Microbes in aerobic and anaerobic waste treatment

Microbes at Work: From Wastes to Resources

Volumn , Issue , 2010, Pages 1-34

  Insam, Heribert ^a   Franke Whittle, Ingrid ^a   Goberna, Marta ^a  

^a UNIVERSITY OF INNSBRUCK   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 78049237399     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-3-642-04043-6_1     Document Type: Chapter

References (195)

1. Alexander M (1977) Introduction to soil microbiology. Wiley, New York
2. Alfreider A, Peters S, Tebbe CC, Rangger A, Insam H (2002) Microbial community dynamics during composting of organic matter as determined by 16S ribosomal DNA analysis. Compost Sci Util 10:303-312
3. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143-169
4. Bagge E, Sahlström L, Albihn A (2005) The effect of hygienic treatment on the microbial flora of biowaste at biogas plants. Water Res 39:4879-4886
5. Balk M, Weijma J, Stams AJM (2002) Thermotoga lettingae, sp. nov., a novel thermophilic, methanol-degrading bacterium isolated from a thermophilic anaerobic reactor. Int J Syst Evol Microbiol 52:1361-1368
6. Balk M, Weijma J, Friedrich MW, Stams AJM (2003) Methanol utilization by a novel thermophilic homoacetogenic bacterium, Moorella mulderi sp. nov., isolated from a bioreactor. Arch Microbiol 179:315-320
7. Bastida F, Hernández T, Garćia C (2010) Soil degradation and rehabilitation: microorganisms and functionality. In: Insam H, Franke-Whittle IH, Goberna M (eds) Microbes at work. From wastes to resources. Springer, Heidelberg, pp 253-270
8. Beffa T, Blanc M, Lyon PF, Vogt G, Marchiani M, Fischer JL, Aragno M (1996) Isolation of Thermus strains from hot composts (60 to 80 degrees C). Appl Environ Microbiol 62:1723-1727
9. Bonin AS, Boone DR (2006) The order Methanobacteriales. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes. A handbook on the biology of bacteria, vol 3. Springer, New York, pp 231-243
10. Boone DR, Chynoweth DP, Mah RA, Smith PH, Wilkie AC (1993) Ecology and microbiology of biogasification. Biomass Bioenerg 5:191-202
11. Braun R, Drosg B, Bochmann G, Weiß S, Kirchmayr R (2010) Recent developments in bio-energy recovery through fermentation. In: Insam H, Franke-Whittle IH, Goberna M (eds) Microbes at work. From wastes to resources. Springer, New York, pp 35-58
12. Briones A, Raskin L (2003) Diversity and dynamics of microbial communities in engineered environments and their implications for process stability. Curr Opin Biotechnol 14:270-276
13. Browne CA (1933) The spontaneous heating and ignition of hay and other agricultural products. Science 77:223-229
14. Bruns MA, Hanson JR, Mefford J, Scow KM (2001) Isolate PM1 populations are dominant and novel methyl tert-butyl ether-degrading bacteria in compost biofilter enrichments. Environ Microbiol 3:220-225
15. 2 profiles and methane formation during the maturation phase of composting. Compost Sci Util 14:86-89
16. Chachkhiani M, Dabert P, Abzianidze T, Partskhaladze G, Tsiklauri L, Dudauri TGJJ (2004) 16S rDNA characterisation of bacterial and archaeal communities during start-up of anaerobic thermophilic digestion of cattle manure. Bioresource Technol 93:227-232
17. Chen AC, Ueda K, Sekiguchi Y, Ohashi A, Harada H (2003) Molecular detection and direct enumeration of methanogenic archaea and methanotrophic bacteria in domestic solid waste landfill soils. Biotechnol Lett 25:1563-1569
18. Chouari R, Le Paslier D, Daegelen P, Ginestet P, Weissenbach J, Sghir A (2005) Novel predominant archaeal and bacterial groups revealed by molecular analysis of an anaerobic sludge digester. Environ Microbiol 7:1104-1115
19. Chynoweth DP, Pullammanappallil P (1996) Anaerobic digestion of municipal solid wastes. In: Palmisano AC, Barlaz MA (eds) Microbiology of solid wastes. CRC Press, Florida, pp 71-114
20. Collins G, Woods A, McHugh S, Carton MW, O'Flaherty V (2003) Microbial community structure and methanogenic activity during start-up of psychrophilic anaerobic digesters treating synthetic industrial wastewaters. FEMS Microbiol Ecol 46:159-170
21. Collins G, Kavanagh S, McHugh S, Connaughton S, Kearney A, Rice O, Carrig C, Scully C, Bhreathnach N, Mahony T, Madden P, Enright AM, O'Flaherty V (2006) Accessing the black box of microbial diversity and ecophysiology: Recent advances through polyphasic experiments. J Environ Sci Health A 41:897-922
22. Connaughton S, Collins G, O'Flaherty V (2006) Development of microbial community structure and activity in a high-rate anaerobic bioreactor at 18°C. Water Res 40:1009-1017
23. Cook KSG, Sayler GS (2003) Environmental application of array technology: promise, problems and practicalities. Curr Opin Biotechnol 14:311-318
24. Curtis TP, Sloan WT (2004) Prokaryotic diversity and its limits: microbial community structure in nature and implications for microbial ecology. Curr Opin Microbiol 7:221-226
25. Danon M (2008) Suppression of Sclerotium rolfsii in compost: characterization and function of the microbial populations. The Hebrew University of Jerusalem. PhD thesis
26. Danon M, Franke-Whittle IH, Insam H, Chen Y, Hadar Y (2008) Molecular analysis of bacterial community succession during prolonged compost curing. FEMS Microbiol Ecol 65:133-144
27. de Bertoldi M, Vallini G, Pera A, Zucconi F (1982) Comparison of three windrow compost systems. BioCycle 23(2):45-50
28. de Bertoldi M, Vallini G, Pera A (1983) The biology of composting: a review. Waste Manag Res 1:157-176
29. Dees PM, Ghiorse WC (2001) Microbial diversity in hot synthetic compost as revealed by PCR-amplified rRNA sequences from cultivated isolates and extracted DNA. FEMS Microbiol Ecol 35:207-216
30. Delbes C, Moletta R, Godon JJ (2000) Monitoring of activity dynamics of an anaerobic digester bacterial community using 16S rRNA polymerase chain reaction-single-strand conformation polymorphism analysis. Environ Microbiol 2:506-515
31. DeLong EF, Wickham GS, Pace NR (1989) Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 243:1360-1363
32. Demirel B, Scherer P (2008) The roles of acetotrophic and hydrogenotrophic methanogens during anarobic conversion biomass to methane: a review. Rev Environ Sci Biotechnol 7:173-190
33. Dighe AS, Shouche YS, Ranade DR (1998) Selenomonas lipolytica sp. nov., an obligately anaerobic bacterium possessing lipolytic activity. Int J Syst Bacteriol 48:783-791
34. Domínguez J, Aira M, Gómez-Brandón M (2010) Vermicomposting: earthworms enhance the work of microbes. In: Insam H, Franke-Whittle IH, Goberna M (eds) Microbes at work. From wastes to resources. Springer, Heidelberg, pp 93-114
35. Drake HL, Küsel K, Matthies C (2006) Acetogenic prokaryotes. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes. A handbook on the biology of bacteria, vol 2. Springer, New York, USA, pp 354-420
36. Eicker A (1981) The occurrence and nature of sulphur crystals in phase I mushroom compost. Mushroom Sci 11:27-34
37. Eylar OR, Schmidt RL (1959) A survey of heterotrophic microorganisms from soil for ability to form nitrite and nitrate. J Gen Microbiol 20:473-481
38. Farrelly V, Rainey FA, Stackebrandt E (1995) Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl Environ Microbiol 61:2798-2801
39. Felske A, Wolterink A, Van Lis R, De Vos WM, Akkermans ADL (2000) Response of a soil bacterial community to grassland succession as monitored by 16S rRNA levels of the predominant ribotypes. Appl Environ Microbiol 66:3998-4003
40. Fernández A, Huang S, Seston S, Xing J, Hickey R, Criddle C, Tiedje J (1999) How stable is stable? Function versus community composition. Appl Environ Microbiol 65:3697-3704
41. Finstein MS, Morris ML (1975) Microbiology of municipal solid waste composting. Adv Appl Microbiol 19:113-151
42. Focht DD, Chang AC (1975) Nitrification and denitrification processes related to waste water treatment. Adv Appl Microbiol 19:153-186
43. Fracchia L, Dohrmann AB, Martinotti MG, Tebbe CC (2006) Bacterial diversity in a finished compost and vermicompost: differences revealed by cultivation-independent analyses of PCR-amplified 16S rRNA genes. Appl Microbiol Biotechnol 71:942-952
44. Francou C, Poitrenaud M, Houot S (2005) Stabilization of organic matter during composting: influence of process and feedstocks. Compost Sci Util 13:72-83
45. Franke-Whittle IH, Klammer SH, Insam H (2005) Design and application of an oligonucleotide microarray for the investigation of compost microbial communities. J Microbiol Methods 62:37-56
46. Franke-Whittle IH, Knapp BA, Fuchs J, Kaufmann R, Insam H (2009a) Application of COMPO-CHIP microarray to investigate the bacterial communities of different composts. Microb Ecol 57:510-521
47. Franke-Whittle IH, Goberna M, Pfister V, Insam H (2009b) Design and development of the ANAEROCHIP microarray for investigation of methanogenic communities. J Microbiol Methods 79:279-288
48. Friedrich M, Springer N, Ludwig W, Schink B (1996) Phylogenetic positions of Desulfofustis glycolicus gen. nov., sp. nov., and Syntrophobotulus glycolicus gen. nov., sp. nov., two new strict anaerobes growing with glycolic acid. Int J Syst Bacteriol 46:1065-1069
49. Fuchs JG (2010) Interactions between beneficial and harmful micro-organisms: from the composting process to compost application. In: Insam H, Franke-Whittle IH, Goberna M (eds) Microbes at work. From wastes to resources. Springer, Heidelberg, pp 213-230
50. Gallert C, Winter J (2005) Bacterial metabolism in wastewater treatment systems. In: Jördening HJ, Winter J (eds) Environmental biotechnology. Concepts and applications. Wiley-VCH Verlag Gmbh & Co KGaA, Weinheim, pp 1-48
51. Garćia JL, Ollivier B, Whitman WB (2006) The order Methanomicrobiales. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes. A handbook on the biology of bacteria, vol 3. Springer, New York, pp 208-230
52. Goberna M, Franke-Whittle IH, Insam H (2008) Fingerprinting the microbial communities in organic wastes using oligonucleotide microarrays and real-time PCR. In: Abstract volume of the II international meeting of soil enzimology. Recycling of organic wastes in environmental restoration and global change. Burgos, Spain, p 36
53. 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
54. Godon JJ, Zumstein E, Dabert P, Habouzit F, Moletta R (1997) Microbial 16S rDNA diversity in an anaerobic digester. Water Sci Technol 36:49-55
55. Green SJ, Michel FC Jr, Hadar Y, Minz D (2004) Similarity of bacterial communities in sawdustand straw-amended cow manure composts. FEMS Microbiol Lett 233:115-123
56. Griffin DM (1985) A comparison of the roles of bacteria and fungi. In: Leadbetter ER, Poindexter JS (eds) Bacteria in nature, vol 1. Plenum Publishing, London, pp 221-255
57. Guschin DY, Mobarry BK, Proudnikov D, Stahl DA, Rittmann BE, Mirzabekov AD (1997) Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology. Appl Environ Microbiol 63:2397-2402
58. Harmsen HJM, Wullings B, Akkermans ADL, Ludwig W, Stams AJM (1993) Phylogenetic analysis of Syntrophobacter woliniii reveals a relationship with sulphate-reducing bacteria. Arch Microbiol 160:238-240
59. Hatamoto M, Imachi H, Yashiro Y, Ohashi A, Harada H (2007) Diversity of anaerobic microorganisms involved in long-chain fatty acid degradation in methanogenic sludges as revealed by RNA-based stable isotope probing. Appl Environ Microbiol 73:4119-4127
60. Hatamoto M, Imachi H, Yashiro Y, Ohashi A, Harada H (2008) Detection of active butyratedegrading microorganisms in methanogenic sludges by RNA-based stable isotope probing. Appl Environ Microbiol 74:3610-3614
61. Hattori S, Kamagata Y, Hanada S, Shoun H (2000) Thermacetogenium phaeum gen. nov., sp. nov., a strictly anaerobic, thermophilic, syntrophic acetate-oxidizing bacterium. Int J Syst Evol Microbiol 50:1601-1609
62. He PJ, Lu F, Shao LM, Zhang H (2009) Characterization of methanogenesis using stable isotopic probing. Prog Chem 21:540-549
63. Hirsch P, Overrein L, Alexander M (1961) Formation of nitrite and nitrate by actinobacteria and fungi. J Bacteriol 82:442-448
64. Hora TS, Iyengar MRS (1960) Nitrification by soil fungi. Arch Mikrobiol 35:252-257
65. 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
66. Huang LN, Chen YQ, Zhou H, Luo S, Lan CY, Qu LH (2003) Characterization of methanogenic archaea in the leachate of a closed municipal solid waste landfill. FEMS Microbiol Ecol 46:171-177
67. Hultman J, Kurola J, Raininsalo A, Kontro M, Romantschuk M (2010) Utility of molecular tools for optimization of large scale composting. In: Insam H, Franke-Whittle IH, Goberna M (eds) Microbes at work. From wastes to resources. Springer, Heidelberg, pp 135-152
68. Ianotti EL, Fischer JR, Sievers DM (1982) Characterization of bacteria from a swine manure digester. Appl Environ Microbiol 43:136-143
69. Innerebner G, Knapp B, Vasara T, Romantschuk M, Insam H (2006) Traceability of ammoniaoxidising bacteria in compost-treated soils. Soil Biol Biochem 38:1092-1100
70. Insam H, de Bertoldi M (2007) Microbiology of the composting process. In: Diaz LF, de Bertoldi M, Bidlingmaier W, Stentiford E (eds) Compost science and technology. Elsevier, Amsterdam, pp 25-48
71. Insam H, Wett B (2008) Control of GHG emission at the microbial community level. Waste Manage 28:699-706
72. Jäckel U, Thummes K, Kämpfer P (2005) Thermophilic methane production and oxidation in compost. FEMS Microbiol Ecol 52:175-184
73. Juste A, Thomma BPHJ, Lievens B (2008) Recent advances in molecular techniques to study microbial communities in food-associated matrices and processes. Food Microbiol 25:745-761
74. Karakashev D, Batstone DJ, Angelidaki I (2005) Influence of environmental conditions on methanogenic compositions in anaerobic biogas reactors. Appl Environ Microbiol 71:331-338
75. Kendall MM, Boone DR (2006) The order Methanosarcinales. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes. A handbook on the biology of bacteria, vol 3. Springer-Verlag, New York, USA, pp 244-256
76. Klocke M, Nettmann E, Bergmann I, Mundt K, Souidi K, Mumme J, Linke B (2008) Characterization of the methanogenic archaea within two-phase biogas reactor systems operated with plant biomass. Syst Appl Microbiol 31:190-205
77. Knapp B, Ros M, Insam H (2010) Do composts affect the soil microbial community? In: Insam H, Franke-Whittle IH, Goberna M (eds) Microbes at work. From wastes to resources. Springer, Heidelberg, pp 271-292
78. Krause DO, Denman SE, Mackie RI, Morrison M, Rae AL, Attwood GT, McSweeney CS (2003) Opportunities to improve fibre degradation in the rumen: microbiology, ecology, and genomics. FEMS Microbiol Rev 27:663-693
79. Krause L, Diaz NN, Edwards RA, Gartemann K-H, Krömeke H, Neuweger H, Pnhler A, Runte KJ, Schlnter A, Stoye J, Szczepanowski R, Tauch A, Goesmann A (2008) Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor: genome research in the light of ultrafast sequencing technologies. J Biotechnol 136:91-101
80. Laloui-Carpentier W, Li T, Vigneron V, Mazéas L, Bouchez T (2006) Methanogenic diversity and activity in municipal solid waste landfill leachates. Anton Leeuw Int JG89:423-434
81. LaPara TM, Nakatsu CH, Pantea LM, Alleman JE (2002) Stability of the bacterial communities supported by a seven-stage biological process treating pharmaceutical wastewater as revealed by PCR-DGGE. Water Res 36:638-646
82. Leclerc M, Delgènes JP, Godon JJ (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
83. Levén L, Eriksson ARB, Schnürer A (2007) Effect of process temperature on bacterial and archaeal communities in two methanogenic bioreactors treating organic household waste. FEMS Microbiol Ecol 59:683-693
84. Liesack W, Stackebrandt E (1992) Unculturable microbes detected by molecular sequences and probes. Biodivers Conserv 1:250-262
85. Liu WT, Marsh TL, Cheung 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
86. Liu WT, Chan CO, Fang HH (2002) Microbial community dynamics during start-up of acidogenic anaerobic reactors. Water Res 36:3203-3210
87. Loehr RC (1974) Agricultural waste management. Academic, New York, USA
88. Lott Fischer J (1998) Avoidance of biorisks of composting by thermohygienization: influence of the type of system and management on the occurrence of the potentially pathogenic mold Aspergillus fumigatus and fecal indicator bacteria. Thesis, Université de Neuchâtel, Switzerland
89. Loy A, Bodrossy L (2006) Highly parallel microbial diagnostics using oligonucleotide microarrays. Clin Chim Acta 363:106-119
90. Loy A, Lehner A, Lee N, Adamczyk J, Meier H, Ernst J, Schleifer K-H, Wagner M (2002) Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl Environ Microb 68:5064-5081
91. Lueders T, Friedrich MW (2003) Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. Appl Environ Microbiol 69:320-326
92. Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS (2002) Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev 66:507-577
93. Macario AJL, Conway de Macario E (1988) Quantitative inmunologic analysis of the methanogenic microflora of digestors reveals considerable diversity. Appl Environ Microbiol 54:79-86
94. Macedo AJ, Timmis KN, Wolf-Rainer A (2007) Widespread capacity to metabolize polychlorinated biphenyls by diverse microbial communities in soils with no significant exposure to PCB contamination. Environ Microbiol 9:1890-1897
95. Madsen EL (2006) The use of stable isotope probing techniques in bioreactor and field studies on bioremediation. Curr Opin Biotechnol 17:92-97
96. Malin C, Illmer P (2008) Ability of DNA content and DGGE analysis to reflect the performance condition of an anaerobic biowaste fermenter. Microbiol Res 163:503-511
97. Manz W, Amann R, Ludwig W, Wagner M, Schleifer KH (1992) Phylogenetic oligonucleotide probes for the major subclasses of Proteobacteria: problems and solutions. Syst Appl Microbiol 15:593-600
98. Marshall KC, Alexander M (1962) Nitrification by Aspergillus flavus. J Bacteriol 83:572-578
99. McHugh S, Carton M, Mahony T, O'Flaherty V (2003) Methanogenic population structure in a variety of anaerobic bioreactors. FEMS Microbiol Lett 219:297-304
100. McMahon KD, Stroot PG, Mackie RI, Raskin L (2001) Anaerobic codigestion of municipal solid waste and biosolids under various mixing conditions - II: microbial population dynamics. Water Res 35:1817-1827
101. McMahon KD, Zheng D, Stams AJM, Mackie RI, Raskin L (2004) Microbial population dynamics during start-up and overload conditions of anaerobic digesters treating municipal solid waste and sewage sludge. Biotechnol Bioeng 87:823-834
102. Michel FC Jr, Marsh TJ, Reddy CA (2002) Bacterial community structure during yard trimmings composting. In: Insam H, Riddech N, Klammer S (eds) Microbiology of composting. Springer-Verlag, Heidelberg, pp 25-42
103. Minz D, Green SJ, Ofek M, Hadar Y (2010) Compost microbial populations and interactions with plants. In: Insam H, Franke-Whittle IH, Goberna M (eds) Microbes at work. From wastes to resources. Springer, Heidelberg, pp 231-252
104. Mladenovska Z, Dabrowski S, Ahring B (2003) Anaerobic digestion of manure and mixture of manure with lipids: biogas reactor performance and microbial community analysis. Water Sci Technol 48:271-278
105. Monis PT, Giglio S (2006) Nucleic acid amplification-based techniques for pathogen detection and identification. Infect Genet Evol 6:2-12
106. Montero B, Morales JL, Sales D, Solera R (2008) Evolution of microorganisms in thermophilicdry anaerobic digestion. Bioresource Technol 99:3233-3243
107. Mosier N, Wyman C, Dale B, Elander R, Lee YY, Holtzapple M, Ladisch M (2005) Features of promising technologies for pretreatment of lignocellulosic biomass. Bioresource Technol 96:673-686
108. Mountfort DO, Brulla WJ, Krumholz LR, Bryant MP (1984) Syntrophus buswellii gen. nov. sp. nov.: a benzoate catabolizer from methanogenic ecosystems. Int J Syst Bacteriol 34:216-217
109. Moyer CL, Dobbs FC, Karl DM (1994) Estimation of diversity and community structure through restriction fragment length polymorphism distribution analysis of bacterial 16S rRNA genes from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii. Appl Environ Microbiol 60:871-879
110. Muyzer G, Stams AJM (2008) The ecology and biotechnology of sulphate-reducing bacteria. Nat Rev Microbiol 6:441-454
111. Muyzer G, de Waal EC, Uitterlinden AG (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
112. Nakashimada Y, Srinivasan K, Murakami M, Nishio N (2000) Direct conversion of cellulose to methane by anaerobic fungus Neocallimastix frontalis and defined methanogens. Biotechnol Lett 22:223-227
113. Nishida T, Fujimura T, Omasa T, Katakura Y, Suga K-I, Shioya S (2003) Changes in microflora duding composting of an aquatic plant, Brazilian elodea. J Chem Eng Jpn 36:1201-1205
114. Nocker A, Burr M, Camper A (2007) Genotypic microbial community profiling: a critical technical review. Microb Ecol 54:276-289
115. Ntougias S, Zervakis GI, Kavroulakis N, Ehaliotis C, Papadopoulou KK (2004) Bacterial diversity in spent mushroom compost assessed by amplified rDNA restriction analysis and sequencing of cultivated isolates. Syst Appl Microbiol 27:746-754
116. O'Flaherty V, Collins G, Mahony T (2006) The microbiology and biochemistry of anaerobic bioreactors with relevance to domestic sewage treatment. Rev Environ Sci Biotechnol 5:39-55
117. Ortega-Charleston L (2008) Hyperthermophilic anaerobic digestion of food waste. PhD Thesis, McGill University, Montreal
118. Pedro MS, Haruta S, Hazaka M, Shimada R, Yoshida C, Hiura K, Ishii M, Igarashi Y (2001) Denaturing gradient gel electrophoresis analyses of microbial community from field-scale composter. J Biosci Bioeng 91:159-165
119. Pérez-Piqueres A, Edel-Hermann V, Alabouvette C, Steinberg C (2006) Response of soil microbial communities to compost amendments. Soil Biol Biochem 38:460-470
120. Plugge CM, van Lier J B, Stams AJM (2010) Syntrophic communities in methane formation from high strength wastewaters. In: Insam H, Franke-Whittle IH, Goberna M (eds) Microbes at work. From wastes to resources. Springer-Verlag, New York, pp 59-78
121. Polz MF, Cavanaugh CM (1998) Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol 64:3724-3730
122. Qiu Y-L, Hanada S, Ohashi A, Harada H, Kamagata Y, Sekiguchi Y (2008) Syntrophorhabdus aromaticivorans gen. nov., sp. nov., the first cultured anaerobe capable of degrading phenol to acetate in obligate syntrophic associations with a hydrogenotrophic methanogen. Appl Environ Microbiol 74:2051-2058
123. Ramsay IR, Pullammanappallil PC (2001) Protein degradation during anaerobic wastewater treatment: derivation of stoichiometry. Biodegradation 12:247-257
124. Raskin L, Poulsen LK, Noguera DR, Rittmann B, Stahl DA (1994a) Quantification of methanogenic groups in anaerobic biological reactors by oligonucleotide probe hybridization. Appl Environ Microbiol 60:1241-1248
125. Raskin L, Stromley JM, Rittmann B, Stahl DA (1994b) Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens. Appl Environ Microbiol 60:1232-1240
126. Ren Z, Ward TE, Logan BE, Regan JM (2007) Characterization of the cellulolytic and hydrogenproducing activities of six mesophilic Clostridium species. J Appl Microbiol 103:2258-2266
127. Rincón B, Raposo F, Borja R, González JM, Portillo MC, Saiz-Jiménez C (2006) Performance and microbial communities of a continuous stirred tank anaerobic reactor treating two-phases olive mill solid wastes at low organic loading rates. J Biotechnol 121:534-543
128. Roest K, Altinbas M, Paulo PL, Heilig HGHJ, Akkermans ADL, Smidt H, de Vos WM, Stams AJM (2005a) Enrichment and detection of microorganisms involved in direct and indirect methanogenesis from methanol in an anaerobic thermophilic bioreactor. Microb Ecol 50:440-446
129. Roest K, Heilig HGHJ, Smidt H, deVos WM, Stams AJM, Akkermans ADL (2005b) Community analysis of a full-scale anaerobic bioreactor treating paper mill wastewater. Syst Appl Microbiol 28:175-185
130. Roller C, Wagner M, Amann R, Ludwig W, Schleifer K-H (1994) In situ probing of Gram-positive bacteria with high DNA G + C content using 23S rRNA-targeted oligonucleotides. Microbiology 140:2849-2858
131. Ros M, Klammer S, Knapp B, Aichberger K, Insam H (2006) Long term effects of compost amendment of soil on functional and structural diversity and microbial activity. Soil Use Manag 22:209-218
132. Ryckeboer J, Mergaert J, Vaes K, Klammer S, De Clercq D, Coosemans J, Insam H, Swings J (2003) A survey of bacteria and fungi occurring during composting and self-heating processes. Ann Microbiol 53:349-410
133. Sahlström L (2003) A review of survival of pathogenic bacteria in organic waste used in biogas plants. Bioresource Technol 87:161-166
134. Sahlström L, Aspan A, Bagge E, Danielsson-Tham ML, Albihn A (2004) Bacterial pathogen incidences in sludge from Swedish sewage treatment plants. Water Res 38:1989-1994
135. Sarada R, Joseph R (1994) Characterization and enumeration of microorganisms associated with anaerobic digestion of tomato-processing waste. Bioresource Technol 49:261-265
136. Sawayama S, Tsukahara K, Yagishita T (2006) Phylogenetic description of immobilized methanogenic community using real-time PCR in a fixed-bed anaerobic digester. Bioresource Technol 97:69-76
137. Schink B (1997) Energetics of syntrophic cooperation in methanogenic degradation. Microbiol Mol Biol Rev 61:262-280
138. Schink B, Stams AJM (2006) Syntrophism among prokaryotes. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes. A handbook on the biology of bacteria, vol 2. Springer-Verlag, New York, USA, pp 309-335
139. Schloss PD, Hay AG, Wilson DB, Walker LP (2003) Tracking temporal changes of bacterial community fingerprints during the initial stages of composting. FEMS Microbiol Ecol 46:1-9
140. Schlüter A, Bekel T, Diaz NN, Dondrup M, Eichenlaub R, Gartemann K-H, Krahn I, Krause L, Krömeke H, Kruse O, Mussgnug JH, Neuweger H, Niehaus K, Pnhler A, Runte KJ, Szczepanowski R, Tauch A, Tilker A, Viehöver P, Goesmann A (2008) The metagenome of a biogasproducing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology: genome research in the light of ultrafast sequencing technologies. J Biotechnol 136:77-90
141. Schmitz RA, Daniel R, Deppenmeier U, Gottschalk G (2006) The anaerobic way of life. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes. A handbook on the biology of bacteria, vol 2. Springer-Verlag, New York, USA, pp 86-101
142. Schnürer A, Schink B, Svensson BH (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
143. Schwarz WH (2001) The cellulosome and cellulose degradation by anaerobic bacteria. Appl Microbiol Biotechnol 56:634-649
144. Scully C, Collins G, O'Flaherty V (2005) Assessment of anaerobic wastewater treatment failure using terminal restriction fragment length polymorphism analysis. J Appl Microbiol 99:1463-1471
145. Sekiguchi Y (2006) Yet-to-be cultured microorganisms relevant to methane fermentation process. Microbes Environ 21:1-15
146. Sekiguchi Y, Kamagata Y, Nakamura K, Ohashi A, Harada H (2000) Syntrophothermus lipocalidus gen. nov., sp. nov., a novel thermophilic, syntrophic, fatty-acid-oxidizing anaerobe which utilizes isobutyrate. Int J Syst Evol Microbiol 50:771-779
147. Sessitsch A, Gyamfi S, Stralis-Pavese N, Weilharter A, Pfeifer U (2002) RNA isolation from soil for bacterial community and functional analysis: evaluation of different extraction and soil conservation protocols. J Microbiol Methods 51:171-179
148. Sharma VK, Hagen JC (1995) Isolation and characterization of Clostridium hobsonii comb. nov. Bioresource Technol 51:61-74
149. Shigematsu T, Tang Y, Kawaguchi H, Ninomiya K, Kijima J, Kobayashi T, Morimura S, Kida K (2003) Effect of dilution rate on structure of a mesophilic acetate-degrading methanogenic community during continuous cultivation. J Biosci Bioeng 96:547-558
150. Small J, Call DR, Brockman FJ, Straub TM, Chandler DP (2001) Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays. Appl Environ Microbiol 67:4708-4716
151. Smith KS, Ingram-Smith C (2007) Methanosaeta, the forgotten methanogen? Trends Microbiol 15:150-155
152. Smith A, Hubbard H, Huber D (2004) Archaeal diversity of a thermophilic methanogenic pilot scale digester treating poultry farm waste. In: Proceedings of the 10th Anaerobic Digestion Conference, Montréal, Canada, 1574-1577
153. Sokolova TG, Kostrikina NA, Chernyh NA, Tourova TP, Kolganova TV, Bonch-Osmolovskaya EA (2002) Carboxydocella thermautotrophica gen. nov., sp. nov., a novel anaerobic, CO-utilizing thermophile from a Kamchatkan hot spring. Int J Syst Evol Microbiol 52:1961-1967
154. Sokolova TG, González JM, Kostrikina NA, Chernyh NA, Slepova TV, Bonch-Osmolovskaya EA, Robb FT (2004) Thermosinus carboxydivorans gen. nov., sp. nov., a new anaerobic, thermophilic, carbon-monoxideoxidizing, hydrogenogenic bacterium from a hot pool of Yellowstone National Park. Int J Syst Evol Microbiol 54:2353-2359
155. Sousa DZ (2006) Ecology and physiology of anaerobic microbial communities that degrade long chain fatty acids. PhD Thesis, Universidade do Minho
156. Sousa DZ, Pereira MA, Smidt H, Stams AJM, Alves MM (2007) Molecular assessment of complex microbial communities degrading long-chain fatty acids in methanogenic bioreactors. FEMS Microbiol Ecol 60:252-265
157. Stackebrandt E, Rainey FA, Ward-Rainey NL (1997) Proposal for a new heirarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 47:479-491
158. Stams AJM, Elferink SJWHO, Westermann P (2003) Metabolic interactions between methanogenic consortia and anaerobic respiring bacteria. In: Sheper T (ed) Advances in biochemical engineering/biotechnology. Springer-Verlag, Berlin, pp 31-56
159. Stams AJM, de Bok FAM, Plugge CM, van Eekert JD, Schraa G (2006) Exocellular electron transfer in anaerobic microbial communities. Environ Microbiol 8:371-382
160. Strom PF (1985) Effect of temperature on bacterial diversity in thermophilic solid-waste composting. Appl Environ Microbiol 50:899-905
161. Suzuki M, Giovannoni S (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62:625-630
162. Talbot G, Roy C, Topp E, Palin MF, Massé D (2004) Monitoring microbial diversity and function in swine manure anaerobic digesters by length heterogeneity PCR (LH-PCR). In: Anaerobic Digestion 10th World Congress Proceedings, Aug. 29th-Sept 2nd, Montreal, vol 3, pp 1594-1598
163. 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
164. Tang Y, Shigematsu T, Ikbal MS, Kida K (2004) The effects of micro-aeration on the phylogenic diversity of microorganisms in a thermophilic anaerobic municipal solid-waste digester. Water Res 38:2537-2550
165. Tang Y, Shigematsu T, Morimura S, Kida K (2005) Microbial community analysis of mesophilic anaerobic protein degradation process using bovine serum albumin (BSA)-fed continuous cultivation. J Biosci Bioeng 99:150-164
166. Tarlera S, Muxí L, Soubes M, Stams AJM (1997) Calaromator proteoclasticus sp. nov., a new moderately thermophilic anareobic proteolytic bacterium. Int J Syst Bacteriol 47:651-656
167. Thummes K, Kämpfer P, Jäckel U (2007a) Temporal change of composition and potential activity of the thermophilic archaeal community during the composting of organic material. Syst Appl Microbiol 30:418-429
168. Thummes K, Schäfer J, Kämpfer P, Jäckel U (2007b) Thermophilic methanogenic archaea in compost material: occurrence, persistence and possible mechanisms for their distribution to other environments. Syst Appl Microbiol 30:634-643
169. Tiquia SM (2005) Microbial community dynamics in manure composts based on 16S and 18S rDNA T-RFLP profiles. Environ Technol 26:1101-1113
170. Torsvik VL, Goksoyr J, Daae FL (1990) High diversity in DNA of soil bacteria. Appl Environ Microbiol 56:782-787
171. Ueno Y, Haruta S, Ishii M, Igarashi Y (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 Biot 57:65-73
172. US-EPA (Environmental Protection Agency) (2006) Anaerobic digestion: benefits for waste management, agriculture, energy and environment. Available at: http://www.dcmnr.gov. ie/NR/rdonlyres/287C17F6-13D2-48B9-882C-2060512A573E/0/EPAappendix.pdf. Accessed 26 July 2006
173. Vinnerås B, Schönning C, Nordin A (2006) Identification of the microbiological community in biogas systems and evaluation of microbial risks from gas usage. Sci Total Environ 367:606-615
174. Vinnerås B, Agostini F, Jönsson H (2010) Sanitation by composting. In: Insam H, Franke-Whittle IH, Goberna M (eds) Microbes at work. From wastes to resources. Springer, Heidelberg, pp 171-192
175. Vogels GD, Van der Drift C (1976) Degradation of purines and pyrimidines by microorganisms. Bacteriol Rev 40:403-468
176. Wagner R (1994) The regulation of ribosomal RNA synthesis and bacterial cell growth. Arch Microbiol 161:100-109
177. Waksman SA (1932) Principles of soil microbiology. Williams & Wilkins, Baltimore, MD
178. Wang LF, Rakela J, Laskus T (1997) Head-to-tail primer tandem repeats generated in hemi-nested PCR. Mol Cell Probes 11:385-387
179. Ward DM, Bateson MM, Weller R, Ruff-Roberts AL (1992) Ribosomal RNA analysis of microorganisms as they occur in nature. Adv Microb Ecol 12:219-286
180. Ward AJ, Hobbs PJ, Holliman PJ, Jones DL (2008) Optimisation of the anaerobic digestion of agricultural resources. Bioresource Technol 99:7928-7940
181. Wéry N, Lhoutellier C, Ducray F, Delgenès JP, Godon JJ (2008) Behaviour of pathogenic and indicator bacteria during urban wastewater treatment and sludge composting, as revealed by quantitative PCR. Water Res 42:53-62
182. Wett B, Insam H (2010) Biogas technology: Controlled gas flow for enhanced mixing, heating, and desulfurization. In: Insam H, Franke-Whittle IH, Goberna M (eds) Microbes at work. From wastes to resources. Springer, Heidelberg, pp 79-92
183. Whitehead TR, Cotta MA (1999) Phylogenetic diversity of methanogenic archaea in swine waste storage pits. FEMS Microbiol Lett 179:223-226
184. Whitman W, Jeanthon C (2006) Methanococcales. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes. A handbook on the biology of bacteria, vol 3. Springer-Verlag, New York, USA, pp 257-273
185. Wilson DB (2008) Three microbial strategies for plant cell wall degradation. Ann New York Acad Sci 1125:289-297
186. Yamada T, Miyauchi K, Ueda H, Ueda Y, Sugawara H, Nakai Y, Endo G (2007) Composting cattle dung wastes by using a hyperthermophilic pre-treatment process: characterization by physicochemical and molecular biological analysis. J Biosci Bioeng 104:408-415
187. Yazdani SS, Gonzalez R (2007) Anaerobic fermentation of glycerol: a path to economic viability for the biofuels industry: energy biotechnology/environmental biotechnology. Curr Opin Biotechnol 18:213-219
188. Yu Y, Kim J, Hwang S (2006) Use of real-time PCR for group-specific quantification of aceticlastic methanogens in anaerobic processes: population dynamics and community structures. Biotechnol Bioeng 93:424-433
189. Zhang B, He P-J, Lü F, Shao L-M, Wang P (2007) Extracellular enzyme activities during regulated hydrolysis of high-solid organic wastes. Water Res 41:4468-4478
190. Zhao HW, Viraraghavan T (2004) Analysis of the performance of an anaerobic digestion system at the Regina wastewater treatment plant. Bioresource Technol 95:301-307
191. Zheng D, Raskin L (2000) Quantification of Methanosaeta species in anaerobic bioreactors using genus- and species-specific hybridization probes. Microb Ecol 39:246-262
192. Zinder SH (1993) Physiological ecology of methanogens. In: Ferrry JG (ed) Methanogenesis: ecology, physiology, biochemistry and genetics. Springer-Verlag, New York, pp 128-206
193. Zinder SH, Koch M (1984) Non-acetoclastic methanogenesis from acetate: acetate oxidation by a thermophilic syntrophic coculture. Arch Microbiol 138:263-272
194. Zinder SH, Cardwell SC, Anguish T, Lee M, Koch M (1984) Methanogenesis in a thermophilic anaerobic digestor: Methanothrix sp. as an important aceticlastic methanogen. Appl Environ Microbiol 47:796-807
195. Zumstein E, Moletta R, Godon JJ (2000) Examination of two years of community dynamics in an anaerobic bioreactor using fluorescence polymerase chain reaction (PCR) single-strand conformation polymorphism analysis. Environ Microbiol 2:69-78