Use of order-specific primers to investigate the methanogenic diversity in acetate enrichment system

Journal of Industrial Microbiology and Biotechnology

Volumn 35, Issue 11, 2008, Pages 1345-1352

  Shin, Seung Gu ^a   Lee, Changsoo ^b   Hwang, Kwanghyun ^a   Ahn, Johng Hwa ^c   Hwang, Seokhwan ^a  

^a Pohang University of Science and Technology (POSTECH)   (South Korea)

^b NATIONAL UNIVERSITY OF IRELAND   (Ireland)

^c Kangwon National University   (South Korea)

Author keywords

Denaturing gradient gel electrophoresis; Diversity of methanogens; Order specific primers; Real time quantitative PCR; Taxonomic level

Indexed keywords

ACETIC ACID;

ANAEROBIC DIGESTION; ARCHAEBACTERIUM; CONFERENCE PAPER; DENATURING GRADIENT GEL ELECTROPHORESIS; ENRICHMENT CULTURE; METHANOBACTERIALES; METHANOMICROBIALES; METHANOSARCINA; MICROBIAL DIVERSITY; MICROBIAL POPULATION DYNAMICS; NONHUMAN; NUCLEOTIDE SEQUENCE; REAL TIME POLYMERASE CHAIN REACTION; TAXONOMIC RANK; UNINDEXED SEQUENCE;

ACETATES; BIODIVERSITY; BIOREACTORS; DNA PRIMERS; DNA, ARCHAEAL; ELECTROPHORESIS, POLYACRYLAMIDE GEL; EURYARCHAEOTA; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; SPECIES SPECIFICITY;

METHANOBACTERIALES; METHANOMICROBIALES; METHANOSARCINALES; OTUS;

EID: 54049126447     PISSN: 13675435     EISSN: 14765535     Source Type: Journal    
DOI: 10.1007/s10295-008-0417-7     Document Type: Conference Paper

References (38)

1. Atlas RM (1993) Handbook of microbiological media, CRC Press, Boca Raton
2. S Ayyadevara JJ Thaden RJ Shmookler Reis 2000 Discrimination of primer 3′-nucleotide mismatch by Taq DNA polymerase during polymerase chain reaction Anal Biochem 284 11 18
3. GC Baker JJ Smith DA Cowan 2003 Review and re-analysis of domain-specific 16S primers J Microbiol Methods 55 541 555
4. N Banning F Brock JC Fry RJ Parkes ERC Hornibrook AJ Weightman 2005 Investigation of the methanogen population structure and activity in a brackish lake sediment Environ Microbiol 7 947 960
5. Batstone DJ (2002) Anaerobic Digestion Model No. 1, IWA Publishing, London
6. E Ben-Dov OH Shapiro N Siboni A Kushmaro 2006 Advantage of using inosine at the 3′ termini of 16S rRNA gene universal primers for the study of microbial diversity Appl Environ Microbiol 72 6902 6906
7. S Connaughton G Collins V O'Flaherty 2006 Development of microbial community structure and actvity in a high-rate anaerobic bioreactor at 18 °C Water Res 40 1009 1017
8. Eaton AD, Clesceri LS, Greenberg AE (2005) Standard methods for the examination of water and wastewater. American Public Health Association, Washington, D.C
9. LJ Forney X Zhou CJ Brown 2004 Molecular microbial ecology: land of the one-eyed king Curr Opin Microbiol 7 210 220
10. PE Galand H Fritze K Yrjala 2003 Microsite-dependent changes in methanogenic populations in a boreal oligotrophic fen Environ Microbiol 5 1133 1143
11. Garrity GM, Holt JG (2001) Phylum AII. Euryarchaeota phy. nov. In: Boone DR (ed) Bergey's manual of systematic bacteriology, Springer, New York
12. ME Griffin KD McMahon RI Mackie L Raskin 1998 Methanogenic population dynamics during start-up of anaerobic digesters treating municipal solid waste and biosolids Biotechnol Bioeng 57 342 355
13. L Høj RA Olsen VL Torsvik 2005 Archaeal communities in High Arctic wetlands at Spitsbergen, Norway (78°N) as characterized by 16S rRNA gene fingerprinting FEMS Microbiol Ecol 53 89 101
14. T Hori S Haruta Y Ueno M Ishii Y Igarashi 2006 Dynamic transition of a methanogenic population in response to the concentration of volatile fatty acids in a thermophilic anaerobic digester Appl Environ Microbiol 72 1623 1630
15. D Karakashev DJ Batstone I Angelidaki 2005 Influence of environmental conditions on methanogenic compositions in anaerobic biogas reactors Appl Environ Microbiol 71 331 338
16. J Kim C Lee SG Shin S Hwang 2008 Correlation of microbial mass with ATP and DNA concentrations in acidogenesis of whey permeate Biodegradation 19 187 195
17. M Leclerc C Delbes R Moletta JJ Godon 2001 Single strand conformation polymorphism monitoring of 16 S rDNA Archaea during start-up of an anaerobic digester FEMS Microbiol Ecol 34 213 220
18. M Leclerc J-P Delgenes J-J Godon 2004 Diversity of the archaeal community in 44 anaerobic digesters as determined by single strand conformation polymorphism analysis and 16S rDNA sequencing Environ Microbiol 6 809 819
19. C Lee J Kim H Do S Hwang 2008 Monitoring thiocyanate-degrading microbial community in relation to changes in process performance in mixed culture systems near washout Water Res 42 1254 1262
20. J Lim H Do SG Shin S Hwang 2008 Primer and probe sets for group-specific quantification of the genera Nitrosomonas and Nitrosospira using real-time PCR Biotechnol Bioeng 99 1374 1383
21. WT Liu OC Chan HH Fang 2002 Microbial community dynamics during start-up of acidogenic anaerobic reactors Water Res 36 3203 3210
22. G Muyzer EC de Waal AG Uitterlinden 1993 Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA Appl Environ Microbiol 59 695 700
23. B Nüsslein K-J Chin W Eckert R Conrad 2001 Evidence for anaerobic syntrophic acetate oxidation during methane production in the profundal sediment of subtropical Lake Kinneret (Israel) Environ Microbiol 3 460 470
24. K Obata O Segawa M Yakabe Y Ishida T Kuroita K Ikeda B Kawakami Y Kawamura M Yohda T Matsunaga H Tajima 2001 Development of a novel method for operating magnetic particles, magtration technology, and its use for automating nucleic acid purification J Biosci Bioeng 91 500 503
25. L Øvreås L Forney FL Daae V Torsvik 1997 Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA Appl Environ Microbiol 63 3367 3373
26. Rittmann BE, McCarty PL (2001) Environmental biotechnology: principles and applications. McGraw-Hill, New York
27. K Roest HG Heilig H Smidt WM de Vos AJ Stams AD Akkermans 2005 Community analysis of a full-scale anaerobic bioreactor treating paper mill wastewater Syst Appl Microbiol 28 175 185
28. A Schnürer B Schink BH Svensson 1996 Clostridium ultunense sp. nov., a mesophilic bacterium oxidizing acetate in syntrophic association with a hydrogenotrophic methanogenic bacterium Int J Syst Bacteriol 46 1145 1152
29. Shuler ML, Kargi F (2001) Bioprocess engineering: basic concepts, Prentice Hall, Upper Saddle River
30. KS Smith C Ingram-Smith 2007 Methanosaeta, the forgotten methanogen? Trends Microbiol 15 150 155
31. Speece RE (1996) Anaerobic biotechnology for industrial wastewaters, Archae Press, Nashville
32. Y Ueno S Haruta M Ishii Y Igarashi 2001 Changes in product formation and bacterial community by dilution rate on carbohydrate fermentation by methanogenic microflora in continuous flow stirred tank reactor Appl Microbiol Biotechnol 57 65 73
33. Y Ueno S Haruta M Ishii Y Igarashi 2001 Microbial community in anaerobic hydrogen-producing microflora enriched from sludge compost Appl Microbiol Biotechnol 57 555 562
34. C Wawer G Muyzer 1995 Genetic diversity of Desulfovibrio spp. in environmental samples analyzed by denaturing gradient gel electrophoresis of [NiFe] hydrogenase gene fragments Appl Environ Microbiol 61 2203 2210
35. Y Yu J Kim S Hwang 2006 Use of real-time PCR for group-specific quantification of aceticlastic methanogens in anaerobic processes: population dynamics and community structures Biotechnol Bioeng 93 424
36. Y Yu C Lee S Hwang 2005 Analysis of community structures in anaerobic processes using a quantitative real-time PCR method Water Sci Technol 52 85 91
37. Y Yu C Lee J Kim S Hwang 2005 Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction Biotechnol Bioeng 89 670 679
38. Zinder SH (1993) Physiological ecology of methanogens. In: Ferry JG (ed) Methanogenesis. Chapman & Hall, New York