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the Taylor lab

TOOLS FOR FUNGAL SEQUENCE ANALYSIS AND IDENTIFICATION

Fungi have a 1 billion year evolutionary history, number perhaps 1.5 million species, and are hence extremely diverse phylogenetically and functionally. They play dominant roles in decomposition of recalcitrant substrates and plant nutrient acquisition, and thus influence net primary productivity, carbon sequestration in soil, and the biogeochemical cycling of key elements such as nitrogen and phosphorus. Despite their importance, fungi have often been ignored in ecological studies. Our goal is to understand how the evolutionary history of fungi has shaped their ecology, present distribution, and their communities.

2011 MSA Annual Meeting in Fairbanks

Video from MSA Auction 2009

Lab photo - 2005

People who frequent the lab :

• Mike Anderson
• Robert Burgess
• Catharine Catranis
• Daniel Glass
• John Haight
• Ian Herriott
• Becky Hewitt
• Sarah Hopkins
• Michaela Swanson
• Lee Taylor (PI)
• Ina Timling
• Claudia Thresher

Collaborators:

• Gary Andersen
• Todd Desantis
• John Freudenstein
• Shawn Houston
• Gary Laursen
• Mary Beth Leigh
• Melissa McCormick
• Don Natvig
• Chad Nusbaum
• Diane O'Brien
• Clare Robinson
• Roger Ruess
• Jyotsna Sharma
• Robert Sinsabaugh
• Donald (Skip) Walker
• Jeff Welker
• Dennis Whigham
• Matthew Wooller

Former lab members:

• Seth Adams
• Daphne Attla
• Michelle Augustyn
• Britt Arnesen
• Liz Bent
• Michael Booth
• Luke Bruner
• Kelley Calhoun
• Shelley DeWilde
• Jessica Eichmiller
• József Geml
• Hope Gray
• Lisa Grubisha
• Scott Hayden
• Dan Hepler
• Scott Hillard
• Jason Hunt
• La Tia Jackson
• Thomas Larsen
• Jack McFarland
• Mitali Patil
• Cortney Pylant
• Keane Richards

Useful Items:

Search all GenBank Fungal ITS or LSU Sequences With or Without Environmental Sequences

PCR Primers for Orchid Fungi

Funded projects:

NSF: Ecosystem-level Consequences of Mutualist Partner Choice in Alder across a Forest Successional Sequence in Interior Alaska

NSF: IPY: A Community Genomics Investigation of Fungal Adaptation to Cold

NSF: Metagenomics of Alaskan Fungi (view the BioScience article or listen to the report on the Alaska Public Radio Network to learn more about the project)

NSF: Impacts of Fungi on Orchid Distribution

Bonanza Creek Long Term Ecological Research (LTER)

Publications:

Timling I, Taylor DL. 2012. Peeking through a frosty window: Molecular insights into fungal diversity in arctic soil. Fungal Ecology Online Early DOI 10.1016/j.funeco.2012.01.009

Grubisha L, Levsen N, Olson MS, Taylor DL. 2012. Intercontinental divergence in the Populus-associated ectomycorrhizal fungus, Tricholoma populinum. New Phytologist 194(2): 548–560.

McCormick MK, Taylor DL, Juhaszova K, Burnett RK, Whigham DF, O'Neill J.  2012.  Limitations on orchid recruitment: not a simple picture.  Molecular Ecology 21(6): 1511–1523.

Geml J, Kauff F, Brochmann C, Lutzoni F, Laursen GA, Redhead, SA, Taylor DL.  2012.  Frequent circumarctic and rare transequatorial dispersals in the lichenised agaric genus Lichenomphalia (Hygrophoraceae, Basidiomycota).  Fungal Biology 116(3): 388-400.

Geml J, Timling I, Robinson CH, Lennon N, Nusbaum HC, Brochmann C, Noordeloos ME, Taylor DL.  2012.  An arctic community of symbiotic fungi assembled by long-distance dispersers: phylogenetic diversity of ectomycorrhizal basidiomycetes in Svalbard based on soil and sporocarp DNA.  Journal of Biogeography 39(1): 74-88.

Hopkins S, Taylor DL. 2011. Characterization of polymorphic microsatellite loci in the mycoheterotrophic orchid Corallorhiza maculata with cross-species amplification in Corallorhiza mertensiana. American Journal of Botany Primer Notes 98(9): e253-e255.

Bent E, Kiekel P, Brenton R, Taylor DL. 2011. Root-associated ectomycorrhizal fungi shared by various boreal forest seedlings naturally regenerating after a fire in Interior Alaska and correlation of different fungi with host growth responses. Appl. Environ. Microbiol. 77: 3351-3359.

Taylor DL and Houston S. 2011. A Bioinformatics pipeline for sequence-based analyses of fungal biodiversity. In Fungal Genomics, Xu, Jin-Rong; Bluhm, Burton H. (Eds.) Methods in Molecular Biology (722) 141-155.

Kennedy A, Taylor DL, Watson L. 2011. Mycorrhizal specificity in the fully mycoheterotrophic Hexalectris Raf. (Orchidaceae: Epidendroideae). Molecular Ecology 20: 1303–1316. Supplemental Table S1. Supplemental Figure S1.

Taylor DL, Herriott IC, Stone KE, McFarland JW, Booth MG, Leigh MB.  2010. Structure and resilience of fungal communities in Alaskan boreal forest soils.  Canadian Journal of Forest Research. 40(7): 1288–1301.

Chapin FS, McGuire AD, Ruess RW, Hollingsworth TN, Mack MC, Johnstone JF, Kasischke ES, Euskirchen ES, Jones J, Jorgenson MT, Kielland K, Kofinas GP, Turetsky MR, Yarie J, Lloyd AH, and Taylor DL. 2010.  Resilience of Alaska’s boreal forest to climatic change. Canadian Journal of Forest Research. 40(7): 1360–1370.

Geml J, Laursen GA, Herriott IC, McFarland JM, Booth MG, Lennon N, Nusbaum HC, Taylor DL.  2010. Phylogenetic and ecological analyses of soil and sporocarp DNA sequences reveal high diversity and strong habitat partitioning in the boreal ectomycorrhizal genus Russula Pers. (Russulales; Basidiomycota).  New Phytologist. 187(2): 494-507.

Geml J, Kauff K, Brochmann C, Taylor DL.  2010. Surviving climate changes: high genetic diversity and transoceanic gene flow in two arctic-alpine lichens, Flavocetraria cucullata and F. nivalis (Parmeliaceae, Ascomycota).  Journal of Biogeography 37(8): 1529–1542.

Geml J, Kauff F, Laursen GA, Taylor DL.  2010.  Genetic studies point to Beringia as a biodiversity hotspot for high-latitude fungi.  Alaska Park Science 8(2):  37-41.

Leigh MB, Neufeld J, Taylor DL. 2010. Clone libraries of ribosomal RNA gene sequences for characterization of bacterial and fungal communities. In Handbook of Hydrocarbon and Lipid Microbiology. Timmis KN, McGenity T, Meer JR, Lorenzo V, eds. Springer, Berlin Heidelberg. pp 3969-3993.

Barrett CF, Freudenstein JV, Taylor DL, and Urmas Kõljalg U. 2010. Rangewide analysis of fungal associations in the fully mycoheterotrophic Corallorhiza striata complex (Orchidaceae) reveals extreme specificity on ectomycorrhizal Tomentella (Thelephoraceae) across North America. American Journal of Botany 97 (3): 628-643.

Bent EL, Taylor DL. 2010. Direct amplification of DNA from fresh and preserved ectomycorrhizal root tips.  Journal of Microbiological Methods. 80 (2): 206-208.

Geml J, Tulloss RE, Laursen GA, Sazanova NA, Taylor DL. 2010. Phylogeographic analyses of a boreal-temperate ectomycorrhizal basidiomycete, Amanita muscaria, suggest forest refugia in Alaska during the last glacial maximum. In: Relict Species: Phylogeography and Conservation Biology. Habel, Jan Christian; Assmann, Thorsten (Eds.) Springer-Verlag, Berlin Heidelberg, pp. 173-186. PROOF PDF

Larsen T, Taylor DL, Leigh MB, O’Brien DM. 2009. Stable isotope fingerprinting: a novel method for identifying plant, fungal, or bacterial origins of amino acids. Ecology 90 (12): 3526-3535.

McCormick MK, Whigham DF, O’Neill JP, Becker JJ, Werner S, Rasmussen HN, Bruns TD, Taylor DL. 2009. Abundance and distribution of Corallorhiza odontorhiza reflects variations in climate and ectomycorrhizae. Ecological Monographs 79(4): 619-635.

Anderson MD, Ruess RR, Myrold DD, Taylor DL. 2009. Host species and habitat aVect nodulation by specific Frankia genotypes in two species of Alnus in interior Alaska. Oecologia 160 (4): 619-630.

Geml J, Laursen GA, Timling I, McFarland J, Booth MG, Lennon N, Nusbaum HC, Taylor DL. 2009. Molecular phylogenetic biodiversity assessment of arctic and boreal ectomycorrhizal Lactarius Pers. (Russulales; Basidiomycota) in Alaska, based on soil and sporocarp DNA. Molecular Ecology 18: 2213–2227.

Geml J, Laursen GA, Taylor DL.  2008.  Molecular diversity assessment of arctic and boreal Agaricus taxa.  Mycologia 100: 577-589.

Geml J, Tulloss RE, Laursen GA, Sazanova NA, Taylor DL.  2008.  Evidence for strong inter- and intracontinental phylogeographic structure in Amanita muscaria, a wind-dispersed ectomycorrhizal basidiomycete. Molecular Phylogenetics and Evolution 48(2): 694-701.

Tranchida Lombardo V, Hopkins SE, Selosse MA, Cozzolino S and Taylor DL.  2008.  Isolation and characterization of new polymorphic microsatellite loci in the mixotrophic orchid Limodorum abortivum L. Swartz (Orchidaceae).  Molecular Ecology Resources 8(4): 742-752.

Taylor DL, Booth MG, McFarland JW, Herriott IC, Lennon NJ, Nusbaum C & Marr TG.  2008.  Increasing ecological inference from high throughput sequencing of fungi in the environment through a tagging approach.  Molecular Ecology Resources 8(4): 742 - 752.  Supplemental Material - Table S1.

Taylor DL & McCormick MK.  2008.  Internal transcribed spacer primers and sequences for improved characterization of basidiomycetous orchid mycorrhizas.  New Phytologist 177: 1020–1033.  Supplemental Material - Figures s1-s4.  Supplemental Material - Table s1.

Bidartondo MI, et al. 2008. Preserving accuracy in GenBank. Science 319(5870): 1616.

Geml J, Laursen GA, Nusbaum HC, Taylor DL. 2007. Two new species of Agaricus from the Subantarctic. Mycotaxon 100: 193-208.

Shefferson RP, Taylor DL, Weiss M, Garnica S, McCormick MK, Adams S, Gray HM, McFarland JW, Kull T, Tali K, Yukawa T, Kawahara T, Miyoshi K, Lee Y-I. 2007. The evolutionary history of mycorrhizal specificity among Lady's Slipper orchids. Evolution 61: 1380-1390.

Taylor DL, Herriott IC, Long J, O'Neill K. 2007. TOPO-TA is A-OK: A test of phylogenetic bias in fungal environmental clone library construction. Environmental Microbiology 9: 1329-1334. Supplemental Material.

Simms EL, Taylor DL, Povich J, Shefferson RP, Sachs JL, Urbina M, Tausczik Y. 2006. An empirical test of partner choice mechanisms in a wild legume-rhizobium interaction. Proceedings of the Royal Society of London 273:77-81.

Geml J, Laursen GA, O’Neill K, Nusbaum HC, Taylor DL. 2006. Beringian origins and cryptic speciation events in the Fly Agaric (Amanita muscaria). Molecular Ecology 15:225-239.

Shefferson RP, Weiss M, Kull T, Taylor DL. 2005. High specificity generally characterizes mycorrhizal association in rare lady's slipper orchids, genus Cypripedium. Molecular Ecology 14:613-626.

Lilleskov EA, Bruns TD, Horton TR, Taylor DL, Grogan P 2004. Detection of forest stand-level spatial structure in ectomychorrhizal fungal communties. FEMS Microbiology Ecology 49:319-332.

Taylor DL 2004. Myco-heterotroph-fungus marriages - is fidelity over-rated? New Phytologist: 163:217-221.

Taylor DL, Bruns TD, & Hodges, SA 2004. Evidence for mycorrhizal races in a cheating orchid. Proceedings of the Royal Society of London 271:35-43.

Taylor DL, Bruns TD, Szaro TM, & Hodges SA. 2003. Divergence in mycorrhizal specialization within Hexalectris spicata, a nonphotosynthetic desert orchid. American Journal of Botany 90:1168-1179.

Taylor DL, Bruns TD, Leake JR & Read DJ. 2002. Mycorrhizal specificity and function in myco-heterotrophic plants. In: The Ecology of Mycorrhizas. Ecological Studies vol. 157. Ian R. Sanders and Marcel van der Heijden, eds. pp 375-414. Berlin: Springer-Verlag. (NOTE: this pdf is from the page proofs, and is not identical to the published version)

Simms EL & Taylor DL. 2002. Partner choice in nitrogen fixation mutualisms of legumes and rhizobia. Integrative and Comparative Biology 42:369-380.

McKendrick SL, Leake JR, Taylor DL & Read DJ.2002 Symbiotic germination and development of the myco-heterotrophic orchid Neottia nidus-avis in nature and its requirement for locally distributed Sebacina spp. New Phytologist 154:233-247.

Bruns TD, Bidartondo MI, & Taylor DL. 2002. Host specificity in ectomycorrhizal communities: What do the exceptions tell us? Integrative and Comparative Biology 42:352-359.

Kristiansen KA, Taylor DL, Kjøller R, Rasmussen & Rosendahl S. 2001. Identification of mycorrhizal fungi from single pelotons of Dactylorhiza majalis (Orchidaceae) using single-strand conformation polymorphism and mitochondrial ribosomal large subunit DNA sequences. Molecular Ecology 10:2089-2093.

Taylor DL. 2000 A new dawn – the ecological genetics of mycorrhizal fungi. New Phytologist 147:236-239.

McKendrick SL, Leake JR, Taylor DL & Read DJ. 2000. Symbiotic germination and development of myco-heterotrophic plants in nature: ontogeny of Corallorhiza trifida and characterization of its mycorrhizal fungi. New Phytologist 145:523-537.

Taylor DL & TD Bruns. 1999 Population, habitat and genetic correlates of mycorrhizal specialization in the 'cheating' orchids Corallorhiza maculata and C. mertensiana. Molecular Ecology 8:1719-1732.

Taylor DL & Bruns TD. 1999. Community structure of ectomycorrhizal fungi in a Pinus muricata forest: minimal overlap between the mature forest and resistant propagule communities. Molecular Ecology 8:1837-1850.

Bruns TD, Szaro TM, Gardes M, Cullings KW, Pan JJ, Taylor DL, Horton TR, Kretzer A, Garbelotto M & Li Y. 1998. A sequence database for the identification of ectomycorrhizal Basidiomycetes by phylogenetic analysis. Molecular Ecology 7:257-272.

Taylor DL & Bruns TD. 1997 Independent, specialized invasions of ectomycorrhizal mutualism by two nonphotosynthetic orchids. Proceedings of the National Academy of Sciences USA 94:4510-4515