University of Calgary

Michael Francis Hynes

  • Professor
  • Microbiology

Research Interests

Research activities have included studies on symbiotic nitrogen fixation, and on development of vector and gene transfer systems for various bacteria of agricultural significance (rumen bacteria, biological control agents, plant-growth promoting bacteria). Our major effort has been directed towards understanding the role of very large plasmids in the free-living and symbiotic life of Rhizobium spp., that form nitrogen fixing nodules on the roots of various legume host plants. Plasmid encoded loci involved in the catabolism of a wide variety of carbon sources have been identified in R. leguminosarum, and the role of these genes in the ability of the bacterium to compete with other bacteria, and to survive as a rhizosphere organism, is being investigated. Studies are also ongoing on partitioning systems that make these plasmids so stable.  More recently, we have been examining plasmid transfer in the rhizobia, with emphasis on a previously unstudied conjugation system identified on plasmid pRleVF39b. Another major area of research has been the study of chemotaxis and motility in rhizobia, and the regulation of genes involved in these processes. Other lab interests include work on bacteriocins, bacteriophage and IS elements.  We have recently done a lot of work on rhizobiophage genomics and ecology, and hope to continue this work. 

Graduate Student

Greenwood, Paige  M.Sc. Regulation of plasmid transfer in rhizobia
Nandun Dulmini Wathugala Ph.D. Conjugation of plasmid pRleVF39b
Deborah Buhlers M.Sc. Adonitol catabolic loci on rhizobial plasmids
Amina Alghamdi M.Sc. Atypical type I rhizobial conjugation systems
Maria Augusta Schmidt   PDF Regulation of rhizobial motility

Selected Publications


  • Scharf BE, Hynes MF, Alexandre GM (2016) Chemotaxis signaling systems in model beneficial plant-bacteria associations.  Plant Molec. Biol. 90:549-559  (doi: 10.1007/s11103-016-0432-4)
  • Halmillawewa AP, Restrepo-Córdoba M, Perry BJ, Yost CK, Hynes MF (2016) Characterization of the temperate phage vB_RleM_PPF1 and its site-specific integration into the Rhizobium leguminosarum F1 genome.  Mol. Genet. Genom. 191:349-362 (doi:10.​1007/​s00438-015-1113-8)
  • Ramsay JP, Tester LGL, Major AS, Sullivan JT, Edgar CD, Kleffmann T, Patterson-House JR, Hall DA, Tate WP, Hynes MF, Ronson CW (2015) Ribosomal frameshifting and dual-target antiactivation restrict quorum-sensing-activated  transfer of a mobile genetic element.  Proc. Natl. Acad. Sci. USA . 112:4104-4109 (doi:10.1073/pnas.1501574112 )
  • Halmillawewa AP, Restrepo-Córdoba M, Yost CK, Hynes MF (2015)  Genomic and phenotypic characterization of Rhizobium gallicum phage vB_RglS_P106B. Microbiology 61:611-620. (doi: 10.1099/mic.0.000022)
  • Yip CB, Ding H, Hynes MF (2015) Counter transcribed RNAs of Rhizobium leguminosarum repABC plasmids exerts incompatibility effects only when highly expressed.  Plasmid 78:37-47 (doi:10.1016/j.plasmid.2014.12.003)
  • Tambalo DD, Yost CK, and Hynes MF (2015) Motility and chemotaxis in the rhizobia, In: Biological Nitrogen Fixation  edited by Frans De Bruijn. Wiley and Sons, Hoboken New Jersey, Chapter 33, pages 337-348
  • Tambalo, DD,  Vanderlinde EM, Robinson S, Halmillawewa A, Hynes MF, and Yost CK (2014) Legume seed extracts and Physcomitrella patens extracts influence swarming behaviour in Rhizobium leguminosarum.  Can. J. Microbiol. 60:15-24
  • Vanderlinde EM, Hynes MF, and Yost CK (2014) Homoserine catabolism by Rhizobium leguminosarum  bv. viciae 3841 requires a plasmid-borne gene cluster that also affects competitiveness for nodulation.  Environ. Microbiol.  16:205-217  (DOI: 10.1111/1462-2920.12196)
  • Ronson CW, Hynes MF, Ramsay JP, and Sullivan JT (2013) Symbiosis islands.  In “Brenner's Encyclopedia of Genetics” 2nd edition, edited S. Maloy and K. Hughes. Elsevier publishers. pp 598-600.  (DOI 10.1016/B978-0-12-374984-0.01497-2)
  • Ding H, Yip CB, and Hynes MF (2013) Genetic characterization of a novel rhizobial plasmid conjugation system in Rhizobium leguminosarum bv. viciae strain VF39SM.  J. Bacteriol. 195:328-339. (DOI: 10.1128/JB.01234-12)
  • Ramsay JP,  Major AS, Komarovsky VL, Sullivan JT, Dy R, Hynes MF, Salmond GP, Ronson CW (2013) A widely conserved molecular switch controls quorum sensing and symbiosis island transfer in Mesorhizobium loti through expression of a novel antiactivator. Mol. Microbiol. 87:1-13. (DOI doi: 10.1111/mmi.12079)
  • Ding H, Yip CB, Geddes BA, Oresnik IJ, and Hynes MF (2012) Glycerol utilization by Rhizobium leguminosarum requires an ABC transporter and affects competition for nodulation. Microbiology 158:1369-1378. doi: 10.1099/mic.0.057281-0
  • Tambalo DD, Bustard DE, Del Bel KL, Koval SF, Khan MF, and Hynes MF (2010) Characterization and functional analysis of seven flagellin genes in Rhizobium leguminosarum BMC Microbiology 10:219 doi:10.1186/1471-2180-10-219
  • Tambalo DD, Yost CK, and Hynes MF (2010) Characterization of swarming motility in Rhizobium leguminosarum bv. viciae.  FEMS Microbiology Lett. 307:165-174 DOI: 10.1111/j.1574-6968.2010.01982.x
  • Tambalo DD, Del Bel KL, Bustard DE, Greenwood PR, Steedman AE, and Hynes MF (2010) Regulation of flagellar, motility and chemotaxis genes in Rhizobium leguminosarum by the VisN/R-Rem cascade. Microbiology 156:1673-1685   DOI:10.1099/mic.0.035386-0
  • Perrine-Walker FM, Hynes MF, Rolfe BG and Hocart CH (2009) Strain competition and agar affect the interaction of rhizobia with rice. Can J. Microbiol. 55:1217-1223
  • Ding H, and Hynes MF (2009) Plasmid transfer systems in the rhizobia. Can J. Microbiol. 55:917-927
  • Crossman LC, Castillo-Ramírez S, McAnnula C, Lozano L, Vernikos GS, Acosta JL, Ghazoui ZF, Hernández-González I, Meakin G, Walker AW, Hynes MF, Young JP, Downie JA, Romero D, Johnston AW, Dávila G, Parkhill J, González V (2008) A common genomic framework for a diverse assembly of plasmids in the symbiotic nitrogen fixing bacteria. PLoS ONE.3:e2567
  • Poole PS, Hynes MF, Johnston AWB, Tiwari RP, Reeve WG, and Downie, JA (2008) Physiology of root nodule bacteria. In “Nitrogen-fixing leguminous symbioses” edited by M.J. Dilworth, E.K. James,  J. Sprent,, and W.E. Newton.  Springer NY.  pp. 241-292
  • Miller LD, Yost CK, Hynes MF, and Alexandre G (2007) The major chemotaxis gene cluster of Rhizobium leguminosarum bv. viciae is essential for competitive nodulation. Mol. Microbiol.  63:348-362
  • Yost CK,  Rath AM,  Noel TC, and Hynes MF (2006) Characterization of genes involved in erythritol catabolism in Rhizobium leguminosarum bv. viciae. . Microbiology 152:2061-2074





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