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Advancement of Functional Genomics of a Model Species of Neurospora and Its Use for Ecological Genomics of Soil Fungi

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Book cover Genomics of Soil- and Plant-Associated Fungi

Part of the book series: Soil Biology ((SOILBIOL,volume 36))

Abstract

Our daily life is deeply interwoven with diverse filamentous fungi. These fungi are essential to many ecosystem functions. The estimates of the potential number of fungi predicted to occur on Earth are between 1.5 million and over five million species. We know, however, very little of the biology and ecological functions of most of these fungal species. Only few chosen fungal species have been used for systematic studies on diverse biological problems. Since there is a limited amount of resources in learning fungal biology, it is beneficial to have a model organism, in which new techniques are tested and detailed genetic and molecular mechanisms elucidated for diverse biological phenomena. However, a concerted and creative effort by a group of researchers is necessary to address ecological questions in non-model and non-laboratory microorganisms. By doing so, we can translate genomics data from the few fungal model organisms into the real-world function of the purported functional groups of saprotrophs, pathogens, mycorrhizae, and endophytes. Neurospora crassa has been a successful filamentous fungal model organism: its study has greatly advanced our understanding of its physiology, biochemistry, and molecular makeup, but surprisingly little about its ecology.

We have a focused goal in this chapter. We will summarize recent advances of genomics and post-genomics tools in the model fungal organism Neurospora. Then, we will summarize current efforts in genomics studies in Neurospora and soil fungi. Our hope is to shed light on how genomics studies in the model organism Neurospora can be extrapolated to advance our understanding of the ecological functions and biology of soil fungi. Our emphasis will be more on the current advancement in two topics, photobiology and lignocellulose metabolism.

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References

  • Andersen MR, Nielsen J (2009) Current status of systems biology in Aspergilli. Fungal Genet Biol 46(Suppl 1):S180–S190

    Article  PubMed  CAS  Google Scholar 

  • Avalos J, Estrada AF (2010) Regulation by light in Fusarium. Fungal Genet Biol 47:930–938

    Article  PubMed  CAS  Google Scholar 

  • Bahn YS, Xue C, Idnurm A, Rutherford JC, Heitman J, Cardenas ME (2007) Sensing the environment: lessons from fungi. Nat Rev Microbiol 5:57–69

    Article  PubMed  CAS  Google Scholar 

  • Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3:e3376

    Article  PubMed  CAS  Google Scholar 

  • Ballario P, Macino G (1997) White collar proteins: PASsing the light signal in Neurospora crassa. Trends Microbiol 5:458–462

    Article  PubMed  CAS  Google Scholar 

  • Ballario P, Vittorioso P, Magrelli A, Talora C, Cabibbo A, Macino G (1996) White collar-1, a central regulator of blue light responses in Neurospora, is a zinc finger protein. EMBO J 15:1650–1657

    PubMed  CAS  Google Scholar 

  • Ballario P, Talora C, Galli D, Linden H, Macino G (1998) Roles in dimerization and blue light photoresponse of the PAS and LOV domains of Neurospora crassa white collar proteins. Mol Microbiol 29:719–729

    Article  PubMed  CAS  Google Scholar 

  • Baxter JW, Dighton J (2001) Ectomycorrhizal diversity alters growth and nutrient acquisition of gray birch (Betula populifolia Marshall) seedlings in host-symbiont culture conditions. New Phytol 152:139–149

    Article  Google Scholar 

  • Baxter JW, Dighton J (2005) Phosphorus source alters host plant response to ectomycorrhizal diversity. Mycorrhiza 15:513–523

    Article  PubMed  CAS  Google Scholar 

  • Bayram O, Braus GH, Fischer R, Rodriguez-Romero J (2010) Spotlight on Aspergillus nidulans photosensory systems. Fungal Genet Biol 47:900–908

    Article  PubMed  CAS  Google Scholar 

  • Beeson WT, Phillips CM, Cate JH, Marletta MA (2012) Oxidative cleavage of cellulose by fungal copper-dependent polysaccharide monooxygenases. J Am Chem Soc 134:890–892

    Article  PubMed  CAS  Google Scholar 

  • Bohlin C, Praestgaard E, Baumann MJ, Borch K, Praestgaard J, Monrad RN, Westh P (2013) A comparative study of hydrolysis and transglycosylation activities of fungal beta-glucosidases. Appl Microbiol Biotechnol 97:159–169

    Article  PubMed  CAS  Google Scholar 

  • Chen CH, Dunlap JC, Loros JJ (2010) Neurospora illuminates fungal photoreception. Fungal Genet Biol 47:922–929

    Article  PubMed  Google Scholar 

  • Cheng P, Yang Y, Heintzen C, Liu Y (2001) Coiled-coil domain-mediated FRQ-FRQ interaction is essential for its circadian clock function in Neurospora. EMBO J 20:101–108

    Article  PubMed  CAS  Google Scholar 

  • Coradetti ST, Craig JP, Xiong Y, Shock T, Tian C, Glass NL (2012) Conserved and essential transcription factors for cellulase gene expression in ascomycete fungi. Proc Natl Acad Sci U S A 109:7397–7402

    Article  PubMed  CAS  Google Scholar 

  • Corrochano LM (2007) Fungal photoreceptors: sensory molecules for fungal development and behaviour. Photochem Photobiol Sci 6:725–736

    Article  PubMed  CAS  Google Scholar 

  • Corrochano LM, Garre V (2010) Photobiology in the Zygomycota: multiple photoreceptor genes for complex responses to light. Fungal Genet Biol 47:893–899

    Article  PubMed  CAS  Google Scholar 

  • Coutinho PM, Andersen MR, Kolenova K, van Kuyk PA, Benoit I, Gruben BS, Trejo-Aguilar B, Visser H, van Solingen P, Pakula T, Seiboth B, Battaglia E, Aguilar-Osorio G, de Jong JF, Ohm RA, Aguilar M, Henrissat B, Nielsen J, Stalbrand H, de Vries RP (2009) Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus nidulans and comparison to Aspergillus niger and Aspergillus oryzae. Fungal Genet Biol 46(Suppl 1):S161–S169

    Article  PubMed  CAS  Google Scholar 

  • Dadachova E, Casadevall A (2008) Ionizing radiation: how fungi cope, adapt, and exploit with the help of melanin. Curr Opin Microbiol 11:525–531

    Article  PubMed  CAS  Google Scholar 

  • Dadachova E, Bryan RA, Huang X, Moadel T, Schweitzer AD, Aisen P, Nosanchuk JD, Casadevall A (2007) Ionizing radiation changes the electronic properties of melanin and enhances the growth of melanized fungi. PLoS One 2:e457

    Article  PubMed  CAS  Google Scholar 

  • De Sordi L, Muhlschlegel FA (2009) Quorum sensing and fungal-bacterial interactions in Candida albicans: a communicative network regulating microbial coexistence and virulence. FEMS Yeast Res 9:990–999

    Article  PubMed  CAS  Google Scholar 

  • Degli-Innocenti F, Russo VE (1984) Isolation of new white collar mutants of Neurospora crassa and studies on their behavior in the blue light-induced formation of protoperithecia. J Bacteriol 159:757–761

    PubMed  CAS  Google Scholar 

  • Denault DL, Loros JJ, Dunlap JC (2001) WC-2 mediates WC-1-FRQ interaction within the PAS protein-linked circadian feedback loop of Neurospora. EMBO J 20:109–117

    Article  PubMed  CAS  Google Scholar 

  • Dettman JR, Anderson JB, Kohn LM (2010) Genome-wide investigation of reproductive isolation in experimental lineages and natural species of Neurospora: identifying candidate regions by microarray-based genotyping and mapping. Evolution 64:694–709

    Article  PubMed  CAS  Google Scholar 

  • Dighton J, Mascarenhas M, Arbuckle-Keil GA (2001) Changing resources: assessment of leaf litter carbohydrate resource change at a microbial scale of resolution. Soil Biol Biochem 33:1429–1432

    Article  CAS  Google Scholar 

  • Dighton J, Tugay T, Zhdanova N (2008) Fungi and ionizing radiation from radionuclides. FEMS Microbiol Lett 281:109–120

    Article  PubMed  CAS  Google Scholar 

  • DOE Office of Biological and Environmental Research. DOE office of biological and environmental research: biofuels strategic plan. http://science.energy.gov/~/media/ber/pdf/biofuels_strategic_plan.pdf

  • Dogaris I, Gkounta O, Mamma D, Kekos D (2012) Bioconversion of dilute-acid pretreated sorghum bagasse to ethanol by Neurospora crassa. Appl Microbiol Biotechnol 95:541–550

    Article  PubMed  CAS  Google Scholar 

  • Dogaris I, Mamma D, Kekos D (2013) Biotechnological production of ethanol from renewable resources by Neurospora crassa: an alternative to conventional yeast fermentations? Appl Microbiol Biotechnol 97:1457–1473

    Article  PubMed  CAS  Google Scholar 

  • Dunlap JC, Borkovich KA, Henn MR, Turner GE, Sachs MS, Glass NL, McCluskey K, Plamann M, Galagan JE, Birren BW, Weiss RL, Townsend JP, Loros JJ, Nelson MA, Lambreghts R, Colot HV, Park G, Collopy P, Ringelberg C, Crew C, Litvinkova L, De Caprio D, Hood HM, Curilla S, Shi M, Crawford M, Koerhsen M, Montgomery P, Larson L, Pearson M, Kasuga T, Tian C, Basturkmen M, Altamirano L, Xu J (2007) Enabling a community to dissect an organism: overview of the Neurospora functional genomics project. Adv Genet 57:49–96

    Article  PubMed  CAS  Google Scholar 

  • Durrell LW, Shields LA (1960) Fungi isolated in culture from soils of the Nevada test site. Mycologia 52:636–641

    Article  Google Scholar 

  • Eastwood DC, Floudas D, Binder M, Majcherczyk A, Schneider P, Aerts A, Asiegbu FO, Baker SE, Barry K, Bendiksby M, Blumentritt M, Coutinho PM, Cullen D, de Vries RP, Gathman A, Goodell B, Henrissat B, Ihrmark K, Kauserud H, Kohler A, LaButti K, Lapidus A, Lavin JL, Lee YH, Lindquist E, Lilly W, Lucas S, Morin E, Murat C, Oguiza JA, Park J, Pisabarro AG, Riley R, Rosling A, Salamov A, Schmidt O, Schmutz J, Skrede I, Stenlid J, Wiebenga A, Xie X, Kues U, Hibbett DS, Hoffmeister D, Hogberg N, Martin F, Grigoriev IV, Watkinson SC (2011) The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi. Science 333:762–765

    Article  PubMed  CAS  Google Scholar 

  • Elias-Arnanz M, Padmanabhan S, Murillo FJ (2011) Light-dependent gene regulation in nonphototrophic bacteria. Curr Opin Microbiol 14:128–135

    Article  PubMed  CAS  Google Scholar 

  • Eriksson K-EL, Blanchette RA, Ander P (1991) Microbial and enzymatic degradation of wood and wood components. Springer, Berlin

    Google Scholar 

  • Fan Z, Wu W, Hildebrand A, Kasuga T, Zhang R, Xiong X (2012) A novel biochemical route for fuels and chemicals production from cellulosic biomass. PLoS One 7:e31693

    Article  PubMed  CAS  Google Scholar 

  • Fernandez-Fueyo E, Ruiz-Dueñas FJ, Ferreira P, Floudas D, Hibbett DS, Canessa P, Larrondo LF, James TY, Seelenfreund D, Lobos S, Polanco R, Tello M, Honda Y, Watanabe T, Watanabe T, Ryu JS, Kubicek CP, Schmoll M, Gaskell J, Hammel KE, St John FJ, Vanden Wymelenberg A, Sabat G, Splinter BonDurant S, Syed K, Yadav JS, Doddapaneni H, Subramanian V, Lavin JL, Oguiza JA, Perez G, Pisabarro AG, Ramirez L, Santoyo F, Master E, Coutinho PM, Henrissat B, Lombard V, Magnuson JK, Kuees U, Hori C, Igarashi K, Samejima M, Held BW, Barry KW, LaButti KM, Lapidus A, Lindquist EA, Lucas SM, Riley R, Salamov AA, Hoffmeister D, Schwenk D, Hadar Y, Yarden O, de Vries RP, Wiebenga A, Stenlid J, Eastwood D, Grigoriev IV, Berka RM, Blanchette RA, Kersten P, Martinez AT, Vicuna R, Cullen D (2012) Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis. Proc Natl Acad Sci U S A 109:5458–5463

    Article  PubMed  CAS  Google Scholar 

  • Frankland JC (1966) Succession of fungi on decaying petioles of Pteridium aquilinum. J Ecol 54:41–63

    Article  Google Scholar 

  • Frankland JC (1992) Mechanisms in fungal succession. In: Caroll G, Wicklow DT (eds) The fungal community: its organization and role in the ecosystem. Marcel Dekker, New York

    Google Scholar 

  • Frankland JC (1998) Fungal succession – unravelling the unpredictable. Mycol Res 102:1–15

    Article  Google Scholar 

  • Froehlich AC, Liu Y, Loros JJ, Dunlap JC (2002) White Collar-1, a circadian blue light photoreceptor, binding to the frequency promoter. Science 297:815–819

    Article  PubMed  CAS  Google Scholar 

  • Fu C, Iyer P, Herkal A, Abdullah J, Stout A, Free SJ (2011) Identification and characterization of genes required for cell-to-cell fusion in Neurospora crassa. Eukaryot Cell 10:1100–1109

    Article  PubMed  CAS  Google Scholar 

  • Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, Jaffe D, FitzHugh W, Ma LJ, Smirnov S, Purcell S, Rehman B, Elkins T, Engels R, Wang S, Nielsen CB, Butler J, Endrizzi M, Qui D, Ianakiev P, Bell-Pedersen D, Nelson MA, Werner-Washburne M, Selitrennikoff CP, Kinsey JA, Braun EL, Zelter A, Schulte U, Kothe GO, Jedd G, Mewes W, Staben C, Marcotte E, Greenberg D, Roy A, Foley K, Naylor J, Stange-Thomann N, Barrett R, Gnerre S, Kamal M, Kamvysselis M, Mauceli E, Bielke C, Rudd S, Frishman D, Krystofova S, Rasmussen C, Metzenberg RL, Perkins DD, Kroken S, Cogoni C, Macino G, Catcheside D, Li W, Pratt RJ, Osmani SA, DeSouza CP, Glass L, Orbach MJ, Berglund JA, Voelker R, Yarden O, Plamann M, Seiler S, Dunlap J, Radford A, Aramayo R, Natvig DO, Alex LA, Mannhaupt G, Ebbole DJ, Freitag M, Paulsen I, Sachs MS, Lander ES, Nusbaum C, Birren B (2003) The genome sequence of the filamentous fungus Neurospora crassa. Nature 422:859–868

    Article  PubMed  CAS  Google Scholar 

  • Gallo ME, Porras-Alfaro A, Odenbach KJ, Sinsabaugh RL (2009) Photoacceleration of plant litter decomposition in an arid environment. Soil Biol Biochem 41:1433–1441

    Article  CAS  Google Scholar 

  • Gauslaa Y, Solhaug KA (2001) Fungal melanins as a sun screen for symbiotic green algae in the lichen Lobaria pulmonaria. Oecologia 126:462–471

    Article  Google Scholar 

  • Gooch VD, Mehra A, Larrondo LF, Fox J, Touroutoutoudis M, Loros JJ, Dunlap JC (2008) Fully codon-optimized luciferase uncovers novel temperature characteristics of the Neurospora clock. Eukaryot Cell 7:28–37

    Article  PubMed  CAS  Google Scholar 

  • Haferburg G, Kothe E (2010) Metallomics: lessons for metalliferous soil remediation. Appl Microbiol Biotechnol 87:1271–1280

    Article  PubMed  CAS  Google Scholar 

  • Hammond TM, Xiao H, Boone EC, Perdue TD, Pukkila PJ, Shiu PK (2011) SAD-3, a putative helicase required for meiotic silencing by unpaired DNA, interacts with other components of the silencing machinery. G3 (Bethesda) 1:369–376

    Article  CAS  Google Scholar 

  • He Q, Cheng P, Yang Y, Wang L, Gardner KH, Liu Y (2002) White collar-1, a DNA binding transcription factor and a light sensor. Science 297:840–843

    Article  PubMed  CAS  Google Scholar 

  • Heintzen C, Liu Y (2007) The Neurospora crassa circadian clock. Adv Genet 58:25–66

    Article  PubMed  CAS  Google Scholar 

  • Heintzen C, Loros JJ, Dunlap JC (2001) The PAS protein VIVID defines a clock-associated feedback loop that represses light input, modulates gating, and regulates clock resetting. Cell 104:453–464

    Article  PubMed  CAS  Google Scholar 

  • Honda S, Selker EU (2009) Tools for fungal proteomics: multifunctional neurospora vectors for gene replacement, protein expression and protein purification. Genetics 182:11–23

    Article  PubMed  CAS  Google Scholar 

  • Hurley JM, Chen CH, Loros JJ, Dunlap JC (2012) Light-inducible system for tunable protein expression in Neurospora crassa. G3 (Bethesda) 2:1207–1212

    Article  CAS  Google Scholar 

  • Jacobson DJ, Dettman JR, Adams RI, Boesl C, Sultana S, Roenneberg T, Merrow M, Duarte M, Marques I, Ushakova A, Carneiro P, Videira A, Navarro-Sampedro L, Olmedo M, Corrochano LM, Taylor JW (2006) New findings of Neurospora in Europe and comparisons of diversity in temperate climates on continental scales. Mycologia 98:550–559

    Article  PubMed  Google Scholar 

  • Karpenko YV, Redchitz TI, Zheltonozhsky VA, Dighton J, Zhdanova NN (2006) Comparative responses of microscopic fungi to ionizing radiation and light. Folia Microbiol 51:45–49

    Article  CAS  Google Scholar 

  • Kellner H, Zak DR, Vandenbol M (2010) Fungi unearthed: transcripts encoding lignocellulolytic and chitinolytic enzymes in forest soil. PLoS One 5:e10971

    Article  PubMed  CAS  Google Scholar 

  • Kume A, Nasahara KN, Nagai S, Muraoka H (2011) The ratio of transmitted near-infrared radiation to photosynthetically active radiation (PAR) increases in proportion to the adsorbed PAR in the canopy. J Plant Res 124:99–106

    Article  PubMed  Google Scholar 

  • Lammers K, Dighton J, Arbuckle-Keil GA (2009) FT-IR study of the changes in carbohydrate chemistry of three New Jersey pine barrens leaf litters during simulated control burning. Soil Biol Biochem 41:340–347

    Article  CAS  Google Scholar 

  • Larrondo LF, Loros JJ, Dunlap JC (2012) High-resolution spatiotemporal analysis of gene expression in real time: in vivo analysis of circadian rhythms in Neurospora crassa using a FREQUENCY-luciferase translational reporter. Fungal Genet Biol 49:681–683

    Article  PubMed  CAS  Google Scholar 

  • Lee K, Dighton J (2010) Neurospora, a potential fungal organism for experimental and evolutionary ecology. Fungal Biol Rev 24:85–89

    Article  Google Scholar 

  • Lee K, Loros JJ, Dunlap JC (2000) Interconnected feedback loops in the Neurospora circadian system. Science 289:107–110

    Article  PubMed  CAS  Google Scholar 

  • Lewis ZA, Shiver AL, Stiffler N, Miller MR, Johnson EA, Selker EU (2007) High-density detection of restriction-site-associated DNA markers for rapid mapping of mutated loci in Neurospora. Genetics 177:1163–1171

    Article  PubMed  CAS  Google Scholar 

  • Li X, Beeson WT IV, Phillips CM, Marletta MA, Cate JH (2012) Structural basis for substrate targeting and catalysis by fungal polysaccharide monooxygenases. Structure 20:1051–1061

    Article  PubMed  CAS  Google Scholar 

  • Linden H, Macino G (1997) White collar 2, a partner in blue-light signal transduction, controlling expression of light-regulated genes in Neurospora crassa. EMBO J 16:98–109

    Article  PubMed  CAS  Google Scholar 

  • Linden H, Rodriguez-Franco M, Macino G (1997) Mutants of Neurospora crassa defective in regulation of blue light perception. Mol Gen Genet 254:111–118

    Article  PubMed  CAS  Google Scholar 

  • Longoni P, Rodolfi M, Pantaleoni L, Doria E, Concia L, Picco AM, Cella R (2012) Functional analysis of the degradation of cellulosic substrates by a Chaetomium globosum endophytic isolate. Appl Environ Microbiol 78:3693–3705

    Article  PubMed  CAS  Google Scholar 

  • Lorito M, Woo SL, Harman GE, Monte E (2010) Translational research on Tricholoma: from ‘omics to the field. Annu Rev Phytopathol 48:395–417

    Article  PubMed  CAS  Google Scholar 

  • Lundell TK, Makela MR, Hilden K (2010) Lignin-modifying enzymes in filamentous basidiomycetes–ecological, functional and phylogenetic review. J Basic Microbiol 50:5–20

    Article  PubMed  CAS  Google Scholar 

  • Nargang FE, Adames K, Rub C, Cheung S, Easton N, Nargang CE, Chae MS (2012) Identification of genes required for alternative oxidase production in the Neurospora crassa gene knockout library. G3 (Bethesda) 2:1345–1356

    Article  CAS  Google Scholar 

  • Nevalainen KM, Te’o VS, Bergquist PL (2005) Heterologous protein expression in filamentous fungi. Trends Biotechnol 23:468–474

    Article  PubMed  CAS  Google Scholar 

  • Nix-Stohr S, Moshe R, Dighton J (2008) Effects of propagule density and survival strategies on establishment and growth: further investigations in the phylloplane fungal model system. Microb Ecol 55:38–44

    Article  PubMed  Google Scholar 

  • Oberle-Kilic J, Dighton J, Arbuckle-Keil G (2013) Atomic force microscopy and micro-ATR-FT-IR imaging reveals fungal enzyme activity at the hyphal scale of resolution. Mycology 4:1–10. doi:10.1080/21501203.2012.759631

    Google Scholar 

  • Pandit A, Maheshwari R (1996) Life-history of Neurospora intermedia in a sugar cane field. J Biosci 21:57–79

    Article  Google Scholar 

  • Park G, Servin JA, Turner GE, Altamirano L, Colot HV, Collopy P, Litvinkova L, Li L, Jones CA, Diala FG, Dunlap JC, Borkovich KA (2011) Global analysis of serine-threonine protein kinase genes in Neurospora crassa. Eukaryot Cell 10:1553–1564

    Article  PubMed  CAS  Google Scholar 

  • Phillips CM, Beeson WT, Cate JH, Marletta MA (2011) Cellobiose dehydrogenase and a copper-dependent polysaccharide monooxygenase potentiate cellulose degradation by Neurospora crassa. ACS Chem Biol 6:1399–1406

    Article  PubMed  CAS  Google Scholar 

  • Ponge JF (1990) Ecological study of a forest humus by observing a small volume. 1. Penetration of Pine litter by mycorrhizal fungi. Eur J For Pathol 20:290–303

    Article  Google Scholar 

  • Ponge JF (1991) Succession of fungi and fauna during decomposition of needles in a small area of scots pine litter. Plant Soil 138:99–113

    Article  Google Scholar 

  • Purschwitz J, Muller S, Kastner C, Schoser M, Haas H, Espeso EA, Atoui A, Calvo AM, Fischer R (2008) Functional and physical interaction of blue- and red-light sensors in Aspergillus nidulans. Curr Biol 18:255–259

    Article  PubMed  CAS  Google Scholar 

  • Rockwell NC, Lagarias JC (2010) A brief history of phytochromes. Chemphyschem 11:1172–1180

    Article  PubMed  CAS  Google Scholar 

  • Rodriguez-Romero J, Hedtke M, Kastner C, Muller S, Fischer R (2010) Fungi, hidden in soil or up in the air: light makes a difference. Annu Rev Microbiol 64:585–610

    Article  PubMed  CAS  Google Scholar 

  • Rossouw D, Naes T, Bauer FF (2008) Linking gene regulation and the exo-metabolome: a comparative transcriptomics approach to identify genes that impact on the production of volatile aroma compounds in yeast. BMC Genomics 9:530

    Article  PubMed  CAS  Google Scholar 

  • Roux A, Payne SM, Gilmore MS (2009) Microbial telesensing: probing the environment for friends, foes, and food. Cell Host Microbe 6:115–124

    Article  PubMed  CAS  Google Scholar 

  • Rowe HC, Renaut S, Guggisberg A (2011) RAD in the realm of next-generation sequencing technologies. Mol Ecol 20:3499–3502

    PubMed  CAS  Google Scholar 

  • Ryu JS, Shary S, Houtman CJ, Panisko EA, Korripally P, St. John FJ, Crooks C, Siika-aho M, Magnuson JK, Hammel KE (2011) Proteomic and functional analysis of the cellulase system expressed by Postia placenta during brown rot of solid wood. Appl Environ Microbiol 77:7933–7941

    Article  PubMed  CAS  Google Scholar 

  • Sanchez C (2009) Lignocellulosic residues: biodegradation and bioconversion by fungi. Biotechnol Adv 27:185–194

    Article  PubMed  CAS  Google Scholar 

  • Šašek V (2005) Potential of ligninolytic Basidiomycetes to degrade organopollutants. In: Deshmukh SK, Rai MK (eds) Biodiversity of fungi: their role in human life. Science, Enfield, NH, pp 155–184

    Google Scholar 

  • Schmoll M, Tian C, Sun J, Tisch D, Glass NL (2012) Unravelling the molecular basis for light modulated cellulase gene expression – the role of photoreceptors in Neurospora crassa. BMC Genomics 13:127

    Article  PubMed  CAS  Google Scholar 

  • Schwerdtfeger C, Linden H (2000) Localization and light-dependent phosphorylation of white collar 1 and 2, the two central components of blue light signaling in Neurospora crassa. Eur J Biochem 267:414–422

    Article  PubMed  CAS  Google Scholar 

  • Schwerdtfeger C, Linden H (2001) Blue light adaptation and desensitization of light signal transduction in Neurospora crassa. Mol Microbiol 39:1080–1087

    Article  PubMed  CAS  Google Scholar 

  • Sharrock RA (2008) The phytochrome red/far-red photoreceptor superfamily. Genome Biol 9:230

    Article  PubMed  CAS  Google Scholar 

  • Sinsabaugh RL (2005) Fungal enzymes at the community scale. In: Dighton J, White JF Jr, Oudemans P (eds) The fungal community: its organization and role in the ecosystem. CRC, Boca Raton, pp 349–360

    Chapter  Google Scholar 

  • Šnajdr J, Cajthaml T, Valášková V, Merhautová V, Petránková M, Spetz P, Leppänen K, Baldrian P (2011) Transformation of Quercus petraea litter: successive changes in litter chemistry are reflected in differential enzyme activity and changes in the microbial community composition. FEMS Microbiol Ecol 75:291–303

    Article  PubMed  CAS  Google Scholar 

  • Stohr SN, Dighton J (2004) Effects of species diversity on establishment and coexistence: a phylloplane fungal community model system. Microb Ecol 48:431–438

    Article  PubMed  CAS  Google Scholar 

  • Stursova M, Zifcakova L, Leigh MB, Burgess R, Baldrian P (2012) Cellulose utilization in forest litter and soil: identification of bacterial and fungal decomposers. FEMS Microbiol Ecol 80:735–746

    Article  PubMed  CAS  Google Scholar 

  • Sun J, Glass NL (2011) Identification of the CRE-1 cellulolytic regulon in Neurospora crassa. PLoS One 6:e25654

    Article  PubMed  CAS  Google Scholar 

  • Sun J, Phillips CM, Anderson CT, Beeson WT, Marletta MA, Glass NL (2011a) Expression and characterization of the Neurospora crassa endoglucanase GH5-1. Protein Expr Purif 75:147–154

    Article  PubMed  CAS  Google Scholar 

  • Sun X, Zhang H, Zhang Z, Wang Y, Li S (2011b) Involvement of a helix-loop-helix transcription factor CHC-1 in CO(2)-mediated conidiation suppression in Neurospora crassa. Fungal Genet Biol 48:1077–1086

    Article  PubMed  CAS  Google Scholar 

  • Sun J, Tian C, Diamond S, Glass NL (2012) Deciphering transcriptional regulatory mechanisms associated with hemicellulose degradation in Neurospora crassa. Eukaryot Cell 11:482–493

    Article  PubMed  CAS  Google Scholar 

  • Swift MJ, Heal OW, Anderson JM (1979) Decomposition in terrestrial ecosystems. University of California Press, Berkeley

    Google Scholar 

  • Talora C, Franchi L, Linden H, Ballario P, Macino G (1999) Role of a white collar-1-white collar-2 complex in blue-light signal transduction. EMBO J 18:4961–4968

    Article  PubMed  CAS  Google Scholar 

  • Tian C, Beeson WT, Iavarone AT, Sun J, Marletta MA, Cate JH, Glass NL (2009) Systems analysis of plant cell wall degradation by the model filamentous fungus Neurospora crassa. Proc Natl Acad Sci U S A 106:22157–22162

    Article  PubMed  CAS  Google Scholar 

  • Tugay T, Zhdanova NN, Zheltonozhsky V, Sadovnikov L, Dighton J (2006) The influence of ionizing radiation on spore germination and emergent hyphal growth response reactions of microfungi. Mycologia 98:521–527

    Article  PubMed  Google Scholar 

  • Turner GE (2011) Phenotypic analysis of Neurospora crassa gene deletion strains. Methods Mol Biol 722:191–198

    Article  PubMed  CAS  Google Scholar 

  • Urich T, Lanzen A, Qi J, Huson DH, Schleper C, Schuster SC (2008) Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS One 3:e2527

    Article  PubMed  CAS  Google Scholar 

  • van Elsas JD, Boersma FGH (2011) A review of molecular methods to study the microbiota of soil and the mycosphere. Eur J Soil Biol 47:77–87

    Article  Google Scholar 

  • Watters MK, Boersma M, Johnson M, Reyes C, Westrick E, Lindamood E (2011) A screen for Neurospora knockout mutants displaying growth rate dependent branch density. Fungal Biol 115:296–301

    Article  PubMed  Google Scholar 

  • Wilson DB (2008) Three microbial strategies for plant cell wall degradation. Ann N Y Acad Sci 1125:289–297

    Article  PubMed  CAS  Google Scholar 

  • Yadav SK, Singla-Preek SL, Pareek A (2010) Transcriptome analysis. In: Varma A, Oelmüller R (eds) Soil biology. Springer, Berlin, pp 111–131

    Google Scholar 

  • Zhdanova NN, Vasilevskaya AI, Artyshkova LV, Sadovnikov YS, Lashko TN, Gavrilyuk VI, Dighton J (1994) Changes in micromycete communities in soil in response to pollution by long-lived radionuclides emitted in the chernobyl accident. Mycol Res 98:789–795

    Article  CAS  Google Scholar 

  • Znameroski EA, Coradetti ST, Roche CM, Tsai JC, Iavarone AT, Cate JH, Glass NL (2012) Induction of lignocellulose-degrading enzymes in Neurospora crassa by cellodextrins. Proc Natl Acad Sci U S A 109:6012–6017

    Article  PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Center for Computational and Integrative Biology, Department of Biology, Rutgers University, Camden, NJ, 08102 1411, USA

    Kwangwon Lee

  2. Rutgers Pinelands Field Station, 501 Four Mile Road, 206, New Lisbon, NJ, 08057, USA

    John Dighton

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  1. Kwangwon Lee
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  2. John Dighton
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Correspondence to Kwangwon Lee .

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Editors and Affiliations

  1. Dep. of Biology, Technion – Israel Inst. of Technology, Haifa, Israel

    Benjamin A. Horwitz

  2. Central Institute for Cotton Research, Nagpur, India

    Prasun K. Mukherjee

  3. Central Institute for Cotton Research, Nagpur, India

    Mala Mukherjee

  4. Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria

    Christian P. Kubicek

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Lee, K., Dighton, J. (2013). Advancement of Functional Genomics of a Model Species of Neurospora and Its Use for Ecological Genomics of Soil Fungi. In: Horwitz, B., Mukherjee, P., Mukherjee, M., Kubicek, C. (eds) Genomics of Soil- and Plant-Associated Fungi. Soil Biology, vol 36. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-39339-6_3

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