Discrimination of shifts in a soil microbial community assosciated with TNT-contamination using a functional ANOVA of 16S rRNA hybridized to oligonucleotide microarrays
Eyers, Laurent; Smoot, James C.; Smoot, Laura M.et al.
2006 • In Environmental Science and Technology, 40, p. 5867-5873
[en] A functional ANOVA analysis of the thermal dissociation
of RNA hybridized to DNA microarrays was used to
improve discrimination between two soil microbial
communities. Following hybridization of in vitro transcribed
16S rRNA derived from uncontaminated and 2,4,6-
trinitrotoluene contaminated soils to an oligonucleotide
microarray containing group- and species-specific perfect
match (PM) probes and mismatch (MM) variants, thermal
dissociation was used to analyze the nucleic acid bound to
each PM-MM probe set. Functional ANOVA of the
dissociation curves generally discriminated PM-MM probe
sets when Td values (temperature at 50% probe-target
dissociation) could not. Maximum discrimination for many
PM and MM probes often occurred at temperatures
greater than theTd. Comparison of signal intensities measured
prior to dissociation analysis from hybridizations of the
two soil samples revealed significant differences in domain-,
group-, and species-specific probes. Functional ANOVA
showed significantly different dissociation curves for 11 PM
probes when hybridizations from the two soil samples
were compared, even though initial signal intensities for 3
of the 11 did not vary.
Disciplines :
Environmental sciences & ecology
Author, co-author :
Eyers, Laurent; University o Louvain > Unit of Bioengineering and Institute of Statistics
Smoot, James C.
Smoot, Laura M.
Bugli, Céline
Urakawa, Hidetoshi
McMurry, Zack
Siripong, Slil
El Fantroussi, Said
Lambert, Philippe ; Université de Liège - ULiège > Institut des sciences humaines et sociales > Méthodes quantitatives en sciences sociales
Agathos, Spiros N.
Stahl, David A.
Language :
English
Title :
Discrimination of shifts in a soil microbial community assosciated with TNT-contamination using a functional ANOVA of 16S rRNA hybridized to oligonucleotide microarrays
Publication date :
2006
Journal title :
Environmental Science and Technology
ISSN :
0013-936X
eISSN :
1520-5851
Publisher :
American Chemical Society, Washington, United States - District of Columbia
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.
Zhou, J. Microarrays for bacterial detection and microbial community analysis. Curr. Opin. Microbiol. 2003, 6, 288-294.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Esteve-Nunez, A.; Ramos, J. L. Metabolism of 2,4,6-trinitro-toluene by Pseudomonas sp. JLR11. Environ. Sci. Technol. 1998, 32, 3802-3808.
Maniatis, T.; Fritsch, E. F.; Sambrook, J. Molecular Cloning: A Laboratory Manual; Cold Spring Harbor Laboratory Press: New York, 1982.
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.
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.
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.
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.
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.
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.
Polz, M. F.; Cavanaugh, C. M. Bias in template-to-product ratios in multitemplate PCR. Appl. Environ. Microbiol. 1998, 64, 3724-3730.
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.
