Fungi in Consolidated Bioprocessing of Lignocellulosic Materials

  • Anastasia P. Galanopoulou
  • Dimitris G. HatzinikolaouEmail author
Part of the Fungal Biology book series (FUNGBIO)


Second generation biorefineries are based on the efficient exploitation of the carbon stored in lignocellulosic biomass. Many fungal genera have the capacity to enzymatically degrade lignocellulose, while other can transform the resulting degradation products into compounds of economical value, such as biofuels. The possibility of performing both tasks in a single vessel and, ideally, by a single microbial strain is described by the term consolidated bioprocessing (CBP). This strategy is in principle applicable to the production of a broad range of compounds using plant biomass as raw material. In this chapter we will discuss the progress, problems, and prospects of CBP systems that exploit fungal species as their main biocatalyst. Since most of the relevant research has been conducted toward the production of bioethanol, our approach will focus on the efforts to either engineer ethanologenic strains for cellulase and hemicellulase production or to increase the fermentative capacity of natural biomass degraders. Finally, we will give an overview of fungal lignocellulose CBP processes for the production of additional higher value-added chemicals.


Fungi Yeasts Cellulose Hemicellulose Lignocellulose Consolidated bioprocessing Simultaneous saccharification and fermentation Bioethanol Organic acids 


  1. Aden AJ, Bozell HJ, White J, Manheim A (2004) Top value added chemicals from biomass. Volume I: results of screening for potential candidates from sugars and synthesis gas. In: Werpy T, Petersen G (eds) Pacific Northwest National Laboratory (PNNL), National Renewable Energy Laboratory (NREL) and Office of Biomass Program (EERE)Google Scholar
  2. Adsul M, Singhvi M, Gaikaiwari S, Gokhale D (2011) Development of biocatalysts for production of commodity chemicals from lignocellulosic biomass. Bioresour Technol 102(6):4304–4312PubMedCrossRefGoogle Scholar
  3. Albergaria H, Arneborg N (2016) Dominance of Saccharomyces cerevisiae in alcoholic fermentation processes: role of physiological fitness and microbial interactions. Appl Microbiol Biotechnol 100(5):2035–2046PubMedCrossRefGoogle Scholar
  4. Ali SS, Khan M, Fagan B, Mullins E, Doohan FM (2012) Exploiting the inter-strain divergence of Fusarium oxysporum for microbial bioprocessing of lignocellulose to bioethanol. AMB Express 2(1):1–9CrossRefGoogle Scholar
  5. Ali SS, Nugent B, Mullins E, Doohan FM (2013) Insights from the fungus Fusarium oxysporum point to high affinity glucose transporters as targets for enhancing ethanol production from lignocellulose. PLoS ONE 8(1):e54701PubMedPubMedCentralCrossRefGoogle Scholar
  6. Ali SS, Khan M, Mullins E, Doohan FM (2014) Identification of Fusarium oxysporum genes associated with lignocellulose bioconversion competency. Bioenergy Res 7(1):110–119CrossRefGoogle Scholar
  7. Ali SS, Nugent B, Mullins E, Doohan FM (2016) Fungal-mediated consolidated bioprocessing: the potential of Fusarium oxysporum for the lignocellulosic ethanol industry. AMB Express 6(1):1–13CrossRefGoogle Scholar
  8. Alvira P, Tomás-Pejó E, Ballesteros M, Negro MJ (2010) Pretreatment technologies for an efficient bioethanol production process based on enzymatic hydrolysis: a review. Bioresour Technol 101(13):4851–4861PubMedCrossRefGoogle Scholar
  9. Amore A, Faraco V (2012) Potential of fungi as category I Consolidated BioProcessing organisms for cellulosic ethanol production. Renew Sustain Energy Rev 16(5):3286–3301CrossRefGoogle Scholar
  10. Anasontzis G, Zerva A, Stathopoulou P, Haralampidis K, Diallinas G, Karagouni A, Hatzinikolaou D (2011) Homologous overexpression of xylanase in Fusarium oxysporum increases ethanol productivity during consolidated bioprocessing (CBP) of lignocellulosics. J Biotechnol 152(1–2):16–23PubMedCrossRefGoogle Scholar
  11. Anasontzis GE, Kourtoglou E, Mamma D, Villas-Boâs SG, Hatzinikolaou DG, Christakopoulos P (2014) Constitutive homologous expression of phosphoglucomutase and transaldolase increases the metabolic flux of Fusarium oxysporum. Microb Cell Fact 13(1):1–13CrossRefGoogle Scholar
  12. Anasontzis GE, Kourtoglou E, Villas-Boas SG, Hatzinikolaou DG, Christakopoulos P (2016) Metabolic engineering of Fusarium oxysporum to improve its ethanol-producing capability. Front Microbiol 7:632Google Scholar
  13. Ballesteros I, Ballesteros M, CabaÑas A, Carrasco J, MartÍn C, Negro MJ, Saez F, Saez R (1991) Selection of thermotolerant yeasts for simultaneous saccharification and fermentation (SSF) of cellulose to ethanol. Appl Biochem Biotechnol 28–29(1):307–315PubMedCrossRefGoogle Scholar
  14. Ballesteros M, Oliva JM, Negro MJ, Manzanares P, Ballesteros I (2004) Ethanol from lignocellulosic materials by a simultaneous saccharification and fermentation process (SFS) with Kluyveromyces marxianus CECT 10875. Process Biochem 39(12):1843–1848CrossRefGoogle Scholar
  15. Barron N, Marchant R, McHale L, McHale AP (1995) Studies on the use of a thermotolerant strain of Kluyveromyces marxianus in simultaneous saccharification and ethanol formation from cellulose. Appl Microbiol Biotechnol 43(3):518–520CrossRefGoogle Scholar
  16. Bayer EA, Belaich JP, Shoham Y, Lamed R (2004) The cellulosomes: multienzyme machines for degradation of plant cell wall polysaccharides. Ann Rev Microbiol 58:521–554CrossRefGoogle Scholar
  17. Blazeck J, Hill A, Liu L, Knight R, Miller J, Pan A, Otoupal P, Alper HS (2014) Harnessing Yarrowia lipolytica lipogenesis to create a platform for lipid and biofuel production. Nat Commun 5Google Scholar
  18. Boyle M, Barron N, McHale AP (1997) Simultaneous saccharification and fermentation of straw to ethanol using the thermotolerant yeast strain Kluyveromyces marxianus imb3. Biotechnol Lett 19(1):49–51CrossRefGoogle Scholar
  19. Brink J, Vries RP (2011) Fungal enzyme sets for plant polysaccharide degradation. Appl Microbiol Biotechnol 91(6):1477–1492PubMedPubMedCentralCrossRefGoogle Scholar
  20. Brown SH, Bashkirova L, Berka R, Chandler T, Doty T, McCall K, McCulloch M, McFarland S, Thompson S, Yaver D, Berry A (2013) Metabolic engineering of Aspergillus oryzae NRRL 3488 for increased production of l-malic acid. Appl Microbiol Biotechnol 97(20):8903–8912PubMedCrossRefGoogle Scholar
  21. Cai Z, Zhang B, Li Y (2012) Engineering Saccharomyces cerevisiae for efficient anaerobic xylose fermentation: reflections and perspectives. Biotechnol J 7(1):34–46PubMedCrossRefGoogle Scholar
  22. Carta FS, Soccol CR, Ramos LP, Fontana JD (1999) Production of fumaric acid by fermentation of enzymatic hydrolysates derived from cassava bagasse. Bioresour Technol 68(1):23–28CrossRefGoogle Scholar
  23. Chang J-J, Ho C-Y, Ho F-J, Tsai T-Y, Ke H-M, Wang C, Chen H-L, Shih M-C, Huang C-C, Li W-H (2012) PGASO: a synthetic biology tool for engineering a cellulolytic yeast. Biotechnol Biofuels 5(1):53PubMedPubMedCentralCrossRefGoogle Scholar
  24. Chang J-J, Ho F-J, Ho C-Y, Wu Y-C, Hou Y-H, Huang C-C, Shih M-C, Li W-H (2013) Assembling a cellulase cocktail and a cellodextrin transporter into a yeast host for CBP ethanol production. Biotechnol Biofuels 6(1):19PubMedPubMedCentralCrossRefGoogle Scholar
  25. Charoensopharat K, Thanonkeo P, Thanonkeo S, Yamada M (2015) Ethanol production from Jerusalem artichoke tubers at high temperature by newly isolated thermotolerant inulin-utilizing yeast Kluyveromyces marxianus using consolidated bioprocessing. Antonie Van Leeuwenhoek 108(1):173–190PubMedCrossRefGoogle Scholar
  26. Chen R, Dou J (2015) Biofuels and bio-based chemicals from lignocellulose: metabolic engineering strategies in strain development. Biotechnol Lett 38(2):213–221PubMedCrossRefGoogle Scholar
  27. Chen H, Fu X (2016) Industrial technologies for bioethanol production from lignocellulosic biomass. Renew Sustain Energy Rev 57:468–478CrossRefGoogle Scholar
  28. Chi Z, Wang Z-P, Wang G-Y, Khan I, Chi Z-M (2016) Microbial biosynthesis and secretion of l-malic acid and its applications. Crit Rev Biotechnol 36(1):99–107PubMedCrossRefGoogle Scholar
  29. Choudhary J, Singh S, Nain L (2016) Thermotolerant fermenting yeasts for simultaneous saccharification fermentation of lignocellulosic biomass. Electron J Biotechnol 21:82–92CrossRefGoogle Scholar
  30. Christakopoulos P, Macris BJ, Kekos D (1989) Direct fermentation of cellulose to ethanol by Fusarium oxysporum. Enzyme Microb Technol 11(4):236–239CrossRefGoogle Scholar
  31. Cragg SM, Beckham GT, Bruce NC, Bugg TDH, Distel DL, Dupree P, Etxabe AG, Goodell BS, Jellison J, McGeehan JE, McQueen-Mason SJ, Schnorr K, Walton PH, Watts JEM, Zimmer M (2015) Lignocellulose degradation mechanisms across the Tree of Life. Curr Opin Chem Biol 29:108–119PubMedCrossRefGoogle Scholar
  32. de Albuquerque TL, da Silva IJ Jr, de Macedo GR, Rocha MVP (2014) Biotechnological production of xylitol from lignocellulosic wastes: a review. Process Biochem 49(11):1779–1789CrossRefGoogle Scholar
  33. de Siqueira FG, de Siqueira EG, Jaramillo PMD, Silveira MHL, Andreaus J, Couto FA, Batista LR, Filho EXF (2010) The potential of agro-industrial residues for production of holocellulase from filamentous fungi. Int Biodeterior Biodegradation 64(1):20–26CrossRefGoogle Scholar
  34. Della-Bianca BE, Basso TO, Stambuk BU, Basso LC, Gombert AK (2012) What do we know about the yeast strains from the Brazilian fuel ethanol industry? Appl Microbiol Biotechnol 97(3):979–991PubMedCrossRefGoogle Scholar
  35. Den Haan R, Van Zyl WH (2003) Enhanced xylan degradation and utilisation by Pichia stipitis overproducing fungal xylanolytic enzymes. Enzyme Microb Technol 33(5):620–628CrossRefGoogle Scholar
  36. den Haan R, van Rensburg E, Rose SH, Görgens JF, van Zyl WH (2015) Progress and challenges in the engineering of non-cellulolytic microorganisms for consolidated bioprocessing. Curr Opin Biotechnol 33:32–38CrossRefGoogle Scholar
  37. Deneyer A, Renders T, Van Aelst J, Van den Bosch S, Gabriëls D, Sels BF (2015) Alkane production from biomass: chemo-, bio- and integrated catalytic approaches. Curr Opin Chem Biol 29:40–48PubMedCrossRefGoogle Scholar
  38. Dugar D, Stephanopoulos G (2011) Relative potential of biosynthetic pathways for biofuels and bio-based products. Nat Biotechnol 29(12):1074–1078PubMedCrossRefGoogle Scholar
  39. Eiteman MA, Ramalingam S (2015) Microbial production of lactic acid. Biotechnol Lett 37(5):955–972PubMedCrossRefGoogle Scholar
  40. Elkins JG, Raman B, Keller M (2010) Engineered microbial systems for enhanced conversion of lignocellulosic biomass. Curr Opin Biotechnol 21(5):657–662PubMedCrossRefGoogle Scholar
  41. Enari TM, Suihko ML (1983) Ethanol production by fermentation of pentoses and hexoses from cellulosic materials. Crit Rev Biotechnol 1(3):229–240CrossRefGoogle Scholar
  42. Fan J-X, Yang Q, Liu Z-H, Huang X-M, Song J-Z, Chen Z-X, Sun Y, Liang Q, Wang S (2010) The characterization of transaldolase gene tal from Pichia stipitis and its heterologous expression in Fusarium oxysporum. Mol Biol Rep 38(3):1831–1840PubMedCrossRefGoogle Scholar
  43. Fan J-X, Yang X-X, Song J-Z, Huang X-M, Cheng Z-X, Yao L, Juba OS, Liang Q, Yang Q, Odeph M, Sun Y, Wang Y (2011) Heterologous expression of transaldolase gene Tal from Saccharomyces cerevisiae in Fusarium oxysporum for enhanced bioethanol production. Appl Biochem Biotechnol 164(7):1023–1036PubMedCrossRefGoogle Scholar
  44. Feng C, Zou S, Liu C, Yang H, Zhang K, Ma Y, Hong J, Zhang M (2016) Ethanol production from acid- and alkali-pretreated corncob by endoglucanase and β-glucosidase co-expressing Saccharomyces cerevisiae subject to the expression of heterologous genes and nutrition added. World J Microbiol Biotechnol 32(5):1–7CrossRefGoogle Scholar
  45. Fonseca GG, Heinzle E, Wittmann C, Gombert AK (2008) The yeast Kluyveromyces marxianus and its biotechnological potential. Appl Microbiol Biotechnol 79(3):339–354PubMedCrossRefGoogle Scholar
  46. Galbe M, Sassner P, Wingren A, Zacchi G (2007) Process engineering economics of bioethanol production. In: Olsson L (ed) Biofuels. Springer, Berlin Heidelberg, pp 303–327Google Scholar
  47. Gangl IC, Weigand WA, Keller FA (1990) Economic comparison of calcium fumarate and sodium fumarate production by Rhizopus arrhizus. Appl Biochem Biotechnol 24–25(1):663–677CrossRefGoogle Scholar
  48. Gao J, Weng H, Zhu D, Yuan M, Guan F, Xi Y (2008) Production and characterization of cellulolytic enzymes from the thermoacidophilic fungal Aspergillus terreus M11 under solid-state cultivation of corn stover. Bioresour Technol 99(16):7623–7629PubMedCrossRefGoogle Scholar
  49. García-Aparicio MP, Oliva JM, Manzanares P, Ballesteros M, Ballesteros I, González A, Negro MJ (2011) Second-generation ethanol production from steam exploded barley straw by Kluyveromyces marxianus CECT 10875. Fuel 90(4):1624–1630CrossRefGoogle Scholar
  50. Gianoulis TA, Griffin MA, Spakowicz DJ, Dunican BF, Alpha CJ, Sboner A, Sismour AM, Kodira C, Egholm M, Church GM, Gerstein MB, Strobel SA (2012) Genomic analysis of the hydrocarbon-producing, cellulolytic, endophytic fungus ascocoryne sarcoides. PLoS Genet 8(3):e1002558Google Scholar
  51. Gong C-S, Maun CM, Tsao GT (1981) Direct fermentation of cellulose to ethanol by a cellulolytic filamentous fungus, Monilia sp. Biotechnol Lett 3(2):77–82CrossRefGoogle Scholar
  52. Guerriero G, Hausman J-F, Strauss J, Ertan H, Siddiqui KS (2015) Destructuring plant biomass: Focus on fungal and extremophilic cell wall hydrolases. Plant Sci 234:180–193PubMedPubMedCentralCrossRefGoogle Scholar
  53. Guirimand G, Sasaki K, Inokuma K, Bamba T, Hasunuma T, Kondo A (2016) Cell surface engineering of Saccharomyces cerevisiae combined with membrane separation technology for xylitol production from rice straw hydrolysate. Appl Microbiol Biotechnol 100(8):3477–3487PubMedCrossRefGoogle Scholar
  54. Guo L, Zhang J, Hu F, Dy Ryu D, Bao J (2013a) Consolidated bioprocessing of highly concentrated jerusalem artichoke tubers for simultaneous saccharification and ethanol fermentation. Biotechnol Bioeng 110(10):2606–2615PubMedCrossRefGoogle Scholar
  55. Guo X, Zhang R, Li Z, Dai D, Li C, Zhou X (2013b) A novel pathway construction in Candida tropicalis for direct xylitol conversion from corncob xylan. Bioresour Technol 128:547–552PubMedCrossRefGoogle Scholar
  56. Guo Z, Duquesne S, Bozonnet S, Cioci G, Nicaud J-M, Marty A, O’Donohue MJ (2015) Development of cellobiose-degrading ability in Yarrowia lipolytica strain by overexpression of endogenous genes. Biotechnol Biofuels 8(1):1–16CrossRefGoogle Scholar
  57. Hahn-Hägerdal B, Galbe M, Gorwa-Grauslund MF, Lidén G, Zacchi G (2006) Bio-ethanol—the fuel of tomorrow from the residues of today. Trends Biotechnol 24(12):549–556PubMedCrossRefGoogle Scholar
  58. Harner NK, Wen X, Bajwa PK, Austin GD, Ho C-Y, Habash MB, Trevors JT, Lee H (2014) Genetic improvement of native xylose-fermenting yeasts for ethanol production. J Ind Microbiol Biotechnol 42(1):1–20PubMedCrossRefGoogle Scholar
  59. Hasunuma T, Ishii J, Kondo A (2015) Rational design and evolutional fine tuning of Saccharomyces cerevisiae for biomass breakdown. Curr Opin Chem Biol 29:1–9PubMedCrossRefGoogle Scholar
  60. Hennessy RC, Doohan F, Mullins E (2013) Generating phenotypic diversity in a fungal biocatalyst to investigate alcohol stress tolerance encountered during microbial cellulosic biofuel production. PLoS ONE 8(10):e77501PubMedPubMedCentralCrossRefGoogle Scholar
  61. Herrera Bravo de Laguna I, Toledo Marante FJ, Mioso R (2015). Enzymes and bioproducts produced by the ascomycete fungus Paecilomyces variotii. J Appl Microbiol 119:1455–1466Google Scholar
  62. Ho DP, Ngo HH, Guo W (2014) A mini review on renewable sources for biofuel. Bioresour Technol 169:742–749PubMedCrossRefGoogle Scholar
  63. Hong J, Wang Y, Kumagai H, Tamaki H (2007) Construction of thermotolerant yeast expressing thermostable cellulase genes. J Biotechnol 130(2):114–123PubMedCrossRefGoogle Scholar
  64. Hong S-J, Kim HJ, Kim J-W, Lee D-H, Seo J-H (2014) Optimizing promoters and secretory signal sequences for producing ethanol from inulin by recombinant Saccharomyces cerevisiae carrying Kluyveromyces marxianus inulinase. Bioprocess Biosyst Eng 38(2):263–272PubMedCrossRefGoogle Scholar
  65. Hu N, Yuan B, Sun J, Wang S-A, Li F-L (2012) Thermotolerant Kluyveromyces marxianus and Saccharomyces cerevisiae strains representing potentials for bioethanol production from Jerusalem artichoke by consolidated bioprocessing. Appl Microbiol Biotechnol 95(5):1359–1368PubMedCrossRefGoogle Scholar
  66. Huang J, Chen D, Wei Y, Wang Q, Li Z, Chen Y, Huang R (2014) Direct Ethanol production from lignocellulosic sugars and sugarcane bagasse by a recombinant Trichoderma reesei strain HJ48. Sci World J 2014:8Google Scholar
  67. Isroi R, Millati S, Syamsiah C, Niklasson MN, Cahyanto K Lundquist, Taherzadeh MJ (2011) Biological pretreatment of lignocelluloses with white-rot fungi and its applications: a review. BioResources 6(4):5224–5259Google Scholar
  68. Jäger G, Büchs J (2012) Biocatalytic conversion of lignocellulose to platform chemicals. Biotechnol J 7(9):1122–1136PubMedCrossRefGoogle Scholar
  69. Jin M, Balan V, Gunawan C, Dale BE (2011) Consolidated bioprocessing (CBP) performance of Clostridium phytofermentans on AFEX-treated corn stover for ethanol production. Biotechnol Bioeng 108(6):1290–1297PubMedCrossRefGoogle Scholar
  70. John RP, Anisha GS, Nampoothiri KM, Pandey A (2009) Direct lactic acid fermentation: Focus on simultaneous saccharification and lactic acid production. Biotechnol Adv 27(2):145–152Google Scholar
  71. Kawaguchi H, Hasunuma T, Ogino C, Kondo A (2016) Bioprocessing of bio-based chemicals produced from lignocellulosic feedstocks. Curr Opin Biotechnol 42:30–39PubMedCrossRefGoogle Scholar
  72. Kim S, Kim CH (2014) Evaluation of whole Jerusalem artichoke (Helianthus tuberosus L.) for consolidated bioprocessing ethanol production. Renew Energy 65:83–91CrossRefGoogle Scholar
  73. Kircher M (2015) Sustainability of biofuels and renewable chemicals production from biomass. Curr Opin Chem Biol 29:26–31PubMedCrossRefGoogle Scholar
  74. Klement T, Büchs J (2013) Itaconic acid—a biotechnological process in change. Bioresour Technol 135:422–431PubMedCrossRefGoogle Scholar
  75. Klement T, Milker S, Jäger G, Grande PM, Domínguez de María P, Büchs J (2012) Biomass pretreatment affects Ustilago maydis in producing itaconic acid. Microb Cell Fact 11(1):1–13CrossRefGoogle Scholar
  76. Kourtoglou E, Anasontzis GE, Mamma D, Topakas E, Hatzinikolaou DG, Christakopoulos P (2011) Constitutive expression, purification and characterization of a phosphoglucomutase from Fusarium oxysporum. Enzyme Microb Technol 48(3):217–224PubMedCrossRefGoogle Scholar
  77. Kricka W, Fitzpatrick J, Bond U (2014) Metabolic engineering of yeasts by heterologous enzyme production for degradation of cellulose and hemicellulose from biomass: a perspective. Front Microbiol 5Google Scholar
  78. Kück U, Hoff B (2010) New tools for the genetic manipulation of filamentous fungi. Appl Microbiol Biotechnol 86(1):51–62PubMedCrossRefGoogle Scholar
  79. la Grange D, den Haan R, van Zyl W (2010) Engineering cellulolytic ability into bioprocessing organisms. Appl Microbiol Biotechnol 87(4):1195–1208PubMedCrossRefGoogle Scholar
  80. Lane S, Zhang S, Wei N, Rao C, Jin Y-S (2015) Development and physiological characterization of cellobiose-consuming Yarrowia lipolytica. Biotechnol Bioeng 112(5):1012–1022PubMedCrossRefGoogle Scholar
  81. Lara CA, Santos RO, Cadete RM, Ferreira C, Marques S, Gírio F, Oliveira ES, Rosa CA, Fonseca C (2014) Identification and characterisation of xylanolytic yeasts isolated from decaying wood and sugarcane bagasse in Brazil. Antonie van Leeuwenhoek Int J Gen Mol Microbiol 105(6):1107–1119CrossRefGoogle Scholar
  82. Lark N, Xia Y, Qin C-G, Gong CS, Tsao GT (1997) Production of ethanol from recycled paper sludge using cellulase and yeast, Kluveromyces marxianus. Biomass Bioenergy 12(2):135–143CrossRefGoogle Scholar
  83. Larran A, Jozami E, Vicario L, Feldman SR, Podestá FE, Permingeat HR (2015) Evaluation of biological pretreatments to increase the efficiency of the saccharification process using Spartina argentinensis as a biomass resource. Bioresour Technol 194:320–325PubMedCrossRefGoogle Scholar
  84. Lee H, Biely P, Latta RK, Barbosa MFS, Schneider H (1986) Utilization of xylan by yeasts and its conversion to ethanol by Pichia stipitis strains. Appl Environ Microbiol 52(2):320–324PubMedPubMedCentralGoogle Scholar
  85. Li X, Liu Y, Yang Y, Zhang H, Wang H, Wu Y, Zhang M, Sun T, Cheng J, Wu X, Pan L, Jiang S, Wu H (2014) High levels of malic acid production by the bioconversion of corn straw hydrolyte using an isolated Rhizopus delemar strain. Biotechnol Bioprocess Eng 19(3):478–492CrossRefGoogle Scholar
  86. Liaud N, Rosso M-N, Fabre N, Crapart S, Herpoël-Gimbert I, Sigoillot J-C, Raouche S, Levasseur A (2015) L-lactic acid production by Aspergillus brasiliensis overexpressing the heterologous ldha gene from Rhizopus oryzae. Microb Cell Fact 14(1):1–9CrossRefGoogle Scholar
  87. Linger JG, Adney WS, Darzins A (2010) Heterologous expression and extracellular secretion of cellulolytic enzymes by Zymomonas mobilis. Appl Environ Microbiol 76(19):6360–6369PubMedPubMedCentralCrossRefGoogle Scholar
  88. Long X-H, Shao H-B, Liu L, Liu L-P, Liu Z-P (2016) Jerusalem artichoke: a sustainable biomass feedstock for biorefinery. Renew Sustain Energy Rev 54:1382–1388CrossRefGoogle Scholar
  89. Luo Z, Bao J (2015) Secretive expression of heterologous β-glucosidase in Zymomonas mobilis. Bioresour Bioprocess 2(1):1–6CrossRefGoogle Scholar
  90. Lynd LR, van Zyl WH, McBride JE, Laser M (2005) Consolidated bioprocessing of cellulosic biomass: an update. Curr Opin Biotechnol 16(5): 577–583Google Scholar
  91. Lynd LR, Laser MS, Bransby D, Dale BE, Davison B, Hamilton R, Himmel M, Keller M, McMillan JD, Sheehan J, Wyman CE (2008) How biotech can transform biofuels. Nat Biotechnol 26(2):169–172PubMedCrossRefGoogle Scholar
  92. Mallette N, Pankratz EM, Parker AE, Strobel GA, Busse SC, Carlson RP, Peyton BM (2014) Evaluation of cellulose as a substrate for hydrocarbon fuel production by Ascocoryne sarcoides (NRRL 50072). J Sustain Bioenergy Syst 4:33–49CrossRefGoogle Scholar
  93. Matsushika A, Inoue H, Kodaki T, Sawayama S (2009) Ethanol production from xylose in engineered Saccharomyces cerevisiae strains: current state and perspectives. Appl Microbiol Biotechnol 84(1):37–53PubMedCrossRefGoogle Scholar
  94. Matsuzaki C, Nakagawa A, Koyanagi T, Tanaka K, Minami H, Tamaki H, Katayama T, Yamamoto K, Kumagai H (2012) Kluyveromyces marxianus-based platform for direct ethanol fermentation and recovery from cellulosic materials under air-ventilated conditions. J Biosci Bioeng 113(5):604–607PubMedCrossRefGoogle Scholar
  95. Mazzoli R, Lamberti C, Pessione E (2012) Engineering new metabolic capabilities in bacteria: lessons from recombinant cellulolytic strategies. Trends Biotechnol 30(2):111–119PubMedCrossRefGoogle Scholar
  96. Menon V, Rao M (2012) Trends in bioconversion of lignocellulose: Biofuels, platform chemicals & biorefinery concept. Prog Energy Combust Sci 38(4):522–550CrossRefGoogle Scholar
  97. Millati R, Edebo L, Taherzadeh MJ (2005) Performance of Rhizopus, Rhizomucor, and Mucor in ethanol production from glucose, xylose, and wood hydrolyzates. Enzyme Microb Technol 36(2–3):294–300CrossRefGoogle Scholar
  98. Mondala AH (2015) Direct fungal fermentation of lignocellulosic biomass into itaconic, fumaric, and malic acids: current and future prospects. J Ind Microbiol Biotechnol 42(4):487–506PubMedCrossRefGoogle Scholar
  99. Morosoli R, Zalce E, Durand S (1993) Secretion of a Cryptococcus albidus xylanase in Pichia stipitis resulting in a xylan fermenting transformant. Curr Genet 24(1):94–99PubMedCrossRefGoogle Scholar
  100. Moysés DN, Reis VCB, de Almeida JRM, de Moraes LMP, Torres FAG (2016) Xylose fermentation by Saccharomyces cerevisiae: Challenges and prospects. Int J Mol Sci 17(3)Google Scholar
  101. Naik SN, Goud VV, Rout PK, Dalai AK (2010) Production of first and second generation biofuels: a comprehensive review. Renew Sustain Energy Rev 14(2):578–597CrossRefGoogle Scholar
  102. Narayanaswamy N, Dheeran P, Verma S, Kumar S (2013) Biological pretreatment of lignocellulosic biomass for enzymatic saccharification. In: Fang Z (ed) Pretreatment techniques for biofuels and biorefineries. Springer, Berlin Heidelberg, pp 3–34CrossRefGoogle Scholar
  103. Narra M, Dixit G, Divecha J, Madamwar D, Shah AR (2012) Production of cellulases by solid state fermentation with Aspergillus terreus and enzymatic hydrolysis of mild alkali-treated rice straw. Bioresour Technol 121:355–361PubMedCrossRefGoogle Scholar
  104. Narron RH, Kim H, Chang H-M, Jameel H, Park S (2016) Biomass pretreatments capable of enabling lignin valorization in a biorefinery process. Curr Opin Biotechnol 38:39–46PubMedCrossRefGoogle Scholar
  105. Nevalainen H, Peterson R (2014) Making recombinant proteins in filamentous fungi- are we expecting too much? Front Microbiol 5Google Scholar
  106. Okabe M, Lies D, Kanamasa S, Park E (2009) Biotechnological production of itaconic acid and its biosynthesis in Aspergillus terreus. Appl Microbiol Biotechnol 84(4):597–606PubMedCrossRefGoogle Scholar
  107. Olson DG, McBride JE, Joe Shaw A, Lynd LR (2012) Recent progress in consolidated bioprocessing. Curr Opin Biotechnol 23(3):396–405PubMedCrossRefGoogle Scholar
  108. Panagiotou G, Christakopoulos P, Olsson L (2005a) The influence of different cultivation conditions on the metabolome of Fusarium oxysporum. J Biotechnol 118(3):304–315PubMedCrossRefGoogle Scholar
  109. Panagiotou G, Christakopoulos P, Villas-Boas SG, Olsson L (2005b) Fermentation performance and intracellular metabolite profiling of Fusarium oxysporum cultivated on a glucose–xylose mixture. Enzyme Microb Technol 36(1):100–106CrossRefGoogle Scholar
  110. Panagiotou G, Villas-Bôas SG, Christakopoulos P, Nielsen J, Olsson L (2005c) Intracellular metabolite profiling of Fusarium oxysporum converting glucose to ethanol. J Biotechnol 115(4):425–434PubMedCrossRefGoogle Scholar
  111. Papanek B, Biswas R, Rydzak T, Guss AM (2015) Elimination of metabolic pathways to all traditional fermentation products increases ethanol yields in Clostridium thermocellum. Metab Eng 32:49–54PubMedCrossRefGoogle Scholar
  112. Park Y-C, Oh EJ, Jo J-H, Jin Y-S, Seo J-H (2016) Recent advances in biological production of sugar alcohols. Curr Opin Biotechnol 37:105–113PubMedCrossRefGoogle Scholar
  113. Peitersen N (1975) Cellulase and protein production from mixed cultures of Trichoderma viride and a yeast. Biotechnol Bioeng 17(9):1291–1299PubMedCrossRefGoogle Scholar
  114. Pessani NK, Atiyeh HK, Wilkins MR, Bellmer DD, Banat IM (2011) Simultaneous saccharification and fermentation of Kanlow switchgrass by thermotolerant Kluyveromyces marxianus IMB3: the effect of enzyme loading, temperature and higher solid loadings. Bioresour Technol 102(22):10618–10624PubMedCrossRefGoogle Scholar
  115. Puseenam A, Tanapongpipat S, Roongsawang N (2015) Co-expression of endoxylanase and endoglucanase in Scheffersomyces stipitis and its application in ethanol production. Appl Biochem Biotechnol 177(8):1690–1700PubMedCrossRefGoogle Scholar
  116. Rabemanolontsoa H, Saka S (2016) Various pretreatments of lignocellulosics. Bioresour Technol 199:83–91PubMedCrossRefGoogle Scholar
  117. Riscaldati E, Moresi M, Federici F, Petruccioli M (2000) Direct ammonium fumarate production by Rhizopus arrhizus under phosphorous limitation. Biotechnol Lett 22(13):1043–1047CrossRefGoogle Scholar
  118. Riyaz-Ul-Hassan S, Strobel G, Geary B, Sears J (2013) An endophytic Nodulisporium sp. from central America producing volatile organic compounds with both biological and fuel potential. J Microbiol Biotechnol 23(1):29–35PubMedCrossRefGoogle Scholar
  119. Rowlands WN, Masters A, Maschmeyer T (2008) The biorefinery—challenges, opportunities, and an Australian perspective. Bull Sci Technol Soc 28(2):149–158CrossRefGoogle Scholar
  120. Rumbold K, van Buijsen H, Overkamp K, van Groenestijn J, Punt P, Werf M (2009) Microbial production host selection for converting second-generation feedstocks into bioproducts. Microb Cell Fact 8(1):64PubMedPubMedCentralCrossRefGoogle Scholar
  121. Saha BC, Qureshi N, Kennedy GJ, Cotta MA (2016) Biological pretreatment of corn stover with white-rot fungus for improved enzymatic hydrolysis. Int Biodeterior Biodegradation 109:29–35CrossRefGoogle Scholar
  122. Sànchez Nogué V, Karhumaa K (2015) Xylose fermentation as a challenge for commercialization of lignocellulosic fuels and chemicals. Biotechnol Lett 37(4):761–772PubMedCrossRefGoogle Scholar
  123. Sander JD, Joung JK (2014) CRISPR-Cas systems for editing, regulating and targeting genomes. Nat Biotechnol 32(4):347–355PubMedPubMedCentralCrossRefGoogle Scholar
  124. Seidl V, Seiboth B (2010) Trichoderma reesei: genetic approaches to improving strain efficiency. Biofuels 1(2):343–354CrossRefGoogle Scholar
  125. Sims RE, Mabee W, Saddler JN, Taylor M (2010) An overview of second generation biofuel technologies. Bioresour Technol 101(6):1570–1580PubMedCrossRefGoogle Scholar
  126. Sindhu R, Binod P, Pandey A (2016) Biological pretreatment of lignocellulosic biomass—an overview. Bioresour Technol 199:76–82PubMedCrossRefGoogle Scholar
  127. Singh A, Kumar P (1991) Fusarium oxysporum: status in bioethanol production. Crit Rev Biotechnol 11(2):129–147PubMedCrossRefGoogle Scholar
  128. Singh A, Kumar P, Schügerl K (1992). Bioconversion of cellulosic materials to ethanol by filamentous fungi. Enzymes and products from bacteria fungi and plant cells, vol 45. Springer, Berlin Heidelberg, pp 29–55Google Scholar
  129. Stephanopoulos G (2007) Challenges in engineering microbes for biofuels production. Science 315(5813):801–804PubMedCrossRefGoogle Scholar
  130. Strobel G (2011) Muscodor species- endophytes with biological promise. Phytochem Rev 10(2):165–172CrossRefGoogle Scholar
  131. Strobel GA (2015) Bioprospecting—fuels from fungi. Biotechnol Lett 37(5):973–982PubMedCrossRefGoogle Scholar
  132. Suryawati L, Wilkins MR, Bellmer DD, Huhnke RL, Maness NO, Banat IM (2008) Simultaneous saccharification and fermentation of Kanlow switchgrass pretreated by hydrothermolysis using Kluyveromyces marxianus IMB4. Biotechnol Bioeng 101(5):894–902PubMedCrossRefGoogle Scholar
  133. Szczodrak J (1988) Enzymatic hydrolysis and fermentation of pretreated wheat straw to ethanol. Biotechnol Bioeng 32(6):771–776PubMedCrossRefGoogle Scholar
  134. Szczodrak J (1989) Use of cellulases from a β-glucosidase-hyperproducing mutant of Trichoderma reesei in simultaneous saccharification and fermentation of wheat straw. Biotechnol Bioeng 33(9):1112–1116PubMedCrossRefGoogle Scholar
  135. Tomás-Pejó E, Oliva JM, González A, Ballesteros I, Ballesteros M (2009) Bioethanol production from wheat straw by the thermotolerant yeast Kluyveromyces marxianus CECT 10875 in a simultaneous saccharification and fermentation fed-batch process. Fuel 88(11):2142–2147CrossRefGoogle Scholar
  136. Ulber R, Sieker T, Tippkötter N, Bart HJ, Dimitrova D, Heinzle E, Neuner A (2010) Grassilage als Rohstoff für die chemische Industrie. Chem Ing Tech 82(8):1153–1159CrossRefGoogle Scholar
  137. Van Dyk JS, Pletschke BI (2012) A review of lignocellulose bioconversion using enzymatic hydrolysis and synergistic cooperation between enzymes—factors affecting enzymes, conversion and synergy. Biotechnol Adv 30(6):1458–1480PubMedCrossRefGoogle Scholar
  138. van Zyl W, Lynd L, den Haan R, McBride J (2007) Consolidated bioprocessing for bioethanol production using Saccharomyces cerevisiae. In: Olsson L (ed) Biofuels, vol 108. Springer, Berlin Heidelberg, pp 205–235CrossRefGoogle Scholar
  139. Vially G, Marchal R, Guilbert N (2009) L(+) Lactate production from carbohydrates and lignocellulosic materials by Rhizopus oryzae UMIP 4.77. World J Microbiol Biotechnol 26(4):607–614CrossRefGoogle Scholar
  140. Vijayakumar J, Aravindan R, Viruthagiri T (2008) Recent trends in the production, purification and application of lactic acid. Chem Biochem Eng Q 22(2):245–264Google Scholar
  141. Vinuselvi P, Lee SK (2012) Engineered Escherichia coli capable of co-utilization of cellobiose and xylose. Enzyme Microb Technol 50(1):1–4PubMedCrossRefGoogle Scholar
  142. Wagner JM, Alper HS (2015) Synthetic biology and molecular genetics in non-conventional yeasts: current tools and future advances. Fungal Genet BiolGoogle Scholar
  143. Wang G, Huang D, Li Y, Wen J, Jia X (2015) A metabolic-based approach to improve xylose utilization for fumaric acid production from acid pretreated wheat bran by Rhizopus oryzae. Bioresour Technol 180:119–127PubMedCrossRefGoogle Scholar
  144. West TP (2011) Malic acid production from thin stillage by Aspergillus species. Biotechnol Lett 33(12):2463–2467PubMedCrossRefGoogle Scholar
  145. Wikandari R, Millati R, Lennartsson PR, Harmayani E, Taherzadeh MJ (2012) Isolation and characterization of zygomycetes fungi from tempe for ethanol production and biomass applications. Appl Biochem Biotechnol 167(6):1501–1512PubMedCrossRefGoogle Scholar
  146. Wu JF, Lastick SM, Updegraff DM (1986) Ethanol production from sugars derived from plant biomass by a novel fungus. Nature 321:887–888CrossRefGoogle Scholar
  147. Xu Q, Singh A, Himmel ME (2009) Perspectives and new directions for the production of bioethanol using consolidated bioprocessing of lignocellulose. Curr Opin Biotechnol 20(3):364–371PubMedCrossRefGoogle Scholar
  148. Xu C, Qin Y, Li Y, Ji Y, Huang J, Song H, Xu J (2010a) Factors influencing cellulosome activity in consolidated bioprocessing of cellulosic ethanol. Bioresour Technol 101(24):9560–9569PubMedCrossRefGoogle Scholar
  149. Xu Q, Li S, Fu Y, Tai C, Huang H (2010b) Two-stage utilization of corn straw by Rhizopus oryzae for fumaric acid production. Bioresour Technol 101(15):6262–6264PubMedCrossRefGoogle Scholar
  150. Yee KL, Rodriguez M Jr, Thompson OA, Fu C, Wang Z-Y, Davison BH, Mielenz JR (2014) Consolidated bioprocessing of transgenic switchgrass by an engineered and evolved Clostridium thermocellum strain. Biotechnol Biofuels 7(1):1–6CrossRefGoogle Scholar
  151. Yuan WJ, Zhao XQ, Ge XM, Bai FW (2008) Ethanol fermentation with Kluyveromyces marxianus from Jerusalem artichoke grown in salina and irrigated with a mixture of seawater and freshwater. J Appl Microbiol 105(6):2076–2083PubMedCrossRefGoogle Scholar
  152. Yuan WJ, Chang BL, Ren JG, Liu JP, Bai FW, Li YY (2012) Consolidated bioprocessing strategy for ethanol production from Jerusalem artichoke tubers by Kluyveromyces marxianus under high gravity conditions. J Appl Microbiol 112(1):38–44PubMedCrossRefGoogle Scholar
  153. Yuan W-J, Li N-N, Zhao X-Q, Chen L-J, Kong L, Bai F-W (2013a) Engineering an industrial Saccharomyces cerevisiae strain with the inulinase gene for more efficient ethanol production from Jerusalem artichoke tubers. Eng Life Sci 13(5):472–478CrossRefGoogle Scholar
  154. Yuan W, Zhao X, Chen L, Bai F (2013b) Improved ethanol production in Jerusalem artichoke tubers by overexpression of inulinase gene in Kluyveromyces marxianus. Biotechnol Bioprocess Eng 18(4):721–727CrossRefGoogle Scholar
  155. Zerva AP, Stathopoulou PM, Katsifas EA, Karagouni AD, Hatzinikolaou DG (2012) The filamentous fungus Paecilomyces variotii as a potential candidate for bioethanol production via consolidated bioprocessing of lignocellulosics. New Biotechnol 29S:S5CrossRefGoogle Scholar
  156. Zhang ZY, Jin B, Kelly JM (2007) Production of lactic acid from renewable materials by Rhizopus fungi. Biochem Eng J 35(3):251–263CrossRefGoogle Scholar
  157. Zhang GC, Liu JJ, Kong II, Kwak S, Jin YS (2015a) Combining C6 and C5 sugar metabolism for enhancing microbial bioconversion. Curr Opin Chem Biol 29:49–57PubMedCrossRefGoogle Scholar
  158. Zhang L, Li X, Yong Q, Yang S-T, Ouyang J, Yu S (2015b) Simultaneous saccharification and fermentation of xylo-oligosaccharides manufacturing waste residue for l-lactic acid production by Rhizopus oryzae. Biochem Eng J 94:92–99CrossRefGoogle Scholar
  159. Zhou Y, Du J, Tsao GT (2000) Mycelial pellet formation by Rhizopus oryzae ATCC 20344. Appl Biochem and Biotechnol Part A Enzyme Eng Biotechnol 84–86:779–789CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Anastasia P. Galanopoulou
    • 1
  • Dimitris G. Hatzinikolaou
    • 1
    Email author
  1. 1.Microbial Biotechnology Group (MBG), Department of BiologyNational and Kapodistrian University of AthensAtticaGreece

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