Advertisement

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

  • Kwangwon Lee
  • John Dighton
Chapter
Part of the Soil Biology book series (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.

Keywords

Fungal Species Fungal Community Lignocellulosic Biomass Soil Fungus Cellulosic Biofuel 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. Andersen MR, Nielsen J (2009) Current status of systems biology in Aspergilli. Fungal Genet Biol 46(Suppl 1):S180–S190PubMedCrossRefGoogle Scholar
  2. Avalos J, Estrada AF (2010) Regulation by light in Fusarium. Fungal Genet Biol 47:930–938PubMedCrossRefGoogle Scholar
  3. Bahn YS, Xue C, Idnurm A, Rutherford JC, Heitman J, Cardenas ME (2007) Sensing the environment: lessons from fungi. Nat Rev Microbiol 5:57–69PubMedCrossRefGoogle Scholar
  4. 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:e3376PubMedCrossRefGoogle Scholar
  5. Ballario P, Macino G (1997) White collar proteins: PASsing the light signal in Neurospora crassa. Trends Microbiol 5:458–462PubMedCrossRefGoogle Scholar
  6. 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 15:1650–1657PubMedGoogle Scholar
  7. 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 29:719–729PubMedCrossRefGoogle Scholar
  8. 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 152:139–149CrossRefGoogle Scholar
  9. Baxter JW, Dighton J (2005) Phosphorus source alters host plant response to ectomycorrhizal diversity. Mycorrhiza 15:513–523PubMedCrossRefGoogle Scholar
  10. Bayram O, Braus GH, Fischer R, Rodriguez-Romero J (2010) Spotlight on Aspergillus nidulans photosensory systems. Fungal Genet Biol 47:900–908PubMedCrossRefGoogle Scholar
  11. Beeson WT, Phillips CM, Cate JH, Marletta MA (2012) Oxidative cleavage of cellulose by fungal copper-dependent polysaccharide monooxygenases. J Am Chem Soc 134:890–892PubMedCrossRefGoogle Scholar
  12. 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 97:159–169PubMedCrossRefGoogle Scholar
  13. Chen CH, Dunlap JC, Loros JJ (2010) Neurospora illuminates fungal photoreception. Fungal Genet Biol 47:922–929PubMedCrossRefGoogle Scholar
  14. 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 20:101–108PubMedCrossRefGoogle Scholar
  15. 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 109:7397–7402PubMedCrossRefGoogle Scholar
  16. Corrochano LM (2007) Fungal photoreceptors: sensory molecules for fungal development and behaviour. Photochem Photobiol Sci 6:725–736PubMedCrossRefGoogle Scholar
  17. Corrochano LM, Garre V (2010) Photobiology in the Zygomycota: multiple photoreceptor genes for complex responses to light. Fungal Genet Biol 47:893–899PubMedCrossRefGoogle Scholar
  18. 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–S169PubMedCrossRefGoogle Scholar
  19. Dadachova E, Casadevall A (2008) Ionizing radiation: how fungi cope, adapt, and exploit with the help of melanin. Curr Opin Microbiol 11:525–531PubMedCrossRefGoogle Scholar
  20. 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:e457PubMedCrossRefGoogle Scholar
  21. 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 9:990–999PubMedCrossRefGoogle Scholar
  22. 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 159:757–761PubMedGoogle Scholar
  23. 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 20:109–117PubMedCrossRefGoogle Scholar
  24. 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 64:694–709PubMedCrossRefGoogle Scholar
  25. 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 33:1429–1432CrossRefGoogle Scholar
  26. Dighton J, Tugay T, Zhdanova N (2008) Fungi and ionizing radiation from radionuclides. FEMS Microbiol Lett 281:109–120PubMedCrossRefGoogle Scholar
  27. 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
  28. Dogaris I, Gkounta O, Mamma D, Kekos D (2012) Bioconversion of dilute-acid pretreated sorghum bagasse to ethanol by Neurospora crassa. Appl Microbiol Biotechnol 95:541–550PubMedCrossRefGoogle Scholar
  29. 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 97:1457–1473PubMedCrossRefGoogle Scholar
  30. 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 57:49–96PubMedCrossRefGoogle Scholar
  31. Durrell LW, Shields LA (1960) Fungi isolated in culture from soils of the Nevada test site. Mycologia 52:636–641CrossRefGoogle Scholar
  32. 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 333:762–765PubMedCrossRefGoogle Scholar
  33. Elias-Arnanz M, Padmanabhan S, Murillo FJ (2011) Light-dependent gene regulation in nonphototrophic bacteria. Curr Opin Microbiol 14:128–135PubMedCrossRefGoogle Scholar
  34. Eriksson K-EL, Blanchette RA, Ander P (1991) Microbial and enzymatic degradation of wood and wood components. Springer, BerlinGoogle Scholar
  35. 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:e31693PubMedCrossRefGoogle Scholar
  36. 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 109:5458–5463PubMedCrossRefGoogle Scholar
  37. Frankland JC (1966) Succession of fungi on decaying petioles of Pteridium aquilinum. J Ecol 54:41–63CrossRefGoogle Scholar
  38. 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 YorkGoogle Scholar
  39. Frankland JC (1998) Fungal succession – unravelling the unpredictable. Mycol Res 102:1–15CrossRefGoogle Scholar
  40. Froehlich AC, Liu Y, Loros JJ, Dunlap JC (2002) White Collar-1, a circadian blue light photoreceptor, binding to the frequency promoter. Science 297:815–819PubMedCrossRefGoogle Scholar
  41. 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 10:1100–1109PubMedCrossRefGoogle Scholar
  42. 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 422:859–868PubMedCrossRefGoogle Scholar
  43. Gallo ME, Porras-Alfaro A, Odenbach KJ, Sinsabaugh RL (2009) Photoacceleration of plant litter decomposition in an arid environment. Soil Biol Biochem 41:1433–1441CrossRefGoogle Scholar
  44. Gauslaa Y, Solhaug KA (2001) Fungal melanins as a sun screen for symbiotic green algae in the lichen Lobaria pulmonaria. Oecologia 126:462–471CrossRefGoogle Scholar
  45. 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 7:28–37PubMedCrossRefGoogle Scholar
  46. Haferburg G, Kothe E (2010) Metallomics: lessons for metalliferous soil remediation. Appl Microbiol Biotechnol 87:1271–1280PubMedCrossRefGoogle Scholar
  47. 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) 1:369–376CrossRefGoogle Scholar
  48. 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 297:840–843PubMedCrossRefGoogle Scholar
  49. Heintzen C, Liu Y (2007) The Neurospora crassa circadian clock. Adv Genet 58:25–66PubMedCrossRefGoogle Scholar
  50. 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 104:453–464PubMedCrossRefGoogle Scholar
  51. Honda S, Selker EU (2009) Tools for fungal proteomics: multifunctional neurospora vectors for gene replacement, protein expression and protein purification. Genetics 182:11–23PubMedCrossRefGoogle Scholar
  52. Hurley JM, Chen CH, Loros JJ, Dunlap JC (2012) Light-inducible system for tunable protein expression in Neurospora crassa. G3 (Bethesda) 2:1207–1212CrossRefGoogle Scholar
  53. 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 98:550–559PubMedCrossRefGoogle Scholar
  54. Karpenko YV, Redchitz TI, Zheltonozhsky VA, Dighton J, Zhdanova NN (2006) Comparative responses of microscopic fungi to ionizing radiation and light. Folia Microbiol 51:45–49CrossRefGoogle Scholar
  55. Kellner H, Zak DR, Vandenbol M (2010) Fungi unearthed: transcripts encoding lignocellulolytic and chitinolytic enzymes in forest soil. PLoS One 5:e10971PubMedCrossRefGoogle Scholar
  56. 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 124:99–106PubMedCrossRefGoogle Scholar
  57. 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 41:340–347CrossRefGoogle Scholar
  58. 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 49:681–683PubMedCrossRefGoogle Scholar
  59. Lee K, Dighton J (2010) Neurospora, a potential fungal organism for experimental and evolutionary ecology. Fungal Biol Rev 24:85–89CrossRefGoogle Scholar
  60. Lee K, Loros JJ, Dunlap JC (2000) Interconnected feedback loops in the Neurospora circadian system. Science 289:107–110PubMedCrossRefGoogle Scholar
  61. 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 177:1163–1171PubMedCrossRefGoogle Scholar
  62. Li X, Beeson WT IV, Phillips CM, Marletta MA, Cate JH (2012) Structural basis for substrate targeting and catalysis by fungal polysaccharide monooxygenases. Structure 20:1051–1061PubMedCrossRefGoogle Scholar
  63. 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 16:98–109PubMedCrossRefGoogle Scholar
  64. Linden H, Rodriguez-Franco M, Macino G (1997) Mutants of Neurospora crassa defective in regulation of blue light perception. Mol Gen Genet 254:111–118PubMedCrossRefGoogle Scholar
  65. 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 78:3693–3705PubMedCrossRefGoogle Scholar
  66. Lorito M, Woo SL, Harman GE, Monte E (2010) Translational research on Tricholoma: from ‘omics to the field. Annu Rev Phytopathol 48:395–417PubMedCrossRefGoogle Scholar
  67. Lundell TK, Makela MR, Hilden K (2010) Lignin-modifying enzymes in filamentous basidiomycetes–ecological, functional and phylogenetic review. J Basic Microbiol 50:5–20PubMedCrossRefGoogle Scholar
  68. 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) 2:1345–1356CrossRefGoogle Scholar
  69. Nevalainen KM, Te’o VS, Bergquist PL (2005) Heterologous protein expression in filamentous fungi. Trends Biotechnol 23:468–474PubMedCrossRefGoogle Scholar
  70. 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 55:38–44PubMedCrossRefGoogle Scholar
  71. 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
  72. Pandit A, Maheshwari R (1996) Life-history of Neurospora intermedia in a sugar cane field. J Biosci 21:57–79CrossRefGoogle Scholar
  73. 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 10:1553–1564PubMedCrossRefGoogle Scholar
  74. 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 6:1399–1406PubMedCrossRefGoogle Scholar
  75. 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 20:290–303CrossRefGoogle Scholar
  76. Ponge JF (1991) Succession of fungi and fauna during decomposition of needles in a small area of scots pine litter. Plant Soil 138:99–113CrossRefGoogle Scholar
  77. 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 18:255–259PubMedCrossRefGoogle Scholar
  78. Rockwell NC, Lagarias JC (2010) A brief history of phytochromes. Chemphyschem 11:1172–1180PubMedCrossRefGoogle Scholar
  79. 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 64:585–610PubMedCrossRefGoogle Scholar
  80. 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 9:530PubMedCrossRefGoogle Scholar
  81. Roux A, Payne SM, Gilmore MS (2009) Microbial telesensing: probing the environment for friends, foes, and food. Cell Host Microbe 6:115–124PubMedCrossRefGoogle Scholar
  82. Rowe HC, Renaut S, Guggisberg A (2011) RAD in the realm of next-generation sequencing technologies. Mol Ecol 20:3499–3502PubMedGoogle Scholar
  83. 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 77:7933–7941PubMedCrossRefGoogle Scholar
  84. Sanchez C (2009) Lignocellulosic residues: biodegradation and bioconversion by fungi. Biotechnol Adv 27:185–194PubMedCrossRefGoogle Scholar
  85. 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 155–184Google Scholar
  86. 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 13:127PubMedCrossRefGoogle Scholar
  87. 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 267:414–422PubMedCrossRefGoogle Scholar
  88. Schwerdtfeger C, Linden H (2001) Blue light adaptation and desensitization of light signal transduction in Neurospora crassa. Mol Microbiol 39:1080–1087PubMedCrossRefGoogle Scholar
  89. Sharrock RA (2008) The phytochrome red/far-red photoreceptor superfamily. Genome Biol 9:230PubMedCrossRefGoogle Scholar
  90. 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 349–360CrossRefGoogle Scholar
  91. 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 75:291–303PubMedCrossRefGoogle Scholar
  92. Stohr SN, Dighton J (2004) Effects of species diversity on establishment and coexistence: a phylloplane fungal community model system. Microb Ecol 48:431–438PubMedCrossRefGoogle Scholar
  93. 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 80:735–746PubMedCrossRefGoogle Scholar
  94. Sun J, Glass NL (2011) Identification of the CRE-1 cellulolytic regulon in Neurospora crassa. PLoS One 6:e25654PubMedCrossRefGoogle Scholar
  95. 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 75:147–154PubMedCrossRefGoogle Scholar
  96. 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 48:1077–1086PubMedCrossRefGoogle Scholar
  97. Sun J, Tian C, Diamond S, Glass NL (2012) Deciphering transcriptional regulatory mechanisms associated with hemicellulose degradation in Neurospora crassa. Eukaryot Cell 11:482–493PubMedCrossRefGoogle Scholar
  98. Swift MJ, Heal OW, Anderson JM (1979) Decomposition in terrestrial ecosystems. University of California Press, BerkeleyGoogle Scholar
  99. 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 18:4961–4968PubMedCrossRefGoogle Scholar
  100. 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 106:22157–22162PubMedCrossRefGoogle Scholar
  101. 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 98:521–527PubMedCrossRefGoogle Scholar
  102. Turner GE (2011) Phenotypic analysis of Neurospora crassa gene deletion strains. Methods Mol Biol 722:191–198PubMedCrossRefGoogle Scholar
  103. 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:e2527PubMedCrossRefGoogle Scholar
  104. van Elsas JD, Boersma FGH (2011) A review of molecular methods to study the microbiota of soil and the mycosphere. Eur J Soil Biol 47:77–87CrossRefGoogle Scholar
  105. 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 115:296–301PubMedCrossRefGoogle Scholar
  106. Wilson DB (2008) Three microbial strategies for plant cell wall degradation. Ann N Y Acad Sci 1125:289–297PubMedCrossRefGoogle Scholar
  107. Yadav SK, Singla-Preek SL, Pareek A (2010) Transcriptome analysis. In: Varma A, Oelmüller R (eds) Soil biology. Springer, Berlin, pp 111–131Google Scholar
  108. 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 98:789–795CrossRefGoogle Scholar
  109. 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 109:6012–6017PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  1. 1.Center for Computational and Integrative Biology, Department of BiologyRutgers UniversityCamdenUSA
  2. 2.Rutgers Pinelands Field StationNew LisbonUSA

Personalised recommendations