Martin Filion

Image Martin Filion
Research scientist - Plant bacteriology and microbial ecology

Development of alternative approaches for controlling diseases and promoting plant productivity using plant beneficial bacteria

Current research and/or projects

  • Control of plant pathogens by using plant beneficial Pseudomonas spp.

  • Biofertilization and improved crop yields using plant growth promoting rhizobacteria.

  • Rhizocompetence of plant beneficial bacteria and development of approaches to promote their presence under field conditions.

  • Soil health and characterization of taxonomic and functional microbial diversity under field conditions.

  • Development of molecular diagnostic tools to track targeted bacteria under soil conditions.

  • Population genetics and spatio-temporal monitoring of bacterial plant pathogens.

  • Functional genomics of plant beneficial Pseudomonas spp.


Professional activities / interests

Senior Editor, Phytopathology

Editor, Canadian Journal of Microbiology

Associate Editor, Frontiers in Microbiology

Associate Editor, Canadian Journal of Plant Pathology

Editorial Board Member, Applied and Environmental Microbiology

Editorial Board Member, Microorganisms


Key publications


83)     Balthazar C, D.L. Joly, M Filion. 2022. Exploiting Beneficial Pseudomonas spp. for Cannabis Production. Frontiers in Microbiology 12:


82)     Biessy A, M Filion. 2022. Biological control of potato common scab by plant-beneficial bacteria. Biological Control 165: 104808.


81)     Biessy A, M Ciotola, M Cadieux, D Albert, M Filion. 2022. Complete genome sequences of five Burkholderia strains with biocontrol acticity against various lettuce pathogens. Microbiology Resource Announcements 11: e01120-21


80)     Zboralski A, A Biessy, M Filion. 2022. Bridging the gap: Type III secretion systems in plant-beneficial bacteria. Microorganisms 10: 187. doi: 10.3390/microorganisms10010187.



79)     Léger G, A Novinscak, A Biessy, S Lamarre, M Filion. 2021. In tuber biocontrol of potato late blight by a collection of phenazine-1-carboxylic acid-producing Pseudomonas spp. Microorganisms 9: 2525.

78)     Novinscak A, C Goyer, C Wilson, BJ Zebarth, DL Burton, M Chantigny, M Filion. Seasonal changes in the abundance and activity of bacterial and fungal denitrifying communities associated with different compost amendments. Canadian Journal of Microbiology 99: 1-12.


77)    Comeau D, C Balthazar, A Novinscak, N Bouhamdani, DL Joly, M Filion. Interactions between Bacillus Spp., Pseudomonas spp. and Cannabis sativa promote plant growth. Frontiers in Microbiology 12: 715758. doi: 10.3389/fmicb.2021.715758. 


76)    Hudec C, A Biessy, A Novinscak, R St-Onge, S Lamarre, J Blom, M Filion. 2021. Comparative genomics potato of common scab-causing Streptomyces spp, displaying varying virulence. Frontiers in Microbiology: doi10.3389/fmicb.2021.716522.


75)    Balthazar C, A Novinscak, G Cantin, D.L. Joly, M Filion. 2021. Biocontrol Activity of Bacillus spp. and Pseudomonas spp. Against Botrytis cinerea and Other Cannabis Fungal Pathogens. Phytopathology: In press.


74)    Biessy A, A Novinscak, R St-Onge, G Léger, A Zboralski, M Filion. 2021. Inhibition of three potato pathogens by phenazine-producing Pseudomonas spp. is associated with multiple biocontrol-related traits. mSphere 6: e0042721. doi: 10.1128/mSphere.00427-21.


73)    Biessy A, M Filion. 2021. Phloroglucinol derivatives in plant-beneficial Pseudomonas spp.: biosynthesis, regulation, and functions. Metabolites 11: 82 doi: 10.3390/metabo11030182.

72)    Hudec C, A Novinscak, M Filion. 2021. Diversity and virulence of Streptomyces spp. causing potato common scab in Prince Edward Island, Canada. Phytopathology.

71) Novinscak A, A Zboralski, R Roquigny, M Filion. 2021. Genomics and functional traits required for successful use of biofertilizers. P. 45-56 dans: Biofertilizers: Advances in bio-inoculants, Volume 1. Rakshit A, VS Meena, M Parihar, HB Singh, AK Singh, ed. Springer, Pays-Bas. 302 pages.


70)     Zboralski A, M Filion. 2020. Genetic factors involved in rhizosphere colonization by phytobeneficial Pseudomonas spp. Computational and Structural Biotechnology Journal 18: 3539-3554.

69)     Novinscak A, M Filion. 2020. Comparison of talc- and peat-based carriers for the development of phytobeneficial Pseudomonas bioformulations promoting plant growth. Frontiers in Sustainable Food Systems.

68)     Balthazar C, G Cantin, A Novinscak, DL Joly, M Filion. 2020. Expression of Defense Responses in Cannabis Primed by Pseudomonas and/or Bacillus Strains and Infected by Botrytis cinerea. Frontiers in Plant Science. doi: 10.3389/fpls.2020.572112.

67)     Jiménez JA, A Novinscak, M Filion. 2020. Inoculation with the plant-growth-promoting rhizobacterium Pseudomonas fluorescens LBUM677 impacts the rhizosphere microbiome of three oilseed crops. Frontiers in Microbiology.

66)     Novinscak A, A Zboralski, R Roquigny, M Filion. 2020. Microbiome genomics and functional traits for agricultural sustainability. P. 279-298 In: The Plant Microbiome in Sustainable Agriculture, First Edition. Srivastava, AK, PL Kashyap, M Srivastava. John Wiley & Sons, UK,  301 pages. 

65)     Comeau D, A Novinscak, DL Joly, M Filion. 2020. Spatio-temporal and cultivar-dependent variations in the Cannabis microbiome. Frontiers in Microbiology 11: 491.  doi: 10.3389/fmicb.2020.00491.

64)     Zboralski A, A Biessy, M-C Savoie, A Novinscak, M Filion. 2020. Metabolic and genomic traits of phytobeneficial phenazine-producing Pseudomonas spp. are linked to rhizosphere colonization in Arabidopsis thaliana and Solanum tuberosum. Applied and Environmental Microbiology 66: e02443-19.

63)     Jiménez JA, A Novinscak, M Filion. 2020. Pseudomonas fluorescens LBUM677 differentially increases plant biomass, total oil content and lipid composition in three oilseed crops. Journal of Applied Microbiology 128:1119-1127.

62)     Arseneault T, R Roquigny, A Novinscak, C Goyer, M Filion. 2020. Phenazine-1-carboxylic acid-producing Pseudomonas synxantha LBUM223 alters the transcriptome of Streptomyces scabies, the causal agent of potato common scab. Physiological and Molecular Plant Pathology 110.


61)     Biessy A, A Novinscak, J Blom, G Léger, LS Thomashow, FM Cazorla, D Josic, M Filion. 2019. Diversity of phytobeneficial traits revealed by whole-genome analysis of worldwide-isolated phenazine-producing Pseudomonas spp. Environmental Microbiology. doi: 10.1111/1462-2920.14476.

60)     Novinscak A, M Filion. 2019. Persistence of Pseudomonas fluorescens LBUM677 in the rhizosphere of corn gromwell (Buglossoides arvensis) under field conditions and its impact on seed oil and stearidonic acid bioaccumulation. Journal of Applied Microbiology. 127: 208-218.

59)     Novinscak A, DL Joly, M Filion. 2019. Complete Genome Sequence of the Plant Growth-Promoting Rhizobacterium Pseudomonas fluorescens LBUM677. Microbiology Resource Announcements. doi: 10.1128/MRA.00438-19.


58)     Filion M, M Surette. 2018. Rhizobacterial strain and uses for enhancing total lipid yields in an oilseed crop. American Patent No. 15/471,135

57)     Roquigny R, A Novinscak, T Arseneault, DL Joly, M Filion. 2018. Transcriptome alteration in Phytophthora infestans in response to phenazine-1-carboxylic acid production by Pseudomonas fluorescens strain LBUM223. BMC Genomics 19: 474. doi: 10.1186/s12864-018-4852-1.

56)     Biessy A, M Filion. 2018. Phenazines in plant-beneficial Pseudomonas spp.: biosynthesis, regulation and genomics. Environmental Microbiology 20: 3905-3917.

55)     Roquigny R, A Novinscak, G Léger, N Marcoux, DL Joly, M Filion. 2018. Deciphering the rhizosphere and geocaulosphere microbiomes of potato following inoculation with the biocontrol agent Pseudomonas fluorescens strain LBUM223. Phytobiomes 2: 92-99.

54)     Novinscak A, M Filion. 2018 Enhancing total lipid and stearidonic acid yields in Buglossoides arvensis through PGPR inoculation. Journal of Applied Microbiology 125: 203-215.


53)     Paulin MM, A Novinscak, C Lanteigne, VJ Gadkar, M Filion. 2017. Interaction between DAPG and HCN producing Pseudomonas brassicacearum LBUM300 and Clavibacter michiganensis subsp. michiganensis in the rhizosphere of tomato. Applied and Environmental Microbiology 83: e00073-17.

52)     Morrison CK, T Arseneault, A Novinscak, M Filion. 2017. Phenazine-1-carboxylic acid production by Pseudomonas fluorescensLBUM636 alters Phytophtora infestans's growth and late blight development. Phytopathology 107: 273-279.

51)     Tatti E, C Goyer, BJ Zebarth, S Wertz, DL Burton, MH Chantigny, M Filion, J Zeng. 2017. Over-winter dynamics of soil bacterial denitrifiers and nitrite ammonifiers influenced by crop residues with different carbon to nitrogen ratios. Applied Soil Ecology 110: 53-64.

50)     Arseneault T, M Filion. 2017. Biocontrol through antibiosis: Exploring the role played by subinhibitory concentrations of antibiotics in soil and their impact on plant pathogens. Canadian Journal of Plant Pathology 39: 267-274.

49)     Roquigny R, A Novinscak, A Biessy, M Filion. 2017. Pseudomonadaceae: from biocontrol to plant growth promotion. p. 39-68 in: Microbes for sustainability - rhizotrophs. Menhaz, S. ed. Springer, India.

48)     Zboralski A, A Biessy, M Filion. 2017. Rhizosphere colonization by plant-beneficial Pseudomonas spp.: Thriving in a heterogeneous and challenging environment. p. 197-217 in: Advances in PGPR Research. Singh, H.B. ed. CABI, United Kingdom.


47)     Wertz S, C Goyer, BJ Zebarth, E Tatti, DL Burton, MH Chantigny, M Filion. 2016. The amplitude of soil freeze-thaw cycles influences temporal dynamics of N2O emissions and denitrifier transcriptional activity and community composition. Biology and Fertility of Soils. 52: 1149-1162.

46)     Morrison C, A Novinscak A, VJ Gadkar, M Filion. 2016. Complete genome sequence of Pseudomonas fluorescens LBUM636, a strain with biocontrol capabilities against late blight of potato. Genome Announcements. 4(3):e00446-16. doi:10.1128/genomeA.00446-16.

45)     Arseneault A, C Goyer, M Filion. 2016. Biocontrol of potato common scab is associated with high Pseudomonas fluorescens LBUM223 populations and phenazine-1-carboxylic acid biosynthetic transcripts accumulation in the potato geocaulosphere. Phytopathology 106: 963-970.

44)     Novinscak A, C Goyer, BJ Zebarth, DL Burton, MH Chantigny, M Filion. 2016. Characterization of the prevalence and diversity of soil fungal denitrifiers using a novel P450nor gene detection assay. Applied and Environmental Microbiology 82: 4560-4569.

43)     Novinscak A, VJ Gadkar, DL Joly, M Filion. 2016. Complete genome sequence of Pseudomonas brassicacearum LBUM300, a disease-suppressive bacterium with antagonistic activity towards fungal, oomycete and bacterial plant pathogens. Genome Announcements. 4: doi: 10.1128/genomeA.01623-15.

42)     Arseneault T, M Filion. 2016. Phenazine-producing Pseudomonas spp. as biocontrol agents of plant pathogens. p. 53-68 in: Microbial inoculants in sustainable agricultural productivity. DP Singh et al. eds. Springer, India.


41)     Arseneault A, C Goyer, M Filion. 2015. Pseudomonas fluorescens LBUM223 increases potato yield and reduces common scab symptoms in the field. Phytopathology 105: 1311-1317.

40)     Tatti E, C Goyer, DL Burton, S Wertz, BJ Zebarth, M Chantigny, M Filion. 2015. Tillage management and seasonal effects on denitrifier community abundance, gene expression and structure over winter. Microbial Ecology 70: 795-808.

39)     Gadkar VJ, M Filion. 2015. Validation of endogenous reference genes in Buglossoides arvensis for normalizing RT-qPCR-based gene expression data. SpringerPlus 4: 178-189.

38)     Roquigny R, T Arseneault, VJ Gadkar, A Novinscak, DL Joly, M Filion. 2015. Complete genome sequence of biocontrol strain Pseudomonas fluorescens LBUM223. Genome Announcements 3: doi: 10.1128/genomeA.00443-15.


37)     Arseneault T, CMJ Pieterse, M Gérin-Ouellet, C Goyer, M Filion. 2014. Long-term induction of defense gene expression in potato by Pseudomonas sp. LBUM223 and Streptomyces scabies. Phytopathology 104:926-932.

36)     Gadkar VJ, M Filion. 2014. Fidelity and representativeness of two isothermal multiple displacement amplification systems to pre-amplify limiting amounts of total RNA. Molecular Biotechnology 56: 377-385.

35)     Tatti E, C Goyer, M Chantigny, S Wertz, BJ Zebarth, DL Burton, M Filion. 2014. Influences of over winter conditions on denitrification and nitrous oxide-producing microorganism abundance and structure in an agricultural soil amended with different nitrogen sources. Agriculture, Ecosystems and Environment 183: 47-59.

34)     Gadkar VJ, M Filion. 2014. New developments in quantitative real-time polymerase chain reaction technology. Current Issues in Molecular Biology 16: 1-6.


33)     Arseneault T, C Goyer, M Filion. 2013. Phenazine production by Pseudomonas sp. LBUM223 contributes to the biocontrol of potato common scab. Phytopathology. 103:995-1000.

32)     Wertz S, C Goyer, BJ Zebarth, DL Burton, E Tatti, MH Chantigny, M Filion. 2013. Effects of temperature near the freezing point on N2O emissions, denitrification and the abundance and structure of nitrifying and denitrifying soil communities. FEMS Microbiology Ecology 83: 242-254.

31)     Gadkar VJ, M Filion. 2013. Development of a versatile TaqMan compliant anchor sequence to quantify bacterial gene transcripts from RNA samples containing carryover genomic DNA. BMC Biotechnology 13: 7 doi 10 :1186/1472-6750- 13-7.

30)     Gadkar VJ, M Filion. 2013. Quantitative real-time polymerase chain reaction for tracking microbial gene expression in complex environmental matrices. Current Issues in Molecular Biology 15: 45-58.

29)     Gadkar, VJ, M Filion. 2013. A linear concatenation strategy to construct 5' enriched amplified cDNA libraries using multiple displacement amplification. Molecular Biotechnology 54: 541-550.

28)     Novinscak A, C Goyer, CE Dandie, M Filion. 2013. Abundance, diversity and spatio-temporal dynamics of nirS- harbouring denitrifiers in a potato field over the course of a growth season. Systematic and Applied Microbiology 36: 112-115.

27)     Paulin M, M Filion. 2013. Engineering the rhizosphere for agricultural and environmental sustainability. p. 251-271 in: Applications of microbial engineering. VK Gupta et al. eds. CRC Press. Boca Raton, FL, USA.


26)     Lanteigne C, VJ Gadkar, T Wallon, A Novinscak, M Filion. 2012. Production of DAPG and HCN by Pseudomonas sp. LBUM300 contributes to the biocontrol of bacterial canker of tomato. Phytopathology 102: 967-973.

25)     Gadkar VJ, M Filion. 2012. Studying microbial gene expression in complex environmental matrices using quantitative real-time polymerase chain reaction. P. 163-180 in: Quantitative real-time PCR in applied microbiology. M Filion ed. Caister Academic Press. Norfolk, United Kingdom.

24)     Gadkar VJ, M Filion. 2012. Future trends in quantitative real-time polymerase chain reaction technology and their implication in applied microbiology. p. 233-238 in: Quantitative real-time PCR in applied microbiology. M Filion ed. Caister Academic Press. Norfolk, United Kingdom.

23)     Filion M (ed). 2012. Quantitative real-time PCR in applied microbiology. Caister Academic Press. Norfolk, United Kingdom. 238 pages.


22)     Gadkar VJ, M Filion. 2011. A novel method to perform genomic walks using a combination of single strand DNA circularization and rolling circle amplification. Journal of Microbiological Methods 87: 38-43.

21)     Novinscak A, M Filion. 2011. Effect of soil clay content on RNA isolation and on detection and quantification of bacterial gene transcripts in soil by quantitative reverse transcription-PCR. Applied and Environmental Microbiology 77: 6249-6252.

20)     DeCoste NJ, VJ Gadkar, M Filion. 2011. Relative and absolute quantitative real-time PCR-based quantification of hcnC and phlD gene transcripts in natural soil spiked with Pseudomonas sp. strain LBUM300. Applied and Environmental Microbiology 77: 41-47.

19)     St-Onge R, VJ Gadkar, T Arseneault, C Goyer, M Filion. 2011. The ability of Pseudomonas sp. LBUM223 to produce phenazine-1-carboxylic acid affects the growth of Streptomyces scabies, the expression of thaxtomin biosynthesis genes and the biological control potential against common scab of potato. FEMS Microbiology Ecology 75: 173-183.


18)     St-Onge R, C Goyer, M Filion. 2010. Pseudomonas spp. can inhibit Streptomyces scabies growth and repress the expression of genes involved in pathogenesis. Journal of bacteriology and Parasitology 1:101 doi: 10.4172/2155- 9597.1000101.

17)     DeCoste NJ, VJ Gadkar, M Filion. 2010. Verticillium dahliae alters Pseudomonas spp. populations and HCN gene expression in the rhizosphere of strawberry. Canadian Journal of Microbiology 56: 906-915.

16)     Karpowicz E, A Novinscak, F Bärlocher, M Filion. 2010. qPCR quantification and genetic characterization of Clostridium perfringens populations in biosolids composted for two years. Journal of Applied Microbiology 108: 571-581.


15)     Paulin MM, A Novinscak, M St-Arnaud, C Goyer, N DeCoste, J-P Privé, J Owen, M Filion. 2009. Transcriptional activity of antifungal metabolite encoding genes phlD and hcnBC in Pseudomonas spp. using qRT-PCR. FEMS Microbiology Ecology 68: 212-222.

14)     Novinscak A, N DeCoste, C Surette, M Filion. 2009. Characterization of bacterial and fungal communities in composted biosolids over a two year period using denaturing gradient gel electrophoresis. Canadian Journal of Microbiology 55: 375-387.


13)     St-Onge R, C Goyer, R Coffin, M Filion. 2008. Genetic diversity of Streptomyces spp. causing common scab of potato in Eastern Canada. Systematic and Applied Microbiology 31: 474-484.

12)     Filion M. 2008. Do transgenic plants affect rhizobacteria populations? Microbial Biotechnology 1: 463-475.

11)     Novinscak A, C Surette, C Allain, M Filion. 2008. Application of molecular technologies to monitor the microbial content of biosolids and composted biosolids. Water Science and Technology 57: 471-477.


10)     LeBlanc PM, RC Hamelin, M Filion. 2007. Alteration of soil rhizosphere communities following genetic transformation of white spruce. Applied and Environmental Microbiology 73: 4128-4234.

9)       Novinscak A, C Surette, M Filion. 2007. Quantification of Salmonella spp. in composted biosolids using a TaqMan qPCR assay. Journal of Microbiological Methods 70: 119-126.

8)       Goyer C, M Filion. 2007. La galle commune: stratégie de lutte. Conference proceeding published in: Colloque sur la pomme de terre: changeons nos façons de faire, p.11-15. Conférence du Centre de référence en Agriculture et Agroelimentaire du Québec.

7)       Novinscak A, C Surette, C Allain, M Filion. 2007. Application of molecular technologies to monitor the microbial content of biosolids and composted biosolids. Conference proceeding published in: Moving forward, wastewater biosolids sustainability: technical, managerial, and public synergy, p. 303-309. International Water Association specialist conferences on wastewater biosolids sustainability.


6)       Yergeau E, M Filion, V Vujanovic, M St-Arnaud. 2005. A PCR-denaturing gradient gel electrophoresis (DGGE) approach to assess Fusarium diversity in asparagus. Journal of Microbiological Methods 60: 143-154.


5)       Filion M, RC Hamelin, L Bernier, M St-Arnaud. 2004. Molecular profiling of rhizosphere microbial communities associated with healthy and diseased black spruce (Picea mariana) seedlings grown in nursery. Applied & Environmental Microbiology 70: 3541-3551.


4)       Filion M, M St-Arnaud, SH Jabaji-Hare. 2003. Quantification of Fusarium solani f. sp. phaseoli in mycorrhizal bean plants and surrounding mycorrhizosphere soil using real-time PCR and direct isolations on selective media. Phytopathology 93: 229-235.

3)       Filion M, M St-Arnaud, SH Jabaji-Hare. 2003. Direct quantification of fungal DNA from soil substrate using real-time PCR. Journal of Microbiological Methods 53: 67-76.


2)       Filion M, M St-Arnaud, C Guillon, C Hamel, SH Jabaji-Hare. 2001. Suitability of Glomus intraradices in vitro produced spores and root segment inoculum for the establishment of a mycorrhizosphere in an experimental microcosm. Canadian Journal of Botany 79: 879-885.


1)      Filion M, M St-Arnaud, JA Fortin. 1999. Direct interactions between the arbuscular mycorrhizal fungus Glomus intraradices and different rhizosphere microorganisms. New Phytologist 141: 525-533.