Metatranscriptomics of contaminated soil
The microbial response to the polycyclic aromatic hydrocarbon Phenanthrene in soil was evaluated by 454 sequencing of extracted RNA. SEED subsystem annotation showed a marked increase in transcripts involved in aromatic compound metabolism, respiration, stress responses and amino acid metabolism, and concurrent decreases in virulence, motility, chemotaxis, carbohydrate and DNA metabolism transcripts. Annotation based on the NCBI Refseq database showed that phenanthrene addition led to an increase of 1.8 - 33 fold in the abundance of dioxygenase, stress response and detoxification transcripts, whereas those of general metabolism were little affected. Heavy Metal P-type ATPases transcripts were significantly more abundant in the phenanthrene-amended soil, and this is the first time these proteins were associated with 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. Taxonomic identity of the most abundant transcript groups revealed that the actinobacteria were responsible for most of the de novo expression of 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 in soil microbes that can be explored further. |  |  | |