Culture-independent characterization of archaeal biodiversity in swine confinement building bioaerosols

Applied and Environmental Microbiology

Volumn 75, Issue 17, 2009, Pages 5445-5450

  Nehmé, Benjamin ^a,b   Gilbert, Yan ^a,b   Létourneau, Valérie ^a,b   Forster, Robert J ^c   Veillette, Marc ^a   Villemur, Richard ^d   Duchaine, Caroline ^a  

^a LAVAL UNIVERSITY   (Canada)

^b UNIVERSITÉ LAVAL   (Canada)

^c AGRICULTURE AND AGRI FOOD CANADA   (Canada)

^d INRS INSTITUT ARMAND FRAPPIER   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

16S RRNA GENE; ARCHAEA; ARCHAEAL; BIOAEROSOLS; DENATURING GRADIENT GEL ELECTROPHORESIS; GELATIN FILTERS; GENOMIC DNA; HIGH CONCENTRATION; INSTITUTE OF OCCUPATIONAL MEDICINES; METHANOGENIC ARCHAEA; MICROBIAL BIOMASS; MICROBIAL COMMUNITIES; PCR AMPLIFICATION; PIG MANURES; SWINE OPERATIONS;

AMPLIFICATION; BACTERIOLOGY; BIODIVERSITY; BIOMASS; ELECTROPHORESIS; GELATION; MOLECULAR BIOLOGY; NUCLEIC ACIDS;

MANURES;

GENOMIC DNA; RNA 16S;

AEROSOL; BIODIVERSITY; BIOMASS; DNA; ELECTROKINESIS; GENE EXPRESSION; MANURE; MICROBIAL COMMUNITY; MOLECULAR ECOLOGY; PIG; POLYMERASE CHAIN REACTION; PROKARYOTE; RNA;

AEROSOL; AIR; ARCHAEBACTERIUM; ARTICLE; BIODIVERSITY; CONCENTRATION RESPONSE; CONTROLLED STUDY; DNA EXTRACTION; FINGER DERMATOGLYPHICS; GEL ELECTROPHORESIS; GENE AMPLIFICATION; GENE CASSETTE; GENE LIBRARY; MANURE; METHANOGENIC ARCHAEON; METHANOSPHAERA STADTMANAE; MICROBIAL BIOMASS; MICROBIAL COMMUNITY; MOLECULAR ECOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; OCCUPATIONAL MEDICINE; POLYMERASE CHAIN REACTION; SEASONAL VARIATION; SUMMER; SWINE; WINTER;

AEROSOLS; AIR MICROBIOLOGY; ANIMALS; ARCHAEA; BIODIVERSITY; CLUSTER ANALYSIS; DNA FINGERPRINTING; DNA, ARCHAEAL; DNA, RIBOSOMAL; GENES, RRNA; HOUSING, ANIMAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, ARCHAEAL; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; SWINE;

ARCHAEA; METHANOSPHAERA STADTMANAE; SUIDAE;

EID: 69449102372     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.00726-09     Document Type: Article

References (27)

1. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
2. Amann, R. I., W. Ludwig, and K.-H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
3. Baker, G. C., J. J. Smith, and D. A. Cowan. 2003. Review and re-analysis of domain-specific 16S primers. J. Microbiol. Methods 55:541-555.
4. Brodie, E. L., T. Z. DeSantis, J. P. Parker, I. X. Zubietta, Y. M. Piceno, and G. L. Andersen. 2007. Urban aerosols harbor diverse and dynamic bacterial populations. Proc. Natl. Acad. Sci. USA 104:299-304.
5. Cole, J. R., B. Chai, T. L. Marsh, R. J. Farris, Q. Wang, S. A. Kulam, S. Chandra, D. M. McGarrell, T. M. Schmidt, G. M. Garrity, and J. M. Tiedje. 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.
6. Crook, B., J. F. Robertson, S. A. Glass, E. M. Botheroyd, J. Lacey, and M. D. Topping. 1991. Airborne dust, ammonia, microorganisms, and antigens in pig confinement houses and the respiratory health of exposed farm workers. Am. Ind. Hyg. Assoc. J. 52:271-279.
7. Duchaine, C., Y. Grimard, and C. Cormier. 2000. Influence of building maintenance, environmental factors, and seasons on airborne contaminants of swine confinement buildings. Am. Ind. Hyg. Assoc. J. 61:56.
8. Elberson, M. A., and K. R. Sowers. 1997. Isolation of an aceticlastic strain of Methanosarcina siciliae from marine canyon sediments and emendation of the species description for Methanosarcina siciliae. Int. J. Syst. Bacteriol. 47:1258-1261.
9. Godon, J.-J., E. Zumstein, P. Dabert, F. Habouzit, and R. Moletta. 1997. Molecular microbial diversity of an anaerobic digestor as determined by smallsubunit rDNA sequence analysis. Appl. Environ. Microbiol. 63:2802-2813.
10. Jurgens, G., K. Lindstrom, and A. Saano. 1997. Novel group within the kingdom Crenarchaeota from boreal forest soil. Appl. Environ. Microbiol. 63:803-805.
11. Kim, K. Y., H. J. Ko, H. T. Kim, Y. S. Kim, Y. M. Roh, and C. N. Kim. 2007. Effect of ventilation rate on gradient of aerial contaminants in the confinement pig building. Environ. Res. 103:352-357.
12. Lane, D. J. 1991. 16S/23S rRNA sequencing, p. 115-175. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. Wiley, Chichester, United Kingdom.
13. Leser, T. D., J. Z. Amenuvor, T. K. Jensen, R. H. Lindecrona, M. Boye, and K. Moller. 2002. Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited. Appl. Environ. Microbiol. 68:673-690.
14. Ludwig, W., O. Strunk, R. Westram, L. Richter, H. Meier, Yadhukumar, A. Buchner, T. Lai, S. Steppi, G. Jobb, W. Förster, I. Brettske, S. Gerber, A. W. Ginhart, O. Gross, S. Grumann, M. May, B. Nonhoff, B. Reichel, R. Strehlow, A. Stamatakis, N. Stuckmann, A. Vilbig, M. Lenke, T. Ludwig, A. Bode, and K.-H. Schleifer. 2004. ARB: a software environment for sequence data. Nucleic Acids Res. 32:1363-1371. (Pubitemid 38854737)
15. Maron, P. A., D. P. H. Lejon, E. Carvalho, K. Bizet, P. Lemanceau, L. Ranjard, and C. Mougel. 2005. Assessing genetic structure and diversity of airborne bacterial communities by DNA fingerprinting and 16S rDNA clone library. Atmos. Environ. 39:3687-3695.
16. Miller, T. L., and M. J. Wolin. 1985. Methanosphaera stadtmanae gen. nov., sp. nov.: a species that forms methane by reducing methanol with hydrogen. Arch. Microbiol. 141:116-122.
17. Moletta, M., J. P. Delgenes, and J. J. Godon. 2007. Differences in the aerosolization behavior of microorganisms as revealed through their transport by biogas. Sci. Total Environ. 379:75-88.
18. Muyzer, G. 1999. DGGE/TGGE a method for identifying genes from natural ecosystems. Curr. Opin. Microbiol. 2:317-322.
19. Muyzer, G., E. C. De Waal, and A. G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59:695-700.
20. Nehme, B., V. Létourneau, R. J. Forster, M. Veillette, and C. Duchaine. 2008. Culture-independent approach of the bacterial bioaerosol diversity in the standard swine confinement buildings, and assessment of the seasonal effect. Environ. Microbiol. 10:665-675.
21. Ovreas, L., L. Forney, F. L. Daae, and V. Torsvik. 1997. Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl. Environ. Microbiol. 63:3367-3373.
22. Snell-Castro, R., J. J. Godon, J. P. Delgenes, and P. Dabert. 2005. Characterisation of the microbial diversity in a pig manure storage pit using small subunit rDNA sequence analysis. FEMS Microbiol. Ecol. 52:229-242.
23. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
24. Thorne, P. S., and C. Duchaine. 2007. Airborne bacteria and endotoxin, p. 989-1004. In C. J. Hurst, R. M. Crawford, J. L. Garland, D. A. Lipson, A. L. Mills, and L. D. Stetzenbach (ed.), Manual of environmental microbiology, 3rd ed. ASM Press, Washington, DC.
25. Whitehead, T. R., and M. A. Cotta. 1999. Phylogenetic diversity of methanogenic archaea in swine waste storage pits. FEMS Microbiol. Lett. 179:223-226.
26. Whitford, M., R. Teather, and R. Forster. 2001. Phylogenetic analysis of methanogens from the bovine rumen. BMC Microbiol. 1:5. (Pubitemid 38904587)
27. Yu, Y., C. Lee, J. Kim, and S. Hwang. 2005. Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction. Biotechnol. Bioeng. 89:670-679.