Recent publications from the Vilgalys lab


Gregory Bonito, Khalid Hameed, Merje Toome-Heller, Rosaria Healy, Chantal Reid, Hui-Ling Liao, and Rytas Vilgalys.  Atractiella rhizophila, a novel endorrhizal fungus adapted to the root microbiome of Populus and diverse plant hosts”.  Mycologia (accepted)

Lisa M. Rosenthal, Karl-Henrik Larsson, Sara Branco, Judy A. Chung, Sydney I. Glassman, Hui-Ling Liao, Kabir G. Peay, Dylan P. Smith, Jennifer M. Talbot, John W. Taylor, Else C. Vellinga, Rytas Vilgalys, Thomas D. Bruns. 2016.  Survey of corticioid fungi in North American pinaceous forests reveals hyperdiversity, underpopulated sequence databases, and species that are potentially ectomycorrhizal.  Mycologia (accepted)

Liao, H.-L., Y. Chen, and R. Vilgalys. 2016. Metatranscriptomic Study of Common and Host-Specific Patterns of Gene Expression between Pines and Their Symbiotic Ectomycorrhizal Fungi in the Genus Suillus.  PLoS Genet 12(10): e1006348. doi:10.1371/journal.pgen.1006348

Branco, S., K. Bi, H.-L. Liao, P. Gladieux, H. Badouin, C. E. Ellison, N. H. Nguyen, R. Vilgalys, K. G. Peay, J. W. Taylor, and T. D. Bruns. 2016. Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes. Mol Ecol, doi: 10.1111/mec.13892.

Spatafora, J. W., Y. Chang, G. L. Benny, K. Lazarus, M. E. Smith, M. L. Berbee, G. Bonito, N. Corradi, I. Grigoriev, A. Gryganskyi, T. Y. James, K. O’Donnell, R. W. Roberson, T. N. Taylor, J. Uehling, R. Vilgalys, M. M. White, and J. E. Stajich. 2016. A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia 108:1028–1046.

Li, Z., Q. Yao, S. P. Dearth, M. R. Entler, H. F. Castro Gonzalez, J. K. Uehling, R. J. Vilgalys, G. B. Hurst, S. R. Campagna, J. L. Labbé, and C. Pan. 2016. Integrated Proteomics and Metabolomics Suggests Symbiotic Metabolism and Multimodal Regulation in a Fungal-Endobacterial System. Environmental Microbiology doi: 10.1111/1462-2920.13605.

Bonito, G., K. Hameed, R. Ventura, J. Krishnan, C. W. Schadt, and R. Vilgalys. 2016. Isolating a functionally relevant guild of fungi from the root microbiome of Populus. Fungal Ecology 22:35–42. Elsevier Ltd.

Johansen, R. B., P. Johnston, P. Mieczkowski, G. L. W. Perry, M. S. Robeson, B. R. Burns, and R. Vilgalys. 2016. Fungal Ecology. Fungal Ecology 23:141–155.

González, D., M. Rodriguez-Carres, T. Boekhout, J. Stalpers, E. E. Kuramae, A. K. Nakatani, R. Vilgalys, and M. A. Cubeta. 2016. Phylogenetic relationships of. Fungal Biology 120:603–619.

Ekblad, A., A. Mikusinska, G. I. Ågren, L. Menichetti, H. Wallander, R. Vilgalys, A. Bahr, and U. Eriksson. 2016. Production and turnover of ectomycorrhizal extramatrical mycelial biomass and necromass under elevated CO2 and nitrogen fertilization. The New Phytologist.  doi: 10.1111/nph.13961


Branco, S., P. Gladieux, C. E. Ellison, A. Kuo, K. LaButti, A. Lipzen, I. V. Grigoriev, H.-L. Liao, R. Vilgalys, K. G. Peay, J. W. Taylor, and T. D. Bruns. 2015. Genetic isolation between two recently diverged populations of a symbiotic fungus. Molecular Ecology 24:2747–2758.

 Guevara, G. G., G. Bonito, E. Cázares, R. A. Healy, R. Vilgalys, and J. Trappe. 2015. Novel Tuber spp. (Tuberaceae, Pezizales) in the Puberulum Group from Mexico. 7:367–374.

Glassman, S. I., Peay, K. G., Talbot, J. M., Smith, D. P., Chung, J. A., Taylor, J. W., et al. (2015). A continental view of pine-associated ectomycorrhizal fungal spore banks: a quiescent functional guild with a strong biogeographic pattern. The New Phytologist, n/a–n/a. doi:10.1111/nph.13240


Kuske, C. R., C. N. Hesse, J. F. Challacombe, D. Cullen, J. R. Herr, R. C. Mueller, A. Tsang, and R. Vilgalys. 2015. Prospects and challenges for fungal metatranscriptomics of complex communities. Fungal Ecology

Bonito, G., Reynolds, H., Robeson, M. S., Nelson, J., Hodkinson, B. P., Tuskan, G., et al. (2014). Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants. Molecular Ecology, 23(13), 3356–3370. doi:10.1111/mec.12821

Cubeta, M. A., Thomas, E., Dean, R. A., Jabaji, S., Neate, S. M., Tavantzis, S., et al. (2014). Draft Genome Sequence of the Plant-Pathogenic Soil Fungus Rhizoctonia solani Anastomosis Group 3 Strain Rhs1AP. Genome Announcements, 2(5). doi:10.1128/genomeA.01072-14

Liao, H. L., Chen, Y., Bruns, T. D., Peay, K. G., Taylor, J. W., Branco, S., et al. (2014). Metatranscriptomic analysis of ectomycorrhizal roots reveals genes associated with Piloderma-Pinus symbiosis: improved methodologies for assessing gene expression in situ. Environmental Microbiology …, 16(12), 3730–3742. doi:10.1111/1462-2920.12619

Losada, L., Pakala, S. B., Fedorova, N. D., Joardar, V., Shabalina, S. A., Hostetler, J., et al. (2014). Mobile elements and mitochondrial genome expansion in the soil fungus and potato pathogen Rhizoctonia solani AG-3. FEMS Microbiology Letters., 352(2), 165–173. doi:10.1111/1574-6968.12387

Talbot, J. M., Bruns, T. D., Taylor, J. W., Smith, D. P., Branco, S., Glassman, S. I., et al. (2014). Endemism and functional convergence across the North American soil mycobiome. Proceedings of the National Academy of Sciences, 111(17), 6341–6346. doi:10.1073/pnas.1402584111


Benítez, M.-S., Hersh, M. H., Vilgalys, R., & Clark, J. S. (2013). Pathogen regulation of plant diversity via effective specialization. Trends in Ecology & Evolution (Personal Edition), 28(12), 705–711. doi:10.1016/j.tree.2013.09.005

Bonito, G., Smith, M. E., Nowak, M., Healy, R. A., Guevara, G., Cázares, E., et al. (2013). PLOS ONE: Historical Biogeography and Diversification of Truffles in the Tuberaceae and Their Newly Identified Southern Hemisphere Sister Lineage. PLoS ONE, 8(1), e52765. doi:10.1371/journal.pone.0052765.s003

Golonka, A. M., & Vilgalys, R. (2013). Nectar Inhabiting Yeasts in Virginian Populations of Silene latifolia (Caryophyllaceae) and Coflowering Species. The American Midland Naturalist.

Gryganskyi, A. P., Humber, R. A., Smith, M. E., Hodge, K., Huang, B., Voigt, K., & Vilgalys, R. (2013a). Phylogenetic lineages in Entomophthoromycota. Persoonia – Molecular Phylogeny and Evolution of Fungi, 30(1), 94–105. doi:10.3767/003158513X666330

Gryganskyi, A. P., Humber, R. A., Smith, M. E., Miadlikowska, J., Wu, S., Voigt, K., et al. (2013b). Molecular phylogeny of the Entomophthoromycota (vol 65, pg 682, 2012). Molecular Phylogenetics and Evolution, 66(3), 1099–1099. doi:10.1016/j.ympev.2012.11.001

Gryganskyi, A. P., Humber, R. A., Stajich, J. E., Mullens, B., Anishchenko, I. M., & Vilgalys, R. (2013c). Sequential Utilization of Hosts from Different Fly Families by Genetically Distinct, Sympatric Populations within the Entomophthora muscae Species Complex. PLoS ONE, 8(8), e71168. doi:10.1371/journal.pone.0071168.s002

Guevara, G., Bonito, G., Trappe, J. M., Cázares, E., Williams, G., Healy, R. A., et al. (2013). New North American truffles (Tuber spp.) and their ectomycorrhizal associations. Mycologia, 105(1), 194–209. doi:10.3852/12-087

Healy, R. A., Smith, M. E., Bonito, G. M., Pfister, D. H., Ge, Z. W., Guevara, G. G., et al. (2013). High diversity and widespread occurrence of mitotic spore mats in ectomycorrhizal Pezizales. Molecular Ecology, 22(6), 1717–1732. doi:10.1111/mec.12135

Husbands, D. R., Henkel, T. W., Bonito, G., Vilgalys, R., & Smith, M. E. (2013). New species of Xerocomus (Boletales) from the Guiana Shield, with notes on their mycorrhizal status and fruiting occurrence. Mycologia, 105(2), 422–435. doi:10.3852/12-146

Lodge, D. J., Padamsee, M., Matheny, P. B., Aime, M. C., Cantrell, S. A., Boertmann, D., et al. (2013). Molecular phylogeny, morphology, pigment chemistry and ecology in Hygrophoraceae (Agaricales). Fungal Diversity. doi:10.1007/s13225-013-0259-0

Shakya, M., Gottel, N., Castro, H., Yang, Z. K., Gunter, L., Labbé, J., et al. (2013). A Multifactor Analysis of Fungal and Bacterial Community Structure in the Root Microbiome of Mature Populus deltoides Trees. PLoS ONE, 8(10), e76382. doi:10.1371/journal.pone.0076382

Smith, M. E., Henkel, T. W., Uehling, J. K., Fremier, A. K., Clarke, H. D., & Vilgalys, R. (2013). The Ectomycorrhizal Fungal Community in a Neotropical Forest Dominated by the Endemic Dipterocarp Pakaraimaea dipterocarpacea. PLoS ONE, 8(1), e55160. doi:10.1371/journal.pone.0055160.t003

Weber, C. F., Vilgalys, R., & Kuske, C. R. (2013). Changes in Fungal Community Composition in Response to Elevated Atmospheric CO2 and Nitrogen Fertilization Varies with Soil Horizon. Frontiers in Microbiology, 4, 1–14. doi:10.3389/fmicb.2013.00078/abstract


Bonito, G., Matthew E Smith, Brenneman, T., & Vilgalys, R. (2012a). Assessing ectomycorrhizal fungal spore banks of truffle producing soils with pecan seedling trap-plants. Plant and Soil, 356(1-2), 357–366. doi:10.1007/s11104-012-1127-5

Bonito, G., Smith, M. E., Brenneman, T., & Vilgalys, R. (2012b). Assessing ectomycorrhizal fungal spore banks of truffle producing soils with pecan seedling trap-plants. Plant and Soil, 356(1-2), 357–366. doi:10.1007/s11104-012-1127-5

Dunbar, J., Eichorst, S. A., Gallegos-Graves, L. V., Silva, S., Xie, G., Hengartner, N. W., et al. (2012). Common bacterial responses in six ecosystems exposed to 10 years of elevated atmospheric carbon dioxide. Environmental Microbiology …, 14(5), 1145–1158. doi:10.1111/j.1462-2920.2011.02695.x

Gryganskyi, A. P., Humber, R. A., Smith, M. E., Miadlikowska, J., Miadlikovska, J., Wu, S., et al. (2012). Molecular phylogeny of the Entomophthoromycota. Molecular Phylogenetics and Evolution, 65(2), 682–694. doi:10.1016/j.ympev.2012.07.026

Hersh, M., Vilgalys, R., & Clark, J. (2012). Evaluating the impacts of multiple generalist fungal pathogens on temperate tree seedling survival. Ecology.

Talbot, J. M., Bruns, T. D., Smith, D. P., Branco, S., Glassman, S. I., Erlandson, S., et al. (2012). Independent roles of ectomycorrhizal and saprotrophic communities in soil organic matter decomposition. Soil Biology and Biochemistry.

Uehling, J. K., Henkel, T. W., Aime, M. C., Vilgalys, R., & Matthew E Smith. (2012a). New species of Clavulina (Cantharellales, Basidiomycota) with resupinate and effused basidiomata from the Guiana Shield. Mycologia, 104(2), 547–556. doi:10.3852/11-130

Uehling, J. K., Henkel, T. W., Vilgalys, R., & Matthew E Smith. (2012b). Membranomyces species are common ectomycorrhizal symbionts in Northern Hemisphere forests. Mycorrhiza. doi:10.1007/s00572-012-0457-8


Baroni TY, Hofstetter V, Largent DL, Vilgalys R: Entocybe is proposed as a new genus in the Entolomataceae (Agaricomycetes, Basidiomycota) based on morphological and molecular evidence. North American Fungi 2011, 6:1–19.

Bonito G, Brenneman T, Vilgalys R. 2011. Ectomycorrhizal fungal diversity in orchards of cultivated pecan (carya illinoinensis; juglandaceae). Mycorrhiza 21: 601-612. 0940-6360

Bonito G, Trappe JM, Donovan S, Vilgalys R: The Asian black truffle Tuber indicum can form ectomycorrhizas with North American host plants and complete its life cycle in non-native soils. Fungal Ecology 2011, 4:83–93.  1754-5048

Gottel NR, Castro HF, Kerley M, Yang Z, Pelletier DA, Podar M, Karpinets T, Uberbacher E, Tuskan GA, Vilgalys R, Doktycz MJ, Schadt CW. 2011. Distinct microbial communities within the endosphere and rhizosphere of populus deltoides roots across contrasting soil types. Applied and Environmental Microbiology 77: 5934-5944. 10.1128/AEM.05255-11

Henkel TW, Aime MC, Chin MML, Miller SL, Vilgalys R, Matthew E Smith: Ectomycorrhizal fungal sporocarp diversity and discovery of new taxa in Dicymbe monodominant forests of the Guiana Shield. Biodivers Conserv 2011, doi:10.1007/s10531-011-0166-1.

Porter TM, Martin W, James TY, Longcore JE, Gleason FH, Adler PH, Letcher PM, Vilgalys R. 2011. Molecular phylogeny of the Blastocladiomycota (Fungi) based on nuclear ribosomal DNA. Fungal Biology 115: 381-392. 10.1016/j.funbio.2011.02.004

Smith ME, Henkel TW, Catherine Aime M, Fremier AK, Vilgalys R. 2011. Ectomycorrhizal fungal diversity and community structure on three co-occurring leguminous canopy tree species in a neotropical rainforest. New Phytologist 192: 699-712. 10.1111/j.1469-8137.2011.03844.x

Weber CF, Zak DR, Hungate BA, Jackson RB, Vilgalys R, Evans RD, Schadt CW, Megonigal JP, Kuske CR. 2011. Responses of soil cellulolytic fungal communities to elevated atmospheric co(2)  are complex and variable across five ecosystems. Environmental Microbiology 13: 2778-2793. 10.1111/j.1462-2920.2011.02548.x


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