Abstract
A sustainable and rational use of the existing resources with limited generation of residues and using environmentally friendly processes is a current concern that is being addressed under the concepts of green chemistry and circular economy. Biotechnological processes, namely, the use of microorganisms and/or enzymes to cost-efficiently produce and convert renewable biological resources and waste streams into valuable products across several economic sectors (such as food, feed, bio-based products, and bioenergy), comprise a powerful alternative. The so-called circular bioeconomy is currently taking advantage of the recent developments in omics techniques, gene editing, systems, and synthetic biology, as well as of the novel technological developments of bioreactors and downstream processes. In addition, the potential of many existing residues from different sources, which remain to be mapped and thoroughly characterized, is largely unexplored and represents a great opportunity to design new products and processes, hence a great opportunity for the economy, for the environment, and ultimately for the society.
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
Abbreviations
- ATPS:
-
Aqueous two-phase systems
- CCR:
-
Carbon catabolite repression
- cmc:
-
Critical micelle concentration
- COS:
-
Chitooligosaccharides
- CRISPR-Cas9:
-
Clustered regularly interspaced short palindromic repeats-associated caspase 9 endonuclease
- CSL:
-
Corn step liquor
- DNA:
-
Deoxyribonucleic acid
- E24:
-
Emulsifying index
- epPCR:
-
Error-prone polymerase chain reaction
- FOS:
-
Fructooligosaccharides
- GOS:
-
Galactooligosaccharides
- IMO:
-
Isomaltooligosaccharides
- NGS:
-
New-generation sequencing
- OMW:
-
Olive mill wastewater
- PCR:
-
Polymerase chain reaction
- PEG:
-
Polyethylene glycol
- PUF:
-
Polyurethane foam
- RL:
-
Rhamnolipid
- SmF:
-
Submerged fermentation
- SSF:
-
Solid state fermentation
- ST:
-
Surface tension
- STR:
-
Stirred tank reactor
- XOS:
-
Xylooligosaccharides
References
Aachary AA, Gobinath D, Srinivasan K, Prapulla SG (2015) Protective effect of xylooligosaccharides from corncob on 1,2-dimethylhydrazine induced colon cancer in rats. Bioact Carbohydr Diet Fibre 5:146–152. https://doi.org/10.1016/j.bcdf.2015.03.004
Abdallah II, Pramastya H, van Merkerk R, Sukrasno QWJ (2019) Metabolic engineering of Bacillus subtilis toward taxadiene biosynthesis as the first committed step for taxol production. Front Microbiol 10:1–11. https://doi.org/10.3389/fmicb.2019.00218
Abdelaal AS, Jawed K, Yazdani SS (2019) CRISPR/Cas9-mediated engineering of Escherichia coli for n-butanol production from xylose in defined medium. J Ind Microbiol Biotechnol:1–11. https://doi.org/10.1007/s10295-019-02180-8
Abdel-Mawgoud AM, Aboulwafa MM, Hassouna NAH (2008) Optimization of surfactin production by Bacillus subtilis isolate BS5. Appl Biochem Biotechnol 150:305–325. https://doi.org/10.1007/s12010-008-8155-x
Abdullah R, Naeem N, Aftab M, Kaleem A, Iqtedar M, Iftikhar T, Naz S (2018) Enhanced production of alpha amylase by exploiting novel bacterial co-culture technique employing solid state fermentation. Iran J Sci Technol Trans A Sci 42:305–312. https://doi.org/10.1007/s40995-016-0015-x
Adamberg S, Sumeri I, Uusna R, Ambalam P, Kondepudi KK, Adamberg K, Wadström T, Ljungh A (2014) Survival and synergistic growth of mixed cultures of bifidobacteria and lactobacilli combined with prebiotic oligosaccharides in a gastrointestinal tract simulator. Microb Ecol Health Dis 25:1–9. https://doi.org/10.3402/mehd.v25.23062
Adhyaru DN, Bhatt NS, Modi HA, Divecha J (2016) Insight on xylanase from Aspergillus tubingensis FDHN1: production, high yielding recovery optimization through statistical approach and application. Biocatal Agric Biotechnol 6:51–57. https://doi.org/10.1016/j.bcab.2016.01.014
Aguiar-Pulido V, Huang W, Suarez-Ulloa V, Cickovski T, Mathee K, Narasimhan G (2016) Metagenomics, metatranscriptomics, and metabolomics approaches for microbiome analysis. Evol Bioinform Online 12(Suppl 1):5–16. https://doi.org/10.4137/EBO.S36436
Aguieiras ECG, De Barros DSN, Fernandez-Lafuente R, Freire DMG (2018) Production of lipases in cottonseed meal and application of the fermented solid as biocatalyst in esterification and transesterification reactions. Renew Energy 130:574–581. https://doi.org/10.1016/j.renene.2018.06.095
Aguilar O, Albiter V, Serrano-Carreón L, Rito-Palomares M (2006) Direct comparison between ion-exchange chromatography and aqueous two-phase processes for the partial purification of penicillin acylase produced by E. coli. J Chromatogr B 835:77–83. https://doi.org/10.1016/j.jchromb.2006.03.016
Aguilar A, Wohlgemuth R, Twardowski T (2018) Perspectives on bioeconomy. N Biotechnol 40:181–184. https://doi.org/10.1016/j.nbt.2017.06.012
Ahmad T, Singh RS, Gupta G, Sharma A, Kaur B (2019) Metagenomics in the search for industrial enzymes. In: Singhania RR, Pandey A, Larroche C (eds) Singh RS. Elsevier, Advances in enzyme technology, pp 419–451. https://doi.org/10.1016/B978-0-444-64114-4.00015-7
Ai H, Liu M, Yu P, Zhang S, Suo Y, Luo P, Li S, Wang J (2015) Improved welan gum production by Alcaligenes sp. ATCC31555 from pretreated cane molasses. Carbohydr Polym 129:35–43. https://doi.org/10.1016/j.carbpol.2015.04.0330
Akpinar O, Ak O, Kavas A, Bakir U, Yilmaz L (2007) Enzymatic production of xylooligosaccharides from cotton stalks. J Agric Food Chem 55:5544–5551. https://doi.org/10.1021/jf063580d
Al-Askar AA, Saber WIA, Ghoneem KM, Rashad YM (2018) Oxalic acid as the main molecule produced by Trichoderma asperellum MG323528 fermented on corn stover based medium. Biotechnology 17:95–103. https://doi.org/10.3923/biotech.2018.95.103
Al-Bhary SN, Al-Wahaibi YM, Elshafie AE, Al-Bemani AS, Joshi SJ, Al-Makhmari HS, Al-Sulaimani HS (2013) Biosurfactant production by Bacillus subtilis B20 using date molasses and its possible application in enhanced oil recovery. Int Biodeter Biodegr 81:141–146. https://doi.org/10.1016/j.ibiod.2012.01.006
Ali O, Moftah S, Grbav S (2012) Adding value to the oil cake as a waste from oil processing industry: production of lipase and protease by Candida utilis in solid state fermentation. Appl Biochem Biotechnol 166:348–364. https://doi.org/10.1007/s12010-011-9429-2
Allen EE, Banfield JF (2005) Community genomics in microbial ecology and evolution. Nat Rev Microbiol 3(6):489–498. https://doi.org/10.1038/nrmicro1157
Al-Wahaibi Y, Joshi S, Al-Bahry S, Elshafie A, Al-Bemani A, Shibulal B (2014) Biosurfactant production by Bacillus subtilis B30 and its application in enhancing oil recovery. Colloids Surf B Biointerfaces 114:324–333. https://doi.org/10.1016/j.colsurfb.2013.09.022
Ameen A, Raza S (2017) Metaproteomics approaches and techniques: a review. Int J Adv Sci Res Manag 3(5):49–51. https://doi.org/10.7439/ijasr.v3i5.4167
Amorim C, Silvério SC, Silva SP, Coelho E, Coimbra MA, Prather KLJ, Rodrigues LR (2018) Single-step production of arabino-xylooligosaccharides by recombinant Bacillus subtilis 3610 cultivated in brewers’ spent grain. Carbohydr Polym 199:546–554. https://doi.org/10.1016/j.carbpol.2018.07.017
Amorim C, Silvério SC, Gonçales RFS, Pinheiro AC, Silva SP, Coelho E, Coimbra MA, Prather KLJ, Rodrigues LR (2019a) Downscale fermentation for xylooligosaccharides production by recombinant Bacillus subtilis 3610. Carbohydr Polym 205:176–183. https://doi.org/10.1016/j.carbpol.2018.09.088
Amorim C, Silvério SC, Rodrigues LR (2019b) One-step process for producing prebiotic arabino-xylooligosaccharides from brewer’s spent grain employing Trichoderma species. Food Chem 270:86–94. https://doi.org/10.1016/j.foodchem.2018.07.080
Anandharamakrishnan C, Raghavendra SN, Barhate RS, Hanumesh U, Raghavarao KSMS (2005) Aqueous two-phase extraction for recovery of proteins from cheese whey. Food Bioprod Process 83:191–197. https://doi.org/10.1205/fbp.03403
Andri P, Meyer AS, Jensen PA, Dam-johansen K (2010) Reactor design for minimizing product inhibition during enzymatic lignocellulose hydrolysis: I Significance and mechanism of cellobiose and glucose inhibition on cellulolytic enzymes. Biotechnol Adv 28:308–324. https://doi.org/10.1016/j.biotechadv.2010.01.003
Antunes S, Freitas F, Alves VD, Grandfils C, Reis MAM (2015) Conversion of cheese whey into a fucose- and glucuronic acid-rich extracellular polysaccharide by Enterobacter A47. J Biotechnol 210:1–7. https://doi.org/10.1016/j.jbiotec.2015.05.013
Antunes S, Freitas F, Sevrin C, Grandfils C, Reis MAM (2017) Production of FucoPol by Enterobacter A47 using waste tomato paste by-product as sole carbon source. Bioresour Technol 227:66–73. https://doi.org/10.1016/j.biortech.2016.12.018
Aparna A, Srinikethan G, Smith H (2012) Production and characterization of biosurfactant produced by a novel Pseudomonas sp. 2B. Colloids Surf B Biointerfaces 95:23–29. https://doi.org/10.1016/j.colsurfb.2012.01.043
Aragon CC, Santos AF, Ruiz-Matute AI, Corzo N, Guisan JM, Monti R, Mateo C (2013) Continuous production of xylooligosaccharides in a packed bed reactor with immobilized–stabilized biocatalysts of xylanase from Aspergillus versicolor. J Mol Catal B: Enzym 98:8–14. https://doi.org/10.1016/j.molcatb.2013.09.017
Ashok A, Doriya K, Ram D, Rao M, Kumar DS (2018) Design of solid state bioreactor for industrial applications: an overview to conventional bioreactors. Biocatal Agric Biotechnol 9:11–18. https://doi.org/10.1016/j.bcab.2016.10.014
Ashwini A, Ramya HN, Ramkumar C, Reddy KR, Kulkarni RV, Abinaya V, Naveen S, Raghu AV (2019) Reactive mechanism and the applications of bioactive prebiotics for human health: review. J Microbiol Methods 159:128–137. https://doi.org/10.1016/j.mimet.2019.02.019
Assis DJ, Brandão LV, Costa LAS, Figueiredo TVB, Sousa LS, Padilha FF, Druzian JI (2014) A study of the effects of aeration and agitation on the properties and production of xanthan gum from crude glycerin derived from biodiesel using the response surface methodology. Appl Biochem Biotechnol 172:2769–2785. https://doi.org/10.1007/s12010-014-0723-7
Ávila SNS, Gutarra MLE, Fernandez-Lafuente R, Cavalcanti EDC, Freire DMG (2018) Multipurpose fixed-bed bioreactor to simplify lipase production by solid-state fermentation and application in biocatalysis. Biochem Eng J 144:1–7. https://doi.org/10.1016/j.bej.2018.12.024
Babu IS, Ramappa S, Mahesh DG, Kumari KS, Kumari KS, Subba G (2008) Optimization of medium constituents for the production of fructosyltransferase (ftase) by Bacillus subtilis using response surface methodology. Res J Microbiol 3:114–121. https://doi.org/10.3923/jm.2008.114.121
Bach E, Anna S’, Daroit DJ, Corrêa APF, Segalin J, Brandelli A (2012) Production, one-step purification, and characterization of a keratinolytic protease from Serratia marcescens P3. Process Biochem 47:2455–2462. https://doi.org/10.1016/j.procbio.2012.10.007
Badhwar P, Kumar P, Dubey KK (2019) Extractive fermentation for process integration and amplified pullulan production by A. pullulans in aqueous two-phase systems. Sci Rep 9:32. https://doi.org/10.1038/s41598-018-37314-y
Balderas-Hernández VE, Correia K, Mahadevan R (2018) Inactivation of the transcription factor mig1 (YGL035C) in Saccharomyces cerevisiae improves tolerance towards monocarboxylic weak acids: acetic, formic and levulinic acid. J Ind Microbiol Biotechnol 45:735–751. https://doi.org/10.1007/s10295-018-2053-1
Banik RM, Santhiagu A, Upadhayay SN (2007) Optimization of nutrients for gellan gum production by Sphingomonas paucimobilis ATCC-31461 in molasses based medium using response surface methodology. Bioresour Technol 98:792–797. https://doi.org/10.1016/j.biortech.2006.03.012
Barbosa MDFS, Silva DO, Pinheiro AJR, Guimarães WV, Borges AC (1985) Production of beta-d-galactosidase from Kluyveromyces fragilis grown in cheese whey. J Dairy Sci 68:1618–1623. https://doi.org/10.3168/jds.s0022-0302(85)81004-3
Barbosa R, Pereira MS, Jahn L (2019) Screening of Aspergillus, Bacillus and Trichoderma strains and influence of substrates on auxin and phytases production through solid-state fermentation. Biocatal Agric Biotechnol 19:101165. https://doi.org/10.1016/j.bcab.2019.101165
Batista-García RA, Sánchez-Carbente MR, Talia P, Jackson SA, O’Leary ND, Dobson ADW et al (2016) From lignocellulosic metagenomes to lignocellulolytic genes: trends, challenges and future prospects. Biofuels Bioprod Biorefin 10(6):864–882. https://doi.org/10.1002/bbb.1709
Béjà O, Aravind L, Koonin EV, Suzuki MT, Hadd A, Nguyen LP et al (2000) Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289(5486):1902–1906. https://doi.org/10.1126/science.289.5486.1902
Belo I, Pinheiro R, Mota M (2003) Fed-batch cultivation of Saccharomyces cerevisiae in a hyperbaric bioreactor. Biotechnol Prog 19:665–671. https://doi.org/10.1021/bp0257067
Benincasa M, Accorsini FR (2008) Pseudomonas aeruginosa LBI production as an integrated process using the wastes from sunflower-oil refining as a substrate. Bioresour Technol 99:3843–3849. https://doi.org/10.1016/j.biortech.2007.06.048
Berini F, Casciello C, Marcone GL, Marinelli F (2017) Metagenomics: novel enzymes from non-culturable microbes. FEMS Microbiol Lett 364(21). https://doi.org/10.1093/femsle/fnx211
Bi P-Y, Li D-Q, Dong L-R (2009) A novel technique for the separation and concentration of penicillin G from fermentation broth: aqueous two-phase flotation. Sep Purif Technol 69:205–209. https://doi.org/10.1016/j.seppur.2009.07.019
Bi P-Y, Dong H-R, Yuan Y-C (2010) Application of aqueous two-phase flotation in the separation and concentration of puerarin from Puerariae extract. Sep Purif Technol 75:402–406. https://doi.org/10.1016/j.seppur.2010.09.010
Bi P-Y, Chang L, Mu Y-L, Liu J-Y, Wu Y, Geng X, Wei Y (2013) Separation and concentration of baicalin from Scutellaria Baicalensis Georgi extract by aqueous two-phase flotation. Sep Purif Technol 116:454–457. https://doi.org/10.1016/j.seppur.2013.06.024
Bian J, Peng P, Peng F, Xiao X, Xu F, Sun RC (2014) Microwave-assisted acid hydrolysis to produce xylooligosaccharides from sugarcane bagasse hemicelluloses. Food Chem 156:7–13. https://doi.org/10.1016/j.foodchem.2014.01.112
Bockmühl D, Jassoy C, Nieveler S, Scholtysse R, Wadl A, Waldmann-Laue M (2007) Prebiotic cosmetics: an alternative to antibacterial products. Int J Cosmet Sci 29:63–64. https://doi.org/10.1111/j.1467-2494.2007.00355_2.x
Boland MJ, Hesselink PGM, Papamichael N, Hustedt H (1991) Extractive purification of enzymes from animal tissue using two phase systems: pilot scale studies. J Biotechnol 19:19–34. https://doi.org/10.1016/0168-1656(91)90072-4
Bommarius AS, Blum JK, Abrahamson MJ (2011) Status of protein engineering for biocatalysts: how to design an industrially useful biocatalyst. Curr Opin Chem Biol 15:194–200. https://doi.org/10.1016/j.cbpa.2010.11.011
Bowen CH, Dai B, Sargent CJ, Bai W, Ladiwala P, Feng H, Huang W, Kaplan DL, Galazka JM, Zhang F (2018) Recombinant spidroins fully replicate primary mechanical properties of natural spider silk. Biomacromolecules 19:3853–3860. https://doi.org/10.1021/acs.biomac.8b00980
Bragg L, Tyson GW (2014) Metagenomics using next-generation sequencing. Methods Mol Biol 1096:183–201. https://doi.org/10.1007/978-1-62703-712-9_15
Caballero A, Ramos JL (2017) Enhancing ethanol yields through D-xylose and L-arabinose co-fermentation after construction of a novel high efficient L-arabinose-fermenting Saccharomyces cerevisiae strain. Microbiology 163:442–452. https://doi.org/10.1099/mic.0.000437
Caramihai M, Severin I (2013) Biomass now—sustainable growth and use. In: IntechOpen (ed) Bioprocess modeling and control
Cardoso B, Silvério SC, Abrunhosa L, Teixeira JA, Rodrigues LR (2017) β-galactosidase from Aspergillus lacticoffeatus: a promising biocatalyst for the synthesis of novel prebiotics. Int J Food Microbiol 257:67–74. https://doi.org/10.1016/j.ijfoodmicro.2017.06.013
Carvalho AFA, Neto PO, Silva DF, Pastore GM (2013) Xylo-oligosaccharides from lignocellulosic materials: chemical structure, health benefits and production by chemical and enzymatic hydrolysis. Food Res Int 51:75–85. https://doi.org/10.1016/j.foodres.2012.11.021
Castilla IA, Woods DF, Reen FJ, O'Gara F (2018) Harnessing marine biocatalytic reservoirs for green chemistry applications through metagenomic technologies. Mar Drugs 16(7). https://doi.org/10.3390/md16070227
Castro AM, Castilho LR, Freire DMG (2015) Performance of a fixed-bed solid-state fermentation bioreactor with forced aeration for the production of hydrolases by Aspergillus awamori. Biochem Eng J 93:303–308. https://doi.org/10.1016/j.bej.2014.10.016
Cavalcanti EDAC, Gutarra MLE, Freire DMG, Castilho LDR, Sant’Anna Júnior GL (2005) Lipase production by solid-state fermentation in fixed-bed bioreactors. Brazilian Arch Biol Technol 48:79–84. https://doi.org/10.1590/S1516-89132005000400010
Cerda A, Gea T, Vargas-garcía MC, Sánchez A (2017) Towards a competitive solid state fermentation: cellulases production from coffee husk by sequential batch operation and role of microbial diversity. Sci Total Environ 589:56–65. https://doi.org/10.1016/j.scitotenv.2017.02.184
Chae TU, Choi SY, Ryu JY, Lee SY (2018) Production of ethylene glycol from xylose by metabolically engineered Escherichia coli. AIChE J 64:4193–4200. https://doi.org/10.1002/aic.16339
Chapla D, Pandit P, Shah A (2012) Production of xylooligosaccharides from corncob xylan by fungal xylanase and their utilization by probiotics. Bioresour Technol 115:215–221. https://doi.org/10.1016/j.biortech.2011.10.083
Cheirsilp B, Kitcha S (2015) Solid state fermentation by cellulolytic oleaginous fungi for direct conversion of lignocellulosic biomass into lipids: fed-batch and repeated-batch fermentations. Ind Crop Prod 66:73–80. https://doi.org/10.1016/j.indcrop.2014.12.035
Chen K, Arnold FH (1993) Tuning the activity of an enzyme for unusual environments: Sequential random mutagenesis of subtilisin E for catalysis in dimethylformamide. Proc Natl Acad Sci U S A 90:5618–5622. https://doi.org/10.1073/pnas.90.12.5618
Chen JYH-P, Wang C-H (1991) Lactose hydrolysis by β-galactosidase in aqueous two-phase systems. J Ferment Bioeng 71:168–175. https://doi.org/10.1016/0922-338X(91)90104-O
Chen C, Sun N, Li D, Long S, Tang X, Xiao G, Wang L (2018) Optimization and characterization of biosurfactant production from kitchen waste oil using Pseudomonas aeruginosa. Environ Sci Pollut Res Int 25:14934–14943. https://doi.org/10.1007/s11356-018-1691-1
Chen C, Lin J, Wang W, Huang H, Li S (2019a) Cost-effective production of surfactin from xylose-rich corncob hydrolysate using Bacillus subtilis BS-37. Waste Biomass Valor 10:341–347. https://doi.org/10.1007/s12649-017-0052-5
Chen M, Lu J, Cheng Y, Li Q, Wang H (2019b) Novel process for the coproduction of xylo-oligosaccharide and glucose from reed scraps of reed pulp mill. Carbohydr Polym 215:82–89. https://doi.org/10.1016/j.carbpol.2019.03.068
Chew PL, Annuar MSM, Show PL, Ling TC (2015) Extractive bioconversion of poly-ε-caprolactone by Burkholderia cepacia lipase in aqueous two-phase system. Biochem Eng J 101:9–17. https://doi.org/10.1016/j.bej.2015.04.015
Chisti MY, Moo-Young M (1987) Airlift reactors: characteristics, applications and design considerations. Chem Eng Commun 60:195–242. https://doi.org/10.1080/00986448708912017
Cláudio AFM, Marques CFC, Boal-Palheiros I, Freire MG, Coutinho JAP (2014) Development of back-extraction and recyclability routes for ionic-liquid-bases aqueous two-phase systems. Green Chem 16:259–268. https://doi.org/10.1039/c3gc41999a
Cordisco E, Haidar CN, Coscueta ER, Nerli BB, Malpiedi LP (2016) Integrated extraction and purification of soy isoflavones by using aqueous micellar systems. Food Chem 213:514–520. https://doi.org/10.1016/j.foodchem.2016.07.001
Courtin CM, Swennen K, Verjans P, Delcour JA (2009) Heat and pH stability of prebiotic arabinoxylooligosaccharides, xylooligosaccharides and fructooligosaccharides. Food Chem 112:831–837. https://doi.org/10.1016/j.foodchem.2008.06.039
Couto MR, Rodrigues JL, Rodrigues LR (2017) Optimization of fermentation conditions for the production of curcumin by engineered Escherichia coli. J R Soc Interface 14:1–8. https://doi.org/10.1098/rsif.2017.0470
Couto MR, Gudiña EJ, Ferreira D, Teixeira JA, Rodrigues LR (2019) The biopolymer produced by Rhizobium viscosum CECT 908 is a promising agent for application in microbial enhanced oil recovery. N Biotechnol 49:144–150. https://doi.org/10.1016/j.nbt.2018.11.002
Cruz JM, Hughes C, Quilty B, Montagnolli RN, Bidoia ED (2018) Agricultural feedstock supplemented with manganese for biosurfactant production by Bacillus subtilis. Waste Biomass Valor 9:613–618. https://doi.org/10.1007/s12649-017-0019-6
Cunha JT, Soares PO, Romaní A, Thevelein JM, Domingues L (2019) Xylose fermentation efficiency of industrial Saccharomyces cerevisiae yeast with separate or combined xylose reductase/xylitol dehydrogenase and xylose isomerase pathways. Biotechnol Biofuels 12:1–14. https://doi.org/10.1186/s13068-019-1360-8
Dahiya S, Kumar AN, Sravan JS, Chatterjee S, Sarkar O, Mohan SV (2018) Food waste biorefinery: sustainable strategy for circular bioeconomy. Bioresour Technol 248:2–12. https://doi.org/10.1016/j.biortech.2017.07.176
Darabzadeh N, Hamidi-Esfahani Z, Hejazi P (2019) Optimization of cellulase production under solid-state fermentation by a new mutant strain of Trichoderma reesei. Food Sci Nutr 7:572–578. https://doi.org/10.1002/fsn3.852
Das K, Mukherjee AK (2007) Comparison of lipopeptide biosurfactants production by Bacillus subtilis strains in submerged and solid state fermentation systems using a cheap carbon source: some industrial applications of biosurfactants. Process Biochem 42:1191–1199. https://doi.org/10.1016/j.procbio.2007.05.011
De Wit M, Faaij A (2010) European biomass resource potential and costs. Biomass Bioenergy 34(2):188–202. https://doi.org/10.1016/j.biombioe.2009.07.011
DeCastro ME, Rodriguez-Belmonte E, Gonzalez-Siso MI (2016) Metagenomics of thermophiles with a focus on discovery of novel thermozymes. Front Microbiol 7(1521). https://doi.org/10.3389/fmicb.2016.01521
Delmont TO, Robe P, Cecillon S, Clark IM, Constancias F, Simonet P et al (2011) Accessing the soil metagenome for studies of microbial diversity. Appl Environ Microbiol 77(4):1315–1324. https://doi.org/10.1128/AEM.01526-10
DeLong EF (2005) Microbial community genomics in the ocean. Nat Rev Microbiol 3(6):459–469. https://doi.org/10.1038/nrmicro1158
Denard CA, Ren H, Zhao H (2015) Improving and repurposing biocatalysts via directed evolution. Curr Opin Chem Biol 25:55–64. https://doi.org/10.1016/j.cbpa.2014.12.036
Devesa-Rey R, Vecino X, Varela-Alende JL, Barral MT, Cruz JM, Moldes AB (2011) Valorization of winery wastes vs. the costs of not recycling. Waste Manag 31(11):2327–2335. https://doi.org/10.1016/j.wasman.2011.06.001
Dhillon GS, Oberoi HS, Kaur S, Bansal S, Brar SK (2011) Value-addition of agricultural wastes for augmented cellulase and xylanase production through solid-state tray fermentation employing mixed-culture of fungi. Ind Crop Prod 34:1160–1167. https://doi.org/10.1016/j.indcrop.2011.04.001
Doudna JA, Charpentier E (2014) The new frontier of genome engineering with CRISPR-Cas9. Science 346(6213):1258096. https://doi.org/10.1126/science.1258096
Duarte C, Gudiña EJ, Lima CF, Rodrigues LR (2014) Effects of biosurfactants on the viability and proliferation of human breast cancer cells. AMB Express 4:40. https://doi.org/10.1186/s13568-014-0040-0
Durand A (2003) Bioreactor designs for solid state fermentation. Biochem Eng J 13:113–125. https://doi.org/10.1016/S1369-703X(02)00124-9
Dursun D, Dalgiç AC (2016) Optimization of astaxanthin pigment bioprocessing by four different yeast species using wheat wastes. Biocatal Agric Biotechnol 7:1–6. https://doi.org/10.1016/j.bcab.2016.04.006
Eiteman MA, Lee SA, Altman E (2008) A co-fermentation strategy to consume sugar mixtures effectively. J Biol Eng 2:1–8. https://doi.org/10.1186/1754-1611-2-3
Elbersen B, Startisky I, Hengeveld G, Schelhaas MJ, Naeff H (2012) Atlas of EU biomass potentials—deliverable 3.3: spatially detailed and quantified overview of EU biomass potential taking into account the main criteria determining biomass availability from different sources, IEE 08 653 SI2. 529 241.
Elegbede JA, Lateef A (2017) Valorization of corn-cob by fungal isolates for production of xylanase in submerged and solid state fermentation media and potential biotechnological applications. Waste and Biomass Valorization 9:1273–1287. https://doi.org/10.1007/s12649-017-9932-y
El-Housseiny GS, Aboshanab KM, Aboulwafa MM, Hassouna NA (2016) Optimization of rhamnolipid production by Pseudomonas aeruginosa isolate P6. J Surfactant Deterg 19:943–955. https://doi.org/10.1007/s11743-016-1845-4
El-Shishtawy RM, Mohamed SA, Asiri AM, Gomaa AM, Ibrahim IH (2014) Solid fermentation of wheat bran for hydrolytic enzymes production and saccharification content by a local isolate Bacillus megatherium. BMC Biotechnol 14:1–8. https://doi.org/10.1186/1472-6750-14-29
de Faria AF, Teodoro-Martínez DS, de Oliveira Barbosa GN, Vaz BG, Silva IS, García JS, Tótola MR, Eberlin MN, Grossman M, Alves OL, Durrant LR (2011) Production and structural characterization of surfactin (C14/Leu7) produced by Bacillus subtilis isolate LSFM-05 grown on raw glycerol from the biodiesel industry. Process Biochem 46:1951–1957. https://doi.org/10.1016/j.procbio.2011.07.001
Farinas CS (2015) Developments in solid-state fermentation for the production of biomass-degrading enzymes for the bioenergy sector. Renew Sustain Energy Rev 52:179–188. https://doi.org/10.1016/j.rser.2015.07.092
Faryar R, Linares-Pastén JA, Immerzeel P, Mamo G, Andersson M, Stålbrand H, Karlsson EN (2015) Production of prebiotic xylooligosaccharides from alkaline extracted wheat straw using the K80R-variant of a thermostable alkali-tolerant xylanase. Food Bioprod Process 93:1–10. https://doi.org/10.1016/j.fbp.2014.11.004
Fernandes MLP, Jorge JA, Henrique LHS (2017) Characterization of an extracellular β-D-fructofuranosidase produced by Aspergillus niveus during solid-state fermentation (SSF) of cassava husk. J Food Biochem 42:1–10. https://doi.org/10.1111/jfbc.12443
Ferreira A, Rocha F, Mota A, Teixeira JA (2017) Characterization of industrial bioreactors: mixing, heat, and mass transfer. In: Larroche C, Sanroman M, Du G, Pandey A (eds) Current developments in biotechnology and bioengineering: bioprocesses, bioreactors and controls, Elsevier B.V., pp 563–592
Flores AD, Ayla EZ, Nielsen DR, Wang X (2019) Engineering a synthetic, catabolically-orthogonal co-culture cystem for enhanced conversion of lignocellulose-derived sugars to ethanol. ACS Synth Biol 8:1089–1099. https://doi.org/10.1021/acssynbio.9b00007
de França IWL, Lima AP, Lemos JAM, Lemos CGF, Melo VMM, Santana HB, Gonçalves LRB (2015) Production of a biosurfactant by Bacillus subtilis ICA56 aiming bioremediation of impacted soils. Catal Today 255:10–15. https://doi.org/10.1016/j.cattod.2015.01.046
Gadhe A, Mudliar S, Pandey R, Elumalai S, Satpute D (2011) Statistical optimization of process parameters for the production of vanillic acid by solid-state fermentation of groundnut shell waste using response surface methodology. J Chem Technol Biotechnol 86:1535–1541. https://doi.org/10.1002/jctb.2671
Ganguly S, Nandi S (2015) Process optimization of lipase catalyzed synthesis of diesters in a packed bed reactor. Biochem Eng J:1–4. https://doi.org/10.1016/j.bej.2015.03.020
Gaurav, SG (2017) Prebiotics: ingredients, applications and global markets BCC research. https://www.bccresearch.com/market-research/food-and-beverage/prebiotics-ingredients-applications-and-global-markets.html. Accessed 21 Apr 2019.
George S, Jayachandran K (2009) Analysis of rhamnolipid biosurfactants produced through submerged fermentation using orange fruit peelings as sole carbon source. Appl Biochem Biotechnol 158:694–705. https://doi.org/10.1007/s12010-008-8337-6
George S, Jayachandran K (2013) Production and characterization of rhamnolipid biosurfactant from waste frying coconut oil using a novel Pseudomonas aeruginosa D. J Appl Microbiol 114:373–383. https://doi.org/10.1111/jam.12069
Gibson GR, Roberfroid MB (1995) Dietary modulation of the human colonic microbiota:introducing the concept of prebiotics. J Nutr 125:1401–1412. https://doi.org/10.1093/jn/125.6.1401
Gibson GR, Hutkins R, Sanders ME, Prescott SL, Reimer RA, Salminen SJ, Scott K, Stanton C, Swanson KS, Cani PD, Verbeke K, Reid G (2017) The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics. Nat Rev Gastroenterol Hepatol 14:491–502. https://doi.org/10.1038/nrgastro.2017.75
Global Market Insights, Inc. (2017) Prebiotics market size by ingredient (inulin, GOS, FOS, MOS), by application (animal feed, food & beverages [dairy, cereals, baked goods, fermented meat, dry foods], dietary supplements [food, nutrition, infant formulations]), industry analysis report, regional outlook, application potential, price trends, competitive market share & forecast, 2017–2024. https://www.gminsights.com/industry-analysis/prebiotics-market. Accessed 23 June 2019
Göksungur Y, Uzunogullari P, Dagbagli S (2011) Optimization of pullulan production from hydrolysed potato starch waste by response surface methodology. Carbohydr Polym 83:1330–1337. https://doi.org/10.1016/j.carbpol.2010.09.047
Goodwin S, McPherson JD, McCombie WR (2016) Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 17(6):333–351. https://doi.org/10.1038/nrg.2016.49
Görke B, Stülke J (2008) Carbon catabolite repression in bacteria: many ways to make the most out of nutrients. Nat Rev Microbiol 6:613–624. https://doi.org/10.1038/nrmicro1932
Graedel TE (2002) Green chemistry and sustainable development. In: Clark J, Macquarrie DJ (eds) Handbook of green chemistry and technology. Blackwell Science Ltd., Oxford, pp 56–61
Grand Market Insights Research (2018) Biosurfactants market worth over $2.7 bn by 2024. https://www.gminsights.com/pressrelease/biosurfactants-market-size. Accessed 8 June 2019.
Gudiña EJ, Rangarajan V, Sen R, Rodrigues LR (2013) Potential therapeutic applications of biosurfactants. Trends Pharmacol Sci 34:667–675. https://doi.org/10.1016/j.tips.2013.10.002
Gudiña EJ, Rodrigues AI, Alves E, Domingues MR, Teixeira JA, Rodrigues LR (2015a) Bioconversion of agro-industrial by-products in rhamnolipids toward applications in enhanced oil recovery and bioremediation. Bioresour Technol 177:87–93. https://doi.org/10.1016/j.biortech.2014.11.069
Gudiña EJ, Fernandes EC, Rodrigues AI, Teixeira JA, Rodrigues LR (2015b) Biosurfactant production by Bacillus subtilis using corn step liquor as culture medium. Front Microbiol 6:59. https://doi.org/10.3389/fmicb.2015.00059
Gudiña EJ, Rodrigues AI, de Freitas V, Azevedo Z, Teixeira JA, Rodrigues LR (2016) Valorization of agro-industrial wastes towards the production of rhamnolipids. Bioresour Technol 212:144–150. https://doi.org/10.1016/j.biortech.2016.04.027
Gullon P, Romani A, Vila C, Garrote G, Parajo JC (2012) Potential of hydrothermal treatments in lignocellulose biorefineries. Biofuels Bioprod Biorefin 6(2):219–232. https://doi.org/10.1002/bbb.339
Gunasekar V, Reshma KR, Treesa G, Gowdhaman D, Ponnusami V (2014) Xanthan from sulphuric acid treated tapioca pulp: influence of acid concentration on xanthan fermentation. Carbohydr Polym 102:669–673. https://doi.org/10.1016/j.carbpol.2013.11.006
Guneser O, Demirkol A, Karagul Y, Ozmen S, Isleten M, Elibol M (2017) Biotechnology and industrial microbiology production of flavor compounds from olive mill waste by Rhizopus oryzae and Candida tropicalis. Braz J Microbiol 48:275–285. https://doi.org/10.1016/j.bjm.2016.08.003
Gurpilhares DB, Pessoa A, Roberto IC (2015) Process integration for the disruption of Candida guilliermondii cultivated in rice straw hydrolysate and recovery of glucose-6-phosphate dehydrogenase by aqueous two-phase systems. Appl Biochem Biotechnol 176:1596–1612. https://doi.org/10.1007/s12010-015-1664-5
Haba E, Pinazo A, Jauregui O, Espuny MJ, Infante MR, Manresa A (2003) Physicochemical characterization and antimicrobial properties of rhamnolipids produced by Pseudomonas aeruginosa 47T2 NCBIM 40044. Biotechnol Bioeng 81:316–322. https://doi.org/10.1002/bit.10474
Hahn-Hägerdal B, Karhumaa K, Jeppsson M, Gorwa-Grauslund MF (2007) Metabolic engineering for pentose utilization in Saccharomyces cerevisiae. In: Olsson L (ed) Biofuels. Springer, New York, pp 147–177
Halperin SO, Tou CJ, Wong EB, Modavi C, Schaffer DV, Dueber JE (2018) CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window. Nature 560:248–252. https://doi.org/10.1038/s41586-018-0384-8
Hamrouni R, Molinet J, Miché L, Carboué Q, Dupuy N, Masmoudi A, Roussos S (2019) Production of coconut aroma in solid-state cultivation: screening and identification of Trichoderma strains for 6-pentyl-alpha-pyrone and conidia production. J Chem. https://doi.org/10.1155/2019/8562384
Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5(10):245–249
Hector RE, Mertens JA (2017) A synthetic hybrid promoter for xylose-regulated control of gene expression in Saccharomyces yeasts. Mol Biotechnol 59:24–33. https://doi.org/10.1007/s12033-016-9991-5
Hu Y, Du C, Leu S, Jing H, Li X, Sze C, Lin K (2018) Valorisation of textile waste by fungal solid state fermentation: An example of circular waste-based biorefinery. Resour Conserv Recycl 129:27–35. https://doi.org/10.1016/j.resconrec.2017.09.024
Hutkins RW, Krumbeck JA, Bindels LB, Cani PD, Fahey G, Goh YJ, Sanders ME (2016) Prebiotics: why definitions matter. Curr Opin Biotechnol 37:1–7. https://doi.org/10.1016/j.copbio.2015.09.001
Illanes A, Cauerhff A, Wilson L, Castro GR (2012) Recent trends in biocatalysis engineering. Bioresour Technol 115:48–57. https://doi.org/10.1016/j.biortech.2011.12.050
Iqbal M, Tao Y, Xie S, Zhu Y, Chen D, Wang X, Huang L, Peng D, Sattar A, Shabbir MAB, Hussain HI, Ahmed S, Yuan Z (2016) Aqueous two-phase system (ATPS): an overview and advances in its applications. Biol Proced Online 18:18. https://doi.org/10.1186/s12575-016-0048-8
Jiang B, Na J, Wang L, Li D, Liu C, Feng Z (2019) Eco-innovation in reusing food by-products: separation of ovalbumin from salted egg white aqueous two-phase system of PEG 1000/(NH4)2SO4. Polymers 11:238. https://doi.org/10.3390/polym11020238
Jiao JY, Wang HX, Zeng Y, Shen YM (2006) Enrichment for microbes living in association with plant tissues. J Appl Microbiol 100(4):830–837. https://doi.org/10.1111/j.1365-2672.2006.02830.x
Jiménez-Quero A, Pollet E, Zhao M, Marchioni E, Averous L, Phalip V (2017) Fungal fermentation of lignocellulosic biomass for itaconic and fumaric acid production. J Microbiol Biotechnol 27:1–8. https://doi.org/10.4014/jmb.1607.07057
Joshi S, Bharucha C, Jha S, Yadav S, Nerurkar A, Desai AJ (2008) Biosurfactant production using molasses and whey under thermophilic conditions. Bioresour Technol 99:195–199. https://doi.org/10.1016/j.biortech.2006.12.010
Jullesson D, David F, Pfleger B, Nielsen J (2015) Impact of synthetic biology and metabolic engineering on industrial production of fine chemicals. Biotechnol Adv 33:1395–1402. https://doi.org/10.1016/j.biotechadv.2015.02.011
Jung I-Y, Lee J-W, Min W-K, Park Y-C, Seo J-H (2015) Simultaneous conversion of glucose and xylose to 3-hydroxypropionic acid in engineered Escherichia coli by modulation of sugar transport and glycerol synthesis. Bioresour Technol 198:709–716. https://doi.org/10.1016/j.biortech.2015.09.079
Kalaivani S, Regupathi I (2013) Partitioning studies of α-lactalbumin in environmental friendly poly(ethylene glycol)-citrate salt aqueous two phase systems. Bioprocess Biosyst Eng 36:1475–1483. https://doi.org/10.1007/s00449-013-0910-x
Kalogiannis S, Iakovidou G, Liakopoulou-Kyrikiades M, Kyriakidis A, Skaracis GN (2003) Optimization of xanthan gum production by Xanthomonas campestris grown in molasses. Process Biochem 39:249–256. https://doi.org/10.1016/S0032-9592(03)00067-0
Kaur P, Ghoshal G, Jain A (2019) Bio-utilization of fruits and vegetables waste to produce β-carotene in solid-state fermentation: characterization and antioxidant activity. Process Biochem 76:155–164. https://doi.org/10.1016/j.procbio.2018.10.007
Khanahmadi M, Roostaazad R, Safekordi A, Bozorgmehri R, Mitchell DA (2004) Investigating the use of cooling surfaces in solid-state fermentation tray bioreactors: modelling and experimentation. J Chem Technol Biotechnol 79:1228–1242. https://doi.org/10.1002/jctb.1117
Khanahmadi M, Roostaazad R, Mitchell DA, Miranzadeh M, Bozorgmehri R, Safekordi A (2006) Bed moisture estimation by monitoring of air stream temperature rise in packed-bed solid-state fermentation. Chem Eng Sci 61:5654–5663. https://doi.org/10.1016/j.ces.2006.04.039
Khanahmadi M, Arezi I, Amiri M, Miranzadeh M (2018) Bioprocessing of agro-industrial residues for optimization of xylanase production by solid- state fermentation in flask and tray bioreactor. Biocatal Agric Biotechnol 13:272–282. https://doi.org/10.1016/j.bcab.2018.01.005
Kim J-H, 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 88:1077–1085. https://doi.org/10.1007/s00253-010-2839-1
Kim HJ, Jeong H, Lee SJ (2018) Synthetic biology for microbial heavy metal biosensors. Anal Bioanal Chem 410:1191–1203. https://doi.org/10.1007/s00216-017-0751-6
Ko KC, Lee JH, Han Y, Choi JH, Song JJ (2013) A novel multifunctional cellulolytic enzyme screened from metagenomics resources representing ruminal bacteria. Biochem Biophys Res Commun 441:567–572. https://doi.org/10.1016/j.bbrc.2013.10.120
Kumar V, Satyanarayana T (2011) Applicability of thermo-alkali stable and cellulose free xylanase from a novel thermo-halo-alkaliphilic Bacillus haloduransin producing xyloligosaccharides. Biotechnol Lett 33:2279–2285. https://doi.org/10.1007/s10529-011-0698-1
Kumar V, Satyanarayana T (2015) Generation of xylooligosaccharides from microwave irradiated agroresidues using recombinant thermo-alkali-stable endoxylanase of the polyextremophilic bacterium Bacillus halodurans expressed in Pichia pastoris. Bioresour Technol 179:382–389. https://doi.org/10.1016/j.biortech.2014.12.049
Kumar D, Jain VK, Shanker G, Sri A (2003) Utilisation of fruits waste for citric acid production by solid state fermentation. Process Biochem 38:1725–1729. https://doi.org/10.1016/S0032-9592(02)00253-4
Kumar B, Bhardwaj N, Alam A, Agrawal K, Prasad H, Verma P (2018) Production, purification and characterization of an acid/alkali and thermo tolerant cellulase from Schizophyllum commune NAIMCC-F-03379 and its application in hydrolysis of lignocellulosic wastes. AMB Expr 8:173. https://doi.org/10.1186/s13568-018-0696-y
Kung SH, Lund S, Murarka A, McPhee D, Paddon CJ (2018) Approaches and recent developments for the commercial production of semi-synthetic artemisinin. Front Plant Sci 9:1–7. https://doi.org/10.3389/fpls.2018.00087
van de Lagemaat J, Pyle DL (2004) Solid-state fermentation: a continuous process for fungal tannase production. Biotechnol Bioeng 87:924–929. https://doi.org/10.1002/bit.20206
Lan G, Fan Q, Liu Y, Chen C, Li G, Liu Y, Yin X (2015) Rhamnolipid production from waste cooking oil using Pseudomonas SWP-4. Biochem Eng J 101:44–54. https://doi.org/10.1016/j.bej.2015.05.001
Lawford HG, Rousseau JD (2002) Performance testing of Zymomonas mobilis metabolically engineered for cofermentation of glucose, xylose, and arabinose. In: Finkelstein M, McMillan JD, Davison BH (eds) Biotechnology for fuels and chemicals. Humana Press, New York, pp 429–448
Lee SK, Chou H, Ham TS, Lee TS, Keasling JD (2008) Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels. Curr Opin Biotechnol 19:556–563. https://doi.org/10.1016/j.copbio.2008.10.014
Lee SY, Khoiroh I, Ooi CW, Ling TC, Show PL (2017) Recent advances in protein extraction using ionic liquid-based aqueous two-phase systems. Sep Purif Rev 46:291–304. https://doi.org/10.1080/15422119.2017.1279628
Lemes CL, Silvério SC, Rodrigues S, Rodrigues LR (2019) Integrated strategy for purification of esterase from Aureobasidium pullulans. Sep Purif Technol 209:409–418. https://doi.org/10.1016/j.seppur.2018.07.062
Leong YK, Lan JC-W, Loh H-S, Ling TC, Ooi CW, Show PL (2016) Thermoseparating aqueous two-phase systems: recent trends and mechanisms. J Sep Sci 39:640–647. https://doi.org/10.1002/jssc.201500667
Leong HY, Ooi CW, Law CL, Julkifle AL, Ling TC, Show PL (2018) Application of liquid biphasic flotation for betacyanins extraction from peel and flesh of Hylocereus polyrhizus and antioxidant activity evaluation. Sep Purif Technol 201:156–166. https://doi.org/10.1016/j.seppur.2018.03.008
Leong YK, Show P-L, Lan JC-W, Krishnamoorthy R, Chu D-T, Nagarajan D, Yen H-W, Chang J-S (2019) Application of thermo-separating aqueous two-phase system in extractive bioconversion of polyhydroxyalkanoates by Cupriavidus necator H16. Bioresour Technol 287:121474. https://doi.org/10.1016/j.biortech.2019.121474
Léon-González G, González-Valdez J, Mayolo-Deloisa R-PM (2016) Intensified fractionation of brewery yeast waste for the recovery of invertase using aqueous two-phase systems. Biotechnol Appl Biochem 63:886–894. https://doi.org/10.1002/bab.1435
Li Z, Liu X, Pei Y, Wang J, He M (2012) Design of environmentally friendly ionic liquid aqueous two-phase systems for the efficient and high activity extraction of proteins. Green Chem 14:2941–2950. https://doi.org/10.1039/c2gc35890e
Li H, Schmitz O, Alper HS (2016a) Enabling glucose/xylose co-transport in yeast through the directed evolution of a sugar transporter. Appl Microbiol Biotechnol 100:10215–10223. https://doi.org/10.1007/s00253-016-7879-8
Li P, Li T, Zeng Y, Li X, Jiang X, Wang Y, Xie T, Zhang Y (2016b) Biosynthesis of xanthan gum by Xanthomonas campestris LRELP-1 using kitchen waste as the sole substrate. Carbohydr Polym 151:684–691. https://doi.org/10.1016/j.carbpol.2016.06.017
Li P, Fu X, Zhang L, Zhang Z, Li J, Li S (2017) The transcription factors Hsf1 and Msn2 of thermotolerant Kluyveromyces marxianus promote cell growth and ethanol fermentation of Saccharomyces cerevisiae at high temperatures. Biotechnol Biofuels 10:1–13. https://doi.org/10.1186/s13068-017-0984-9
Li G, Fu Y, Dang W, Hu R, Xue H (2019) The effects of aqueous ammonia-pretreated rice straw as solid substrate on laccase production by solid-state fermentation. Bioprocess Biosyst Eng 42:567–574. https://doi.org/10.1007/s00449-018-02060-y
Liao L-C, Ho CS, Wu W-T (1999) Bioconversion with whole cell penicillin acylase in aqueous two-phase systems. Process Biochem 34:417–420. https://doi.org/10.1016/S0032-9592(98)00099-5
Lin C, Wu C, Tran D, Shih M, Li W, Wu C (2011) Mixed culture fermentation from lignocellulosic materials using thermophilic lignocellulose-degrading anaerobes. Process Biochem 46:489–493. https://doi.org/10.1016/j.procbio.2010.09.024
Lin CSK, Koutinas AA, Stamatelatou K, Mubofu EB, Matharu AS, Kopsahelis N, Pfaltzgraff LA, Clark JH, Papanikolaou S, Kwan TH, Luque R (2014) Current and future trends in food waste valorization for the production of chemicals, materials and fuels: a global perspective. Biofuels Bioprod Biorefin 8(5):686–715. https://doi.org/10.1002/bbb.1506
Lin YK, Show PL, Yap YJ, Ariff AB, Annuar MSM, Lai OM, Tang TK, Juan JC, Ling TC (2016) Production of γ-cyclodextrin by Bacillus cereus cyclodextrin glycosyltransferase using extractive bioconversion in polymer-salt aqueous two-phase system. J Biosci Bioeng 121:692–696. https://doi.org/10.1016/j.jbiosc.2015.11.001
Linares-Pastén JA, Aronsson A, Karlsson EN (2018) Structural considerations on the use of endo-xylanases for the production of prebiotic xylooligosaccharides from biomass. Curr Protein Pept Sci 19:48–67. https://doi.org/10.2174/1389203717666160923155209
Linde GA, Magagnin G, Alberto J, Costa V, Bertolin TE, Colauto NB (2007) Column bioreactor use for optimization of pectinase production in solid substrate cultivation. Braz J Microbiol 38:557–562. https://doi.org/10.1590/S1517-83822007000300033
Liu Y, Li C, Meng X, Yan Y (2016) Biodiesel synthesis directly catalyzed by the fermented solid of Burkholderia cenocepacia via solid state fermentation. Fuel Process Technol 106:303–309. https://doi.org/10.1016/j.fuproc.2012.08.013
Liu MQ, Huo WK, Xu X, Weng XY (2017a) Recombinant Bacillus amyloliquefaciens xylanase A expressed in Pichia pastoris and generation of xylooligosaccharides from xylans and wheat bran. Int J Biol Macromol 105:656–663. https://doi.org/10.1016/j.ijbiomac.2017.07.073
Liu R, Hooker NH, Parasidis E, Simons CT (2017b) A natural experiment: using immersive technologies to study the impact of “all-natural” labeling on perceived food quality, nutritional content, and liking. J Food Sci. https://doi.org/10.1111/1750-3841.13639
Liu X, Liu Y, Jiang Z, Liu H, Yang S, Yan Q (2018) Biochemical characterization of a novel xylanase from Paenibacillus barengoltzii and its application in xylooligosaccharides production from corncobs. Food Chem 264:310–318. https://doi.org/10.1016/j.foodchem.2018.05.023
Lonsane BK, Ghildyal NP, Budiatman S, Ramakrishna SV (1985) Engineering aspects of solid state fermentation. Enzyme Microb Technol 7:258–265
Lopes VRO, Farias MA, Belo IMP, Coelho MAZ (2016) Nitrogen sources on tpomw valorization through solid state fermentation performed by Yarrowia Lipolytica. Brazilian J Chem Eng 33:261–270. https://doi.org/10.1590/0104-6632.20160332s20150146
López-Pérez M, Viniegra-González G (2015) Production of protein and metabolites by yeast grown in solid state fermentation: present status and perspectives. J Chem Technol Biotechnol 91:1224–1231. https://doi.org/10.1002/jctb.4819
Madhavan A, Sindhu R, Parameswaran B, Sukumaran RK, Pandey A (2017) Metagenome analysis: a powerful tool for enzyme bioprospecting. Appl Biochem Biotechnol 183(2):636–651. https://doi.org/10.1007/s12010-017-2568-3
Majidian P, Tabatabaei M, Zeinolabedini M, Naghshbandi MP, Chisti Y (2018) Metabolic engineering of microorganisms for biofuel production. Renew Sustain Energy Rev 82:3863–3885. https://doi.org/10.1016/j.rser.2017.10.085
Manan MA, Webb C (2017) Design aspects of solid state fermentation as applied to microbial bioprocessing. J Appl Biotechnol Bioeng 4:91. https://doi.org/10.15406/jabb.2017.04.00094
Mano MCR, Neri-Numa IA, da Silva JB, Paulino BN, Pessoa MG, Pastore GM (2018) Oligosaccharide biotechnology: an approach of prebiotic revolution on the industry. App Microbiol Biotechnol 102:17–37. https://doi.org/10.1007/s00253-017-8564-2
Markets and Markets (2015) Surfactants market worth $42,120.4 million by 2020. http://www.prnewswire.com/news-releases/surfactants-market-worth-421204-million-by-2020-506134181.html. Accessed 8 June 2019
Martínez-Avila O, Sánchez A, Font X (2018a) Bioproduction of 2-phenylethanol and 2-phenethyl acetate by Kluyveromyces marxianus through the solid-state fermentation of sugarcane bagasse. Appl Microbiol Biotechnol 102:4703–4716. https://doi.org/10.1007/s00253-018-8964-y
Martínez-Avila O, Sánchez A, Font X, Barrena R (2018b) Enhancing the bioproduction of value-added aroma compounds via solid-state fermentation of sugarcane bagasse and sugar beet molasses: operational strategies and scaling-up of the process. Bioresour Technol 263:136–144. https://doi.org/10.1016/j.biortech.2018.04.106
Martínez-Avila O, Sánchez A, Barrena R, Font X (2019) Fed-batch and sequential-batch approaches to enhance the bioproduction of 2-phenylethanol and 2-phenethyl acetate in solid-state fermentation residue-based systems. J Agric Food Chem 67:3389–3399. https://doi.org/10.1021/acs.jafc.9b00524
Maruthamuthu M (2017) Novel bacterial enzymes for plant biomass degradation discovered by meta-omics approach. University of Groningen
Mathew S, Aronsson A, Karlsson EN, Adlercreutz P (2018) Xylo- and arabinoxylooligosaccharides from wheat bran by endoxylanases, utilisation by probiotic bacteria, and structural studies of the enzymes. Appl Microbiol Biotechnol 102:3105–3120. https://doi.org/10.1007/s00253-018-8823-x
Mehta A, Prasad GS, Choudhury AR (2014) Cost effective production of pullulan from agri-industrial residues using response surface methodology. Int J Biol Macromol 64:252–256. https://doi.org/10.1016/j.ijbiomac.2013.12.011
Mejía-Manzano LA, Barba-Dávila BA, Vázquez-Villegas P (2019) Improved extraction of the natural anticancerigen pristimerin from Mortonia greggii root bark using green solvents and aqueous two-phase systems. Sep Purif Technol 211:667–672. https://doi.org/10.1016/j.seppur.2018.08.056
Mejias L, Cerda A, Barrena R, Gea T (2018) Microbial strategies for cellulase and xylanase production through solid-state fermentation of digestate from biowaste. Sustainability 10:2433. https://doi.org/10.3390/su10072433
Melikoglu M, Lin CSK, Webb C (2015) Solid state fermentation of waste bread pieces by Aspergillus awamori: analysing the effects of airflow rate on enzyme production in packed bed bioreactors. Food Bioprod Process 95:63–75. https://doi.org/10.1016/j.fbp.2015.03.011
Mitchell DA, Krieger N, Stuart DM, Pandey A (2000) New developments in solid-state fermentation. II: Rational approaches to the design, operation and scale-up of bioreactors. Process Biochem 35:1211–1225. https://doi.org/10.1016/S0032-9592(00)00157-6
Montella S, Amore A, Faraco V (2016) Metagenomics for the development of new biocatalysts to advance lignocellulose saccharification for bioeconomic development. Crit Rev Biotechnol 36(6):998–1009. https://doi.org/10.3109/07388551.2015.1083939
Moore JC, Arnold FH (1996) Directed evolution of a paranitrobenzyl esterase for aqueous organic solvents. Nat Biotechnol 14:458–467. https://doi.org/10.1038/nbt0496-458
Moreira S, Silvério SC, Macedo EA, Milagres AMF, Teixeira JA, Mussatto SI (2013) Recovery of Peniophora cinerea laccase using aqueous two-phase systems composed by ethylene oxide/propylene oxide copolymer and potassium phosphate salts. J Chromatogr A 1321:14–20. https://doi.org/10.1016/j.chroma.2013.10.056
Moshtagh B, Hawboldt K, Zhang B (2018) Optimization of biosurfactant production by Bacillus subtilis N3-1P using the brewery waste as the carbon source. Environ Technol 14:1–10. https://doi.org/10.1080/09593330.2018.1473502
Narang S, Sahai V, Bisaria VS (2001) Optimization of xylanase production by Melanocarpus albomyces IIS68 in solid state fermentation using response surface methodology. J Biosci Bioeng 91:425–427. https://doi.org/10.1016/s1389-1723(01)80164-x
Ngara TR, Zhang H (2018) Recent advances in function-based metagenomic screening. Genomics Proteomics Bioinformatics 16(6):405–415. https://doi.org/10.1016/j.gpb.2018.01.002
Niknezhad SV, Asadollahi MA, Zamani A, Biria D, Doostmohammadi M (2015) Optimization of xanthan gum production using cheese whey and response surface methodology. Food Sci Biotechnol 24:453–460. https://doi.org/10.1007/s10068-015-0060-9
Nitschke M, Pastore GM (2006) Production and properties of a surfactant obtained from Bacillus subtilis grown on cassava wastewater. Bioresour Technol 97:336–341. https://doi.org/10.1016/j.biortech.2005.02.044
Nitschke M, Costa SG, Haddad R, Gonçalves LAG, Alves NC, Eberlin MN, Contiero J (2008) Oil wastes as unconventional substrates for rhamnolipid biosurfactant production by Pseudomonas aeruginosa LBI. Biotechnol Prog 21:1562–1566. https://doi.org/10.1021/bp050198x
Oliveira DWF, Sousa JR, França IWL, Felix AKN, Martins JJL, Gonçalves LRB (2013) Kinetic study of biosurfactant production by Bacillus subtilis LAMI005 grown in clarified cashew apple juice. Colloids Surf B Biointerfaces 101:34–43. https://doi.org/10.1016/j.colsurfb.2012.06.011
Oliveira F, Salgado JM, Abrunhosa L, Pérez-Rodríguez N, Domínguez JM, Venâncio A, Belo I (2017a) Optimization of lipase production by solid-state fermentation of olive pomace: from flask to laboratory-scale packed-bed bioreactor. Bioprocess Biosyst Eng 40:1123–1132. https://doi.org/10.1007/s00449-017-1774-2
Oliveira F, Salgado JM, Pérez-Rodríguez N, Domínguez JM, Venâncio A, Belo I (2017b) Lipase production by solid-state fermentation of olive pomace in tray-type and pressurized bioreactors. J Chem Technol Biotechnol 93:1312–1319. https://doi.org/10.1002/jctb.5492
Oliveira AC, Amorim GM, Azevêdo JAG, Mateus G, Freire DMG (2018) Solid-state fermentation of co-products from palm oil processing: production of lipase and xylanase and effects on chemical composition. Biocatal Biotransformation 36:381–388. https://doi.org/10.1080/10242422.2018.1425400
Oyarce P, Meester B, Fonseca F, Vries L, Goeminne G, Pallidis A, Rycke R, Tsuji Y, Li Y, Van den Bosch S (2019) Introducing curcumin biosynthesis in Arabidopsis enhances lignocellulosic biomass processing. Nat Plants 5:225–237. https://doi.org/10.1038/s41477-018-0350-3
Ozdal M, Gurkok S, Ozdal OG (2017) Optimization of rhamnolipid production by Pseudomonas aeruginosa OG1 using waste frying oil and chicken feather peptone. 3 Biotech 7:117. https://doi.org/10.1007/s13205-017-0774-x
Paddon CJ, Keasling JD (2014) Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development. Nat Rev Microbiol 12:355–367. https://doi.org/10.1038/nrmicro3240
Paithankar A, Rewatkar A (2014) Oil cakes as substrate for improved lipase production in solid state fermentation. Int J Microbiol Res 3:71. https://doi.org/10.9790/3008-09413138
Palaniappan A, Balasubramaniam VG, Antony U (2017) Prebiotic potential of xylooligosaccharides derived from finger millet seed coat. Food Biotechnol 31:264–280. https://doi.org/10.1080/08905436.2017.1369433
Pandey A (2003) Solid-state fermentation. Biochem Eng J 13:81–84. https://doi.org/10.1016/S1369-703X(02)00121-3
Pandey A, Soccol CR, Mitchell D (2000) New developments in solid state fermentation: I-bioprocesses and products. Process Biochem 35:1153–1169. https://doi.org/10.1016/S0032-9592(00)00152-7
Panigrahi S, Velraj P, Rao TS (2019) Functional microbial diversity in contaminated environment and application in bioremediation. Microbial diversity in the genomic era. Academic Press, pp 359–385. https://doi.org/10.1016/b978-0-12-814849-5.00021-6
Pathania S, Sharma S, Kumari K (2018) Solid state fermentation of BSG for citric acid production. Indian J Nat Prod Resour 9:70–74
Paula RG, Antoniêto ACC, Ribeiro LFC, Srivastava N, O’Donovan A, Mishra P, Gupta VK, Silva RN (2019) Engineered microbial host selection for value-added bioproducts from lignocellulose. Biotechnol Adv 37(6):107347. https://doi.org/10.1016/j.biotechadv.2019.02.003
Pérez-Armendáriz B, Cal-y-Mayor-Luna C, El-Kassis EG, Ortega-Martínez LD (2019) Use of waste canola oil as a low-cost substrate for rhamnolipid production using Pseudomonas aeruginosa. AMB Express 9:61. https://doi.org/10.1186/s13568-019-0784-7
Phong WN, Show PL, Teh WH, Teh TX, Lim MY, Nazri NSB, Tan CH, Chang J-S, Ling TC (2017) Protein recovery from wet microalgae using liquid biphasic flotation (LBF). Bioresour Technol 244:1329–1336. https://doi.org/10.1016/j.biortech.2017.05.165
Phong WN, Show PL, Chow YH, Ling TC (2018) Recovery of biotechnological products using aqueous two-phase systems. J Biosci Bioeng 126:273–281. https://doi.org/10.1016/j.jbiosc.2018.03.005
Protzko RJ, Latimer LN, Martinho Z, de Reus E, Seibert T, Benz JP, Dueber JE (2018) Engineering Saccharomyces cerevisiae for co-utilization of D-galacturonic acid and D-glucose from citrus peel waste. Nat Commun 9:5059. https://doi.org/10.1038/s41467-018-07589-w
Purohit A, Rai SK, Chownk M, Sangwan RS, Yadav SK (2017) Xylanase from Acinetobacter pittii MASK 25 and developed magnetic cross-linked xylanase aggregate produce predominantly xylopentose and xylohexose from agro biomass. Bioresour Technol 244:793–799. https://doi.org/10.1016/j.biortech.2017.08.034
Qiao W, Tao J, Luo Y, Tang T (2018) Microbial oil production from solid-state fermentation by a newly isolated oleaginous fungus, Mucor circinelloides Q531 from mulberry branches. R Soc Open Sci 5:180551. https://doi.org/10.1098/rsos.180551
Qureshi AS, Khushk I, Ali HC, Chisti Y, Ahmad A, Majeed H (2016) Coproduction of protease and amylase by thermophilic Bacillus sp. BBXS-2 using open solid-state fermentation of lignocellulosic biomass. Biocatal Agric Biotechnol 8:146–151. https://doi.org/10.1016/j.bcab.2016.09.006
Rabausch U, Juergensen J, Ilmberger N, Böhnke S, Fischer S, Schubach B, Schulte M, Streit WR (2013) Functional screening of metagenome and genome libraries for detection of novel flavonoid-modifying enzymes. Appl Environ Microbiol 79:4551–4563. https://doi.org/10.1128/AEM.01077-13
Raja S, Murty VR (2013) Optimization of aqueous two-phase systems for the recovery of soluble proteins from tannery wastewater using response surface methodology. J Eng 2013:217483. https://doi.org/10.1155/2013/217483
Rajagopalan G, Shanmugavelu K, Yang KL (2017) Production of prebiotic -xylooligosaccharides from alkali pretreated mahogany and mango wood sawdust by using purified xylanase of Clostridium strain BOH3. Carbohydr Polym 167:158–166. https://doi.org/10.1016/j.carbpol.2017.03.021
Ramalakshmi S, Ramanan RN, Ariff AB, Ooi CW (2014) Liquid-liquid equilibrium of primary and secondary aqueous two-phase systems composed of sucrose + triton X114 + water at different temperatures. J Chem Eng Data 59:2756–2762. https://doi.org/10.1021/je500571k
Ramírez IM, Tsaousi K, Rudden M, Marchant R, Alameda EJ, Román MG, Banat IM (2015) Rhamnolipid and surfactin production from olive oil mill waste as a sole carbon source. Bioresour Technol 198:231–236. https://doi.org/10.1016/j.biortech.2015.09.012
Ran L, Yang C, Xu M, Yi Z, Ren D, Yi L (2019) Enhanced aqueous two-phase extraction of proanthocyanidins from grape seeds by using ionic liquids as adjuvants. Sep Purif Technol 226:154–161. https://doi.org/10.1016/j.seppur.2019.05.089
Redden H, Alper HS (2015) The development and characterization of synthetic minimal yeast promoters. Nat Commun 6:1–9. https://doi.org/10.1038/ncomms8810
Reddy SS, Krishnan C (2016a) Production of high-pure xylooligosaccharides from sugarcane bagasse using crude β-xylosidase-free xylanase of Bacillus subtilis KCX006 and their bifidogenic function. LWT—Food Sci Technol 65:237–245. https://doi.org/10.1016/j.lwt.2015.08.013
Reddy SS, Krishnan C (2016b) Production of xylooligosaccharides in SSF by Bacillus subtilis KCX006 producing β-xylosidase-free endo-xylanase and multiple xylan debranching enzymes. Prep Biochem Biotechnol 46:49–55. https://doi.org/10.1080/10826068.2014.970694
Renata H, Wang J, Arnold FH (2015) Expanding the enzyme universe: accessing non-natural reactions by mechanism-guided directed evolution. Angew Chem 54:3351–3367. https://doi.org/10.1002/anie.201409470
The Market Reports (2018) Global Xylo-oligosaccharide (XOS) market by manufacturers, regions, type and application, forecast to 2023. https://www.themarketreports.com/report/global-xylo-oligosaccharide-xos-market-by-manufacturers-regions-type-and-application-forecast-to-2023. Accessed 23 June 2019.
Rito-Palomares M, Lyddiatt A (2002) Process integration using aqueous two-phase partition for the recovery of intracellular proteins. Chem Eng J 87:313–319. https://doi.org/10.1016/S1385-8947(01)00241-8
Rodrigues JL, Rodrigues LR (2017a) Synthetic biology: perspectives in industrial biotechnology. In: Pandey A, Teixiera J (eds) . Foundations of biotechnology and bioengineering. Current developments in biotechnology and bioengineering, Elsevier, pp 239–269
Rodrigues JL, Rodrigues LR (2017b) Potential applications of the Escherichia coli heat shock response in synthetic biology. Trends Biotechnol 36:186–198. https://doi.org/10.1016/j.tibtech.2017.10.014
Rodrigues JL, Sousa M, Prather KL, Kluskens LD, Rodrigues LR (2014) Selection of Escherichia coli heat shock promoters towards their application as stress probes. J Biotechnol 188:61–71. https://doi.org/10.1016/j.jbiotec.2014.08.005
Rodrigues J, Araújo R, Prather K, Kluskens L, Rodrigues L (2015a) Heterologous production of caffeic acid from tyrosine in Escherichia coli. Enzyme Microb Technol 71:36–44. https://doi.org/10.1016/j.enzmictec.2015.01.001
Rodrigues J, Araújo R, Prather K, Kluskens L, Rodrigues L (2015b) Production of curcuminoids from tyrosine by a metabolically engineered Escherichia coli using caffeic acid as an intermediate. Biotechnol J 10:599–609. https://doi.org/10.1002/biot.201400637
Rodrigues JL, Prather KL, Kluskens L, Rodrigues L (2015c) Heterologous production of curcuminoids. Microbiol Mol Biol Rev 79:39–60. https://doi.org/10.1128/MMBR.00031-14
Rodrigues JL, Couto MR, Araújo RG, Prather KL, Kluskens L, Rodrigues LR (2017a) Hydroxycinnamic acids and curcumin production in engineered Escherichia coli using heat shock promoters. Biochem Eng J 125:41–49. https://doi.org/10.1016/j.bej.2017.05.015
Rodrigues JL, Ferreira D, Rodrigues LR (2017b) Synthetic biology strategies towards the development of new bioinspired technologies for medical applications. In: Rodrigues L, Mota M (eds) Bioinspired materials for medical applications. Woodhead Publishing, United Kingdom, pp 451–497
Roelants S, Van Renterghem L, Maes K, Everaert B, Vanlerberghe B, Demaeseneire S, Soetaert W (2019) Microbial biosurfactants: from lab to market. In: Banat IM, Thavasi R (eds) Microbial biosurfactants and their environmental and industrial applications. CRC Press, Boca Raton. https://doi.org/10.1201/b21950
Ruiz HA, Rodríguez-Jasso RM, Rodríguez R, Contreras-Esquivel JC, Aguilar CN (2012) Pectinase production from lemon peel pomace as support and carbon source in solid-state fermentation column-tray bioreactor. Biochem Eng J 65:90–95. https://doi.org/10.1016/j.bej.2012.03.007
Sadh PK, Duhan S, Duhan JS (2018) Agro-industrial wastes and their utilization using solid state fermentation: a review. Bioresour Bioprocess 5:1. https://doi.org/10.1186/s40643-017-0187-z
Saha MLAL (1997) Citric acid fermentation by magnetic rotating biological contactors using Aspergillus niger AJ 117173. J Ferment Bioeng 84:244–248. https://doi.org/10.1016/S0922-338X(97)82062-4
Saithi S, Tongta A (2016) Phytase production of Aspergillus niger on soybean meal by solid-state fermentation using a rotating drum bioreactor. Agric Agric Sci Procedia 11:25–30. https://doi.org/10.1016/j.aaspro.2016.12.005
Salah RB, Chaari K, Besbes S, Ktari N, Blecker C, Deroanne C, Attia H (2015) Optimisation of xanthan gum production by palm date (Phoenix dactylifera L.) juice by-products using response surface methodology. Food Chem 121:627–633. https://doi.org/10.1016/j.foodchem.2009.12.077
Salas-Veizaga DM, Villagomez R, Linares-Pastén JA, Carrasco C, Álvarez MT, Adlercreutz P, Karlsson EN (2017) Extraction of glucuronoarabinoxylan from quinoa stalks (chenopodium quinoa willd.) and evaluation of xylooligosaccharides produced by GH10 and GH11 xylanases. J Agric Food Chem 65:8663–8673. https://doi.org/10.1021/acs.jafc.7b01737
Salum TFC, Villeneuve P, Barea B, Itsuo C, Cristina L, Alexander D, Krieger N (2010) Synthesis of biodiesel in column fixed-bed bioreactor using the fermented solid produced by Burkholderia cepacia LTEB11. Process Biochem 45:1348–1354. https://doi.org/10.1016/j.procbio.2010.05.004
Samanta AK, Jayapal N, Kolte AP, Senani S, Sridhar M, Suresh KP, Sampath KT (2012) Enzymatic production of xylooligosaccharides from alkali solubilized xylan of natural grass (Sehima nervosum). Bioresour Technol 112:199–205. https://doi.org/10.1016/j.biortech.2012.02.036
Samanta AK, Jayapal N, Jayaram C, Roy S, Kolte AP, Senani S, Sridhar M (2015) Xylooligosaccharides as prebiotics from agricultural by-products: production and applications. Bioact Carbohydr Diet Fibre 5:62–71. https://doi.org/10.1016/j.bcdf.2014.12.003
Samykannu M, Achary A (2017) Utilization of agro-industry residue for rhamnolipid production by Pseudomonas aeruginosa AMB AS7 and its application in chromium removal. Appl Biochem Biotechnol 183:70–90. https://doi.org/10.1007/s12010-017-2431-6
Sankaran R, Show PL, Yap YJ, Tao Y, Ling TC, Tomohisa K (2018a) Green technology of liquid biphasic flotation for enzyme recobery utilizing recycling surfactant and sorbitol. Clean Technol Environ Policy 20:2001–2012. https://doi.org/10.1007/s10098-018-1523-5
Sankaran R, Show PL, Lee SY, Yap YJ, Ling TC (2018b) Integration process of fermentation and liquid flotation for lipase separation from Burkholderia cepacia. Bioresour Technol 250:306–316. https://doi.org/10.1016/j.biortech.2017.11.050
Saravanan S, Rao JR, Nair BU, Ramasami T (2008) Aqueous two-phase poly(ethylene glycol)-poly(acrylic acid) system for protein partitioning: influence of molecular weight, pH and temperature. Process Biochem 43:905–911. https://doi.org/10.1016/j.procbio.2008.04.011
Sathi-Reddy K, Yahya-Khan M, Archana K, Reddy G, Hameeda B (2016) Utilization of mango kernel oil for the rhamnolipid production by Pseudomonas aeruginosa DR1 towards its application as biocontrol agent. Bioresour Technol 221:291–299. https://doi.org/10.1016/j.biortech.2016.09.041
Savvides AL, Katsifas EA, Hatzinikolaou DG, Karagouni AD (2012) Xanthan production by Xanthomonas campestris using whey permeate medium. World J Microbiol Biotechnol 28:2759–2764. https://doi.org/10.1007/s11274-012-1087-1
Scarlat N, Martinov M, Dallemand JF (2010) Assessment of the availability of agricultural crop residues in the European Union: potential and limitations for bioenergy use. Waste Manag 30:1889–1897. https://doi.org/10.1016/j.wasman.2010.04.016
Scoma A, Rebecchi S, Bertin L, Fava F (2016) High impact biowastes from South European agroindustries as feedstock for second-generation biorefineries. Crit Rev Biotechnol 36:175–189. https://doi.org/10.3109/07388551.2014.947238
Searle S, Malins C (2013) Availability of cellulosic residues and wastes in the EU. International Council on Clean Transportation, Washington, DC
Seesuriyachan P, Kawee-ai A, Chaiyaso T (2017) Green and chemical-free process of enzymatic xylooligosaccharide production from corncob: enhancement of the yields using a strategy of lignocellulosic destructuration by ultra-high pressure pretreatment. Bioresour Technol 241:537–544. https://doi.org/10.1016/j.biortech.2017.05.193
Sharma N, Prasad GS, Choudhury AR (2013) Utilization of corn steep liquor for biosynthesis of pullulan, an important exopolysaccharide. Carbohydr Polym 93:95–101. https://doi.org/10.1016/j.carbpol.2012.06.059
Sheldon RA, Woodley JM (2018) Role of biocatalysis in sustainable chemistry. Chem Rev 118:801–838. https://doi.org/10.1021/acs.chemrev.7b00203
Shojaosadati SA, Babaeipour V (2002) Citric acid production from apple pomace in multi-layer packed bed solid-state bioreactor. Process Biochem 37:909–914. https://doi.org/10.1016/S0032-9592(01)00294-1
Show PL, Tan CP, Anuar MS, Ariff A, Yusof YA, Chen SK, Ling TC (2012) Extractive fermentation for improved production and recovery of lipase derived from Burkholderia cepacian using a thermoseparating polymer in aqueous two systems. Bioresour Technol 116:226–233. https://doi.org/10.1016/j.biortech.2011.09.131
Silva TM, Minim LA, Maffia MC, Coimbra JSR, Minim VPR, da Silva LHM (2007) Equilibrium data for poly(propylene glycol) + sucrose + water and poly(propylene glycol) + fructose + water systems from (15 to 45) °C. J Chem Eng Data 52:1649–1652. https://doi.org/10.1021/je700031d
da Silva MB, Rossi DM, Ayub MA (2017) Screening of filamentous fungi to produce xylanase and xylooligosaccharides in submerged and solid-state cultivations on rice husk, soybean hull, and spent malt as substrates. World J Microbiol Biotechnol 33:58. https://doi.org/10.1007/s11274-017-2226-5
Silva C, Martins M, Jing S, Fu J, Cavaco-Paulo A (2018) Practical insights on enzyme stabilization. Crit Ver Biotechnol 38:335–350. https://doi.org/10.1080/07388551.2017.1355294
Simon C, Daniel R (2011) Metagenomic analyses: past and future trends. Appl Environ Microbiol 77(4):1153–1161. https://doi.org/10.1128/AEM.02345-10
Singh RD, Banerjee J, Sasmal S, Muir J, Arora A (2018) High xylan recovery using two stage alkali pre-treatment process from high lignin biomass and its valorization to xylooligosaccharides of low degree of polymerisation. Bioresour Technol 256:110–117. https://doi.org/10.1016/j.biortech.2018.02.009
Singhania RR, Patel AK, Soccol CR, Pandey A (2009) Recent advances in solid-state fermentation. Biochem Eng J 44:13–18. https://doi.org/10.1016/j.bej.2008.10.019
Sjöling S, Cowan DA (2008) Metagenomics: microbial community genomes revealed. In: Margesin R, Schinner F, Marx JC, Gerday C (eds) Psychrophiles: from biodiversity to biotechnology. Springer, Berlin, pp 313–332. https://doi.org/10.1007/978-3-540-74335-4_18
Soccol CR, Iloki I, Marin B, Raimbault M (1994) Comparative production of alpha-amylase, glucoamylase and protein enrichment of raw and cooked cassava by rhizopus strains in submerged and solid state. J Food Sci Technol 31:320–323
Soccol CR, Scopel E, Alberto L, Letti J, Karp SG, Woiciechowski AL, Porto L, Vandenberghe DS (2017) Recent developments and innovations in solid state fermentation. Biotechnol Res Innov 1:52–71. https://doi.org/10.1016/j.biori.2017.01.002
Sofía M, Rodríguez-Jasso RM, Michelin M, Flores-Gallegos AC (2018) Bioreactor design for enzymatic hydrolysis of biomass under the biorefinery concept. Chem Eng J 347:119–136. https://doi.org/10.1016/j.cej.2018.04.057
Sousa M, Melo VMM, Rodrigues S, Santana HB, Gonçalves LRB (2012) Screening of biosurfactant-producing Bacillus strains using glycerol from the biodiesel synthesis as main carbon source. Bioprocess Biosyst Eng 35:897–906. https://doi.org/10.1007/s00449-011-0674-0
Spier MR, Porto L, Vandenberghe DS, Bianchi A, Medeiros P, Soccol CR (2011) Application of different types of bioreactors in bioprocesses. In: Bioreactors: design, properties and applications. Nova Science Publishers, Hauppauge, pp 53–87
Sripokar P, Chaijan M, Benjakul S, Yoshida A, Klomklao S (2017) Aqueous two-phase partitioning of liver proteinase from albacore tuna (Thunnus alalunga): application to starry triggerfish (Abalistes stellaris) muscle hydrolysis. Int J Food Prop 52:51600–51612. https://doi.org/10.1080/10942912.2017.1350705
Stemmer WPC (1994) Rapid evolution of a protein in vitro by DNA shuffling. Nature 370:389–391. https://doi.org/10.1038/370389a0
Sun Z, Wikmark Y, Baeckvall J-E, Reetz MT (2016) New concepts for increasing the efficiency in directed evolution of stereoselective enzymes. Chem A Eur J 22(15):5046–5054. https://doi.org/10.1002/chem.201504406
Teles ASC, Chávez DWH, Oliveira RA, Bon EPS, Terzi SC, Souza EF, Gottschalk LMF, Tonon RV (2019) Use of grape pomace for the production of hydrolytic enzymes by solid-state fermentation and recovery of its bioactive compounds. Food Res Int 120:441–448. https://doi.org/10.1016/j.foodres.2018.10.083
Tjerneld F, Johansson G, Joelsson M (1987) Affinity liquid-liquid extraction of lactate dehydrogenase on a large scale. Biotechnol Bioeng 30:809–816. https://doi.org/10.1002/bit.260300702
Try S, De-Coninck J, Voilley A, Chunhieng T, Waché Y (2017) Solid state fermentation for the production of γ-decalactones by Yarrowia lipolytica. Process Biochem 64:9–15. https://doi.org/10.1016/j.procbio.2017.10.004
Tsuji Y, Vanholme R, Tobimatsu Y, Ishikawa Y, Foster CE, Kamimura N, Hishiyama S, Hashimoto S, Shino A, Hara H (2015) Introduction of chemically labile substructures into Arabidopsis lignin through the use of LigD, the Cα-dehydrogenase from Sphingobium sp. strain SYK-6. Plant Biotechnol J 13:821–832. https://doi.org/10.1111/pbi.12316
Ufarte L, Potocki-Veronese G, Laville E (2015) Discovery of new protein families and functions: new challenges in functional metagenomics for biotechnologies and microbial ecology. Front Microbiol 6(563). https://doi.org/10.3389/fmicb.2015.00563
Uygut MA, Tanyildizi MŞ (2018) Optimization of alpha-amylase production by Bacillus amyloliquefaciens grown on orange peels. Iran J Sci Technol Trans A Sci 42:443–449. https://doi.org/10.1007/s40995-016-0077-9
Vea EB, Romeo D, Thomsen M (2018) Biowaste valorisation in a future circular bioeconomy. Procedia CIRP 69:591–596. https://doi.org/10.1016/j.procir.2017.11.062
Wang C, Dong D, Wang H, Müller K, Qin Y, Wang H, Wu W (2016) Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition. Biotechnol Biofuels 9:22. https://doi.org/10.1186/s13068-016-0440-2
Wang Y, Xian M, Feng X, Liu M, Zhao G (2018) Biosynthesis of ethylene glycol from d-xylose in recombinant Escherichia coli. Bioengineered 9:233–241. https://doi.org/10.1080/21655979.2018.1478489
Wang X, Yang J, Yang S, Jiang Y (2019) Unraveling the genetic basis of fast L-arabinose consumption on top of recombinant xylose-fermenting Saccharomyces cerevisiae. Biotechnol Bioeng 116:283–293. https://doi.org/10.1002/bit.26827
Weber W, Fussenegger M (2012) Emerging biomedical applications of synthetic biology. Nat Rev Genet 13:21–35. https://doi.org/10.1038/nrg3094
Werner S, Maschke RW, Eibl D, Eibl R (2018) Bioreactor technology for sustainable production of plant cell-derived products. In: Bioprocessing of plant in vitro systems, pp 413–432
Westfall PJ, Pitera DJ, Lenihan JR, Eng D, Woolard FX, Regentin R, Horning T, Tsuruta H, Melis DJ, Owens A, Fickesa S, Diolaa D, Benjamina KR, Keasling JD, Leavella MD, McPheea DJ, Renningera NS, Newmana JD, Paddona CJ (2012) Production of amorphadiene in yeast, and its conversion to dihydroartemisinic acid, precursor to the antimalarial agent artemisinin. Proc Natl A Sci 109:E111–E118. https://doi.org/10.1073/pnas.1110740109
WHO—World Health Organization (2017) Cardiovascular diseases (CVDs) https://www.who.int/news-room/fact-sheets/detail/cardiovascular-diseases-(cvds). Accessed 23 June 2019
WHO—World Health Organization (2018) Global report on diabetes. https://apps.who.int/iris/bitstream/handle/10665/204871/9789241565257_eng.pdf.jsessionid=AB2C916A6DBA6120F68D15F7A47BF5BC?sequence=1. Accessed 23 June 2019
Winans K, Kendall A, Deng H (2017) The history and current applications of the circular economy concept. Renew Sustain Energy Rev 68:825–833. https://doi.org/10.1016/j.rser.2016.09.123
Wu S, Lu M, Chen J, Fang Y, Wu L, Xu Y, Wang S (2016) Production of pullulan from raw potato starch hydrolysates by a new strain of Aureobasidium pullulans. Int J Biol Macromol 82:740–743. https://doi.org/10.1016/j.ijbiomac.2015.09.075
Wu H, Li H, Xue Y, Luo G, Gan L, Liu J, Mao L, Long M (2017) High efficiency co-production of ferulic acid and xylooligosaccharides from wheat bran by recombinant xylanase and feruloyl esterase. Biochem Eng J 120:41–48. https://doi.org/10.1016/j.bej.2017.01.001
Wysokinska Z (2016) The “New” environmental policy of the European Union: a path to development of a circular economy and mitigation of the negative effects of climate change. Comp Econ Res 19:57–73. https://doi.org/10.1515/cer-2016-0013
Xia T, Eiteman MA, Altman E (2012) Simultaneous utilization of glucose, xylose and arabinose in the presence of acetate by a consortium of Escherichia coli strains. Microb Cell Fact 11:77. https://doi.org/10.1186/1475-2859-11-77
Xu K, Wang Y, Huang Y, Li N, Wen Q (2015) A green Deep eutectic solvent-based aqueous two-phase system for protein extracting. Anal Chim Acta 864:9–20. https://doi.org/10.1016/j.aca.2015.01.026
Xu G, Hao C, Tian S, Gao F, Sun W, Sun R (2017) A method for the preparation of curcumin by ultrasonic-assisted ammonium sulfate/ethanol aqueous two phase extraction. J Chromatogr B Analyt Technol Biomed Life Sci 1041-1041:167–174. https://doi.org/10.1016/j.jchromb.2016.12.029
Yang F, Mitra P, Zhang L, Prak L, Verhertbruggen Y, Kim JS, Sun L, Zheng K, Tang K, Auer M (2013) Engineering secondary cell wall deposition in plants. Plant Biotechnol J 11:325–335. https://doi.org/10.1111/pbi.12016
Yang J, Summanen PH, Henning SM, Hsu M, Lam H, Huang J, Tseng C-H, Dowd SE, Finegold SM, Heber D, Li Z (2015) Xylooligosaccharide supplementation alters gut bacteria in both healthy and prediabetic adults: a pilot study. Front Physiol 6:216. https://doi.org/10.3389/fphys.2015.00216
Yao W, Nokes SE (2013) The use of co-culturing in solid substrate cultivation and possible solutions to scientific challenges. Biofuels Bioprod Biorefin 7:361–372. https://doi.org/10.1002/bbb.1389
Yen H, Chang J (2015) Growth of oleaginous Rhodotorula glutinis in an internal-loop airlift bioreactor by using lignocellulosic biomass hydrolysate as the carbon source. J Biosci Bioeng 119:580–584. https://doi.org/10.1016/j.jbiosc.2014.10.001
Zafra G, Taylor TD, Absalón AE, Cortés-Espinosa DV (2016) Comparative metagenomic analysis of PAH degradation in soil by a mixed microbial consortium. J Hazard Mater 318:702–710. https://doi.org/10.1016/j.jhazmat.2016.07.060
Zeng X, Miao W, Zeng H, Zhao K, Zhou Y, Zhang J, Zhao Q, Tursun D, Xu D, Li F (2018) Production of natamycin by Streptomyces gilvosporeus Z28 through solid-state fermentation using agro-industrial residues. Bioresour Technol 273:377–385. https://doi.org/10.1016/j.biortech.2018.11.009
Zhang H, Xu Y, Yu S (2017) Co-production of functional xylooligosaccharides and fermentable sugars from corncob with effective acetic acid prehydrolysis. Bioresour Technol 234:343–349. https://doi.org/10.1016/j.biortech.2017.02.094
Zhong J (2010) Recent advances in bioreactor engineering. Korean J Chem Eng 27:1035–1041. https://doi.org/10.1007/s11814-010-0277-5
Acknowledgements
C.A. and A.C. acknowledge their grants (UMINHO/BPD/4/2019 and UMINHO/BPD/37/2018, respectively) from Portuguese Foundation for Science and Technology (FCT). The study received financial support from FCT under the scope of the strategic funding of UID/BIO/04469/2013 unit, COMPETE 2020 (POCI-01-0145-FEDER-006684), and the projects FoSynBio (POCI-01-0145-FEDER-029549) and Lignozymes (POCI-01-0145-FEDER-029773). The authors also acknowledge BioTecNorte operation (NORTE-01-0145-FEDER-000004) and the project MultiBiorefinery (POCI-01-0145-FEDER-016403) funded by the European Regional Development Fund under the scope of Norte2020—Programa Operacional Regional do Norte.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Gudiña, E.J. et al. (2020). Biotech Green Approaches to Unravel the Potential of Residues into Valuable Products. In: Inamuddin, Asiri, A. (eds) Sustainable Green Chemical Processes and their Allied Applications. Nanotechnology in the Life Sciences. Springer, Cham. https://doi.org/10.1007/978-3-030-42284-4_5
Download citation
DOI: https://doi.org/10.1007/978-3-030-42284-4_5
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-42283-7
Online ISBN: 978-3-030-42284-4
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)