Discrimination of shifts in a soil microbial community associated with TNT-contamination using a functional ANOVA of 16S rRNA hybridized to oligonucleotide microarrays

Environmental Science and Technology

Volumn 40, Issue 19, 2006, Pages 5867-5873

  Eyers, Laurent ^a   Smoot, James C ^b   Smoot, Laura M ^b   Bugli, Céline ^a   Urakawa, Hidetoshi ^c   McMurry, Zack ^b   Siripong, Slil ^d   El Fantroussi, Said ^a   Lambert, Philippe ^a   Agathos, Spiros N ^a   Stahl, David A ^b  

^a UNIVERSITÉ CATHOLIQUE DE LOUVAIN   (Belgium)

^b UNIVERSITY OF WASHINGTON   (United States)

^c UNIVERSITY OF TOKYO   (Japan)

^d Northwestern University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANOVA ANALYSIS; HYBRIDIZATIONS; OLIGONUCLEOTIDE MICROARRAYS;

CONTAMINATION; MICROORGANISMS; OLIGOMERS; RNA; TOLUENE;

SOIL POLLUTION;

BACTERIAL DNA; BACTERIAL RNA; RNA 16S; TRINITROTOLUENE;

CONTAMINATION; MICROORGANISMS; OLIGOMERS; RNA; SOIL POLLUTION; TOLUENE;

ARRAY; CHEMICAL COMPOUND; DNA; HYBRIDIZATION; MICROBIAL COMMUNITY; RNA; SOIL MICROORGANISM;

ANALYSIS OF VARIANCE; ARTICLE; BACTERIUM DETECTION; BACTERIUM IDENTIFICATION; DNA MICROARRAY; DNA PROBE; NONHUMAN; RNA HYBRIDIZATION; SOIL MICROFLORA; SOIL POLLUTION;

ANALYSIS OF VARIANCE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PSEUDOMONAS PUTIDA; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SOIL MICROBIOLOGY; SOIL POLLUTANTS; TRINITROTOLUENE;

EID: 33749395359     PISSN: 0013936X     EISSN: None     Source Type: Journal    
DOI: 10.1021/es0609093     Document Type: Article

References (21)

1. Keramas, G.; Bang, D. D.; Lund, M.; Madsen, M.; Rasmussen, S. E.; Bunkenborg, H.; Telleman, P.; Christensen, C. B. V. Development of a sensitive DNA microarray suitable for rapid detection of Campylobacter spp. Mol. Cell. Probes 2003, 17, 187-196.
2. Zhou, J. Microarrays for bacterial detection and microbial community analysis. Curr. Opin. Microbiol. 2003, 6, 288-294.
3. Loy, A.; Lehner, A.; Lee, N.; Adamczyk, J.; Meier, H.; Ernst, J.; Schleifer, K.; Wagner, M. Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl. Environ. Microbiol. 2002, 68, 5064-5081.
4. Small, J.; Call, D. R.; Brockman, F. J.; Straub, T. M.; Chandler, T. M. Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays. Appl. Environ. Microbiol. 2001, 67, 4708-4716.
5. Wang, R. F.; Beggs, M. L.; Robertson, L. A.; Cerniglia, C. E. Design and evaluation of oligonucleotide-microarray method for the detection of human intestinal bacteria in fecal samples. FEMS Microbiol. Ecol. 2002, 213, 175-182.
6. El Fantroussi, S.; Urakawa, H.; Bernhard, A. E.; Kelly, J. J.; Noble, P. A.; Smidt, H.; Yershov, G. M.; Stahl, D. A. Direct profiling of environmental microbial populations by thermal dissociation analysis of native rRNAs hybridized to oligonucleotide microarrays. Appl. Environ. Microbiol. 2003, 69, 2377-2382.
7. Reyes-Lopez, M. A.; Mendez-Tenorio, A.; Maldonado-Rodriguez, R.; Doktycz, M. J.; Fleming, J. T.; Beattie, K. L. Fingerprinting of prokaryotic 16S rRNA genes using oligodeoxyribonucleotide microarrays and virtual hybridization. Nucleic Acids Res. 2003, 31, 779-789.
8. Liu, W. T.; Mirzabekov, A. D.; Stahl, D. A. Optimization of an oligonucleotide microchip for microbial identification studies: a non-equilibrium dissociation approach. Environ. Microbiol. 2001, 3, 619-629.
9. Urakawa, H.; El Fantroussi, S.; Smidt, H.; Smoot, J. C.; Tribou, E. H.; Kelly, J. J.; Noble, P.A.; Stahl, D. A. Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays. Appl. Environ. Microbiol. 2003, 69, 2848-2856.
10. Fuller, M. E.; Manning, J. F. Evidence for differential effects of 2,4,6-trinitrotoluene and other munitions compounds on specific subpopulations of soil microbial communities. Environ. Toxicol. Chem. 1998, 17, 2185-2195.
11. Eyers, L.; Stenuit, B.; El Fantroussi, S.; Agathos, S. N. Microbial ecology of TNT-contaminated soils and anaerobic TNT biodegradation processes. In Proceedings of the 103rd general meeting of the American Society for Microbiology; Washington, DC, 2003.
12. Esteve-Nunez, A.; Ramos, J. L. Metabolism of 2,4,6-trinitro-toluene by Pseudomonas sp. JLR11. Environ. Sci. Technol. 1998, 32, 3802-3808.
13. Maniatis, T.; Fritsch, E. F.; Sambrook, J. Molecular Cloning: A Laboratory Manual; Cold Spring Harbor Laboratory Press: New York, 1982.
14. Bavykin, S. G.; Akowski, J. P.; Zakhariev, V. M.; Barsky, V. E.; Perov, A. N.; Mirzabekov, A. D. Portable system for microbial sample preparation and oligonucleotide microarray analysis. Appl. Environ. Microbiol 2001, 67, 922-928.
15. Bugli, C.; Lambert, P. Functional ANOVA with random functional effects: an application to event-related potentials modelling for electroencephalograms analysis. Stat. Med. 2006, in press.
16. Hacia, J. G.; Brody, L. C.; Chee, M. S.; Fodor, M. S.; Collins, F. S. Detection of heterozygous mutations in BRCA1 using high density oligonucleotides arrays and two-colour fluorescent analysis. Nat. Genet. 1996, 14, 441-447.
17. Pozhitkov, A.; Chernov, B.; Yershov, G.; Noble, P. A. Evaluation of gel-pad oligonucleotide microarray technology by using artificial neural networks. Appl. Environ. Microbiol. 2005, 71, 8663-8676.
18. White, A. M.; Daly, D. S.; Willse, A. R.; Protic, M.; Chandler, D. P. Automated microarray image analysis toolbox for matlab. Bioinformatics 2005, 21, 3578-3579.
19. Suzuki, M. T.; Giovannoni, S. J. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 1996, 62, 625-630.
20. Polz, M. F.; Cavanaugh, C. M. Bias in template-to-product ratios in multitemplate PCR. Appl. Environ. Microbiol. 1998, 64, 3724-3730.
21. Fuller, M. E.; Manning, J. F. Aerobic Gram-positive and Gram-negative bacteria exhibit differential sensitivity to and transformation of 2,4,6-trinitrotoluene (TNT). Curr. Microbiol. 1997, 35, 77-83.