Comparative metatranscriptomics reveals widespread community responses during phenanthrene degradation in soil
Article first published online: 25 MAY 2012
© 2012 Society for Applied Microbiology and Blackwell Publishing Ltd
Special Issue: Microbial Communities - Structure, Behaviour, Evolution
Volume 14, Issue 9, pages 2577–2588, September 2012
How to Cite
de Menezes, A., Clipson, N. and Doyle, E. (2012), Comparative metatranscriptomics reveals widespread community responses during phenanthrene degradation in soil. Environmental Microbiology, 14: 2577–2588. doi: 10.1111/j.1462-2920.2012.02781.x
- Issue published online: 4 SEP 2012
- Article first published online: 25 MAY 2012
- Received 16 January, 2012; revised 23 March, 2012; accepted 24 April, 2012.
Soil microbial community response to phenanthrene was evaluated by metatranscriptomics. A marked increase in transcripts involved in aromatic compound metabolism, respiration and stress responses, and concurrent decreases in virulence, carbohydrate, DNA metabolism and phosphorus metabolism transcripts was revealed. Phenanthrene addition led to a 1.8-fold to 33-fold increase in the abundance of dioxygenase, stress response and detoxification transcripts, whereas those of general metabolism were little affected. Heavy metal P-type ATPases and thioredoxin transcripts were more abundant in the phenanthrene-amended soil, and this is the first time these proteins have been associated with polycyclic aromatic hydrocarbon (PAH) stress in microorganisms. Annotation with custom databases constructed with bacterial or fungal PAH metabolism protein sequences showed that increases in PAH-degradatory gene expression occurred for all gene groups investigated. Taxonomic determination of mRNA transcripts showed widespread changes in the bacteria, archaea and fungi, and the actinobacteria were responsible for most of the de novo expression of transcripts associated with dioxygenases, stress response and detoxification genes. This is the first report of an experimental metatranscriptomic study detailing microbial community responses to a pollutant in soil, and offers information on novel in situ effects of PAHs on soil microbes that can be explored further.