Skip to main content
SpringerLink
Log in

Microbial Metabolomics in Biomass Waste Management

  • Chapter
  • First Online:
Microbial Metabolomics

  • 1889 Accesses

Abstract

Agricultural processes, especially harvesting and post-harvesting, generate considerable amounts of biomass waste every year, the majority of which is incinerated or ends up in landfill. However, this biomass has, instead, the potential to be utilised for various applications including the production of biofuels and numerous medicinal and important industrial metabolites. Numerous bacteria, especially thermophilic species, and fungi have the ability to degrade complex biomass substrates to simpler, useful products which have wide commercial applications. The wide variability in biomass composition and the low degradation capability of individual microbes, however, has limited the utilisation of these wastes. In recent years, the field of metabolomics has been successfully applied to identify the many limiting factors of bioconversion processes. Metabolic profiling has also helped to identify the critical points in microbial metabolic pathways to not only overcome these limiting factors, but also increase the production of valuable by-products products. This chapter reviews the application of microbial metabolomics to increase the efficiency of biomass degradation. It will describe recent advances and future aspects of microbial metabolite profiling and metabolic engineering processes to optimise the production of various compounds of medicinal and industrial interest.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Adarme-Vega TC, Lim DKY, Timmins M, Vernen F, Li Y, Schenk PM (2012) Microalgal biofactories: a promising approach towards sustainable omega-3 fatty acid production. Microb Cell Fact 11:96

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Alonso ÁM, Castro R, Rodrı́guez MC, Guillén DA, Barroso CG (2004) Study of the antioxidant power of brandies and vinegars derived from Sherry wines and correlation with their content in polyphenols. Food Res Int 37:715–721

    Article  CAS  Google Scholar 

  • Alonso ÁM, Guillén DA, Barroso CG, Puertas B, García A (2002) Determination of antioxidant activity of wine byproducts and its correlation with polyphenolic content. J Agr Food Chem 50:5832–5836

    Article  CAS  Google Scholar 

  • Alvira P, Tomás-Pejó E, Ballesteros M, Negro MJ (2010) Pretreatment technologies for an efficient bioethanol production process based on enzymatic hydrolysis: a review. Bioresour Technol 101:4851–4861

    Article  CAS  PubMed  Google Scholar 

  • Ando H, Sakaki T, Kokusho T, Shibata M, Uemura Y, Hatate Y (2000) Decomposition behavior of plant biomass in hot-compressed water. Ind Eng Chem Res 39:3688–3693

    Article  CAS  Google Scholar 

  • Antoniewicz MR (2013) Using multiple tracers for 13C metabolic flux analysis. In: Alper SH (ed) Systems metabolic engineering: methods and protocols. Humana Press, Totowa

    Google Scholar 

  • Arora DS, Sharma RK (2010) Ligninolytic fungal laccases and their biotechnological applications. Appl Biochem Biotechn 160:1760–1788

    Article  CAS  Google Scholar 

  • Arvanitoyannis IS, Ladas D, Mavromatis A (2006) Potential uses and applications of treated wine waste: a review. Int J Food Sci Tech 41:475–487

    Article  CAS  Google Scholar 

  • Bak JS, Ko JK, Choi IG, Park YC, Seo J-H, Kim KH (2009) Fungal pretreatment of lignocellulose by Phanerochaete chrysosporium to produce ethanol from rice straw. Biotechnol Bioeng 104:471–482

    Article  CAS  PubMed  Google Scholar 

  • Baucher M, Monties B, Montagu MV, Boerjan W (1998) Biosynthesis and genetic engineering of lignin. Crit Rev Plant Sci 17:125–197

    Article  CAS  Google Scholar 

  • Beale D, Barratt R, Marlow D, Dunn M, Palombo E, Morrison P, Key C (2013) Application of metabolomics to understanding biofilms in water distribution systems: a pilot study. Biofouling 29:283–294

    Article  CAS  PubMed  Google Scholar 

  • Beale D, Karpe A, Mcleod J, Gondalia S, Muster T, Othman M, Palombo E, Joshi D (2016) An ‘omics’ approach towards the understanding of laboratory scale anaerobic digesters treating municipal wastewater activated sludge. Water Res 88:346–357

    Article  CAS  PubMed  Google Scholar 

  • Beale DJ, Morrison PD, Palombo EA (2014) Detection of Listeria in milk using non-targeted metabolic profiling of Listeria monocytogenes: a proof-of-concept application. Food Control 42:343–346

    Article  CAS  Google Scholar 

  • Bi H, Krausz K, Manna S, Li F, Johnson C, Gonzalez F (2013) Optimization of harvesting, extraction, and analytical protocols for UPLC-ESI-MS-based metabolomic analysis of adherent mammalian cancer cells. Anal Bioanal Chem 405:5279–5289

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Boerjan W, Ralph J, Baucher M (2003) Lignin biosynthesis. Annu Rev Plant Biol 54:519–546

    Article  CAS  PubMed  Google Scholar 

  • Brethauer S, Studer MH (2014) Consolidated bioprocessing of lignocellulose by a microbial consortium. Energy Environ Sci 7:1446–1453

    Article  CAS  Google Scholar 

  • Brijwani K, Oberoi HS, Vadlani PV (2010) Production of a cellulolytic enzyme system in mixed-culture solid-state fermentation of soybean hulls supplemented with wheat bran. Process Biochem 45:120–128

    Article  CAS  Google Scholar 

  • Brink J, Vries RP (2011) Fungal enzyme sets for plant polysaccharide degradation. Appl Microbiol Biot 91:1477–1492

    Article  CAS  Google Scholar 

  • Brune A (2014) Symbiotic digestion of lignocellulose in termite guts. Nat Rev Microbiol 12:168–180

    Article  CAS  PubMed  Google Scholar 

  • Budarin VL, Clark JH, Lanigan BA, Shuttleworth P, Macquarrie DJ (2010) Microwave assisted decomposition of cellulose: a new thermochemical route for biomass exploitation. Bioresour Technol 101:3776–3779

    Article  CAS  PubMed  Google Scholar 

  • Carbonell P, Parutto P, Baudier C, Junot C, Faulon J-L (2014) Retropath: automated pipeline for embedded metabolic circuits. ACS Synth Biol 3:565–577

    Article  CAS  PubMed  Google Scholar 

  • Cattaneo C, Spertino S, Boatti L, Icardi S, Cavaletto M (2014) Protein fingerprinting in the choice of cellulase cocktails for the conversion of lignocellulosic biomass. Anal Method 6:4046–4055

    Article  CAS  Google Scholar 

  • Chen R (2015) The sweet branch of metabolic engineering: cherry-picking the low-hanging sugary fruits. Microb Cell Fact 14:197

    Article  PubMed  PubMed Central  Google Scholar 

  • Cheng X-Y, Liu C-Z (2012) Fungal pretreatment enhances hydrogen production via thermophilic fermentation of cornstalk. Appl Energ 91:1–6

    Article  CAS  Google Scholar 

  • Chu Y, Wei Y, Yuan X, Shi X (2011) Bioconversion of wheat stalk to hydrogen by dark fermentation: effect of different mixed microflora on hydrogen yield and cellulose solubilisation. Bioresour Technol 102:3805–3809

    Article  CAS  PubMed  Google Scholar 

  • Couto SR, Sanromán MÁ (2006) Application of solid-state fermentation to food industry—a review. J Food Eng 76:291–302

    Article  CAS  Google Scholar 

  • Cui J, Zhang J, Zhu X, Bai F, Feng Y, Guan W, Cui Q (2013) Separation and quantification of water-soluble cellular metabolites in Clostridium thermocellum using liquid chromatography-isotope dilution tandem mass spectrometry. Anal Lett 46:2767–2786

    Article  CAS  Google Scholar 

  • de Melo MMR, Silvestre AJD, Silva CM (2014) Supercritical fluid extraction of vegetable matrices: applications, trends and future perspectives of a convincing green technology. J Supercrit Fluids 92:115–176

    Article  CAS  Google Scholar 

  • Diblasi L, Arrighi F, Silva J, Bardón A, Cartagena E (2015) Penicillium commune metabolic profile as a promising source of antipathogenic natural products. Nat Prod Res 29:1–7

    Article  CAS  Google Scholar 

  • Ding M-Z, Lu H, Cheng J-S, Chen Y, Jiang J, Qiao B, Li B-Z, Yuan Y-J (2012) Comparative metabolomic study of Penicillium chrysogenum during pilot and industrial penicillin fermentations. Appl Biochem Biotechnol 168:1223–1238

    Article  CAS  PubMed  Google Scholar 

  • Dixon RA, Gang DR, Charlton AJ, Fiehn O, Kuiper HA, Reynolds TL, Tjeerdema RS, Jeffery EH, German JB, Ridley WP (2006) Applications of metabolomics in agriculture. J Agr Food Chem 54:8984–8994

    Article  CAS  Google Scholar 

  • Draper J, Lloyd A, Goodacre R, Beckmann M (2013) Flow infusion electrospray ionisation mass spectrometry for high throughput, non-targeted metabolite fingerprinting: a review. Metabolomics 9:4–29

    Article  CAS  Google Scholar 

  • Draper J, Rasmussen S, Zubair H (2011) Metabolite analysis and metabolomics in the study of biotrophic interactions between plants and microbes. In: Annual plant reviews, vol 43. Wiley-Blackwell, New York

    Google Scholar 

  • Driouch H, Melzer G, Wittmann C (2012) Integration of in vivo and in silico metabolic fluxes for improvement of recombinant protein production. Metab Eng 14:47–58

    Article  CAS  PubMed  Google Scholar 

  • Duarte G, Moreira L, Jaramillo P, Filho E (2012) Biomass-derived inhibitors of holocellulases. Bioenerg Res 5:768–777

    Article  CAS  Google Scholar 

  • Ehrhardt C, Arapitsas P, Stefanini M, Flick G, Mattivi F (2014) Analysis of the phenolic composition of fungus-resistant grape varieties cultivated in Italy and Germany using UHPLC-MS/MS. J Mass Spectrom 49:860–869

    Article  CAS  PubMed  Google Scholar 

  • Ellis DI, Goodacre R (2012) Metabolomics-assisted synthetic biology. Curr Opin Biotechnol 23:22–28

    Article  CAS  PubMed  Google Scholar 

  • Eriksson KL, Blanchette RA, Ander P (1990) Microbial and enzymatic degradation of wood and wood components. Springer, Berlin

    Book  Google Scholar 

  • FAO (2015) FAOSTAT domain [Online]. Rome: The Food and Agriculture Organization of the United Nations. Available: http://faostat3.fao.org/faostat-gateway/go/to/download/Q/QD/E[accessed]

  • Fernandes AN, Thomas LH, Altaner CM, Callow P, Forsyth VT, Apperley DC, Kennedy CJ, Jarvis MC (2011) Nanostructure of cellulose microfibrils in spruce wood. Proc Natl Acad Sci USA 108:E1195–E1203

    Article  PubMed  PubMed Central  Google Scholar 

  • Fiehn O (2002) Metabolomics—the link between genotypes and phenotypes. Plant Mol Biol 48:155–171

    Article  CAS  PubMed  Google Scholar 

  • Fraatz MA, Naeve S, Hausherr V, Zorn H, Blank LM (2014) A minimal growth medium for the basidiomycete Pleurotus sapidus for metabolic flux analysis. Fungal Biol Biotechnol 1:9

    Article  Google Scholar 

  • Georgieva TI, Mikkelsen MJ, Ahring BKR (2007) High ethanol tolerance of the thermophilic anaerobic ethanol producer Thermoanaerobacter BG1L1. Cent Eur J Biol 2:364–377

    CAS  Google Scholar 

  • Godelmann R, Fang F, Humpfer E, Schütz B, Bansbach M, Schäfer H, Spraul M (2013) Targeted and nontargeted wine analysis by 1 h nmr spectroscopy combined with multivariate statistical analysis. Differentiation of important parameters: grape variety, geographical origin, year of vintage. J Agr Food Chem 61:5610–5619

    Article  CAS  Google Scholar 

  • González-Centeno M, Rosselló C, Simal S, Garau M, López F, Femenia A (2010) Physico-chemical properties of cell wall materials obtained from ten grape varieties and their byproducts: grape pomaces and stems. LWT-Food Sci Technol 43:1580–1586

    Article  CAS  Google Scholar 

  • Goto M, Obuchi R, Hirose T, Sakaki T, Shibata M (2004) Hydrothermal conversion of municipal organic waste into resources. Bioresour Technol 93:279–284

    Article  CAS  PubMed  Google Scholar 

  • Gupte A, Madamwar D (1997) Solid state fermentation of lignocellulosic waste for cellulase and β-glucosidase production by cocultivation of Aspergillus ellipticus and Aspergillus fumigatus. Biotechnol Progr 13:166–169

    Article  CAS  Google Scholar 

  • Haghighi Mood S, Hossein Golfeshan A, Tabatabaei M, Salehi Jouzani G, Najafi GH, Gholami M, Ardjmand M (2013) Lignocellulosic biomass to bioethanol, a comprehensive review with a focus on pretreatment. Renew Sustain Energy Rev 27:77–93

    Article  CAS  Google Scholar 

  • Harris DM, Corbin K, Wang T, Gutierrez R, Bertolo AL, Petti C, Smilgies D-M, Estevez JM, Bonetta D, Urbanowicz BR, Ehrhardt DW, Somerville CR, Rose JKC, Hong M, Debolt S (2012) Cellulose microfibril crystallinity is reduced by mutating C-terminal transmembrane region residues CESA1A903 V and CESA3T942I of cellulose synthase. Proc Natl Acad Sci USA 109:4098–4103

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hartl L, Kubicek CP, Seiboth B (2007) Induction of the gal pathway and cellulase genes involves no transcriptional inducer function of the galactokinase in Hypocrea jecorina. J Biol Chem 282:18654–18659

    Article  CAS  PubMed  Google Scholar 

  • Hasunuma T, Ishii J, Kondo A (2015) Rational design and evolutional fine tuning of Saccharomyces cerevisiae for biomass breakdown. Curr Opin Chem Biol 29:1–9

    Article  CAS  PubMed  Google Scholar 

  • Hasunuma T, Kondo A (2012) Development of yeast cell factories for consolidated bioprocessing of lignocellulose to bioethanol through cell surface engineering. Biotechnol Adv 30:1207–1218

    Article  CAS  PubMed  Google Scholar 

  • Hideno A, Inoue H, Tsukahara K, Yano S, Fang X, Endo T, Sawayama S (2011) Production and characterization of cellulases and hemicellulases by Acremonium cellulolyticus using rice straw subjected to various pretreatments as the carbon source. Enzyme Microb Technol 48:162–168

    Article  CAS  PubMed  Google Scholar 

  • Higuchi T (2006) Look back over the studies of lignin biochemistry. J Wood Sci 52:2–8

    Article  CAS  Google Scholar 

  • Hölker U, Lenz J (2005a) Solid-state fermentation—are there any biotechnological advantages? Curr Opi Microbiol 8:301–306

    Article  CAS  Google Scholar 

  • Hölker U, Lenz J (2005b) Solid-state fermentation—are there any biotechnological advantages? Curr Opin Microbiol 8:301–306

    Article  PubMed  CAS  Google Scholar 

  • Hong Y-S, Martinez A, Liger-Belair G, Jeandet P, Nuzillard J-M, Cilindre C (2012) Metabolomics reveals simultaneous influences of plant defence system and fungal growth in Botrytis cinerea-infected Vitis vinifera cv. Chardonnay berries. J Exp Bot 63:5773–5785

    Article  CAS  PubMed  Google Scholar 

  • Hori H, Elbein AD (1985) Biosynthesis of plant cell wall polysaccharides. In: Higuchi T (ed) Biosynthesis and biodegradation of wood components. Academic Press, Orlando

    Google Scholar 

  • Huang D, Wang R, Du W, Wang G, Xia M (2015) Activation of glycerol metabolic pathway by evolutionary engineering of Rhizopus oryzae to strengthen the fumaric acid biosynthesis from crude glycerol. Bioresour Technol 196:263–272

    Article  CAS  PubMed  Google Scholar 

  • Humphrey A (1998) Shake flask to fermentor: what have we learned? Biotechnol Prog 14:3–7

    Article  CAS  Google Scholar 

  • Jones OA, Dias DA, Callahan DL, Kouremenos KA, Beale DJ, Roessner U (2015) The use of metabolomics in the study of metals in biological systems. Metallomics 7:29–38

    Article  CAS  PubMed  Google Scholar 

  • Jones OAH, Sdepanian S, Lofts S, Svendsen C, Spurgeon DJ, Maguire ML, Griffin JL (2014) Metabolomic analysis of soil communities can be used for pollution assessment. Environ Toxicol Chem 33:61–64

    Article  CAS  PubMed  Google Scholar 

  • Juhász T, Szengyel Z, Réczey K, Siika-Aho M, Viikari L (2005) Characterization of cellulases and hemicellulases produced by Trichoderma reesei on various carbon sources. Process Biochem 40:3519–3525

    Article  CAS  Google Scholar 

  • Kamei I, Nitta T, Nagano Y, Yamaguchi M, Yamasaki Y, Meguro S (2014) Evaluation of spent mushroom waste from Lentinula edodes cultivation for consolidated bioprocessing fermentation by Phlebia sp. MG-60. Int Biodet Biodegr 94:57–62

    Article  CAS  Google Scholar 

  • Karimi K, Shafiei M, Kumar R (2013) Progress in physical and chemical pretreatment of lignocellulosic biomass. In: Gupta VK, Tuohy MG (eds) Biofuel technologies. Springer, Berlin

    Google Scholar 

  • Karpe A, Beale D, Morrison P, Harding I, Palombo E (2015a) Untargeted metabolic profiling of Vitis vinifera during fungal degradation. FEMS Microbiol Lett 362. Article fnv060

    Google Scholar 

  • Karpe AV, Beale DJ, Godhani N, Morrison PD, Harding IH, Palombo EA (2015b) Untargeted metabolic profiling of winery-derived biomass waste degradation by Aspergillus niger. J Chem Technol Biotechnol. doi:10.1002/jctb.4749

    Google Scholar 

  • Karpe AV, Beale DJ, Morrison PD, Harding IH Palombo EA (2015c) Untargeted metabolic profiling of Vitis vinifera during fungal degradation. FEMS Microbiol Lett 362, fnv060

    Google Scholar 

  • Karpe AV, Harding IH, Palombo EA (2014) Comparative degradation of hydrothermal pretreated winery grape wastes by various fungi. Ind Crop Prod 59:228–233

    Article  CAS  Google Scholar 

  • Kato H, Izumi Y, Hasunuma T, Matsuda F, Kondo A (2012) Widely targeted metabolic profiling analysis of yeast central metabolites. J Biosci Bioeng 113:665–673

    Article  CAS  PubMed  Google Scholar 

  • Kausar H, Sariah M, Mohd Saud H, Zahangir Alam M, Razi Ismail M (2010) Development of compatible lignocellulolytic fungal consortium for rapid composting of rice straw. Int Biodeter Biodegr 64:594–600

    Article  CAS  Google Scholar 

  • Khuong LD, Kondo R, de Leon R, Kim Anh T, Shimizu K, Kamei I (2014) Bioethanol production from alkaline-pretreated sugarcane bagasse by consolidated bioprocessing using Phlebia sp. MG-60. Int Biodet Biodegr 88:62–68

    Article  CAS  Google Scholar 

  • Kim T-Y, Wang D, Kim AK, Lau E, Lin AJ, Liem DA, Zhang J, Zong NC, Lam MPY, Ping P (2012) Metabolic labeling reveals proteome dynamics of mouse mitochondria. Mol Cell Proteomics 11:1586–1594

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kingston-Smith AH, Davies TE, Stevens PR, Mur LA (2013) Comparative metabolite fingerprinting of the rumen system during colonisation of three forage grass (Lolium perenne L.) varieties. PLoS ONE 8:e82801

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kosmides AK, Kamisoglu K, Calvano SE, Corbett SA, Androulakis IP (2013) Metabolomic fingerprinting: challenges and opportunities. Criti Rev Biomed Eng 41:205–221

    Article  Google Scholar 

  • Kouremenos KA, Pitt J, Marriott PJ (2010) Metabolic profiling of infant urine using comprehensive two-dimensional gas chromatography: application to the diagnosis of organic acidurias and biomarker discovery. J Chromatogr A 1217:104–111

    Article  CAS  PubMed  Google Scholar 

  • Kovacs K, Macrelli S, Szakacs G, Zacchi G (2009) Enzymatic hydrolysis of steam-pretreated lignocellulosic materials with Trichoderma atroviride enzymes produced in-house. Biotechnol Biofuels 2:14

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Krull R, Cordes C, Horn H, Kampen I, Kwade A, Neu TR, Nörtemann B (2010) Morphology of filamentous fungi: linking cellular biology to process engineering using Aspergillus niger. Adv Biochem Eng Biotechnol 121:1–21

    CAS  PubMed  Google Scholar 

  • Kubicek CP (2013) Systems biological approaches towards understanding cellulase production by Trichoderma reesei. J Biotechnol 163:133–142

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kumar R, Singh S, Singh O (2008) Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol 35:377–391

    Article  CAS  PubMed  Google Scholar 

  • Lee J (1997) Biological conversion of lignocellulosic biomass to ethanol. J Biotechnol 56:1–24

    Article  CAS  PubMed  Google Scholar 

  • Liu H-Q, Feng Y, Zhao D-Q, Jiang J-X (2012) Evaluation of cellulases produced from four fungi cultured on furfural residues and microcrystalline cellulose. Biodegradation 23:465–472

    Article  CAS  PubMed  Google Scholar 

  • Lu J, Weerasiri RR, Liu Y, Wang W, Ji S, Lee I (2013) Enzyme production by the mixed fungal culture with nano-shear pretreated biomass and lignocellulose hydrolysis. Biotechnol Bioeng 110:2123–2130

    Article  CAS  PubMed  Google Scholar 

  • Lynd LR, Zyl WHV, McBride JE, Laser M (2005) Consolidated bioprocessing of cellulosic biomass: an update. Curr Opin Biotech 16:577–583

    Article  CAS  PubMed  Google Scholar 

  • Ma X, Zheng X, Zhang M, Yang X, Chen L, Huang L, Cao S (2014) Electron beam irradiation of bamboo chips: degradation of cellulose and hemicelluloses. Cellulose 21:3865–3870

    Article  CAS  Google Scholar 

  • Maeda RN, Serpa VI, Rocha VAL, Mesquita RAA, Anna LMMS, de Castro AM, Driemeier CE, Pereira N Jr, Polikarpov I (2011) Enzymatic hydrolysis of pretreated sugar cane bagasse using Penicillium funiculosum and Trichoderma harzianum cellulases. Process Biochem 46:1196–1201

    Article  CAS  Google Scholar 

  • Maier K, Hofmann U, Bauer A, Niebel A, Vacun G, Reuss M, Mauch K (2009) Quantification of statin effects on hepatic cholesterol synthesis by transient 13C-flux analysis. Metab Eng 11:292–309

    Article  CAS  PubMed  Google Scholar 

  • Marcinowska R, Trygg J, Wolf-Watz H, Mortiz T, Surowiec I (2011) Optimization of a sample preparation method for the metabolomic analysis of clinically relevant bacteria. J Microbiol Methods 87:24–31

    Article  CAS  PubMed  Google Scholar 

  • Martins I, Garcia H, Varela A, Núñez O, Planchon S, Galceran MT, Renaut J, Rebelo LPN, Silva Pereira C (2014) Investigating Aspergillus nidulans secretome during colonisation of cork cell walls. J Prot 98:175–188

    Article  CAS  Google Scholar 

  • Matsuzaki F, Shimizu M, Wariishi H (2008) Proteomic and metabolomic analyses of the white-rot fungus Phanerochaete chrysosporium exposed to exogenous benzoic acid. J Proteome Res 7:2342–2350

    Article  CAS  PubMed  Google Scholar 

  • Maynard AD (2015) Navigating the fourth industrial revolution. Nat Nanotechnol 10:1005–1006

    Article  CAS  PubMed  Google Scholar 

  • Meijer S, Otero J, Olivares R, Andersen MR, Olsson L, Nielsen J (2009) Overexpression of isocitrate lyase—glyoxylate bypass influence on metabolism in Aspergillus niger. Metab Eng 11:107–116

    Article  CAS  PubMed  Google Scholar 

  • Meinert S, Rapp S, Schmitz K, Noack S, Kornfeld G, Hardiman T (2013) Quantitative quenching evaluation and direct intracellular metabolite analysis in Penicillium chrysogenum. Anal Biochem 438:47–52

    Article  CAS  PubMed  Google Scholar 

  • Merino S, Cherry J (2007) Progress and challenges in enzyme development for biomass utilization. In: Olsson L (ed) Biofuels. Springer, Berlin

    Google Scholar 

  • Nelson CJ, Li L, Millar AH (2014) Quantitative analysis of protein turnover in plants. Proteomics 14:579–592

    Article  CAS  PubMed  Google Scholar 

  • Ng JSY, Ryan U, Trengove RD, Maker GL (2012) Development of an untargeted metabolomics method for the analysis of human faecal samples using Cryptosporidium-infected samples. Mol Biochem Parasitol 185:145–150

    Article  CAS  PubMed  Google Scholar 

  • Niklas J, Schneider K, Heinzle E (2010) Metabolic flux analysis in eukaryotes. Curr Opin Biotechnol 21:63–69

    Article  CAS  PubMed  Google Scholar 

  • O’Neill MA, Ishii T, Albersheim P, Darvill AG (2004) Rhamnogalacturanan II: structure and function of a borate cross-linked cell wall pectic polysaccharide. Annu Rev Plant Biol 55:109–139

    Article  PubMed  CAS  Google Scholar 

  • O’Sullivan A (1997) Cellulose: the structure slowly unravels. Cellulose 4:173–207

    Article  Google Scholar 

  • Ogura T, Date Y, Kikuchi J (2013) Differences in cellulosic supramolecular structure of compositionally similar rice straw affect biomass metabolism by paddy soil microbiota. PLoS ONE 8:e66919

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Olson DG, McBride JE, Joe Shaw A, Lynd LR (2012) Recent progress in consolidated bioprocessing. Curr Opin Biotechnol 23:396–405

    Article  CAS  PubMed  Google Scholar 

  • Ortiz ME, Bleckwedel J, Raya RR, Mozzi F (2013) Biotechnological and in situ food production of polyols by lactic acid bacteria. Appl Microbiol Biotechnol 97:4713–4726

    Article  CAS  PubMed  Google Scholar 

  • Papini M, Nookaew I, Siewers V, Nielsen J (2012) Physiological characterization of recombinant Saccharomyces cerevisiae expressing the Aspergillus nidulans phosphoketolase pathway: validation of activity through 13C-based metabolic flux analysis. Appl Microbiol Biotechnol 95:1001–1010

    Article  CAS  PubMed  Google Scholar 

  • Pedersen H, Carlsen M, Nielsen J (1999) Identification of enzymes and quantification of metabolic fluxes in the wild type and in a recombinant Aspergillus oryzae strain. Appl Environ Microb 65:11–19

    CAS  Google Scholar 

  • Pirota RPB, Delabona P, Farinas C (2014) Simplification of the biomass to ethanol conversion process by using the whole medium of filamentous fungi cultivated under solid-state fermentation. BioEnerg Res 7:744–752

    Article  CAS  Google Scholar 

  • Pribowo A, Arantes V, Saddler JN (2012) The adsorption and enzyme activity profiles of specific Trichoderma reesei cellulase/xylanase components when hydrolyzing steam pretreated corn stover. Enzyme Microb Technol 50:195–203

    Article  CAS  PubMed  Google Scholar 

  • Putri SP, Nakayama Y, Matsuda F, Uchikata T, Kobayashi S, Matsubara A, Fukusaki E (2013) Current metabolomics: practical applications. J Biosci Bioeng 115:579–589

    Article  CAS  PubMed  Google Scholar 

  • Qi-He C, Krügener S, Hirth T, Rupp S, Zibek S (2011) Co-cultured production of lignin-modifying enzymes with white-rot fungi. Appl Biochem Biotechnol 165:700–718

    Article  PubMed  CAS  Google Scholar 

  • Ralph J, Lundquist K, Brunow G, Lu F, Kim H, Schatz PF, Marita JM, Hatfield RD, Ralph SA, Christensen JH, Boerjan W (2004) Lignins: natural polymers from oxidative coupling of 4-hydroxyphenyl- propanoids. Phytochem Rev 3:29–60

    Article  CAS  Google Scholar 

  • Rani KS, Seenayya G (1999) High ethanol tolerance of new isolates of Clostridium thermocellum strains SS21 and SS22. World J Microbiol Biotechnol 15:173–178

    Article  Google Scholar 

  • Rautio J, Smit B, Wiebe M, Penttila M, Saloheimo M (2006) Transcriptional monitoring of steady state and effects of anaerobic phases in chemostat cultures of the filamentous fungus Trichoderma reesei. BMC Genom 7:247

    Article  CAS  Google Scholar 

  • Rehman MSU, Kim I, Chisti Y, Han J-I (2013) Use of ultrasound in the production of bioethanol from lignocellulosic biomass. EEST Part A: Energy Sci Res 30:1391–1410

    Google Scholar 

  • Rodríguez A, Carnicero A, Perestelo F, De La Fuente G, Milstein O, Falcón MA (1994) Effect of Penicillium chrysogenum on lignin transformation. Appl Environ Microbiol 60:2971–2976

    PubMed  PubMed Central  Google Scholar 

  • Roessner U, Bowne J (2009) What is metabolomics all about? Biotechniques 46:363

    Article  CAS  PubMed  Google Scholar 

  • Rumbold K, van Buijsen HJJ, Overkamp KM, van Groenestijn JW, Punt PJ, van der Werf MJ (2009) Microbial production host selection for converting second-generation feedstocks into bioproducts. Microb Cell Fact 8:64

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Sánchez C (2009) Lignocellulosic residues: biodegradation and bioconversion by fungi. Biotechnol Adv 27:185–194

    Article  PubMed  CAS  Google Scholar 

  • Sarkar N, Ghosh SK, Bannerjee S, Aikat K (2012) Bioethanol production from agricultural wastes: an overview. Renew Energy 37:19–27

    Article  CAS  Google Scholar 

  • Saunders EC, Souza DP, Chambers JM, Ng M, Pyke J, McConville MJ (2015) Use of 13C stable isotope labelling for pathway and metabolic flux analysis in Leishmania parasites. In: Peacock C (ed) Parasite genomics protocols. Springer, New York

    Google Scholar 

  • Seiboth B, Gamauf C, Pail M, Hartl L, Kubicek CP (2007) The D-xylose reductase of Hypocrea jecorina is the major aldose reductase in pentose and D-galactose catabolism and necessary for β-galactosidase and cellulase induction by lactose. Mol Microbiol 66:890–900

    Article  CAS  PubMed  Google Scholar 

  • Shevchenko SM, Chang K, Robinson J, Saddler JN (2000) Optimization of monosaccharide recovery by post-hydrolysis of the water-soluble hemicellulose component after steam explosion of softwood chips. Bioresour Technol 72:207–211

    Article  CAS  Google Scholar 

  • Shulaev V (2006) Metabolomics technology and bioinformatics. Brief Bioinform 7:128–139

    Article  CAS  PubMed  Google Scholar 

  • Stone BA (1958) Biochemistry of cellulose and related polysaccharides. Nature 182:687–690

    Article  CAS  PubMed  Google Scholar 

  • Strong PJ, Burgess JE (2008) Treatment methods for wine-related and distillery wastewaters: a review. Bioremediat J 12:70–87

    Article  CAS  Google Scholar 

  • Studholme DJ, Harris B, le Cocq K, Winsbury R, Perera V, Ryder L, Beale M, Ward J, Thornton CR, Grant M (2013) Investigating the beneficial traits of Trichoderma hamatum GD12 for sustainable agriculture—insights from genomics. Front Plant Sci 4:258

    Article  PubMed  PubMed Central  Google Scholar 

  • Takeda H, Yoneyama F, Kawai S, Hashimoto W, Murata K (2011) Bioethanol production from marine biomass alginate by metabolically engineered bacteria. Energy Environ Sci 4:2575–2581

    Article  CAS  Google Scholar 

  • Tian F, Xie Z-L, Zhao L-Z, Guo J, Han X-B, Xie L-F, Wang Y, Chang X-Y (2015) Comparative secretome analysis of Fusarium sp. Q7-31T during liquid fermentation using oat straw as a carbon source. Ann Microbiol 65:1–10

    Article  CAS  Google Scholar 

  • Udatha DBRKG, Rasmussen S, Sicheritz-Pontén T, Panagiotou G (2013) Targeted metabolic engineering guided by computational analysis of single-nucleotide polymorphisms (SNPs). In: Alper SH (ed) Systems metabolic engineering: methods and protocols. Humana Press, Totowa

    Google Scholar 

  • Vanholme R, Demedts B, Morreel K, Ralph J, Boerjan W (2010) Lignin biosynthesis and structure. Plant Physiol 153:895–905

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Velmurugan R, Muthukumar K (2012) Sono-assisted enzymatic saccharification of sugarcane bagasse for bioethanol production. Biochem Eng J 63:1–9

    Article  CAS  Google Scholar 

  • Villas-Bôas SG, Noel S, Lane GA, Attwood G, Cookson A (2006) Extracellular metabolomics: a metabolic footprinting approach to assess fiber degradation in complex media. Anal Biochem 349:297–305

    Article  PubMed  CAS  Google Scholar 

  • Vivas M, Nunes C, Coimbra M, Solla A (2014) Maternal effects and carbohydrate changes of Pinus pinaster after inoculation with Fusarium circinatum. Trees 28:373–379

    Article  CAS  Google Scholar 

  • Waeonukul R, Kosugi A, Tachaapaikoon C, Pason P, Ratanakhanokchai K, Prawitwong P, Deng L, Saito M, Mori Y (2012) Efficient saccharification of ammonia soaked rice straw by combination of Clostridium thermocellum cellulosome and Thermoanaerobacter brockii β-glucosidase. Bioresour Technol 107:352–357

    Article  CAS  PubMed  Google Scholar 

  • Wagner JM, Alper HS (2016) Synthetic biology and molecular genetics in non-conventional yeasts: current tools and future advances. Fungal Genet Biol 89:126–136

    Article  CAS  PubMed  Google Scholar 

  • Wang X, Jin M, Balan V, Jones AD, Li X, Li BZ, Dale BE, Yuan YJ (2014) Comparative metabolic profiling revealed limitations in xylose-fermenting yeast during co-fermentation of glucose and xylose in the presence of inhibitors. Biotechnol Bioeng 111:152–164

    Article  CAS  PubMed  Google Scholar 

  • Wiethölter N, Graeßner B, Mierau M, Willats WGT, Knox JP, Moerschbacher BM (2003) Isolation and characterisation of the homogalacturonan from type II cell walls of the commelinoid monocot wheat using HF-solvolysis. Carbohydr Res 338:423–431

    Article  PubMed  Google Scholar 

  • Williams TC, Averesch NJH, Winter G, Plan MR, Vickers CE, Nielsen LK, Krömer JO (2015) Quorum-sensing linked RNA interference for dynamic metabolic pathway control in Saccharomyces cerevisiae. Metab Eng 29:124–134

    Article  CAS  PubMed  Google Scholar 

  • Yamazawa A, Iikura T, Shino A, Date Y, Kikuchi J (2013) Solid-, solution-, and gas-state NMR monitoring of 13C-cellulose degradation in an anaerobic microbial ecosystem. Molecules 18:9021–9033

    Article  CAS  PubMed  Google Scholar 

  • Yang Q, Wu S, Lou R, Lv G (2010a) Analysis of wheat straw lignin by thermogravimetry and pyrolysis-gas chromatography/mass spectrometry. J Anal Appl Pyrol 87:65–69

    Article  CAS  Google Scholar 

  • Yang X-Y, Chen W-P, Rendahl AK, Hegeman AD, Gray WM, Cohen JD (2010b) Measuring the turnover rates of Arabidopsis proteins using deuterium oxide: an auxin signaling case study. Plant J 63:680–695

    Article  CAS  PubMed  Google Scholar 

  • Yuan Y, Du J, Zhao H (2013) Customized optimization of metabolic pathways by combinatorial transcriptional engineering. In: Alper SH (ed) Systems metabolic engineering: methods and protocols. Humana Press, Totowa

    Google Scholar 

  • Zha Y, Westerhuis JA, Muilwijk B, Overkamp KM, Nijmeijer BM, Coulier L, Smilde AK, Punt PJ (2014) Identifying inhibitory compounds in lignocellulosic biomass hydrolysates using an exometabolomics approach. BMC Biotechnol 14:22

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zuroff T, Curtis W (2012) Developing symbiotic consortia for lignocellulosic biofuel production. Appl Microbiol Biotechnol 93:1–13

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Chemistry and Biotechnology, Swinburne University of Technology, PO Box 218, Hawthorn, Melbourne, Victoria, 3122, Australia

    Avinash V. Karpe, Ian H. Harding & Enzo A. Palombo

  2. Land and Water, Commonwealth Scientific and Industrial Research Organization (CSIRO), PO Box 2583, Brisbane, Queensland, 4002, Australia

    Avinash V. Karpe & David J. Beale

Authors
  1. Avinash V. Karpe
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. David J. Beale
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ian H. Harding
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Enzo A. Palombo
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Avinash V. Karpe .

Editor information

Editors and Affiliations

  1. Land and Water, CSIRO, Dutton Park, Queensland, Australia

    David J. Beale

  2. Metabolomics Australia, Bio21 Molecular Science & Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia

    Konstantinos A. Kouremenos

  3. Swinburne University of Technology, Hawthorn, Victoria, Australia

    Enzo A. Palombo

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer International Publishing Switzerland

About this chapter

Cite this chapter

Karpe, A.V., Beale, D.J., Harding, I.H., Palombo, E.A. (2016). Microbial Metabolomics in Biomass Waste Management. In: Beale, D., Kouremenos, K., Palombo, E. (eds) Microbial Metabolomics. Springer, Cham. https://doi.org/10.1007/978-3-319-46326-1_9

Download citation

Publish with us

Policies and ethics

Search

Navigation