Gregory Bonito, Ph.D.

Gregory Bonito

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Associate Professor - Mycology, plant-fungal interactions, truffle ecology, evolution of bacterial endosymbiosis in fungi
Department of Plant, Soil and Microbial Sciences



P.h.D, Biology, Duke University
M.S., Conservation Ecology & Sustainable Development, University of Georgia
B.S. Ecology & Environmental Biology, Appalachian State University

Our lab studies the ecology and evolution of plant-fungal-bacterial associations, with a particular interest in belowground root associated fungi including truffles, mushrooms & molds. These organisms provide important links between plants and soils, and are functionally important to plant health and nutrition as well as nutrient cycles and the flow of energy through terrestrial ecosystems.

Our research makes use of phylogenetics, high-throughput sequencing, isotope tracers and –omics approaches to better understand:

  1. Phylogenetic and functional diversity of root-associated fungi.
  2. Environmental and genetic factors that structure root microbiome communities.
  3. The evolution and functional relevance of bacterial symbionts of fungi.

Our lab research has applications pertinent to agriculture, forestry, and in the sustainability of terrestrial life support systems.

General areas of expertise:

Mycology, plant-fungal interactions, truffle ecology, evolution of bacterial endosymbiosis in fungi; Fungal systematics; truffle biology; plant-fungal-bacterial interactions.


PLP 847/PLB 847/MMG 847 - Advanced Mycology -
Fall 2022

Course description - Advanced Mycology is a four-credit lecture and lab-based course that will provide graduate students and advanced undergraduates with current research and techniques in fungal biology, ecology, evolution, and genomics. In class sections, students will revisit foundational literature in mycology, will lead scholarly discussion and will present. Laboratories will involve classical and modern laboratory techniques in mycology, and research employing high throughput sequencing technologies, bioinformatics computation and ecological statistics to address student-driven research questions. 


Peer-Reviewed Publications

  1. Healy RA, Horner HT, Bonito G, McLaughlin DJ, Smith ME. 2017. An ultrastructural study of spore wall development and septal pores in species of the Pachyphlodes (Pezizaceae, Pezizales) lineage, with a description of the new species Pachyphlodes annagardnerae. Mycological Progress.
  2. Desirò A, Rimington W, Jacob A, Vande Pol N, Smith M, Trappe J, Bidartondo M, Bonito G. 2017. Multigene Phylogeny of Endogonales, an Early Diverging Lineage of Fungi Associated with Plants. IMA Fungus.
  3. Hejase H, VandePol N, Bonito G, Edger P, Liu K. 2017. Coal-Miner: A Statistical Method for GWA Studies of Quantitative Traits with Complex Evolutionary Origins. ISMB
  4. Ge ZW, Brenneman T, Bonito G, Smith ME. 2017. Soil pH and mineral nutrients strongly influence truffles and other ectomycorrhizal fungi associated with commercial pecans (Carya illinoinensis). Plant and Soil. DOI 10.1007/s11104-017-3312-z
  5. Torres-Cruz T, Billingsley Tobias TL, Almatruk M, Hesse CN, Kuske CR, Desirò D, Benucci GMN, Bonito G, Stajich J, Dunlap C, Arnold AE, Porras-Alfaro A. 2017. Bifiguratus adelaidae gen. et sp. nov., a new lineage of Mucoromycotina with endophytic and soil-dwelling strains. Mycologia.
  6. Fechner N, Bonito G, Bougher NL, Lebel T, Halling RE. 2017. New species of Austroboletus (Boletaceae) in Australia. Mycological Progress.
  7. Uehling J, Gryganskyi A, Hameed K, Tschaplinski T, Misztal PK, Wu S, Desirò A, Vande Pol N, Du Z, Zienkiewicz A, Zienkiewicz K, Morin E, Tisserant E, Splivallo R, Hainaut M, Henrissat B, Ohm R, Kuo A, Yan J, Lipzen A, Nolan M, LaButti K, Barry K, Goldstein AH, Labbé J, Schadt C, Tuskan G, Grigoriev I, Martin F, Vilgalys R, Bonito G. 2017. Genome sequencing reveals origins of a unique bacterial endosymbiosis in the earliest lineages of terrestrial Fungi. Environmental Microbiology.
  8. Bonito G, Hameed K, Toome-Heller M,  Healy R, Reid C, Liao HL, Aime MC, Schadt CW, Vilgalys R. 2017. Atractiella rhizophila, a novel endorrhizal fungus within the rust lineage (Puccinomycotina) adapted to the root microbiome of Populus and a broad diversity of plant hosts. Mycology.
  9. Velez JM, Tschaplinski TJ, Vilgalys R, Schadt CW, Bonito G, Hameed K, Hamilton C. 2017. Characterization of a novel, ubiquitous fungal endophyte from the rhizosphere and root endosphere of Poplar trees. Fungal Ecology.
  10. Marozzi G, Sánchez S, Benucci GMN, Bonito G, Falini LB, Albertini E, Donnini D. 2017. Mycorrhization of Pecan (Carya illinoinensis) with black truffles: Tuber brumale and Tuber melanosporum. Mycorrhiza.
  11. Spatafora JW, Chang Y, Benny GL, Lazarus K, Smith ME, Berbee ML, Bonito G, Corradi N, Grigoriev I, Gryganskyi A, James TY, O’Donnell K, Taylor TN, Uehling J, Vilgalys R, White M, Stajich JE. 2016. Zygomycete Genealogy of Life (ZyGoLife): a phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia.
  12. Healy RA, Zurier H, Bonito G, Smith ME, Pfister DH. 2016. Mycorrhizal detection of native and non-native truffles in a historic arboretum and the discovery of a new North American species, Tuber arnoldianum sp. nov. Mycorrhiza. doi 10.1007/s00572-016-0713-4
  13. Berch S. and Bonito G. 2016. Truffle diversity (Tuber) in British Columbia. Mycorrhiza. doi. 10.1007/s00572-016-0695-2
  14. Bonito G, Hameed K, Krishnan J, Ventura R, Vilgalys R. 2016. Isolating a functionally relevant guild of fungi from the root microbiome of Populus. Fungal Ecology. 22: 35-42.
  15. Benucci GMN, Bonito G. 2016. The truffle microbiome: Species and geography effects on bacteria associated with fruiting bodies of hypogeous Pezizales. FEMS Microbiology Letters. 72:4-8. doi: 10.1007/s00248-016-0755-3.
  16. SchusterTM, StajsicV, Bonito G. 2016. False Polygonaceae Smut: First Record of Sphacelotheca polygoni-serrulati Maire for Victoria, Australia. Muelleria.  34: 82-101.
  17. Benucci GMN, Lefevre C, Bonito G. 2016. Characterizing fungal root-associated communities and soils in Douglas-Fir (Pseudotsuga menziesii) stands that naturally produce truffles (Tuber oregonense & Tuber gibbosum). Mycorrhiza. 26: 367-376. doi:10.1007/s00572-015-0677-9.
  18. Henkel TW, Obase K, Husbands D, Uehling JK, Bonito G, Aime CM, Smith ME. 2016. New Boletaceae taxa from Guyana: Binderoboletus segoi gen. et sp. nov., Guyanaporus albipodus gen. et sp. nov., Singerocomus rubriflavus gen. et sp. nov., and a new combination for Xerocomus inundabilis. Mycologia. Doi:10.3852/15-075
  19. Guevara-Guerrero G, Bonito G., Cazares-Gonzalez E, Healy R, Vilgalys R, Trappe J. 2015. Novel Tuber spp. (Tuberaceae, Pezizales) in the Puberulum group in Mexico. Ascomycetes. 7(6): 367-374.
  20. Tedersoo L, Bahram M, Polme S, Koljalg U, Yorou NS, Wijesundera R, Ruiz LV, Vasco-Palacios AM, Thu PQ, Suija A, Smith ME, Sharp C, Saluveer E, Saitta A, Rosas M, Riit T, Ratkowsky D, Pritsch K, Poldmaa K, Piepenbring M, Phosri C, Peterson M, Parts K, Partel K, Otsing E, Nouhra E, Njouonkou AL, Nilsson RH, Morgado LN, Mayor J, May TW, Majuakim L, Lodge DJ, Lee SS, Larsson KH, Kohout P, Hosaka K, Hiiesalu I, Henkel TW, Harend H, Guo LD, Greslebin A, Grelet G, Geml J, Gates G, Dunstan W, Dunk C, Drenkhan R, Dearnaley J, De Kesel A, Dang T, Chen X, Buegger F, Brearley FQ, Bonito G, Anslan S, Abell S, Abarenkov K (2014) Global diversity and geography of soil fungi. Science. 346: 6213. Doi: 10.1126/science.1256688
  21. Bonito G, Reynolds H, Hodkinson B, Nelson J, Tuskan G, Robeson M, Schadt C, Vilgalys R (2014) Plant host and soil origin influence fungal and bacterial assemblages in the rhizosphere of woody plants. Molecular Ecology. 23: 3356-3370.
  22. Berch S and Bonito G (2014) Cultivation of Tuber melanosporum and T. aestivum (Tuberaceae) in British Columbia, Canada. Mycorrhiza. 24: 473-479.
  23. Shakya M, Gottel N, Castro H, Yang Z, Gunter L, Labbé J, Muchero W, Bonito G, Vilgalys R, Tuskan G, Podar M, Schadt C (2013) A multifactor analysis of fungal and bacterial community structure in the root microbiome of mature Populus deltoides trees. PlosONE. 8(10):e76382. doi: 10.1371/journal.pone.0076382.
  24. Smith ME, Gryganskyi A, Bonito G, Nouhra E, Moreno_Arroyo B, Benny G (2013) A Phylogenetic analysis of the genus Modicella reveals an independent evolutionary origin of sporocarp-forming fungi in the Mortierellales. Fungal Biology & Genetics. doi: 10.1016/j.fgb.2013.10.001
  25. Bonito G, Smith M, Nowak M, Healy R, Guevara G, Cázares E, Kinoshita A, Nouhra E, Domínguez L, Tedersoo L, Murat C, Wang Y, Moreno B, Pfister D, Nara K, Zambonelli A, Trappe J, Vilgalys R (2013) Historical biogeography and diversification of truffles in the Tuberaceae and its newly identified sister lineage. PLoS ONE. 8(1): e52765. doi:10.1371/journal.pone.0052765
  26. Benucci GMN, Bonito G, Baciarelli Falini L, Donnini D, Bencivenga M (2013) Mycorrhizal inoculation of pecan seedlings with some marketable truffles. Acta Mycologica. 47(2): 179-184.
  27. Wang XH, Benucci GMN, Xie XD, Bonito G, Leisola M, Liu PG, Shamekh S (2013) Morphological, mycorrhizal and molecular characterization of Finnish truffles belonging to the Tuber anniae species-complex. Fungal Ecology. 6(4):269-280.
  28. Healy R, Smith ME, Bonito G, Pfister DH, Ge Z-W, Guevara G, Williams G, Stafford K, Kumar L, Lee T, Hobart C, Trappe J, Vilgalys R, McLaughlin D (2013) High diversity and widespread occurrence of mitotic spore mats in ectomycorrhizal Pezizales. Molecular Ecology. 22(6)1717-1732. doi: 10.1111/mec.12135
  29. Guevara G, Bonito G, Trappe J, Cázares E, Williams G, Healy R, Schadt  C, Vilgalys R (2013) New North American truffles (Tuber spp.) and their ectomycorrhizal associations. Mycologia. 2013 105(1): 194-209. doi:10.3852/12-087
  30. Husbands D, Henkel T, Bonito G, Vilgalys V, Smith M (2012) New species of Xerocomus (Boletales) from the Guiana Shield, with notes on their mycorrhizal status and fruiting occurrence. Mycologia. doi: 10.3852/12-146
  31. Bonito G, Smith M, Brenneman T, Vilgalys R (2012) Assessing ectomycorrhizal fungal spore banks of truffle producing soils with pecan seedling trap-plants. Plant and Soil. 356: 357-366. doi:10.1007/s11104-012-1127-5.
  32. Benucci G, Bonito G, Baciarelli Falini L, Bencivenga M (2012) Mycorrhization of Pecan trees (Carya illinoinensis) with commercial truffle species: Tuber aestivum Vittad. and Tuber borchii Vittad. Mycorrhiza. Mycologia. 22(5):383-392. doi:10.1007/s00572-011-0413-z
  33. Tedersoo L, Abarenkov K, Nilsson H, Schüβler A, GreletG, Kohout P, Oja J, Bonito G, Veldre V, Jairus T, Ryberg M, Larsson K, Kõljalg U (2011) Tidying up International Nucleotide Sequence Databases (INSD): ecological, geographical and sequence quality annotation of ITS sequences of mycorrhizal fungi. PLoS ONE. 6: e24940.
  34. Bonito G, Brenneman T, Vilgalys R (2011) Ectomycorrhizal fungal diversity in orchards of cultivated pecan (Carya illinoinensis; Juglandaceae). Mycorrhiza. 21: 601-612.
  35. Bonito G, Trappe J, Donovan S, Vilgalys R (2011) The Asian black truffle Tuber indicum can form ectomycorrhizae with North American host plants and can complete its life cycle in non-native soils. Fungal Ecology. 4: 83-93. doi: 10.1016/j.funeco.2010.08.003
  36. Bonito G, Brenneman T, Vilgalys R (2011) Tuber ectomycorrhizae on Pecan trees (Carya illinoinensis; Juglandaceae). Proceedings from the 3rd International Congress on Tuber. Spoleto, Italy. Acta Botanica Yunnanica Supp. XVI: 39-51.
  37. Gryganskyi AP, LeeSC, Litvintseva AP, SmithME, Bonito G, Porter TM, Anishchenko IM, Heitman J, Vilgalys R (2011) Structure, function, and phylogeny of the mating locus in the Rhizopus oryzae complex. PLoS ONE. 5(12): e15273. doi:10.1371/journal.pone.0015273
  38. Bonito G, Gryganskyi A, Vilgalys R, Trappe J (2010) A global meta-analysis of Tuber ITS rDNA sequences: species diversity, host specificity, and long-distance dispersal. Molecular Ecology 19: 4994-5008. doi: 10.1111/j.1365-294X.2010.04855.x
  39. Bonito G, Trappe J, Rawlinson P, Vilgalys R (2010) Improved resolution of major clades within Tuber and taxonomy of species within the Tuber gibbosum complex. Mycologia 101: (5) 1042-1057.
  40. Trappe M, Trappe J, Bonito G (2010) Kalapuya brunnea gen. & sp. nov. and its relationship to the other sequestrate genera in Morchellaceae. Mycologia 101: (5) 1058-1065.
  41. Bonito G, Isikhuemhen O, Vilgalys R (2010) Identification of fungi associated with municipal compost using DNA-based techniques. Bioresource Technology.101: (3) 1021-1027.
  42. Bonito G (2009) Fast DNA-based identification of the black truffle Tuber melanosporum using direct PCR and species-specific primers. FEMS Microbiology Letters. 301: (2) 171-175.
  43. Bonito G, Trappe J, Vilgalys R (2009) North American truffles in the Tuberaceae: Molecular and morphological perspectives. Proceedings of the 5th International Workshop on Edible Mycorrhizal Mushrooms. Chuxiong, China. Acta Botanica Yunnanica. Supplement XVI.
  44. Schoch C, and 63 other authors (2009) The Ascomycota tree of life: A phylum wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits. Systematic Biology. 58 (2): 224-239.
  45. Healy R, Bonito G, Guevara G (2009). Pachyphloeus marronius, a new truffle species from Iowa and Mexico. Mycotaxon. 107: 61-71.
  46. Healy R, Bonito G, and Trappe J. (2009) Calongea, a new genus of hypogeous Pezizaceae. Anales del Jardin Botanico de Madrid. 66: (1) 25-32.
  47. Guevara, G, Bonito G, Cázares E, Rodríguez J, Vilgalys R, Trappe J (2008). A new species of black truffle from Mexico, Tuber regimontanum. Mexican Journal of Mycology. 26:17-20.
  48. Iotti M, Amicucci A, Bonito G, Bonuso E, Stocchi V, Zambonelli A (2007). Selection of a set of specific primers for the identification of Tuber rufum: a truffle species with high genetic variability. FEMS Microbiology Letters. 277: (2) 223-231.
  49. Collins SL, Bettencourt LMA, Hagberg A, Larkey L, Brown RF, Moore DI, Bonito G, Delin KA, Jackson SP, Johnson DW, Burleigh SC, Woodrow RR, McAuley JM. (2006) New Opportunities in ecological sensing using wireless sensor networks. Frontiers in Ecology and the Environment. 4: 402-407.
  50. Bonito, GM, Coleman, D.C., Haines, B.L. and Cabrera, M.L. (2003). Can nitrogen budgets explain differences in soil nitrogen mineralization rates between oak pine and northern hardwood stands? Forest Ecology and Management. 276(1):563-574.



  1. Zambonelli A and Bonito G (Eds) (2013) Edible Ectomycorrhizal Mushrooms: Current knowledge and future prospects. Soil Biology Series: 34. Springer.


Peer Reviewed Reports and Book Chapters:

  1. Wright C, Gryganskyi A, Bonito G. 2016. Fungi and Composting. In: Fungal Applications in Sustainable Environmental Biotechnology. Ed. Diane Purchase. Fungal Biology Series: 34. Springer.
  2. Bonito G and Smith ME. 2016.General systematic position of the truffles: Evolutionary theories. In. True truffles (Tuber spp.) of the world: Soil Ecology, Systematics and Biochemistry. Springer. Eds. Zambonelli A, Iotti M, Murat C.
  3. Healy R, Bonito G, Smith ME. 2016.A brief overview of the systematics, taxonomy, and ecology of the Tuber rufum clade. In. True truffles (Tuber spp.)of the world: Soil Ecology, Systematics and Biochemistry. Springer. Eds. Zambonelli A, Iotti M, Murat C.
  4. Payen T, Murat C, Bonito G. 2014. Truffle phylogenomics: New insights into truffle evolution and truffle life cycle. Fungi. (Ed) Francis Martin. Elsevier.
  5. Martin F and Bonito G. 2013. Ten years of genomics for ectomycorrhizal fungi: what have we achieved and where are we heading? In: Edible Ectomycorrhizal Mushrooms: Current knowledge and future prospects. (Eds) A. Zambonelli and G. Bonito. Soil Biology Series: 34. Springer.
  6. Smith M and Bonito G. 2013. Systematics and ecology of ectomycorrhizal mushrooms. In: Edible Ectomycorrhizal Mushrooms: Current knowledge and future prospects. (Eds) A. Zambonelli and G. Bonito. Soil Biology Series: 34. Springer.
  7. Benucci GN, Bonito G, Donnini D, Baciarelli Falini L, Di Massimo G, and Bencivenga M. 2013. Truffles, timber, food, and fuel: Possibilities in multi-cropping truffles with economically important plants. In: Edible Ectomycorrhizal Mushrooms: Current knowledge and future prospects. (Eds) A. Zambonelli and G. Bonito. Soil Biology Series: 34. Springer.
  8. Pregenzer A, Parmenter RR, Passell H, Vande Castle J, Budge T, Bonito G. 2004. Sustainability in arid grasslands: New technology applications for management. In:  Biodiversity in Drylands.  Oxford University Press.
  9. Estrin D, Michener W, Bonito G, and the workshop participants. 2003. Environmental cyberinfrastructure needs for distributed sensor networks: A report from a National Science Foundation sponsored workshop. Scripps Institution of Oceanography,La Jolla,CA. August 12-14, 2003.
  10. Nagel D, Hughes D and Bonito G. 2003. Environmental sensor networks. In: Any signal, any scale, anywhere: Multi-sector crisis management consortium- conference proceedings. Arlington, VA Jan 11- 13, 2002.
  11. Bonito G and Michner W. 2002. In-situ environmental sensor technology highlights. In: Proceedings of the 2002 National Conference on Environmental Science and Technology. Greensboro, North Carolina, September 8-10, 2002. Battelle Press. Pp.185-194.
  12. Goodin D and Bonito G. 2002. In situ Sensors. In: Scalable Information networks for the environment conference proceedings. San Diego Supercomputer Center October 29-31, 2001. 


Invention Disclosures:

  1. Weisenberger A, Bonito G, Reid C, Smith M. 2015. Method and apparatus to image biological interactions in plants. Invention disclosure #1343
  2. Vilgaly R, Bonito G., Hameed K, Lipkowitz J, Schadt C. 2014. Plant growth promoting fungi. Invention disclosure #4331


Non-peer reviewed publications:

  1. Grupe AC, Brenneman T, Bonito G, Smith ME(2016) The Pecan Truffle (Tuber lyonii): a gourmet truffle native to the Southeastern USA. (EDIS PP330). Gainesville: University of Florida Institute of Food and Agricultural Sciences.
  2. Bonito G, Hallan H, Volk T, Adams G (2016) May is Morel Month in Michigan. MSU Extension Bulletin E2755.
  3. Bonito G, Benucci GMN, Miesel J, Cregg B (2016) Mushroom and truffle specialty crop resources for the Michigan Christmas tree industry. Christmas Tree Journal.
  4. Sharma J, Trela B, Wang S, Smith M, Bonito G (2012) Pecan truffle (Tuber lyonii) in Texas. Pecan South Magazine. Fall: 19-24.
  5. Smith M, Bonito G, Sharma J, Long J, Long B, Brenneman T (2012) Pecan truffles (Tuber lyonii): what we know and what we need to know. Georgia Pecan Magazine. Spring: 52-59.
  6. Le Tacon F, Wang YW, Jeandroz S, Bonito G, Murat C (2009) Phylogénie et paléogéographie des truffes. Société d'horticulture et d'histoire naturelle de l'Hérault.
  7. Bonito G, Vilgalys R, Isikhuemhen O (2008) Second annual truffle biotechnology workshop.    Inoculum. 59(5).
  8. Bonito G and Casarez E (2007) Truffling, South of the border. Inoculum. 58: (32).
  9. Michener W and Bonito G (2003) Ecoinformatics training for field stations. The LTER Network Newsletter (1):10.
  10. Bonito G (2001) An in-situ environmental sensor resource - Web Site
  11. Bonito G, Porter D, and Davis D (2001) Brochure: Mushrooms and fungi at the Georgia State Botanical Garden, Athens, GA.