Dr. Franck Stefani

Image Franck Stefani
Research scientist
  • Curator of the Canadian Collection of Arbuscular Mycorrhizal Fungi (CCAMF)
  • Soil microbiome and numerical ecology
  • Taxonomy, systematics and genetics of arbuscular mycorrhizal fungi
  • In vivo and in vitro cultures of arbuscular mycorrhizal fungi

Current research and/or projects

The research carried out in the Mycorrhizal Symbiosis Laboratory aims to improve knowledge of the soil microbiome in general and of the diversity of arbuscular mycorrhizal fungi in particular, and to understand how to maximise their benefits to plants and soil fertility. To achieve these research objectives, laboratory activities are carried out by AAFC technicians Dr. Lobna Abdellatif and Claudia Banchini, and PhD student Simon Thériault (co-supervision Prof. M. Hijri - Université de Montréal). The team also manages the Canadian Collection of Arbuscular Mycorrhizal Fungi (CCAMF). In the long term, this research program will contribute to the transition to sustainable agriculture.


Lab alumni: 

PDF: Dr Vasilis Kokkoris 2018-2020 (co-supervision Dr J. Dettman - AAFC and prof. N. Corradi - UOttawa)

Master students: 

  • Dane Goh 2018-2021 (co-supervision prof. A MacLean - UOttawa)
  • Louis Paré 2019-2022 (co-supervision prof. L. Bernier  - ULaval)

PhD student:

  • Jean-Marc Kyalamakasa Kaumbu (co-supervision prof. Damase P. Khasa - ULaval)

Research and/or project statements

  • Stefani F / Canadian Government, Departmental A-base funding / Canadian Survey of Soil Biodiversity / $ 450K / 2021-2024.
  • Hambleton S / Canadian Government, Departmental A-base funding / Fungal and Bacterial Biosystematics - bridging taxonomy and “omics” technology in agricultural research and regulation/ $ 3,000K / 2019-2025. Stefani: participant, responsible for objective "Taxonomy, molecular systematics and metagenomics of arbuscular mycorrhizal fungi".
  • Lybaert A / Canadian Government, Departmental A-base funding / Management and enhancement of AAFC's biological collections / $ 3,000K / 2019-2025. Stefani: participant, curator of the Canadian collection of Arbuscular Mycorrhizal Fungi (CCAMF).


  1. Stefani F, Beguin J, Paré D, Morency M-J, Martineau C, Fortin JA, Thiffault N, Séguin A. 2023. Does wood mulch trigger microbially mediated positive plant-soil feedback in degraded boreal forest sites? A post hoc study. Front Plant Sci 14, 1122445. https://doi.org/10.3389/fmicb.2022.937912

  2. Paré L, Banchini C, Hamel C, Bernier L, Stefani F. 2022. A simple and low-cost technique to initiate single-spore cultures of arbuscular mycorrhizal fungi using a superabsorbent polymer. Symbiosis 88:61–73. https://doi.org/10.1007/s13199-022-00878-5

  3. Goh D, Martin JGA, Banchini C, MacLean AM, Stefani F. 2022. RocTest: A standardized method to assess the performance of root organ cultures in the propagation of arbuscular mycorrhizal fungi. Front Microbiol 13, 937912. https://doi.org/10.3389/fmicb.2022.937912

  4. Serghi EU, Kokkoris V, Cornell C, Dettman J, Stefani F, Corradi N. 2021. Homo- and Dikaryons of the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis Differ in Life History Strategy. Front Plant Sci 12, 715377. https://doi.org/10.3389/fpls.2021.715377

  5. Cornell C, Kokkoris V, Turcu B, Dettman J, Stefani F, Corradi N. (2021). The arbuscular mycorrhizal fungus Rhizophagus irregularis harmonizes nuclear dynamics in the presence of distinct abiotic factors. Fungal Genetics Biology 158, 103639. https://doi.org/10.1016/j.fgb.2021.103639

  6. Serghi EU, Kokkoris V, Cornell C, Dettman J, Stefani F, Corradi N. (2021). Homo- and dikaryons of the arbuscular mycorrhizal fungus Rhizophagus irregularis differ in life history strategy. Frontiers in Plant Science 12, 715377. https://doi.org/10.3389/fpls.2021.715377

  7. Savard M, Martineau C, Laganière J, Bégin C, Marion J, Smirnoff A, Stefani F, Bergeron J, Rheault K, Paré D, Séguin A. (2021). Nitrogen isotopes in the soil-to-tree continuum – Tree-rings express the soil biogeochemistry of boreal forests exposed to moderate airborne emissions. Science of the Total Environment 146581. https://doi.org/10.1016/j.scitotenv.2021.146581

  8. Kokkoris V, Chagnon P-L,Yildirir G, Clarke K, Goh D, MacLean A M, Dettman J, Stefani F, Corradi N. (2021). Host identity influences nuclear dynamics in arbuscular mycorrhizal fungi. Current Biology 31: 1-8. https://doi.org/10.1016/j.cub.2021.01.035

  9. Stefani F, Dupont S, Laterrière M, Knox R, Ruan Y, Hamel C, Hijri M. (2020). Similar arbuscular mycorrhizal fungal communities in 31 durum wheat cultivars (Triticum turgidum L. var. durum) under field conditions in eastern Canada. Frontiers in Plant Science 11: 1206. https://doi.org/10.3389/fpls.2020.01206

  10. Kokkoris V, Stefani F, Dalpé Y, Dettman J, Corradi N. (2020). Nuclear dynamics in the arbuscular mycorrhizal fungi. Trends in Plant Science  25(8): 765-778. https://doi.org/10.1016/j.tplants.2020.05.002

  11. Stefani F, Bencherif K, Sabourin S, Hadj-Sahraoui A, Banchini C, Séguin S, Dalpé Y. (2020). Taxonomic assignment of arbuscular mycorrhizal fungi in an 18S metagenomic dataset: a case study with saltcedar (Tamarix aphylla). Mycorrhiza 30: 243–255. https://doi.org/10.1007/s00572-020-00946-y

  12. Pacé M, Fenton NJ, Paré D, Stefani F, Massicotte HB, Tackaberry LE, Bergeron Y. (2018). Lichens contribute to open woodland stability in the boreal forest through detrimental effects on pine growth and root ectomycorrhizal development. Ecosystems 22(1): 189-201. https://doi.org/10.1007/s10021-018-0262-0

  13. Stefani F, Isabel N, Morency M-J, Lamothe M, Nadeau S, Lachance D, Li EHY, Greer C, Yergeau E, Pinno BD, Séguin A. (2018). The impact of reconstructed soils following oil sands exploitation on aspen and its associated belowground microbiome. Scientific Reports 8: 2761. https://doi.org/10.1038/s41598-018-20783-6

  14. Yu J, Baninasab B, Xu S, Tabori M, Zhang Y, Wang X, DeSchiffart I, Dalpé Y, Stefani F, Séguin S, Ma B, Xu C and Khanizadeh S. (2017). Effect of arbuscular mycorrhizal fungi on tolerance and growth of selected spring wheat (Triticum aestivum L.) lines under salinity stress. Journal of Food, Agriculture & Environment 15: 40–47. https://doi.org/10.1234/4.2017.5459

  15. Klopfenstein NB et al. (2017). Insights into the phylogeny of Northern Hemisphere Armillaria: Neighbor-net and Bayesian analyses of translation elongation factor 1-α gene sequences. Mycologia 109 (1): 75-91. http://doi.org/10.1080/00275514.2017.1286572

  16. Badri A, Stefani F, Lachance G, Roy-Arcand L, Beaudet D, Vialle A, Hijri M. (2016). Molecular diagnostic toolkit for Rhizophagus irregularis isolate DAOM- 197198 using quantitative PCR assay targeting the mitochondrial genome. Mycorrhiza 26 (7): 721-733. http://doi.org/10.1007/s00572-016-0708-1

  17. Bell TH, Stefani F, Abram K, Champagne J, Yergeau E, Hijri M, St-Arnaud M. (2016). A Diverse soil microbiome degrades more crude oil than specialized bacterial assemblages obtained in culture. Applied and Environmental Microbiology 82: 5530– 5541. http://doi.org/10.1128/AEM.01327-16

  18. Nadimi M, Stefani F, Hijri M. (2016). The large (134.9 kb) mitochondrial genome of the glomeromycete Funneliformis mosseae. Mycorrhiza 26 (7): 747-755. http://doi.org/10.1007/s00572-016-0710-7

  19. Stefani F, Klimaszewski J, Morency M-J, Blais M, Labrie P, Séguin S, Venier L. (2016). Diversity of fungal gut associates of rove beetles (Coleoptera: Staphylinidae) in boreal forest. Fungal Ecology 23: 164-171. https://doi.org/10.1016/j.funeco.2016.05.001

  20. Stefani F, Bell TH, Marchand C, de la Providencia IE, El Yassimi A, St- Arnaud M, Hijri M. (2015). Culture-dependent and independent methods capture different microbial community fractions in hydrocarbon-contaminated soils. PLoSONE, 10: e0128272, https://doi.org/10.1371/journal.pone.0128272

  21. de la Providencia IE, Stefani F, Labridy M, St-Arnaud M, Hijri M. (2015). Arbuscular mycorrhizal fungal diversity in an extreme petroleum hydrocarbon- polluted sedimentation basin. FEMS Microbiology Letters, 362 (12): fnv081. https://doi.org/10.1093/femsle/fnv081

  22. Chapman TF, May TW, Stefani F, Bougher NL, Robinson RM. (2015). Fungal hyphae of Coprinopsis found in a bilby (Macrotis lagotis) burrow spoil- mound. Australasian Mycologist 32: 6-9.

  23. Nadimi M, Stefani F, Hijri M. (2014). The mitochondrial genome of the glomeromycete Rhizophagus sp. DAOM 213198 reveals an unusual organization consisting of two circular chromosomes. Genome Biology and Evolution 7(1): 96–105. https://doi.org/10.1093/gbe/evu268

  24. Hassan SE, Bell TH, Stefani F, Denis D, Hijri M, St-Arnaud M. (2014). Contrasting the community structure of arbuscular mycorrhizal fungi from hydrocarbon- contaminated and uncontaminated soils following willow (Salix spp. L.) planting. PLoSONE 9: e102838. https://doi.org/10.1371/journal.pone.0102838

  25. Stefani F, RH Jones, TW May. (2013). Concordance of seven gene genealogies compared to phenotypic data reveals multiple cryptic species in Australian dermocyboid Cortinarius (Agaricales). Molecular Phylogenetics and Evolution 71: 249-260. https://doi.org/10.1016/j.ympev.2013.10.019

  26. Lamarche J, Stefani F, Séguin A, Hamelin RC. (2011). Impact of endochitinase transformed white spruce on soil fungal communities. FEMS Microbiology Ecology 76: 199-208. https://doi.org/10.1111/j.1574-6941.2011.01041.x

  27. Stefani F and Hamelin RC. (2010). The current state of genetically modified plant on target and non-target fungi. Environmental Reviews 18: 441-475. https://doi.org/10.1139/A10-022

  28. Stefani F, Sokolski S, Wurtz TL, Piché Y, Hamelin RC, Fortin JA, Bérubé JA. (2010). Morchella tomentosa: a unique belowground structure and a new clade of morels. Mycologia 102(5): 1082-1088. https://doi.org/10.3852/09-294

  29. Stefani F, Tanguay P, Piché Y and Hamelin RC. (2010). Impact of endochitinase transformed white spruce on soil fungal biomass and ectendomycorrhizal symbiosis. Applied and Environmental Microbiology 76(8): 2607-2614. https://doi.org/10.1128/AEM.02807-09

  30. Stefani F, Moncalvo J-M, Séguin A, Bérubé JA, Hamelin RC. (2009). Impact study of an 8-year-old transgenic poplar plantation on the ectomycorrhizal fungal community. Applied and Environmental Microbiology 75(23): 7527-7536. https://doi.org/10.1128/AEM.01120-09

  31. Stefani F and Bérubé JA. (2006). Evaluation of foliar fungal endophyte incidence in field-grown transgenic Bt white spruce trees. Canadian Journal of Botany 84: 1573-1580. https://doi.org/10.1139/b06-110

  32. Stefani F and Bérubé JA. (2006). Biodiversity of foliar fungal endophytes in white spruce (Picea glauca) from southern Québec. Canadian Journal of Botany 84: 777-790. https://doi.org/10.1139/b06-022


Professional activities / interests

  • Impact of agricultural practices on soil microbiome and AMF communities
  • New species of AMF
  • Transition from conventionnal agricultural practices to sustainable agricultural practices
  • Soil fertility restoration and carbon sequestration in soil

Education and awards

  • PhD in Forestry Science, Université Laval, 2010
  • DEA (postgraduate research degree programme), specialty in Environmental Sciences, University of Corsica, 2004
  • IUP (Institut Universitaire Professionnel), graduate degree in Environmental Engineering, University of Corsica, 2002
  • BTSA (Advanced Agricultural Technician Certificate), forestry specialty, Lycée agricole de Poisy-Annecy, 2000

International experience and/or work

  • 2016 – Present, Research scientist (Mycology), Laboratory of mycorrhizal symbiosis, Ottawa Research and Development Centre, Agriculture and Agri-Food Canada. Curator of the Canadian Collection of Arbuscular Mycorrhizal Fungi. Adjunct professor at Université Laval, department of forestry, geography and geomatics. Adjunct professor at UOttawa, department of biology.
  • 2015 – 2016, Postdoctoral Fellow (NSERC Visiting Fellowship in Canadian Government Laboratories), NRCAN CFS LFC, Quebec QC. Supervisor: Dr. A. Séguin. Research project: Innovative land reclamation approaches following oil sands mining: a phytoremediation approach based on tree — soil microbiome interactions.
  • 2012 – 2014, Postdoctoral Fellow (NSERC CREATE), Université de Montréal Institut de Recherche en Biologie Végétale, Montréal QC. Supervisor: Prof. M. Hijri. Research projects: i) Molecular identification and quantification of arbuscular mycorrhizal fungi in agricultural soil and bioproducts, Métagénomique des communautés microbiennes présentes dans les sols pollués aux hydrocarbures. ii) Bioremediation and phytoremediation of PAH and heavy metal polluted soils (GenoRem Project – Génome Canada). Molecular identification of the Boletales collections from the Cercles des Mycologues de Montréal.
  • 2010 – 2012, Postdoctoral Fellow, Royal Botanic Gardens Melbourne VIC. Supervisor: Dr. T. May. Research project: Molecular taxonomy and phylogeny of Dermocybe collections (genus Cortinarius) from Southern Australia.

Key publications

  1. Masse, J., Caron, M., Chagnon, P.-L., Thivierge, M.-N., Bélec C. and Stefani, F. 2023. Optimisation des cultures intercalaires pour la préservation des communautés de champignons mycorhiziens arbusculaires dans les champs de Brassicacées. 37th Annual Meeting of the Association québécoise des spécialistes en sciences du sol (AQSSS), Québec, Canada, May 23–25, 2023. Oral presentation.

    2023 - View publication details

  2. Stefani, F., Dupont, S., Laterrière, M., Knox, R., Ruan, Y., Hamel, C., Hijri, M. (2020). Similar Arbuscular Mycorrhizal Fungal Communities in 31 Durum Wheat Cultivars (Triticum turgidum L. var. durum) Under Field Conditions in Eastern Canada. Frontiers in Plant Science, [online] 11 http://dx.doi.org/10.3389/fpls.2020.01206

    2020 - View publication details

  3. Stefani, F., Isabel, N., Morency, M.J., Lamothe, M., Nadeau, S., Lachance, D., Li, E.H.Y., Greer, C., Yergeau, É., Pinno, B.D., Séguin, A. (2018). The impact of reconstructed soils following oil sands exploitation on aspen and its associated belowground microbiome. Scientific Reports, [online] 8(1), http://dx.doi.org/10.1038/s41598-018-20783-6

    2018 - View publication details

  4. F. Stefani (Invited speaker). Identification of arbuscular mycorrhizal fungi: past, present, future. 5eJFM, Dunkerque, France. June 27-29, 2018.

    2018 - View publication details

  5. Stefani, F. 2018. Soil and plant microbiome in the context of the Biodiversity and Bioresources Science Strategy. 3rd ed. AgriScience Day.

    2018 - View publication details

  6. Junjie Yu, Bahram Baninasab, Shuhui Xu, Mirko Tabori, Yuxue Zhang, Xuelian Wang, Ian DeSchiffart, Yolande Dalpé, Franck Stefani , Sylvie Séguin, Baoluo Ma, Chenwu Xu, & Shahrokh Khanizadeh, 2017. Effect of arbuscular mycorrhizal fungi on tolerance and growth of selected spring wheat (Triticum aestivum L.) lines under salinity stress. Journal of Food, Agriculture & Environment (JFAE) Vol.15 (3&4):40- 47

    2017 - View publication details

  7. Stefani, F. 2017. The twisted world of arbuscular mycorrhizal fungi. 2017 Annual Meeting of the Canadian Botanical Association. Waterloo University.

    2017 - View publication details

  8. Klopfenstein, N.B., Stewart, J.E., Ota, Y., Hanna, J.W., Richardson, B.A., Ross-Davis, A.L., Elías-Román, R.D., Korhonen, K., Keča, N., Iturritxa, E., Alvarado-Rosales, D., Solheim, H., Brazee, N.J., Łakomy, P., Cleary, M.R., Hasegawa, E., Kikuchi, T., Garza-Ocañas, F., Tsopelas, P., Rigling, D., Prospero, S., Tsykun, T., Bérubé, J.A., Stefani, F.O.P., Jafarpour, S., Antonín, V., Tomšovský, M., McDonald, G.I., Woodward, S., Kim, M.S. (2017). Insights into the phylogeny of northern hemisphere Armillaria: Neighbor-net and bayesian analyses of translation elongation factor 1-α gene sequences. Mycologia, [online] 109(1), 75-91. http://dx.doi.org/10.1080/00275514.2017.1286572

    2017 - View publication details

  9. Stefani, F., Banchini, C., Dalpé, Y., Cayouette, J., Redhead, S. A. 2017. Exploration of the fungal diversity at ᑕᒥᐅᔭᖅ (Umiujaq, Quebec) through DNA barcoding. Poster and abstract. Canada's Arctic Biodiversity: The Next 150 Years, Museum of Nature Ottawa 2017/01/26 - 2017/01/27.

    2017 - View publication details

Research facility

960 Carling Avenue
Ottawa, ON K1A 0C6


  • Treasurer of the International Mycorrhiza Society (IMS) / 2020 - Present
  • Adjunct professor, department of biology, UOttawa / 2017-Present.
  • Adjunct professor, department of wood science and forestry, Université Laval / 2016-Present.