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
Right arrow Citation Map
Services
Right arrow E-mail this article to a friend
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 Chin, K.-J.
Right arrow Articles by Janssen, P. H.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Chin, K.-J.
Right arrow Articles by Janssen, P. H.
Agricola
Right arrow Articles by Chin, K.-J.
Right arrow Articles by Janssen, P. H.

 Previous Article  |  Next Article 

Applied and Environmental Microbiology, November 1999, p. 5042-5049, Vol. 65, No. 11
0099-2240/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.

Characterization and Identification of Numerically Abundant Culturable Bacteria from the Anoxic Bulk Soil of Rice Paddy Microcosms

Kuk-Jeong Chin,1 Dittmar Hahn,2,dagger Ulf Hengstmann,1 Werner Liesack,1 and Peter H. Janssen1,*

Max-Planck-Institut für terrestrische Mikrobiologie, D-35043 Marburg, Germany,1 and Institute of Terrestrial Ecology, Soil Biology, CH-8952 Schlieren, Switzerland2

Received 29 April 1999/Accepted 23 August 1999

Most-probable-number (liquid serial dilution culture) counts were obtained for polysaccharolytic and saccharolytic fermenting bacteria in the anoxic bulk soil of flooded microcosms containing rice plants. The highest viable counts (up to 2.5 × 108 cells per g [dry weight] of soil) were obtained by using xylan, pectin, or a mixture of seven mono- and disaccharides as the growth substrate. The total cell count for the soil, as determined by using 4',6-diamidino-2-phenylindole staining, was 4.8 × 108 cells per g (dry weight) of soil. The nine strains isolated from the terminal positive tubes in counting experiments which yielded culturable populations that were equivalent to about 5% or more of the total microscopic count population belonged to the division Verrucomicrobia, the Cytophaga-Flavobacterium-Bacteroides division, clostridial cluster XIVa, clostridial cluster IX, Bacillus spp., and the class Actinobacteria. Isolates originating from the terminal positive tubes of liquid dilution series can be expected to be representatives of species whose populations in the soil are large. None of the isolates had 16S rRNA gene sequences identical to 16S rRNA gene sequences of previously described species for which data are available. Eight of the nine strains isolated fermented sugars to acetate and propionate (and some also fermented sugars to succinate). The closest relatives of these strains (except for the two strains of actinobacteria) were as-yet-uncultivated bacteria detected in the same soil sample by cloning PCR-amplified 16S rRNA genes (U. Hengstmann, K.-J. Chin, P. H. Janssen, and W. Liesack, Appl. Environ. Microbiol. 65:5050-5058, 1999). Twelve other isolates, which originated from most-probable-number counting series indicating that the culturable populations were smaller, were less closely related to cloned 16S rRNA genes.

* Corresponding author. Present address: Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3052, Australia. Phone: 61 (3) 9344 5706. Fax: 61 (3) 9347 1540. E-mail: p.janssen{at}microbiology.unimelb.edu.au.

dagger Present address: Department of Biological Sciences, Rutgers University, Newark, NJ 07102.

Applied and Environmental Microbiology, November 1999, p. 5042-5049, Vol. 65, No. 11
0099-2240/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.


This article has been cited by other articles:

  • Koch, I. H., Gich, F., Dunfield, P. F., Overmann, J. (2008). Edaphobacter modestus gen. nov., sp. nov., and Edaphobacter aggregans sp. nov., acidobacteria isolated from alpine and forest soils. Int. J. Syst. Evol. Microbiol. 58: 1114-1122 [Abstract] [Full Text]  
  • Yoon, J., Matsuo, Y., Matsuda, S., Adachi, K., Kasai, H., Yokota, A. (2007). Cerasicoccus arenae gen. nov., sp. nov., a carotenoid-producing marine representative of the family Puniceicoccaceae within the phylum 'Verrucomicrobia', isolated from marine sand. Int. J. Syst. Evol. Microbiol. 57: 2067-2072 [Abstract] [Full Text]  
  • Yoon, J., Yasumoto-Hirose, M., Katsuta, A., Sekiguchi, H., Matsuda, S., Kasai, H., Yokota, A. (2007). Coraliomargarita akajimensis gen. nov., sp. nov., a novel member of the phylum 'Verrucomicrobia' isolated from seawater in Japan. Int. J. Syst. Evol. Microbiol. 57: 959-963 [Abstract] [Full Text]  
  • Choo, Y.-J., Lee, K., Song, J., Cho, J.-C. (2007). Puniceicoccus vermicola gen. nov., sp. nov., a novel marine bacterium, and description of Puniceicoccaceae fam. nov., Puniceicoccales ord. nov., Opitutaceae fam. nov., Opitutales ord. nov. and Opitutae classis nov. in the phylum 'Verrucomicrobia'. Int. J. Syst. Evol. Microbiol. 57: 532-537 [Abstract] [Full Text]  
  • Lee, Y.-J., Romanek, C. S., Mills, G. L., Davis, R. C., Whitman, W. B., Wiegel, J. (2006). Gracilibacter thermotolerans gen. nov., sp. nov., an anaerobic, thermotolerant bacterium from a constructed wetland receiving acid sulfate water.. Int. J. Syst. Evol. Microbiol. 56: 2089-2093 [Abstract] [Full Text]  
  • Cavaletti, L., Monciardini, P., Bamonte, R., Schumann, P., Rohde, M., Sosio, M., Donadio, S. (2006). New lineage of filamentous, spore-forming, gram-positive bacteria from soil.. Appl. Environ. Microbiol. 72: 4360-4369 [Abstract] [Full Text]  
  • Shiratori, H., Ikeno, H., Ayame, S., Kataoka, N., Miya, A., Hosono, K., Beppu, T., Ueda, K. (2006). Isolation and Characterization of a New Clostridium sp. That Performs Effective Cellulosic Waste Digestion in a Thermophilic Methanogenic Bioreactor.. Appl. Environ. Microbiol. 72: 3702-3709 [Abstract] [Full Text]  
  • Martens-Habbena, W., Sass, H. (2006). Sensitive Determination of Microbial Growth by Nucleic Acid Staining in Aqueous Suspension. Appl. Environ. Microbiol. 72: 87-95 [Abstract] [Full Text]  
  • Kopke, B., Wilms, R., Engelen, B., Cypionka, H., Sass, H. (2005). Microbial Diversity in Coastal Subsurface Sediments: a Cultivation Approach Using Various Electron Acceptors and Substrate Gradients. Appl. Environ. Microbiol. 71: 7819-7830 [Abstract] [Full Text]  
  • Sangwan, P., Kovac, S., Davis, K. E. R., Sait, M., Janssen, P. H. (2005). Detection and Cultivation of Soil Verrucomicrobia. Appl. Environ. Microbiol. 71: 8402-8410 [Abstract] [Full Text]  
  • Tyson, G. W., Lo, I., Baker, B. J., Allen, E. E., Hugenholtz, P., Banfield, J. F. (2005). Genome-Directed Isolation of the Key Nitrogen Fixer Leptospirillum ferrodiazotrophum sp. nov. from an Acidophilic Microbial Community. Appl. Environ. Microbiol. 71: 6319-6324 [Abstract] [Full Text]  
  • Xie, C.-H., Yokota, A. (2005). Pleomorphomonas oryzae gen. nov., sp. nov., a nitrogen-fixing bacterium isolated from paddy soil of Oryza sativa. Int. J. Syst. Evol. Microbiol. 55: 1233-1237 [Abstract] [Full Text]  
  • Tamaki, H., Sekiguchi, Y., Hanada, S., Nakamura, K., Nomura, N., Matsumura, M., 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: 2162-2169 [Abstract] [Full Text]  
  • Lueders, T., Pommerenke, B., Friedrich, M. W. (2004). Stable-Isotope Probing of Microorganisms Thriving at Thermodynamic Limits: Syntrophic Propionate Oxidation in Flooded Soil. Appl. Environ. Microbiol. 70: 5778-5786 [Abstract] [Full Text]  
  • Sangwan, P., Chen, X., Hugenholtz, P., Janssen, P. H. (2004). Chthoniobacter flavus gen. nov., sp. nov., the First Pure-Culture Representative of Subdivision Two, Spartobacteria classis nov., of the Phylum Verrucomicrobia. Appl. Environ. Microbiol. 70: 5875-5881 [Abstract] [Full Text]  
  • Stevenson, B. S., Eichorst, S. A., Wertz, J. T., Schmidt, T. M., Breznak, J. A. (2004). New Strategies for Cultivation and Detection of Previously Uncultured Microbes. Appl. Environ. Microbiol. 70: 4748-4755 [Abstract] [Full Text]  
  • Schoenborn, L., Yates, P. S., Grinton, B. E., Hugenholtz, P., Janssen, P. H. (2004). Liquid Serial Dilution Is Inferior to Solid Media for Isolation of Cultures Representative of the Phylum-Level Diversity of Soil Bacteria. Appl. Environ. Microbiol. 70: 4363-4366 [Abstract] [Full Text]  
  • Burrell, P. C., O'Sullivan, C., Song, H., Clarke, W. P., Blackall, L. L. (2004). Identification, Detection, and Spatial Resolution of Clostridium Populations Responsible for Cellulose Degradation in a Methanogenic Landfill Leachate Bioreactor. Appl. Environ. Microbiol. 70: 2414-2419 [Abstract] [Full Text]  
  • Akasaka, H., Ueki, A., Hanada, S., Kamagata, Y., Ueki, K. (2003). Propionicimonas paludicola gen. nov., sp. nov., a novel facultatively anaerobic, Gram-positive, propionate-producing bacterium isolated from plant residue in irrigated rice-field soil. Int. J. Syst. Evol. Microbiol. 53: 1991-1998 [Abstract] [Full Text]  
  • Janssen, P. H., Yates, P. S., Grinton, B. E., Taylor, P. M., Sait, M. (2002). Improved Culturability of Soil Bacteria and Isolation in Pure Culture of Novel Members of the Divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. Appl. Environ. Microbiol. 68: 2391-2396 [Abstract] [Full Text]  
  • Chin, K.-J., Janssen, P. H. (2002). Propionate Formation by Opitutus terrae in Pure Culture and in Mixed Culture with a Hydrogenotrophic Methanogen and Implications for Carbon Fluxes in Anoxic Rice Paddy Soil. Appl. Environ. Microbiol. 68: 2089-2092 [Abstract] [Full Text]  
  • Francis, C. A., Tebo, B. M. (2002). Enzymatic Manganese(II) Oxidation by Metabolically Dormant Spores of Diverse Bacillus Species. Appl. Environ. Microbiol. 68: 874-880 [Abstract] [Full Text]  
  • Weber, S., Stubner, S., Conrad, R. (2001). Bacterial Populations Colonizing and Degrading Rice Straw in Anoxic Paddy Soil. Appl. Environ. Microbiol. 67: 1318-1327 [Abstract] [Full Text]  
  • Barbieri, E., Potenza, L., Rossi, I., Sisti, D., Giomaro, G., Rossetti, S., Beimfohr, C., Stocchi, V. (2000). Phylogenetic Characterization and In Situ Detection of a Cytophaga-Flexibacter-Bacteroides Phylogroup Bacterium in Tuber borchii Vittad. Ectomycorrhizal Mycelium. Appl. Environ. Microbiol. 66: 5035-5042 [Abstract] [Full Text]  
  • Hengstmann, U., Chin, K.-J., Janssen, P. H., Liesack, W. (1999). Comparative Phylogenetic Assignment of Environmental Sequences of Genes Encoding 16S rRNA and Numerically Abundant Culturable Bacteria from an Anoxic Rice Paddy Soil. Appl. Environ. Microbiol. 65: 5050-5058 [Abstract] [Full Text]  


Copyright © 2010 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»