High bacterial diversity of a waste gas-degrading community in an industrial biofilter as shown by a 16S rDNA clone library

Environmental Microbiology

Volumn 4, Issue 11, 2002, Pages 721-734

  Friedrich, Udo ^a,b   Prior, Karola ^a,c   Altendorf, Karlheinz ^a   Lipski, André ^a  

^a UNIVERSITY OF OSNABRÜCK   (Germany)

^b DANISCO   (Germany)

^c UNIVERSITY HOSPITAL MÜNSTER   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; BASE SEQUENCE; BIODEGRADATION, ENVIRONMENTAL; DNA, BACTERIAL; DNA, RIBOSOMAL; FILTRATION; GENE LIBRARY; INDUSTRIAL WASTE; MOLECULAR SEQUENCE DATA; PHYLOGENY; RESTRICTION MAPPING; RNA, RIBOSOMAL, 16S; VARIATION (GENETICS); WASTE MANAGEMENT;

ACTINOBACTERIA; ANIMALIA; BACTERIA (MICROORGANISMS); BACTEROIDETES; DELTAPROTEOBACTERIA; FIRMICUTES; GAMMAPROTEOBACTERIA; PROTEOBACTERIA; THERMOMICROBIA; VERRUCOMICROBIA;

EID: 0036862358     PISSN: 14622912     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1462-2920.2002.00349.x     Document Type: Article

References (55)

1. Ahrens, A., Lipski, A., Klatte, S., Busse, H.J., Auling, G., and Altendorf, K. (1997) Polyphasic classification of proteobacteria isolated from biofilters. System Appl Microbiol 20: 255-267.
2. Amann, R.I., Ludwig, W., and Schleifer, K.-H. (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59: 143-169.
3. Amann, G., Stetter, K.O., Llobet-Brossa, E., Amann, R., and Antón, J. (2000) Direct proof for the presence and expression of two 5% different 16S rRNA genes in individual cells of Haloarcula marismortui. Extremophiles 4: 373-376.
4. Bendinger, B., Kroppenstedt, R.M., Klatte, S., and Altendorf, K. (1992) Chemotaxonomic differentiation of coryneform bacteria isolated from biofilters. Int J Syst Bacteriol 42: 474-486.
5. Borneman, J., Skroch, P.W., O'Sullivan, K.M., Palus, J.A., Rumjanek, N.G., Jansen, J.L. et al. (1996) Molecular microbial diversity of an agricultural soil in Wisconsin. Appl Environ Microbiol 62: 1935-1943.
6. Chandler, D.P., Fredrickson, J.K., and Brockman, F.J. (1997) Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries. Mol Ecol 6: 475-482.
7. Clayton, R.A., Sutton, G., Hinkle, P.S. Jr, Bult, C., and Fields, C. (1995) Intraspecific variation in small-subunit rRNA sequences in GenBank: Why single sequences may not adequately represent prokaryotic taxa. Int J Syst Bacteriol 45: 595-599.
8. Cole, S.T., and Girons, I.S. (1994) Bacterial genomics. FEMS Microbiol Rev 14: 139-160.
9. Crocetti, G.R., Hugenholtz, P., Bond, P.L., Schuler, A., Keller, J., Jenkins, D., and Blackall, L.L. (2000) Identification of polyphosphate-accumulating organisms and design of 16S rRNA-directed probes for their detection and quantitation. Appl Environ Microbiol 66: 1175-1182.
10. Devinny, J.S., Deshusses, M.A., and Webster, T.S. (1999) Biofiltration for Air Pollution Control. Boca Raton: CRC Press LLC.
11. Dunbar, J., Takala, S., Barns, S.M., Davis, J.A., and Kuske, C.R. (1999) Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning. Appl Environ Microbiol 65: 1662-1669.
12. Eder, W., Ludwig, W., and Huber, R. (1999) Novel 16S rRNA gene sequences retrieved from highly saline brine sediments of Kebrit Deep, Red Sea. Arch Microbiol 172: 213-218.
13. Eilers, H., Pernthaler, J., Glöckner, F.O., and Amann, R. (2000) Culturability and in situ abundance of pelagic bacteria from the North Sea. Appl Environ Microbiol 66: 3044-3051.
14. Felske, A., Wolterink, A., Van Lis, R., and Akkermans, A.D.L. (1998) Phylogeny of the main bacterial 16S rRNA sequences in Drentse A grassland soils (The Netherlands). Appl Environ Microbiol 64: 871-879.
15. 2O-producing Xanthomonas-like isolates from biofilters as Stenotrophomonas nitritireducens sp. nov. & Pseudoxanthomonas broegbernensis gen. nov., sp. nov. Int J Syst Evol Microbiol 50: 273-282.
16. Friedrich, U., Naismith, M.M., Altendorf, K., and Lipski, A. (1999) Community analysis of biofilters using fluorescence in situ hybridization including a new probe for the Xanthomonas branch of the class Proteobacteria. Appl Environ Microbiol 65: 3547-3554.
17. Heyndrickx, M., Vauterin, L., Vandamme, P., Kersters, K., and De Vos, P. (1996) Applicability of combined amplified ribosomal DNA restriction analysis (ARDRA) patterns in bacterial phylogeny and taxonomy. J Microbiol Methods 26: 247-259.
18. 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.
19. Itaya, M., and Tanaka, T. (1991) Complete physical map of the Bacillus subtilis 168 chromosome constructed by a gene-directed mutagenesis method. J Mol Biol 220: 631-648.
20. Juretschko, S., Timmermann, G., Schmid, M., Schleifer, K.-H., Pommerening-Röser, A., Koops, H.P., and Wagner, M. (1998) Combined molecular and conventional analyses of nitrifying bacterium diversity in activated sludge: Nitrosococcus mobilis and Nitrospira-like bacteria as dominant populations. Appl Environ Microbiol 64: 3042-3051.
21. Juteau, P., Larocque, R., Rho, D., and LeDuy, A. (1999) Analysis of the relative abundance of different types of bacteria capable of toluene degradation in a compost biofilter. Appl Microbiol Biotechnol 52: 863-868.
22. von Keitz, V., Schramm, A., Altendorf, K., and Lipski, A. (1999) Characterization of microbial communities of biofilters by phospholipid fatty acid analysis and rRNA targeted oligonucleotide probes. System Appl Microbiol 22: 626-634.
23. Kreader, C.A. (1996) Relief of amplification inhibition in PCR with bovine serum albumin or T4 gene 32 protein. Appl Environ Microbiol 62: 1102-1106.
24. Li, L., Kato, C., and Horikoshi, K. (1999) Bacterial diversity in deep-sea sediments from different depths. Biodiv Conserv 8: 659-677.
25. Liefting, L.W., Andersen, M.T., Beever, R.E., Gardner, R.C., and Forster, R.L. (1996) Sequence heterogeneity in the two 16S rRNA genes of Phormium yellow leaf phytoplasma. Appl Environ Microbiol 62: 3133-3139.
26. Lipski, A., and Altendorf, K. (1997) Identification of heterotrophic bacteria isolated from ammonia-supplied experimental biofilters. System Appl Microbiol 20: 448-457.
27. Lipski, A., Klatte, S., Bendinger, B., and Altendorf, K. (1992) Differentiation of Gram-negative, nonfermentative bacteria isolated from biofilters on the basis of fatty acid composition, quinone system, and physiological reaction profiles. Appl Environ Microbiol 58: 2053-2065.
28. Ludwig, W., and Klenk, H.-P. (2001) Overview: A phylogenetic backbone and taxonomic framework for prokaryotic systematics. In Bergey's Manual of Systematic Bacteriology. Garrity, G.M., Boone, D.R., and Castenholz, R., (eds), 2nd edn. Vol one. New York: Springer-Verlag.
29. Maidak, B.L., Cole, J.R., Lilburn, T.G., Parker, C.T., Jr Saxman, P.R., Stredwick, J.M. et al. (2000) The RDP (Ribosomal Database Project) continues. Nucleic Acids Res 28: 173-174.
30. Meyerhans, A., Vartanian, J.P., and Wain-Hobson, S. (1990) DNA recombination during PCR. Nucleic Acids Res 18: 1687-1691.
31. Moyer, C.L., Tiedje, J.M., Dobbs, F.C., and Karl, D.M. (1996) A computer-simulated restriction fragment length polymorphism analysis of bacterial small-subunit rRNA genes: Efficacy of selected tetrameric restriction enzymes for studies of microbial diversity in nature. Appl Environ Microbiol 62: 2501-2507.
32. Muyzer, G., Teske, A., Wirsen, C.O., and Jannasch, H.W. (1995) Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch Microbiol 164: 165-172.
33. Nogales, B., Moore, E.R., Abraham, W.R., and Timmis, K.N. (1999) Identification of the metabolically-active members of a bacterial community in a polychlorinated biphenyl-polluted moorland soil. Environ Microbiol 1: 199-212.
34. Nogales, B., Moore, E.R., Llobet-Brossa, E., Rosselló-Mora, R., Amann, R., and Timmis, K.N. (2001) Combined use of 16S ribosomal DNA and 16S rRNA to study the bacterial community of polychlorinated biphenyl-polluted soil. Appl Environ Microbiol 67: 1874-1884.
35. Polz, M.F., and Cavanaugh, C.M. (1998) Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol 64: 3724-3730.
36. Rainey, F.A., Ward, N., Sly, L.I., and Stackebrandt, E. (1994) Dependence on the taxon composition of clone libraries for PCR amplified, naturally occurring 16S rDNA, on the primer pair and the cloning system used. Experientia 50: 796-797.
37. T contains multiple 16S rRNA genes with heterogeneous intervening sequences. Microbiology 142: 2087-2095.
38. Ravenschlag, K., Sahm, K., Pernthaler, J., and Amann, R. (1999) High bacterial diversity in permanently cold marine sediments. Appl Environ Microbiol 65: 3982-3989.
39. Reischl, U., Feldmann, K., Naumann, L., Gaugler, B.J., Ninet, B., Hirschel, B., and Emler, S. (1998) 16S rRNA sequence diversity in Mycobacterium celatum strains caused by presence of two different copies of 16S rRNA gene. J Clin Microbiol 36: 1761-1764.
40. Reysenbach, A.L., Giver, L.J., Wickham, G.S., and Pace, N.R. (1992) Differential amplification of rRNA genes by polymerase chain reaction. Appl Environ Microbiol 58: 3417-3418.
41. Sakano, Y., and Kerkhof, L. (1998) Assessment of changes in microbial community structure during operation of an ammonia biofilter with molecular tools. Appl Environ Microbiol 64: 4877-4882.
42. Schramm, A., De Beer, D., Wagner, M., and Amann, R. (1998) Identification and activities in situ of Nitrosospira and Nitrospira spp. as dominant populations in a nitrifying fluidized bed reactor. Appl Environ Microbiol 64: 3480-3485.
43. Schuppler, M., Mertens, F., Schön, G., and Göbel, U.B. (1995) Molecular characterization of nocardioform actinomycetes in activated sludge by 16S rRNA analysis. Microbiology 141: 513-521.
44. Smith, C.L., Econome, J.G., Schutt, A., Klco, S., and Cantor, C.R. (1987) A physical map of the Escherichia coli K12 genome. Science 236: 1448-1453.
45. Snaidr, J., Amann, R., Huber, I., Ludwig, W., and Schleifer, K.-H. (1997) Phylogenetic analysis and in situ identification of bacteria in activated sludge. Appl Environ Microbiol 63: 2884-2896.
46. Speksnijder, A.G., Kowalchuk, G.A., De Jong, S., Kline, E., Stephen, J.R., and Laanbroek, H.J. (2001) Microvariation artifacts introduced by PCR and cloning of closely related 16S rRNA gene sequences. Appl Environ Microbiol 67: 469-472.
47. Stackebrandt, E., and Goebel, B.M. (1994) Taxonomic note: A place for DNA:DNA reassociation and 16S rRNA sequence analysis in the present definition in Bacteriology. Int J Syt Bacteriol 44: 846-849.
48. Strunk, O., Gross, O., Reichel, B., May, M., Hermann, S., Stuckman, N. et al. (1999) ARB: A Software Environment for Sequence Data. Munich, Germany: Technische Universität München. Department of Microbiology. http://www.mikro.biologie.tu-muenchen.de.
49. Suzuki, M.T., and Giovannoni, S.J. (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62: 625-630.
50. Wang, G.C.-Y., and Wang, Y. (1996) The frequency of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from different bacterial species. Microbiology 142: 1107-1114.
51. Wang, G.C.-Y., and Wang, Y. (1997) Frequency of formation of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from mixed bacterial genomes. Appl Environ Microbiol 63: 4645-4650.
52. Watanabe, K., Teramoto, M., and Harayama, S. (1999) An outbreak of nonflocculating catabolic populations caused the breakdown of a phenol-digesting activated-sludge process. Appl Environ Microbiol 65: 2813-2819.
53. Yap, W.H., Zhang, Z., and Wang, Y. (1999) Distinct types of rRNA operons exist in the genome of the actinomycete Thermomonospora chromogena and evidence for horizontal transfer of an entire rRNA operon. J Bacteriol 181: 5201-5209.
54. Yu, Z., and Mohn, W. (2001) Bacterial diversity and community structure in an aerated lagoon revealed by ribosomal intergenic spacer analyses and 16S ribosomal DNA sequencing. Appl Environ Microbiol 67: 1565-1574.
55. Zhou, J., Bruns, M.A., and Tiedje, J.M. (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62: 316-322.