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 Chin, K.-J.
Right arrow Articles by Conrad, R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Chin, K.-J.
Right arrow Articles by Conrad, R.
Agricola
Right arrow Articles by Chin, K.-J.
Right arrow Articles by Conrad, R.

 Previous Article  |  Next Article 

Applied and Environmental Microbiology, June 1999, p. 2341-2349, Vol. 65, No. 6
0099-2240/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.

Effect of Temperature on Structure and Function of the Methanogenic Archaeal Community in an Anoxic Rice Field Soil

Kuk-Jeong Chin, Thomas Lukow, and Ralf Conrad*

Max-Planck-Institut für Terrestrische Mikrobiologie, D-35043 Marburg/Lahn, Germany

Received 11 January 1999/Accepted 18 March 1999

Soil temperatures in Italian rice fields typically range between about 15 and 30°C. A change in the incubation temperature of anoxic methanogenic soil slurry from 30°C to 15°C typically resulted in a decrease in the CH4 production rate, a decrease in the steady-state H2 partial pressure, and a transient accumulation of acetate. Previous experiments have shown that these changes were due to an alteration of the carbon and electron flow in the methanogenic degradation pathway of organic matter caused by the temperature shift (K. J. Chin and R. Conrad, FEMS Microbiol. Ecol. 18:85-102, 1995). To investigate how temperature affects the structure of the methanogenic archaeal community, total DNA was extracted from soil slurries incubated at 30 and 15°C. The archaeal small-subunit (SSU) rRNA-encoding genes (rDNA) of these environmental DNA samples were amplified by PCR with an archaeal-specific primer system and used for the generation of clone libraries. Representative rDNA clones (n = 90) were characterized by terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis. T-RFLP analysis produced for the clones terminally labeled fragments with a characteristic length of mostly 185, 284, or 392 bp. Sequence analysis allowed determination of the phylogenetic affiliation of the individual clones with their characteristic T-RFLP fragment lengths and showed that the archaeal community of the anoxic rice soil slurry was dominated by members of the families Methanosarcinaceae (185 bp) and Methanosaetaceae (284 bp), the kingdom Crenarchaeota (185 or 284 bp), and a novel, deeply branching lineage of the (probably methanogenic) kingdom Euryarchaeota (392 bp) that has recently been detected on rice roots (R. Großkopf, S. Stubner, and W. Liesack, Appl. Environ. Microbiol. 64:4983-4989, 1998). The structure of the archaeal community changed when the temperature was shifted from 30°C to 15°C. Before the temperature shift, the clones (n = 30) retrieved from the community were dominated by Crenarchaeota (70%), "novel Euryarchaeota" (23%), and Methanosarcinacaeae (7%). Further incubation at 30°C (n = 30 clones) resulted in a relative increase in members of the Methanosarcinaceae (77%), whereas further incubation at 15°C (n = 30 clones) resulted in a much more diverse community consisting of 33% Methanosarcinaceae, 23% Crenarchaeota, 20% Methanosaetaceae, and 17% novel Euryarchaeota. The appearance of Methanosaetaceae at 15°C was conspicuous. These results demonstrate that the structure of the archaeal community in anoxic rice field soil changed with time and incubation temperature.

* Corresponding author. Mailing address: Max-Planck-Institut für Terrestrische Mikrobiologie, Karl-von-Frisch-Str., D-35043 Marburg/Lahn, Germany. Phone: 49-6421-178 801. Fax: 49-6421-178 809. E-mail: conrad{at}mailer.uni-marburg.de.

Applied and Environmental Microbiology, June 1999, p. 2341-2349, Vol. 65, No. 6
0099-2240/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.


This article has been cited by other articles:

  • Goevert, D., Conrad, R. (2009). Effect of Substrate Concentration on Carbon Isotope Fractionation during Acetoclastic Methanogenesis by Methanosarcina barkeri and M. acetivorans and in Rice Field Soil. Appl. Environ. Microbiol. 75: 2605-2612 [Abstract] [Full Text]  
  • Peng, J., Lu, Z., Rui, J., Lu, Y. (2008). Dynamics of the Methanogenic Archaeal Community during Plant Residue Decomposition in an Anoxic Rice Field Soil. Appl. Environ. Microbiol. 74: 2894-2901 [Abstract] [Full Text]  
  • Singh, B. K., Tate, K. R., Kolipaka, G., Hedley, C. B., Macdonald, C. A., Millard, P., Murrell, J. C. (2007). Effect of Afforestation and Reforestation of Pastures on the Activity and Population Dynamics of Methanotrophic Bacteria. Appl. Environ. Microbiol. 73: 5153-5161 [Abstract] [Full Text]  
  • Murase, J., Noll, M., Frenzel, P. (2006). Impact of Protists on the Activity and Structure of the Bacterial Community in a Rice Field Soil. Appl. Environ. Microbiol. 72: 5436-5444 [Abstract] [Full Text]  
  • Mohanty, S. R., Bodelier, P. L. E., Floris, V., Conrad, R. (2006). Differential Effects of Nitrogenous Fertilizers on Methane-Consuming Microbes in Rice Field and Forest Soils. Appl. Environ. Microbiol. 72: 1346-1354 [Abstract] [Full Text]  
  • Penning, H., Conrad, R. (2006). Effect of Inhibition of Acetoclastic Methanogenesis on Growth of Archaeal Populations in an Anoxic Model Environment. Appl. Environ. Microbiol. 72: 178-184 [Abstract] [Full Text]  
  • Metje, M., Frenzel, P. (2005). Effect of Temperature on Anaerobic Ethanol Oxidation and Methanogenesis in Acidic Peat from a Northern Wetland. Appl. Environ. Microbiol. 71: 8191-8200 [Abstract] [Full Text]  
  • Pernthaler, J., Amann, R. (2005). Fate of Heterotrophic Microbes in Pelagic Habitats: Focus on Populations. Microbiol. Mol. Biol. Rev. 69: 440-461 [Abstract] [Full Text]  
  • Lu, Y., Conrad, R. (2005). In Situ Stable Isotope Probing of Methanogenic Archaea in the Rice Rhizosphere. Science 309: 1088-1090 [Abstract] [Full Text]  
  • Castro, H., Newman, S., Reddy, K. R., Ogram, A. (2005). Distribution and Stability of Sulfate-Reducing Prokaryotic and Hydrogenotrophic Methanogenic Assemblages in Nutrient-Impacted Regions of the Florida Everglades. Appl. Environ. Microbiol. 71: 2695-2704 [Abstract] [Full Text]  
  • Castro, H., Ogram, A., Reddy, K. R. (2004). Phylogenetic Characterization of Methanogenic Assemblages in Eutrophic and Oligotrophic Areas of the Florida Everglades. Appl. Environ. Microbiol. 70: 6559-6568 [Abstract] [Full Text]  
  • Miyamoto, T., Kawahara, M., Minamisawa, K. (2004). Novel Endophytic Nitrogen-Fixing Clostridia from the Grass Miscanthus sinensis as Revealed by Terminal Restriction Fragment Length Polymorphism Analysis. Appl. Environ. Microbiol. 70: 6580-6586 [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]  
  • Donovan, S. E., Purdy, K. J., Kane, M. D., Eggleton, P. (2004). Comparison of Euryarchaea Strains in the Guts and Food-Soil of the Soil-Feeding Termite Cubitermes fungifaber across Different Soil Types. Appl. Environ. Microbiol. 70: 3884-3892 [Abstract] [Full Text]  
  • Pester, M., Friedrich, M. W., Schink, B., Brune, A. (2004). pmoA-Based Analysis of Methanotrophs in a Littoral Lake Sediment Reveals a Diverse and Stable Community in a Dynamic Environment. Appl. Environ. Microbiol. 70: 3138-3142 [Abstract] [Full Text]  
  • Sliwinski, M. K., Goodman, R. M. (2004). Spatial Heterogeneity of Crenarchaeal Assemblages within Mesophilic Soil Ecosystems as Revealed by PCR-Single-Stranded Conformation Polymorphism Profiling. Appl. Environ. Microbiol. 70: 1811-1820 [Abstract] [Full Text]  
  • Kent, A. D., Smith, D. J., Benson, B. J., Triplett, E. W. (2003). Web-Based Phylogenetic Assignment Tool for Analysis of Terminal Restriction Fragment Length Polymorphism Profiles of Microbial Communities. Appl. Environ. Microbiol. 69: 6768-6776 [Abstract] [Full Text]  
  • Schmitt-Wagner, D., Friedrich, M. W., Wagner, B., Brune, A. (2003). Axial Dynamics, Stability, and Interspecies Similarity of Bacterial Community Structure in the Highly Compartmentalized Gut of Soil-Feeding Termites (Cubitermes spp.). Appl. Environ. Microbiol. 69: 6018-6024 [Abstract] [Full Text]  
  • Lueders, T., Friedrich, M. W. (2003). Evaluation of PCR Amplification Bias by Terminal Restriction Fragment Length Polymorphism Analysis of Small-Subunit rRNA and mcrA Genes by Using Defined Template Mixtures of Methanogenic Pure Cultures and Soil DNA Extracts. Appl. Environ. Microbiol. 69: 320-326 [Abstract] [Full Text]  
  • Lueders, T., Friedrich, M. W. (2002). Effects of Amendment with Ferrihydrite and Gypsum on the Structure and Activity of Methanogenic Populations in Rice Field Soil. Appl. Environ. Microbiol. 68: 2484-2494 [Abstract] [Full Text]  
  • Takai, K., Moser, D. P., DeFlaun, M., Onstott, T. C., Fredrickson, J. K. (2001). Archaeal Diversity in Waters from Deep South African Gold Mines. Appl. Environ. Microbiol. 67: 5750-5760 [Abstract] [Full Text]  
  • Friedrich, M. W., Schmitt-Wagner, D., Lueders, T., Brune, A. (2001). Axial Differences in Community Structure of Crenarchaeota and Euryarchaeota in the Highly Compartmentalized Gut of the Soil-Feeding Termite Cubitermes orthognathus. Appl. Environ. Microbiol. 67: 4880-4890 [Abstract] [Full Text]  
  • Braker, G., Ayala-del-Río, H. L., Devol, A. H., Fesefeldt, A., Tiedje, J. M. (2001). Community Structure of Denitrifiers, Bacteria, and Archaea along Redox Gradients in Pacific Northwest Marine Sediments by Terminal Restriction Fragment Length Polymorphism Analysis of Amplified Nitrite Reductase (nirS) and 16S rRNA Genes. Appl. Environ. Microbiol. 67: 1893-1901 [Abstract] [Full Text]  
  • Dunbar, J., Ticknor, L. O., Kuske, C. R. (2001). Phylogenetic Specificity and Reproducibility and New Method for Analysis of Terminal Restriction Fragment Profiles of 16S rRNA Genes from Bacterial Communities. Appl. Environ. Microbiol. 67: 190-197 [Abstract] [Full Text]  
  • Fey, A., Conrad, R. (2000). Effect of Temperature on Carbon and Electron Flow and on the Archaeal Community in Methanogenic Rice Field Soil. Appl. Environ. Microbiol. 66: 4790-4797 [Abstract] [Full Text]  
  • Takai, K., Horikoshi, K. (2000). Rapid Detection and Quantification of Members of the Archaeal Community by Quantitative PCR Using Fluorogenic Probes. Appl. Environ. Microbiol. 66: 5066-5072 [Abstract] [Full Text]  
  • Kim, H., Honda, D., Hanada, S., Kanamori, N., Shibata, S., Miyaki, T., Nakamura, K., Oyaizu, H. (2000). A deeply branched novel phylotype found in Japanese paddy soils. Microbiology 146: 2309-2315 [Abstract] [Full Text]  
  • Lueders, T., Friedrich, M. (2000). Archaeal Population Dynamics during Sequential Reduction Processes in Rice Field Soil. Appl. Environ. Microbiol. 66: 2732-2742 [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»