Comparison of DNA- and RNA-based bacterial community  structures in soil exposed to 2,4-dichlorophenol.
OBJECTIVE
To examine the effect of the pollutant 2,4-dichlorophenol on DNA- and RNA-based bacterial communities in soil.


RESULTS
Soil was exposed to 100 mg kg(-1) of 2,4-dichlorophenol (2,4-DCP), and degradation was monitored over 35 days. DNA and RNA were coextracted, and terminal restriction fragment length polymorphism (T-RFLP) was used to report changes in bacterial communities in response to the presence of the chlorophenol. The phylogenetic composition of the soil during degradation was determined by creating a clone library of amplified 16S rRNA sequences from both DNA and reverse-transcribed RNA from exposed soil. Resulting clones were sequenced, and putative identities were assigned.


CONCLUSIONS
A significant difference between active (RNA-based) and total (DNA-based) bacterial community structure was observed for both T-RFLP and phylogenetic analyses in response to 2,4-DCP, with more pronounced changes seen in RNA-based communities. Phylogenetic analysis indicated the dominance of Proteobacteria in both profiles.


CONCLUSIONS
This study describes the response of soil bacterial communities to the addition of the xenobiotic compound 2,4-DCP, and highlights the importance of including RNA-based 16S rRNA analysis to complement any molecular study in a perturbed soil.
Lillis
L
L
School of Biology and Environmental Science, University College Dublin, Belfield, Dublin, Ireland. lorraine.lillis@ucd.ie
Doyle
E
E
Clipson
N
N
D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D001673:Biodegradation, Environmental; D044822:Biodiversity; D002733:Chlorophenols / Q000494:pharmacology*; D004269:DNA, Bacterial / Q000235:genetics*; D054892:Metagenome / Q000187:drug effects*; D008969:Molecular Sequence Data; D012150:Polymorphism, Restriction Fragment Length; D012329:RNA, Bacterial / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012988:Soil Microbiology; D012989:Soil Pollutants / Q000494:pharmacology*
D002733:Chlorophenols; D004269:DNA, Bacterial; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D012989:Soil Pollutants; C004762:2,4-dichlorophenol