1. Liber J, Minier DH, Stouffer-Hopkins A, Van Wyk J, Longley R, Bonito G. Submitted. Leaf litter fungal communities reflect pre-senescent leaf communities in a temperate forest ecosystem. Fungal Ecology
  2. Benucci GMN, Rennick B, Bonito G Submitted. Patient propagules: do long-term soil archives preserve legacy fungal and bacterial communities? PLoSONE
  3. Bowsher A, Benucci GMN, Bonito G, Shade A. Resubmitted. Seasonal dynamics of core fungi in the switchgrass phyllosphere, and co-occurrence with leaf bacteria. Phytobiomes.
  4. Vandepol N, Liber J, Desiro A, Na H, Kennedy M, Barry K, Grigoriev IV, Miller A, O’Donnell K, Stajich J, Bonito G. Resubmitted. Resolving the Mortierellaceae phylogeny through synthesis of multi-gene phylogenetics and phylogenomics. Fungal Diversity.
  5. Martin et al. Resubmitted. Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits. Nature Ecology and Evolution
  6. Mei Y, Liu CY, Li SH, Guerin-Laguette A, Xiao YJ, Tang P, Wan SP, Bonito G, Wang Y. Resubmitted. Phlebopus roseus, a rare edible bolete from China is associated with insects and plants. Mycologia.
  7. Myers JM, Bonds AE, Simmons DR, Clemons RA, Thapa NA, Longcore JE, Stajich J, James TY. Submitted. In vitro and in silico screenings of early-diverging lineages reveal abundant and diverse mycoviruses throughout kingdom Fungi. mSystems.



  1. Zhu S, Bonito G, Chen Y, and Du Z. 2020. Oleaginous Fungi in Biorefineries. In “Reference Module in Life Sciences” (ISBN 9780128096338), DOI: 10.1016/B978-0-12-819990-9.00004-4. 
  2. Wang X, Peng J, Sun L, Bonito G, Guo Y, Li Y, Fu Y. 2020. Genome sequencing of Paecilomyces penicillatus provides insights into its phylogenetic placement and mycoparasitism mechanisms on morel mushrooms. Pathogens. 9(10), 834; Article 
  3. Martin et al. 2020. Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits. Nature Communications. 11, 5125 (2020). Article
  4. Mei Y, Liu CY, Li SH, Guerin-Laguette A, Xiao YJ, Tang P, Wan SP, Bonito G, Wang Y. In Press. Phlebopus roseus, a rare edible bolete from China is associated with insects and plants. Mycologia
  5. Song GQ, Chen Q, Callow P, Mandujano M, Han XY, Cuenca B, Bonito G, Medina-Mora C, Fulbright DW, Guyer DE. 2020. Efficient Micropropagation of Chestnut Hybrids (Castanea spp.) Using Modified Woody Plant Medium and Zeatin Riboside. Horticulture Plant Journal. doi: 10.1016/j.hpj.2020.09.006 
  6. Bowsher A, Benucci GMN, Bonito G, Shade A. 2020. Seasonal dynamics of core fungi in the switchgrass phyllosphere, and co-occurrence with leaf bacteria. Phytobiomes. doi: 10.1094/PBIOMES-07-20-0051-R 
  7. Myers JM, Bonds AE, Simmons DR, Clemons RA, Thapa NA, Longcore JE, Stajich J, James TY. 2020. In vitro and in silico screenings of early-diverging lineages reveal abundant and diverse mycoviruses throughout kingdom Fungi. mSystems. doi: 10.1128/mBio.02027-20 
  8. Vandepol N, Liber J, Desiro A, Na H, Kennedy M, Barry K, Grigoriev IV, Miller A, O’Donnell K, Stajich J, Bonito G. 2020.  Resolving the Mortierellaceae phylogeny through synthesis of multi-gene phylogenetics and phylogenomics. Fungal Diversity. 
  9. Benucci GMN, Rennick B, Bonito G. 2020. Patient propagules: do long-term soil archives preserve legacy fungal and bacterial communities? PLoSONE. 15(8): e0237368.
  10. Liber J, Bryson A, Bonito G, Du ZY. 2020. Harvesting microalgae for food and energy. Small Methods. doi: 10.1002/smtd.202000349
  11. Eberhart J, Trappe J, Piña Páez C, Bonito G. 2020. Tuber luomae, a new spiny-spored truffle species from the Pacific Northwest, USA. Fungal Systematics and Evolution 6: 299–304. doi: 10.3114/fuse.2020.06.15
  12. Zhang K, Bonito G, Hsu CM, Hameed K, Vilgalys R, Liao HL. 2020. Mortierella elongata increases plant biomass among non-leguminous crop species. Agronomy10, 754. doi: 10.3390/agronomy10050754 
  13. Longley R, Noel ZA, Benucci GMN, Chilvers MI, Trail F, Bonito G. 2020. Crop management impacts the soybean (Glycine max) microbiome. Frontiers in Microbiology. 11:1116. doi: 10.3389/fmicb.2020.01116 
  14. Benucci GMN, Burnard D, Shepherd LD, Bonito G, Munkacsi A. 2020. Evidence for co-evolutionary history of early diverging Lycopodiaceae plants with fungi. Frontiers in Plant Biology. Article




  1. Benucci GMN, Haridas S, Labutti K, Marozzi G, Antonielli L, Sanchez S, Marco P, Wang X, Barry K, Lipzen A, Chovatia M, Hundley H, Baciarelli Falini L, Murat C, Martin F, Albertini E, Donnini D, Grigoriev IV, Bonito G. 2019. Draft genome sequence of the ectomycorrhizal ascomycete Sphaerosporella brunnea. Genome Announcements. Microbiology Resource Announcements 8 (50). doi: 10.1128/MRA.00857-19.
  2. Longley R, Benucci GMN, Mills G, Bonito G. 2019. Fungal and bacterial community dynamics in substrates during the cultivation of morels (Morchella rufobrunnea) indoors. FEMS Microbiology Notes. doi: 10.1093/femsle/fnz215
  3. Benucci GMN, Longley R, Zhang P, Zhao Q, Bonito G, Yu Fuqiang. 2019. Microbial communities associated with the cultivated black morel Morchella sextelata in greenhouses. PeerJ. doi: 10.7717/peerj.7744
  4. Uehling JK, Entler M, Meredith H, Millet L, Timm C, Aufrecht J, Bonito G, Engle N, Labbé JL, Doktycz MJ, Retterer S, Spatafora J, Stajich JE, Tschaplinski T, Vilgalys R. 2019. Microfluidics and metabolomics reveal symbiotic bacterial-fungal interactions between Mortierella elongata and Burkholderia include metabolite exchange. Frontiers in Microbiology. doi:10.3389/fmicb.2019.02163
  5. Du ZY, Kienkiewicz, Vande Pol N, Ostrom N, Benning C, Bonito G. 2019. Algal fungal symbiosis leads to photosynthetic mycelium. eLife.. 8:e47815 DOI: 10.7554/eLife.47815
  6. McCoy AG, Roth MG, Shay R, Jayawardana MA, Longley RM, Bonito G, Chilvers MI. 2019. Utilizing Next Generation Sequencing to Identify Fungal Species Associated with the Tar Spot Complex of Corn. Phytobiomes.
  7. Bonito G, Benucci GMN, Hameed K, Weighill D, Jones P, Chen KH, Jacobson D, Schadt C, Vilgalys R. 2019. Fungal-bacterial networks in the Populus rhizobiome are impacted by soil properties and host genotype. Frontiers in Microbiology. 10: 481.
  8. Abel EP, Ayres V, Birnbaum E, Bollen G, Bonito G, Bredeweg T, Clause H, Couture A, DeVore J, Dietrich M, Ellison P, Engle J, Ferrieri R, Fitzsimmons J, Friedman M, Georgobiani D, Graves S, Greene J, Lapi S, Loveless CS, Mastren T, Martinez-Gomez C, Mittig W, Morrissey D, Peaslee G, Pellemoine F, Robertson JD, Ronningen R, Shaughnessy D, Scielzo N, Scott M, Severin G, Shusterman J, Singh J, Stoyer M, Sutherlin L, Visser A, McGuinness S, Wilkinson J. 2019. Isotope Harvesting at FRIB: Additional opportunities for scientific discovery. Journal of Physics G: Nuclear and Particle Physics. 46: 100501.
  9. Khmelnitsky O, Davoodian N, Singh P, Raspé O, Lee S, Fechner N, Bonito G, Lebel T, Halling RE. 2019. Ionosporus: A new genus for Boletus longipes (Boletaceae), with a new species, I. australis, from Australia. Mycological Progress. 18(3): 439–451.
  10. Millet LJ, Aufrecht J, Labbé J, Uehling J, Vilgalys R, Estes ML, Guennoc CM, Deveau A, Olsson A, Bonito G, Doktycz MJ, Retterer ST. 2019. Increasing access to microfluidics for studying fungi and other branched biological structures. Fungal Biology and Biotechnology. 6 (1): 1.
  11. Wang X, Peng J, Sun L, Bonito G, Wang J, Cui W, Fu Y, Li Y. 2019. Genome sequencing illustrates the genetic basis of the pharmacological properties of Gloeostereum incarnatum. Genes. 1(10): 3 E188. doi: 10.3390/genes10030188
  12. Liao HL, Bonito G, Rojas JA, Hameed K, Wu S, Schadt CW, Labbé JL, Tuskan G, Martin FM, Greigoriev IV, Vilgalys R. 2019. Fungal endophytes of Populus trichocarpa alter host phenotype, gene expression and rhizobiome composition. Molecular Plant Microbial Interaction.
  13. Chang Y, Desirò A, Na H, Sandor L, Lipzen A, Clum A, Barry K, Grigoriev IV, Martin FM, Stajich JE, Smith ME, Bonito G, Spatafora JW. 2019. Phylogenomics of Endogonaceae and evolution of mycorrhizas within Mucoromycota. New Phytologist. 222(1): 511-525. doi:101111/nph15613.
  14. Benucci GMN, Bonito V, Bonito G. 2019. Fungal, Bacterial, and Archaeal diversity in soils beneath native and introduced plants in Fiji, South Pacific. Microbial Ecology. 78(1): 136-146. https://doiorg/101007/s00248-018-1266-1




  1. Zhi-Yan D, Alvaro J, Hyden B, Zienkiewicz K, Benning N, Zienkiewicz A, Bonito G, Benning C. 2018. Enhancing oil production and harvest by combining the marine alga Nannochloropsis oceanica and the oleaginous fungus Mortierella elongata. Biotechnology for Biofuels. 11:174.
  2. Hejase HA, Vande Pol N, Bonito GM, Liu KJ. 2018. FastNet: Fast and Accurate Statistical Inference of Phylogenetic Networks Using Large-Scale Genomic Sequence Data. In: Blanchette M., Ouangraoua A. (eds) Comparative Genomics. RECOMB-CG 2018. Lecture Notes in Computer Science, vol 11183. Pp.242-259. Springer, Cham.
  3. Misztal, Pawel K., Despoina S. Lymperopoulou, Rachel I. Adams, Russell A. Scott, Steven E. Lindow, Thomas Bruns, John W. Taylor, GM Bonito, R Vilgalys, A Goldstein. 2018. Emission Factors of Microbial Volatile Organic Compounds from Environmental Bacteria and Fungi. Environmental Science & Technology 52 (15): 8272–82.
  4. Aime MC, Urbina H, Liber J, Bonito G, Oono R. 2018. Two new endophytic Atractiellomycetes, Atractidochium hillariae and Proceropycnis hameedii. Mycologia. 110:1, 136-146.
  5. Grupe A, Sulzbacher MA, Grebenc T, Healy R, Bonito G, Smith ME. 2018. Tuber brennemanii and Tuber floridanum: two new Tuber species (Pezizales, Ascomycota) are among the most commonly detected ectomycorrhizal taxa within commercial pecan (Carya illinoinensis) orchards. Mycologia. 21:1-11. doi: 10.1080/00275514.2018.1490121
  6. Chen KH, Liao HL, Arnold AE, Bonito GM, Lutzoni F. 2018. RNA-Based Analyses Reveal Fungal Communities Structured by a Senescence Gradient in the Moss Dicranum scoparium and the Presence of Putative Multi-Trophic Fungi. The New Phytologist 218 (4): 1597–1611.
  7. Deveau A, Bonito GM, Uehling J, Paoletti M, Becker M, Bindschedler S, Hacquard S, Bonfante P, Wick L. 2018. Bacterial-Fungal Interactions: Ecology, Mechanisms and Challenges. FEMS Microbiology Reviews 42 (3): 335–52.
  8. Desirò, Alessandro, Zhen Hao, Julian A. Liber, Gian Maria Niccolò Benucci, David Lowry, Robert Roberson, and Bonito GM. 2018. Mycoplasma-Related Endobacteria within Mortierellomycotina Fungi: Diversity, Distribution and Functional Insights into Their Lifestyle. The ISME Journal 12 (7): 1743–57.
  9. Guevara G, Bonito G, Smith ME, Healy R, Grupe II AC, Cázares E, Castellano MA, Trappe JM. 2018. Tuber aztecorum sp. nov., a truffle species from Mexico belonging to the Maculatum clade (Tuberaceae, Pezizales). MycoKeys 30: 61-72.
  10. Páez CP, Bonito GM, Guevara-Guerrero G, Castellano MA, Garibay-Orijel R, Trappe JM, Rámirez RP. 2018. Description and distribution of Tuber incognitum sp. nov. and Tuber anniae in the Trans-Mexican Volcanic Belt. MycoKeys. 2018 Oct 11;(41):17-27. doi: 10.3897/mycokeys.41.28130. eCollection 2018
  11. Healy RA, Horner HT, Bonito G, McLaughlin DJ, Smith ME. 2018. 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.




  1. 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. 8 (2), 245-264.
  2. 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. International Society for Computational Biology. 107-114.
  3. Gdanetz K, Benucci GMN, VandePol NV, Bonito G. 2017. CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences. BMC Bioinformatics. 1(18)538-542.
  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. Mycologia.
  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.




  1. 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.
  2. 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
  3. Berch S. and Bonito G. 2016. Truffle diversity (Tuber) in British Columbia. Mycorrhiza. doi. 10.1007/s00572-016-0695-2
  4. 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.
  5. 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.
  6. Schuster TM, Stajsic V, Bonito G. 2016. False Polygonaceae Smut: First Record of Sphacelotheca polygoni-serrulati Maire for Victoria, Australia. Muelleria. 34: 82-101.
  7. 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.
  8. 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.  




  1. 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.




  1. 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
  2. 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.
  3. Berch S and Bonito G (2014) Cultivation of Tuber melanosporum and T. aestivum (Tuberaceae) in British Columbia, Canada. Mycorrhiza. 24: 473-479.
  4. 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.
  5. 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
  6. 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
  7. 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.
  8. 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.
  9. 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
  10. 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
  11. 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
  12. 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.
  13. 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
  14. 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.
  15. Bonito G, Brenneman T, Vilgalys R (2011) Ectomycorrhizal fungal diversity in orchards of cultivated pecan (Carya illinoinensis; Juglandaceae). Mycorrhiza. 21: 601-612.
  16. 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
  17. 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.
  18. 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
  19. 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
  20. 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.
  21. 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.
  22. Bonito G, Isikhuemhen O, Vilgalys R (2010) Identification of fungi associated with municipal compost using DNA-based techniques. Bioresource Technology.101: (3) 1021-1027.
  23. 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.
  24. 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.
  25. 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.
  26. Healy R, Bonito G, Guevara G (2009). Pachyphloeus marronius, a new truffle species from Iowa and Mexico. Mycotaxon. 107: 61-71.
  27. 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.
  28. 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.
  29. 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.
  30. 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.
  31. Bonito GM, Coleman DC, Haines BL, Cabrera ML (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.



Non-peer reviewed publications

  1. Miesel, J., G. Bonito, and M. Sakalidis. 2019. Which organisms benefit from biochar: microbes, weeds, or conifer seedlings? Great Lakes Christmas Tree Journal 15(1):8-9.
  2. 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.
  3. Bonito G, Hallan H, Volk T, Adams G (2016) May is Morel Month in Michigan. MSU Extension Bulletin E2755.
  4. E O Bonito, G. M., Benucci, G. M. N., Miesel, J. R., & Cregg, B. M. (2016, July). Mushroom and truffle specialty crop resources for the Michigan Christmas tree industry. Great Lakes Christmas Tree Journal, 11(3), pp. 8-9.
  5. Sharma J, Trela B, Wang S, Smith M, Bonito G (2012) Pecan truffle (Tuber lyonii) in Texas. Pecan South Magazine. Fall: 19-24.
  6. 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.
  7. 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.
  8. Bonito G, Vilgalys R, Isikhuemhen O (2008) Second annual truffle biotechnology workshop. Inoculum. 59(5).
  9. Bonito G and Casarez E (2007) Truffling, South of the border. Inoculum. 58: (32).
  10. Michener W and Bonito G (2003) Ecoinformatics training for field stations. The LTER Network Newsletter (1):10.
  11. Bonito G (2001) An in-situ environmental sensor resource - Website
  12. Bonito G, Porter D, and Davis D (2001) Brochure: Mushrooms and fungi at the Georgia State Botanical Garden, Athens, GA.