Novel predominant archaeal and bacterial groups revealed by molecular analysis of an anaerobic sludge digester

Environmental Microbiology

Volumn 7, Issue 8, 2005, Pages 1104-1115

  Chouari, Rakia ^a   Le Paslier, Denis ^a   Daegelen, Patrick ^a   Ginestet, Philippe ^b   Weissenbach, Jean ^a   Sghir, Abdelghani ^a  

^a UNIVERSITÉ D EVRY VAL D ESSONNE   (France)

^b CIRSEE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEAL DNA; BACTERIAL DNA; RIBOSOME DNA; RNA 16S; RNA 23S;

ANAEROBIC GROWTH; ARCHAEBACTERIUM; ARTICLE; BACTERIUM; CLASSIFICATION; DNA SEQUENCE; GENE LIBRARY; GENETICS; GROWTH, DEVELOPMENT AND AGING; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA GENE; SEWAGE;

ANAEROBIOSIS; ARCHAEA; BACTERIA; DNA, ARCHAEAL; DNA, BACTERIAL; DNA, RIBOSOMAL; GENE LIBRARY; GENES, RRNA; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; RNA, RIBOSOMAL, 23S; SEQUENCE ANALYSIS, DNA; SEWAGE;

ACTINOBACTERIA; ACTINOBACTERIA (CLASS); ARCHAEA; BACTEROIDETES; BACTEROIDETES PHYLUM; CHLOROFLEXI; CHLOROFLEXI (CLASS); CRENARCHAEOTA; EURYARCHAEOTA; FIRMICUTES; OTUS; PLANCTOMYCETES; POSIBACTERIA; PROKARYOTA; PROTEOBACTERIA; SYNERGISTES; THERMOTOGALES;

EID: 22744444875     PISSN: 14622912     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2005.00795.x     Document Type: Article

References (51)

1. 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.
2. Archer, D.B., and Kirsop, B.H. (1990) The microbiology and control of anaerobic digestion. In Anaerobic Digestion: A Waste Treatment Technology. Wheatley, A. (ed.). London, England: Elsevier Science Publishing, pp. 43-89.
3. Balch, W.E., Fox, G.E., Magrum, L.J., Woese, C.R., and Wolfe, R.S. (1979) Methanogens: reevaluation, of a unique biological group. Microbiol Rev 43: 260-296.
4. Bjornsson, L., Hugenholtz, P., Tyson, G.W., and Blackall, L.L. (2002) Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal. Microbiology 148: 2309-2318.
5. Brosius, J., Palmer, M.L., Kennedy, P.J., and Noller, H.F. (1978) Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coll. Proc Natl Acad Sci USA 75: 4801-4805.
6. Chandler, D.P., Brockman, F.J., Bailey, T.J., and Fredrickson, J.K. (1998) Phylogenetic diversity of Archaea and Bacteria in a deep subsurface paleosol. Microb Ecol 36: 37-50.
7. Chouari, R., Le Paslier, D., Daegelen, P., Ginestet, P., Weissenbach, J., and Sghir, A. (2003) Molecular evidence for novel planctomycete diversity in a municipal wastewater treatment plant. Appl Environ Microbiol 69: 7354-7363.
8. Chouari, R., Le Paslier, D., Dauga, C., Daegelen, P., Weissenbach, J., and Sghir, A. (2005) Novel major bacterial candidate division within a municipal anaerobic sludge digester. Appl Environ Microbiol 71, in press.
9. Chynoweth, D.P., Bosch, G., Earle, J.F., Legrand, R., and Liu, K. (1991) A novel process for anaerobic composting of municipal solid waste. Appl Biochem Biotechnol 28-29: 421-432.
10. Cole, J.R., Chai, B., Marsh, T.L., Farris, R.J., Wang, Q., Kulam, S.A., et al. (2003) The ribosomal database project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31: 442-443.
11. 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.
12. Dabert, P., Sialve, B., Delgenes, J.P., Moletta, R., and Godon, J.J. (2001) Characterisation of the microbial 16S rDNA diversity of an aerobic phosphorus-removal ecosystem and monitoring of its transition to nitrate respiration. Appl Microbiol Biotechnol 55: 500-509.
13. Daims, H., Ramsing, N.B., Schleifer, K.H., and Wagner, M. (2001) Cultivation-independent, semiautomatic determination of absolute bacterial cell numbers in environmental samples by fluorescence in situ hybridization. Appl Environ Microbiol 67: 5810-5818.
14. De los Reyes, F.L., Ritter, W., and Raskin, L. (1997) Group-specific small-subunit rRNA hybridization probes to characterize filamentous foaming in activated sludge systems. Appl Environ Microbiol 63: 1107-1117.
15. De los Reyes, M.F., De los Reyes, F.L., III, Hernandez, M., and Raskin, L. (1998) Quantification of Gordona amarae strains in foaming activated sludge and anaerobic digester systems with oligonucleotide hybridization probes. Appl Environ Microbiol 64: 2503-2512.
16. DeLong, E.F. (1992) Archaea in coastal marine environments. Proc Natl Acad Sci USA 89: 5685-5689.
17. Derakshani, M., Lukow, T., and Liesack, W. (2001) Novel Bacterial lineages at the (Sub)division level as detected by signature nucleotide-targeted recovery of 16S rRNA genes from bulk soil and rice roots of flooded rice microcosms. Appl Environ Microbiol 67: 623-631.
18. Dojka, M.A., Hugenholtz, P., Haack, S.K., and Pace, N.R. (1998) Microbial diversity in hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl Environ Microbiol 64: 3869-3877.
19. Doré, J., Sghir, A., Hannequart-Gramet, G., Corthier, G., and Pochart, P. (1998) Design and evaluation of a 16S rRNA-targeted oligonucleotide probe for specific detection and quantitation of human faecal Bacteroides populations. Syst Appl Microbiol 1: 65-71.
20. Farrelly, V., Rainey, F.A., and Stackebrandt, E. (1995) Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl Environ Microbiol 61: 2798-2801.
21. Gich, F., Garcia-Gil, J., and Overmann, J. (2001) Previously unknown and phylogenetically diverse members of the green non-sulfur bacteria are indigenous to freshwater lakes. Arch Microbiol 177: 1-10.
22. Godon, J.J., Zumstein, E., Dabert, P., Habouzit, F., and Moletta, R. (1997) Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis. Appl Environ Microbiol 63: 2802-2813.
23. Goebel, B.M., and Stackebrandt, E. (1994) Cultural and phylogenetic analysis of mixed microbial populations found in natural and commercial bioleaching environments. Appl Environ Microbiol 60: 1614-1621.
24. Good, I.J. (1953) The population frequencies of species and the estimation of population parameters. Biometrika 40: 237-264.
25. Harmsen, H.J., Kengen, H.M., Akkermans, A.D., Stams, A.J., and de Vos, W.M. (1996) Detection and localization of syntrophic propionate-oxidizing bacteria in granular sludge by in situ hybridization using 16S rRNA-based oligonucleotide probes. Appl Environ Microbiol 62: 1656-1663.
26. Holt, J.G., and Lewin, R.A. (1968) Herpetosiphon aurantiacus gen. et sp. n., a new filamentous gliding organism. J Bacteriol 95: 2407-2408.
27. Hugenholtz, P., and Goebel, B.M. (2001) The polymerase chain reaction as a tool to investigate microbial diversity in environmental samples. In Environmental Molecular Microbiology: Protocols and Applications. Rochelle, P.A. (ed.). New York, USA: Horizon Scientific, pp. 31-42.
28. Hugenholtz, P., Pitulle, C., Hershberger, K.L., and Pace, N.R. (1998) Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol 180: 366-376.
29. Juretschko, S., Loy, A., Lehner, A., and Wagner, M. (2002) The microbial community composition of a nitrifying-denitrifying activated sludge from an industrial sewage treatment plant analyzed by the full-cycle rRNA approach. Syst Appl Microbiol 25: 84-99.
30. Lim, E.L., Amaral, L.A., Caron, D.A., and DeLong, E.F. (1993) Application of rRNA-based probes for observing marine nanoplanktonic protists. Appl Environ Microbiol 59: 1647-1655.
31. MacGregor, B.J., Toze, S., Alm, E.W., Sharp, R., Ziemer, C.J., and Stahl, D.A. (2001) Distribution and abundance of Gram-positive bacteria in the environment: development of a group-specific probe. J Microbiol Methods 44: 193-203.
32. Manz, W., Amann, R., Ludwig, W., Wagner, M., and Schleifer, K.-H. (1992) Phylogenetic oligodeoxynucleotide probes for the major subclasses of proteobacteria; problems and solutions. Syst Appl Microbiol 15: 593-600.
33. Manz, W., Amann, R., Ludwig, W., Vancanneyt, M., and Schleifer, K.H. (1996) Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum Cytophaga-Flavobacter-Bacteroides in the natural environment. Microbiology 142: 1097-1106.
34. Marchesi, J.R., Sato, T., Weightman, A.J., Martin, T.A., Fry, J.C., Hiom, S.J., et al. (1998) Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol 64: 795-799.
35. Neef, A., Amann, R., Schlesner, H., and Schleifer, K.H. (1998) Monitoring a widespread bacterial group: in situ detection of planctomycetes with 16S rRNA-targeted probes. Microbiology 144: 3257-3266.
36. Oyaizu, H., Debrunner-Vossbrinck, B., Mandelco, L., Studier, J.A., and Woese, C.R. (1987) The green non-sulfur bacteria: a deep branching in the eubacterial line of descent. Syst Appl Microbiol 9: 47-53.
37. Rappé, M.S., Kemp, P.F., and Giovannoni, S.J. (1997) Phylogenetic diversity of marine coastal picoplankton 16S rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina. Limnol Oceanogr 42: 811-826.
38. Raskin, L., Stromley, J.M., Rittmann, B.E., and Stahl, D.A. (1994) Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens. Appl Environ Microbiol 60: 1232-1240.
39. 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.
40. Sekiguchi, Y., Kamagata, Y., Syutsubo, K., Ohashi, A., Harada, H., and Nakamura, K. (1998) Phylogenetic diversity of mesophilic and thermophilic granular sludges determined by 16S rRNA gene analysis. Microbiology 144: 2655-2665.
41. Sekiguchi, Y., Takahashi, H., Kamagata, Y., Ohashi, A., and Harada, H. (2001) In situ detection, isolation, and physiological properties of a thin filamentous microorganism abundant in methanogenic granular sludges: a novel isolate affiliated with a clone cluster, the green non-sulfur bacteria, subdivision I. Appl Environ Microbiol 67: 5740-5749.
42. Sekiguchi, Y., Yamada, T., Hanada, S., Ohashi, A., Harada, H., and Kamagata, Y. (2003) Anaerolinea thermophila gen. nov., sp. nov. and Caldilinea aerophila gen. nov., sp. nov., novel filamentous thermophiles that represent a previously uncultured lineage of the domain Bacteria at the subphylum level. Int J Syst Evol Microbiol 53: 1843-1851.
43. Sghir, A., Gramet, G., Suau, A., Rochet, V., Pochart, P., and Dore, J. (2000) Quantification of bacterial groups within human fecal flora by oligonucleotide probe hybridization. Appl Environ Microbiol 66: 2263-2266.
44. 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.
45. Stahl, D.A., Flesher, B., Mansfield, H.R., and Montgomery, L. (1988) Use of phylogenetically based hybridization probes for studies of ruminai microbial ecology. Appl Environ Microbiol 54: 1079-1084.
46. Suau, A., Bonnet, R., Sutren, M., Godon, J.J., Gibson, G.R., Collins, M.D., and Dore, J. (1999) Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl Environ Microbiol 65: 4799-4807.
47. 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.
48. Von Wintzingerode, F., Gobel, U.B., and Stackebrandt, E. (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21: 213-229.
49. Watanabe, K., Kodama, Y., Hamamura, N., and Kaku, N. (2002) Diversity, abundance, and activity of archaeal populations in oil-contaminated groundwater accumulated at the bottom of an underground crude oil storage cavity. Appl Environ Microbiol 68: 3899-3907.
50. Wu, W.M., Mahendra, K.J., Conway de Macario, E., Thiele, J.H., and Zeikus, J.G. (1992) Microbiol composition and characterization of prevalent methanogens and acetogens isolated from syntrophic methanogenic granules. Appl Microbiol Biotechnol 38: 282-290.
51. Zheng, D., Alm, E.W., Stahl, D.A., and Raskin, L. (1996) Characterization of universal small subunit rRNA hybridization probes for quantitative molecular microbial ecology studies. Appl Environ Microbiol 62: 4504-4513.