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

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.