Quantitative detection of previously characterized syntrophic bacteria in anaerobic wastewater treatment systems by sequence-specific rRNA cleavage method

Water Research

Volumn 46, Issue 7, 2012, Pages 2167-2175

  Narihiro, Takashi ^a   Terada, Takeshi ^a   Ohashi, Akiko ^a   Kamagata, Yoichi ^a,b   Nakamura, Kazunori ^a   Sekiguchi, Yuji ^a  

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

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

Author keywords

Anaerobic wastewater treatment process; RNase H method; Syntroph

Indexed keywords

BACTERIA; FATTY ACIDS; RNA;

ANAEROBIC WASTE WATER TREATMENT; HETEROTROPHIC BACTERIAS; METHANOGENIC COMMUNITY; METHANOGENIC CONDITION; QUANTITATIVE DETECTION; QUANTITATIVE MONITORING; RNASE H; SYNTROPH;

WASTEWATER TREATMENT;

FATTY ACID; RIBOSOME RNA;

ANOXIC CONDITIONS; BACTERIUM; DETECTION METHOD; HETEROTROPHY; METHANOGENESIS; MICROBIAL COMMUNITY; MONITORING SYSTEM; POPULATION DISTRIBUTION; PROKARYOTE; QUANTITATIVE ANALYSIS; RELATEDNESS; RNA; WASTEWATER; WATER TREATMENT;

ANAEROBIC WASTEWATER TREATMENT; ARTICLE; BACTERIAL STRAIN; BACTERIUM; BACTERIUM DETECTION; CHLOROFLEXI; FIRMICUTES; IN SITU HYBRIDIZATION; METHANOGENIC BACTERIUM; NITROSPIRAE; NONHUMAN; PELOTOMACULUM; PRIORITY JOURNAL; PROTEOBACTERIA; QUANTITATIVE ANALYSIS; RNA CLEAVAGE; RNA EXTRACTION; SLUDGE TREATMENT; SMITHELLA; SYNTROPHIC BACTERIUM; SYNTROPHOBACTER; WATER TREATMENT;

CHLOROFLEXI; CHLOROFLEXI (CLASS); PELOTOMACULUM; PROKARYOTA; SMITHELLA; SYNTROPHOBACTER;

EID: 84858081964     PISSN: 00431354     EISSN: 18792448     Source Type: Journal    
DOI: 10.1016/j.watres.2012.01.034     Document Type: Article

References (51)

1. Arbeli Z., Brenner A., Abeliovich A. Treatment of high-strength dairy wastewater in an anaerobic deep reservoir: analysis of the methanogenic fermentation pathway and the rate-limiting step. Water Research 2006, 40(19):3653-3659.
2. Ariesyady H.D., Ito T., Okabe S. Functional bacterial and archaeal community structures of major trophic groups in a full-scale anaerobic sludge digester. Water Research 2007, 41(7):1554-1568.
3. Bjornsson L., Hugenholtz P., Tyson G.W., Blackall L.L. Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal. Microbiology-SGM 2002, 148(8):2309-2318.
4. Brosius J., Palmer M.L., Kennedy P.J., Noller H.F. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proceedings of National Academy of Sciences of the United States of America 1978, 75(10):4801-4805.
5. Chen S.Y., Liu X.L., Dong X.Z. Syntrophobacter sulfatireducens sp. nov., a novel syntrophic, propionate-oxidizing bacterium isolated from UASB reactors. International Journal of Systematic and Evolutionary Microbiology 2005, 55(3):1319-1324.
6. Chouari R., Le Paslier D., Daegelen P., Ginestet P., Weissenbach J., Sghir A. Novel predominant archaeal and bacterial groups revealed by molecular analysis of an anaerobic sludge digester. Environmental Microbiology 2005, 7(8):1104-1115.
7. de Bok F.A.M., Harmsen H.J.M., Plugge C.M., de Vries M.C., Akkermans A.D.L., de Vos W.M., Stams A.J.M. The first true obligately syntrophic propionate-oxidizing bacterium, Pelotomaculum schinkii sp. nov., co-cultured with Methanospirillum hungatei, and emended description of the genus Pelotomaculum. International Journal of Systematic and Evolutionary Microbiology 2005, 55(4):1697-1703.
8. Elferink S.J.W.H.O., Boschker H.T.S., Stams A.J.M. Identification of sulfate reducers and Syntrophobacter sp. in anaerobic granular sludge by fatty-acid biomarkers and 16S rRNA probing. Geomicrobiology Journal 1998, 15(1):3-17.
9. Fernandez N., Sierra-Alvarez R., Field J.A., Amils R., Sanz J.L. Microbial community dynamics in a chemolithotrophic denitrification reactor inoculated with methanogenic granular sludge. Chemosphere 2008, 70(3):462-474.
10. Garrity G.M., Holt J.G. Phylum BVIII. Nitrospirae phy. nov. Bergey's Manual 2001, 451-464. Springer-Verlag, New York. second ed. D.R. Boone, R.W. Castenholz, G.M. Garrity (Eds.).
11. Gich F., Garcia-Gil J., Overmann J. Previously unknown and phylogenetically diverse members of the green nonsulfur bacteria are indigenous to freshwater lakes. Archives of Microbiology 2001, 177(1):1-10.
12. Hansen K.H., Ahring B.K., Raskin L. Quantification of syntrophic fatty acid-beta-oxidizing bacteria in a mesophilic biogas reactor by oligonucleotide probe hybridization. Applied and Environmental Microbiology 1999, 65(11):4767-4774.
13. Harmsen H.J.M., Akkermans A.D.L., Stams A.J.M., deVos W.M. Population dynamics of propionate-oxidizing bacteria under methanogenic and sulfidogenic conditions in anaerobic granular sludge. Applied and Environmental Microbiology 1996, 62(6):2163-2168.
14. Harmsen H.J.M., Kengen K.M.P., Akkermans A.D.L., Stams A.J.M. Phylogenetic analysis of two syntrophic propionate-oxidizing bacteria in enrichments cultures. Systematic and Applied Microbiology 1995, 18(1):67-73.
15. Hattori S. Syntrophic acetate-oxidizing microbes in methanogenic environments. Microbes and Environments 2008, 23(2):118-127.
16. Huang Z., Szostak J.W. Selective labeling and detection of specific RNAs in an RNA mixture. Analytical Biochemistry 2003, 315(1):129-133.
17. Iguchi A., Terada T., Narihiro T., Yamaguchi T., Kamagata Y., Sekiguchi Y. In situ detection and quantification of uncultured members of the phylum Nitrospirae abundant in methanogenic wastewater treatment systems. Microbes and Environments 2009, 24(2):97-104.
18. Imachi H., Sakai S., Ohashi A., Harada H., Hanada S., Kamagata Y., Sekiguchi Y. Pelotomaculum propionicicum sp. nov., an anaerobic, mesophilic, obligately syntrophic, propionate-oxidizing bacterium. International Journal of Systematic and Evolutionary Microbiology 2007, 57(7):1487-1492.
19. Imachi H., Sekiguchi Y., Kamagata Y., Hanada S., Ohashi A., Harada H. Pelotomaculum thermopropionicum gen. nov., sp. nov., an anaerobic, thermophilic, syntrophic propionate-oxidizing bacterium. International Journal of Systematic and Evolutionary Microbiology 2002, 52(5):1729-1735.
20. Imachi H., Sekiguchi Y., Kamagata Y., Loy A., Qiu Y.L., Hugenholtz P., Kimura N., Wagner M., Ohashi A., Harada H. Non-sulfate-reducing, syntrophic bacteria affiliated with Desulfotomaculum cluster I are widely distributed in methanogenic environments. Applied and Environmental Microbiology 2006, 72(3):2080-2091.
21. Kato S., Watanabe K. Ecological and evolutionary interactions in syntrophic methanogenic consortia. Microbes and Environments 2010, 25(3):145-151.
22. Kleerebezem R., Macarie H. Treating industrial wastewater: anaerobic digestion comes of age. Chemical Engineering 2003, 110(4):56-64.
23. Kuever J., Schink B. Genus I. Syntrophus Mountfort, Brulla, Krumholtz and Bryant 1984. Bergey's Manual of Systematic Bacteriology 2005, 1033-1035. Springer, New York, USA. G.M. Garrity (Ed.).
24. Lettinga G. Anaerobic digestion and wastewater treatment systems. Antonie van Leeuwenhoek 1995, 67(1):3-28.
25. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar, Buchner A., Lai T., Steppi S., Jobb G., Forster W., Brettske I., Gerber S., Ginhart A.W., 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 K.H. ARB: a software environment for sequence data. Nucleic Acids Research 2004, 32(4):1363-1371.
26. McCarty P.L. The development of anaerobic treatment and its future. Water Science and Technology 2001, 44(8):149-156.
27. McInerney M.J., Stams A.J.M., Boone D.R. Genus I. Syntrophobacter Boone and Bryant 1984. Bergey's Manual of Systematic Bacteriology 2005, 1021-1027. Springer, New York, USA. G.M. Garrity (Ed.).
28. McMahon K.D., Zheng D.D., Stams A.J.M., Mackie R.I., Raskin L. Microbial population dynamics during start-up and overload conditions of anaerobic digesters treating municipal solid waste and sewage sludge. Biotechnology and Bioengineering 2004, 87(7):823-834.
29. Miura Y., Watanabe Y., Okabe S. Significance of Chloroflexi in performance of submerged membrane bioreactors (MBR) treating municipal wastewater. Environmental Science and Technology 2007, 41(22):7787-7794.
30. Narihiro T., Sekiguchi Y. Microbial communities in anaerobic digestion processes for waste and wastewater treatment: a microbiological update. Current Opinion in Biotechnology 2007, 18(3):273-278.
31. Narihiro T., Terada T., Kikuchi K., Iguchi A., Ikeda M., Yamauchi T., Shiraishi K., Kamagata Y., Nakamura K., Sekiguchi Y. Comparative analysis of bacterial and archaeal communities in methanogenic sludge granules from upflow anaerobic sludge blanket reactors treating various food-processing, high-strength organic wastewaters. Microbes and Environments 2009, 24(2):88-96.
32. Narihiro T., Terada T., Ohashi A., Wu J.H., Liu W.T., Araki N., Kamagata Y., Nakamura K., Sekiguchi Y. Quantitative detection of culturable methanogenic archaea abundance in anaerobic treatment systems using the sequence-specific rRNA cleavage method. ISME Journal 2009, 3(5):522-535.
33. Okabe S., Oshiki M., Kamagata Y., Yamaguchi N., Toyofuku M., Yawata Y., Tashiro Y., Nomura N., Ohta H., Ohkuma M., Hiraishi A., Minamisawa K. A great leap forward in microbial ecology. Microbes and Environments 2010, 25(4):230-240.
34. Qiu Y.L., Sekiguchi Y., Hanada S., Imachi H., Tseng I.C., Cheng S.S., Ohashi A., Harada H., Kamagata Y. Pelotomaculum terephthalicum sp. nov. and Pelotomaculum isophthalicum sp. nov.: two anaerobic bacteria that degrade phthalate isomers in syntrophic association with hydrogenotrophic methanogens. Archives of Microbiology 2006, 185(3):172-182.
35. Scheid D., Stubner S. Structure and diversity of Gram-negative sulfate-reducing bacteria on rice roots. FEMS Microbiology Ecology 2001, 36(2-3):175-183.
36. Schink B. Energetics of syntrophic cooperation in methanogenic degradation. Microbiology and Molecular Biology Reviews 1997, 61(2):262-280.
37. Sekiguchi Y. Yet-to-be cultured microorganisms relevant to methane fermentation processes. Microbes and Environments 2006, 21(1):1-15.
38. Sekiguchi Y., Imachi H., Susilorukmi A., Muramatsu M., Ohashi A., Harada H., Hanada S., Kamagata Y. Tepidanaerobacter syntrophicus gen. nov., sp. nov., an anaerobic, moderately thermophilic, syntrophic alcohol- and lactate-degrading bacterium isolated from thermophilic digested sludges. International Journal of Systematic and Evolutionary Microbiology 2006, 56(7):1621-1629.
39. Sekiguchi Y., Muramatsu M., Imachi H., Narihiro T., Ohashi A., Harada H., Hanada S., Kamagata Y. Thermodesulfovibrio aggregans sp. nov. and Thermodesulfovibrio thiophilus sp. nov., anaerobic, thermophilic, sulfate-reducing bacteria isolated from thermophilic methanogenic sludge, and emended description of the genus Thermodesulfovibrio. International Journal of Systematic and Evolutionary Microbiology 2008, 58(11):2541-2548.
40. Sekiguchi Y., Takahashi H., Kamagata Y., Ohashi A., Harada H. 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. Applied and Environmental Microbiology 2001, 67(12):5740-5749.
41. Sekiguchi Y., Yamada T., Hanada S., Ohashi A., Harada H., Kamagata Y. 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. International Journal of Systematic and Evolutionary Microbiology 2003, 53(6):1843-1851.
42. Sobieraj M., Boone D.R. Genus IV. Smithella Liu, Balkwill, Aldrich, Drake and Boone 1999. Bergey's Manual of Systematic Bacteriology 2005, 1039-1040. Springer, New York, USA. G.M. Garrity (Ed.).
43. Speece R.E., Boonyakitsombut S., Kim M., Azbar N., Ursillo P. Overview of anaerobic treatment: thermophilic and propionate implications. Water Environment Research 2006, 78(5):460-473.
44. Stams A.J., Plugge C.M. Electron transfer in syntrophic communities of anaerobic bacteria and archaea. Nature Reviews Microbiology 2009, 7(8):568-577.
45. Uyeno Y., Sekiguchi Y., Sunaga A., Yoshida H., Kamagata Y. Sequence-specific cleavage of small-subunit (SSU) rRNA with oligonucleotides and RNase H: a rapid and simple approach to SSU rRNA-based quantitative detection of microorganisms. Applied and Environmental Microbiology 2004, 70(6):3650-3663.
46. Westerholm M., Müller B., Arthurson V., Schnürer A. Changes in the acetogenic population in a mesophilic anaerobic digester in response to increasing ammonia concentration. Microbes and Environments 2011, 26(4):347-353.
47. Yamada T., Imachi H., Ohashi A., Harada H., Hanada S., Kamagata Y., Sekiguchi Y. 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. International Journal of Systematic and Evolutionary Microbiology 2007, 57(10):2299-2306.
48. Yamada T., Sekiguchi Y. Cultivation of uncultured Chloroflexi subphyla: significance and ecophysiology of formary uncultured Chloroflexi 'subphylum I' with natural and biotechnological relevance. Microbes and Environments 2009, 24(3):205-216.
49. Yamada T., Sekiguchi Y., Hanada S., Imachi H., Ohashi A., Harada H., Kamagata Y. 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. International Journal of Systematic and Evolutionary Microbiology 2006, 56(6):1331-1340.
50. Yamada T., Sekiguchi Y., Imachi H., Kamagata Y., Ohashi A., Harada H. Diversity, localization, and physiological properties of filamentous microbes belonging to Chloroflexi subphylum I in mesophilic and thermophilic methanogenic sludge granules. Applied and Environmental Microbiology 2005, 71(11):7493-7503.
51. Zheng D., Angenent L.T., Raskin L. Monitoring granule formation in anaerobic upflow bioreactors using oligonucleotide hybridization probes. Biotechnology and Bioengineering 2006, 94(3):458-472.