Improved growth media and culture techniques for genetic analysis and assessment of biomass utilization by Caldicellulosiruptor bescii

Journal of Industrial Microbiology and Biotechnology

Volumn 40, Issue 1, 2013, Pages 41-49

  Farkas, Joel ^a,b   Chung, Daehwan ^a,b   Cha, Minseok ^a,b   Copeland, Jennifer ^a,b   Grayeski, Philip ^a,b   Westpheling, Janet ^a,b  

^a University of Georgia   (United States)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

Biomass utilization; Caldicellulosiruptor; Defined growth media

Indexed keywords

CARBON; DNA;

ARTICLE; BACTERIUM CULTURE; BIOMASS; BIOMASS ALLOCATION; CALDICELLULOSIRUPTOR BESCII; CARBON SOURCE; CULTURE MEDIUM; CYTOLYSIS; ELECTROPORATION; GENETIC ANALYSIS; GENETIC MANIPULATION; GENETIC TRANSFORMATION; GROWTH INHIBITION; NONHUMAN; OPTICAL DENSITY; OSMOLARITY; OSMOTIC STRESS; THERMOPHILIC BACTERIUM;

AGAR; BIOMASS; CELL CULTURE TECHNIQUES; CULTURE MEDIA; CULTURE TECHNIQUES; GRAM-POSITIVE BACTERIA; TRANSFORMATION, BACTERIAL;

BACTERIA (MICROORGANISMS); CALDICELLULOSIRUPTOR;

EID: 84873710352     PISSN: 13675435     EISSN: 14765535     Source Type: Journal    
DOI: 10.1007/s10295-012-1202-1     Document Type: Article

References (30)

1. Adams MW, Holden JF, Menon AL, Schut GJ, Grunden AM, Hou C, Hutchins AM, Jenny FE Jr, Kim C, Ma K, Pan G, Roy R, Sapra R, Story SV, Verhagen MF (2001) Key role for sulfur in peptide metabolism and in regulation of three hydrogenases in the hyperthermophilic archaeon Pyrococcus furiosus. J Bacteriol 183(2):716-724
2. Blumer-Schuette SE, Giannone RJ, Zurawski JV, Ozdemir I, Ma Q, Yin Y, Xu Y, Kataeva I, Poole FL II, Adams MW, Hamilton-Brehm SD, Elkins JG, Larimer FW, Land ML, Hauser LJ, Cottingham RW, Hettich RL, Kelly RM (2012) Caldicellulosiruptor core and pangenomes reveal determinants for noncellulosomal thermophilic deconstruction of plant biomass. J Bacteriol 194(15):4015-4028. doi: 10.1128/JB.00266-12
3. Blumer-Schuette SE, Kataeva I, Westpheling J, Adams MW, Kelly RM (2008) Extremely thermophilic microorganisms for biomass conversion: status and prospects. Curr Opin Biotechnol 19(3):210-217. doi: 10.1016/j.copbio.2008.04.007
4. Blumer-Schuette SE, Ozdemir I, Mistry D, Lucas S, Lapidus A, Cheng JF, Goodwin LA, Pitluck S, Land ML, Hauser LJ, Woyke T, Mikhailova N, Pati A, Kyrpides NC, Ivanova N, Detter JC, Walston-Davenport K, Han S, Adams MW, Kelly RM (2011) Complete genome sequences for the anaerobic, extremely thermophilic plant biomass-degrading bacteria Caldicellulosiruptor hydrothermalis, Caldicellulosiruptor kristjanssonii, Caldicellulosiruptor kronotskyensis, Caldicellulosiruptor owensenis, and Caldicellulosiruptor lactoaceticus. J Bacteriol. doi: 10.1128/JB.01515-10
5. Bredholt S, Sonne-Hansen J, Nielsen P, Mathrani IM, Ahring BK (1999) Caldicellulosiruptor kristjanssonii sp. nov., a cellulolytic, extremely thermophilic, anaerobic bacterium. Int J Syst Bacteriol 49(Pt 3):991-996
6. Chung D, Farkas J, Cha M, Westpheling J (2012) A replicating shuttle vector for Caldicellulosiruptor species. In preparation
7. Chung D, Farkas J, Huddleston JR, Olivar E, Westpheling J (2012) Methylation by a unique α-class N4-cytosine methyltransferase is required for DNA transformation of Caldicellulosiruptor bescii DSM6725. PLoS One 7(8):e43844
8. Chung D, Huddleston JR, Farkas J, Westpheling J (2011) Identification and characterization of CbeI, a novel thermostable restriction enzyme from Caldicellulosiruptor bescii DSM 6725 and a member of a new subfamily of HaeIII-like enzymes J Ind Microbiol Biotechnol 38(11):1867-1877
9. Dam P, Kataeva I, Yang SJ, Zhou F, Yin Y, Chou W, Poole FL, 2nd, Westpheling J, Hettich R, Giannone R, Lewis DL, Kelly R, Gilbert HJ, Henrissat B, Xu Y, Adams MW (2011) Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptor bescii DSM 6725. Nucleic Acids Res. doi: 10.1093/nar/gkq1281
10. Elkins JG, Lochner A, Hamilton-Brehm SD, Davenport KW, Podar M, Brown SD, Land ML, Hauser LJ, Klingeman DM, Raman B, Goodwin LA, Tapia R, Meincke LJ, Detter JC, Bruce DC, Han CS, Palumbo AV, Cottingham RW, Keller M, Graham DE (2010) Complete genome sequence of the cellulolytic thermophile Caldicellulosiruptor obsidiansis OB47T. J Bacteriol 192(22):6099-6100. doi: 10.1128/JB.00950-10
11. Hamilton-Brehm SD, Mosher JJ, Vishnivetskaya T, Podar M, Carroll S, Allman S, Phelps TJ, Keller M, Elkins JG (2010) Caldicellulosiruptor obsidiansis sp. nov., an anaerobic, extremely thermophilic, cellulolytic bacterium isolated from Obsidian Pool, Yellowstone National Park. Appl Environ Microbiol 76(4):1014-1020. doi: 10.1128/AEM.01903-09
12. Holwerda EK, Hirst KD, Lynd LR (2012) A defined growth medium with very low background carbon for culturing Clostridium thermocellum. J Ind Microbiol Biotechnol. doi: 10.1007/s10295-012-1091-3
13. Huang CY, Patel BK, Mah RA, Baresi L (1998) Caldicellulosiruptor owensensis sp. nov., an anaerobic, extremely thermophilic, xylanolytic bacterium. Int J Syst Bacteriol 48 (Pt 1):91-97
14. Kataeva IA, Yang SJ, Dam P, Poole FL II, Yin Y, Zhou F, Chou WC, Xu Y, Goodwin L, Sims DR, Detter JC, Hauser LJ, Westpheling J, Adams MW (2009) Genome sequence of the anaerobic, thermophilic, and cellulolytic bacterium "Anaerocellum thermophilum" DSM 6725. J Bacteriol 191(11):3760-3761. doi: 10.1128/JB.00256-09
15. Ljunggren M, Willquist K, Zacchi G, van Niel EW (2011) A kinetic model for quantitative evaluation of the effect of hydrogen and osmolarity on hydrogen production by Caldicellulosiruptor saccharolyticus. Biotechnol Biofuels 4(1):31. doi: 10.1186/1754-6834-4-31
16. Miroshnichenko ML, Kublanov IV, Kostrikina NA, Tourova TP, Kolganova TV, Birkeland NK, Bonch-Osmolovskaya EA (2008) Caldicellulosiruptor kronotskyensis sp. nov. and Caldicellulosiruptor hydrothermalis sp. nov., two extremely thermophilic, cellulolytic, anaerobic bacteria from Kamchatka thermal springs. Int J Syst Evol Microbiol 58(Pt 6):1492-1496. doi: 10.1099/ijs.0.65236-0
17. Mladenovska Z, Mathrani IM, Ahring BK (1995) Isolation and Characterization of Caldicellulosiruptor lactoaceticus sp. nov., an extremely thermophilic, cellulolytic, anaerobic bacterium. Arch Microbiol 163(3):223-230
18. Nielsen P, Mathrani IM, Ahring BK (1993) Thermoanaerobium acetigenum spec nov., a new anaerobic, extremely thermophilic, xylanolytic non-spore-forming bacterium isolated from an Icelandic hot-spring. Arch Microbiol 159(5):460-464
19. Onyenwoke RU, Lee YJ, Dabrowski S, Ahring BK, Wiegel J (2006) Reclassification of Thermoanaerobium acetigenum as Caldicellulosiruptor acetigenus comb. nov and emendation of the genus description. Int J Syst Evol Micr 56:1391-1395. doi: 10.1099/Ijs.0.63723-0
20. Rainey FA, Donnison AM, Janssen PH, Saul D, Rodrigo A, Bergquist PL, Daniel RM, Stackebrandt E, Morgan HW (1994) Description of Caldicellulosiruptor saccharolyticus gen. nov., sp. nov: an obligately anaerobic, extremely thermophilic, cellulolytic bacterium. FEMS Microbiol Lett 120(3):263-266
21. Sigma-Aldrich (2012) Phytagel product information
22. Svetlichnyi VA, Svetlichnaya TP, Chernykh NA, Zavarzin GA (1990) Anaerocellum thermophilum gen. nov sp. nov. an extremely thermophilic cellulolytic eubacterium isolated from hot-springs in the valley of geysers. Microbiology 59(5):598-604
23. van de Werken HJ, Verhaart MR, VanFossen AL, Willquist K, Lewis DL, Nichols JD, Goorissen HP, Mongodin EF, Nelson KE, van Niel EW, Stams AJ, Ward DE, de Vos WM, van der Oost J, Kelly RM, Kengen SW (2008) Hydrogenomics of the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus. Appl Environ Microbiol 74(21):6720-6729. doi: 10.1128/AEM.00968-08
24. van Niel EW, Claassen PA, Stams AJ (2003) Substrate and product inhibition of hydrogen production by the extreme thermophile, Caldicellulosiruptor saccharolyticus. Biotechnol Bioeng 81(3):255-262. doi: 10.1002/bit.10463
25. Vanfossen AL, Ozdemir I, Zelin SL, Kelly RM (2011) Glycoside hydrolase inventory drives plant polysaccharide deconstruction by the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus. Biotechnol Bioeng. doi: 10.1002/bit.23093
26. Widdel F, Kohring GW, Mayer F (1983) Studies on dissimilatory sulfate-reducing bacteria that decompose fatty-acids III. Characterization of the Filamentous Gliding Desulfonema limicola gen. nov sp. nov., and Desulfonema magnum sp. nov. Arch Microbiol 134(4):286-294
27. Willquist K, Claassen PAM, van Niel EWJ (2009) Evaluation of the influence of CO2 on hydrogen production by Caldicellulosiruptor saccharolyticus. Int J Hydrogen Energy 34(11):4718-4726
28. Wolin EA, Wolin MJ, Wolfe RS (1963) Formation of methane by bacterial extracts. J Biol Chem 238:2882-2886
29. Yang SJ, Kataeva I, Hamilton-Brehm SD, Engle NL, Tschaplinski TJ, Doeppke C, Davis M, Westpheling J, Adams MW (2009) Efficient degradation of lignocellulosic plant biomass, without pretreatment, by the thermophilic anaerobe "Anaerocellum thermophilum" DSM 6725. Appl Environ Microbiol 75(14):4762-4769. doi: 10.1128/AEM.00236-09
30. Yang SJ, Kataeva I, Wiegel J, Yin Y, Dam P, Xu Y, Westpheling J, Adams MW (2010) Classification of 'Anaerocellum thermophilum' strain DSM 6725 as Caldicellulosiruptor bescii sp. nov. Int J Syst Evol Microbiol 60(Pt 9):2011-2015. doi: 10.1099/ijs.0.017731-0