Abstract
This chapter explores the main microbial breeding techniques for 1G and 2G bioethanol production, including classical genetic strategies (induced mutations, clonal selection, sexual hybridization, artificial hybridization, and evolutionary engineering) and those based on genetic transformation (deletion and regulation of genes, pooled-segregant whole genome sequence analysis, and CRISPR/CAS9 system). Saccharomyces cerevisiae has long been a popular model organism for breeding biological research; however, genetic manipulation of non-model microorganisms (e.g., Z. mobilis and Escherichia coli) has also been explored mainly for 2G ethanol production. Tools based on classical genetics are generally random and, therefore, less efficient. However, these techniques have the advantage of not needing prior knowledge about the gene of interest (facilitated procedure), and the microorganisms generated are not considered genetically modified. On the other hand, modifications based on genetic transformation result in more targeted improvements and overproduction of metabolites, although they are more expensive techniques and require extensive knowledge of intracellular biochemical pathways and regulatory mechanisms.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Abdel-Fattah WR et al (2000) Isolation of thermotolerant ethanologenic yeasts and use of selected strains in industrial scale fermentation in an Egyptian distillery. Biotechnol Bioeng 68(5):531–535. https://doi.org/10.1002/(SICI)1097-0290(20000605)68:5<531::AID-BIT7>3.0.CO;2-Y
Adegboye MF et al (2021) Bioprospecting of microbial strains for biofuel production: metabolic engineering, applications, and challenges. Biotechnol Biofuels 14(1):1–21. https://doi.org/10.1186/s13068-020-01853-2
Ahmad QUA et al (2017) Moderate alkali-thermophilic ethanologenesis by locally isolated Bacillus licheniformis from Pakistan employing sugarcane bagasse: a comparative aspect of aseptic and non-aseptic fermentations. Biotechnol Biofuels 10(1):1–20. https://doi.org/10.1186/s13068-017-0785-1
Aikawa S et al (2018) Characterization and high-quality draft genome sequence of Herbivorax saccincola A7, an anaerobic, alkaliphilic, thermophilic, cellulolytic, and xylanolytic bacterium. Syst Appl Microbiol 41(4):261–269. https://doi.org/10.1016/j.syapm.2018.01.010
Argueso JL et al (2009) Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production. Genome Res 19(12):2258–2270. https://doi.org/10.1101/gr.091777.109
Babrzadeh F et al (2012) Whole-genome sequencing of the efficient industrial fuel-ethanol fermentative Saccharomyces cerevisiae strain CAT-1. Mol Gen Genomics 287(6):485–494. https://doi.org/10.1007/s00438-012-0695-7
Banat IM, Nigam P, Marchant R (1992) Isolation of thermotolerant, fermentative yeasts growing at 52°C and producing ethanol at 45°C and 50°C. World J Microbiol Biotechnol 8(3):259–263. https://doi.org/10.1007/BF01201874
Basso LC et al (2008) Yeast selection for fuel ethanol production in Brazil. FEMS Yeast Res 8(7):1155–1163. https://doi.org/10.1111/j.1567-1364.2008.00428.x
Borneman AR et al (2011) Whole-genome comparison reveals novel genetic elements that characterize the genome of industrial strains of Saccharomyces cerevisiae. PLoS Genet 7(2). https://doi.org/10.1371/journal.pgen.1001287
Brexó RP, Sant’Ana AS (2017) Impact and significance of microbial contamination during fermentation for bioethanol production. Renew Sust Energ Rev 73(February 2016):423–434. https://doi.org/10.1016/j.rser.2017.01.151
Brown SD et al (2013) Genome sequences of industrially relevant Saccharomyces cerevisiae strain M3707, isolated from a sample of distillers yeast and four haploid derivatives. Genome Announc 1(3). https://doi.org/10.1128/genomeA.00323-13
Chaudhary N, Qazi JI, Irfan M (2017) Isolation and identification of cellulolytic and ethanologenic bacteria from soil. Iran J Sci Technol Trans A Sci 41(3):551–555. https://doi.org/10.1007/s40995-017-0282-1
Chen MT et al (2012) Generation of diploid Pichia pastoris strains by mating and their application for recombinant protein production. Microb Cell Factories 11:1–18. https://doi.org/10.1186/1475-2859-11-91
Chen Z et al (2015) Characteristics and kinetic study on pyrolysis of five lignocellulosic biomass via thermogravimetric analysis. Bioresour Technol 192:441–450. https://doi.org/10.1016/j.biortech.2015.05.062
Choi GW et al (2010) Bioethanol production by a flocculent hybrid, CHFY0321 obtained by protoplast fusion between Saccharomyces cerevisiae and Saccharomyces bayanus. Biomass Bioenergy 34(8):1232–1242. https://doi.org/10.1016/j.biombioe.2010.03.018
Choudhary J, Singh S, Nain L (2017) Bioprospecting thermotolerant ethanologenic yeasts for simultaneous saccharification and fermentation from diverse environments. J Biosci Bioeng 123(3):342–346. https://doi.org/10.1016/j.jbiosc.2016.10.007
Costa AC et al (2001) Factorial design and simulation for the optimization and determination of control structures for an extractive alcoholic fermentation. Process Biochem 37(2):125–137. https://doi.org/10.1016/S0032-9592(01)00188-1
Coutouné N et al (2017) Draft genome sequence of Saccharomyces cerevisiae Barra Grande (BG-1), a Brazilian industrial bioethanol- producing strain. Genome 5(September):1–2. https://doi.org/10.1128/genomeA.00111-17
da Silva-Filho EA et al (2005) Yeast population dynamics of industrial fuel-ethanol fermentation process assessed by PCR-fingerprinting. Antonie Van Leeuwenhoek 88(1):13–23. https://doi.org/10.1007/s10482-004-7283-8
Dandi ND, Dandi BN, Chaudhari AB (2013) Bioprospecting of thermo- and osmo-tolerant fungi from mango pulp-peel compost for bioethanol production. Anton Leeuw Int J Gen Mol Microbiol 103(4):723–736. https://doi.org/10.1007/s10482-012-9854-4
Darvasi A, Soller M (1995) Advanced intercross lines, an experimental population for fine genetic mapping. In: Genetics. Elsevier, New York, pp 1199–1207
de Melo Pereira GV et al (2020) An updated review on bacterial community composition of traditional fermented milk products: what next-generation sequencing has revealed so far? Crit Rev Food Sci Nutr 0(0):1–20. https://doi.org/10.1080/10408398.2020.1848787
De Souza Liberal AT et al (2005) Contaminant yeast detection in industrial ethanol fermentation must by rDNA-PCR. Lett Appl Microbiol 40(1):19–23. https://doi.org/10.1111/j.1472-765X.2004.01618.x
De Souza Liberal AT et al (2007) Identification of Dekkera bruxellensis as a major contaminant yeast in continuous fuel ethanol fermentation. J Appl Microbiol 102(2):538–547. https://doi.org/10.1111/j.1365-2672.2006.03082.x
Della-Bianca BE, Gombert AK (2013) Stress tolerance and growth physiology of yeast strains from the Brazilian fuel ethanol industry. Anton Leeuw Int J Gen Mol Microbiol 104(6):1083–1095. https://doi.org/10.1007/s10482-013-0030-2
Dhaliwal SS et al (2011) Enhanced ethanol production from sugarcane juice by galactose adaptation of a newly isolated thermotolerant strain of Pichia kudriavzevii. Bioresour Technol 102(10):5968–5975. https://doi.org/10.1016/j.biortech.2011.02.015
DiCarlo JE et al (2013) Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res 41(7):4336–4343. https://doi.org/10.1093/nar/gkt135
Dubey R, Jakeer S, Gaur NA (2016) Screening of natural yeast isolates under the effects of stresses associated with second-generation biofuel production. J Biosci Bioeng 121(5):509–516. https://doi.org/10.1016/j.jbiosc.2015.09.006
Ekblom R, Wolf JBW (2014) A field guide to whole-genome sequencing, assembly and annotation. Evol Appl 7(9):1026–1042. https://doi.org/10.1111/eva.12178
Favaro L et al (2013) Exploring grape marc as trove for new thermotolerant and inhibitor-tolerant Saccharomyces cerevisiae strains for second-generation bioethanol production. Biotechnol Biofuels 6(1):1–14. https://doi.org/10.1186/1754-6834-6-168
Favaro L, Jansen T, van Zyl WH (2019) Exploring industrial and natural Saccharomyces cerevisiae strains for the bio-based economy from biomass: the case of bioethanol. Crit Rev Biotechnol 39(6):800–816. https://doi.org/10.1080/07388551.2019.1619157
Fay JC, Benavides JA (2005) Evidence for domesticated and wild populations of saccharomyces cerevisiae. PLoS Genet 1(1):0066–0071. https://doi.org/10.1371/journal.pgen.0010005
Field SJ et al (2015) Identification of furfural resistant strains of Saccharomyces cerevisiae and Saccharomyces paradoxus from a collection of environmental and industrial isolates. Biotechnol Biofuels 8(1):1–8. https://doi.org/10.1186/s13068-015-0217-z
Fong JCN et al (2006) Isolation and characterization of two novel ethanol-tolerant facultative-anaerobic thermophilic bacteria strains from waste compost. Extremophiles 10(5):363–372. https://doi.org/10.1007/s00792-006-0507-2
Fraczek MG, Naseeb S, Delneri D (2018) History of genome editing in yeast. Yeast 35(5):361–368. https://doi.org/10.1002/yea.3308
Fu N, Peiris P (2008) Co-fermentation of a mixture of glucose and xylose to ethanol by Zymomonas mobilis and Pachysolen tannophilus. World J Microbiol Biotechnol 24(7):1091–1097. https://doi.org/10.1007/s11274-007-9613-2
Fu N et al (2009) A novel co-culture process with Zymomonas mobilis and Pichia stipitis for efficient ethanol production on glucose/xylose mixtures. Enzym Microb Technol 45(3):210–217. https://doi.org/10.1016/j.enzmictec.2009.04.006
Fujitomi K et al (2012) Deletion of the PHO13 gene in Saccharomyces cerevisiae improves ethanol production from lignocellulosic hydrolysate in the presence of acetic and formic acids, and furfural. Bioresour Technol 111:161–166. https://doi.org/10.1016/j.biortech.2012.01.161
Gallagher D et al (2018) Dynamic bacterial and fungal microbiomes during sweet sorghum ensiling impact bioethanol production. Bioresour Technol 264(March):163–173. https://doi.org/10.1016/j.biortech.2018.05.053
Gao Y et al (2014) Ethanol production from high solids loading of alkali-pretreated sugarcane bagasse with an SSF process. Bioresources 9(2):3466–3479. https://doi.org/10.15376/biores.9.2.3466-3479
García-Pedrajas MD et al (2010) Molecular and cell biology methods for fungi. Springer Protocols 638:55–76. https://doi.org/10.1007/978-1-60761-611-5
Garrigues S, Martínez-Reyes N, de Vries RP (2021) Genetic engineering for strain improvement in filamentous fungi. In: Zaragoza Ó, Casadevall A (eds) Encyclopedia of mycology. Elsevier, Kidlington, pp 489–504. https://doi.org/10.1016/b978-0-12-819990-9.00006-8
Ge J et al (2014) Construction and analysis of high-ethanol-producing fusants with co-fermentation ability through protoplast fusion and double labeling technology. PLoS One 9(9). https://doi.org/10.1371/journal.pone.0108311
Gerke JP, Chen CTL, Cohen BA (2006) Natural isolates of Saccharomyces cerevisiae display complex genetic variation in sporulation efficiency. Genetics 174(2):985–997. https://doi.org/10.1534/genetics.106.058453
Giudici P et al (2005) Strategies and perspectives for genetic improvement of wine yeasts. Appl Microbiol Biotechnol 66(6):622–628. https://doi.org/10.1007/s00253-004-1784-2
Goffeau A et al (1996) Life with 6000 genes. Science 274(October):546–567
González-Siso MI et al (2015) Improved bioethanol production in an engineered Kluyveromyces lactis strain shifted from respiratory to fermentative metabolism by deletion of NDI1. Microb Biotechnol 8(2):319–330. https://doi.org/10.1111/1751-7915.12160
Greig D et al (1997) Greig, Plays 1. Methuen, London, pp 2–5
Gurdo N et al (2018) Improved robustness of an ethanologenic yeast strain through adaptive evolution in acetic acid is associated with its enzymatic antioxidant ability. J Appl Microbiol. https://doi.org/10.1111/jam.13917
Haber JE (2012) Mating-type genes and MAT switching in Saccharomyces cerevisiae. Genetics 191(1):33–64. https://doi.org/10.1534/genetics.111.134577
He MX et al (2014) Zymomonas mobilis: a novel platform for future biorefineries. Biotechnol Biofuels 7(1):1–15. https://doi.org/10.1186/1754-6834-7-101
Hemmati N, Lightfoot DA, Fakhoury A (2012) A mutated yeast strain with enhanced ethanol production efficiency and stress tolerance. Atlas J Biol 2(2):100–115. https://doi.org/10.5147/ajb.2012.0092
Hicks JB, Herskowitz I (1977) Interconversion of yeast mating types. II. Restoration of mating ability to sterile mutants in homothallic and heterothallic strains. Genetics 85(3):373–393. https://doi.org/10.1093/genetics/85.3.373
Horinouchi T, Maeda T, Kotani H, Furusawa C (2020) Suppression of antibiotic resistance evolution by single-gene deletion. Sci Rep 10(1):1–9
Hubmann G et al (2013) Quantitative trait analysis of yeast biodiversity yields novel gene tools for metabolic engineering. Metab Eng 17(1):68–81. https://doi.org/10.1016/j.ymben.2013.02.006
Jacobus AP et al (2021) Saccharomyces cerevisiae strains used industrially for bioethanol production. Essays Biochem 65(2):147–161. https://doi.org/10.1042/ebc20200160
Jessen JE, Orlygsson J (2012) Production of ethanol from sugars and lignocellulosic biomass by thermoanaerobacter J1 isolated from a hot spring in Iceland. J Biomed Biotechnol 2012. https://doi.org/10.1155/2012/186982
Jin ZH et al (2009) Enhanced production of spinosad in saccharopolyspora spinosa by genome shuffling. Appl Biochem Biotechnol 159(3):655–663. https://doi.org/10.1007/s12010-008-8500-0
Karp SG et al (2021) Bioeconomy and biofuels: the case of sugarcane ethanol in Brazil. Biofuels Bioprod Biorefin 15(3):899–912. https://doi.org/10.1002/BBB.2195
Katz Ezov T et al (2010) Heterothallism in Saccharomyces cerevisiae isolates from nature: effect of HO locus on the mode of reproduction. Mol Ecol 19(1):121–131. https://doi.org/10.1111/j.1365-294X.2009.04436.x
Kaushal R, Sharma N, Dogra V (2016) Molecular characterization of glycosyl hydrolases of Trichoderma harzianum WF5 - a potential strain isolated from decaying wood and their application in bioconversion of poplar wood to ethanol under separate hydrolysis and fermentation. Biomass Bioenergy 85:243–251. https://doi.org/10.1016/j.biombioe.2015.12.010
Kim JH, Block DE, Mills DA (2010) Simultaneous consumption of pentose and hexose sugars: an optimal microbial phenotype for efficient fermentation of lignocellulosic biomass. Appl Microbiol Biotechnol 88(5):1077–1085. https://doi.org/10.1007/s00253-010-2839-1
Kim SR et al (2015) Deletion of PHO13, encoding haloacid dehalogenase type IIA phosphatase, results in upregulation of the pentose phosphate pathway in Saccharomyces cerevisiae. Appl Environ Microbiol 81(5):1601–1609. https://doi.org/10.1128/AEM.03474-14
Koutinas M et al (2016) High temperature alcoholic fermentation of orange peel by the newly isolated thermotolerant Pichia kudriavzevii KVMP10. Lett Appl Microbiol 62(1):75–83. https://doi.org/10.1111/lam.12514
Kuhad RC et al (2011) Bioethanol production from pentose sugars: current status and future prospects. Renew Sust Energ Rev 15(9):4950–4962. https://doi.org/10.1016/J.RSER.2011.07.058
Kumar D, Singh V (2019) Bioethanol production from corn. In: Serna-Saldivar SO (ed) Corn, 3rd edn. AACC International Press, St Paul, pp 615–631
Kumari R, Pramanik K (2012) Improvement of multiple stress tolerance in yeast strain by sequential mutagenesis for enhanced bioethanol production. J Biosci Bioeng 114(6):622–629. https://doi.org/10.1016/j.jbiosc.2012.07.007
Kvitek DJ, Will JL, Gasch AP (2008) Variations in stress sensitivity and genomic expression in diverse S. cerevisiae isolates. PLoS Genet 4(10):31–35. https://doi.org/10.1371/journal.pgen.1000223
Larsen L, Nielsen P, Ahring BK (1997) Thermoanaerobacter mathranii sp. nov., an ethanol-producing, extremely thermophilic anaerobic bacterium from a hot spring in Iceland. Arch Microbiol 168(2):114–119. https://doi.org/10.1007/s002030050476
Legras JL et al (2007) Bread, beer and wine: Saccharomyces cerevisiae diversity reflects human history. Mol Ecol 16(10):2091–2102. https://doi.org/10.1111/j.1365-294X.2007.03266.x
Limayem A, Ricke SC (2012) Lignocellulosic biomass for bioethanol production: current perspectives, potential issues and future prospects. Prog Energy Combust Sci 38(4):449–467. https://doi.org/10.1016/j.pecs.2012.03.002
Lippman ZB, Zamir D (2007) Heterosis: revisiting the magic. Trends Genet 23(2):60–66. https://doi.org/10.1016/j.tig.2006.12.006
Liti G, Louis EJ (2012) Advances in quantitative trait analysis in yeast. PLoS Genet 8(8):e1002912. https://doi.org/10.1371/journal.pgen.1002912
Liti G et al (2009) Population genomics of domestic and wild yeasts. Nature 458(7236):337–341. https://doi.org/10.1038/nature07743
Loaces I et al (2016) Improved glycerol to ethanol conversion by E. coli using a metagenomic fragment isolated from an anaerobic reactor. J Ind Microbiol Biotechnol 43(10):1405–1416. https://doi.org/10.1007/s10295-016-1818-7
Loaces I, Schein S, Noya F (2017) Ethanol production by Escherichia coli from Arundo donax biomass under SSF, SHF or CBP process configurations and in situ production of a multifunctional glucanase and xylanase. Bioresour Technol 224:307–313. https://doi.org/10.1016/j.biortech.2016.10.075
Lv W, Yu Z (2013) Isolation and characterization of two thermophilic cellulolytic strains of Clostridium thermocellum from a compost sample. J Appl Microbiol 114(4):1001–1007. https://doi.org/10.1111/jam.12112
MacKay TFC, Stone EA, Ayroles JF (2009) The genetics of quantitative traits: challenges and prospects. Nat Rev Genet 10(8):565–577. https://doi.org/10.1038/nrg2612
Madeira-Jr JV, Gombert AK (2018) Towards high-temperature fuel ethanol production using Kluyveromyces marxianus: on the search for plug-in strains for the Brazilian sugarcane-based biorefinery. Biomass Bioenergy 119(March):217–228. https://doi.org/10.1016/j.biombioe.2018.09.010
Magwene PM, Willis JH, Kelly JK (2011a) The statistics of bulk segregant analysis using next generation sequencing. PLoS Comput Biol 7(11):e1002255. https://doi.org/10.1371/journal.pcbi.1002255
Magwene PM et al (2011b) Outcrossing, mitotic recombination, and life-history trade-offs shape genome evolution in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 108(5):1987–1992. https://doi.org/10.1073/pnas.1012544108
Mans R, Daran JMG, Pronk JT (2018) Under pressure: evolutionary engineering of yeast strains for improved performance in fuels and chemicals production. Curr Opin Biotechnol 50:47–56. https://doi.org/10.1016/j.copbio.2017.10.011
McGovern PE et al (2004) Fermented beverages of pre- and proto-historic China. Proc Natl Acad Sci U S A 101(51):17593–17598. https://doi.org/10.1073/pnas.0407921102
McMillan JD, Beckham GT (2017) Thinking big: towards ideal strains and processes for large-scale aerobic biofuels production. Microb Biotechnol 10(1):40–42. https://doi.org/10.1111/1751-7915.12471
Meijnen JP et al (2016) Polygenic analysis and targeted improvement of the complex trait of high acetic acid tolerance in the yeast Saccharomyces cerevisiae. Biotechnol Biofuels 9(1):5. https://doi.org/10.1186/s13068-015-0421-x
Min K et al (2016) Candida albicans gene deletion with a transient CRISPR-Cas9 system. mSphere 1(3):e00130–e00116. https://doi.org/10.1128/msphere.00130-16
Mobini-Dehkordi M et al (2008) Isolation of a novel mutant strain of Saccharomyces cerevisiae by an ethyl methane sulfonate-induced mutagenesis approach as a high producer of bioethanol. J Biosci Bioeng 105(4):403–408. https://doi.org/10.1263/jbb.105.403
Modig T, Lidén G, Taherzadeh MJ (2002) Inhibition effects of furfural on alcohol dehydrogenase, aldehyde dehydrogenase and pyruvate dehydrogenase. Biochem J 363(3):769–776. https://doi.org/10.1042/0264-6021:3630769
Moreno AD et al (2013) Comparing cell viability and ethanol fermentation of the thermotolerant yeast Kluyveromyces marxianus and Saccharomyces cerevisiae on steam-exploded biomass treated with laccase. Bioresour Technol 135:239–245. https://doi.org/10.1016/j.biortech.2012.11.095
Mukherjee V et al (2014) Phenotypic evaluation of natural and industrial Saccharomyces yeasts for different traits desirable in industrial bioethanol production. Appl Microbiol Biotechnol 98(22):9483–9498. https://doi.org/10.1007/s00253-014-6090-z
Muthaiyan A, Limayem A, Ricke SC (2011) Antimicrobial strategies for limiting bacterial contaminants in fuel bioethanol fermentations. Prog Energy Combust Sci 37(3):351–370. https://doi.org/10.1016/j.pecs.2010.06.005
Nieduszynski CA, Liti G (2011) From sequence to function: insights from natural variation in budding yeasts. Biochim Biophys Acta Gen Subj 1810(10):959–966. https://doi.org/10.1016/j.bbagen.2011.02.004
Ota A et al (2013) Production of ethanol from mannitol by the yeast strain Saccharomyces paradoxus NBRC 0259. J Biosci Bioeng 116(3):327–332. https://doi.org/10.1016/j.jbiosc.2013.03.018
Parisutham V, Kim TH, Lee SK (2014) Feasibilities of consolidated bioprocessing microbes: from pretreatment to biofuel production. Bioresour Technol 161:431–440. https://doi.org/10.1016/j.biortech.2014.03.114
Pereira FB et al (2014) Industrial robust yeast isolates with great potential for fermentation of lignocellulosic biomass. Bioresour Technol 161:192–199. https://doi.org/10.1016/j.biortech.2014.03.043
Pereira GVM et al (2020) Lactic acid bacteria: what coffee industry should know? Curr Opin Food Sci 31:1–8. https://doi.org/10.1016/j.cofs.2019.07.004
Peris D et al (2017a) Hybridization and adaptive evolution of diverse Saccharomyces species for cellulosic biofuel production. Biotechnol Biofuels 10(1):1–19. https://doi.org/10.1186/s13068-017-0763-7
Peris D et al (2017b) Hybridization and adaptive evolution of diverse Saccharomyces species for cellulosic biofuel production. Biotechnol Biofuels 10(1):78. https://doi.org/10.1186/s13068-017-0763-7
Peter J et al (2018) Genome evolution across 1,011 Saccharomyces cerevisiae isolates species-wide genetic and phenotypic diversity. Nature
Pretorius IS (2000) Tailoring wine yeast for the new millennium: novel approaches to the ancient art of winemaking. Yeast 16(8):675–729. https://doi.org/10.1002/1097-0061(20000615)16:8<675::aid-yea585>3.3.co;2-2
Rainieri S, Pretorius IS (2000) Selection and improvement of wine yeasts. Ann Microbiol 50(1):15–31
Reuter JA, Spacek DV, Snyder MP (2015) High-throughput sequencing technologies. Mol Cell 58(4):586–597. https://doi.org/10.1016/j.molcel.2015.05.004
Rodrussamee N, Sattayawat P, Yamada M (2018) Highly efficient conversion of xylose to ethanol without glucose repression by newly isolated thermotolerant Spathaspora passalidarum CMUWF1-2. BMC Microbiol 18(1):1–11. https://doi.org/10.1186/s12866-018-1218-4
Romero-Frasca E et al (2021) Bioprospecting of wild type ethanologenic yeast for ethanol fuel production from wastewater-grown microalgae. Biotechnol Biofuels 14(1):1–10. https://doi.org/10.1186/s13068-021-01925-x
Ruyters S et al (2015) Assessing the potential of wild yeasts for bioethanol production. J Ind Microbiol Biotechnol 42(1):39–48. https://doi.org/10.1007/s10295-014-1544-y
Sandberg TE et al (2019) The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology. Metab Eng 56(August):1–16. https://doi.org/10.1016/j.ymben.2019.08.004
Santos F et al (2020) Production of second-generation ethanol from sugarcane. In: Sugarcane biorefinery, technology and perspectives. Elsevier, New York, pp 195–228. https://doi.org/10.1016/B978-0-12-814236-3.00011-1
Sauer B (1987) Functional expression of the cre-lox site-specific recombination system in the yeast Saccharomyces cerevisiae. Mol Cell Biol 7(6):2087–2096. https://doi.org/10.1128/mcb.7.6.2087-2096.1987
Schnable PS, Springer NM (2013) Progress toward understanding heterosis in crop plants. Annu Rev Plant Biol 64:71–88. https://doi.org/10.1146/annurev-arplant-042110-103827
Scully SM, Orlygsson J (2015) Recent advances in second generation ethanol production by thermophilic bacteria. Energies 8(1):1–30. https://doi.org/10.3390/en8010001
Selim KA et al (2018) Bioethanol a microbial biofuel metabolite; new insights of yeasts metabolic engineering. Fermentation 4(1). https://doi.org/10.3390/fermentation4010016
Selmecki AM et al (2015) Polyploidy can drive rapid adaptation in yeast. Nature 519(7543):349–351. https://doi.org/10.1038/nature14187
Shahid S, Tajwar R, Akhtar MW (2018) A novel trifunctional, family GH10 enzyme from Acidothermus cellulolyticus 11B, exhibiting endo-xylanase, arabinofuranosidase and acetyl xylan esterase activities. Extremophiles 22(1):109–119. https://doi.org/10.1007/s00792-017-0981-8
Shapira R et al (2014) Extensive heterosis in growth of yeast hybrids is explained by a combination of genetic models. Heredity 113(4):316–326. https://doi.org/10.1038/hdy.2014.33
Sicard D, Legras JL (2011) Bread, beer and wine: yeast domestication in the Saccharomyces sensu stricto complex. C R Biol 334(3):229–236. https://doi.org/10.1016/j.crvi.2010.12.016
Signori L et al (2014) Effect of oxygenation and temperature on glucose-xylose fermentation in Kluyveromyces marxianus CBS712 strain. Microb Cell Factories 13(1):1–13. https://doi.org/10.1186/1475-2859-13-51
Singh N et al (2018) Bioethanol production potential of a novel thermophilic isolate Thermoanaerobacter sp. DBT-IOC-X2 isolated from Chumathang hot spring. Biomass Bioenergy 116(January):122–130. https://doi.org/10.1016/j.biombioe.2018.05.009
Sipiczki M (2008) Interspecies hybridization and recombination in Saccharomyces wine yeasts. FEMS Yeast Res 8(7):996–1007. https://doi.org/10.1111/j.1567-1364.2008.00369.x
Stambuk BU (2019) Yeasts: the leading figures on bioethanol production. In: Ethanol as a green alternative fuel: insight and perspectives. Nova Science Publishers, New York, pp 57–92
Stambuk BU et al (2009) Industrial fuel ethanol yeasts contain adaptive copy number changes in genes involved in vitamin B1 and B6 biosynthesis. Genome Res 19(12):2271–2278. https://doi.org/10.1101/gr.094276.109
Steensels J et al (2014) Improving industrial yeast strains: exploiting natural and artificial diversity. FEMS Microbiol Rev 38(5):947–995. https://doi.org/10.1111/1574-6976.12073
Storici F, Lewis LK, Resnick MA (2001) In vivo site-directed mutagenesis using oligonucleotides. Nat Biotechnol 19(8):773–776. https://doi.org/10.1038/90837
Sukwong P et al (2020) Improvement of bioethanol production by Saccharomyces cerevisiae through the deletion of GLK1, MIG1 and MIG2 and overexpression of PGM2 using the red seaweed Gracilaria verrucosa. Process Biochem 89:134–145. https://doi.org/10.1016/j.procbio.2019.10.030
Swinnen S, Thevelein JM, Nevoigt E (2012a) Genetic mapping of quantitative phenotypic traits in Saccharomyces cerevisiae. FEMS Yeast Res 12(2):215–227. https://doi.org/10.1111/j.1567-1364.2011.00777.x
Swinnen S et al (2012b) Identification of novel causative genes determining the complex trait of high ethanol tolerance in yeast using pooled-segregant whole-genome sequence analysis. Genome Res 22(5):975–984. https://doi.org/10.1101/gr.131698.111
Swinnen S et al (2014) The fraction of cells that resume growth after acetic acid addition is a strain-dependent parameter of acetic acid tolerance in Saccharomyces cerevisiae. FEMS Yeast Res 14(4):642–653. https://doi.org/10.1111/1567-1364.12151
Takabatake A, Kawazoe N, Izawa S (2015) Plasma membrane proteins Yro2 and Mrh1 are required for acetic acid tolerance in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 99(6):2805–2814. https://doi.org/10.1007/s00253-014-6278-2
Tan F et al (2016) Using global transcription machinery engineering (gTME) to improve ethanol tolerance of Zymomonas mobilis. Microb Cell Factories 15(1):1–9. https://doi.org/10.1186/s12934-015-0398-y
Tan H et al (2018) A bifunctional cellulase–xylanase of a new Chryseobacterium strain isolated from the dung of a straw-fed cattle. Microb Biotechnol 11(2):381–398. https://doi.org/10.1111/1751-7915.13034
Tao X et al (2012) A novel strategy to construct yeast saccharomyces cerevisiae strains for very high gravity fermentation. PLoS One 7(2). https://doi.org/10.1371/journal.pone.0031235
Tiwari S et al (2020) Xylanolytic and Ethanologenic potential of gut associated yeasts from different species of termites from India. Mycobiology 48(6):501–511. https://doi.org/10.1080/12298093.2020.1830742
Tomás AF et al (2013) Extreme thermophilic ethanol production from rapeseed straw: using the newly isolated Thermoanaerobacter pentosaceus and combining it with Saccharomyces cerevisiae in a two-step process. Biotechnol Bioeng 110(6):1574–1582. https://doi.org/10.1002/bit.24813
Tran DT et al (2011) Ethanol production from lignocelluloses by native strain Klebsiella oxytoca THLC0409. Waste Biomass Valorization 2(4):389–396. https://doi.org/10.1007/s12649-011-9082-6
Turner P, Mamo G, Karlsson EN (2007) Potential and utilization of thermophiles and thermostable enzymes in biorefining. Microb Cell Factories 6:1–23. https://doi.org/10.1186/1475-2859-6-9
Udom N et al (2019) Coordination of the cell wall integrity and high-osmolarity glycerol pathways in response to ethanol stress in Saccharomyces cerevisiae. Appl Environ Microbiol 85(15):e00551–e00519. https://doi.org/10.1128/AEM.00551-19
Voordeckers K et al (2015) Adaptation to high ethanol reveals complex evolutionary pathways. PLoS Genet 11(11):1–31. https://doi.org/10.1371/journal.pgen.1005635
Waghmare PR et al (2014) Production and characterization of cellulolytic enzymes by isolated klebsiella sp. PRW-1 using agricultural waste biomass. Emir J Food Agric 26(1):44–59. https://doi.org/10.9755/ejfa.v26i1.15296
Wallace-Salinas V et al (2015) Cell periphery-related proteins as major genomic targets behind the adaptive evolution of an industrial Saccharomyces cerevisiae strain to combined heat and hydrolysate stress. BMC Genomics 16(1):1–16. https://doi.org/10.1186/s12864-015-1737-4
Wang Z et al (2019) QTL analysis reveals genomic variants linked to high-temperature fermentation performance in the industrial yeast. Biotechnol Biofuels 12(1):59. https://doi.org/10.1186/s13068-019-1398-7
Wang L et al (2021) Improving multiple stress-tolerance of a flocculating industrial Saccharomyces cerevisiae strain by random mutagenesis and hybridization. Process Biochem 102:275–285. https://doi.org/10.1016/j.procbio.2020.12.022
Watanabe T et al (2011) A UV-induced mutant of Pichia stipitis with increased ethanol production from xylose and selection of a spontaneous mutant with increased ethanol tolerance. Bioresour Technol 102(2):1844–1848. https://doi.org/10.1016/j.biortech.2010.09.087
Widyasti E et al (2018) Biodegradation of fibrillated oil palm trunk fiber by a novel thermophilic, anaerobic, xylanolytic bacterium Caldicoprobacter sp. CL-2 isolated from compost. Enzym Microb Technol 111:21–28. https://doi.org/10.1016/j.enzmictec.2017.12.009
Xu H et al (2016) PHO13 deletion-induced transcriptional activation prevents sedoheptulose accumulation during xylose metabolism in engineered Saccharomyces cerevisiae. Metab Eng 34:88–96. https://doi.org/10.1016/j.ymben.2015.12.007
Xue T et al (2018) Improved bioethanol production using CRISPR/Cas9 to disrupt the ADH2 gene in Saccharomyces cerevisiae. World J Microbiol Biotechnol 34(154):1–12. https://doi.org/10.1007/s11274-018-2518-4
Yadav P et al (2018) Production, purification, and characterization of thermostable alkaline xylanase from Anoxybacillus kamchatkensis NASTPD13. Front Bioeng Biotechnol 6(May). https://doi.org/10.3389/fbioe.2018.00065
Yi S et al (2018) Screening and mutation of Saccharomyces cerevisiae UV-20 with a high yield of second generation bioethanol and high tolerance of temperature, glucose and ethanol. Indian J Microbiol 58(4):440–447. https://doi.org/10.1007/s12088-018-0741-1
Zhang M et al (2017) Deletion of acetate transporter gene ADY2 improved tolerance of Saccharomyces cerevisiae against multiple stresses and enhanced ethanol production in the presence of acetic acid. Bioresour Technol 245:1461–1468. https://doi.org/10.1016/j.biortech.2017.05.191
Zhang K et al (2018) Genetic characterization and modification of a bioethanol-producing yeast strain. Appl Microbiol Biotechnol 102(5):2213–2223. https://doi.org/10.1007/s00253-017-8727-1
Zhang Q et al (2019) Adaptive evolution and selection of stress-resistant Saccharomyces cerevisiae for very high-gravity bioethanol fermentation. Electron J Biotechnol 41:88–94. https://doi.org/10.1016/j.ejbt.2019.06.003
Zheng DQ et al (2012) Genome sequencing and genetic breeding of a bioethanol Saccharomyces cerevisiae strain YJS329. BMC Genomics 13(1). https://doi.org/10.1186/1471-2164-13-479
Zheng Y et al (2021) Genetic diversity for accelerating microbial adaptive laboratory evolution. ACS Synth Biol 10(7):1574–1586. https://doi.org/10.1021/acssynbio.0c00589
Zhou XG et al (2010) The next-generation sequencing technology: a technology review and future perspective. Sci China Life Sci 53(1):44–57. https://doi.org/10.1007/s11427-010-0023-6
Acknowledgements
The authors acknowledge the financial support given by CNPq and CAPES.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2022 The Author(s), under exclusive license to Springer Nature Switzerland AG
About this chapter
Cite this chapter
de Melo Pereira, G.V. et al. (2022). Microorganisms and Genetic Improvement for First and Second Generation Bioethanol Production. In: Soccol, C.R., Amarante Guimarães Pereira, G., Dussap, CG., Porto de Souza Vandenberghe, L. (eds) Liquid Biofuels: Bioethanol. Biofuel and Biorefinery Technologies, vol 12. Springer, Cham. https://doi.org/10.1007/978-3-031-01241-9_3
Download citation
DOI: https://doi.org/10.1007/978-3-031-01241-9_3
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-031-01240-2
Online ISBN: 978-3-031-01241-9
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)