Distinctive Responses of Metabolically Active Microbiota to Acidification in a Thermophilic Anaerobic Digester

Microbial Ecology

Volumn 61, Issue 3, 2011, Pages 595-605

  Akuzawa, Masateru ^a   Hori, Tomoyuki ^a,b   Haruta, Shin ^a,c   Ueno, Yoshiyuki ^d   Ishii, Masaharu ^a   Igarashi, Yasuo ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^c TOKYO METROPOLITAN UNIVERSITY   (Japan)

^d KAJIMA TECHNICAL RESEARCH INSTITUTE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ACID; BACTERIAL DNA; FORMATE TETRAHYDROFOLATE LIGASE; RNA 16S; VOLATILE FATTY ACID;

ANAEROBIC GROWTH; ARTICLE; BACTERIAL GENE; BIOREACTOR; BIOSYNTHESIS; CHLOROFLEXI; DNA SEQUENCE; GENE EXPRESSION PROFILING; GENE LIBRARY; GENETICS; METABOLISM; METHODOLOGY; MICROBIOLOGY; PH; PHYLOGENY; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SEWAGE;

ACIDS; ANAEROBIOSIS; BIOREACTORS; CHLOROFLEXI; DNA, BACTERIAL; FATTY ACIDS, VOLATILE; FORMATE-TETRAHYDROFOLATE LIGASE; GENE EXPRESSION PROFILING; GENE LIBRARY; GENES, BACTERIAL; HYDROGEN-ION CONCENTRATION; PHYLOGENY; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; WASTE DISPOSAL, FLUID;

BACTERIA (MICROORGANISMS); CHLOROFLEXI; CHLOROFLEXI (CLASS); THERMOANAEROBACTERIUM; UNIDENTIFIED BACTERIUM;

EID: 79953746426     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-010-9788-1     Document Type: Article

References (56)

1. Boone DR, Whitman WB, Rouviere P (1993) Diversity and taxonomy of methanogens. In: Ferry JG (ed) methanogens. Chapman and Hall, inc., New York, pp 35-80.
2. Brauer SL, Cadillo-Quiroz H, Yashiro E, Yavitt JB, Zinder SH (2006) Isolation of a novel acidiphilic methanogen from an acidic peat bog. Nature 442: 192-194.
3. Cadillo-Quiroz H, Yashiro E, Yavitt JB, Zinder SH (2008) Characterization of the archaeal community in a minerotrophic fen and terminal restriction fragment length polymorphism-directed isolation of a novel hydrogenotrophic methanogen. Appl Environ Microbiol 74: 2059-2068.
4. Cord-Ruwisch R, Mercz TI, Hoh C-Y, Strong GE (1997) Dissolved hydrogen concentration as an on-line control parameter for the automated operation and optimization of anaerobic digesters. Biotechnol Bioeng 56: 626-634.
5. Cresson R, Dabert P, Bernet N (2009) Microbiology and performance of a methanogenic biofilm reactor during the start-up period. J Appl Microbiol 106: 863-876.
6. Delbes C, Moletta R, Godon J (2001) Bacterial and archaeal 16S rDNA and 16S rRNA dynamics during an acetate crisis in an anaerobic digestor ecosystem. FEMS Microbiol Ecol 35: 19-26.
7. Drake HL (1994) Acetogenesis. Chapman and Hall, New York.
8. Drake HL, Daniel SL (2004) Physiology of the thermophilic acetogen Moorella thermoacetica. Res Microbiol 155: 869-883.
9. Dunbar J, Ticknor LO, Kuske CR (2001) Phylogenetic specificity and reproducibility and new method for analysis of terminal restriction fragment profiles of 16S rRNA genes from bacterial communities. Appl Environ Microbiol 67: 190-197.
10. Eichler S, Christen R, Holtje C, Westphal P, Botel J, Brettar I, Mehling A, Hofle MG (2006) Composition and dynamics of bacterial communities of a drinking water supply system as assessed by RNA- and DNA-based 16S rRNA gene fingerprinting. Appl Environ Microbiol 72: 1858-1872.
11. Felsenstein J (2005) PHYLIP (phylogeny inference package). Department of Genome Sciences, University of Washington, Seattle.
12. Goberna M, Insam H, Franke-Whittle IH (2009) Effect of biowaste sludge maturation on the diversity of thermophilic bacteria and archaea in an anaerobic reactor. Appl Environ Microbiol 75: 2566-2572.
13. Henderson G, Naylor GE, Leahy SC, Janssen PH (2010) Presence of novel, potentially homoacetogenic bacteria in the rumen as determined by analysis of formyltetrahydrofolate synthetase sequences from ruminants. Appl Environ Microbiol 76: 2058-2066.
14. Hori T, Haruta S, Ueno Y, Ishii M, Igarashi Y (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. Hori T, Haruta S, Ueno Y, Ishii M, Igarashi Y (2006) Direct comparison of single-strand conformation polymorphism (SSCP) and denaturing gradient gel electrophoresis (DGGE) to characterize a microbial community on the basis of 16S rRNA gene fragments. J Microbiol Methods 66: 165-169.
16. Hori T, Noll M, Igarashi Y, Friedrich MW, Conrad R (2007) Identification of acetate-assimilating microorganisms under methanogenic conditions in anoxic rice field soil by comparative stable isotope probing of RNA. Appl Environ Microbiol 73: 101-109.
17. 13C-acetate probing. ISME J 4: 267-278.
18. Hugenholtz P, Stackebrandt E (2004) Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description). Int J Syst Evol Microbiol 54: 2049-2051.
19. Juottonen H, Tuittila ES, Juutinen S, Fritze H, Yrjala K (2008) Seasonality of rDNA- and rRNA-derived archaeal communities and methanogenic potential in a boreal mire. ISME J 2: 1157-1168.
20. Kemnitz D, Kolb S, Conrad R (2005) Phenotypic characterization of Rice Cluster III archaea without prior isolation by applying quantitative polymerase chain reaction to an enrichment culture. Environ Microbiol 7: 553-565.
21. 2-dependent methanogenesis in a west Siberian peat bog at low pH values and isolation of an acidophilic Methanobacterium strain. Appl Environ Microbiol 73: 2344-2348.
22. Kublanov IV, Prokofeva MI, Kostrikina NA, Kolganova TV, Tourova TP, Wiegel J, Bonch-Osmolovskaya EA (2007) Thermoanaerobacterium aciditolerans sp. nov., a moderate thermoacidophile from a Kamchatka hot spring. Int J Syst Evol Microbiol 57: 260-264.
23. Leaphart AB, Friez MJ, Lovell CR (2003) Formyltetrahydrofolate synthetase sequences from salt marsh plant roots reveal a diversity of acetogenic bacteria and other bacterial functional groups. Appl Environ Microbiol 69: 693-696.
24. Lee C, Kim J, Hwang K, O'Flaherty V, Hwang S (2009) Quantitative analysis of methanogenic community dynamics in three anaerobic batch digesters treating different wastewaters. Water Res 43: 157-165.
25. Leigh JA, Mayer F, Wolfe RS (1981) Acetogenium kivui, a new thermophilic hydrogen-oxidizing acetogenic bacterium. Arch Microbiol 129: 275-280.
26. Lettinga G (1995) Anaerobic digestion and wastewater treatment systems. Antonie Leeuwenhoek 67: 3-28.
27. Lins P, Malin C, Wagner AO, Illmer P (2010) Reduction of accumulated volatile fatty acids by an acetate-degrading enrichment culture. FEMS Microbiol Ecol 71: 469-478.
28. Liu WT, Marsh TL, Cheng H, Forney LJ (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63: 4516-4522.
29. Lovell CR, Leaphart AB (2005) Community-level analysis: key genes of CO2-reductive acetogenesis. Methods Enzymol 397: 454-469.
30. Lu F, Shao LM, Bru V, Godon JJ, He PJ (2009) Synergetic effect of pH and biochemical components on bacterial diversity during mesophilic anaerobic fermentation of biomass-origin waste. J Appl Microbiol 106: 580-591.
31. Ludwig W, Strunk O, Klugbauer S, Klugbauer N, Weizenegger M, Neumaier J, Bachleitner M, Schleifer KH (1998) Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19: 554-568.
32. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar BA, Lai T, Steppi S, Jobb G, Forster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, Konig A, Liss T, Lussmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer KH (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363-1371.
33. Lueders T, Friedrich MW (2002) Effects of amendment with ferrihydrite and gypsum on the structure and activity of methanogenic populations in rice field soil. Appl Environ Microbiol 68: 2484-2494.
34. Lueders T, Wagner B, Claus P, Friedrich MW (2004) Stable isotope probing of rRNA and DNA reveals a dynamic methylotroph community and trophic interactions with fungi and protozoa in oxic rice field soil. Environ Microbiol 6: 60-72.
35. Miura Y, Watanabe Y, Okabe S (2007) Significance of Chloroflexi in performance of submerged membrane bioreactors (MBR) treating municipal wastewater. Environ Sci Technol 41: 7787-7794.
36. Narihiro T, Sekiguchi Y (2007) Microbial communities in anaerobic digestion processes for waste and wastewater treatment: a microbiological update. Curr Opin Biotechnol 18: 273-278.
37. Noll M, Matthies D, Frenzel P, Derakshani M, Liesack W (2005) Succession of bacterial community structure and diversity in a paddy soil oxygen gradient. Environ Microbiol 7: 382-395.
38. Pester M, Brune A (2006) Expression profiles of fhs (FTHFS) genes support the hypothesis that spirochaetes dominate reductive acetogenesis in the hindgut of lower termites. Environ Microbiol 8: 1261-1270.
39. Qiu YL, Sekiguchi Y, Hanada S, Imachi H, Tseng IC, Cheng SS, Ohashi A, Harada H, Kamagata Y (2006) Pelotomaculum terephthalicum sp. nov. and Pelotomaculum isophthalicum sp. nov.: two anaerobic bacteria that degrade phthalate isomers in syntrophic association with hydrogenotrophic methanogens. Arch Microbiol 185: 172-182.
40. Roy CS, Talbot G, Topp E, Beaulieu C, Palin MF, Masse DI (2009) Bacterial community dynamics in an anaerobic plug-flow type bioreactor treating swine manure. Water Res 43: 21-32.
41. Schink B (1997) Energetics of syntrophic cooperation in methanogenic degradation. Microbiol Mol Biol Rev 61: 262-280.
42. Schoen MA, Sperl D, Gadermaier M, Goberna M, Franke-Whittle I, Insam H, Ablinger J, Wett B (2009) Population dynamics at digester overload conditions. Bioresour Technol 100: 5648-5655.
43. Sekiguchi Y, Takahashi H, Kamagata Y, Ohashi A, Harada H (2001) In situ detection, isolation, and physiological properties of a thin filamentous microorganism abundant in methanogenic granular sludges: a novel isolate affiliated with a clone cluster, the green non-sulfur bacteria, subdivision I. Appl Environ Microbiol 67: 5740-5749.
44. Sekiguchi Y, Yamada T, Hanada S, Ohashi A, Harada H, Kamagata Y (2003) Anaerolinea thermophila gen. nov., sp. nov. and Caldilinea aerophila gen. nov., sp. nov., novel filamentous thermophiles that represent a previously uncultured lineage of the domain Bacteria at the subphylum level. Int J Syst Evol Microbiol 53: 1843-1851.
45. Shigematsu T, Tang Y, Kobayashi T, Kawaguchi H, Morimura S, Kida K (2004) Effect of dilution rate on metabolic pathway shift between aceticlastic and nonaceticlastic methanogenesis in chemostat cultivation. Appl Environ Microbiol 70: 4048-4052.
46. Speece RE (1996) Anaerobic biotechnology for industrial wastewaters. Archae, Nashville.
47. Stackebrandt E, Goebel BM (1994) A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44: 846-849.
48. Talbot G, Topp E, Palin MF, Masse DI (2008) Evaluation of molecular methods used for establishing the interactions and functions of microorganisms in anaerobic bioreactors. Water Res 42: 513-537.
49. Thevenieau F, Fardeau ML, Ollivier B, Joulian C, Baena S (2007) Desulfomicrobium thermophilum sp. nov., a novel thermophilic sulphate-reducing bacterium isolated from a terrestrial hot spring in Colombia. Extremophiles 11: 295-303.
50. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882.
51. Yamada T, Sekiguchi Y, Imachi H, Kamagata Y, Ohashi A, Harada H (2005) Diversity, localization, and physiological properties of filamentous microbes belonging to Chloroflexi subphylum I in mesophilic and thermophilic methanogenic sludge granules. Appl Environ Microbiol 71: 7493-7503.
52. Yamada T, Sekiguchi Y, Hanada S, Imachi H, Ohashi A, Harada H, Kamagata Y (2006) Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi. Int J Syst Evol Microbiol 56: 1331-1340.
53. Yamada T, Imachi H, Ohashi A, Harada H, Hanada S, Kamagata Y, Sekiguchi Y (2007) Bellilinea caldifistulae gen. nov., sp. nov. and Longilinea arvoryzae gen. nov., sp. nov., strictly anaerobic, filamentous bacteria of the phylum Chloroflexi isolated from methanogenic propionate-degrading consortia. Int J Syst Evol Microbiol 57: 2299-2306.
54. Yamada T, Yamauchi T, Shiraishi K, Hugenholtz P, Ohashi A, Harada H, Kamagata Y, Nakamura K, Sekiguchi Y (2007) Characterization of filamentous bacteria, belonging to candidate phylum KSB3, that are associated with bulking in methanogenic granular sludges. ISME J 1: 246-255.
55. Zehnder AJB (1978) Ecology of methane formation. In: Mitchell R (ed) Water pollution microbiology, vol 2. Wiley, London, pp 349-376.
56. Zehnder AJB, Stumm W (1988) Geochemistry and biochemistry of anaerobic habitats. In: Zehnder AJB (ed) Biology of anaerobic microorganisms. Wiley Interscience, New York, pp 1-38.