Gregory Bonito

Assistant Professor - Mycology, plant-fungal interactions, truffle ecology, evolution of bacterial endosymbiosis in fungi.

Gregory Bonito


Molecular Plant Science Building
1066 Bogue Street Rm 3270
East Lansing, MI 48824-6254

Phone: (517) 884-6958

Lab Website

Click here to see a list of Gregory Bonito's publications on Google Scholar.


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

Research Interests:

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 the (1) phylogenetic and functional diversity of root-associated fungi, (2) environmental and genetic factors that structure root microbiome communities, and (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: 

Fungal systematics; truffle biology; plant-fungal-bacterial interactions.



Peer-Reviewed Papers

  1. Bonito G, Reynolds H, Hodkinson B, Nelson J, Tuskan G, Robeson M, Schadt C, Vilgalys R (accepted) Plant host and soil origin influence fungal and bacterial assemblages in the rhizosphere of woody plants. Molecular Ecology.
  2. Berch S and Bonito G (2014) Cultivation of Tuber melanosporum and T. aestivum (Tuberaceae) in British Columbia, Canada. Mycorrhiza
  3. 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.
  4. 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
  5. 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
  6. 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.
  7. 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.
  8. 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
  9. 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
  10. 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
  11. 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.
  12. 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
  13. Tedersoo L, Abarenkov K, Nilsson H, Schüβler A, Grelet G, 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.
  14. Bonito G, Brenneman T, Vilgalys R (2011) Ectomycorrhizal fungal diversity in orchards of cultivated pecan (Carya illinoinensis; Juglandaceae). Mycorrhiza. 21: 601-612. 
  15. 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
  16. 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.
  17. Gryganskyi AP, Lee SC, Litvintseva AP, Smith ME, 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
  18. 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
  19. 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. 
  20. 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.
  21. Bonito G, Isikhuemhen O, Vilgalys R (2010) Identification of fungi associated with municipal compost using DNA-based techniques. Bioresource Technology.101: (3) 1021-1027.
  22. 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.
  23. 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.
  24. 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.
  25. Healy R, Bonito G, Guevara G (2009). Pachyphloeus marronius, a new truffle species from Iowa and Mexico. Mycotaxon. 107: 61-71.
  26. 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.
  27. 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.
  28. 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.
  29. Collins SL, Bettencourt LMA, Hagberg A, Larkey L, Brown RF, Moore DI, Bonito GM, 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.
  30. 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.


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

Reports and Book Chapters 

  1. Payen T, Murat C, Bonito G (In press) Truffle phylogenomics. Fungi. (Ed) Francis Martin. Elsevier.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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. 
  8. 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.
  9. 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.  

Non-peer reviewed publications

  1. Sharma J, Trela B, Wang S, Smith M, Bonito G (2012) Pecan truffle (Tuber lyonii) in Texas. Pecan South Magazine. Fall: 19-24.
  2.  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.
  3.  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.
  4. Bonito G, Vilgalys R, Isikhuemhen O (2008) Second annual truffle biotechnology workshop.
  5. Inoculum. 59(5).
  6. Bonito G and Casarez E (2007) Truffling, South of the border. Inoculum. 58: (32).


  1. Weisenberger A, Bonito G, Reid C, Smith M (2013) 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.