Phylogenetic identity, growth-response time and rRNA operon copy number of soil bacteria indicate different stages of community succession

Environmental Microbiology

Volumn 9, Issue 10, 2007, Pages 2464-2474

  Shrestha, Pravin Malla ^a   Noll, Matthias ^a,b   Liesack, Werner ^a  

^a MAX PLANCK INSTITUTE FOR TERRESTRIAL MICROBIOLOGY   (Germany)

^b BAM FEDERAL INSTITUTE FOR MATERIALS RESEARCH AND TESTING   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ACTINOBACTERIA; ARTICLE; BACILLUS; BACTERIUM; GENE DOSAGE; GENETICS; GROWTH, DEVELOPMENT AND AGING; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OPERON; PHYLOGENY; PROTEOBACTERIA; RESTRICTION FRAGMENT LENGTH POLYMORPHISM;

ACTINOBACTERIA; BACILLUS; BACTERIA; BASE SEQUENCE; GENE DOSAGE; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; PROTEOBACTERIA; RRNA OPERON; SOIL MICROBIOLOGY;

ACTINOBACTERIA; ALPHAPROTEOBACTERIA; BACILLI (CLASS); BACTERIA (MICROORGANISMS); BETAPROTEOBACTERIA; GAMMAPROTEOBACTERIA;

EID: 34548401606     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2007.01364.x     Document Type: Article

References (38)

1. Andrews, J.H. Harris, R.F. (1986) r- and K-selection and microbial ecology. Adv Microb Ecol 9 : 99 147.
2. Balestra, G.M. Misaghi, I.J. (1997) Increasing the efficiency of the plate counting method for estimating bacterial diversity. J Microbiol Methods 30 : 111 117.
3. Buesing, N. Gessner, M.O. (2002) Comparison of detachment procedures for direct counts of bacteria associated with sediment particles, plant litter, and epiphytic biofilms. Aquat Microb Ecol 27 : 29 36.
4. Chin, K.J., Hahn, D., Hengstmann, U., Liesack, W. Janssen, P.H. (1999) Characterization and identification of numerically abundant culturable bacteria from the anoxic bulk soil of rice paddy microcosms. Appl Environ Microbiol 65 : 5042 5049.
5. Dang, H. Lovell, C.R. (2000) Bacterial primary colonization and early succession on surface in marine waters as determined by amplified rRNA gene restriction analysis and sequence analysis of 16S rRNA genes. Appl Environ Microbiol 66 : 467 475.
6. Davis, K.E.R., Joseph, S.J. Janssen, P.H. (2005) Effects of growth medium, inoculum size, and incubation time on the culturability and isolation of soil bacteria. Appl Environ Microbiol 71 : 826 834.
7. De Leij, F.A.A.M., Whipps, J.M. Lynch, J.M. (1993) The use of colony development for the characterization of bacterial communities in soil and on roots. Microb Ecol 27 : 81 97.
8. Dighe, A.S., Jangid, K., Gonzalez, J.M., Pidiyar, V.J., Patole, M.S., Ranade, D.R. Shouche, Y.S. (2004) Comparison of 16S rRNA gene sequences of genus Methanobrevibacter. BMC Microbiol 4 : 20.
9. Garland, J.L., Cook, K.L., Adams, J.L. Kerkhof, L. (2001) Culturability as an indicator of succession in microbial communities. Microb Ecol 42 : 150 158.
10. 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.
11. Holzapfel-Pschorn, A., Conrad, R. Seiler, W. (1985) Production, oxidation, and emission of methane in rice paddies. FEMS Microbiol Ecol 31 : 343 351.
12. 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.
13. Klappenbach, J.A., Dunbar, J.M. Schmidt, T.M. (2000) rRNA operon copy number reflects ecological strategies of bacteria. Appl Environ Microbiol 29 : 1328 1333.
14. Koch, A.L. (1994) Growth measurement. In Methods for General and Molecular Bacteriology. Gerhardt, P., Murray, R.G.E., Wood, W.A. Krieg, N.R. (eds). Washington, DC, USA : American Society for Microbiology, pp. 248 277.
15. Kristufek, V., Elhottova, D., Chronakova, A., Dostalkova, I., Picek, T. Kalcik, J. (2005) Growth strategy of heterotrophic bacterial population along successional sequence on spoil of brown coal colliery substrate. Folia Microbiol 50 : 427 435.
16. Krüger, M., Frenzel, P. Conrad, R. (2001) Microbial processes influencing methane emission from rice fields. Global Change Biol 7 : 49 63.
17. Kuwae, T. Hosokawa, Y. (1999) Determination of the abundance and biovolume of bacteria in sediments by dual staining with 4′,6-diamidino-2- phenylindole and acridine orange: relationship to dispersion treatment and sediment characteristics. Appl Environ Microbiol 65 : 3407 3412.
18. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, et al. (2004) ARB: a software environment for sequence data. Nucleic Acid Res 32 : 1363 1371.
19. MacArthur, R.H. Wilson, E.O. (1967) The Theory of Island Biogeography. Princeton, UK : Princeton University Press.
20. McDaniel, J.A. Capone, D.G. (1985) A comparison of procedures for the separation of aquatic bacteria from sediments for subsequent direct enumeration. J Microbiol Methods 3 : 291 302.
21. Martiny, A.C., Jørgensen, T.M., Albrechtsen, H.J., Arvin, E. 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.
22. Mitsui, H., Gorlach, K., Lee, H.J., Hattori, R. Hattori, T. (1997) Incubation time and media requirements of culturable bacteria from different phylogenetic groups. J Microbiol Methods 30 : 103 110.
23. Mott, I.E.C., Stickler, D.J., Coakely, W.T. Bott, T.R. (1998) The removal of bacterial biofilm from water-filled tubes using axially propagated ultrasound. J Appl Microbiol 84 : 509 514.
24. Nemergut, D.R., Anderson, S.P., Cleveland, C.C., Martin, A.P., Miller, A.E., Seimon, A. Schmidt, S.K. (2007) Microbial community succession in an unvegetated, recently deglaciated soil. Microb Ecol 53 : 110 122.
25. Noll, M., Matthies, D., Frenzel, P., Derakshani, M. Liesack, W. (2005) Succession of bacterial community structure and diversity in a paddy soil oxygen gradient. Environ Microbiol 7 : 382 395.
26. Olsen, R.A. Bakken, L.R. (1987) Viability of soil bacteria: optimization of plate-counting technique and comparison between total counts and plate counts within different size groups. Microb Ecol 13 : 59 74.
27. Reasoner, D.J. Geldreich, E.E. (1985) A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 49 : 1 7.
28. Sambrook, J. Russell, D.W. (2001) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor, NY, USA : Cold Spring Harbor Laboratory Press.
29. Schmidt, H.A., Strimmer, K., Vingron, M. Haeseler, A.V. (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18 : 502 504.
30. Schoniger, M. von Haeseler, A. (1994) A stochastic model for the evolution of autocorrelated DNA sequences. Mol Phylogenet Evol 3 : 240 247.
31. Shayne, J.J., Hugenholtz, P., Sangwan, P., Osborne, C.A. Janssen, P.H. (2003) Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl Environ Microbiol 69 : 7210 7215.
32. Sigler, W.V. Zeyer, J. (2004) Colony-forming analysis of bacterial community succession in deglaciated soils indicates pioneer stress-tolerant opportunists. Microb Ecol 48 : 316 323.
33. Sigler, W.V., Crivii, S. Zeyer, J. (2002) Bacterial succession in glacial forefield soils characterized by community structure, activity and opportunistic growth dynamics. Microb Ecol 44 : 306 316.
34. Stackebrandt, E. Goebel, B.M. (1994) Taxonomic note; a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44 : 846 849.
35. Weinbauer, M.G., Beckmann, C. Höfle, M.G. (1998) Utility of green fluorescent nucleic acid dyes and aluminium oxide membrane filters for rapid epifluorescence enumeration of soil and sediment bacteria. Appl Environ Microbiol 64 : 5000 5003.
36. Wilson, K. (1999) Preparation of genomic DNA from bacteria. In Current Protocols in Molecular Biology. Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Smith, J.A., Seidman, J.G. Struhl, K. (eds). New York, NY, USA : John Wiley & Sons, pp. 2.4.1 2. 4.5.
37. Zarda, B., Hahn, D., Chatzinotas, A., Schonhuber, W., Neef, A., Amann, R.I. Zeyer, J. (1997) Analysis of bacterial community structure in bulk soil by in situ hybridization. Arch Microbiol 168 : 185 192.
38. Zhu, H., Qu, F. Zhu, L.H. (1993) Isolation of genomic DNAs from plants, fungi and bacteria using benzyl chloride. Nucleic Acid Res 21 : 5279 5280.