Amplified ribosomal DNA restriction analysis of free-living bacteria present in the headbox of a Canadian paper machine

Canadian Journal of Microbiology

Volumn 55, Issue 7, 2009, Pages 810-817

  Prince, Véronique ^a   Simao Beaunoir, Anne Marie ^a   Beaulieu, Carole ^a  

^a UNIVERSITÉ DE SHERBROOKE   (Canada)

Author keywords

Geobacillus; Principal component analysis; Pseudomonas; Pseudoxanthomonas; Schlegelella

Indexed keywords

BACTERIAL COMMUNITY; BACTERIAL CONTAMINANTS; BACTERIAL CONTAMINATION; BACTERIAL GENUS; BACTERIAL POPULATION; CANADIAN MILLS; CLONE LIBRARY; CONTROL METHODS; GEOBACILLUS; HEADBOX; METABOLIC PROFILES; PAPER MACHINE; PSEUDOMONAS; PSEUDOXANTHOMONAS; RIBOSOMAL DNA; SCHLEGELELLA; TEMPORAL VARIATION;

BACTERIOLOGY; CLONING; DNA; GENES; HEADBOXES; LIBRARIES; NUCLEIC ACIDS; PAPER PRODUCTS; PAPERMAKING; PAPERMAKING MACHINERY; WATER ANALYSIS;

PRINCIPAL COMPONENT ANALYSIS;

RNA 16S;

CLONE; DNA; MACHINERY; METABOLISM; MICROBIAL ACTIVITY; POLLUTANT; POPULATION GROWTH; PRINCIPAL COMPONENT ANALYSIS;

AMPLIFIED RIBOSOMAL DNA RESTRICTION ANALYSIS; ARTICLE; BACTERIUM; BACTERIUM COLONY; BACTERIUM CONTAMINATION; BEIJERINCKIACEAE; BURKHOLDERIALES; CHELATOCOCCUS; COMAMONADACEAE; GEOBACILLUS; HYDROGENOPHILACEAE; HYDROGENOPHILUS; MACHINE; MEIOTHERMUS; MICROBIAL COMMUNITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PSEUDOMONAS; PSEUDOXANTHOMONAS; SCHLEGELELLA; TEPIDIMONAS; THERMACEAE; XANTHOMONADACEAE;

BACTERIA; CANADA; DNA, BACTERIAL; DNA, RIBOSOMAL; EQUIPMENT CONTAMINATION; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; SEASONS; WATER MICROBIOLOGY;

BACTERIOLOGY; CLONES; GENES; HEAD BOXES; LIBRARIES; NUCLEIC ACIDS; PAPER MACHINES; PAPER MAKING; PAPER PRODUCTS; WATER ANALYSIS;

BACTERIA (MICROORGANISMS); CHELATOCOCCUS; GEOBACILLUS; HYDROGENOPHILUS; MEIOTHERMUS; PSEUDOMONAS; PSEUDOXANTHOMONAS; SCHLEGELELLA; TEPIDIMONAS;

EID: 68149087784     PISSN: 00084166     EISSN: None     Source Type: Journal    
DOI: 10.1139/W09-036     Document Type: Article

References (46)

1. Albuquerque, L., Tiago, I., Veríssimo, A., and da Costa, M.S. 2006. Tepidimonas thermarum sp. nov., a new slightly thermophilic betaproteobacterium isolated from the Elisenquelle in Aachen and emended description of the genus Tepidimonas. Syst. Appl. Microbiol. 29: 450-456. doi:10.1016/j.syapm.2005.12. 004. PMID:16410043.
2. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410. PMID:2231712.
3. 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. PMID: 7535888.
4. Bennett, C. 1985. Control of microbial problems and corrosion in closed systems. Paper Technol. Ind. 26: 331-335.
5. Brümmer, I.H.M., Fehr, W., and Wagner-Döbler, I. 2000. Biofilm community structure in polluted rivers: abundance of dominant phylogenetic groups over a complete annual cycle. Appl. Environ. Microbiol. 66: 3078-3082. doi:10.1128/AEM.66.7.3078- 3082.2000. PMID:10877809.
6. Chen, M.Y., Lin, G.H., Lin, Y.T., and Tsay, S.S. 2002. Meiothermus taiwanensis sp.nov., a novel filamentous, thermophilic species isolated in Taiwan. Int. J. Syst. Evol. Microbiol. 52: 1647- 1654. doi:10.1099/ijs.0.02189- 0. PMID:12361269.
7. Chen, T.L., Chou, Y.J., Chen, W.M., Arun, B., and Young, C.C. 2006. Tepidimonas taiwanensis sp. nov., a novel alkaline-protease-producing bacterium isolated from a hot spring. Extremophiles, 10: 35-40. doi:10.1007/s00792-005- 0469-9. PMID: 16215773.
8. Chung, A.P., Rainey, F., Nobre, M.F., Burghardt, J., and da Costa, M.S. 1997. Meiothermus cerbereus sp. nov., a new slightly thermophilic species with high levels of 3-hydroxy fatty acids. Int. J. Syst. Bacteriol. 47: 1225-1230. PMID:9336933.
9. 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. doi:10.1093/nar/gkg039. PMID:12520046. (Pubitemid 36150424)
10. Cole, J.R., Chai, B., Farris, R.J., Wang, Q., Kulam-Syed-Mohideen, A.S., McGarrell, D.M., et al. 2007. The Ribosomal Database Project (RDP-II): introducing myRDP Space and quality controlled public data. Nucleic Acids Res. 35: D169-D172. doi:10. 1093/nar/gkl889. PMID:17090583. (Pubitemid 46056192)
11. Crosby, L.D., and Criddle, C.S. 2003. Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity. Biotechniques, 34: 790-794. PMID: 12703304.
12. Desjardins, E., and Beaulieu, C. 2003. Identification of bacteria contaminating pulp and a paper machine in a Canadian paper mill. J. Ind. Microbiol. Biotechnol. 30: 141-145. PMID: 12715250.
13. 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. PMID:10103265.
14. Ekman, J., Kosonen, M., Jokela, S., Kolari, M., Korhonen, P., and Salkinoja-Salonen, M. 2007. Detection and quantitation of colored deposit-forming Meiothermus spp. in paper industry processes and end products. J. Ind. Microbiol. Biotechnol. 34: 203- 211. doi:10.1007/s10295-006-0187-z. PMID:17131103.
15. Findlay, R.H., and Watling, L. 1998. Seasonal variation in the structure of a marine benthic microbial community. Microb. Ecol. 36: 23-30. doi:10.1007/s002489900089. PMID:9622561.
16. Freitas, M., Rainey, F.A., Nobre, M.F., Silvestre, A.J.D., and da Costa, M.S. 2003. Tepidimonas aquatica sp. nov., a new slightly thermophilic β-proteobacterium isolated from a hot water tank. Syst. Appl. Microbiol. 26: 376-381. doi:10.1078/ 072320203322497400. PMID:14529180.
17. Gordon, D.A., and Giovannoni, S.J. 1996. Detection of stratified microbial populations related to Chlorobium and Fibrobacter species in the Atlantic and Pacific oceans. Appl. Environ. Microbiol. 62: 1171-1177. PMID:8919778.
18. Haack, S.K., Garchow, H., Klug, M.J., and Forney, L.J. 1995. Analysis of factors affecting the accuracy, reproductibility, and interpretation of microbial community carbon source utilization patterns. Appl. Environ. Microbiol. 61: 1458-1468. PMID: 16534996.
19. Hayashi, N.R., Ishida, T., Yokota, A., Kodama, T., and Igarashi, Y. 1999. Hydrogenophilus thermoluteolus gen. nov., sp. nov., a thermophilic, facultatively chemolithoautotrophic, hydrogen-oxidizing bacterium. Int. J. Syst. Bacteriol. 49: 783-786. PMID: 10319503.
20. Ingrassia, I., Roques, C., and Prévost, F. 2001. Preliminary experiments for ARDRA validation on flora associated with intestinal mucosa. Lait, 81: 263-280. doi:10.1051/lait:2001130. (Pubitemid 33238224)
21. Kashama, J. 2007. Caracterisation physiologique des populations bactériennes contaminant les machines des pâtes et papier. Mémoire de maîtrise, Université de Sherbrooke, Sherbrooke, Que.
22. Keith-Roach, M.J., Bryan, N.D., Bardgett, R.D., and Livens, F.R. 2002. Seasonal changes in the microbial community of a salt marsh, measured by phospholipids fatty acid analysis. Biogeochemistry, 60: 77-96. doi:10.1023/A:1016553225977.
23. Kolari, M., Nuutinen, J., and Salkinoja-Salonen, M.S. 2001. Mechanisms of biofilm formation in paper machine by Bacillus species: the role of Deinococcus geothermalis. J. Ind. Microbiol. Biotechnol. 27: 343-351. doi:10.1038/sj.jim. 7000201. PMID: 11773998.
24. Kolari, M., Nuutinen, J., Rainey, F.A., and Salkinoja-Salonen, M.S. 2003. Colored moderately thermophilic bacteria in paper-machine biofilms. J. Ind. Microbiol. Biotechnol. 30: 225-238. PMID:12700951.
25. Lagacé, L., Pitre, M., Jacques, M., and Roy, D. 2004. Identification of the bacterial community of maple sap by using amplified ribosomal DNA (rRNA) restriction analysis and rDNA sequencing. Appl. Environ. Microbiol. 70: 2052-2060. doi:10.1128/ AEM.70.4.2052-2060.2004. PMID:15066796.
26. Lahtinen, T., Kosonen, M., Tiirola, M., Vuento, M., and Oker-Blom, C. 2006. Diversity of bacteria contaminating paper machines. J. Ind. Microbiol. Biotechnol. 33: 734-740. doi:10.1007/ s10295-006-0105-114 PMID:16520979.
27. Liesack, W., Weyland, H., and Stackebrandt, E. 1991. Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed-culture of strict barophilic bacteria. Microb. Ecol. 21: 191-198. doi:10.1007/ BF02539153.
28. Lütke-Eversloh, T., Elbanna, K., Cnockaert, M.C., Mergaert, J., Swings, J., Manaia, C.M., and Steinbuchel, A. 2004. Caenibacterium thermophilum is a later synonym of Schlegelella thermodepolymerans. J. Syst. Evol. Microbiol. 50: 1933-1935. doi:10. 1099/ijs.0.63204-0.
29. Merk, S., Neubauer, H., Meyer, H., and Greiser-Wilke, I. 2001. Comparison of different methods for the isolation of Burkholderia cepacia DNA from pure cultures and waste water. Int. J. Hyg. Environ. Health, 204: 127-131. doi:10.1078/1438-4639- 00083. PMID:11759155.
30. Meyerhans, A., Vartanian, J.-P., and Wain-Hobson, S. 1990. DNA recombination during PCR. Nucleic Acids Res. 18: 1687-1691. doi:10.1093/nar/18. 7.1687. PMID:2186361.
31. Moreira, C., Rainey, F.A., Nobre, M.F., da Silva, M.T., and da Costa, M.S. 2000. Tepidimonas ignava gen. nov., sp. nov., a new chemolithoheterotrophic and slightly thermophilic member of the β-Proteobacteria. Int. J. Syst. Evol. Microbiol. 50: 735-742. PMID:10758883.
32. Moyer, C.L., Dobbs, F.C., and Karl, D.M. 1994. Estimation of diversity and community structure through restriction fragment length polymorphism distribution analysis of bacterial 16S rRNA genes from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii. Appl. Environ. Microbiol. 60: 871-879. PMID:7512808.
33. Prévost, K., Couture, G., Shipley, J.W., Brzezinski, R., and Beaulieu, C. 2006. Effect of chitosan and a biocontrol streptomycete on field and potato tuber bacterial communities. BioControl, 51: 533-546. doi:10.1007/s10526-005-4240-z. (Pubitemid 44389291)
34. 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. PMID:1280061.
35. Rowbottom, R.S. 1988. Bacteria cause fatal explosion at corrugating medium mill. Pulp Paper Can. 90: 75-81.
36. Safade, T.L. 1988. Tackling the slime problem in a paper-mill. Paper Technol. Ind. 29: 280-285.
37. Saw, J.H., Mountain, B.W., Feng, L., Omelchenko, M.V., Hou, S., Saito, J.A., et al. 2008. Encapsulated in silica: genome, proteome, and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1. Genome Biol. 9: R161. doi:10.1186/ gb-2008-9-11-r161. PMID:19014707.
38. Stöhr, R., Waberski, A., Liesack, W., Völker, H., Wehmeyer, U., and Thomm, M. 2001. Hydrogenophilus hirschii sp. nov., a novel thermophilic hydrogen-oxidizing b-proteobacterium isolated from Yellowstone National Park. Int. J. Syst. Evol. Microbiol. 51: 481-488. PMID:11321094.
39. Suihko, M.-L., Sinkko, H., Partanen, L., Mattila-Sandholm, T., Salkinoja-Salonen, M., and Raaska, L. 2004. Description of heterotrophic bacteria occurring in paper mills and paper products. J. Appl. Microbiol. 97: 1228-1235. doi:10.1111/j.1365-2672.2004. 02416.x. PMID:15546414.
40. Väätänen, P., and Niemelä, S.I. 1983. Factors regulating the density of bacteria in process waters of a paper mill. J. Appl. Bacteriol. 54: 367-371. PMID:6348015.
41. Väisänen, O.M., Mentu, J., and Salkinoja-Salonen, M.S. 1991. Bacteria in food packaging paper and board. J. Appl. Bacteriol. 71: 130-133. PMID:1917722.
42. Väisänen, O.M., Nurmiaho-Lassila, E.-L., Marmo, S.A., and Salikinoja-Salonen, M.S. 1994. Structure and composition of biological slimes on paper and board machines. Appl. Environ. Microbiol. 60: 641-653. PMID:16349191.
43. Väisänen, O.M., Weber, A., Bennasar, A., Rainey, F.A., Busse, H.J., and Salkinoja-Salonen, M.S. 1998. Microbial communities of printing paper machines. J. Appl. Microbiol. 84: 1069-1084. doi:10.1046/j.1365-2672.1998.00447. x. PMID:9717292.
44. Verschuere, L., Fievez, V., Van Vooren, L., and Verstraete, W. 1997. The contribution of individual populations to the Biolog pattern of model microbial communities. FEMS Microbiol. Ecol. 24: 353-362. doi:10.1111/j.1574-6941.1997. tb00452.x.
45. Ward, D.M., Weller, R., and Bateson, M.M. 1990. 16S rRNA sequences reveal uncultured inhabitants of a well-studied thermal community. FEMS Microbiol. Rev. 6: 105-115. PMID:2117459.
46. Wilmotte, A., Van der Auwera, G., and De Wachter, R. 1993. Structure of the 16S ribosomal RNA of the thermophilic cynobacterium Chlorogloeopsis HTF ('Mastigocladus laminosus HTF') strain PCC7518, and phylogenetic analysis. FEBS Lett. 317: 96-100. doi:10.1016/0014-5793(93)81499-P. PMID: 8428640.