Changes in hydrogenase genetic diversity and proteomic patterns in mixed-culture dark fermentation of mono-, di- and tri-saccharides

International Journal of Hydrogen Energy

Volumn 36, Issue 18, 2011, Pages 11654-11665

  Quéméneur, Marianne ^a   Hamelin, Jérôme ^a   Benomar, Saida ^b   Guidici Orticoni, Marie Thérse ^b   Latrille, Eric ^a   Steyer, Jean Philippe ^a   Trably, Eric ^a  

^a LABORATOIRE DE BIOTECHNOLOGIE DE L ENVIRONNEMENT   (France)

^b CNRS   (France)

Author keywords

Anaerobic digestion; CE SSCP; Clostridium; hydA functional genes; Hydrogen; Substrate

Indexed keywords

BATCH EXPERIMENTS; CE-SSCP; CELLOBIOSE; DARK FERMENTATION; GENETIC DIVERSITY; HYDA FUNCTIONAL GENES; HYDROGENASES; LOW COSTS; MALTOTRIOSE; METABOLIC ROUTES; MIXED CULTURES; ORGANIC WASTES; PRODUCTION EFFICIENCY; PRODUCTION PERFORMANCE; PROTEOMIC ANALYSIS; PROTEOMIC APPROACHES;

CARBOHYDRATES; CHAIN LENGTH; FERMENTATION; GENES; GLUCOSE; HYDROGEN; SEWAGE; SUGAR (SUCROSE); VOLATILE FATTY ACIDS;

ANAEROBIC DIGESTION;

EID: 80052151179     PISSN: 03603199     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ijhydene.2011.06.010     Document Type: Article

References (67)

1. F.R. Hawkes, R. Dinsdale, D.L. Hawkes, and I. Hussy Sustainable fermentative hydrogen production: challenges for process optimisation Int J Hydrogen Energy 27 11 and 12 2002 1339 1347
2. F.R. Hawkes, I. Hussy, G. Kyazze, R. Dinsdale, and D.L. Hawkes Continuous dark fermentative hydrogen production by mesophilic microflora: principles and progress Int J Hydrogen Energy 32 2 2007 172 184 (Pubitemid 46108351)
3. X.M. Guo, E. Trably, E. Latrille, H. Carrere, and J.P. Steyer Hydrogen production from agricultural waste by dark fermentation: a review Int J Hydrogen Energy 35 19 2010 10660 10673
4. H.S. Shin, J.H. Youn, and S.H. Kim Hydrogen production from food waste in anaerobic mesophilic and thermophilic acidogenesis Int J Hydrogen Energy 29 13 2004 1355 1363
5. M.L. Chong, V. Sabaratnam, Y. Shirai, and M.A. Hassan Biohydrogen production from biomass and industrial wastes by dark fermentation Int J Hydrogen Energy 34 8 2009 3277 3287
6. J.T. Kraemer, and D.M. Bagley Improving the yield from fermentative hydrogen production Biotechnol Lett 29 5 2007 685 695 (Pubitemid 46569216)
7. C.A. Aceves-Lara, E. Latrille, and J.P. Steyer Optimal control of hydrogen production in a continuous anaerobic fermentation bioreactor Int J Hydrogen Energy 35 19 2010 10710 10718
8. C.L. Li, and H.H.P. Fang Fermentative hydrogen production from wastewater and solid wastes by mixed cultures Crit Rev Environ Sci Tech 37 1 2007 1 39 (Pubitemid 44720064)
9. J.L. Wang, and W. Wan Factors influencing fermentative hydrogen production: a review Int J Hydrogen Energy 34 2 2009 799 811
10. M. Quéméneur, J. Hamelin, E. Latrille, J.-P. Steyer, and E. Trably Functional versus phylogenetic fingerprint analyses for monitoring hydrogen-producing bacterial populations in dark fermentation cultures Int J Hydrogen Energy 36 6 2011 3870 3879
11. W.J. Mitchell Carbohydrate uptake and utilization by Clostridium beijerinckii NCIMB 8052 Anaerobe 2 6 1996 379 384 (Pubitemid 27089310)
12. M.D. Servinsky, J.T. Kiel, N.F. Dupuy, and C.J. Sund Transcriptional analysis of differential carbohydrate utilization by Clostridium acetobutylicum Microbiology 156 2010 3478 3491
13. H. Yokoyama, N. Moriya, H. Ohmori, M. Waki, A. Ogino, and Y. Tanaka Community analysis of hydrogen-producing extreme thermophilic anaerobic microflora enriched from cow manure with five substrates Appl Microbiol Biotechnol 77 1 2007 213 222 (Pubitemid 47573321)
14. S. Singh, A.K. Sudhakaran, P.M. Sarma, S. Subudhi, A.K. Mandal, and G. Gandham Dark fermentative biohydrogen production by mesophilic bacterial consortia isolated from riverbed sediments Int J Hydrogen Energy 35 19 2010 10645 10652
15. Y. Huang, W.M. Zong, X. Yan, R.F. Wang, C.L. Hemme, and J.Z. Zhou Succession of the bacterial community and dynamics of hydrogen producers in a hydrogen-producing bioreactor Appl Environ Microbiol 76 10 2010 3387 3390
16. M. Quéméneur, J. Hamelin, E. Latrille, J.-P. Steyer, and E. Trably Development and application of a functional CE-SSCP fingerprinting method based on [Fe-Fe]-hydrogenase genes for monitoring hydrogen-producing Clostridium in mixed cultures Int J Hydrogen Energy 35 24 2010 13158 13167
17. X. Wang, D. Hoefel, C.P. Saint, P.T. Monis, and B. Jin The isolation and microbial community analysis of hydrogen producing bacteria from activated sludge J Appl Microbiol 103 5 2007 1415 1423 (Pubitemid 47620539)
18. 2-producing bacterial communities from a heat-treated soil inoculum Appl Microbiol Biotechnol 66 2 2004 166 173 (Pubitemid 40068783)
19. M.F. Temudo, G. Muyzer, R. Kleerebezem, and M.C.M. van Loosdrecht Diversity of microbial communities in open mixed culture fermentations: impact of the pH and carbon source Appl Microbiol Biotechnol 80 6 2008 1121 1130
20. D.F. Xing, N.Q. Ren, and B.E. Rittmann Genetic diversity of hydrogen-producing bacteria in an acidophilic ethanol-H-2-coproducing system, analyzed using the Fe-hydrogenase gene Appl Environ Microbiol 74 4 2008 1232 1239 (Pubitemid 351287095)
21. J.H. Jo, C.O. Jeon, D.S. Lee, and J.M. Park Process stability and microbial community structure in anaerobic hydrogen-producing microflora from food waste containing kimchi J Biotechnol 131 3 2007 300 308 (Pubitemid 47371165)
22. H. Janssen, C. Doring, A. Ehrenreich, B. Voigt, M. Hecker, and H. Bahl A proteomic and transcriptional view of acidogenic and solventogenic steady-state cells of Clostridium acetobutylicum in a chemostat culture Appl Microbiol Biotechnol 87 6 2010 2209 2226
23. S. Schaffer, N. Isci, B. Zickner, and P. Durre Changes in protein synthesis and identification of proteins specifically induced during solventogenesis in Clostridium acetobutylicum Electrophoresis 23 1 2002 110 121
24. E. Stackebrandt, I. Kramer, J. Swiderski, and H. Hippe Phylogenetic basis for a taxonomic dissection of the genus Clostridium FEMS Immunol Med Microbiol 24 3 1999 253 258 (Pubitemid 29332600)
25. M.D. Collins, P.A. Lawson, A. Willems, J.J. Cordoba, J. Fernandezgarayzabal, and P. Garcia The phylogeny of the genus Clostridium - proposal of 5 new genera and 11 new species combinations Int J Syst Bacteriol 44 4 1994 812 826 (Pubitemid 24315163)
26. O. Schmidt, H.L. Drake, and M.A. Horn Hitherto unknown [Fe-Fe]-hydrogenase gene diversity in anaerobes and anoxic enrichments from a moderately acidic fen Appl Environ Microbiol 76 6 2010 2027 2031
27. C.H. Hung, C.H. Cheng, L.H. Cheng, C.M. Liang, and C.Y. Lin Application of Clostridium-specific PCR primers on the analysis of dark fermentation hydrogen-producing bacterial community Int J Hydrogen Energy 33 5 2008 1586 1592
28. P.M. Vignais, and B. Billoud Occurrence, classification, and biological function of hydrogenases: an overview Chem Rev 107 10 2007 4206 4272 (Pubitemid 350041744)
29. K.E.S. Tolvanen, V.P. Santala, and M.T. Karp [FeFe]-hydrogenase gene quantification and melting curve analysis from hydrogen-fermenting bioreactor samples Int J Hydrogen Energy 35 8 2010 3433 3439
30. K.E.S. Tolvanen, P.E.P. Koskinen, A.I. Ylikoski, P.K. Ollikka, I.A. Hemmila, and J.A. Puhakka Quantitative monitoring of a hydrogen-producing Clostridium butyricum strain from a continuous-flow, mixed culture bioreactor employing real-time PCR Int J Hydrogen Energy 33 2 2008 542 549 (Pubitemid 351210664)
31. C. Delbes, R. Moletta, and J.J. Godon Bacterial and archaeal 16S rDNA and 16S rRNA dynamics during an acetate crisis in an anaerobic digestor ecosystem FEMS Microbiol Ecol 35 1 2001 19 26 (Pubitemid 32436358)
32. D.H. Lee, Y.G. Zo, and S.J. Kim Nonradioactive method to study genetic profiles of natural bacterial communities by PCR-single-strand-conformation polymorphism Appl Environ Microbiol 62 9 1996 3112 3120
33. M.I. Van Dyke, and A.J. McCarthy Molecular biological detection and characterization of Clostridium populations in municipal landfill sites Appl Environ Microbiol 68 4 2002 2049 2053 (Pubitemid 34280020)
34. P. Peu, H. Brugere, A.M. Pourcher, M. Kerouredan, J.J. Godon, and J.P. Delgenes Dynamics of a pig slurry microbial community during anaerobic storage and management Appl Environ Microbiol 72 5 2006 3578 3585 (Pubitemid 43728013)
35. R.J. Michelland, S. Dejean, S. Combes, L. Fortun-Lamothe, and L. Cauquil StatFingerprints: a friendly graphical interface program for processing and analysis of microbial fingerprint profiles Mol Ecol Resour 9 5 2009 1359 1363
36. Team RDC R: a language and environment for statistical computing 2009 R Foundation for Statistical Computing Vienna, Austria
37. N. Fromin, J. Hamelin, S. Tarnawski, D. Roesti, K. Jourdain-Miserez, and N. Forestier Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns Environ Microbiol 4 11 2002 634 643 (Pubitemid 35442251)
38. K.R. Clarke Nonparametric multivariate analyses of changes in community structure Aust J Ecol 18 1 1993 117 143 (Pubitemid 24409223)
39. E.H. Simpson Measurement of diversity Nature 163 1949 688
40. J.D. Thompson, D.G. Higgins, and T.J. Gibson CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res 22 1994 4673 4680 (Pubitemid 24354800)
41. T. Hall BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT Nucleic Acids Symp Ser 41 1999 95 98
42. M. Kimura A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequence J Mol Biol 16 1980 111 120 (Pubitemid 11166431)
43. N. Saitou, and M. Nei The neighbor-joining method: a new method for reconstructing phylogenetic trees Mol Biol Evol 4 1987 406 425
44. J. Felsenstein Confidence-Limits on Phylogenies - an approach using the bootstrap Evolution 39 4 1985 783 791
45. M. Gouy, S. Guindon, and O. Gascuel SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building Mol Biol Evol 27 2 2010 221 224
46. M. Guiral, L. Prunetti, S. Lignon, R. Lebrun, D. Moinier, and M.T. Giudici-Orticoni New insights into the respiratory chains of the chemolithoautotrophic and hyperthermophilic bacterium Aquifex aeolicus J Proteome Res 8 4 2009 1717 1730
47. 2-reducing supercomplex spanning both inner and outer membranes, isolated from the extreme acidophile Acidithiobacillus ferrooxidans J Biol Chem 283 38 2008 25803 25811
48. P.M. Vignais, B. Billoud, and J. Meyer Classification and phylogeny of hydrogenases FEMS Microbiol Rev 25 4 2001 455 501 (Pubitemid 32778469)
49. M. Ferchichi, E. Crabbe, W. Hintz, G.H. Gil, and A. Almadidy Influence of culture parameters on biological hydrogen production by Clostridium saccharoperbutylacetonicum ATCC 27021 World J Microbiol Biotechnol 21 6-7 2005 855 862 (Pubitemid 41680497)
50. C.J. Chou, K.R. Shockley, S.B. Conners, D.L. Lewis, D.A. Comfort, and M.W.W. Adams Impact of substrate glycoside linkage. And elemental sulfur on bioenergetics, of and hydrogen production by the hyperthermophilic archaeon Pyrococcus furiosus Appl Environ Microbiol 73 21 2007 6842 6853 (Pubitemid 350076802)
51. G. Davila-Vazquez, F. Alatriste-Mondragon, A. de Leon-Rodriguez, and E. Razo-Flores Fermentative hydrogen production in batch experiments using lactose, cheese whey and glucose: influence of initial substrate concentration and pH Int J Hydrogen Energy 33 19 2008 4989 4997
52. Y. Mu, X.J. Zheng, H.Q. Yu, and R.F. Zhu Biological hydrogen production by anaerobic sludge at various temperatures Int J Hydrogen Energy 31 6 2006 780 785
53. H.L. Chin, Z.S. Chen, and C.P. Chou Fedbatch operation using Clostridium acetobutylicum suspension culture as biocatalyst for enhancing hydrogen production Biotechnol Progr 19 2 2003 383 388 (Pubitemid 36420987)
54. W.M. Alalayah, M.S. Kalil, A.A.H. Kadhum, J.M. Jahim, and N.M. Alauj Hydrogen production using Clostridium saccharoperbutylacetonicum N1-4 (ATCC 13564) Int J Hydrogen Energy 33 24 2008 7392 7396
55. Z. Ren, T.E. Ward, B.E. Logan, and J.M. Regan Characterization of the cellulolytic and hydrogen-producing activities of six mesophilic Clostridium species J Appl Microbiol 103 6 2007 2258 2266 (Pubitemid 350191173)
56. J. Mounier, C. Monnet, T. Vallaeys, R. Arditi, A.S. Sarthou, and A. Helias Microbial interactions within a cheese microbial community Appl Environ Microbiol 74 1 2008 172 181
57. C. Allison, and G.T. Macfarlane Physiological and nutritional determinants of protease secretion by Clostridium sporogenes: characterization of six extracellular proteases Appl Microbiol Biotechnol 37 1992 152 159
58. S.L. Li, L.M. Whang, Y.C. Chao, Y.H. Wang, Y.F. Wang, and C.J. Hsiao Effects of hydraulic retention time on anaerobic hydrogenation performance and microbial ecology of bioreactors fed with glucose-peptone and starch-peptone Int J Hydrogen Energy 35 1 2010 61 70
59. 2 in simulated and actual landfill samples Environ Technol 24 4 2003 435 443
60. H.Q. Yu, and Y. Mu Biological hydrogen production in a UASB reactor with granules. II: reactor performance in 3-year operation Biotechnol Bioeng 94 5 2006 988 995 (Pubitemid 44186905)
61. H.B. Ding, G.Y.A. Tan, and J.Y. Wang Caproate formation in mixed-culture fermentative hydrogen production Bioresour Technol 101 24 2010 9550 9559
62. S. Keis, R. Shaheen, and D.T. Jones Emended descriptions of Clostridium acetobutylicum and Clostridium beijerinckii, and descriptions of Clostridium saccharoperbutylacetonicum sp. nov. and Clostridium saccharobutylicum sp. nov Int J Syst Evol Microbiol 51 2001 2095 2103 (Pubitemid 33107430)
63. T. Duangmanee, S.I. Padmasiri, J.J. Simmons, L. Raskin, and S. Sung Hydrogen production by anaerobic microbial communities exposed to repeated heat treatments Water Environ Res 79 9 2007 975 983 (Pubitemid 351631043)
64. E. Petitdemange, F. Caillet, J. Giallo, and C. Gaudin Clostridium cellulolyticum sp. nov., a cellulolytic, mesophilic species from decayed grass Int J Syst Bacteriol 34 2 1984 155 159 (Pubitemid 14103603)
65. H. Seedorf, W.F. Fricke, B. Veith, H. Bruggemann, H. Liesegang, and A. Strittimatter The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features P Natl Acad Sci USA 105 6 2008 2128 2133 (Pubitemid 351439476)
66. M. Calusinska, T. Happe, B. Joris, and A. Wilmotte The surprising diversity of clostridial hydrogenases: a comparative genomic perspective Microbiology 156 2010 1575 1588
67. P.M. Pereira, Q. He, F.M.A. Valente, A.V. Xavier, J.Z. Zhou, and I.A.C. Pereira Energy metabolism in Desulfovibrio vulgaris Hildenborough: insights from transcriptome analysis Ant Leeuw Int J G 93 4 2008 347 362