2023
M.N. Nickerson, L.P. Moore, J.M. U'Ren. 2023. Impact of polyphenolic compounds on the in vitro growth of oak-associated endophytic and saprotrophic fungi. Fungal Ecology, 62: 101226. https://doi.org/10.1016/j.funeco.2023.101226
L. Fauchery, M. Koriabine, L.P. Moore, Y, Yoshinaga, K. Barry, A. Kohler, J.M. U'Ren. 2023. Tissue Cultivation, Preparation, and Extraction of High Molecular Weight DNA for Single-Molecule Genome Sequencing of Plant-Associated Fungi. In. Methods in Molecular Biology. Eds. F. Martin & S. Uroz. Volume 2605, pgs. 79-102. 10.1007/978-1-0716-2871-3_5
2022
J.P. Shaffer, et al. 2022. Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity. Nature Microbiology. https://doi.org/10.1038/s41564-022-01266-x.
M.E.E. Franco, J.H. Wisecaver, A.E. Arnold, Y-M. Ju, J.C. Slot, S. Ahrendt, L.P. Moore, K.E. Eastman, K. Scott, Z. Konkel, JGI Team, E. Drula, B. Henrissat, H-M. Hsieh, K. Youens-Clark, F. Lutzoni, J. Miadlikowska, D.C. Eastwood, R.C. Hamelin, I.V. Grigoriev, J.M. U’Ren. 2022. Ecological generalism drives hyperdiversity of secondary metabolite gene clusters in xylarialean endophytes. New Phytologist. 233: 1317–1330. https://doi.org/10.1111/nph.17873
2021
A.J. Ponsero, B.H. Hurwitz, N. Magain, J. Miadlikowska, F. Lutzoni, J.M. U'Ren. 2021. Cyanolichen microbiome contains novel viruses that encode genes to promote microbial metabolism. ISME Communications 1:56. https://doi.org/10.1038/s43705-021-00060-w
J.M. U'Ren, N.B. Zimmerman. 2021. Oaks provide new perspective on seed microbiome assembly. New Phytologist, 230: 1293–1295 (Invited Commentary). https://doi.org/10.1111/nph.17305
A.E. Arnold, A.H. Harrington, Y-L. Huang, J.M. U'Ren, N.C. Massimo, V. Knight-Connoni, P. Inderbitzin. 2021. Coniochaeta elegans sp. nov., Coniochaeta montana sp. nov. and Coniochaeta nivea sp. nov., three new species of endophytes with distinctive morphology and functional traits. International Journal of Systematic and Evolutionary Microbiology 71:005003.
A.E. Arnold, A.H. Harrington, J.M. U'Ren, S. Oita, P. Inderbitzin. 2021. Two new endophytic species enrich the Coniochaeta endophytica/C. prunicola clade: Coniochaeta lutea sp. nov. and C. palaoa sp. nov. Plant and Fungal Systematics 66: 66–78. https://doi.org/10.35535/pfsyst-2021-0006
W. Qu, E.M.K. Wijeratne, B.P. Bashyal, J. Xu, Y-M. Xu, M.X. Liu, M.C. Inácio, A.E. Arnold, J.M. U’Ren, A.A.L. Gunatilaka. 2021. Strobiloscyphones A–F, 6-Isopentylsphaeropsidones and other metabolites from Strobiloscypha sp. AZ0266, a leaf-associated fungus of Douglas fir. Journal of Natural Products 84: 2575–2586. https://doi.org/10.1021/acs.jnatprod.1c00662
S. Oita, A. Ibáñez, F. Lutzoni, J. Miadlikowsk, J. Geml, L.A. Lewis, E.F.Y. Hom, I. Carbone, J.M. U’Ren, A.E. Arnold. 2021. Climate and seasonality drive the richness and composition of tropical fungal endophytes at a landscape scale. Communications Biology 4: 313. https://doi.org/10.1038/s42003-021-01826-7
S. Oita, J. Carey, I. Kline, A. Ibáñez, N. Yang, E.F.Y. Hom, I. Carbone, J. M. U’Ren, A.E. Arnold. 2021. Methodological approaches frame insights into endophyte richness and community composition. Microbial Ecology 82: 21–34. https://doi.org/10.1007/s00248-020-01654-y
2020
L. Selbmann, Z. Benkő, C. Coleine, S. de Hoog, C. Donati, I. Druzhinina, T. Emri, C.L. Ettinger, A.S. Gladfelter, A.A. Gorbushina, I.V. Grigoriev, M. Grube, N. Gunde-Cimerman, Z. Á. Karányi, B. Kocsis, T. Kubressoian, I. Miklós, M. Miskei, L. Muggia, T. Northen, M. Novak-Babič, C. Pennacchio, W.P. Pfliegler, I. Pòcsi, V. Prigione, M. Riquelme, N. Segata, J. Schumacher, E. Shelest, K. Sterflinger, D. Tesei, J.M U’Ren, G.C. Varese, X. Vázquez-Campos, V.A. Vicente, E.M. Souza, P. Zalar, A.K. Walker, J.E. Stajich. 2020. Shed Light in the DaRk LineagES of the Fungal Tree of Life—STRES. Life 10: 362. https://doi.org/10.3390/life10120362
Y.M. Xu, A.E. Arnold, J.M. U'Ren, L.J. Xuan, W.Q. Wang, A.A.L. Gunatilaka. 2020. Teratopyrones A–C, Dimeric Naphtho-γ-Pyrones and other metabolites from Teratosphaeria sp. AK1128, a fungal endophyte of Equisetum arvense. Molecules 25: 5058; https://doi.org/10.3390/molecules25215058.
A. Apprill, C. Miller, J. M. U’Ren, M. S. Leslie, L. Weber, R. Baird, J. Robbins, S. Landry, M. Niemeyer, G. Waring, A. Bogolomoni. 2020. Host phylogeny shapes marine mammal skin microbiomes. Royal Society Open Science. https://doi.org/10.1098/rsos.192046
2019
J.M. U'Ren, F. Lutzoni, J. Miadlikowska, N.B. Zimmerman, I. Carbone, G. May, A.E. Arnold. 2019. Host availability drives distributions of fungal endophytes in the imperiled boreal realm, Nature Ecology and Evolution 3: 1430–1437. https://doi.org/10.1038/s41559-019-0975-2
K. Dietzel, D. Valle, N. Fierer, J.M. U'Ren, A. Barberán. 2019. Geographical distribution of fungal plant pathogens in dust across the United States. Frontiers in Ecology and Evolution https://doi.org/10.3389/fevo.2019.00304
I. Carbone, J.B. White, J. Miadlikowska, A.E. Arnold, M.A. Miller, N. Magain, J.M. U'Ren, F. Lutzoni. 2019. T-BAS Version 2.1: Tree-Based Alignment Selector toolkit for evolutionary placement of DNA sequences and viewing alignments and specimen metadata on curated and custom trees. Microbiology Resource Announcements, https://doi.org/10.1128/MRA.00328-19
A. H. Harrington, M. del Olmo-Ruiz, J.M. U’Ren, K. Garcia, D.C. Sandberg, Y.L. Huang, M.T. Hoffman, A.E. Arnold. 2019. Coniochaeta endophytica sp. nov., a foliar endophyte associated with healthy photosynthetic tissue of Platycladus orientalis (Cupressaceae). Plant and Fungal Systematics 64: 65–79. https://doi.org/10.2478/pfs-2019-0008
M.J. Taylor, R.W. Mannan, J.M. U'Ren, N.P. Garber, R.E. Gallery, A.E. Arnold. 2019. Age-related variation in the oral microbiome of urban Cooper's hawks (Accipiter cooperii). BMC Microbiology 19: 47. https://doi.org/10.1186/s12866-019-1413-y
2018
Huang, Y.-L., E.A. Bowman, N.C. Massimo, N.P. Garber, J.M. U’Ren, D.C. Sandberg, A.E. Arnold. 2018. Using collections data to infer biogeographic, environmental, and host structure in communities of endophytic fungi. Mycologia, 110:1, 47–6. https://doi.org/10.1080/00275514.2018.1442078.
Padumadasa, C., Y.-M. Xu, E.M. Kithsiri Wijeratne, P. Espinosa, J.M. U’Ren, A.E. Arnold, A.A.L. Gunatilaka. 2018. Cytotoxic and non-cytotoxic metabolites from Teratosphaeria sp. FL2137, a fungus associated with Pinus clausa. Journal of Natural Products, J. Nat. Prod. 81: 616–624. https://doi.org/10.1021/acs.jnatprod.7b00838
B.L. Hurwitz, A. Ponsero, J. Thorton, Jr., J.M. U'Ren. 2018. Phage Hunters: computational strategies for finding phages in large-scale 'omics datasets. Virus Research. 244: 110–115. https://doi.org/10.1016/j.virusres.2017.10.019
2017
C. Sarmientoa, P-C. Zalamea, J.W. Dalling, A.S. Davis, S.M. Stump, J.M. U’Ren, A.E. Arnold. 2017. Soilborne fungi have host affinity and host-specific effects on seed germination and survival in a lowland tropical forest. Proceedings of the National Academy of Sciences USA. 114: 11458–11463. https://doi.org/10.1093/bioinformatics/btw808
J. Schaffer, J.M. U’Ren, R.E. Gallery, D.A.. Baltrus, A.E. Arnold. 2017. An endohyphal bacterium (Chitinophaga, Bacteroidetes) Alters carbon source use by Fusarium keratoplasticum (F. solani Species Complex, Nectriaceae). Frontiers in Microbiology 8:350. https://doi.org/10.3389/fmicb.2017.00350
I. Carbone, J.B. White, J. Miadlikowska, A.E. Arnold, M.A. Miller, F. Kauff, C. Schoch, J.M. U'Ren, G. May & F. Lutzoni. 2017. T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads, and metadata visualization, Bioinformatics 33: 1160–1168. https://doi.org/10.1093/bioinformatics/btw808
2016
J.M. U’Ren & A.E. Arnold. 2016. Diversity, distributions, and host associations of fungal communities in living, senescent, and fallen leaves at five sites across North America, Peer J e2768. https://doi.org/10.7717/peerj.2768
J.M. U’Ren, J. Miadlikowska, N. Zimmerman, J.E. Stajich, F. Lutzoni & A.E. Arnold. 2016. Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota). Molecular Phylogenetics and Evolution 98: 210–232. https://doi.org/10.1016/j.ympev.2016.02.010
B.L. Hurwitz & J.M. U’Ren. 2016. Viral metabolic reprogramming in marine ecosystems. Current Opinion in Microbiology 31: 161–168. https://doi.org/10.1016/j.mib.2016.04.002
B.L. Hurwitz, J.M. U’Ren & K. Youens-Clark. 2016. Computational prospecting in the great viral unknown. FEMS Microbiology Reviews. http://dx.doi.org/10.1093/femsle/fnw077.
2015
J.M. U'Ren, J.H. Wisecaver, A.L. Paek, B.L. Dunn & B.L. Hurwitz. 2015. Draft genome sequence of the ale-fermenting Saccharomyces cerevisiae strain GSY2239. Genome Announcements 3: 4. https://doi.org/10.1128/genomeA.00776-15
K.E.M. Wijeratne, G.M.K.B. Gunaherath, V.M. Chapla, J. Tillotson, F. de la Cruz, M. Kang, J.M. U’Ren, A.R. Araujo, A.E. Arnold, E. Chapman & AA.L. Gunatilaka. 2015. Oxaspirol B with p97 inhibitory activity and other oxaspirols from Lecythophora sp. FL1375 and FL1031, endolichenic fungal strains inhabiting Parmotrema tinctorum and Cladonia evansii. Journal of Natural Products 79:340–352. https://doi.org/10.1021/acs.jnatprod.5b00986
P.L. Chagnon, J.M. U'Ren, J. Miadlikowska, F. Lutzoni & A.E. Arnold. 2015. Interaction type influences ecological network structure more than local abiotic conditions: evidence from endophytic and endolichenic fungi at a continental scale. Oecologia https://doi.org/10.1007/s004442-015-3457-5.
Y-M. Xu, J. Mafezoli, M.C.F. de Oliveira, J.M. U’Ren, A.E. Arnold & A.A.L. Gunatilaka. 2015. Anteaglonialides A–F and Palmarumycins CE1–CE3 from Anteaglonium sp. FL0768, a fungal endophyte of the spikemoss Selaginella arenicola. Natural Product Communications 78: 2738–2747.
H. Wei H, Y.M. Xu, P. Espinosa-Artiles, M.X. Liu, J.G. Luo, J.M. U'Ren, A.E. Arnold & A.A.L. Gunatilaka. 2015. Sesquiterpenes and other constituents of Xylaria sp. NC1214, a fungal endophyte of the moss Hypnum sp. Phytochemistry 118: 102–8.
Y-L. Huang, M.M.N. Devan, J.M. U’Ren, S.H. Furr & A.E. Arnold. 2015. Pervasive effects of wildfire on foliar endophyte communities in montane forest trees. Microbial Ecology doi 10.1007/s00248-015-0664-x.
Y-M. Xu, B.P. Bashyal, M.X. Liu, P. Espinosa-Artiles, J.M. U'Ren, A.E. Arnold & A.A.L. Gunatilaka. 2015. Cytotoxic cytochalasins and other metabolites from Xylariaceae sp. FL0390, a fungal endophyte of Spanish moss. Natural Product Communications 10: 1655–1658.
N.C. Massimo, M.M.N. Devan, K.R. Arendt, M.H. Wilch, J.M. Riddle, S.H. Furr, C. Steen, J.M. U’Ren, D.C. Sandberg & A.E. Arnold. 2015. Fungal Endophytes in aboveground tissues of desert plants: infrequent in culture, but highly diverse and distinctive symbionts. Microbial Ecology 70: 61–76.
K-H. Chen, J. Miadlikowska, K. Molnár, A.E. Arnold, J.M. U’Ren, E. Gaya, C. Gueidan & F. Lutzoni. 2015. Phylogenetic analyses of eurotiomycetous endophytes reveal their close affinities to Chaetothyriales, Eurotiales and a new order – Phaeomoniellales. Molecular Phylogenetics and Evolution 85: 117–130.
2014
J.M. U’Ren, J.M. Riddle, J.T. Monacell, I. Carbone, J. Miadlikowska & A.E. Arnold. 2014. Tissue storage and primer selection influence pyrosequencing-based inferences of diversity and community composition of endolichenic and endophytic fungi. Molecular Ecology Resources 14: 1032–1048.
J-G. Luo, X. Wang, Y-M. Xu, J.M. U'Ren, A.E. Arnold, L-Y. Kong & A.A.L. Gunatilaka. 2014. Delitschiapyrone A, a Pyrone–naphthalenone Adduct bearing a new pentacyclic ring system from the leaf-associated fungus Delitschia sp. FL1581. Organic Letters 6: 5944–5947.
R. Oono, F. Lutzoni, A.E. Arnold, L. Kaye, J.M. U’Ren, G. May & I. Carbone. 2014. Genetic variation in horizontally transmitted fungal endophytes of pine needles reveals population structure in cryptic species. American Journal of Botany 101: 1362–1374.
2012
J.M. U'Ren, F. Lutzoni, J. Miadlikowska, A.D. Laetsch & A.E. Arnold. 2012. Host- and geographic structure of endophytic and endolichenic fungal communities at a continental scale. American Journal of Botany. 99: 898–914.
E.M.K. Wijeratne, B.P. Bashyal, M.X. Liu, D.D. Rocha, G.M. Kamal, B. Gunaherath, J.M. U’Ren, M.K. Gunatilaka, A.E. Arnold, L. Whitesell & A.A.L. Gunatilaka. 2012. Geopyxins A – E, ent-kaurane diterpenoids from endolichenic fungal strains, Geopyxis aff. majalis and Geopyxis sp. AZ0066: structure-activity relationships of geopyxins and their analogues. Journal of Natural Products. 75: 361–369.
2011
X-N Wang, B.P. Bashyal, E.M.K. Wijeratne, J.M. U’Ren, M.X. Liu, M.K. Gunatilaka, A.E. Arnold & A.A.L. Gunatilaka. 2011. Smardaesidins A – G, new isopimarane and 20-nor-isopimarane diterpenoids from Smardaea sp., a fungal endophyte of the moss Ceratodon purpureus. Journal of Natural Products. 74: 2052–2061.
2010
J.M. U'Ren, F. Lutzoni, J. Miadlikowska & A.E. Arnold. 2010. Community analysis reveals close affinities between endophytic and endolichenic fungi in mosses and lichens. Microbial Ecology 60: 340–353.
2009
J.M. U’Ren. 2009. Is the hope for a cellulosic biofuel a lot of rot? Environmental Microbiology. 11: 2475–2476.
T.S. Simonson, R.T. Okinaka, B. Wang, W.R. Easterday, L. Huynh, J.M. U'Ren, M. Dukerich, S.R. Zanecki, L.J. Kenefic, J. Beaudry, et al. 2009. Bacillus anthracis in China and its relationship to worldwide lineages. BMC Microbiology 9: 71.
J.M. U’Ren, J.W. Dalling, R.E. Gallery, D.R. Maddison, E.C. Davis, C.M. Gibson & A.E. Arnold. 2009. Diversity and evolutionary origins of fungi associated with seeds of a neotropical pioneer tree: a case study for analyzing environmental samples of fungi. Mycological Research 113: 432–449.
2007
J.M. U’Ren, H. Hornstra, T. Pearson, J.M. Schupp, B. Leadem, S. Georgia, R.W. Sermswan & P. Keim. 2007. Fine scale genetic diversity among Burkholderia pseudomallei soil isolates in Northeast Thailand. Journal of Applied and Environmental Microbiology 73: 6678–6681.
T. Pearson, J.M. U’Ren, J.M. Schupp, G. Allan, P.G. Foster, M.J. Mayo, D.Gal, J. Low Choy, R. Leadem Daugherty, S. Kachur, et al. 2007. VNTR analysis of selected outbreaks of Burkholderia pseudomallei in Australia. Infection, Genetics and Evolution 7: 416–423.
M. N. Van Ert, W.R. Easterday, L.Y. Huynh, R.T Okinaka, M.E. Hugh Jones, J. Ravel, S.R. Zanecki, T. Pearson, T.S. Simonson, J.M. U’Ren, et al. 2007. Global genetic population structure of Bacillus anthracis. PLoS One 5:e461.
J.M. U’Ren, J.M. Schupp, T. Pearson, H. Hornstra, C.L. Clark Friedman, K.L. Smith, R.R. Leadem Daugherty, S.D. Rhoton, B. Leadem, S. Georgia, et al. 2007. Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping. BMC Microbiology 7: 23.
M.N. Van Ert, W.R. Easterday, T.S. Simonson, J.M. U’Ren, T. Pearson, L.J. Kenefic, J.D. Busch, L.Y. Huynh, M. Dukerich, C.B. Trim, et al. 2007. Strain-specific single nucleotide polymorphism assays for the Bacillus anthracis Ames strain. Journal of Clinical Microbiology 45: 47–53.
2005
J.M. U’Ren, M.N. Van Ert, J.M. Schupp, W.R. Easterday, T. Simonson, R. Okinaka, T. Pearson & P. Keim. 2005. Use of a real-time PCR TaqMan assay for rapid identification and differentiation of Burkholderia pseudomallei and Burkholderia mallei. Journal of Clinical Microbiology 43: 5771–5774.
2004
T. Pearson, J. Busch, J. Ravel, T. Read, S. Rhoton, J.M. U’Ren, T. Simonson, S. Kachur, R. Leadem, M. Cardon, et al. 2004. Phylogenetic discovery bias in Bacillus anthracis using single nucleotide polymorphisms from whole genome sequencing. Proceedings of the National Academy of Sciences USA 101: 13536–13541.
M.I. Tenaillon, J. U'Ren, O. Tenaillon & B.S. Gaut. 2004. Selection versus demography: a multilocus investigation of the domestication process in maize. Molecular Biology and Evolution 21: 1214–1225.