Source: UNIVERSITY OF CALIFORNIA, BERKELEY submitted to NRP
FUNGAL EVOLUTION: PATHOGEN, SYMBIONT AND SAPROBE POPULATION GENETICS/GENOMICS AND IDENTIFICATION
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
HATCH
Reporting Frequency
Annual
Accession No.
1004011
Grant No.
(N/A)
Cumulative Award Amt.
(N/A)
Proposal No.
(N/A)
Multistate No.
(N/A)
Project Start Date
Oct 1, 2014
Project End Date
Sep 30, 2019
Grant Year
(N/A)
Program Code
[(N/A)]- (N/A)
Recipient Organization
UNIVERSITY OF CALIFORNIA, BERKELEY
(N/A)
BERKELEY,CA 94720
Performing Department
Microbial Biology
Non Technical Summary
We developed molecular methods to recognize fungal species by genetic isolation in nature and continue to apply this approach to model and socially important fungi. We discovered mate choice in microbes and aim to find the genes that allow female fungi to reject suitors from other species. We have conducted the first comparative genomic study of a human pathogenic fungus and now aim to extend our efforts to account for population variation. To associate phenotypic and genetic variation, we have used quantitative trail locus mapping and now are moving to whole genome association mapping, following the lead of human geneticists. We have profiled RNA transcription in Coccidioides using microarrays of 1000 genes and now are moving to profiling all genes by sequencing the RNAs. We aim to automate identification of fungi to support ecological and agricultural research.
Animal Health Component
20%
Research Effort Categories
Basic
70%
Applied
20%
Developmental
10%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2124020108010%
2124020110230%
3114020108010%
3114020110210%
3114020117010%
7024020110210%
7124020108010%
7124020117010%
Knowledge Area
212 - Pathogens and Nematodes Affecting Plants; 311 - Animal Diseases; 702 - Requirements and Function of Nutrients and Other Food Components; 712 - Protect Food from Contamination by Pathogenic Microorganisms, Parasites, and Naturally Occurring Toxins;

Subject Of Investigation
4020 - Fungi;

Field Of Science
1102 - Mycology; 1080 - Genetics; 1170 - Epidemiology;
Goals / Objectives
1. We aim to characterize the ability of 30 fungi isolated from decaying biofuel plants to deconstruct plant cell walls with the goal of improving enzymes used to convert plant biomass to transportation fuels.2. We aim to use genome wide association to find genes behind traits of thermophilic yeasts important to their use in producing biofuels.3. We aim to use next-generation-sequencing of mRNA from Neurospora discreta to investigate the role of fungi in global climate change in the Boreal Forest.4. We aim to use population genomics with two populations of ectomycorrhizal fungi to study their adaptation to coastal and montane forests.5. We aim to use population genomics of Neurospora discreta collected throughout western North America to study gene flow and adaptation in this fungus, which is capable of bioconversion of plant biomass.
Project Methods
We characterize the genomes of fungi using next-generation-sequencing (Ellison et al., 2011) and characterize phenotypes using the appropriate laboratory experiments (Ellison et al., 2011; Ellison et al., 2014; Palma-Guerrero et al., 2013). The next-generation-sequencing protocols are constantly changing. Currently, we use Illumina, paired-end sequencing for both full genomic sequencing and PCR amplicon based sequencing. To analyze the data, we use the facilities of the Computational Genomics Resource Laboratory at UC, Berkeley, of which Taylor is one of two founding, faculty Co-Directors.

Progress 10/01/16 to 09/30/17

Outputs
Target Audience:Our research is aimed at scientists in industry or academia who could benefit from ecology of mycobiomes, from using natural variation to aid studies of molecular development, who could benefit from using new methods of assessing fungi in indoor air, or who could benefit from knowing genes important to natural adaptation in human pathogenic fungi. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Two former postdocs now have asst. prof. positions Brano at Montana State Univ and Ellison at Rutgers One former postdoc now has a staff position at the California Dept of Pub Health, Adams How have the results been disseminated to communities of interest?We have presented reserach progress at meeting in the USA (Stanford, Washington DC) and abroad (Czech Republic, Taiwan, S. Korea) We have published our research: 228. Taylor JW, Branco S, Gao C, Hann-Soden C, Montoya L, Sylvain I, Gladieux P. 2017. Sources of fungal genetic variation and associating it with phenotypic diversity. Microbiol Spectrum 5(5): FUNK-0057-2016. doi:10.1128/microbiolspec.FUNK-0057-2016. 227. Branco, Sara, Ke Bi, Hui-Ling Liao, Pierre Gladieux, H.l.ne Badoui, Christopher E. Ellison, Nhu H. Nguyen, Rytas Vilgalys, Kabir G. Peay, John W. Taylor, Thomas D. Bruns. 2017. Continental-level population differentiation and environmentaladaptation inthe mushroomSuillus brevipes.Molecular Ecology 26:2063-2076 226. Adams, R. I., Lymperopoulou, D. S., Misztal, P. K., Pessotti, R. D., Behie, S. W., Tian, Y. L., Goldstein, A. H., Lindow, S. E., Nazaroff, W. W., Taylor, J. W., Traxler, M. F., Bruns, T. D., 2017. Microbes and associated soluble and volatile chemicals on periodically wet household surfaces. Microbiome. 5, Article number 128, DOI:10.1186/s40168-017-0347-6 225. Hagen, F., Lumbsch, H. T., Arsenijevic, V. A., Badali, H., Bertout, S., Billmyre, R. B., Bragulat, M. R., Cabanes, F. J., Carbia, M., Chakrabarti, A., Chaturvedi, S., Chaturvedi, V., Chen, M., Chowdhary, A., Colom, M. F., Cornely, O. A., Crous, P. W., Cuetara, M. S., Diaz, M. R., Espinel-Ingroff, A., Fakhim, H., Falk, R., Fang, W. J., Herkert, P. F., Rodriguez, C. F., Fraser, J. A., Gene, J., Guarro, J., Idnurm, A., Illnait-Zaragozi, M. T., Khan, Z., Khayhan, K., Kolecka, A., Kurtzman, C. P., Lagrou, K., Liao, W. Q., Linares, C., Meis, J. F., Nielsen, K., Nyazika, T. K., Pan, W., Pekmezovic, M., Polacheck, I., Posteraro, B., Telles, F. D., Romeo, O., Sanchez, M., Sampaio, A., Sanguinetti, M., Sriburee, P., Sugita, T., Taj-Aldeen, S. J., Takashima, M., Taylor, J. W., Theelen, B., Tomazin, R., Verweij, P. E., Wahyuningsih, R., Wang, P., Boekhoutiii, T., 2017. Importance of Resolving Fungal Nomenclature: the Case of Multiple Pathogenic Species in the Cryptococcus Genus. Msphere. 2 (4) Article Number:e00238-17 DOI:10.1128/mSphere.00238-17 What do you plan to do during the next reporting period to accomplish the goals?We continue to conduct research on the variation in fungi with grants funded by the DOE and the Office of the President of the Univ. of Calif

Impacts
What was accomplished under these goals? 1 was completed in previous reports 2 is in progress 3 is in progress 4. is complete with the publicatin of Branco et la. 2017. 5. is in progress In addition: We have developed methods to assess fungi and bacteria in indoor air (Adams et al 2017) We have reviewed the extent of genetic variation in fungi (Taylor et al2017) We have contributed to the debate over naming of species of fungi (Hagen et al. 2017)

Publications

  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Hagen, F., Lumbsch, H. T., Arsenijevic, V. A., Badali, H., Bertout, S., Billmyre, R. B., Bragulat, M. R., Cabanes, F. J., Carbia, M., Chakrabarti, A., Chaturvedi, S., Chaturvedi, V., Chen, M., Chowdhary, A., Colom, M. F., Cornely, O. A., Crous, P. W., Cuetara, M. S., Diaz, M. R., Espinel-Ingroff, A., Fakhim, H., Falk, R., Fang, W. J., Herkert, P. F., Rodriguez, C. F., Fraser, J. A., Gene, J., Guarro, J., Idnurm, A., Illnait-Zaragozi, M. T., Khan, Z., Khayhan, K., Kolecka, A., Kurtzman, C. P., Lagrou, K., Liao, W. Q., Linares, C., Meis, J. F., Nielsen, K., Nyazika, T. K., Pan, W., Pekmezovic, M., Polacheck, I., Posteraro, B., Telles, F. D., Romeo, O., Sanchez, M., Sampaio, A., Sanguinetti, M., Sriburee, P., Sugita, T., Taj-Aldeen, S. J., Takashima, M., Taylor, J. W., Theelen, B., Tomazin, R., Verweij, P. E., Wahyuningsih, R., Wang, P., Boekhoutiii, T., 2017. Importance of Resolving Fungal Nomenclature: the Case of Multiple Pathogenic Species in the Cryptococcus Genus. Msphere. 2 (4) Article Number: e00238-17 DOI: 10.1128/mSphere.00238-17
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Adams, R. I., Lymperopoulou, D. S., Misztal, P. K., Pessotti, R. D., Behie, S. W., Tian, Y. L., Goldstein, A. H., Lindow, S. E., Nazaroff, W. W., Taylor, J. W., Traxler, M. F., Bruns, T. D., 2017. Microbes and associated soluble and volatile chemicals on periodically wet household surfaces. Microbiome. 5, Article number 128, DOI: 10.1186/s40168-017-0347-6
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Branco, Sara, Ke Bi, Hui-Ling Liao, Pierre Gladieux, H.l.ne Badoui, Christopher E. Ellison, Nhu H. Nguyen, Rytas Vilgalys, Kabir G. Peay, John W. Taylor, Thomas D. Bruns. 2017. Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes. Molecular Ecology 26:2063-2076
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Taylor JW, Branco S, Gao C, Hann-Soden C, Montoya L, Sylvain I, Gladieux P. 2017. Sources of fungal genetic variation and associating it with phenotypic diversity. Microbiol Spectrum 5(5): FUNK-0057-2016. doi:10.1128/microbiolspec.FUNK-0057-2016.


Progress 10/01/15 to 09/30/16

Outputs
Target Audience:Scientists at all levels, from graduate students to professors and agricultural profesionals. Our research is aimed at scientists in industry or academia who could benefit from using natural variation to aid studies of molecular development, who could benefit from using new methods of assessing fungi in indoor air, or who could benefit from knowing genes important to natural adaptation in human pathogenic fungi. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Graduate students. Two are currently being trained, C. Hann-Soden and I. Sylvain. Two previously graduated students have been appointed assistant professors, Dr. Chris Ellison at Rutgers Universtiy and Dr. Thomas Sharpton at Oregon State University. Postdocs. One postdoc, Dr. Rachel Adams won a position at the California State Department of Public Health and also continues as a Research Scientist at Berkeley. A new postdoc, Dr. Cheng Gao, has been engaged to work on the sorghum project. How have the results been disseminated to communities of interest?Our research was published in six , peer-reviewed articles in 2016. Bhangar, S., Adams, R. I., Pasut, W., Huffman, J. A., Arens, E. A., Taylor, J. W., Bruns, T. D., Nazaroff, W. W., 2016. Chamber bioaerosol study: human emissions of size-resolved fluorescent biological aerosol particles. Indoor Air. 26, 193-206. Branco, S., Bi, K., Liao, H.-L., Gladieux, P., Badouin, H., Ellison, C. E., Nguyen, N. H., Vilgalys, R., Peay, K. G., Taylor, J. W., Bruns, T. D., 2016. Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes. Molecular Ecology. doi: 10.1111/mec.13892 Bruns, T. D., Taylor, J. W., 2016. Fungal Symbionts: Comment on "Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism". Science. 351 (6275) doi: 10.1126/science.aad4228 Muñoz, J. F., Farrer, R. A., Desjardins, C. A., Gallo, J. E., Sykes, S., Sakthikumar, S., Misas, E., Whiston, E. A., Bagagli, E., Soares, C. M. A., Teixeira, M. d. M., Taylor, J. W., Clay, O. K., McEwen, J. G., Cuomo, C. A., 2016. Genome Diversity, Recombination, and Virulence across the Major Lineages of Paracoccidioides. mSphere. 1 (5) e00213-16. Pitt, J. I., Taylor, J. W., 2016. (2441) Proposal to conserve the name Aspergillus (Fungi: Eurotiales: Trichocomaceae) with a conserved type to maintain also the name Eurotium. Taxon. 65, 631-632. doi:10.12705/653.17 Taylor, J. W., Goker, M., Pitta, J. I., 2016. Choosing one name for pleomorphic fungi: The example of Aspergillus versus Eurotium, Neosartorya and Emericella. Taxon. 65, 593-601. doi: 10.12705/653.10. Zhang, Y. J., Skaar, I., Sulyok, M., Liu, X. Z., Rao, M. Y., Taylor, J. W., 2016. The Microbiome and Metabolites in Fermented Pu-erh Tea as Revealed by High-Throughput Sequencing and Quantitative Multiplex Metabolite Analysis. Plos One. 11(6): e0157847. doi:10.1371/journal.pone.0157847. What do you plan to do during the next reporting period to accomplish the goals?1. We are putting the finishing touches on a ms comparing on GWAs and reverse ecology in thermophilic yeasts. 2. We have phenotyped cold tolerance in a QTL mapping population of ca. 250 offspring from a cross between cold tolerant and cold susceptible Neurospora crassa parents and have found QTL strongly associated with loci on chromosome 5. We, now, are finishing the analysis and aim to produce a ms in the coming year. 3. We nearly have characterized transcription for strains of Neurospora discreta evolved to grow at elevated temperature and compare them with the progenitors to detect differences in the use of simple and complex carbon sources. This work is being prepared for publication. 4. We have begun a DOE project on the fungi in the rhizosphere and on the roots of sorghum as it experiences drought stress and are analyzing the first year's data. 5. We are investigating a project aimed at associating indoor microbes with asthma.

Impacts
What was accomplished under these goals? We have one publication demonstrating population differentiation, structure and evolution in the fungus Neurospora discreta (Branco et al., 2016). We have used comparative genomics to study reproductive mode and virulence in the animal pathogenic fungus, Paracoccidioides (Muñoz et al., 2016). We have two publications on the use of evolutionary diversity to assign generic names in the fungus, Aspergillus (Pitt and Taylor, 2016; Taylor et al., 2016). We have one publication on the role of occupant in the communities of fungi and bacteria in the built environment, aka, indoor air (Bhangar et al., 2016). We have one publication on the communities of bacteria and fungi that ferment Pu-erh tea, and mycotoxins produced during the fermentation (Zhang et al., 2016). We are actively researching the fungal communities found in sorghum fields as the plants experience drought. We are actively researching the association of the fungal trait of thermal tolerance in a QTL study of Neurospora crassa. We have a total of six publications as noted below. Publications in 2016 Bhangar, S., Adams, R. I., Pasut, W., Huffman, J. A., Arens, E. A., Taylor, J. W., Bruns, T. D., Nazaroff, W. W., 2016. Chamber bioaerosol study: human emissions of size-resolved fluorescent biological aerosol particles. Indoor Air. 26, 193-206. Branco, S., Bi, K., Liao, H.-L., Gladieux, P., Badouin, H., Ellison, C. E., Nguyen, N. H., Vilgalys, R., Peay, K. G., Taylor, J. W., Bruns, T. D., 2016. Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes. Molecular Ecology. doi: 10.1111/mec.13892 Bruns, T. D., Taylor, J. W., 2016. Fungal Symbionts: Comment on "Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism". Science. 351 (6275) doi: 10.1126/science.aad4228 Muñoz, J. F., Farrer, R. A., Desjardins, C. A., Gallo, J. E., Sykes, S., Sakthikumar, S., Misas, E., Whiston, E. A., Bagagli, E., Soares, C. M. A., Teixeira, M. d. M., Taylor, J. W., Clay, O. K., McEwen, J. G., Cuomo, C. A., 2016. Genome Diversity, Recombination, and Virulence across the Major Lineages of Paracoccidioides. mSphere. 1 (5) e00213-16. Pitt, J. I., Taylor, J. W., 2016. (2441) Proposal to conserve the name Aspergillus (Fungi: Eurotiales: Trichocomaceae) with a conserved type to maintain also the name Eurotium. Taxon. 65, 631-632. doi:10.12705/653.17 Taylor, J. W., Goker, M., Pitta, J. I., 2016. Choosing one name for pleomorphic fungi: The example of Aspergillus versus Eurotium, Neosartorya and Emericella. Taxon. 65, 593-601. doi: 10.12705/653.10. Zhang, Y. J., Skaar, I., Sulyok, M., Liu, X. Z., Rao, M. Y., Taylor, J. W., 2016. The Microbiome and Metabolites in Fermented Pu-erh Tea as Revealed by High-Throughput Sequencing and Quantitative Multiplex Metabolite Analysis. Plos One. 11(6): e0157847. doi:10.1371/journal.pone.0157847.

Publications

  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Bhangar, S., Adams, R. I., Pasut, W., Huffman, J. A., Arens, E. A., Taylor, J. W., Bruns, T. D., Nazaroff, W. W., 2016. Chamber bioaerosol study: human emissions of size-resolved fluorescent biological aerosol particles. Indoor Air. 26, 193-206.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Branco, S., Bi, K., Liao, H.-L., Gladieux, P., Badouin, H., Ellison, C. E., Nguyen, N. H., Vilgalys, R., Peay, K. G., Taylor, J. W., Bruns, T. D., 2016. Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes. Molecular Ecology. doi: 10.1111/mec.13892
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Bruns, T. D., Taylor, J. W., 2016. Fungal Symbionts: Comment on "Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism". Science. 351 (6275) doi: 10.1126/science.aad4228
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Mu�oz, J. F., Farrer, R. A., Desjardins, C. A., Gallo, J. E., Sykes, S., Sakthikumar, S., Misas, E., Whiston, E. A., Bagagli, E., Soares, C. M. A., Teixeira, M. d. M., Taylor, J. W., Clay, O. K., McEwen, J. G., Cuomo, C. A., 2016. Genome Diversity, Recombination, and Virulence across the Major Lineages of Paracoccidioides. mSphere. 1 (5) e00213-16.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Pitt, J. I., Taylor, J. W., 2016. (2441) Proposal to conserve the name Aspergillus (Fungi: Eurotiales: Trichocomaceae) with a conserved type to maintain also the name Eurotium. Taxon. 65, 631-632. doi:10.12705/653.17
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Taylor, J. W., Goker, M., Pitta, J. I., 2016. Choosing one name for pleomorphic fungi: The example of Aspergillus versus Eurotium, Neosartorya and Emericella. Taxon. 65, 593-601. doi: 10.12705/653.10.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Zhang, Y. J., Skaar, I., Sulyok, M., Liu, X. Z., Rao, M. Y., Taylor, J. W., 2016. The Microbiome and Metabolites in Fermented Pu-erh Tea as Revealed by High-Throughput Sequencing and Quantitative Multiplex Metabolite Analysis. Plos One. 11(6): e0157847. doi:10.1371/journal.pone.0157847.


Progress 10/01/14 to 09/30/15

Outputs
Target Audience:Our research is aimed at scientists in industry or academia who could benefit from using natural variation to aid studies of molecular development, who could benefit from using new methods of assessing fungi in indoor air, or who could benefit from knowing genes important to natural adaptation in human pathogenic fungi. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Graduate students. Two are currently being trained, C. Hann-Soden and I. Sylvain. Two previously graduated students have been appointed assistant professors, Dr. Chris Ellison at University of California, Berkeley and Dr. Thomas Sharpton at Oregon State University. Postdocs. One postdoc won a position at the University of Paris, Sud. One has been promoted to Research Scientist. One continues in the lab, Dr. Marie Donnelly. How have the results been disseminated to communities of interest?Our research was published in seventeen, peer-reviewed articles and one book chapter in 2015. Shrestha, P., Ibanez, A. B., Bauer, S., Glassman, S. I., Szaro, T. M., Bruns, T. D., Taylor, J. W., 2015. Fungi isolated from Miscanthus and sugarcane: biomass conversion, fungal enzymes, and hydrolysis of plant cell wall polymers. Biotechnology for Biofuels. 8:Article Number:38 DOI:10.1186/s13068-015-0221-3 Natvig, D. O., J. W. Taylor, A. Tsang, M. I. Hutchinson and A. J. Powell (2015). "Mycothermus thermophilus gen. et comb. nov., a new home for the itinerant thermophile Scytalidium thermophilum (Torula thermophila)." Mycologia 107(2): 319-327. Romero-Olivares, Adriana L · John W Taylor · Kathleen K Treseder. 2015. Neurospora discreta as a model to assess adaptation of soil fungi to warming. BMC Evolutionary Biology 15(1):198. DOI:10.1186/s12862-015-0482-2 Branco, S., P. Gladieux, C. E. Ellison, A. Kuo, K. LaButii, 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." Mol Ecol. 24:2747-2758. Glassman, S. I., Peay, K. G., Talbot, J. M., Smith, D. P., Chung, J. A., Taylor, J. W., Vilgalys, R., Bruns, T. D. 2015. A continental view of pine-associated ectomycorrhizal fungal spore banks: a quiescent functional guild with a strong biogeographic pattern. New Phytologist 205:1619-1631. 10.1111/nph.13240 Gladieux, Pierre, Benjamin A Wilson, Fanny Perraudeau, Christopher Hann-Soden, Monika Fischer, Iman Sylvain, David J Jacobson, John W Taylor. 2015. Genomic Sequencing Reveals Historical, Demographic, and Selective Factors Associated with the Diversification of the Fire-Associated Fungus Neurospora discrete. Molecular Ecology 24:5657-5675. doi:10.1111/mec.13417 Taylor, J.W., Hann-Soden, C., Branco, S., Sylvain, I., Ellison, C.E. 2015. Clonal reproduction in fungi. Proceedings of the National Academy of Science 112(29): 8901-8908. Wang, Y., Smith, K. M., Taylor, J. W., Freitag, M., Stajich, J. E., 2015. Endogenous Small RNA Mediates Meiotic Silencing of a Novel DNA Transposon. G3: Genes Genomes Genetics. DOI:10.1534/g3.115.017921 Whiston, E. and J. W. Taylor. 2015. Comparative phylogenomics of pathogenic and non-pathogenic species. G3: Genes, Genomes, Genetics. doi:10.1534/g3.115.022806/-/DC1 Muñoz, José F., Gregory M Gauthier, Christopher A Desjardins, Juan E Gallo, Jason Holder, Thomas D Sullivan, Amber J Marty, John C Carmen, Zehua Chen · Li Ding, Emily A Whiston, Sarah Young, Qiandong Zeng, William E Goldman,. Elaine R Mardis, John W Taylor, Juan G McEwen, Oliver K Clay, Bruce S Klein, Christina A Cuomo. 2015. The Dynamic Genome and Transcriptome of the Human Fungal Pathogen Blastomyces and Close Relative Emmonsia. PLoS Genetics 11(10):e1005493. DOI:10.1371/journal.pgen.1005493 Vilela, R., J. W. Taylor, E. D. Walker and L. Mendoza (2015). "Lagenidium giganteum Pathogenicity in Mammals." Emerging Infectious Diseases 21(2): 290-297. Taylor, J. W. 2015. Evolutionary perspectives on human fungal pathogens. Pp 23-40, In: Casadevall,A., Mitchell, A., Berman, J., Kwon-Chung, K., Perfect, J., Heitman, J. (eds), Human Fungal Pathogens, Cold Spring Harbor Perspectives in Medicine, CSHL Press, Cold Spring Harbor, NY. Thompson, G. R., Stevens, D. A., Clemons, K. V, Fierer, Johnson, R. H., Sykes, J. Rutherford, M. Peterson, J. W. Taylor and V. Chaturvedi (2015). "Call for a California Coccidioidomycosis Consortium to Face the Top Ten Challenges Posed by a Recalcitrant Regional Disease." Mycopathologia 179: 1-9. de Hoog GS, Chaturvedi V, Denning DW, Dyer PS, Frisvad JC, Geiser D, Gräser Y, Guarro J, Haase G, Kwon-Chung KJ, Meis JF, Meyer W, Pitt JI, Samson RA, Taylor JW, Tintelnot K, Vitale RG, Walsh TJ, Lackner M (2015) ISHAM working group on Nomenclature of Medical Fungi. Name changes in medically important fungi and their implications for clinical practice. J Clin Microbiol 53:1056-1062. PMID: 25297326 Adams, Rachel I., Yilin Tian, John W. Taylor, Thomas D. Bruns, Anne Hyvärinen, Martin Täubel. 2015a. Passive dust collectors for assessing airborne microbial material. Microbiome 3(1):46. doi: 10.1186/s40168-015-0112-7. Adams, Rachel I., Seema Bhangar, Wilmer Pasut, Edward A. Arens , John W. Taylor, Steven E. Lindow, William W. Nazaroff, Thomas D. Bruns. 2015b. Chamber Bioaerosol Study: Outdoor Air and Human Occupants as Sources of Indoor Airborne Microbes. PLoS ONE 10(5):e0128022. DOI:10.1371/journal.pone.0128022. Bhangar, S., Adams, R. I., Pasut, W., Huffman, J. A., Arens, E. A., Taylor, J. W., Bruns, T. D., Nazaroff, W. W., 2015. Chamber bioaerosol study: human emissions of size-resolved fluorescent biological aerosol particles. Indoor Air 10.1111/ina.12195 What do you plan to do during the next reporting period to accomplish the goals? 1. We are preparing a ms comparing on GWAs and reverse ecology in thermophilic yeasts. 2. We are phenotyping cold tolerance in a QTL mapping population of ca. 250 offspring from a cross between cold tolerant and cold susceptible N. crassa parents for association with sequence genomes of all progeny. 3. We are close to having characterized transcription for strains of Neurospora discrete evolved to grow at elevated temperature and compare them with the progenitors to detect differences in the use of simple and complex carbon sources. 4. We are beginning a DOE project on the fungi in the rhizosphere and on the roots of sorghum as it experiences drought stress. 5. We are investigating a project aimed at associating indoor microbes with asthma.

Impacts
What was accomplished under these goals? We use nucleic acid variation as a tool to 1) identify fungi, 2) recognize fungal species and populations, 3) identify gene flow among populations, 4) find genes important to adaptation, 5) assign function to unknown genes, 6) characterize fungal communities in soil, air, food and animals, 7) characterize fungal activity in nature through their transcripts and proteins and, 8) understand the contribution of fungi and bacteria to the airborne fungal and bacterial communities. We disseminate our results by publications and presentation at scientific meetings, both posters and oral presentations. We have two publications on biofuel fungi, Shrestha et al. 2015 on enzymes from fungi that best bioconvert energy grasses and Natvig et al. 2015 on the taxonomy of thermophilic fungi. We have phenotypes 50 inividuals of a thermophilic yeast, Kluyveromyces marxianus, and are associating the phenotypes with SNPs scored from the genomes of the same individuals. We have one publication, Romero-Olivares et al. 2015 on the role of fungi in climate change and are working on two more manuscripts for further investigations. We have two publications, Branco et al. 2015, on the population genomics of ectomycorrhizal fungi and adaptation and Glassman et al. 2015, on ecotmycorrhizal spore banks. We have one publication, Gladieux et al. 2015, on population structure, gene flow among populations, and hybridization in Neurospora discrete. We have one publication, Taylor et al., 2015, on clonality in fungi showing that recombination is the default state but that there are many limits to recombination. We have one publication, Wang et al. 2015, on fungal, small RNAs and their role in meiotic silencing. We have six publications on human pathogenic fungi, Whiston and Taylor 2015 showing the unique genes in Coccidioides spp., Muñoz et al. 2015 comparing genomes of the non-Coccidioides pathogens, Blastomyces, Histoplasam and Paracoccidioides, Vilela et al. 2015 on an oomycote pathogen of mosquito larvae that has evolved to attack mammals, Taylor 2015 on evolution of human pathogens, Thompson et al. 2015 on challenges to control of Coccidioides, and deHoog et al. 2015 on the taxonomy of human pathogenic fungi. We have three publications on fungi and bacteria in the build environment, Adams et al. 2015a on the approach, Adams et al. 2015b on experiments in controlled chambers, and Bhangar et al. 2015 a study in parallel to Adams et al. 2015b on particles related to human activity in the same chamber study Our work from previous years has resulted in seventeen publications this year

Publications

  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Shrestha, P., Ibanez, A. B., Bauer, S., Glassman, S. I., Szaro, T. M., Bruns, T. D., Taylor, J. W., 2015. Fungi isolated from Miscanthus and sugarcane: biomass conversion, fungal enzymes, and hydrolysis of plant cell wall polymers. Biotechnology for Biofuels. 8:Article Number:�38 DOI:�10.1186/s13068-015-0221-3
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Natvig, D. O., J. W. Taylor, A. Tsang, M. I. Hutchinson and A. J. Powell (2015). "Mycothermus thermophilus gen. et comb. nov., a new home for the itinerant thermophile Scytalidium thermophilum (Torula thermophila)." Mycologia 107(2): 319-327.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Romero-Olivares, Adriana L � John W Taylor � Kathleen K Treseder. 2015. Neurospora discreta as a model to assess adaptation of soil fungi to warming. BMC Evolutionary Biology 15(1):198. DOI:10.1186/s12862-015-0482-2
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Branco, S., P. Gladieux, C. E. Ellison, A. Kuo, K. LaButii, 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." Mol Ecol. 24:2747-2758.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Glassman, S. I., Peay, K. G., Talbot, J. M., Smith, D. P., Chung, J. A., Taylor, J. W., Vilgalys, R., Bruns, T. D. 2015. A continental view of pine-associated ectomycorrhizal fungal spore banks: a quiescent functional guild with a strong biogeographic pattern. New Phytologist 205:1619-1631. 10.1111/nph.13240
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Gladieux, Pierre, Benjamin A Wilson, Fanny Perraudeau, Christopher Hann-Soden, Monika Fischer, Iman Sylvain, David J Jacobson, John W Taylor. 2015. Genomic Sequencing Reveals Historical, Demographic, and Selective Factors Associated with the Diversification of the Fire-Associated Fungus Neurospora discrete. Molecular Ecology 24:5657-5675. doi:10.1111/mec.13417
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Taylor, J.W., Hann-Soden, C., Branco, S., Sylvain, I., Ellison, C.E.� 2015. Clonal reproduction in fungi. Proceedings of the National Academy of Science 112(29): 8901-8908.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Wang, Y., Smith, K. M., Taylor, J. W., Freitag, M., Stajich, J. E., 2015. Endogenous Small RNA Mediates Meiotic Silencing of a Novel DNA Transposon. G3: Genes|Genomes|Genetics. DOI:10.1534/g3.115.017921�
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Whiston, E. and J. W. Taylor. 2015. Comparative phylogenomics of pathogenic and non-pathogenic species. G3: Genes, Genomes, Genetics. doi:10.1534/g3.115.022806/-/DC1
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Mu�oz, Jos� F., Gregory M Gauthier, Christopher A Desjardins, Juan E Gallo, Jason Holder, Thomas D Sullivan, Amber J Marty, John C Carmen, Zehua Chen � Li Ding, Emily A Whiston, Sarah Young, Qiandong Zeng, William E Goldman,. Elaine R Mardis, John W Taylor, Juan G McEwen, Oliver K Clay, Bruce S Klein, Christina A Cuomo. 2015. The Dynamic Genome and Transcriptome of the Human Fungal Pathogen Blastomyces and Close Relative Emmonsia. PLoS Genetics 11(10):e1005493. DOI:10.1371/journal.pgen.1005493
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Vilela, R., J. W. Taylor, E. D. Walker and L. Mendoza (2015). "Lagenidium giganteum Pathogenicity in Mammals." Emerging Infectious Diseases 21(2): 290-297.
  • Type: Book Chapters Status: Published Year Published: 2015 Citation: Taylor, J. W. 2015. Evolutionary perspectives on human fungal pathogens. Pp 23-40, In: Casadevall,A., Mitchell, A., Berman, J., Kwon-Chung, K., Perfect, J., Heitman, J. (eds), Human Fungal Pathogens, Cold Spring Harbor Perspectives in Medicine, CSHL Press, Cold Spring Harbor, NY.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Thompson, G. R., Stevens, D. A., Clemons, K. V, Fierer, Johnson, R. H., Sykes, J. Rutherford, M. Peterson, J. W. Taylor and V. Chaturvedi (2015). "Call for a California Coccidioidomycosis Consortium to Face the Top Ten Challenges Posed by a Recalcitrant Regional Disease." Mycopathologia 179: 1-9.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: de Hoog GS, Chaturvedi V, Denning DW, Dyer PS, Frisvad JC, Geiser D, Gr�ser Y, Guarro J, Haase G, Kwon-Chung KJ, Meis JF, Meyer W, Pitt JI, Samson RA, Taylor JW, Tintelnot K, Vitale RG, Walsh TJ, Lackner M (2015) ISHAM working group on Nomenclature of Medical Fungi. Name changes in medically important fungi and their implications for clinical practice. J Clin Microbiol 53:1056-1062. PMID: 25297326
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Adams, Rachel I., Yilin Tian, John W. Taylor, Thomas D. Bruns, Anne Hyv�rinen, Martin T�ubel. 2015a. Passive dust collectors for assessing airborne microbial material. Microbiome 3(1):46. doi: 10.1186/s40168-015-0112-7.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Adams, Rachel I., Seema Bhangar, Wilmer Pasut, Edward A. Arens , John W. Taylor, Steven E. Lindow, William W. Nazaroff, Thomas D. Bruns. 2015b. Chamber Bioaerosol Study: Outdoor Air and Human Occupants as Sources of Indoor Airborne Microbes. PLoS ONE 10(5):e0128022. DOI:10.1371/journal.pone.0128022.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Bhangar, S., Adams, R. I., Pasut, W., Huffman, J. A., Arens, E. A., Taylor, J. W., Bruns, T. D., Nazaroff, W. W., 2015. Chamber bioaerosol study: human emissions of size-resolved fluorescent biological aerosol particles. Indoor Air 10.1111/ina.12195