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Soil contamination alters the willow root and rhizosphere metatranscriptome and the root–rhizosphere interactome

The ISME Journalvolume 12pages869884 (2018) | Download Citation


Phytoremediation using willows is thought to be a sustainable alternative to traditional remediation techniques involving excavation, transport, and landfilling. However, the complexity of the interaction between the willow and its associated highly diverse microbial communities makes the optimization of phytoremediation very difficult. Here, we have sequenced the rhizosphere metatranscriptome of four willow species and the plant root metatranscriptome for two willow species growing in petroleum hydrocarbon-contaminated and non-contaminated soils on a former petroleum refinery site. Significant differences in the abundance of transcripts related to different bacterial and fungal taxa were observed between willow species, mostly in contaminated soils. When comparing transcript abundance in contaminated vs. non-contaminated soil for each willow species individually, transcripts for many microbial taxa and functions were significantly more abundant in contaminated rhizosphere soil for Salix eriocephala, S. miyabeana and S. purpurea, in contrast to what was observed in the rhizosphere of S. caprea. This agrees with the previously reported sensitivity of S. caprea to contamination, and the superior tolerance of S. miyabeana and S. purpurea to soil contamination at that site. The root metatranscriptomes of two species were compared and revealed that plants transcripts are mainly influenced by willow species, while microbial transcripts mainly responded to contamination. A comparison of the rhizosphere and root metatranscriptomes in the S. purpurea species revealed a complete reorganization of the linkages between root and rhizosphere pathways when comparing willows growing in contaminated and non-contaminated soils, mainly because of large shifts in the rhizosphere metatranscriptome.

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  1. 1.

    Pulford I, Watson C. Phytoremediation of heavy metal-contaminated land by trees—a review. Environ Int. 2003;29:529–40.

  2. 2.

    Newsholme C. Willows: the genus Salix. Portland: Timber Press; 2003. p. 256.

  3. 3.

    Leigh MB, Prouzova P, Mackova M, Macek T, Nagle DP, Fletcher JS. Polychlorinated biphenyl (PCB)-degrading bacteria associated with trees in a PCB-contaminated site. Appl Environ Microbiol. 2006;72:2331–42.

  4. 4.

    El Amrani A, Dumas A-S, Wick LY, Yergeau E, Berthomé R. “Omics” insights into PAH degradation toward improved green remediation biotechnologies. Environ Sci Technol. 2015;49:11281–91.

  5. 5.

    Bell TH, Pitre FE, Joly S, Yergeau E. Increasing phytoremediation efficiency and reliability using novel ‘omics approaches. Trends Biotechnol. 2014;32:271–80.

  6. 6.

    Gonzalez E, Brereton NJ, Marleau J, Nissim WG, Labrecque M, Pitre FE, et al. Meta-transcriptomics indicates biotic cross-tolerance in willow trees cultivated on petroleum hydrocarbon contaminated soil. BMC Plant Biol. 2015;15:1.

  7. 7.

    Gonzalez E, Pitre F, Pagé A, Marleau J, Guidi Nissim W, St-Arnaud M et al. Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination. Microbiome. 2017 (in revision).

  8. 8.

    Yergeau E, Sanschagrin S, Maynard C, St-Arnaud M, Greer CW. Microbial expression profiles in the rhizosphere of willows depend on soil contamination. ISME J. 2014;8:344–58.

  9. 9.

    Pagé AP, Yergeau É, Greer CW. Salix purpurea stimulates the expression of specific bacterial xenobiotic degradation genes in a soil contaminated with hydrocarbons. PLoS ONE. 2015;10:e0132062.

  10. 10.

    Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, et al. Defining the core Arabidopsis thaliana root microbiome. Nature. 2012;488:86–90.

  11. 11.

    Pérez-Jaramillo JE, Carrión VJ, Bosse M, Ferrão LF, Hollander Md, Garcia AA et al. Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits. ISME J. 2017;11:2244–57.

  12. 12.

    Bulgarelli D, Garrido-Oter R, Münch PC, Weiman A, Dröge J, Pan Y, et al. Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell Host Microbe. 2015;17:392–403.

  13. 13.

    Tardif S, Yergeau É, Tremblay J, Legendre P, Whyte LG, Greer CW. The willow microbiome is influenced by soil petroleum-hydrocarbon concentration with plant compartment-specific effects. Front Microbiol. 2016;7:1363.

  14. 14.

    Hassan SE-D, Bell TH, Stefani FOP, Denis D, Hijri M, St-Arnaud M. Contrasting the community structure of arbuscular mycorrhizal fungi from hydrocarbon-contaminated and uncontaminated soils following willow (Salix spp. L.) planting. PLoS ONE. 2014;9:e102838.

  15. 15.

    Bell TH, El-Din Hassan S, Lauron-Moreau A, Al-Otaibi F, Hijri M, Yergeau E, et al. Reduced linkage between bacterial and fungal rhizosphere communities in hydrocarbon-contaminated soils is related to plant phylogeny. ISME J. 2014;8:331–43.

  16. 16.

    Bell TH, Cloutier-Hurteau B, Al-Otaibi F, Turmel M-C, Yergeau E, Courchesne F, et al. Early rhizosphere microbiome composition is related to the growth and Zn uptake of willows introduced to a former landfill. Environ Microbiol. 2015;17:3025–38.

  17. 17.

    Brereton NJB, Gonzalez E, Marleau J, Guidi W, Labrecque M, Joly S, et al. Comparative transcriptomic approaches exploring contamination stress tolerance in Salix sp. reveal the importance for a metaorganismal de novo assembly approach for non-model plants. Plant Physiol. 2016;171:3–24.

  18. 18.

    Grenier V, Pitre FE, Nissim WG, Labrecque M. Genotypic differences explain most of the response of willow cultivars to petroleum-contaminated soil. Trees. 2015;29:871–81.

  19. 19.

    Yergeau E, Bell TH, Champagne J, Maynard C, Tardif S, Tremblay J, et al. Transplanting soil microbiomes leads to lasting effects on willow growth, but not on the rhizosphere microbiome. Front Microbiol. 2015;6:1436.

  20. 20.

    Gambino G, Perrone I, Gribaudo I. A rapid and effective method for RNA extraction from different tissues of grapevine and other woody plants. Phytochem Anal. 2008;19:520–5.

  21. 21.

    Yergeau E, Bokhorst S, Huiskes AHL, Boschker HTS, Aerts R, Kowalchuk GA. Size and structure of bacterial, fungal and nematode communities along an Antarctic environmental gradient. FEMS Microbiol Ecol. 2007;59:436–51.

  22. 22.

    Yergeau E, Kowalchuk GA. Responses of Antarctic soil microbial communities and associated functions to temperature and freeze-thaw cycle frequency. Environ Microbiol. 2008;10:2223–35.

  23. 23.

    Dorsch M, Stackebrandt E. Some modifications in the procedure of direct sequencing of PCR amplified 16S rDNA. J Microbiol Methods. 1992;16:271–9.

  24. 24.

    Tremblay J, Yergeau E, Fortin N, Cobanli S, Elias M, King TL, et al. Chemical dispersants enhance the activity of oil- and gas condensate-degrading marine bacteria. ISME J. 2017;11:2793–808.

  25. 25.

    Huntemann M, Ivanova NN, Mavromatis K, Tripp HJ, Paez-Espino D, Tennessen K, et al. The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v. 4). Stand Genomic Sci. 2016;11:17.

  26. 26.

    Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139–40.

  27. 27.

    Moran MA, Satinsky B, Gifford SM, Luo H, Rivers A, Chan LK, et al. Sizing up metatranscriptomics. ISME J. 2013;7:237–43.

  28. 28.

    Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486:207.

  29. 29.

    Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, et al. A core gut microbiome in obese and lean twins. Nature. 2009;457:480–4.

  30. 30.

    Siciliano SD, Germida JJ, Banks K, Greer CW. Changes in microbial community composition and function during a polyaromatic hydrocarbon phytoremediation field trial. Appl Environ Microbiol. 2003;69:483–9.

  31. 31.

    Jones DL, Hodge A, Kuzyakov Y. Plant and mycorrhizal regulation of rhizodeposition. New Phytol. 2004;163:459–80.

  32. 32.

    Karst J, Gaster J, Wiley E, Landhäusser SM. Stress differentially causes roots of tree seedlings to exude carbon. Tree Physiol. 2017;37:154–64.

  33. 33.

    Naik D, Smith E, Cumming JR. Rhizosphere carbon deposition, oxidative stress and nutritional changes in two poplar species exposed to aluminum. Tree Physiol. 2009;29:423–36.

  34. 34.

    Qin R, Hirano Y, Brunner I. Exudation of organic acid anions from poplar roots after exposure to Al, Cu and Zn. Tree Physiol. 2007;27:313–20.

  35. 35.

    Esperschutz J, Pritsch K, Gattinger A, Welzl G, Haesler F, Buegger F, et al. Influence of chronic ozone stress on carbon translocation pattern into rhizosphere microbial communities of beech trees (Fagus sylvatica L.) during a growing season. Plant Soil. 2009;323:85–95.

  36. 36.

    Jayne B, Quigley M. Influence of arbuscular mycorrhiza on growth and reproductive response of plants under water deficit: a meta-analysis. Mycorrhiza. 2014;24:109–19.

  37. 37.

    Glassman SI, Casper BB. Biotic contexts alter metal sequestration and AMF effects on plant growth in soils polluted with heavy metals. Ecology. 2012;93:1550–9.

  38. 38.

    Badri DV, Weir TL, van der Lelie D, Vivanco JM. Rhizosphere chemical dialogues: plant–microbe interactions. Curr Opin Biotechnol. 2009;20:642–50.

  39. 39.

    Haichar FeZ, Marol C, Berge O, Rangel-Castro JI, Prosser JI, Balesdent J, et al. Plant host habitat and root exudates shape soil bacterial community structure. ISME J. 2008;2:1221–30.

  40. 40.

    Berg G, Zachow C, Lottmann J, Gotz M, Costa R, Smalla K. Impact of plant species and site on rhizosphere-associated fungi antagonistic to Verticillium dahliae Kleb. Appl Environ Microbiol. 2005;71:4203–13.

  41. 41.

    Kowalchuk GA, Buma DS, de Boer W, Klinkhamer PGL, van Veen JA. Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms. Antonie Van Leeuwenhoek. 2002;81:509–20.

  42. 42.

    Smalla K, Wieland G, Buchner A, Zock A, Parzy J, Kaiser S, et al. Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Appl Environ Microbiol. 2001;67:4742–51.

  43. 43.

    Fletcher JS, Hegde RS. Release of phenols by perennial plant roots and their potential importance in bioremediation. Chemosphere. 1995;31:3009–16.

  44. 44.

    Haby PA, Crowley DE. Biodegradation of 3-chlorobenzoate as affected by rhizodeposition and selected carbon substrates. J Environ Qual. 1996;25:304–10.

  45. 45.

    Isidorov V, Jdanova M. Volatile organic compounds from leaves litter. Chemosphere. 2002;48:975–9.

  46. 46.

    Miya RK, Firestone MK. Enhanced phenanthrene biodegradation in soil by slender oat root exudates and root debris. J Environ Qual. 2001;30:1911–8.

  47. 47.

    Donnelly PK, Hegde RS, Fletcher JS. Growth of PCB-degrading bacteria on compounds from photosynthetic plants. Chemosphere. 1994;28:981–8.

  48. 48.

    Zilber-Rosenberg I, Rosenberg E. Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. FEMS Microbiol Rev. 2008;32:723–35.

  49. 49.

    Rosenberg E, Zilber-Rosenberg I. Microbes drive evolution of animals and plants: the hologenome concept. mBio. 2016;7:e01395–15.

  50. 50.

    Bordenstein SR, Theis KR. Host biology in light of the microbiome: ten principles of holobionts and hologenomes. PLoS Biol. 2015;13:e1002226.

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This project was funded by the Genome Canada and Genome Québec (2010 Large-Scale Applied Research Project Competition grant 2510). Data analyses were carried out on Compute Canada’s infrastructure through EY resource allocation (2016 Resource Allocation competition). Danielle Ouellette and Julie Marleau are gratefully acknowledged for technical assistance. Pétromont is gratefully acknowledged for allowing us access to their site to carry out our field experiment.

Author information


  1. Centre INRS-Institut Armand-Frappier, Institut National de la Recherche Scientifique, Université du Québec, Laval, QC, Canada

    • Etienne Yergeau
  2. National Research Council Canada, Energy, Mining and Environment, Montréal, QC, Canada

    • Julien Tremblay
    • , Christine Maynard
    •  & Charles W. Greer
  3. Institut de recherche en biologie végétale, Jardin botanique de Montréal et Université de Montréal, Montréal, QC, Canada

    • Simon Joly
    • , Michel Labrecque
    • , Frederic E. Pitre
    •  & Marc St-Arnaud


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The authors declare that they have no conflict of interest.

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Correspondence to Etienne Yergeau.

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