16S rRNA-targeted probes for specific detection of Thermoanaerobacterium spp., Thermoanaerobacterium thermosaccharolyticum, and Caldicellulosiruptor spp. by fluorescent in situ hybridization in biohydrogen producing systems

International Journal of Hydrogen Energy

Volumn 33, Issue 21, 2008, Pages 6082-6091

  O Thong, Sompong ^a,b   Prasertsan, Poonsuk ^c   Karakashev, Dimitar ^a   Angelidaki, Irini ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b THAKSIN UNIVERSITY   (Thailand)

^c PRINCE OF SONGKLA UNIVERSITY   (Thailand)

Author keywords

16s rRNA gene oligonucleotide; Caldicellulosiruptor spp.; Fluorescent in situ hybridization; Probe; T. Thermosaccharolyticum; Thermophilic and extreme thermo philic reactor systems; Thermotmaerobacterium spp.

Indexed keywords

BACTERIA; FLUORESCENCE; FLUORESCENCE MICROSCOPY; GAS PRODUCERS; GENES; HYDROGEN; MICROORGANISMS; OLIGONUCLEOTIDES; PALM OIL; PROBES; RNA;

16S RRNA GENE; CALDICELLULOSIRUPTOR SPP; FLUORESCENT IN SITU HYBRIDIZATION; REACTOR SYSTEMS; T. THERMOSACCHAROLYTICUM; THERMOTMAEROBACTERIUM SPP;

HYDROGEN PRODUCTION;

EID: 55049140665     PISSN: 03603199     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ijhydene.2008.07.094     Document Type: Article

References (48)

1. Levin DB, Pitt L, Love M. Biohydrogen production: prospects and limitations to practical application. Int J Hydrogen Energy 2004;29:173-85.
2. Angenent LT, Karim K, Al-Dahhan M, Wrenn BA, Espinosa RD. Production of bioenergy and biochemicals from industrial and agricultural wastewater. Trends Biotechnol 2004;22:476-85.
3. Hawkes FR, Dinsdale R, Hawkes DL, Hussy I. Sustainable fermentative hydrogen production: challenges for process optimization. Int J Hydrogen Energy 2002;27:1339-47.
4. Ustak S, Havrland B, Munoz JOJ, Fernandez EC, Lachman J. Experimental verification of various methods for biological hydrogen production. Int J Hydrogen Energy 2007;32:1736-41.
5. Hawkes FR, Hussy I, Kyazze G, Dinsdale R, Hawkes DL. Continuous dark fermentative hydrogen production by mesophilic microflora: principles and progress. Int J Hydrogen Energy 2007;32:172-84.
6. van Niel EWJ, Claassen PAM, Stams AJM. Substrate and product inhibition of hydrogen production by the extreme thermophile, Caldicellulosiruptor saccharolyticus. Biotechnol Bioeng 2003;81:254-62.
7. Kadar Z, De Vrijek T, van Noorden GE, Budde MAW, Szengyel Z, Reczey K, et al. Yields from glucose, xylose, and paper sludge hydrolysate during hydrogen production by the extreme thermophile Caldicellulosiruptor saccharolyticus. Appl Biochem Biotech 2004;113:497-508.
8. Liu H, Zhang T, Fang HHP. Thermophilic hydrogen production from a cellulose-containing wastewater. Biotechnol Lett 2003;25:365-9.
9. Ahn Y, Park EJ, Oh YK, Park S, Webster G, Weightman AJ. Biofilm microbial community of a thermophilic trickling biofilter used for continuous biohydrogen production. FEMS Microbiol Lett 2005;249:31-8.
10. Kanai T, Imanaka H, Nakajima A, Uwamori K, Omori Y, Fukui T, et al. Continuous hydrogen production by the hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1. J Biotechnol 2005;16:271-82.
11. Islam R, Cicek N, Sparling R, Levin D. Effect of substrate loading on hydrogen production during anaerobic fermentation by Clostridium thermocellum 27405. Appl Microbiol Biotechnol 2006;72:576-83.
12. van Niel EWJ, Budde MAW, de Haas GG, van de Wal FJ, Claassen PAM, Stams AJM. Distinctive properties of high hydrogen producing extreme thermophiles, Cadicellulosiruptor saccharolyticus and Thermotoga elfii. Int J Hydrogen Energy 2002;27:1391-8.
13. Zhang T, Liu H, Fang HHP. Biohydrogen production from starch in wastewater under thermophilic condition. J Environ Manage 2003;69:149-56.
14. Shin HS, Youn JH, Kim HS. Hydrogen production from food waste in anaerobic mesophilic and thermophilic acidogenesis. Int J Hydrogen Energy 2004;29:1355-63.
15. O-Thong S, Prasertsan P, Intrasungkha N, Dhamwichukom S, Birkeland NK. Improvement of biohydrogen production and pollution reduction from palm oil mill effluent with nutrient supplementation at thermophilic condition using an anaerobic sequencing batch reactor. Enzyme Microb Technol 2007;41:583-90.
16. Shin HS, Youn JH. Conversion of food waste into hydrogen by thermophilic acidogenesis. Biodegradation 2005;16:33-44.
17. Ueno Y, Haruta S, Igarashi Y. Microbial community in anaerobic hydrogen producing microflora enriched from sludge compost. Appl Microbiol Biotechnol 2001;57:555-62.
18. Ueno Y, Sasaki D, Fukui H, Haruta S, Ishii M, Igarashi Y. Changes in bacterial community during fermentative hydrogen and acid production from organic waste by thermophilic anaerobic microflora. J Appl Microbiol 2006;101: 331-43.
19. O-Thong S, Prasertsan P, Karakashev D, Angelidaki I. Thermophilic fermentative hydrogen production by the newly isolated Thermoanaerobacterium thermosaccharolyticum PSU-2. Int J Hydrogen Energy 2008;33:1204-14.
20. van Ooteghem SA, Beer SK, Paul CY. Hydrogen production by thermophilic bacteria Thermotoga neapolitana. Appl Biochem Biotech 2002;98-100:177-89.
21. de Vrije T, Mars AE, Budde MAW, Lai MH, Dijkema C, de Waard P, et al. Glycolytic pathway and hydrogen yield studies of the extreme thermophile Caldicellulosiruptor saccharolyticus. Appl Microbiol Biotechnol;74:1358-67.
22. Yokoyama H, Moriya N, Ohmori H, Waki M, Ogino A, Tanaka Y. Community analysis of hydrogen producing extreme thermophilic anaerobic microflora enriched from cow manure with five substrates. Appl Microbiol Biotechnol 2007;77:213-22.
23. de Vrije T, de Haas GG, Tan GB, Keijsers ERP, Classen PAM. Pretreatment of Miscanthus for hydrogen production by Thermotoga elfii. Int J Hydrogen Energy 2002;27:1381-90.
24. Jen JC, Chou CH, Hsu PC, Yu SJ, Chen WE, Lay JJ, et al. Flow-FISH analysis and isolation of clostridial strains in an anaerobic semi-solid bio-hydrogen producing system by hydrogenase gene target. Appl Microbiol Biotechnol 2007;74: 1126-34.
25. Amann R, Glöckner FO, Neef A. Modern methods in subsurface microbiology - in situ identification of microorganisms with nucleic acid probes. FEMS Microbiol Rev 1997;20:191-200.
26. Meier H, Amann R, Ludwig W, Schleifer KH. Specific oligonucleotide probes for in situ detection of a major group of gram-positive bacteria with low DMA G+C content. Syst Appl Microbiol 1999;22:186-96.
27. Loy A, Horn M, Wagner M. ProbeBase: an online resource for rRNA-targeted oligonucleotide probes. Nucleic Acids Res 2003;31:514-6.
28. Loy A, Maixner F, Wagner M, Horn M. probeBase - an online resource for rRNA-targeted oligonucleotide probes: new features 2007. Nucleic Acids Res 2007;35:800-4.
29. Hung HC, Cheng CH, Cheng LH, Liang CM, Lin CY. Application of Clostridium- specific PCR primers on the analysis of dark fermentation hydrogen-producing bacterial community. Int J Hydrogen Energy 2008:33:1586-92.
30. Hung HC, Lee KS, Cheng LH, Huang YH, Lin PJ, Chang JS. Quantitative analysis of a high-rate hydrogen producing microbial community in anaerobic agitated granular sludge bed bioreactors using glucose as substrate. Appl Microbiol Biotechnol 2007;75:693-701.
31. Amann RI, Ludwig W, Schleifer KH. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 1995;59:143-69.
32. Ashelford KE, Weightman AJ, Fry JC. PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database. Nucleic Acids Res 2002;30:3481-9.
33. Cole JR, Chai B, Marsh TL, Farris RJ, Wang Q, Kulam SA, et al. The ribosomal database project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 2003;1:442-3.
34. Altschul SF, Gish W, Miller W, Myers E, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990;215:403-10.
35. Stender H, Fiandaca M, Hyldig-Nielsen JJ, Coull J. PNA for rapid microbiology. J Microbiol Methods 2002;48:1-17.
36. Maidak BL, Cole JR, Lilburn TG, Parker Jr CT, Saxman PR, Farris RJ, et al. The RDP-II (ribosomal database project). Nucleic Acids Res 2001;29:173-4.
37. Aim EW, Oerther DB, Larsen N, Stahl DA, Raskin L. The oligonucleotide probe database. Appl Environ Microbiol 1996; 62:3557-9.
38. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673-80.
39. Fuchs BM, Wallner G, Beisker W, Schwippl I, Ludwig W, Amann R. Flow cytometric analysis of the in situ accessibility of Escherichia coli 16S rRNA for fluorescently labeled oligonucleotide probes. Appl Environ Microbiol 1998;64:4973-82.
40. Gunasekera TS, Dorsch MR, Slade MB, Veal DA. Specific detection of Pseudomonas spp. in milk by fluorescence in situ hybridization using ribosomal RNA directed probes. Appl Microbiol 2003;94:936-45.
41. Schmid M, Twachtmann U, Klein M, Strous M, Juretschko S, Jetten M, et al. Molecular evidence for genus level diversity of bacteria capable of catalyzing anaerobic ammonium oxidation. Syst Appl Microbiol 2000;23:93-106.
42. Daims H, Bruhl A, Amann R, Schleifer KH, Wagner M. The domain-specific probe EUB338 is insufficient for the detection of all bacteria: development and evaluation of a more comprehensive probe set. Syst Appl Microbiol 1999; 22:434-44.
43. Rusch A, Amend JP. Order-specific 16S rRNA-targeted oligonucleotide probes for (hyper) thermophilic archaea and bacteria. Extremophiles 2004;8:357-66.
44. Hugenholtz P, Tyson GW, Blackall LL. Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization. In: Methods in Molecular Biology (Gene Probes). Humana Press; 2001. p. 29-42.
45. Manz W, Amann R, Ludwig W, Wagner M, Schleifer K-H. Phylogenetic oligonucleotide probes for the major subclasses of proteobacteria: problems and solutions. Syst Appl Microbiol 1992;15:593-600.
46. Stahl DA, Amann R. Development and application of nucleic acid probes. In: Stackebrandt E, Goodfellow M, editors. Nucleic acid techniques in bacterial systematics. Chichester, UK: John Wiley & Sons Ltd.; 1991. p. 205-48.
47. Amann RI, Binder BJ, Olson RJ, Chisholm SW, Devereux R, Stahl DA. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol 1990;56:1919-25.
48. Harmsen H, Prieur D, Jeanthon C. Group-specific 16S rRNA-targeted oligonucleotide probes to identify thermophilic bacteria in marine hydrothermal vents. Appl Environ Microbiol 1997;63:4061-8.