Succession of bacterial community structure and diversity in a paddy soil oxygen gradient

Environmental Microbiology

Volumn 7, Issue 3, 2005, Pages 382-395

  Noll, Matthias ^a   Matthies, Diethart ^b   Frenzel, Peter ^a   Derakshani, Manigee ^a   Liesack, Werner ^a  

^a MAX PLANCK INSTITUTE FOR TERRESTRIAL MICROBIOLOGY   (Germany)

^b PHILIPPS UNIVERSITY MARBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); BETAPROTEOBACTERIA; MYXOCOCCALES; NITROSPIRA; VERRUCOMICROBIA;

EID: 14344253895     PISSN: 14622912     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2005.00700.x     Document Type: Article

References (50)

1. Andrews, J.H., and Harris, R.F. (1986) r- and K-selection and microbial ecology. Adv Microb Ecol 9: 99-147.
2. Arth, I., and Frenzel, P. (2000) Nitrification and denitrification in the rhizosphere of rice: the detection of processes by a new multi-channel electrode. Biol Fert Soils 31: 427-435.
3. Baldani, J.I., Pot, B., Kirchhof, G., Falsen, E., Baldani, V.L.D., Olivares, F.L., et al. (1996) Emended description of Herbaspirillum; inclusion of [Pseudomonas] rubrisubalbicans, a mild pathogen, as Herbaspirillum rubrisubalbicans comb, nov., and classification of a group of clinical isolates (EF group 1) as Herbaspirillum species 3. Int J Syst Bacteriol 46: 802-810.
4. Berg, P. (1998) Manual for PROFILE. Version 1.0, pp. 1-12. [WWW document]. URL http://www.ib.uit.no/plantefysiologi/microsensor/lib/downloads
5. Berg, P., Risgaard-Petersen, N., and Rysgaard, S. (1998) Interpretation of measured concentration profiles in sediment pore water. Limnol Oceanogr 43: 1500-1510.
6. Berner, R.A. (1980) Early Diagenesis. A Theoretical Approach. Princeton, UK: Princeton University Press.
7. Blumberg, D.D. (1987) Creating a ribonuclease-free environment. Methods Enzymol 152: 20-24.
8. Bowman, J.P., Sly, L.I., Hayward, A.C., Spiegel, Y., and Stackebrandt, E. (1993) Telluria mixta (Pseudomonas mixta Bowman, Sly, and Hayward 1988) gen. nov., comb. nov., and Telluria chitinolytica, sp. nov., soil-dwelling organisms which actively degrade polysaccharides. Int J Syst Bacteriol 43: 120-124.
9. Broecker, W., and Peng, T. (1974) Gas exchange rates between air and sea. Tellus 17: 21-35.
10. Brune, A., Frenzel, P., and Cypionka, H. (2000) Life at the oxic-anoxic interface: microbial activities and adaptations. FEMS Microbiol Rev 24: 691-710.
11. Collins, M.D., Lawson, P.A., Willems, A., Cordoba, J.J., Fernandez-Garayzabal, J., Garcia, P., et al. (1994) The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int J Syst Bacteriol 44: 812-826.
12. Crank, J. (1980) Mathematics of Diffusion. Oxford, UK: Oxford University Press, pp. 1-424.
13. Daims, H., Nielsen, J.L., Nielsen, P.H., Schleifer, K.H., and Wagner, M. (2001) In situ characterization of Nitrospira-like nitrite-oxidizing bacteria active in wastewater treatment plants. Appl Environ Microbiol 67: 5273-5284.
14. Dawid, W. (2000) Biology and global distribution of myxobacteria in soils. FEMS Microbiol Rev 24: 403-427.
15. Dollhopf, S.L., Hashsham, S.A., and Tiedje, J.M. (2001) Interpreting 16S rDNA T-RFLP data: application of self-organizing maps and principal component analysis to describe community dynamics and convergence. Microb Ecol 42: 495-505.
16. Ehrich, S., Behrens, D., Lebedeva, E., Ludwig, W., and Bock, E. (1995) A new obligately chemolithoautotrophic, nitrite-oxidizing bacterium, Nitrospira moscoviensis sp. nov., and its phylogenetic relationship. Arch Microbiol 164: 16-23.
17. Ferrell, R.T., and Himmelblau, D.M. (1967) Diffusion coefficients of nitrogen and oxygen in water. J Chem Eng Data 12: 111-115.
18. Frenzel, P., Rothfuss, F., and Conrad, R. (1992) Oxygen profiles and methane turnover in a flooded rice microcosm. Biol Fert Soils 14: 84-89.
19. Garrity, G.M., Winters, M., and Searles, D.B. (2001) Taxonomic Outline of the Prokaryotic Genera Bergey's Manual® of Systematic Bacteriology, 2nd edn. New York, USA: Springer.
20. 4 oxidation: the activity in paddy soil by profile studies. Biogeochemistry 48: 341-365.
21. Holzapfel-Pschorn, A., Conrad, R., and Seiler, W. (1985) Production, oxidation and emission of methane in rice paddies. FEMS Microbiol Ecol 31: 343-351.
22. Hugenholtz, P., Goebel, B.M., and Pace, N.R. (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180: 4765-4774.
23. Jongman, R.H.G., Ter Braak, C.J.F., and van Tongeren, O.F.R. (1987) Data Analysis in Community and Landscape Ecology. Wageningen, The Netherlands: Pudoc.
24. Kalmbach, S., Manz, W., Wecke, J., and Szewzyk, U. (1999) Aquabacterium gen. nov., with description of Aquabacterium citratiphilum sp. nov., Aquabacterium parvum sp. nov., and Aquabacterium commune sp. nov., three in situ dominant bacterial species from the Berlin drinking water system. Int J Syst Bacteriol 49: 769-777.
25. Kersters, K., de Vos, P., Gillis, M., Swings, J., Vandamme, P., and Stackebrandt, E. (eds) (2001) Introduction to the proteobacteria. In The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community, 3rd edn, Release 3.7, 2 November 2001, Springer, New York. [WWW document]. URL http://link.springer-ny.com/link/ service/books/10125
26. Klappenbach, J.A., Dunbar, J.M., and Schmidt, T.M. (2000) rRNA operon copy number reflects ecological strategies of bacteria. Appl Environ Microbiol 66: 1328-1333.
27. Lane, D.J. (1991) 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics. Stackebrandt, E., and Goodfellow, M. (eds). Chichester, UK: John Wiley and Sons, pp. 115-175.
28. Liesack, W., Schnell, S., and Revsbech, N.P. (2000) Microbiology of flooded rice paddies. FEMS Microbiol Rev 24: 625-645.
29. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363-1371.
30. Lüdemann, H., Arth, I., and Liesack, W. (2000) Spatial changes in the bacterial community structure along a vertical oxygen gradient in flooded paddy soil cores. Appl Environ Microbiol 66: 754-762.
31. MacArthur, R.H., and Wilson, E.O. (1967) The Theory of Island Biogeography. Princeton, UK: Princeton University Press.
32. Martiny, A.C., Jørgensen, T.M., Albrechtsen, H.J., Arvin, E., and Molin, S. (2003) Long-term succession of structure and diversity of a biofilm formed in a model drinking water distribution system. Appl Environ Microbiol 69: 6899-6907.
33. Pachur, H.J., Denner, H.D., and Walter, H. (1984) A freezing device for sampling the sediment-water interface of lakes. Catena 11: 65-70.
34. Poulsen, L.K., Ballard, G., and Stahl, D.A. (1993) Use of rRNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms. Appl Environ Microbiol 59: 1354-1360.
35. Ratering, S., and Schnell, S. (2000) Localization of iron-reducing activity in paddy soil by profile studies. Biogeochemistry 48: 341-365.
36. Revsbech, N.P. (1989) An oxygen microsensor with a guard cathode. Limnol Oceanogr 34: 474-478.
37. 4 from anoxic paddy soil. Limnol Oceanogr 43: 1511-1518.
38. 4 gradients. In Microbial Mats: Structure, Development and Environmental Significance. Stal, L.J., and Cumette, P. (eds). Berlin, Germany: Springer, pp. 167-172.
39. Sanford, R.A., Cole, J.R., and Tiedje, J.M. (2002) Characterization and description of Anaeromyxobacter dehalogenans gen. nov., sp. nov., an aryl-halorespiring facultative anaerobic myxobacterium. Appl Environ Microbiol 68: 893-900.
40. Schaechter, M., Maaløe, O., and Kjeldgaard, N.O. (1958) Dependency on medium and temperature of cell size and chemical composition during balanced growth of Salmonella typhimurium. J Gen Microbiol 19: 592-606.
41. Schmidt, H.A., Strimmer, K., Vingron, M., and von Haeseler, A. (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18: 502-504.
42. Schoniger, M., and von Haeseler, A. (1994) A stochastic model for the evolution of autocorrelated DNA sequences. Mol Phylogenet Evol 3: 240-247.
43. Schramm, A., de Beer, D., van den Heuvel, J.C., Ottengraf, S., and Amann, R. (1999) Microscale distribution of populations and activities of Nitrosospira and Nitrospira spp. along a macroscale gradient in a nitrifying bioreactor: quantification by in situ hybridization and the use of microsensors. Appl Environ Microbiol 65: 3690-3696.
44. Sharp, R., and MacFarlane, G.T. (2000) Chemostat enrichments of human feces with resistant starch are selective for adherent butyrate-producing clostridia at high dilution rates. Appl Environ Microbiol 66: 4212-4221.
45. Ter Braak, C.J.F., and Šmilauer, P. (1998) Canoco Reference Manual and User's Guide to Canoco for Windows: Software for Canonical Community Ordination (Version 4). Ithaca, USA: Microcomputer Power.
46. Treude, N., Rosencrantz, D., Liesack, W., and Schnell, S. (2003) Strain FAc12, a dissimilatory iron-reducing member of the Anaeromyxobacter subgroup of Myxococcales. FEMS Microbiol Ecol 44: 261-269.
47. Wagner, M., Rath, G., Amann, R., Koops, H.P., and Schleifer, K.H. (1995) In situ identification of ammonia-oxidizing bacteria. Syst Appl Microbiol 18: 251-264.
48. Weber, S., Stubner, S., and Conrad, R. (2001) Bacterial populations colonizing and degrading rice straw in anoxic paddy soil. Appl Environ Microbiol 67: 1318-1327.
49. Yao, H., Conrad, R., Wassmann, R., and Neue, H.U. (1999) Effect of soil characteristics on sequential reduction and methane production in sixteen rice paddy soils from China, the Philippines, and Italy. Biogeochemistry 47: 269-295.
50. Zehnder, A.J.B., and Stumm, W. (1988) Geochemistry and biogeochemistry of anaerobic habitats. In Biology of Anaerobic Microorganisms. Zehnder, A.J.B. (ed.). New York, USA: Wiley Interscience Publications, pp. 1-38.