Advances in industrial microbiome based on microbial consortium for biorefinery

Bioresources and Bioprocessing

Volumn 4, Issue 1, 2017, Pages

  Jiang, Li Li ^a   Zhou, Jin Jie ^a   Quan, Chun Shan ^b   Xiu, Zhi Long ^a  

^a DALIAN UNIVERSITY OF TECHNOLOGY   (China)

^b DALIAN NATIONALITIES UNIVERSITY   (China)

Author keywords

Bio based chemicals; Biofuels; Biomass; Biorefinery; Industrial microbiome; Microbial consortia

Indexed keywords

INDUSTRIAL CHEMICALS; MICROORGANISMS; REFINING;

BIO-BASED CHEMICALS; BIOMASS RESOURCES; BIOREFINERIES; COMPLEX COMPOSITIONS; INDUSTRIAL BIOTECHNOLOGY; INDUSTRIAL MICROBIOME; MICROBIAL CONSORTIUM; MICROBIAL FERMENTATION; MICROBIOME; MULTIPLE PRODUCTS;

BIOMASS;

EID: 85031763242     PISSN: None     EISSN: 21974365     Source Type: Journal    
DOI: 10.1186/s40643-017-0141-0     Document Type: Review

References (82)

1. Alivisatos AP, Blaser MJ, Brodie EL, Chun M, Dangl JL, Donohue TJ, Dorrestein PC, Gilbert JA, Green JL, Jansson JK, Knight R, Maxon ME, McFall-Ngai MJ, Miller JF, Pollard KS, Ruby EG, Taha SA (2015) A unified initiative to harness Earth’s microbiomes. Science 350(6260):507–508
2. Bader J, Mast-Gerlach E, Popovic MK, Bajpai R, Stahl U (2010) Relevance of microbial coculture fermentations in biotechnology. J Appl Microbiol 109(2):371–387
3. Bassler BL, Greenberg EP, Stevens AM (1997) Cross-species induction of luminescence in the quorum sensing bacterium Vibrio harveyi. J Bacteriol 179(12):4043–4045
4. Bernstein HC, Carlson RP (2012) Microbial consortia engineering for cellular factories: in vitro to in silico systems. Comput Struct Biotechnol J 3(4):1–8
5. Bizukojc M, Dietz D, Sun JB, Zeng AP (2010) Metabolic modelling of syntrophic-like growth of a 1,3-propanediol producer Clostridium butyricum and a methanogenic archeon Methanosarcina mazei under anaerobic conditions. Bioprocess Biosyst Eng 33:507–523
6. Brenner K, You L, Arnold FH (2008) Engineering microbial consortia: a new frontier in synthetic biology. Trends Biotechnol 26(9):483–489
7. Chatzifragkou A, Aggelis G, Komaitis M, Zeng AP, Papanikolaou S (2011) Impact of anaerobiosis strategy and bioreactor geometry on the biochemical response of Clostridium butyricum VPI 1718 during 1,3-propanediol fermentation. Bioresourc Technol 102(22):10625–10632
8. Coyte KZ, Schluter J, Foster KR (2015) The ecology of the microbiome: networks, competition, and stability. Science 350(6261):663–666
9. Dias JM, Lemos PC, Serafim LS, Oliveira C, Eiroa M, Albuquerque MG, Ramos AM, Oliveira R, Reis MA (2006) Recent advances in polyhydroxyalkanoate production by mixed aerobic cultures: from the substrate to the final product. Macromol Biosci 6(11):885–906
10. Diaz EE, Stams AJM, Amils R, Sanz JL (2006) Phenotypic properties and microbial diversity of methanogenic granules from a full-scale upflow anaerobic sludge bed reactor treating brewery wastewater. Appl Environ Microbiol 72(7):4942–4949
11. Dietz D, Zeng AP (2014) Efficient production of 1,3-propanediol from fermentation of crude glycerol with mixed cultures in a simple medium. Bioprocess Biosyst Eng 37(2):225–233
12. Diggle SP, Griffin AS, Campbell GS, West SA (2007) Cooperation and conflict in quorum-sensing bacterial populations. Nature 450(7168):411–414
13. Du R, Yan JB, Li SZ, Zhang L, Zhang S, Li J, Zhao G, Qi P (2015) Cellulosic ethanol production by natural bacterial consortia is enhanced by Pseudoxanthomonas taiwanensis. Biotechnol Biofuels 8(1):1–10
14. Dubilier N, McFall-Ngai M, Zhao LP (2015) Great a global microbiome effort. Nature 526(7575):631–634
15. Dürre P (2007) Biobutanol: an attractive biofuel. Biotechnol J 2(12):1525–1534
16. Eiteman MA, Lee SA, Altman E (2008) A co-fermentation strategy to consume sugar mixtures effectively. J Biol Eng 2(1):3–11
17. Escalante AE, Rebolleda-Gómez M, Benítez M, Travisano M (2015) Ecological perspectives on synthetic biology: insights from microbial population biology. Front Microbiol 6(143):1–10
18. Federle MJ, Bassler BL (2003) Interspecies communication in bacteria. J Clin Invest 112(9):1291–1299
19. Gallardo R, Faria C, Rodrigues LR, Pereira MA, Alves MM (2014) Anaerobic granular sludge as a biocatalyst for 1,3-propanediol production from glycerol in continuous bioreactors. Bioresour Technol 155(4):28–33
20. Gambino M, Cappitelli F (2016) Mini-review: biofilm responses to oxidative stress. Biofouling 32(2):167–178
21. Goers L, Freemont P, Polizzi KM (2014) Co-culture systems and technologies: taking synthetic biology to the next level. J R Soc Interface 11(96):1058–1069
22. Gu Y, Jiang Y, Wu H, Liu X, Li Z, Li J, Xiao H, Shen Z, Dong H, Yang Y, Li Y, Jiang W, Yang S (2011) Economical challenges to microbial producers of butanol: feedstock, butanol ratio and titer. Biotechnol J 6(11):1348–1357
23. Hammerschmidt K, Rose CJ, Kerr B, Rainey PB (2014) Life cycles, fitness decoupling and the evolution of multicellularity. Nature 515(7525):75–79
24. Hibbing M, Fuqua C, Parsek M, Peterson SB (2010) Bacterial competition: surviving and thriving in the microbial jungle. Nat Rev Microbiol 8(1):15–25
25. Jiang L, Liu H, Mu Y, Sun Y, Xiu Z (2016) High tolerance to glycerol and high production of 1,3-propanediol in batch fermentations by microbial consortium from marine sludge. Eng Life Sci 1–10. doi:10.1002/elsc.201600215
26. Johnson DT, Taconi KA (2007) The glycerin glut: options for the value-added conversion of crude glycerol resulting from biodiesel production. Environ Prog 26(4):338–348
27. Jolly J, Hitzmann B, Ramalingam S, Ramachandran KB (2014) Biosynthesis of 1,3-propanediol from glycerol with Lactobacillus reuteri: effect of operating variables. J Biosci Bioeng 118(2):188–194
28. Jun SA, Moon C, Kang CH, Kong SW, Sang BI, Um Y (2010) Microbial fed-batch production of 1,3-propanediol using raw glycerol with suspended and immobilized Klebsiella pneumoniae. Appl Biochem Biotechnol 161(161):491–501
29. Kamm B, Schonicke P, Hille C (2016) Green biorefinery—industrial implementation. Food Chem 197:1341–1345
30. Kanjilal B, Noshadi I, Bautista EJ, Srivastava R, Parnas RS (2015) Batch, design optimization, and DNA sequencing study for continuous 1,3-propanediol production from waste glycerol by a soil-based inoculum. Appl Microbiol Biotechnol 99(5):2105–2117
31. Kato S, Haruta S, Cui ZJ, Ishii M, Igarashi Y (2004) Effective cellulose degradation by a mixed-culture system composed of a cellulolytic Clostridium and aerobic non-cellulolytic bacteria. FEMS Microbiol Ecol 51(1):133–142
32. Lee HS, Krajmalinik-Brown R, Zhang H, Rittmann BE (2009) An electron-flow model can predict complex redox reactions in mixed-culture fermentative BioH2: microbial ecology evidence. Biotechnol Bioeng 104(4):687–697
33. Lemos PC, Serafim LS, Reis MA (2006) Synthesis of polyhydroxyalkanoates from different short-chain fatty acids by mixed cultures submitted to aerobic dynamic feeding. J Biotechnol 122(2):226-238
34. Li CL, Fang HHP (2007) Fermentation hydrogen production from wastewater and solid wastes by mixed cultures. Crit Rev Environ Sci Technol 37(1):1–39
35. Lin L, Li T, Dai S, Yu JL, Chen XQ, Wang LY, Wang YG, Hua YJ, Tian B (2016) Autoinducer-2 signaling is involved in regulation of stress-related genes of Deinococcus radiodurans. Arch Microbiol 198(1):43–51
36. Liu B, Christiansen K, Parnas R, Xu Z, Li B (2013) Optimizing the production of hydrogen and 1,3-propanediol in anaerobic fermentation of biodiesel glycerol. Int J Hydrogen Energy 38(8):3196–3205
37. Metsoviti M, Paramithiotis S, Drosinos EH, Galiotou-Panayotou M, Nychas G-JE, Zeng A-P, Papanikolaou S (2012a) Screening of bacterial strains capable of converting biodiesel-derived raw glycerol into 1,3-propanediol, 2,3-butanediol and ethanol. Eng Life Sci 12(1):57–68
38. Metsoviti M, Paraskevaidi K, Koutinas A, Zeng A-P, Papanikolaou S (2012b) Production of 1,3-propanediol, 2,3-butanediol and ethanol by a newly isolated Klebsiella oxytoca strain growing on biodiesel-derived glycerol based media. Process Biochem 47(12):1872–1882
39. Metsoviti M, Zeng AP, Koutinas AA, Papanikolaou S (2013) Enhanced 1,3-propanediol production by a newly isolated Citrobacter freundii strain cultivated on biodiesel-derived waste glycerol through sterile and non-sterile bioprocesses. J Biotechnol 163(4):408–418
40. Miller MB, Bassler BL (2001) Quorum sensing in bacteria. Annu Rev Microbiol 55:165–199
41. Minty JJ, Singer ME, Scholz SA, Bae CH, Ahn JH, Foster CE, Liao JC, Lin XN (2013) Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass. Proc Natl Acad Sci 110(36):14592–14597
42. Moita R, Freches A, Lemos PC (2014) Crude glycerol as feedstock for polyhydroxyalkanoates production by mixed microbial cultures. Water Res 58(3):9–20
43. Nakamura CE, Whited GM (2003) Metabolic engineering for the microbial production of 1,3-propanediol. Curr Opin Biotechnol 14(5):454–459
44. Nishio N, Nakashimada Y (2007) Recent development of anaerobic digestion processes for energy recovery from wastes. J Biosci Bioeng 103(2):105–112
45. Nowak MA (2006) Five rules for the evolution of cooperation. Science 314(5805):1560–1563
46. Oh SE, Ginkel SV, Logan BE (2003) The relative effectiveness of pH control and heat treatment for enhancing biohydrogen gas production. Environ Sci Technol 37(22):5186–5190
47. Olson DG, Mcbride JE, Shaw AJ, Lynd LR (2012) Recent progress in consolidated bioprocessing. Curr Opin Biotechnol 23(3):396–405
48. Park H, Yeo S, Jia Y, Lee J, Yang J, Park S, Shin H, Holzapfel W (2014) Autoinducer-2 associated inhibition by Lactobacillus sakei NR28 reduces virulence of enterohaemorrhagic Escherichia coli O157:H7. Food Control 45:62–69
49. Parsek MR, Greenberg EP (2000) Acyl-homoserine lactone quorum sensing in Gram-negative bacteria: a signaling mechanism involved in associations with higher organisms. Proc Natl Acad Sci 97(16):8789–8793
50. Pereira MC, Thompson JA, Xavier KB (2013) AI-2-mediated signalling in bacteria. FEMS Microbiol Rev 37(2):156–181
51. Raghunandan K, McHunu S, Kumar A, Kumar KS, Govender A, Permaul K, Singh S (2014) Biodegradation of glycerol using bacterial isolates from soil under aerobic conditions. J Environ Sci Health A Tox Hazard Subst Environ Eng 49(1):85–92
52. Rahul M, Matti K, Ville S (2012) Bioconversion of crude glycerol from biodiesel production to hydrogen. Int J Hydrogen Energy 37(17):12198–12204
53. Rodriguez A, Wojtusik M, Ripoll V, Santos VE, Garcia-Ochoa F (2015) 1,3-Propanediol production from glycerol with a novel biocatalyst Shimwellia blattae ATCC 33430: operational conditions and kinetics in batch cultivations. Bioresour Technol 200:830–837
54. Röske I, Sabra W, Nacke H, Daniel R, Zeng AP, Antranikian G, Sahm K (2014) Microbial community composition and dynamics in high-temperature biogas reactors using industrial bioethanol waste as substrate. Appl Microbial Biotechnol 98(21):9095–9106
55. Sabra W, Zeng AP (2014) Mixed microbial cultures for industrial biotechnology: success, chance and challenges, 7th edn. Industrial Biocatalysis, Grunwald
56. Sabra W, Dietz D, Tjahjasari D, Zeng AP (2010) Biosystems analysis and engineering of microbial consortia for industrial biotechnology. Eng Life Sci 10(5):407–421
57. Sabra W, Dietz D, Zeng AP (2013) Substrate limited co-culture for efficient roduction of propionic acid from flour hydrolysate. Appl Microbiol Biotechnol 97:5771–5777
58. Sabra W, Röske I, Sahm K, Antranikian G, Zeng AP (2015) Metabolic and microbial characterization of high-temperature biogas reactors treating stillage from an industrial bioethanol process. Eng Life Sci 15(7):743–750
59. Schertzer JW, Boulette ML, Whiteley M (2009) More than a signal: non-signaling properties of quorum sensing molecules. Trends Microbiol 17(5):189–195
60. Selembo PA, Perez JM, Lloyd WA, Logan BE (2009) High hydrogen production from glycerol or glucose by electrohydrogenesis using microbial electrolysis cells. Int J Hydrogen Energy 34(13):5373–5381
61. Shou W, Ram S, Vilar JMG (2007) Synthetic cooperation in engineered yeast populations. Proc Natl Acad Sci USA 104(6):1877–1882
62. Solomon KV, Haitjema CH, Henske JK, Gilmore SP, Borges-Rivera D, Lipzen A, Brewer HM, Purvine SO, Wright AT, Theodorou MK, Grigoriev IV, Regev A, Thompson DA, O’Malley MA (2016) Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes. Science 351(6278):1192–1195
63. Spiegelman D, Whissell G, Greer CW (2005) A survey of the methods for the characterization of microbial consortia and communities. Can J Microbiol 51(5):355–386
64. Stolyar S, Dien SV, Hillesland KL, Pinel N, Lie TJ, Leigh JA, Stahl DA (2007) Metabolic modeling of a mutualistic microbial community. Mol Syst Biol 3(1):92–106
65. Streit WR, Daniel R, Jaeger KE (2004) Prospecting for biocatalysts and drugs in the genomes of non-cultured microorganisms. Curr Opin Biotechnol 15(4):285–290
66. Sun LH, Song ZY, Sun YQ, Xiu ZL (2010) Dynamic behavior of glycerol–glucose co-fermentation for 1,3-propanediol production by Klebsiella pneumoniae DSM 2026 under micro-aerobic conditions. World J Microbiol Biotechnol 26(8):1401–1407
67. Szymanowska-Powalowska D, Piatkowska J, Leja K (2013) Microbial purification of postfermentation medium after 1,3-PD production from raw glycerol. Biomed Res Int 1:949107–949114
68. Tabasco R, García-Cayuela T, Peláez C, Requena T (2009) Lactobacillus acidophilus La-5 increases lactacin B production when it senses live target bacteria. Int J Food Microbiol 132(2–3):109–116
69. Temudo MF, Muyzer G, Kleerebezem R, van Loosdrecht MC (2008) Diversity of microbial communities in open mixed culture fermentations: impact of the pH and carbon source. Appl Microbiol Biotechnol 80(6):1121–1130
70. Teusink B, Wiersma A, Molenaar D, Francke C, de Vos WM, Siezen RJ, Smid EJ (2006) Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model. J Biol Chem 281(52):40041–40048
71. Vandamme P, Coenye T (2004) Taxonomy of the genus Cupriavidus: a tale of lost and found. Int J Syst Evol Microbiol 54(6):2285–2289
72. Wen ZQ, Wu MB, Lin YJ, Yang LR, Lin JP, Cen PL (2014) Artificial symbiosis for acetone-butanol-ethanol (ABE) fermentation from alkali extracted deshelled corn cobs by co-culture of Clostridium beijerinckii and Clostridium cellulovorans. Microb Cell Fact 13(1):1–11
73. Wilkens E, Ringel AK, Hortig D, Willke T, Vorlop KD (2012) High-level production of 1, 3-propanediol from crude glycerol by Clostridium butyricum AKR102a. Appl Microbiol Biotechnol 93(3):1057–1063
74. Williams P (2007) Quorum sensing, communication and cross-kingdom signalling in the bacterial world. Microbiol 153(12):3923–3938
75. Xiu ZL, Zeng AP (2008) Present state and perspective of downstream processing of biologically produced 1,3-propanediol and 2,3-butanediol. Appl Microbiol Biotechnol 78(6):917–926
76. Xiu ZL, Liu HF, Chen Y, Jiang LL, Sun YQ (2015) A method of fermentation of 1,3-propanediol from glycerol by mixed culture: CN, 104774879A
77. Yang G, Tian JS, Li JL (2007) Fermentation of 1,3-propanediol by a lactate deficient mutant of Klebsiella oxytoca under microaerobic conditions. Appl Microbiol Biotechnol 73(5):1017–1024
78. Yim G, Wang HHM, Davies J (2006) The truth about antibiotics. Int J Med Microbiol 296:163–170
79. Yim G, Wang HMH, Davies J (2007) Antibiotics as signalling molecules. Philos Trans R Soc London B Biol Sci 362:1195–1200
80. Zeng AP, Sabra W (2011) Microbial production of diols as platform chemicals: recent progresses. Curr Opin Biotechnol 22(6):749–757
81. Zhang J, Liu J, Shi Z, Liu L, Chen J (2010) Manipulation of B. megaterium growth for efficient 2-KLG production by K. vulgare. Process Biochem 45(4):602–606
82. Zuroff TR, Curtis WR (2012) Developing symbiotic consortia for lignocellulosic biofuel production. Appl Microbiol Biotechnol 93:1423–1435