Salix purpurea Stimulates the Expression of Specific Bacterial Xenobiotic Degradation Genes in a Soil Contaminated with Hydrocarbons

Abstract

The objectives of this study were to uncover Salix purpurea-microbe xenobiotic degradation systems that could be harnessed in rhizoremediation, and to identify microorganisms that are likely involved in these partnerships. To do so, we tested S. purpurea's ability to stimulate the expression of 10 marker microbial oxygenase genes in a soil contaminated with hydrocarbons. In what appeared to be a detoxification rhizosphere effect, transcripts encoding for alkane 1-monooxygenases, cytochrome P450 monooxygenases, laccase/polyphenol oxidases, and biphenyl 2,3-dioxygenase small subunits were significantly more abundant in the vicinity of the plant's roots than in bulk soil. This gene expression induction is consistent with willows' known rhizoremediation capabilities, and suggests the existence of S. purpurea-microbe systems that target many organic contaminants of interest (i.e. C4-C16 alkanes, fluoranthene, anthracene, benzo(a)pyrene, biphenyl, polychlorinated biphenyls). An enhanced expression of the 4 genes was also observed within the bacterial orders Actinomycetales, Rhodospirillales, Burkholderiales, Alteromonadales, Solirubrobacterales, Caulobacterales, and Rhizobiales, which suggest that members of these taxa are active participants in the exposed partnerships. Although the expression of the other 6 marker genes did not appear to be stimulated by the plant at the community level, signs of additional systems that rest on their expression by members of the orders Solirubrobacterales, Sphingomonadales, Actinomycetales, and Sphingobacteriales were observed. Our study presents the first transcriptomics-based identification of microbes whose xenobiotic degradation activity in soil appears stimulated by a plant. It paints a portrait that contrasts with the current views on these consortia's composition, and opens the door for the development of laboratory test models geared towards the identification of root exudate characteristics that limit the efficiency of current willow-based rhizoremediation applications.

Fig 1. Global influence of S. purpurea on marker microbial gene expression.

Two-dimensional solutions to ordinations, conducted using the non-metric multidimensional scaling (NMDS) method, of global microbial oxygenase transcript abundances measured in bulk contaminated soil samples (brown crosses and shaded areas) and rhizosphere soil samples (green crosses and shaded areas). A) Microbial community-wide expression of the 10 selected genes. B) Taxonomically resolved expression of the 10 selected genes (70 gene-taxon combinations).

Fig 2. Gene-specific assessment of S. purpurea’s influence.

Community-wide transcript abundance of selected microbial oxygenase genes in bulk and rhizosphere soil samples.

Fig 3. Taxonomically resolved assessment of S. purpurea’s influence.

Transcript abundance of identified gene-taxon combinations in bulk and rhizosphere soil samples.