Abstract
Non-renewable fossil fuels such as bitumen, coal, natural gas, oil shale, and petroleum are depleting over the world owing to unrestricted consumption. Biofuels such as biodiesel, biobutanol, bioethanol, and biogas are considered an eco-friendly and cost-effective alternatives of fossil fuels. For energy sustainability, the production of advanced biofuels is required. The advancement of genetic and metabolic engineering in microbial cells played a significant contribution to biofuels overproduction. Essential approaches such as next-generation sequencing technologies and CRISPR/Cas9-mediated genome editing of microbial cells are required for the mass manufacture of biofuels globally. Advanced “omics” approaches are used to construct effective microorganisms for biofuels manufacturing. A new investigation is required to augment the production of lignocellulosic-based biofuels with minimal use of energy. Advanced areas of metabolic engineering are introduced in the manufacture of biofuels by the use of engineered microbial strains. Genetically modified microorganisms are used for the production of biofuels in large quantities at a low-cost.
Similar content being viewed by others
References
Abendroth C, Vilanova C, Günther T, Luschnig O, Porcar M (2015) Eubacteria and archaea communities in seven mesophile anaerobic digester plants in Germany. Biotechnol Biofuels 8:87. https://doi.org/10.1186/s13068-015-0271-6
Adegboye MF, Ojuederie OB, Talia PM, Babalola OO (2021) Bioprospecting of microbial strains for biofuel production: metabolic engineering, applications, and challenges. Biotechnol Biofuels 14:5. https://doi.org/10.1186/s13068-020-01853-2
Aikawa S, Baramee S, Sermsathanaswadi J 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 41:261–269. https://doi.org/10.1016/j.syapm.2018.01.010
Akinosho H, Yee K, Close D, Ragauskas A (2014) The emergence of Clostridium thermocellum as a high utility candidate for consolidated bioprocessing applications. Front Chem 2:66. https://doi.org/10.3389/fchem.2014.00066
Angermayr SA, Hellingwerf KJ, Lindblad P, de Mattos MJ (2009) Energy biotechnology with cyanobacteria. Curr Opin Biotechnol 20:257–263. https://doi.org/10.1016/j.copbio.2009.05.011
Atsumi S, Cann AF, Connor MR, Shen CR, Smith KM, Brynildsen MP, Chou KJY, Hanai T, Liao JC (2008) Metabolic engineering of Escherichia coli for 1-butanol production. Metab Eng 10:305–311. https://doi.org/10.1016/j.ymben.2007.08.003
Atsumi S, Higashide W, Liao JC (2009) Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde. Nat Biotechnol 27:1177–1180. https://doi.org/10.1038/nbt.1586
Awe OW, Zhao Y, Nzihou A, Minh DP, Lyczko N (2017) A review of biogas utilization, purification and upgrading technologies. Waste Biomass Valor 8:267–283
Azad AK, Rasul M, Khan MMK, Sharma SC (2014) Review of biodiesel production from microalgae: a novel source of green energy. Int Green Energy Conf. https://doi.org/10.13140/2.1.3013.0244
Balat M (2011) Production of bioethanol from lignocellulosic materials via the biochemical pathway: a review. Energy Convers Manag 52:858–875
Bao Z, Cobb RE, Zhao H (2016) Accelerated genome engineering through multiplexing. Wiley Interdiscip Rev Syst Biol Med 8:5–21. https://doi.org/10.1002/wsbm.1319
Beloqui A, Nechitaylo TY, Lopez-Cortes N, Ghazi A, Guazzaroni ME, Polaina J et al (2010) Diversity of glycosyl hydrolases from cellulose-depleting communities enriched from casts of two earthworm species. Appl Environ Microbiol 76:5934–5946. https://doi.org/10.1128/AEM.00902-10
Bilal T, Malik B, Hakeem KR (2018) Metagenomic analysis of uncultured microorganisms and their enzymatic attributes. J Microbiol Methods 155:65–69. https://doi.org/10.1016/j.mimet.2018.11.014
Boonsayompoo O, Reungsang A (2013) Thermophilic biohydrogen production from the enzymatic hydrolysate of cellulose fraction of sweet sorghum bagasse by Thermoanaerobacterium thermosaccharolyticum KKU19: optimization of media composition. Int J Hydrogen Energy 38:15777–15786
Brigham C (2019) Perspectives for the biotechnological production of biofuels from CO2 and H2 using Ralstonia eutropha and other “Knallgas” bacteria. Appl Microbiol Biotechnol 103:2113–2120. https://doi.org/10.1007/s00253-019-09636-y
Brown SD, Guss AM, Karpinets TV, Parks JM et al (2011) Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum. Proc Natl Acad Sci 108:13752–13757. https://doi.org/10.1073/pnas.1102444108
Bruder MR, Pyne ME, Moo-Young M, Chung DA, Chou CP (2016) Extending CRISPR-Cas9 technology from genome editing to transcriptional engineering in the genus Clostridium. Appl Environ Microbiol 82:6109–6119. https://doi.org/10.1128/AEM.02128-16
Brunecky R, Chung D, Sarai NS et al (2018) High activity CAZyme cassette for improving biomass degradation in thermophiles. Biotechnol Biofuels 11:22. https://doi.org/10.1186/s13068-018-1014-2
Bugg TD, Rahmanpour R (2015) Enzymatic conversion of lignin into renewable chemicals. Curr Opin Chem Biol 29:10–17. https://doi.org/10.1016/j.cbpa.2015.06.009
Cai D, Chen H, Chen C et al (2016) Gas stripping–pervaporation hybrid process for energy-saving product recovery from acetone–butanol–ethanol (ABE) fermentation broth. Chem Eng J 287:1–10
Caspeta L, Chen Y, Ghiaci P et al (2014) Altered sterol composition renders yeast thermotolerant. Science 346:75–78. https://doi.org/10.1126/science.1258137
Cheon S, Kim HM, Gustavsson M, Lee SY (2016) Recent trends in metabolic engineering of microorganisms for the production of advanced biofuels. Curr Opin Chem Biol 35:10–21. https://doi.org/10.1016/j.cbpa.2016.08.003
Chokhawala HA, Roche CM, Kim T-W et al (2015) Mutagenesis of Trichoderma reesei endoglucanase I: impact of expression host on activity and stability at elevated temperatures. BMC Biotechnol. https://doi.org/10.1186/s12896-015-0118-z
Colin VL, Rodríguez A, Cristóbal HA (2011) The role of synthetic biology in the design of microbial cell factories for biofuel production. J Biomed Biotechnol 2011:601834. https://doi.org/10.1155/2011/601834
Cortes-Tolalpa L, Norder J, van Elsas JD, Falcao Salles J (2018) Halotolerant microbial consortia able to degrade highly recalcitrant plant biomass substrate. Appl Microbiol Biotechnol 102:2913–2927. https://doi.org/10.1007/s00253-017-8714-6
das Neves MA, Kimura T, Shimizu N, Nakajima M (2007) State of the art and future trends of bioethanol production. Dyn Biochem Process Biotechnol Mol Biol 1:1–14
de Gonzalo G, Colpa DI, Habib MH, Fraaije MW (2016) Bacterial enzymes involved in lignin degradation. J Biotechnol 236:110–119. https://doi.org/10.1016/j.jbiotec.2016.08.011
Dellomonaco C, Fava F, Gonzalez R (2010) The path to next generation biofuels: successes and challenges in the era of synthetic biology. Microb Cell Fact 9:3. https://doi.org/10.1186/1475-2859-9-3
Doshi A, Pascoe S, Coglan L, Rainey TJ (2016) Economic and policy issues in the production of algae-based biofuels: a review. Renew Sustain Energy Rev 64:329–337
Dumon C, Song L, Bozonnet S, Fauré R, O’Donohue MJ (2012) Progress and future prospects for pentose-specific biocatalysts in biorefining. Process Biochem 47:346–357
Dutta K, Daverey A, Lin JG (2014) Evolution retrospective for alternative fuels: first to fourth generation. Renew Energy 69:114–122
Fang Z, Fang W, Liu J et al (2010) Cloning and characterization of a beta-glucosidase from marine microbial metagenome with excellent glucose tolerance. J Microbiol Biotechnol 20:1351–1358. https://doi.org/10.4014/jmb.1003.03011
Fang Z, Li T, Wang Q, Zhang X, Peng H, Fang W et al (2011) A bacterial laccase from marine microbial metagenome exhibiting chloride tolerance and dye decolorization ability. Appl Microbiol Biotechnol 89:1103–1110. https://doi.org/10.1007/s00253-010-2934-3
Georgianna DR, Mayfield SP (2012) Exploiting diversity and synthetic biology for the production of algal biofuels. Nature 488:329–335. https://doi.org/10.1038/nature11479
González-Ramos D, de Vries ARG, Grijseels SS et al (2016) A new laboratory evolution approach to select for constitutive acetic acid tolerance in Saccharomyces cerevisiae and identification of causal mutations. Biotechnol Biofuels 9:173. https://doi.org/10.1186/s13068-016-0583-1
Grissa I, Vergnaud G, Pourcel C (2007) The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinform 8:172. https://doi.org/10.1186/1471-2105-8-172
Güllert S, Fischer MA, Turaev D et al (2016) Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies. Biotechnol Biofuels 9:121. https://doi.org/10.1186/s13068-016-0534-x
Gunawardana M, Chang S, Jimenez A et al (2014) Isolation of PCR quality microbial community DNA from heavily contaminated environments. J Microbiol Methods 102:1–7. https://doi.org/10.1016/j.mimet.2014.04.005
Guo D, Zhu J, Deng Z, Liu T (2014) Metabolic engineering of Escherichia coli for production of fatty acid short-chain esters through combination of the fatty acid and 2-keto acid pathways. Metab Eng 22:69–75. https://doi.org/10.1016/j.ymben.2014.01.003
Hahnke S, Langer T, Koeck DE, Klocke M (2016) Description of Proteiniphilum saccharofermentans sp. nov., Petrimonas mucosasp. nov. and Fermentimonas caenicola gen. nov., sp. nov., isolated from mesophilic laboratory-scale biogas reactors, and emended description of the genus Proteiniphilum. Int J Syst Evol Microbiol 66:1466–1475. https://doi.org/10.1099/ijsem.0.000902
Hassa J, Maus I, Off S et al (2018) Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants. Appl Microbiol Biotechnol 102:5045–5063. https://doi.org/10.1007/s00253-018-8976-7
Havlík P, Schneider UA, Schmid E et al (2011) Global land-use implications of first and second generation biofuel targets. Energy Policy 39:5690–5702
Hu Y, Zhang G, Li A, Chen J, Ma L (2008) Cloning and enzymatic characterization of a xylanase gene from a soil-derived metagenomic library with an efficient approach. Appl Microbiol Biotechnol 80:823–830. https://doi.org/10.1007/s00253-008-1636-6
Ilmberger N, Streit WR (2010) Screening for cellulase-encoding clones in metagenomic libraries. Methods Mol Biol 668:177–188. https://doi.org/10.1007/978-1-4939-6691-2_12
Javed MR, Noman M, Shahid M et al (2019) Current situation of biofuel production and its enhancement by CRISPR/Cas9-mediated genome engineering of microbial cells. Microbiol Res 219:1–11. https://doi.org/10.1016/j.micres.2018.10.010
Jiang W, Bikard D, Cox D, Zhang F, Marraffini LA (2013) RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol 31:233–239. https://doi.org/10.1038/nbt.2508
Jiang Y, Xin F, Lu J, Dong W et al (2017) State of the art review of biofuels production from lignocellulose by thermophilic bacteria. Bioresour Technol 245(Pt B):1498–1506. https://doi.org/10.1016/j.biortech.2017.05.142
Joseph RC, Kim NM, Sandoval NR (2018) Recent Developments of the Synthetic Biology Toolkit for Clostridium. Front Microbiol 9:154. https://doi.org/10.3389/fmicb.2018.00154
Jünemann S, Kleinbölting N, Jaenicke S, Henke C et al (2017) Bioinformatics for NGS-based metagenomics and the application to biogas research. J Biotechnol 261:10–23. https://doi.org/10.1016/j.jbiotec.2017.08.012
Jung SK, Parisutham V, Jeong SH, Lee SK (2012) Heterologous expression of plant cell wall degrading enzymes for effective production of cellulosic biofuels. J Biomed Biotechnol 2012:405842. https://doi.org/10.1155/2012/405842
Kanafusa-Shinkai S, Wakayama J, Tsukamoto K et al (2013) Degradation of microcrystalline cellulose and non-pretreated plant biomass by a cell-free extracellular cellulose/hemicellulose system from the extreme thermophilic bacterium Caldicellulosiruptor bescii. J Biosci Bioeng 115:64–70. https://doi.org/10.1016/j.jbiosc.2012.07.019
Kang Q, Appels L, Tan T, Dewil R (2014) Bioethanol from lignocellulosic biomass: current findings determine research priorities. Sci World J 2014:298153. https://doi.org/10.1155/2014/298153
Karimi K, Tabatabaei M, Horváth IS, Kumar R (2015) Recent trends in acetone, butanol, and ethanol (ABE) production. Biofuel Res J 2:301–308
Kim SK, Seong W, Han GH, Lee DH, Lee SG (2017) CRISPR interference-guided multiplex repression of endogenous competing pathway genes for redirecting metabolic flux in Escherichia coli. Microb Cell Fact 16:188. https://doi.org/10.1186/s12934-017-0802-x
Koeck DE, Ludwig W, Wanner G et al (2015) Herbinix hemicellulosilytica gen. nov., sp. nov., a thermophilic cellulose-degrading bacterium isolated from a thermophilic biogas reactor. Int J Syst Evol Microbiol 65:2365–2371. https://doi.org/10.1099/ijs.0.000264
Kurosawa K, Laser J, Sinskey AJ (2015) Tolerance and adaptive evolution of triacylglycerol-producing Rhodococcus opacus to lignocellulose-derived inhibitors. Biotechnol Biofuels 8:76. https://doi.org/10.1186/s13068-015-0258-3
Lan EI, Liao JC (2011) Metabolic engineering of cyanobacteria for 1-butanol production from carbon dioxide. Metab Eng 13:353–363. https://doi.org/10.1016/j.ymben.2011.04.004
Lee LL, Blumer-Schuette SE, Izquierdo JA et al (2018) Genus-wide assessment of lignocellulose utilization in the extremely thermophilic genus Caldicellulosiruptor by genomic, pangenomic, and metagenomic analyses. Appl Environ Microbiol 84:e02694-e2717. https://doi.org/10.1128/AEM.02694-17
Leis B, Angelov A, Mientus M et al (2015) Identification of novel esterase-active enzymes from hot environments by use of the host bacterium Thermus thermophilus. Front Microbiol 6:275. https://doi.org/10.3389/fmicb.2015.00275
Lemos LN, Pereira RV, Quaggio RB et al (2017) Genome-centric analysis of a thermophilic and cellulolytic bacterial consortium derived from composting. Front Microbiol 8:644. https://doi.org/10.3389/fmicb.2017.00644
Liang L, Liu R, Garst AD et al (2017) CRISPR Enabled Trackable genome Engineering for isopropanol production in Escherichia coli. Metab Eng 41:1–10. https://doi.org/10.1016/j.ymben.2017.02.009
Liu N, Yan X, Zhang M et al (2011) Microbiome of fungus-growing termites: a new reservoir for lignocellulase genes. Appl Environ Microbiol 77:48–56. https://doi.org/10.1128/AEM.01521-10
Louwen R, Staals RH, Endtz HP et al (2014) The role of CRISPR-Cas systems in virulence of pathogenic bacteria. Microbiol Mol Biol Rev 78:74–88. https://doi.org/10.1128/MMBR.00039-13
Lu C, Yu L, Varghese S, Yu M, Yang ST (2017) Enhanced robustness in acetone-butanol-ethanol fermentation with engineered Clostridium beijerinckii overexpressing adhE2 and ctfAB. Bioresour Technol 243:1000–1008. https://doi.org/10.1016/j.biortech.2017.07.043
Luo G, Fotidis IA, Angelidaki I (2016) Comparative analysis of taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors by metagenomic sequencing and radioisotopic analysis. Biotechnol Biofuels 9:51. https://doi.org/10.1186/s13068-016-0465-6
Maus I, Koeck DE, Cibis KG et al (2016a) Unravelling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates. Biotechnol Biofuels 9:171. https://doi.org/10.1186/s13068-016-0581-3
Maus I, Cibis KG, Bremges A et al (2016b) Genomic characterization of Defluviitoga tunisiensis L3, a key hydrolytic bacterium in a thermophilic biogas plant and its abundance as determined by metagenome fragment recruitment. J Biotechnol 232:50–60. https://doi.org/10.1016/j.jbiotec.2016.05.001
Maus I, Kim YS, Wibberg D et al (2017) Biphasic study to characterize agricultural biogas plants by high-throughput 16S rRNA gene amplicon sequencing and microscopic analysis. J Microbiol Biotechnol 27:321–334. https://doi.org/10.4014/jmb.1605.05083
Morgan XC, Huttenhower C (2012) Chapter 12: human microbiome analysis. PLoS Comput Biol. https://doi.org/10.1371/journal.pcbi.1002808
Moset V, PoulsenM WR et al (2015) Mesophilic versus thermophilic anaerobic digestion of cattle manure. Methane productivity and microbial ecology. Microb Biotechnol 8:787–800. https://doi.org/10.1111/1751-7915.12271
Mukhopadhyay A (2015) Tolerance engineering in bacteria for the production of advanced biofuels and chemicals. Trends Microbiol 23:498–508. https://doi.org/10.1016/j.tim.2015.04.008
Nasution O, Lee J, Srinivasa K et al (2015) Loss of Dfg5 glycosylphosphatidylinositol-anchored membrane protein confers enhanced heat tolerance in Saccharomyces cerevisiae. Environ Microbiol 17:2721–2734. https://doi.org/10.1111/1462-2920.12649
Nigam PS, Singh A (2011) Production of liquid biofuels from renewable resources. Prog Energy Combust Sci 37:52–68
Pabbathi NPP, Velidandi A, Tavarna T et al (2021) Role of metagenomics in prospecting novel endoglucanases, accentuating functional metagenomics approach in second-generation biofuel production: a review. Biomass Convers Biorefin 7:1–28. https://doi.org/10.1007/s13399-020-01186-y
Palackal N, Lyon CS, Zaidi S et al (2007) A multifunctional hybrid glycosyl hydrolase discovered in an uncultured microbial consortium from ruminant gut. Appl Microbiol Biotechnol 74:113–124. https://doi.org/10.1007/s00253-006-0645-6
Pang H, Zhang P, Duan CJ, Mo XC, Tang JL, Feng JX (2009) Identification of cellulase genes from the metagenomes of compost soils and functional characterization of one novel endoglucanase. Curr Microbiol 58:404–408. https://doi.org/10.1007/s00284-008-9346-y
Přibyl P, Cepák V, Zachleder V (2014) Oil overproduction by means of microalgae. In: Bajpai R, Prokop A, Zappi M (eds) Cultivation of cells and products, vol 1. Springer, Dordrecht, pp 241–273
Prasad RK, Chatterjee S, Mazumder PB et al (2019) Bioethanol production from waste lignocelluloses: a review on microbial degradation potential. Chemosphere 231:588–606. https://doi.org/10.1016/j.chemosphere.2019.05.142
Qiu Y-L, Hanada S, Ohashi A, Harada H, Kamagata Y, Sekiguchi Y (2008) Syntrophorhabdus aromaticivorans gen. Nov., sp. nov., the first cultured anaerobe capable of degrading phenol to acetate in obligate syntrophic associations with a hydrogenotrophic methanogen. Appl Environ Microbiol 74:2051–2058. https://doi.org/10.1128/AEM.02378-07
Raita M, Ibenegbu C, Champreda V, Leak DJ (2016) Production of ethanol by thermophilic oligosaccharide utilising Geobacillus thermoglucosidasius TM242 using palm kernel cake as a renewable feedstock. Biomass Bioenergy 95:45–54
Raschmanová H, Weninger A, Glieder A, Kovar K, Vogl T (2018) Implementing CRISPR-Cas technologies in conventional and non-conventional yeasts: current state and future prospects. Biotechnol Adv 36:641–665. https://doi.org/10.1016/j.biotechadv.2018.01.006
Rathour RK, Ahuja V, Bhatia RK, Bhatt AK (2018) Biobutanol: new era of biofuels. Int J Energy Res. https://doi.org/10.1002/er.4180
Rattanachomsri U, Kanokratana P, Eurwilaichitr L, Igarashi Y, Champreda V (2011) Culture-independent phylogenetic analysis of the microbial community in industrial sugarcane bagasse feedstock piles. Biosci Biotechnol Biochem 75:232–239. https://doi.org/10.1271/bbb.100429
Rodionova M, Poudyal R, Tiwari I et al (2017) Biofuel production: challenges and opportunities. Int J Hydrogen Energy 42:8450–8461
Rodriguez E (2016) Ethical issues in genome editing using Crispr/Cas9 system. J Clin Res Bioeth. https://doi.org/10.4172/2155-9627.1000266
Sakhuja D, Ghai H, Rathour RK, Kumar P, Bhatt AK, Bhatia RK (2021) Cost-effective production of biocatalysts using inexpensive plant biomass: a review. 3 Biotech 11(6):280. https://doi.org/10.1007/s13205-021-02847-z
Sarsekeyeva F, Zayadan BK, Usserbaeva A, Bedbenov VS, Sinetova MA, Los DA (2015) Cyanofuels: biofuels from cyanobacteria. Reality and perspectives. Photosynth Res 125:329–340. https://doi.org/10.1007/s11120-015-0103-3
Schnürer A (2016) Biogas production. Microbiology and technology. Adv Biochem Eng Biotechnol 156:195–234. https://doi.org/10.1007/10_2016_5
Shang M, Chan VJ, Wong DWS, Liao H (2018) A novel method for rapid and sensitive metagenomic activity screening. MethodsX 5:669–675. https://doi.org/10.1016/j.mex.2018.06.011
Shanmugam S, Ngo H-H, Wu Y-R (2019) Advanced CRISPR/Cas-based genome editing tools for microbial biofuels production: a review. Renew Energy. https://doi.org/10.1016/j.renene.2019.10.107
Shen CR, Liao JC (2008) Metabolic engineering of Escherichia coli for 1-butanol and 1-propanol production via the keto-acid pathways. Metab Eng 10:312–320. https://doi.org/10.1016/j.ymben.2008.08.001
Sheng J, Feng X (2015) Metabolic engineering of yeast to produce fatty acid-derived biofuels: bottlenecks and solutions. Front Microbiol 6:554. https://doi.org/10.3389/fmicb.2015.00554
Silva FT, Moreira LR, de Souza FJ, Batista FR, Cardoso VL (2016) Replacement of sugars to hydrogen production by Rhodobacter capsulatus using dark fermentation effluent as substrate. Bioresour Technol 200:72–80. https://doi.org/10.1016/j.biortech.2015.10.002
Simon C, Daniel R (2011) Metagenomic analyses: past and future trends. Appl Environ Microbiol 77:1153–1161. https://doi.org/10.1128/AEM.02345-10
Song Z, Chen L, Wang J, Lu Y, Jiang W, Zhang W (2014) A transcriptional regulator Sll0794 regulates tolerance to biofuel ethanol in photosynthetic Synechocystis sp. PCC 6803. Mol Cell Proteomics 13:3519–3532. https://doi.org/10.1074/mcp.M113.035675
Stolze Y, Zakrzewski M, Maus I et al (2015) Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions. Biotechnol Biofuels 8:14. https://doi.org/10.1186/s13068-014-0193-8
Stolze Y, Bremges A, Rumming M et al (2016) Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants. Biotechnol Biofuels 9:156. https://doi.org/10.1186/s13068-016-0565-3
Taylor MP, Eley KL, Martin S, Tuffin MI, Burton SG, Cowan DA (2009) Thermophilic ethanologenesis: future prospects for second-generation bioethanol production. Trends Biotechnol 27:398–405. https://doi.org/10.1016/j.tibtech.2009.03.006
Tiwari R, Nain L, Labrou NE, Shukla P (2018) Bioprospecting of functional cellulases from metagenome for second generation biofuel production: a review. Crit Rev Microbiol 44:244–257. https://doi.org/10.1080/1040841X.2017.1337713
Tkalec M, Štefanić PP, Cvjetko P, Šikić S, Pavlica M, Balen B (2014) The effects of cadmium-zinc interactions on biochemical responses in tobacco seedlings and adult plants. PLoS ONE 9:e87582. https://doi.org/10.1371/journal.pone.0087582
Ulaganathan K, Goud S, Reddy M, Kayalvili U (2017) Genome engineering for breaking barriers in lignocellulosic bioethanol production. Renew Sustain Energy Rev 74:1080–1107
Visioli LJ, Enzweiler H, Kuhn RC, Schwaab M, Mazutti MA (2014) Recent advances on biobutanol production. Sustain Chem Process 2:15
Wang F, Li F, Chen G, Liu W (2009) Isolation and characterization of novel cellulase genes from uncultured microorganisms in different environmental niches. Microbiol Res 164:650–657. https://doi.org/10.1016/j.micres.2008.12.002
Wang Y, Zhang ZT, Seo SO, Lynn P, Lu T, Jin YS, Blaschek HP (2016) Bacterial genome editing with CRISPR-Cas9: deletion, integration, single nucleotide modification, and desirable “Clean” mutant selection in Clostridium beijerinckii as an example. ACS Synth Biol 5:721–732. https://doi.org/10.1021/acssynbio.6b00060
Wang S, Dong S, Wang Y (2017a) Enhancement of solvent production by overexpressing key genes of the acetone-butanol-ethanol fermentation pathway in Clostridium saccharoperbutylacetonicum N1–4. Bioresour Technol 245:426–433. https://doi.org/10.1016/j.biortech.2017.09.024
Wang S, Dong S, Wang P, Tao Y, Wang Y (2017b) Genome Editing in Clostridium saccharoperbutylacetonicum N1–4 with the CRISPR-Cas9 System. Appl Environ Microbiol. https://doi.org/10.1128/AEM.00233-17
Wang H, Hart DJ, An Y (2019) Functional metagenomic technologies for the discovery of novel enzymes for biomass degradation and biofuel production. Bioenerg Res 12:457–470
Westbrook AW, Miscevic D, Kilpatrick S, Bruder MR, Moo-Young M, Chou CP (2019) Strain engineering for microbial production of value-added chemicals and fuels from glycerol. Biotechnol Adv 37:538–568. https://doi.org/10.1016/j.biotechadv.2018.10.006
Wong DD, Chan VJ, McCormack AA, Batt SB (2010) Cloning and characterization of an exoxylogucanase from rumenal microbial metagenome. Protein Pept Lett 17:803–808. https://doi.org/10.2174/092986610791190381
Xia J, Yang Y, Liu CG, Yang S, Bai FW (2019) Engineering Zymomonas mobilis for Robust Cellulosic Ethanol Production. Trends Biotechnol 37:960–972. https://doi.org/10.1016/j.tibtech.2019.02.002
Xing MN, Zhang XZ, Huang H (2012) Application of metagenomic techniques in mining enzymes from microbial communities for biofuel synthesis. Biotechnol Adv 30:920–929. https://doi.org/10.1016/j.biotechadv.2012.01.021
Yadav M, Vivekanand V (2019) Chaetomium globosporum: a novel laccase producing fungus for improving the hydrolyzability of lignocellulosic biomass. Heliyon. https://doi.org/10.1016/j.heliyon.2019.e01353
Yang S, Fei Q, Zhang Y, Contreras LM, Utturkar SM, Brown SD, Himmel ME, Zhang M (2016) Zymomonas mobilis as a model system for production of biofuels and biochemicals. Microb Biotechnol 9:699–717. https://doi.org/10.1111/1751-7915.12408
Yazdani SS, Gonzalez R (2008) Engineering Escherichia coli for the efficient conversion of glycerol to ethanol and co-products. Metab Eng 10:340–351. https://doi.org/10.1016/j.ymben.2008.08.005
Yu D, Kurola JM, Lähde K, Kymäläinen M, Sinkkonen A, Romantschuk M (2014) Biogas production and methanogenic archaeal community in mesophilic and thermophilic anaerobic co-digestion processes. J Environ Manag 143:54–60. https://doi.org/10.1016/j.jenvman.2014.04.025
Zabed H, Sahu J, Boyce A, Faruq G (2016) Fuel ethanol production from lignocellulosic biomass: an overview on feedstocks and technological approaches. Renew Sust Energy Rev 66:751–774
Zhang Q, Hu J, Lee D-J (2016) Biogas from anaerobic digestion processes. Research updates. Renew Energy 98:108–119
Zhang J, Yu L, Lin M, Yan Q, Yang ST (2017) n-Butanol production from sucrose and sugarcane juice by engineered Clostridium tyrobutyricum overexpressing sucrose catabolism genes and adhE2. Bioresour Technol 233:51–57. https://doi.org/10.1016/j.biortech.2017.02.079
Zhao X-Q, Zi L-H, Bai F-W, Lin H-L, Hao X-M, Yue G-J, Ho NW (2011) Bioethanol from lignocellulosic biomass. Biotechnology in China III: biofuels and Bioenergy. Springer, Berlin, pp 25–51
Zhou YJ, Buijs NA, Zhu Z, Qin J et al (2016) Production of fatty acid-derived oleochemicals and biofuels by synthetic yeast cell factories. Nat Commun 7:11709. https://doi.org/10.1038/ncomms11709
Ziganshin AM, Liebetrau J, Pröter J, Kleinsteuber S (2013) Microbial community structure and dynamics during anaerobic digestion of various agricultural waste materials. Appl Microbiol Biotechnol 97:5161–5174. https://doi.org/10.1007/s00253-013-4867-0
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
None.
Ethical statement
This manuscript does not include any human participants or animals studies.
Rights and permissions
About this article
Cite this article
Banu, J.R., Kumar, G. & Chattopadhyay, I. Management of microbial enzymes for biofuels and biogas production by using metagenomic and genome editing approaches. 3 Biotech 11, 429 (2021). https://doi.org/10.1007/s13205-021-02962-x
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s13205-021-02962-x