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Fungal biodiversity to biotechnology

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Abstract

Fungal habitats include soil, water, and extreme environments. With around 100,000 fungus species already described, it is estimated that 5.1 million fungus species exist on our planet, making fungi one of the largest and most diverse kingdoms of eukaryotes. Fungi show remarkable metabolic features due to a sophisticated genomic network and are important for the production of biotechnological compounds that greatly impact our society in many ways. In this review, we present the current state of knowledge on fungal biodiversity, with special emphasis on filamentous fungi and the most recent discoveries in the field of identification and production of biotechnological compounds. More than 250 fungus species have been studied to produce these biotechnological compounds. This review focuses on three of the branches generally accepted in biotechnological applications, which have been identified by a color code: red, green, and white for pharmaceutical, agricultural, and industrial biotechnology, respectively. We also discuss future prospects for the use of filamentous fungi in biotechnology application.

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References

  • Abe K, Gomi K, Hasegawa F, Machida M (2006) Impact of Aspergillus oryzae genomics on industrial production of metabolites. Mycopathologia 162(3):143–153. doi:10.1007/s11046-006-0049-2

    Article  PubMed  CAS  Google Scholar 

  • Adrio JL, Demain AL (2014) Microbial enzymes: tools for biotechnological processes. Biomolecules 4(1):117–139. doi:10.3390/biom4010117

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Alpha CJ, Campos M, Jacobs-Wagner C, Strobel SA (2015) Mycofumigation by the volatile organic compound-producing fungus Muscodor albus induces bacterial cell death through DNA damage. Appl Environ Microbiol 81(3):1147–1156. doi:10.1128/AEM.03294-14

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • AMFEP (2015) List of commercial enzymes. Association of Manufacturers and Formulators of Enzyme Products. http://www.amfep.org

  • Anand S, Prasad MV, Yadav G, Kumar N, Shehara J, Ansari MZ, Mohanty D (2010) SBSPKS: structure based sequence analysis of polyketide synthases. Nucleic Acids Res 38(Web Server issue):W487–W496. doi:10.1093/nar/gkq340

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Andersen MR (2014) Elucidation of primary metabolic pathways in Aspergillus species: orphaned research in characterizing orphan genes. Brief Funct Genomics 13(6):451–455. doi:10.1093/bfgp/elu029

    Article  PubMed Central  PubMed  Google Scholar 

  • April TM, Foght JM, Currah RS (2000) Hydrocarbon-degrading filamentous fungi isolated from flare pit soils in northern and western Canada. Can J Microbiol 46(1):38–49

    Article  PubMed  CAS  Google Scholar 

  • Aro N, Pakula T, Penttila M (2005) Transcriptional regulation of plant cell wall degradation by filamentous fungi. FEMS Microbiol Rev 29(4):719–739. doi:10.1016/j.femsre.2004.11.006

    Article  PubMed  CAS  Google Scholar 

  • Bafana A, Dutt S, Kumar S, Ahuja PS (2011) Superoxide dismutase: an industrial perspective. Crit Rev Biotechnol 31(1):65–76. doi:10.3109/07388551.2010.490937

    Article  PubMed  CAS  Google Scholar 

  • Baker SE, Thykaer J, Adney WS, Brettin TS, Brockman FJ, D’haeseleer P, Martinez AD, Miller RM, Rokhsar DS, Schadt CW, Torok T, Tuskan G, Bennett J, Berka RM, Briggs SP, Heitman J, Taylor J, Turgeon BG, Werner-Washburne M, Himmel ME (2008) Fungal genome sequencing and bioenergy. Fungal Biology Reviews 22(1):1–5

    Article  Google Scholar 

  • BCC Research (2014) Global Markets for Enzymes in Industrial ApplicationsReport Code: BIO030H. http://www.bccresearch.com/

  • Blackwell M (2011) The fungi: 1, 2, 3. . . 5.1 million species? Am J Bot 98(3):426–438. doi:10.3732/ajb.1000298

    Article  PubMed  Google Scholar 

  • Blin K, Medema MH, Kazempour D, Fischbach MA, Breitling R, Takano E, Weber T (2013) antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers. Nucleic Acids Res 41(Web Server issue):W204–W212. doi:10.1093/nar/gkt449

    Article  PubMed Central  PubMed  Google Scholar 

  • Borges KB, Borges WS, Durán-Patrón R, Pupo MT, Bonato PS, Collado IG (2009) Stereoselective biotransformations using fungi as biocatalysts. Tetrahedron Asymmetry 20:385–397

    Article  CAS  Google Scholar 

  • Bozell JJ, Petersen GR (2010) Technology development for the production of biobased products from biorefinery carbohydrates—the US Department of Energy’s “Top 10” revisited. Critical Review 12:539–554. doi:10.1039/B922014C

    CAS  Google Scholar 

  • Brakhage AA (2013) Regulation of fungal secondary metabolism. Nat Rev Microbiol 11(1):21–32. doi:10.1038/nrmicro2916

    Article  PubMed  CAS  Google Scholar 

  • Brakhage AA, Schroeckh V (2011) Fungal secondary metabolites—strategies to activate silent gene clusters. Fungal Genet Biol 48(1):15–22. doi:10.1016/j.fgb.2010.04.004

    Article  PubMed  CAS  Google Scholar 

  • Brogan DM, Mossialos E (2013) Incentives for new antibiotics: the Options Market for Antibiotics (OMA) model. Global Health 9:58. doi:10.1186/1744-8603-9-58

    Article  PubMed Central  PubMed  Google Scholar 

  • Buaban B, Inoue H, Yano S, Tanapongpipat S, Ruanglek V, Champreda V, Pichyangkura R, Rengpipat S, Eurwilaichitr L (2010) Bioethanol production from ball milled bagasse using an on-site produced fungal enzyme cocktail and xylose-fermenting Pichia stipitis. J Biosci Bioeng 110(1):18–25. doi:10.1016/j.jbiosc.2009.12.003

    Article  PubMed  CAS  Google Scholar 

  • Bushley KE, Raja R, Jaiswal P, Cumbie JS, Nonogaki M, Boyd AE, Owensby CA, Knaus BJ, Elser J, Miller D, Di Y, McPhail KL, Spatafora JW (2013) The genome of Tolypocladium inflatum: evolution, organization, and expression of the cyclosporin biosynthetic gene cluster. PLoS Genet 9(6):e1003496. doi:10.1371/journal.pgen.1003496

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Büttel Z, Díaz R, Dirnberger B, Flak M, Grijseels S, Kwon MJ, Nielsen JCF, Nygård Y, Phule P, Pohl C, Prigent S, Randelovic M, Schütze T, Troppens D, Viggiano A (2015) Unlocking the potential of fungi: the QuantFung project. Fungal Biology and Biotechnology 2:6. doi:10.1186/s40694-015-0016-0

    Article  Google Scholar 

  • Cantrell SA, Casillas-Martinez L, Molina M (2006) Characterization of fungi from hypersaline environments of solar salterns using morphological and molecular techniques. Mycol Res 110(Pt 8):962–970. doi:10.1016/j.mycres.2006.06.005

    Article  PubMed  CAS  Google Scholar 

  • Cantrell SA, Dianese JC, Fell J, Gunde-Cimerman N, Zalar P (2011) Unusual fungal niches. Mycologia 103(6):1161–1174. doi:10.3852/11-108

    Article  PubMed  CAS  Google Scholar 

  • Chambergo FS, Valencia EY, Ferreira-Junior JR, Camilo CM, Campana PT (2012) Conformational stability of recombinant manganese superoxide dismutase from the filamentous fungus Trichoderma reesei. Int J Biol Macromol 50(1):19–24. doi:10.1016/j.ijbiomac.2011.09.015

    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(6):525–531. doi:10.1016/j.mib.2008.09.013

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • DaSilva E (2004) The colours of biotechnology: science, development and humankind. Electron J Biotechnol 7(3). doi:10.2225/vol7-issue3-fulltext

  • Demain AL (2007) The business of biotechnology. Ind Biotechnol 3(3):269–283. doi:10.1089/ind.2007.3.269

    Article  Google Scholar 

  • Demain AL, Adrio JL (2008) Contributions of microorganisms to industrial biology. Mol Biotechnol 38(1):41–55. doi:10.1007/s12033-007-0035-z

    Article  PubMed  CAS  Google Scholar 

  • Dighton J, Tugay T, Zhdanova N (2008) Fungi and ionizing radiation from radionuclides. FEMS Microbiol Lett 281(2):109–120. doi:10.1111/j.1574-6968.2008.01076.x

    Article  PubMed  CAS  Google Scholar 

  • Dufosse L, Fouillaud M, Caro Y, Mapari SA, Sutthiwong N (2014) Filamentous fungi are large-scale producers of pigments and colorants for the food industry. Curr Opin Biotechnol 26:56–61. doi:10.1016/j.copbio.2013.09.007

    Article  PubMed  CAS  Google Scholar 

  • El Aouad N, Perez-Moreno G, Sanchez P, Cantizani J, Ortiz-Lopez FJ, Martin J, Gonzalez-Menendez V, Ruiz-Perez LM, Gonzalez-Pacanowska D, Vicente F, Bills G, Reyes F (2012) Lasionectrin, a naphthopyrone from a Lasionectria sp. J Nat Prod 75(6):1228–1230. doi:10.1021/np3002942

    Article  PubMed  CAS  Google Scholar 

  • El Bondkly AM, El-Gendy MM (2012) Cellulase production from agricultural residues by recombinant fusant strain of a fungal endophyte of the marine sponge Latrunculia corticata for production of ethanol. Antonie Van Leeuwenhoek 101(2):331–346. doi:10.1007/s10482-011-9639-1

    Article  PubMed  CAS  Google Scholar 

  • Erickson B, Nelson J, Winters P (2012) Perspective on opportunities in industrial biotechnology in renewable chemicals. Biotechnol J 7(2):176–185. doi:10.1002/biot.201100069

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Gavrilescu M, Chisti Y (2005) Biotechnology-a sustainable alternative for chemical industry. Biotechnol Adv 23(7–8):471–499. doi:10.1016/j.biotechadv.2005.03.004

    Article  PubMed  CAS  Google Scholar 

  • Godinho VM, Goncalves VN, Santiago IF, Figueredo HM, Vitoreli GA, Schaefer CE, Barbosa EC, Oliveira JG, Alves TM, Zani CL, Junior PA, Murta SM, Romanha AJ, Kroon EG, Cantrell CL, Wedge DE, Duke SO, Ali A, Rosa CA, Rosa LH (2015) Diversity and bioprospection of fungal community present in oligotrophic soil of continental Antarctica. Extremophiles 19(3):585–596. doi:10.1007/s00792-015-0741-6

    Article  PubMed  Google Scholar 

  • Grigoriev IV, Nikitin R, Haridas S, Kuo A, Ohm R, Otillar R, Riley R, Salamov A, Zhao X, Korzeniewski F, Smirnova T, Nordberg H, Dubchak I, Shabalov I (2014) MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res 42(Database issue):D699–D704. doi:10.1093/nar/gkt1183

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Gruninger RJ, Puniya AK, Callaghan TM, Edwards JE, Youssef N, Dagar SS, Fliegerova K, Griffith GW, Forster R, Tsang A, McAllister T, Elshahed MS (2014) Anaerobic fungi (phylum Neocallimastigomycota): advances in understanding their taxonomy, life cycle, ecology, role and biotechnological potential. FEMS Microbiol Ecol 90(1):1–17. doi:10.1111/1574-6941.12383

    Article  PubMed  CAS  Google Scholar 

  • Gutiérrez-Rojas I, Moreno-Sarmiento N, Montoya D (2015) Mecanismos y regulación de la hidrólisis enzimática de celulosa en hongos filamentosos: casos clásicos y nuevos modelos. Rev Iberoam Micol 32(1):1–12. doi:10.1016/j.riam.2013.10.009

    Article  PubMed  Google Scholar 

  • Harms H, Schlosser D, Wick LY (2011) Untapped potential: exploiting fungi in bioremediation of hazardous chemicals. Nat Rev Microbiol 9(3):177–192. doi:10.1038/nrmicro2519

    Article  PubMed  CAS  Google Scholar 

  • Hawksworth DL (2001) The magnitude of fungal diversity: the 1.5 million species estimate revisited. Mycol Res 105(12):1422–1432

    Article  Google Scholar 

  • Heinig U, Scholz S, Jennewein S (2013) Getting to the bottom of Taxol biosynthesis by fungi. Fungal Divers 60:161–170

    Article  Google Scholar 

  • Hibbett DS, Binder M, Bischoff JF, Blackwell M, Cannon PF, Eriksson OE, Huhndorf S, James T, Kirk PM, Lucking R, Thorsten Lumbsch H, Lutzoni F, Matheny PB, McLaughlin DJ, Powell MJ, Redhead S, Schoch CL, Spatafora JW, Stalpers JA, Vilgalys R, Aime MC, Aptroot A, Bauer R, Begerow D, Benny GL, Castlebury LA, Crous PW, Dai YC, Gams W, Geiser DM, Griffith GW, Gueidan C, Hawksworth DL, Hestmark G, Hosaka K, Humber RA, Hyde KD, Ironside JE, Koljalg U, Kurtzman CP, Larsson KH, Lichtwardt R, Longcore J, Miadlikowska J, Miller A, Moncalvo JM, Mozley-Standridge S, Oberwinkler F, Parmasto E, Reeb V, Rogers JD, Roux C, Ryvarden L, Sampaio JP, Schussler A, Sugiyama J, Thorn RG, Tibell L, Untereiner WA, Walker C, Wang Z, Weir A, Weiss M, White MM, Winka K, Yao YJ, Zhang N (2007) A higher-level phylogenetic classification of the fungi. Mycol Res 111(Pt 5):509–547. doi:10.1016/j.mycres.2007.03.004

    Article  PubMed  Google Scholar 

  • Hibbett DS, Ohman A, Glotzer D, Nuhn M, Kirk P, Nilsson RH (2011) Progress in molecular and morphological taxon discovery in fungi and options for formal classification of environmental sequences. Fungal Biology Reviews 25(1):38–47

    Article  Google Scholar 

  • Holladay J, Bozell J, White J, Johnson D (2007) Top value-added chemicals from biomass: volume II - results of screening for potential candidates from biorefinery lignin. Report  PNNL-16983 USDO Energy. http://www.pnl.gov/main/publications/external/technical_reports/PNNL-16983.pdf

  • James TY, Letcher PM, Longcore JE, Mozley-Standridge SE, Porter D, Powell MJ, Griffith GW, Vilgalys R (2006) A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota). Mycologia 98(6):860–871

    Article  PubMed  Google Scholar 

  • Jong E, Higson A, Walsh P, Wellisch M (2012) Product developments in the bio-based chemicals arena. Biofuels Bioprod Biorefin 6(6):606–624

    Article  CAS  Google Scholar 

  • Khaldi N, Seifuddin FT, Turner G, Haft D, Nierman WC, Wolfe KH, Fedorova ND (2010) SMURF: genomic mapping of fungal secondary metabolite clusters. Fungal Genet Biol 47(9):736–741. doi:10.1016/j.fgb.2010.06.003

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Klement T, Buchs J (2013) Itaconic acid—a biotechnological process in change. Bioresour Technol 135:422–431. doi:10.1016/j.biortech.2012.11.141

    Article  PubMed  CAS  Google Scholar 

  • Kubicek CP, Herrera-Estrella A, Seidl-Seiboth V, Martinez DA, Druzhinina IS, Thon M, Zeilinger S, Casas-Flores S, Horwitz BA, Mukherjee PK, Mukherjee M, Kredics L, Alcaraz LD, Aerts A, Antal Z, Atanasova L, Cervantes-Badillo MG, Challacombe J, Chertkov O, McCluskey K, Coulpier F, Deshpande N, von Dohren H, Ebbole DJ, Esquivel-Naranjo EU, Fekete E, Flipphi M, Glaser F, Gomez-Rodriguez EY, Gruber S, Han C, Henrissat B, Hermosa R, Hernandez-Onate M, Karaffa L, Kosti I, Le Crom S, Lindquist E, Lucas S, Lubeck M, Lubeck PS, Margeot A, Metz B, Misra M, Nevalainen H, Omann M, Packer N, Perrone G, Uresti-Rivera EE, Salamov A, Schmoll M, Seiboth B, Shapiro H, Sukno S, Tamayo-Ramos JA, Tisch D, Wiest A, Wilkinson HH, Zhang M, Coutinho PM, Kenerley CM, Monte E, Baker SE, Grigoriev IV (2011) Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma. Genome Biol 12(4):R40. doi:10.1186/gb-2011-12-4-r40

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Kusari S, Singh S, Jayabaskaran C (2014) Rethinking production of Taxol(R) (paclitaxel) using endophyte biotechnology. Trends Biotechnol 32(6):304–311. doi:10.1016/j.tibtech.2014.03.011

    Article  PubMed  CAS  Google Scholar 

  • Lange L (2014) The importance of fungi and mycology for addressing major global challenges*. IMA Fungus 5(2):463–471. doi:10.5598/imafungus.2014.05.02.10

    Article  PubMed Central  PubMed  Google Scholar 

  • Li MH, Ung PM, Zajkowski J, Garneau-Tsodikova S, Sherman DH (2009) Automated genome mining for natural products. BMC Bioinformatics 10:185. doi:10.1186/1471-2105-10-185

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Lotfy WA, Ghanem KM, El-Helow ER (2007) Citric acid production by a novel Aspergillus niger isolate: II. Optimization of process parameters through statistical experimental designs. Bioresour Technol 98(18):3470–3477. doi:10.1016/j.biortech.2006.11.032

    Article  PubMed  CAS  Google Scholar 

  • Lutzoni F, Kauff F, Cox CJ, McLaughlin D, Celio G, Dentinger B, Padamsee M, Hibbett D, James TY, Baloch E, Grube M, Reeb V, Hofstetter V, Schoch C, Arnold AE, Miadlikowska J, Spatafora J, Johnson D, Hambleton S, Crockett M, Shoemaker R, Sung GH, Lucking R, Lumbsch T, O’Donnell K, Binder M, Diederich P, Ertz D, Gueidan C, Hansen K, Harris RC, Hosaka K, Lim YW, Matheny B, Nishida H, Pfister D, Rogers J, Rossman A, Schmitt I, Sipman H, Stone J, Sugiyama J, Yahr R, Vilgalys R (2004) Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. Am J Bot 91(10):1446–1480. doi:10.3732/ajb.91.10.1446

    Article  PubMed  Google Scholar 

  • Mapari SA, Meyer AS, Thrane U (2009) Photostability of natural orange-red and yellow fungal pigments in liquid food model systems. J Agric Food Chem 57(14):6253–6261. doi:10.1021/jf900113q

    Article  PubMed  CAS  Google Scholar 

  • Mapari SA, Nielsen KF, Larsen TO, Frisvad JC, Meyer AS, Thrane U (2005) Exploring fungal biodiversity for the production of water-soluble pigments as potential natural food colorants. Curr Opin Biotechnol 16(2):231–238. doi:10.1016/j.copbio.2005.03.004

    Article  PubMed  CAS  Google Scholar 

  • Mapari SA, Thrane U, Meyer AS (2010) Fungal polyketide azaphilone pigments as future natural food colorants? Trends Biotechnol 28(6):300–307. doi:10.1016/j.tibtech.2010.03.004

    Article  PubMed  CAS  Google Scholar 

  • Martinez-Medina A, Del Mar AM, Pascual JA, Van Wees SC (2014) Phytohormone profiles induced by Trichoderma isolates correspond with their biocontrol and plant growth-promoting activity on melon plants. J Chem Ecol 40(7):804–815. doi:10.1007/s10886-014-0478-1

    Article  PubMed  CAS  Google Scholar 

  • Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P, Fischbach MA, Weber T, Takano E, Breitling R (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 39(Web Server issue):W339–W346. doi:10.1093/nar/gkr466

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Morath SU, Hung R, Bennett JW (2012) Fungal volatile organic compounds: a review with emphasis on their biotechnological potential. Fungal Biology Reviews 26(2–3):73–83. doi:10.1016/j.fbr.2012.07.001

    Article  Google Scholar 

  • Mulder KC, Mulinari F, Franco OL, Soares MS, Magalhaes BS, Parachin NS (2015) Lovastatin production: from molecular basis to industrial process optimization. Biotechnol Adv 33(6 Pt 1):648–665. doi:10.1016/j.biotechadv.2015.04.001

    Article  PubMed  CAS  Google Scholar 

  • Newman DJ, Cragg GM (2015) Endophytic and epiphytic microbes as “sources” of bioactive agents. Front Chem 3:34. doi:10.3389/fchem.2015.00034

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Nutzmann HW, Reyes-Dominguez Y, Scherlach K, Schroeckh V, Horn F, Gacek A, Schumann J, Hertweck C, Strauss J, Brakhage AA (2011) Bacteria-induced natural product formation in the fungus Aspergillus nidulans requires Saga/Ada-mediated histone acetylation. Proc Natl Acad Sci U S A 108(34):14282–14287. doi:10.1073/pnas.1103523108

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • O’Brien HE, Parrent JL, Jackson JA, Moncalvo JM, Vilgalys R (2005) Fungal community analysis by large-scale sequencing of environmental samples. Appl Environ Microbiol 71(9):5544–5550. doi:10.1128/AEM.71.9.5544-5550.2005

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Outterson K, Powers JH, Daniel GW, McClellan MB (2015) Repairing the broken market for antibiotic innovation. Health Aff (Millwood) 34(2):277–285. doi:10.1377/hlthaff.2014.1003

    Article  Google Scholar 

  • Paranjape SR, Chiang YM, Sanchez JF, Entwistle R, Wang CC, Oakley BR, Gamblin TC (2014) Inhibition of Tau aggregation by three Aspergillus nidulans secondary metabolites: 2,omega-dihydroxyemodin, asperthecin, and asperbenzaldehyde. Planta Med 80(1):77–85. doi:10.1055/s-0033-1360180

    Article  PubMed  CAS  Google Scholar 

  • Patel M, Crank M, Dornburg V, Hermann B, Roes L, Hüsing B, Overbeek Lv, Terragni F, Recchia E (2006) Medium and long-term opportunities and risks of the biotechnological production of bulk chemicals from renewable resources—the BREW Project (http://www.projects.science.uu.nl/brew/programme.html)

  • Patel RN (2008) Synthesis of chiral pharmaceutical intermediates by biocatalysis. Coord Chem Rev 252:659–701

    Article  CAS  Google Scholar 

  • Pollard DJ, Woodley JM (2007) Biocatalysis for pharmaceutical intermediates: the future is now. Trends Biotechnol 25(2):66–73. doi:10.1016/j.tibtech.2006.12.005

    Article  PubMed  CAS  Google Scholar 

  • Quin MB, Flynn CM, Schmidt-Dannert C (2014) Traversing the fungal terpenome. Nat Prod Rep 31(10):1449–1473. doi:10.1039/c4np00075g

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Raghukumar C (2008) Marine fungal biotechnology: an ecological perspective. Fungal Divers 31:19–35

    Google Scholar 

  • Rai M, Deshmukh P, Gade A, Ingle A, Kovics GJ, Irinyi L (2009) Phoma Saccardo: distribution, secondary metabolite production and biotechnological applications. Crit Rev Microbiol 35(3):182–196. doi:10.1080/10408410902975992

    Article  PubMed  CAS  Google Scholar 

  • Reddy TB, Thomas AD, Stamatis D, Bertsch J, Isbandi M, Jansson J, Mallajosyula J, Pagani I, Lobos EA, Kyrpides NC (2015) The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification. Nucleic Acids Res 43(Database issue):D1099–D1106. doi:10.1093/nar/gku950

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Robert V, Vu D, Amor AB, van de Wiele N, Brouwer C, Jabas B, Szoke S, Dridi A, Triki M, Ben Daoud S, Chouchen O, Vaas L, de Cock A, Stalpers JA, Stalpers D, Verkley GJ, Groenewald M, Dos Santos FB, Stegehuis G, Li W, Wu L, Zhang R, Ma J, Zhou M, Gorjon SP, Eurwilaichitr L, Ingsriswang S, Hansen K, Schoch C, Robbertse B, Irinyi L, Meyer W, Cardinali G, Hawksworth DL, Taylor JW, Crous PW (2013) MycoBank gearing up for new horizons. IMA Fungus 4(2):371–379. doi:10.5598/imafungus.2013.04.02.16

    Article  PubMed Central  PubMed  Google Scholar 

  • Rodarte-Morales AI, Feijoo G, Moreira MT, Lema JM (2011) Degradation of selected pharmaceutical and personal care products (PPCPs) by white-rot fungi. World J Microbiol Biotechnol 27:1839–1846

    Article  Google Scholar 

  • Rodriguez RJ, White Jr JF, Arnold AE, Redman RS (2009) Fungal endophytes: diversity and functional roles. New Phytol 182(2):314–330. doi:10.1111/j.1469-8137.2009.02773.x

  • Rottig M, Medema MH, Blin K, Weber T, Rausch C, Kohlbacher O (2011) NRPSpredictor2—a web server for predicting NRPS adenylation domain specificity. Nucleic Acids Res 39(Web Server issue):W362–W367. doi:10.1093/nar/gkr323

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Rowley DC, Kelly S, Jensen P, Fenical W (2004) Synthesis and structure-activity relationships of the halovirs, antiviral natural products from a marine-derived fungus. Bioorg Med Chem 12(18):4929–4936. doi:10.1016/j.bmc.2004.06.044

    Article  PubMed  CAS  Google Scholar 

  • SCBD Secretariat of the Convention on Biological Diversity (2014) Global biodiversity outlook 4. Montréal, 155 pages. (https://www.cbd.int/gbo4/)

  • Schmidt FR (2004) Recombinant expression systems in the pharmaceutical industry. Appl Microbiol Biotechnol 65(4):363–372. doi:10.1007/s00253-004-1656-9

    Article  PubMed  CAS  Google Scholar 

  • Schmit JP, Mueller GM (2007) An estimate of the lower limit of global fungal diversity. Biodivers Conserv 16(1):99–111

    Article  Google Scholar 

  • Sergeeva Y, Galanina L, Andrianova D, Feofilova E (2008) Lipids of filamentous fungi as a material for producing biodiesel fuel. Prikl Biokhim Mikrobiol 44(5):576–581

    PubMed  Google Scholar 

  • Singh OV, Kumar R (2007) Biotechnological production of gluconic acid: future implications. Appl Microbiol Biotechnol 75(4):713–722. doi:10.1007/s00253-007-0851-x

    Article  PubMed  CAS  Google Scholar 

  • Spakowicz DJ, Strobel SA (2015) Biosynthesis of hydrocarbons and volatile organic compounds by fungi: bioengineering potential. Appl Microbiol Biotechnol 99(12):4943–4951. doi:10.1007/s00253-015-6641-y

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Stajich JE, Harris T, Brunk BP, Brestelli J, Fischer S, Harb OS, Kissinger JC, Li W, Nayak V, Pinney DF, Stoeckert Jr CJ, Roos DS (2012) FungiDB: an integrated functional genomics database for fungi. Nucleic Acids Res 40(Database issue):D675–D681. doi:10.1093/nar/gkr918

  • Starcevic A, Zucko J, Simunkovic J, Long PF, Cullum J, Hranueli D (2008) ClustScan: an integrated program package for the semi-automatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures. Nucleic Acids Res 36(21):6882–6892. doi:10.1093/nar/gkn685

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Stierle A, Strobel G, Stierle D (1993) Taxol and taxane production by Taxomyces andreanae, an endophytic fungus of Pacific yew. Science 260:214–216. doi:10.1126/science.8097061

  • Strobel G (2006) Muscodor albus and its biological promise. J Ind Microbiol Biotechnol 33(7):514–522. doi:10.1007/s10295-006-0090-7

    Article  PubMed  CAS  Google Scholar 

  • Strobel G (2011) Muscodor species—endophytes with biological promise. Phytochem Rev 10:165–172. doi:10.1007/s11101-010-9163-3

    Article  CAS  Google Scholar 

  • Strobel G (2014) The story of mycodiesel. Curr Opin Microbiol 19:52–58. doi:10.1016/j.mib.2014.06.003

    Article  PubMed  CAS  Google Scholar 

  • Strobel G, Booth E, Schaible G, Mends MT, Sears J, Geary B (2013) The paleobiosphere: a novel device for the in vivo testing of hydrocarbon producing-utilizing microorganisms. Biotechnol Lett 35(4):539–552. doi:10.1007/s10529-012-1123-0

    Article  PubMed  CAS  Google Scholar 

  • Strobel G, Daisy B (2003) Bioprospecting for microbial endophytes and their natural products. Microbiol Mol Biol Rev 67(4):491–502

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Strobel G, Daisy B, Castillo U, Harper J (2004) Natural products from endophytic microorganisms. J Nat Prod 67(2):257–268. doi:10.1021/np030397v

    Article  PubMed  CAS  Google Scholar 

  • Strobel GA (2015) Bioprospecting—fuels from fungi. Biotechnol Lett 37(5):973–982. doi:10.1007/s10529-015-1773-9

    Article  PubMed  CAS  Google Scholar 

  • Strobel GA, Dirkse E, Sears J, Markworth C (2001) Volatile antimicrobials from Muscodor albus, a novel endophytic fungus. Microbiology 147(Pt 11):2943–2950. doi:10.1099/00221287-147-11-2943

    Article  PubMed  CAS  Google Scholar 

  • Tavares S, Ramos AP, Pires AS, Azinheira HG, Caldeirinha P, Link T, Abranches R, Silva Mdo C, Voegele RT, Loureiro J, Talhinhas P (2014) Genome size analyses of Pucciniales reveal the largest fungal genomes. Front Plant Sci 5:422. doi:10.3389/fpls.2014.00422

    Article  PubMed Central  PubMed  Google Scholar 

  • Tedersoo L, Bahram M, Polme S, Koljalg U, Yorou NS, Wijesundera R, Villarreal Ruiz L, Vasco-Palacios AM, Thu PQ, Suija A, Smith ME, Sharp C, Saluveer E, Saitta A, Rosas M, Riit T, Ratkowsky D, Pritsch K, Poldmaa K, Piepenbring M, Phosri C, Peterson M, Parts K, Partel K, Otsing E, Nouhra E, Njouonkou AL, Nilsson RH, Morgado LN, Mayor J, May TW, Majuakim L, Lodge DJ, Lee SS, Larsson KH, Kohout P, Hosaka K, Hiiesalu I, Henkel TW, Harend H, Guo LD, Greslebin A, Grelet G, Geml J, Gates G, Dunstan W, Dunk C, Drenkhan R, Dearnaley J, De Kesel A, Dang T, Chen X, Buegger F, Brearley FQ, Bonito G, Anslan S, Abell S, Abarenkov K (2014) Fungal biogeography. Global diversity and geography of soil fungi. Science 346(6213):1256688. doi:10.1126/science.1256688

    Article  PubMed  CAS  Google Scholar 

  • Teeri TT (2004) Genome sequence of an omnipotent fungus. Nat Biotechnol 22(6):679–680. doi:10.1038/nbt0604-679

    Article  PubMed  CAS  Google Scholar 

  • Tobert JA (2003) Lovastatin and beyond: the history of the HMG-CoA reductase inhibitors. Nat Rev Drug Discov 2(7):517–526. doi:10.1038/nrd1112

    Article  PubMed  CAS  Google Scholar 

  • Tortella GR, Diez MC, Duran N (2005) Fungal diversity and use in decomposition of environmental pollutants. Crit Rev Microbiol 31(4):197–212. doi:10.1080/10408410500304066

    Article  PubMed  CAS  Google Scholar 

  • Tudzynski B (2005) Gibberellin biosynthesis in fungi: genes, enzymes, evolution, and impact on biotechnology. Appl Microbiol Biotechnol 66(6):597–611. doi:10.1007/s00253-004-1805-1

    Article  PubMed  CAS  Google Scholar 

  • Tugay TI, Zheltonozhskaya MV, Sadovnikov LV, Tugay AV, Farfan EB (2011) Effects of ionizing radiation on the antioxidant system of microscopic fungi with radioadaptive properties found in the Chernobyl exclusion zone. Health Phys 101(4):375–382. doi:10.1097/HP.0b013e3181f56bf8

    Article  PubMed  CAS  Google Scholar 

  • Valencia EY, Chambergo FS (2013) Mini-review: Brazilian fungi diversity for biomass degradation. Fungal Genet Biol 60:9–18. doi:10.1016/j.fgb.2013.07.005

    Article  PubMed  CAS  Google Scholar 

  • Van den Berg MA, Albang R, Albermann K, Badger JH, Daran JM, Driessen AJ, Garcia-Estrada C, Fedorova ND, Harris DM, Heijne WH, Joardar V, Kiel JA, Kovalchuk A, Martin JF, Nierman WC, Nijland JG, Pronk JT, Roubos JA, van der Klei IJ, van Peij NN, Veenhuis M, von Dohren H, Wagner C, Wortman J, Bovenberg RA (2008) Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum. Nat Biotechnol 26(10):1161–1168. doi:10.1038/nbt.1498

    Article  PubMed  CAS  Google Scholar 

  • Vega-Sanchez ME, Ronald PC (2010) Genetic and biotechnological approaches for biofuel crop improvement. Curr Opin Biotechnol 21(2):218–224. doi:10.1016/j.copbio.2010.02.002

    Article  PubMed  CAS  Google Scholar 

  • Wan C, Li Y (2012) Fungal pretreatment of lignocellulosic biomass. Biotechnol Adv 30(6):1447–1457. doi:10.1016/j.biotechadv.2012.03.003

    Article  PubMed  CAS  Google Scholar 

  • Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, Lee SY, Fischbach MA, Muller R, Wohlleben W, Breitling R, Takano E, Medema MH (2015) antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res 43(W1):W237–W243. doi:10.1093/nar/gkv437

    Article  PubMed Central  PubMed  Google Scholar 

  • Weber T, Rausch C, Lopez P, Hoof I, Gaykova V, Huson DH, Wohlleben W (2009) CLUSEAN: a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters. J Biotechnol 140(1–2):13–17

    Article  PubMed  CAS  Google Scholar 

  • Werpy T, Petersen G (2004) Top value added chemicals from biomass. Volume I—results of screening for potential candidates from sugars and synthesis gas. Report DOE/GO-102004-1992  USDO Energy. http://www.nrel.gov/docs/fy04osti/35523.pdf

  • Wu X, Jiang S, Liu M, Pan L, Zheng Z, Luo S (2011) Production of L-lactic acid by Rhizopus oryzae using semicontinuous fermentation in bioreactor. J Ind Microbiol Biotechnol 38(4):565–571. doi:10.1007/s10295-010-0804-8

    Article  PubMed  CAS  Google Scholar 

  • Xiao Z, Lin S, Tan C, Lu Y, He L, Huang X, She Z (2015) Asperlones A and B, dinaphthalenone derivatives from a mangrove endophytic fungus Aspergillus sp. 16-5C. Mar Drugs 13(1):366–378. doi:10.3390/md13010366

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Yoder OC, Turgeon BG (2001) Fungal genomics and pathogenicity. Curr Opin Plant Biol 4(4):315–321. doi:10.1016/S1369-5266(00)00179-5

    Article  PubMed  CAS  Google Scholar 

  • Zafar S, Aqil F, Ahmad I (2007) Metal tolerance and biosorption potential of filamentous fungi isolated from metal contaminated agricultural soil. Bioresour Technol 98(13):2557–2561. doi:10.1016/j.biortech.2006.09.051

    Article  PubMed  CAS  Google Scholar 

  • Zhao Z, Liu H, Wang C, Xu JR (2013) Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi. BMC Genomics 14:274. doi:10.1186/1471-2164-14-274

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Zheng Y, Yu X, Zeng J, Chen S (2012) Feasibility of filamentous fungi for biofuel production using hydrolysate from dilute sulfuric acid pretreatment of wheat straw. Biotechnol Biofuels 5(1):50. doi:10.1186/1754-6834-5-50

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Zhou X, Zhu H, Liu L, Lin J, Tang K (2010) A review: recent advances and future prospects of taxol-producing endophytic fungi. Appl Microbiol Biotechnol 86(6):1707–1717. doi:10.1007/s00253-010-2546-y

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

We sincerely apologize to authors of appropriate studies that may have been inadvertently omitted. This work is part of the production of the BIOEN-FAPESP program (Bioenergy grant nos. 2012/50153-5 and 2014/24107-1, São Paulo Research Foundation–FAPESP, Brazil). E.Y.V. is supported by a fellowship from CNPq, Brazil, no. 151264/2014-7.

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  1. Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, Av. Arlindo Bettio, São Paulo, 1000, Brazil

    Felipe S. Chambergo

  2. Instituto de Ciências Biomédicas, Universidade de São Paulo, Av. Prof. Lineu Prestes, São Paulo, 1374, Brazil

    Estela Y. Valencia

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  1. Felipe S. Chambergo
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Correspondence to Felipe S. Chambergo.

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Chambergo, F.S., Valencia, E.Y. Fungal biodiversity to biotechnology. Appl Microbiol Biotechnol 100, 2567–2577 (2016). https://doi.org/10.1007/s00253-016-7305-2

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