Facultative anaerobe Caldibacillus debilis GB1: Characterization and use in a designed aerotolerant, cellulose-degrading coculture with Clostridium thermocellum

Applied and Environmental Microbiology

Volumn 81, Issue 16, 2015, Pages 5567-5573

  Wushke, Scott ^a   Levin, David B ^a   Cicek, Nazim ^a   Sparling, Richard ^a  

^a UNIVERSITY OF MANITOBA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CLOSTRIDIUM; SELF ASSEMBLY;

ANAEROBIC CONDITIONS; ANAEROBIC METABOLISM; CLOSTRIDIUM THERMOCELLUM; CONSOLIDATED BIO-PROCESSING; EXPERIMENTAL CONDITIONS; FACULTATIVE ANAEROBES; PHYSIOLOGICAL DIFFERENCES; RESPIRATORY PROTECTION;

CELLULOSE;

BACTERIUM; BIODEGRADATION; CELLULOSE; METABOLISM; OXIC CONDITIONS; OXIDATION; SYNERGISM;

CALDIBACILLUS; CLOSTRIDIUM THERMOCELLUM;

BACTERIAL DNA; CELLULOSE; LACTIC ACID DERIVATIVE; RIBOSOME DNA; RNA 16S;

AEROBIC METABOLISM; ANAEROBIC GROWTH; BACILLACEAE; BIOTRANSFORMATION; CHEMISTRY; CLASSIFICATION; CLOSTRIDIUM THERMOCELLUM; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MICROBIAL CONSORTIUM; MOLECULAR GENETICS; OXIDATION REDUCTION REACTION;

AEROBIOSIS; ANAEROBIOSIS; BACILLACEAE; BIOTRANSFORMATION; CELLULOSE; CLOSTRIDIUM THERMOCELLUM; DNA, BACTERIAL; DNA, RIBOSOMAL; LACTATES; MICROBIAL CONSORTIA; MOLECULAR SEQUENCE DATA; OXIDATION-REDUCTION; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

EID: 84937865855     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.00735-15     Document Type: Article

References (38)

1. Levin D, Carere C, Cicek N, Sparling R. 2009. Challenges for biohydrogen production via direct lignocellulose fermentation. Int J Hydrogen Energy 34:7390-7403. http://dx.doi.org/10.1016/j.ijhydene.2009.05.091.
2. Lynd LR, Van Zyl WH, McBride JE, Laser M. 2005. Consolidated bioprocessing of cellulosic biomass: an update. Curr Opin Chem Biol 16:577-583. http://dx.doi.org/10.1016/j.copbio.2005.08.009.
3. Biswas R, Prabhu S, Lynd LR, Guss AM. 2014. Increase in ethanol yield via elimination of lactate production in an ethanol-tolerant mutant of Clostridium thermocellum. PLoS One 9:e86389. http://dx.doi.org/10.1371/journal.pone.0086389.
4. Geng A, Ye Y, Qian C, Yan X. 2010. Effect of key factors on hydrogen production from cellulose in a co-culture of Clostridium thermocellum and Clostridium thermopalmarium. Bioresour Technol 101:4029-4033. http://dx.doi.org/10.1016/j.biortech.2010.01.042.
5. Sharma G. 1991. Prospects for ethanol production from cellulose with Clostridium thermocellum-Bacillus stearothermophilus co-cultures. Biotechnol Lett 13:761-764. http://dx.doi.org/10.1007/BF01088183.
6. Kato S, Haruta S, Cui ZJ, Ishii M, Yokota A, Igarashi Y. 2004. Clostridium straminisolvens sp. nov., a moderately thermophilic, aerotolerant and cellulolytic bacterium isolated from a cellulose degrading bacterial community. Int J Syst Evol Microbiol 54:2043-2047. http://dx.doi.org/10.1099/ijs.0.63148-0.
7. Ng TK, Weimer PJ, Zeikus JG. 1977. Cellulolytic and physiological properties of Clostridium thermocellum. Arch Microbiol 114:1-7. http://dx.doi.org/10.1007/BF00429622.
8. Lee WK, Fujisawa T, Kawamura S, Itoh K, Mitsuoka T. 1989. Clostridium intestinalis sp. nov., an aerotolerant species isolated from the feces of cattle and pigs. Int J Syst Bacteriol 39:334-336. http://dx.doi.org/10.1099/00207713-39-3-334.
9. O'Brien RW, Morris JG. 1971. Oxygen and the growth and metabolism of Clostridium acetobutylicum. J Gen Microbiol 68:307-318. http://dx.doi .org/10.1099/00221287-68-3-307.
10. Hillmann F, Döring C, Riebe O, Ehrenreich A, Fischer RJ, Bahl H. 2009. The role of PerR in O2-affected gene expression of Clostridium acetobutylicum. J Bacteriol 191:6082-6093. http://dx.doi.org/10.1128/JB.00351-09.
11. Miyazaki K, Irbis C, Takada J, Matsurra A. 2008. An ability of isolated strains to efficiently cooperate in ethanolic fermentation of agricultural plant refuse under initially aerobic thermophilic conditions: oxygen deletion process appended to consolidated bioprocessing (CBP). Bioresour Technol 99:1768-1775. http://dx.doi.org/10.1016/j.biortech.2007.03.045.
12. Ronan P, Yeung CW, Schellenberg J, Sparling R, Wolfaardt GM, Hausner M. 2013. A versatile and robust aerotolerant microbial community capable of cellulosic ethanol production. Bioresour Technol 129:156-163. http://dx.doi.org/10.1016/j.biortech.2012.10.164.
13. Tran H, Cheirsilp B, Hodgson B, Umsakul K. 2010. Potential use of Bacillus subtilis in a co-culture with Clostridium butylicum for acetonebutanol-ethanol production from cassava starch. Biochem Eng J 48:260-267. http://dx.doi.org/10.1016/j.bej.2009.11.001.
14. Zuroff TR, Xiques SB, Curtis WR. 2013. Consortia-mediated bioprocessing of cellulose to ethanol with a symbiotic Clostridium phytofermentans/yeast co-culture. Biotechnol Biofuels 6:59. http://dx.doi.org/10.1186/1754-6834-6-59.
15. Zuroff TR, Curtis WR. 2012. Developing symbiotic consortia for lignocellulosic biofuel production. Appl Microbiol Biotechnol 93:1423-1435. http://dx.doi.org/10.1007/s00253-011-3762-9.
16. Wushke S, Levin DB, Cicek N, Sparling R. 2013. Characterization of enriched aerotolerant cellulose-degrading communities for biofuels production using differing selection pressures and inoculum sources. Can J Microbiol 59:679-683. http://dx.doi.org/10.1139/cjm-2013-0430.
17. Banat I, Marchant R, Rahman T. 2004. Geobacillus debilis sp. nov., a novel obligately thermophilic bacterium isolated from a cool soil environment, and reassignment of Bacillus pallidus to Geobacillus pallidus comb. nov. Int J Syst Evol Microbiol 54:2197-2201. http://dx.doi.org/10.1099/ijs .0.63231-0.
18. Islam R, Cicek N, Sparling R, Levin D. 2006. Effect of substrate loading on hydrogen production during anaerobic fermentation by Clostridium thermocellum 27405. Appl Microbiol Biotechnol 72:576-583. http://dx .doi.org/10.1007/s00253-006-0316-7.
19. Bradford MM. 1976. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of proteindye binding. Anal Biochem 72:248-254. http://dx.doi.org/10.1016/0003-2697(76)90527-3.
20. Rydzak T, Levin D, Cicek N, Sparling R. 2009. Growth phase-dependant enzyme profile of pyruvate catabolism and end-product formation in Clostridium thermocellum ATCC 27405. J Biotechnol 140:169-175. http://dx.doi.org/10.1016/j.jbiotec.2009.01.022.
21. Ruxton GD. 2006. The unequal variance t-test is an underused alternative to Student's t-test and the Mann-WhitneyUtest. Behav Ecol 17:688-690. http://dx.doi.org/10.1093/beheco/ark016.
22. Ellis LD, Holwerda EK, Hogsett D, Rogers S, Shao X, Tschaplinski T, Lynd LR. 2012. Closing the carbon balance for fermentation by Clostridium thermocellum (ATCC 27405). Bioresour Technol 103:293-299. http://dx.doi.org/10.1016/j.biortech.2011.09.128.
23. Markowitz VM, Ivanova NN, Szeto E, Palaniappan K, Chu K, Dalevi D, Kyrpides NC. 2008. IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res 36:D534-D538. http://dx.doi.org/10.1093/nar/gkm869.
24. Cardinale M, Brusetti L, Quatrini P, Borin S, Puglia AM, Rizzi A, Daffonchio D. 2004. Comparison of different primer sets for use in automated ribosomal intergenic spacer analysis of complex bacterial communities. Appl Environ Microbiol 70:6147-6156. http://dx.doi.org/10.1128/AEM.70.10.6147-6156.2004.
25. Coorevits A, Dinsdale AE, Halket G, Lebbe L, De Vos P, Van Landschoot A, Logan NA. 2012. Taxonomic revision of the genus Geobacillus: emendation of Geobacillus, G. stearothermophilus, G. jurassicus, G. toebii, G. thermodenitrificans and G. thermoglucosidans (nom. corrig., formerly 'thermoglucosidasius'); transfer of Bacillus thermantarcticus to the genus as G. thermantarcticus comb. nov.; proposal of Caldibacillus debilis gen. nov., comb. nov.; transfer of G. tepidamans to Anoxybacillus as A. tepidamans comb. nov.; and proposal of Anoxybacillus caldiproteolyticus sp. nov. Int J Syst Evol Microbiol 62:1470-1485. http://dx.doi.org/10.1099/ijs.0.030346-0.
26. Takahashi N, Abbe K, Takahashi-Abbe S, Yamada T. 1987. Oxygen sensitivity of sugar metabolism and interconversion of pyruvate formatelyase in intact cells of Streptococcus mutans and Streptococcus sanguis. Infect Immun 55:652-656.
27. Cripps R, Eley K, Leak D, Rudd B, Taylor M, Todd M, Boakes S, Martin S, Atkinson T. 2009. Metabolic engineering of Geobacillus thermoglucosidasius for high yield ethanol production. Metab Eng 11:398-408. http://dx.doi.org/10.1016/j.ymben.2009.08.005.
28. Peng H, Wu G, Shao W. 2008. The aldehyde/alcohol dehydrogenase (AdhE) in relation to the ethanol formation in Thermoanaerobacter ethanolicus JW200. Anaerobe 14:125-127. http://dx.doi.org/10.1016/j.anaerobe.2007.09.004.
29. Farmer WR, Liao JC. 1997. Reduction of aerobic acetate production by Escherichia coli. Appl Microbiol Biotechnol 63:3205-3210.
30. Tang YJ, Sapra R, Joyner D, Hazen TC, Myers S, Reichmuth D, Keasling JD. 2009. Analysis of metabolic pathways and fluxes in a newly discovered thermophilic and ethanol tolerant Geobacillus strain. Biotechnol Bioeng 102:1377-1386. http://dx.doi.org/10.1002/bit.22181.
31. Danner H, Neureiter M, Madzingaidzo L, Gartner M, Braun R. 1998. Bacillus stearothermophilus for thermophilic production of L-lactic acid. Appl Biochem Biotechnol 70:895-903. http://dx.doi.org/10.1007/BF02920200.
32. Zigha A, Rosenfeld E, Schmitt P, Duport C. 2007. The redox regulator Fnr is required for fermentative growth and enterotoxin synthesis in Bacillus cereus F4430/73. J Bacteriol 189:2813-2824. http://dx.doi.org/10.1128/JB.01701-06.
33. Fortina MG, Pukall R, Schumann P, Mora D, Parini C, Manachini PL, Stackebrandt E. 2001. Ureibacillus ge. nov., a new genus to accommodate Bacillus thermosphaericus (Andersson et al. 1995), emendation of Ureibacillus thermosphaericus and description of Ureibacillus terrenus sp. nov. Int J Syst Evol Microbiol 51:447-455.
34. Biswas R, Zheng T, Olson DG, Lynd LR, Guss AM. 2015. Elimination of hydrogenase active site assembly blocks H2 production and increases ethanol yield in Clostridium thermocellum. Biotechnol Biofuels 8:20. http://dx.doi.org/10.1186/s13068-015-0204-4.
35. Islam R, Cicek N, Sparling R, Levin D. 2009. Influence of initial cellulose concentration on the carbon flow distribution during batch fermentation by Clostridium thermocellum ATCC 27405. Appl Microbiol Biotechnol 82:141-148. http://dx.doi.org/10.1007/s00253-008-1763-0.
36. He Q, Hemme CL, Jiang H, He Z, Zhou J. 2011. Mechanisms of enhanced cellulosic bioethanol fermentation by co-cultivation of Clostridium and Thermoanaerobacter spp. Bioresour Technol 102:9586-9592. doi.org/10.1016/j.biortech.2011.07.098. http://dx.doi.org/10.1016/j .biortech.2011.07.098.
37. De Beer D, Stoodley P, Roe F, Lewandowski Z. 1994. Effects of biofilm structures on oxygen distribution and mass transport. Biotechnol Bioeng 43:1131-1138. http://dx.doi.org/10.1002/bit.260431118.
38. Stewart PS, Franklin MJ. 2008. Physiological heterogeneity in biofilms. Nat Rev Microbiol 6:199-210. http://dx.doi.org/10.1038/nrmicro1838.