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Increasing access to microfluidics for studying fungi and other branched biological structures.

Millet LJ, Aufrecht J, Labbé J, Uehling J, Vilgalys R, Estes ML, Miquel Guennoc C, Deveau A, Olsson S, Bonito G, Doktycz MJ, Retterer ST.

Fungal Biol Biotechnol. 2019 Jun 10;6:1. doi: 10.1186/s40694-019-0071-z. eCollection 2019. Erratum in: Fungal Biol Biotechnol. 2019 Jul 31;6:10.


Spatiotemporal Transformation in the Alkaloid Profile of Pinus Roots in Response to Mycorrhization.

Veličkovic D, Liao HL, Vilgalys R, Chu RK, Anderton CR.

J Nat Prod. 2019 May 24;82(5):1382-1386. doi: 10.1021/acs.jnatprod.8b01050. Epub 2019 Apr 22.


Fungal-Bacterial Networks in the Populus Rhizobiome Are Impacted by Soil Properties and Host Genotype.

Bonito G, Benucci GMN, Hameed K, Weighill D, Jones P, Chen KH, Jacobson D, Schadt C, Vilgalys R.

Front Microbiol. 2019 Mar 29;10:481. doi: 10.3389/fmicb.2019.00481. eCollection 2019.


Fungal Endophytes of Populus trichocarpa Alter Host Phenotype, Gene Expression, and Rhizobiome Composition.

Liao HL, Bonito G, Rojas JA, Hameed K, Wu S, Schadt CW, Labbé J, Tuskan GA, Martin F, Grigoriev IV, Vilgalys R.

Mol Plant Microbe Interact. 2019 Jul;32(7):853-864. doi: 10.1094/MPMI-05-18-0133-R. Epub 2019 Jun 10.


Phylogenetic taxon definitions for Fungi, Dikarya, Ascomycota and Basidiomycota.

Hibbett DS, Blackwell M, James TY, Spatafora JW, Taylor JW, Vilgalys R.

IMA Fungus. 2018 Jul;9:291-298. doi: 10.5598/imafungus.2018.09.02.05. Epub 2018 Sep 12.


Suilloid fungi as global drivers of pine invasions.

Policelli N, Bruns TD, Vilgalys R, Nuñez MA.

New Phytol. 2019 Apr;222(2):714-725. doi: 10.1111/nph.15660. Epub 2019 Jan 28.


Correction: Metatranscriptomic Study of Common and Host-Specific Patterns of Gene Expression between Pines and Their Symbiotic Ectomycorrhizal Fungi in the Genus Suillus.

Liao HL, Chen Y, Vilgalys R.

PLoS Genet. 2018 Oct 19;14(10):e1007742. doi: 10.1371/journal.pgen.1007742. eCollection 2018 Oct.


Emission Factors of Microbial Volatile Organic Compounds from Environmental Bacteria and Fungi.

Misztal PK, Lymperopoulou DS, Adams RI, Scott RA, Lindow SE, Bruns T, Taylor JW, Uehling J, Bonito G, Vilgalys R, Goldstein AH.

Environ Sci Technol. 2018 Aug 7;52(15):8272-8282. doi: 10.1021/acs.est.8b00806. Epub 2018 Jul 13.


Phylogenetic and Phylogenomic Definition of Rhizopus Species.

Gryganskyi AP, Golan J, Dolatabadi S, Mondo S, Robb S, Idnurm A, Muszewska A, Steczkiewicz K, Masonjones S, Liao HL, Gajdeczka MT, Anike F, Vuek A, Anishchenko IM, Voigt K, de Hoog GS, Smith ME, Heitman J, Vilgalys R, Stajich JE.

G3 (Bethesda). 2018 May 31;8(6):2007-2018. doi: 10.1534/g3.118.200235. Erratum in: G3 (Bethesda). 2019 Aug 8;9(8):2789.


The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome.

Cregger MA, Veach AM, Yang ZK, Crouch MJ, Vilgalys R, Tuskan GA, Schadt CW.

Microbiome. 2018 Feb 12;6(1):31. doi: 10.1186/s40168-018-0413-8.


Investigating niche partitioning of ectomycorrhizal fungi in specialized rooting zones of the monodominant leguminous tree Dicymbe corymbosa.

Smith ME, Henkel TW, Williams GC, Aime MC, Fremier AK, Vilgalys R.

New Phytol. 2017 Jul;215(1):443-453. doi: 10.1111/nph.14570. Epub 2017 May 11.


Hijacked: Co-option of host behavior by entomophthoralean fungi.

Gryganskyi AP, Mullens BA, Gajdeczka MT, Rehner SA, Vilgalys R, Hajek AE.

PLoS Pathog. 2017 May 4;13(5):e1006274. doi: 10.1371/journal.ppat.1006274. eCollection 2017 May. No abstract available.


Survey of corticioid fungi in North American pinaceous forests reveals hyperdiversity, underpopulated sequence databases, and species that are potentially ectomycorrhizal.

Rosenthal LM, Larsson KH, Branco S, Chung JA, Glassman SI, Liao HL, Peay KG, Smith DP, Talbot JM, Taylor JW, Vellinga EC, Vilgalys R, Bruns TD.

Mycologia. 2017;109(1):115-127. doi: 10.1080/00275514.2017.1281677. Epub 2017 Jan 19.


Atractiella rhizophila, sp. nov., an endorrhizal fungus isolated from the Populus root microbiome.

Bonito G, Hameed K, Toome-Heller M, Healy R, Reid C, Liao HL, Aime MC, Schadt C, Vilgalys R.

Mycologia. 2017;109(1):18-26. doi: 10.1080/00275514.2016.1271689. Epub 2017 Jan 9.


Correction: Metatranscriptomic Study of Common and Host-Specific Patterns of Gene Expression between Pines and Their Symbiotic Ectomycorrhizal Fungi in the Genus Suillus.

Liao HL, Chen Y, Vilgalys R.

PLoS Genet. 2017 Jan 26;13(1):e1006575. doi: 10.1371/journal.pgen.1006575. eCollection 2017 Jan.


Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigens.

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.

Environ Microbiol. 2017 Aug;19(8):2964-2983. doi: 10.1111/1462-2920.13669. Epub 2017 Feb 1.


A New Perspective on Sustainable Soil Remediation-Case Study Suggests Novel Fungal Genera Could Facilitate in situ Biodegradation of Hazardous Contaminants.

Czaplicki LM, Cooper E, Ferguson PL, Stapleton HM, Vilgalys R, Gunsch CK.

Remediation (N Y). 2016 Spring;26(2):59-72. Epub 2016 Mar 2.


Integrated proteomics and metabolomics suggests symbiotic metabolism and multimodal regulation in a fungal-endobacterial system.

Li Z, Yao Q, Dearth SP, Entler MR, Castro Gonzalez HF, Uehling JK, Vilgalys RJ, Hurst GB, Campagna SR, Labbé JL, Pan C.

Environ Microbiol. 2017 Mar;19(3):1041-1053. doi: 10.1111/1462-2920.13605. Epub 2017 Jan 30.


Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes.

Branco S, Bi K, Liao HL, Gladieux P, Badouin H, Ellison CE, Nguyen NH, Vilgalys R, Peay KG, Taylor JW, Bruns TD.

Mol Ecol. 2017 Apr;26(7):2063-2076. doi: 10.1111/mec.13892. Epub 2016 Nov 4.


A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data.

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, Roberson RW, Taylor TN, Uehling J, Vilgalys R, White MM, Stajich JE.

Mycologia. 2016 Sep;108(5):1028-1046.


Production and turnover of ectomycorrhizal extramatrical mycelial biomass and necromass under elevated CO2 and nitrogen fertilization.

Ekblad A, Mikusinska A, Ågren GI, Menichetti L, Wallander H, Vilgalys R, Bahr A, Eriksson U.

New Phytol. 2016 Aug;211(3):874-85. doi: 10.1111/nph.13961. Epub 2016 Apr 27.


Phylogenetic relationships of Rhizoctonia fungi within the Cantharellales.

Gónzalez D, Rodriguez-Carres M, Boekhout T, Stalpers J, Kuramae EE, Nakatani AK, Vilgalys R, Cubeta MA.

Fungal Biol. 2016 Apr;120(4):603-619. doi: 10.1016/j.funbio.2016.01.012. Epub 2016 Jan 29.


Genetic isolation between two recently diverged populations of a symbiotic fungus.

Branco S, Gladieux P, Ellison CE, Kuo A, LaButti K, Lipzen A, Grigoriev IV, Liao HL, Vilgalys R, Peay KG, Taylor JW, Bruns TD.

Mol Ecol. 2015 Jun;24(11):2747-58. doi: 10.1111/mec.13132. Epub 2015 Apr 2.


A continental view of pine-associated ectomycorrhizal fungal spore banks: a quiescent functional guild with a strong biogeographic pattern.

Glassman SI, Peay KG, Talbot JM, Smith DP, Chung JA, Taylor JW, Vilgalys R, Bruns TD.

New Phytol. 2015 Mar;205(4):1619-31. doi: 10.1111/nph.13240. Epub 2015 Jan 3.


Draft Genome Sequence of the Plant-Pathogenic Soil Fungus Rhizoctonia solani Anastomosis Group 3 Strain Rhs1AP.

Cubeta MA, Thomas E, Dean RA, Jabaji S, Neate SM, Tavantzis S, Toda T, Vilgalys R, Bharathan N, Fedorova-Abrams N, Pakala SB, Pakala SM, Zafar N, Joardar V, Losada L, Nierman WC.

Genome Announc. 2014 Oct 30;2(5). pii: e01072-14. doi: 10.1128/genomeA.01072-14.


Metatranscriptomic analysis of ectomycorrhizal roots reveals genes associated with Piloderma-Pinus symbiosis: improved methodologies for assessing gene expression in situ.

Liao HL, Chen Y, Bruns TD, Peay KG, Taylor JW, Branco S, Talbot JM, Vilgalys R.

Environ Microbiol. 2014 Dec;16(12):3730-42. doi: 10.1111/1462-2920.12619. Epub 2014 Oct 22.


Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants.

Bonito G, Reynolds H, Robeson MS 2nd, Nelson J, Hodkinson BP, Tuskan G, Schadt CW, Vilgalys R.

Mol Ecol. 2014 Jul;23(13):3356-70. doi: 10.1111/mec.12821.


Endemism and functional convergence across the North American soil mycobiome.

Talbot JM, Bruns TD, Taylor JW, Smith DP, Branco S, Glassman SI, Erlandson S, Vilgalys R, Liao HL, Smith ME, Peay KG.

Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6341-6. doi: 10.1073/pnas.1402584111. Epub 2014 Apr 14.


Mobile elements and mitochondrial genome expansion in the soil fungus and potato pathogen Rhizoctonia solani AG-3.

Losada L, Pakala SB, Fedorova ND, Joardar V, Shabalina SA, Hostetler J, Pakala SM, Zafar N, Thomas E, Rodriguez-Carres M, Dean R, Vilgalys R, Nierman WC, Cubeta MA.

FEMS Microbiol Lett. 2014 Mar;352(2):165-73. doi: 10.1111/1574-6968.12387. Epub 2014 Feb 17.


A multifactor analysis of fungal and bacterial community structure in the root microbiome of mature Populus deltoides trees.

Shakya M, Gottel N, Castro H, Yang ZK, Gunter L, Labbé J, Muchero W, Bonito G, Vilgalys R, Tuskan G, Podar M, Schadt CW.

PLoS One. 2013 Oct 16;8(10):e76382. doi: 10.1371/journal.pone.0076382. eCollection 2013.


Pathogen regulation of plant diversity via effective specialization.

Benítez MS, Hersh MH, Vilgalys R, Clark JS.

Trends Ecol Evol. 2013 Dec;28(12):705-11. doi: 10.1016/j.tree.2013.09.005. Epub 2013 Sep 30.


Phylogenetic lineages in Entomophthoromycota.

Gryganskyi AP, Humber RA, Smith ME, Hodge K, Huang B, Voigt K, Vilgalys R.

Persoonia. 2013 Jun;30:94-105. doi: 10.3767/003158513X666330. Epub 2013 Mar 19.


Sequential utilization of hosts from different fly families by genetically distinct, sympatric populations within the Entomophthora muscae species complex.

Gryganskyi AP, Humber RA, Stajich JE, Mullens B, Anishchenko IM, Vilgalys R.

PLoS One. 2013 Aug 8;8(8):e71168. doi: 10.1371/journal.pone.0071168. eCollection 2013.


Changes in Fungal Community Composition in Response to Elevated Atmospheric CO2 and Nitrogen Fertilization Varies with Soil Horizon.

Weber CF, Vilgalys R, Kuske CR.

Front Microbiol. 2013 Apr 9;4:78. doi: 10.3389/fmicb.2013.00078. eCollection 2013.


The ectomycorrhizal fungal community in a neotropical forest dominated by the endemic dipterocarp Pakaraimaea dipterocarpacea.

Smith ME, Henkel TW, Uehling JK, Fremier AK, Clarke HD, Vilgalys R.

PLoS One. 2013;8(1):e55160. doi: 10.1371/journal.pone.0055160. Epub 2013 Jan 31.


Historical biogeography and diversification of truffles in the Tuberaceae and their newly identified southern hemisphere sister lineage.

Bonito G, Smith ME, Nowak M, Healy RA, Guevara G, Cázares E, Kinoshita A, Nouhra ER, Domínguez LS, Tedersoo L, Murat C, Wang Y, Moreno BA, Pfister DH, Nara K, Zambonelli A, Trappe JM, Vilgalys R.

PLoS One. 2013;8(1):e52765. doi: 10.1371/journal.pone.0052765. Epub 2013 Jan 2.


New species and distribution records for Clavulina (Cantharellales, Basidiomycota) from the Guiana Shield, with a key to the lowland neotropical taxa.

Uehling JK, Henkel TW, Aime MC, Vilgalys R, Smith ME.

Fungal Biol. 2012 Dec;116(12):1263-74. doi: 10.1016/j.funbio.2012.09.004. Epub 2012 Nov 7.


High diversity and widespread occurrence of mitotic spore mats in ectomycorrhizal Pezizales.

Healy RA, Smith ME, Bonito GM, Pfister DH, Ge ZW, Guevara GG, Williams G, Stafford K, Kumar L, Lee T, Hobart C, Trappe J, Vilgalys R, McLaughlin DJ.

Mol Ecol. 2013 Mar;22(6):1717-32. doi: 10.1111/mec.12135. Epub 2012 Dec 3.


New species of Xerocomus (Boletales) from the Guiana Shield, with notes on their mycorrhizal status and fruiting occurrence.

Husbands DR, Henkel TW, Bonito G, Vilgalys R, Smith ME.

Mycologia. 2013 Mar-Apr;105(2):422-35. doi: 10.3852/12-146. Epub 2012 Oct 18.


New North American truffles (Tuber spp.) and their ectomycorrhizal associations.

Guevara G, Bonito G, Trappe JM, Cázares E, Williams G, Healy RA, Schadt C, Vilgalys R.

Mycologia. 2013 Jan-Feb;105(1):194-209. doi: 10.3852/12-087. Epub 2012 Sep 6.


Molecular phylogeny of the Entomophthoromycota.

Gryganskyi AP, Humber RA, Smith ME, Miadlikowska J, Wu S, Voigt K, Walther G, Anishchenko IM, Vilgalys R.

Mol Phylogenet Evol. 2012 Nov;65(2):682-94. doi: 10.1016/j.ympev.2012.07.026. Epub 2012 Aug 2. Erratum in: Mol Phylogenet Evol. 2013 Mar;66(3):1099. Miadlikovska, Jolanta [corrected to Miadlikowska, Jolanta].


Membranomyces species are common ectomycorrhizal symbionts in Northern Hemisphere forests.

Uehling JK, Henkel TW, Vilgalys R, Smith ME.

Mycorrhiza. 2012 Oct;22(7):577-81. doi: 10.1007/s00572-012-0457-8. Epub 2012 Jul 31.


Evaluating the impacts of multiple generalist fungal pathogens on temperate tree seedling survival.

Hersh MH, Vilgalys R, Clark JS.

Ecology. 2012 Mar;93(3):511-20.


Common bacterial responses in six ecosystems exposed to 10 years of elevated atmospheric carbon dioxide.

Dunbar J, Eichorst SA, Gallegos-Graves LV, Silva S, Xie G, Hengartner NW, Evans RD, Hungate BA, Jackson RB, Megonigal JP, Schadt CW, Vilgalys R, Zak DR, Kuske CR.

Environ Microbiol. 2012 May;14(5):1145-58. doi: 10.1111/j.1462-2920.2011.02695.x. Epub 2012 Jan 20.


New species of Clavulina (Cantharellales, Basidiomycota) with resupinate and effused basidiomata from the Guiana Shield.

Uehling JK, Henkel TW, Aime MC, Vilgalys R, Smith ME.

Mycologia. 2012 Mar-Apr;104(2):547-56. doi: 10.3852/11-130. Epub 2011 Nov 8.


Responses of soil cellulolytic fungal communities to elevated atmospheric CO₂ are complex and variable across five ecosystems.

Weber CF, Zak DR, Hungate BA, Jackson RB, Vilgalys R, Evans RD, Schadt CW, Megonigal JP, Kuske CR.

Environ Microbiol. 2011 Oct;13(10):2778-93. doi: 10.1111/j.1462-2920.2011.02548.x. Epub 2011 Sep 1.


Ectomycorrhizal fungal diversity and community structure on three co-occurring leguminous canopy tree species in a Neotropical rainforest.

Smith ME, Henkel TW, Catherine Aime M, Fremier AK, Vilgalys R.

New Phytol. 2011 Nov;192(3):699-712. doi: 10.1111/j.1469-8137.2011.03844.x. Epub 2011 Aug 24.


Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types.

Gottel NR, Castro HF, Kerley M, Yang Z, Pelletier DA, Podar M, Karpinets T, Uberbacher E, Tuskan GA, Vilgalys R, Doktycz MJ, Schadt CW.

Appl Environ Microbiol. 2011 Sep;77(17):5934-44. doi: 10.1128/AEM.05255-11. Epub 2011 Jul 15.


Molecular phylogeny of the Blastocladiomycota (Fungi) based on nuclear ribosomal DNA.

Porter TM, Martin W, James TY, Longcore JE, Gleason FH, Adler PH, Letcher PM, Vilgalys R.

Fungal Biol. 2011 Apr-May;115(4-5):381-92. doi: 10.1016/j.funbio.2011.02.004. Epub 2011 Feb 13.


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