. F., Lipp, J. S., Lever, M. A., Lloyd, K. G., Sorensen, K. B., Anderson, R., Fredricks, H. F., Elvert, M., Kelly, T. J., Schrag, D. P., Sogin, M. L., Brenchley, J. E., Teske, A., House, C. H., Hinrichs, K.-U. (2006). Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. Proc. Natl. Acad. Sci. USA 103: 3846-3851 [Abstract] [Full Text]  
  • Inagaki, F., Nunoura, T., Nakagawa, S., Teske, A., Lever, M., Lauer, A., Suzuki, M., Takai, K., Delwiche, M., Colwell, F. S., Nealson, K. H., Horikoshi, K., D'Hondt, S., Jorgensen, B. B. (2006). Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. Proc. Natl. Acad. Sci. USA 103: 2815-2820 [Abstract] [Full Text]  
  • Ishikawa, M., Nakajima, K., Itamiya, Y., Furukawa, S., Yamamoto, Y., Yamasato, K. (2005). Halolactibacillus halophilus gen. nov., sp. nov. and Halolactibacillus miurensis sp. nov., halophilic and alkaliphilic marine lactic acid bacteria constituting a phylogenetic lineage in Bacillus rRNA group 1. Int. J. Syst. Evol. Microbiol. 55: 2427-2439 [Abstract] [Full Text]  
  • Buchan, A., Gonzalez, J. M., Moran, M. A. (2005). Overview of the Marine Roseobacter Lineage. Appl. Environ. Microbiol. 71: 5665-5677 [Full Text]  
  • Dell'Anno, A., Corinaldesi, C., Stavrakakis, S., Lykousis, V., Danovaro, R. (2005). Pelagic-Benthic Coupling and Diagenesis of Nucleic Acids in a Deep-Sea Continental Margin and an Open-Slope System of the Eastern Mediterranean. Appl. Environ. Microbiol. 71: 6070-6076 [Abstract] [Full Text]  
  • De Wever, A., Muylaert, K., Van der Gucht, K., Pirlot, S., Cocquyt, C., Descy, J.-P., Plisnier, P.-D., Vyverman, W. (2005). Bacterial Community Composition in Lake Tanganyika: Vertical and Horizontal Heterogeneity. Appl. Environ. Microbiol. 71: 5029-5037 [Abstract] [Full Text]  
  • Mills, H. J., Martinez, R. J., Story, S., Sobecky, P. A. (2005). Characterization of Microbial Community Structure in Gulf of Mexico Gas Hydrates: Comparative Analysis of DNA- and RNA-Derived Clone Libraries. Appl. Environ. Microbiol. 71: 3235-3247 [Abstract] [Full Text]  
  • Toffin, L., Zink, K., Kato, C., Pignet, P., Bidault, A., Bienvenu, N., Birrien, J.-L., Prieur, D. (2005). Marinilactibacillus piezotolerans sp. nov., a novel marine lactic acid bacterium isolated from deep sub-seafloor sediment of the Nankai Trough. Int. J. Syst. Evol. Microbiol. 55: 345-351 [Abstract] [Full Text]  
  • Inagaki, F., Tsunogai, U., Suzuki, M., Kosaka, A., Machiyama, H., Takai, K., Nunoura, T., Nealson, K. H., Horikoshi, K. (2004). Characterization of C1-Metabolizing Prokaryotic Communities in Methane Seep Habitats at the Kuroshima Knoll, Southern Ryukyu Arc, by Analyzing pmoA, mmoX, mxaF, mcrA, and 16S rRNA Genes. Appl. Environ. Microbiol. 70: 7445-7455 [Abstract] [Full Text]  
  • Webster, G., Parkes, R. J., Fry, J. C., 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: 5708-5713 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»