Source: http://www.asmscience.org/content/book/10.1128/9781555815547.ch15
Timestamp: 2019-04-21 12:21:07+00:00

Document:
View of a farm-based anaerobic digester in Iowa.
Anaerobic food web. Adapted from Gujer and Zehnder ( 1983 ) and McCarty and Smith ( 1986 ).
Schematic of biological butanol production from waste slurries.
Schematic of a microbial fuel cell for hydrogen generation in the cathode (left panel) and electrical power generation (right panel). The surface of the anodic electrode is positive, and the surface of the cathodic electrode is negative. Electron current is from the anode to the cathode.
1. Agbogbo, F. K., and, M. T. Holtzapple. 2006. Fermentation of rice straw/chicken manure to carboxylic acids using a mixed culture of marine mesophilic microorganisms. Appl. Biochem. Biotechnol. 129-132: 997– 1014.
2. Agbogbo, F. K., and, M. T. Holtzapple. 2007. Fixed-bed fermentation of rice straw and chicken manure using a mixed culture of marine mesophilic microorganisms. Bioresour. Technol. 98: 1586.
3. Aiello-Mazzarri, C.,, G. Coward-Kelly,, F. K. Agbogbo, and, M. T. Holtzapple. 2005. Conversion of municipal solid waste into carboxylic acids by anaerobic countercurrent fermentation: effect of using intermediate lime treatment. Appl. Biochem. Biotechnol. 127: 79– 94.
4. Akin, D. E., and, R. Benner. 1988. Degradation of polysaccharides and lignin by ruminal bacteria and fungi. Appl. Environ. Micro-biol. 54: 1117– 1125.
5. Angelidaki, I., and, B. K. Ahring. 1994. Anaerobic thermophilic digestion of manure at different ammonia loads: effect of temperature. Water Res. 28: 727– 731.
6. Angenent, L. T.,, K. Karim,, M. H. Al-Dahhan,, B. A. Wrenn, and, R. Domínguez-Espinosa. 2004. Production of bioenergy and biochemicals from industrial and agricultural wastewater. Trends Biotechnol. 22: 477– 485.
7. Angenent, L. T.,, S. Sung, and, L. Raskin. 2002. Methanogenic population dynamics during startup of a full-scale anaerobic sequencing batch reactor treating swine waste. Water Res. 36: 4648– 4654.
8. Aspray, T. J.,, S. K. Hansen, and, R. G. Burns. 2005. A soil-based microbial biofilm exposed to 2,4-D: bacterial community development and establishment of conjugative plasmid pJP4. FEMS Micro-biol. Ecol. 54: 317– 327.
9. Azbar, N.,, P. Ursillo, and, R. E. Speece. 2001. Effect of process configuration and substrate complexity on the performance of anaerobic processes. Water Res. 35: 817– 829.
10. Bahl, H.,, W. Andersch,, K. Braun, and, G. Gottschalk. 1982a. Effect of pH and butyrate concentration on the production of acetone and butanol by Clostridium acetobutylicum grown in continuous culture. Appl. Microbiol. Biotechnol. V14: 17.
11. Bahl, H.,, W. Andersch, and, G. Gottschalk. 1982b. Continuous production of acetone and butanol by Clostridium acetobutylicum in a two-stage phosphate limited chemostat. Appl. Microbiol. Biotechnol. V15: 201.
12. Bahl, H.,, M. Gottwald,, A. Kuhn,, V. Rale,, W. Andersch, and, G. Gottschalk. 1986. Nutritional factors affecting the ratio of solvents produced by Clostridium acetobutylicum. Appl. Environ. Micro-biol. 52: 169– 172.
13. Barsoukov, E., and, J. R. Macdonald. 2005. Impedance spectroscopy: theory, experiment, and applications. John Wiley & Sons, Hoboken, NJ.
14. Bathe, S.,, T. V. Mohan,, S. Wuertz, and, M. Hausner. 2004. Bio-augmentation of a sequencing batch biofilm reactor by horizontal gene transfer. Water Sci. Technol. 49: 337– 344.
15. Batstone, D. J., and, J. Keller. 2001. Variation of bulk properties of anaerobic granules with wastewater type. Water Res. 35: 1723– 1729.
16. Batstone, D. J.,, J. Keller,, R. B. Newell, and, M. Newland. 2001. Modelling anaerobic degradation of complex wastewater. II. Parameter estimation and validation using slaughterhouse effluent. Bioresour. Technol. 75: 75– 85.
17. Berlin, A.,, V. Maximenko,, N. Gilkes, and, J. Saddler. 2007. Optimization of enzyme complexes for lignocellulose hydrolysis. Biotechnol. Bioeng. 97: 287– 296.
18. Bond, D. R., and, D. R. Lovley. 2003. Electricity production by Geobacter sulfurreducens attached to electrodes. Appl. Environ. Microbiol. 69: 1548– 1555.
19. Bond, D. R., and, D. R. Lovley. 2005. Evidence for involvement of an electron shuttle in electricity generation by Geothrix fermentans. Appl. Environ. Microbiol. 71: 2186– 2189.
20. Boon, N.,, L. De Gelder,, H. Lievens, and, W. Verstraete. 2002. Bioaugmenting bioreactors for the continuous removal of 3-chloroaniline by slow release approach. Environ. Sci. Technol. 36: 4698.
21. Breznak, J. A., and, A. Brune. 1994. Role of microorganisms in the digestion of lignocellulose by termites. Annu. Rev. Entomol. 39: 453– 487.
22. Brune, A.,, D. Emerson, and, J. A. Breznak. 1995a. The termite gut microflora as an oxygen sink: microelectrode determination of oxygen and pH gradients in guts of lower and higher termites. Appl. Environ. Microbiol. 61: 2681– 2687.
23. Brune, A.,, E. Miambi, and, J. A. Breznak. 1995b. Roles of oxygen and the intestinal microflora in the metabolism of lignin-derived phenylpropanoids and other monoaromatic compounds by termites. Appl. Environ. Microbiol. 61: 2688– 2695.
24. Chan, W. N., and, M. T. Holtzapple. 2003. Conversion of municipal solid wastes to carboxylic acids by thermophilic fermentation. Appl. Biochem. Biotechnol. 111: 93– 112.
25. Chaudhuri, S. K., and, D. R. Lovley. 2003. Electricity generation by direct oxidation of glucose in mediatorless microbial fuel cells. Nat. Biotechnol. 21: 1229– 1232.
26. Chen, Y.,, Y. Inbar,, Y. Hadar, and, R. L. Malcolm. 1989. Chemical properties and solid-state CPMAS 13C-NMR of composted organic matter. Sci. Total Environ. 81/82: 201– 208.
27. Chyi, Y. T., and, R. R. Dague. 1994. Effects of particulate size in anaerobic acidogenesis using cellulose as a sole carbon source. Water Environ. Res. 66: 670– 678.
28. Cleveland, L., and, A. Grimstone. 1964. The fine structure of the flagellate Mixotricha paradoxa and its associated micro-organisms. Proc. R. Soc. London B 159: 668.
29. Contreras, E. M.,, L. Giannuzzi, and, N. E. Zaritzky. 2000. Growth kinetics of the filamentous microorganism Spaerotilus natans in a model system of a food industry wastewater. Water Res. 34: 4455– 4463.
30. Cord-Ruwisch, R.,, D. R. Lovley, and, B. Schink. 1998. Growth of Geobacter sulfurreducens with acetate in syntrophic cooperation with hydrogen-oxidizing anaerobic partners. Appl. Environ. Microbiol. 64: 2232– 2236.
31. Dejonghe, W.,, N. Boon,, D. Seghers,, E. M. Top, and, W. Verstraete. 2001. Bioaugmentation of soils by increasing microbial richness: missing links. Environ. Microbiol. 3: 649.
32. Diaz, E. E.,, A. J. M. Stams,, R. Amils, and, J. L. Sanz. 2006. Phenotypic properties and microbial diversity of methanogenic granules from a full-scale upflow anaerobic sludge bed reactor treating brewery wastewater. Appl. Environ. Microbiol. 72: 4942– 4949.
33. Domke, S. B.,, C. Aiello-Mazzarri, and, M. T. Holtzapple. 2004. Mixed acid fermentation of paper fines and industrial biosludge. Bioresour. Technol. 91: 41.
34. Duran, M., and, R. E. Speece. 1998. Staging of anaerobic processes for reduction of chronically high concentrations of propionic acid. Water Environ. Res. 70: 241– 248.
35. Egli, K.,, C. Langer,, H. R. Siegrist,, A. J. Zehnder,, M. Wagner, and, J. R. Van Der Meer. 2003. Community analysis of ammonia and nitrite oxidizers during start-up of nitritation reactors. Appl. Environ. Microbiol. 69: 3213– 3222.
36. Ekinci, M. S.,, N. Ozcan,, E. Ozkose, and, H. J. Flint. 2001. A study on cellulolytic and hemicellulolytic enzymes of anaerobic rumen bacterium Ruminococcus flavefaciens strain 17. Turk. J. Vet. Anim. Sci. 25: 703– 709.
37. Electric Power Research Institute. 2002. Water and Sustainability, vol. 1. Research Plan. Electric Power Research Institute, Palo Alto, CA.
38. Ezeji, T. C.,, N. Qureshi, and, H. P. Blaschek. 2004. Butanol fermentation research: upstream and downstream manipulations. Chem. Rec. 4: 305– 314.
39. Fang, H. H., and, H. Liu. 2002. Effect of pH on hydrogen production from glucose by a mixed culture. Bioresour. Technol. 82: 87– 93.
40. Fang, H. H. P., and, H. Q. Yu. 2001. Acidification of lactose in waste-water. J. Environ. Eng. 127: 825– 831.
41. Fernandez, A. S.,, S. A. Hashsham,, S. L. Dollhopf,, L. Raskin,, O. Glagoleva,, F. B. Dazzo,, R. F. Hickey,, C. S. Criddle, and, J. M. Tiedje. 2000. Flexible community structure correlates with stable community function in methanogenic bioreactor communities perturbed by glucose. Appl. Environ. Microbiol. 66: 4058– 4067.
42. Fuchs, W.,, H. Binder,, G. Mavrias, and, R. Braun. 2003. Anaerobic treatment of wastewater with high organic content using a stirred tank reactor coupled with a membrane filtration unit. Water Res. 37: 902– 908.
43. Gohil, A., and, G. Nakhla. 2006. Treatment of food industry waste by bench-scale upflow anaerobic sludge blanket-anoxic-aerobic system. Water Environ. Res. 78: 974– 985.
44. Goodridge, L., and, S. T. Adebon. 2003. Bacteriophage biocontrol and bioprocessing: application of phage therapy to industry. SIM News 53: 254– 262.
45. Gorby, Y. A.,, S. Yanina,, J. S. McLean,, K. M. Rosso,, D. Moyles,, A. Dohnalkova,, T. J. Beveridge,, I. S. Chang,, B. H. Kim,, K. S. Kim,, D. E. Culley,, S. B. Reed,, M. F. Romine,, D. A. Saffarini,, E. A. Hill,, L. Shi,, D. A. Elias,, D. W. Kennedy,, G. Pinchuk,, K. Watanabe,, S. Ishii,, B. Logan,, K. H. Nealson, and, J. K. Fredrickson. 2006. Electrically conductive bacterial nanowires produced by Shewanella oneidensis strain MR-1 and other microorganisms. Proc. Natl. Acad. Sci. USA 103: 11358– 11363.
46. Gottschalk, G. 1986. Bacterial Metabolism. Springer-Verlag, New York, NY..
47. Grupe, H., and, G. Gottschalk. 1992. Physiological events in Clostridium acetobutylicum during the shift from acidogenesis to solventogenesis in continuous culture and presentation of a model for shift induction. Appl. Environ. Microbiol. 58: 3896– 3902.
48. Gujer, W., and, A. J. B. Zehnder. 1983. Conversion processes in anaerobic digestion. Water Sci. Technol. 15: 127– 167.
49. Hantula, J.,, A. Kurki,, P. Vuoriranta, and, D. H. Bamford. 1991. Ecology of bacteriophages infecting activated sludge bacteria. Appl. Environ. Microbiol. 57: 2147– 2151.
50. Hao, X.,, P. S. Mir,, M. A. Shah, and, G. R. Travis. 2005. Influence of canola and sunflower diet amendments on cattle feed lot manure. J. Environ. Qual. 34: 1439– 1445.
51. Harper, S. R., and, F. G. Pohland. 1986. Recent developments in hydrogen management during anaerobic biological wastewater treatment. Biotechnol. Bioeng. 28: 585– 602.
52. Hashsham, S. A.,, A. S. Fernandez,, S. L. Dollhopf,, F. B. Dazzo,, R. F. Hickey,, J. M. Tiedje, and, C. S. Criddle. 2000. Parallel processing of substrate correlates with greater functional stability in methanogenic bioreactor communities perturbed by glucose. Appl. Environ. Microbiol. 66: 4050– 4057.
53. Hattori, S.,, Y. Kamagata,, S. Hanada, and, H. Shoun. 2000. Thermacetogenium phaeum gen. nov., sp. nov., a strictly anaerobic, thermophilic, syntrophic acetate-oxidizing bacterium. Int. J. Syst. Evol. Microbiol. 50: 1601– 1609.
54. He, Z., and, L. T. Angenent. 2006. Application of bacterial biocath-odes in microbial fuel cells. Electroanalysis 18: 2009– 2015.
55. He, Z.,, S. D. Minteer, and, L. T. Angenent. 2005. Electricity generation from artificial wastewater with an upflow microbial fuel cell. Environ. Sci. Technol. 39: 5262– 5267.
56. He, Z.,, N. Wagner,, S. D. Minteer, and, L. T. Angenent. 2006. The upflow microbial fuel cell with an interior cathode: assessment of the internal resistance by impedance spectroscopy. Environ. Sci. Technol. 40: 5212– 5217.
57. Holtzapple, M. T.,, R. R. Davison,, M. K. Ross,, S. Albrett-Lee,, M. Nagwani,, C. M. Lee,, C. Lee,, S. Adelson,, W. Kaar,, D. Gaskin,, H. Shirage,, N. S. Chang,, V. S. Chang, and, M. E. Loescher. 1999. Biomass conversion to mixed alcohol fuels using the MixAlco process. Appl. Biochem. Biotechnol. 77–79: 609– 631.
58. Ieropoulos, I. A.,, J. Greenman,, C. Melhuish, and, J. Hart. 2005. Comparative study of three types of microbial fuel cell. Enzyme Microb. Technol. 37: 238– 245.
59. Jones, D. T., and, D. R. Woods. 1986. Acetone-butanol fermentation revisited. Microbiol. Rev. 50: 484– 524.
60. Kato, S.,, S. Haruta,, Z. J. Cui,, M. Ishii, and, Y. Igarashi. 2005. Stable coexistence of five bacterial strains as a cellulose-degrading community. Appl. Environ. Microbiol. 71: 7099– 7106.
61. Katz, E., and, I. Willner. 2003. Probing biomolecular interactions at conductive and semiconductive surfaces by impedance spectroscopy: routes to impedimetric immunosensors, DNA-sensors, and enzyme biosensors. Electroanalysis 15: 913– 947.
62. Kennedy, M.,, D. List, and, Y. Lu. 1999. Apple pomace and products derived from apple pomace: uses, composition, and analysis, p. 75– 120. In H.-F. Linskens and, J. E. Jackson (ed.), Modern Methods of Plant Analysis. Springer-Verlag, Berlin, Germany.
63. Kim, G. T.,, G. Webster,, J. W. T. Wimpenny,, B. H. Kim,, H. J. Kim, and, A. J. Weightman. 2006. Bacterial community structure, compartmentalization and activity in a microbial fuel cell. J. Appl. Microbiol. 101: 698– 710.
64. Kim, H. J.,, H. S. Park,, M. S. Hyun,, I. S. Chang,, M. Kim, and, B. H. Kim. 2002. A mediator-less microbial fuel cell using a metal reducing bacterium, Shewanella putrefaciens. Enzyme Microb. Technol. 30: 145– 152.
65. Kim, J. R.,, B. Min, and, B. E. Logan. 2005. Evaluation of procedures to acclimate a microbial fuel cell for electricity production. Appl. Microbiol. Biotechnol. 68: 23– 30.
66. Kleerebezem, R., and, A. J. M. Stams. 2000. Kinetics of syntrophic cultures: a theoretical treatise on butyrate fermentation. Biotechnol. Bioeng. 67: 529– 543.
67. Kleerebezem, R., and, M. C. M. van Loosdrecht. 2007. Mixed culture biotechnology for bioenergy production. Curr. Opin. Biotechnol. 18: 207– 212.
68. Kraemer, J. T., and, D. M. Bagley. 2005. Continuous fermentative hydrogen production using a two-phase reactor system with recycle. Environ. Sci. Technol. 39: 3819– 3825.
69. Leadbetter, J. R., and, J. A. Breznak. 1996. Physiological ecology of Methanobrevibacter cuticularis sp. nov. and Methanobrevibacter curvatus sp. nov., isolated from the hindgut of the termite Reticulitermes flavipes. Appl. Environ. Microbiol. 62: 3620– 3631.
70. Leadbetter, J. R.,, L. D. Crosby, and, J. A. Breznak. 1998. Methanobrevibacter filiformis sp. nov., a filamentous methanogen from termite hindguts. Arch. Microbiol. 169: 287– 292.
71. Leadbetter, J. R.,, T. M. Schmidt,, J. R. Graber, and, J. A. Breznak. 1999. Acetogenesis from H 2 plus CO 2 by spirochetes from termite guts. Science 283: 686– 689.
72. Lee, M. J., and, S. H. Zinder. 1988. Isolation and characterization of a thermophilic bacterium which oxidizes acetate in syntrophic association with a methanogen and which grows acetogenically on H 2-CO 2. Appl. Environ. Microbiol. 54: 124– 129.
73. Lepisto, S. S., and, J. A. Rintala. 1997. Start-up and operation of laboratory-scale thermophilic upflow anaerobic sludge blanket reactors treating vegetable processing wastewaters. J. Chem. Technol. Biotechnol. 68: 331– 339.
74. Leschine, S. B. 1995. Cellulose degradation in anaerobic environments. Annu. Rev. Microbiol. 49: 399– 426.
75. Ley, R. E.,, P. J. Turnbaugh,, S. Klein, and, J. I. Gordon. 2006. Microbial ecology: human gut microbes associated with obesity. Nature 444: 1022– 1023.
76. Liu, H.,, S. Grot, and, B. E. Logan. 2005. Electrochemically assisted microbial production of hydrogen from acetate. Environ. Sci. Technol. 39: 4317– 4320.
77. Logan, B. E. 2004. Biologically extracting energy from wastewater; biohydrogen production and microbial fuel cells. Environ. Sci. Technol. 38: 160A– 167A.
78. Lu, Z.,, F. Breidt,, V. Plengvidhya, and, H. P. Fleming. 2003. Bacteriophage ecology in commercial sauerkraut fermentations. Appl. Environ. Microbiol. 69: 3192– 3202.
79. Mackie, R. I., and, M. P. Bryant. 1995. Anaerobic digestion of cattle waste at mesophilic and thermophilic conditions. Appl. Microbiol. Biotechnol. 43: 346– 350.
80. Magnuson, T. S.,, A. L. Hodges-Myerson, and, D. R. Lovley. 2000. Characterization of a membrane-bound NADH-dependent Fe(3+) reductase from the dissimilatory Fe(3+)-reducing bacterium Geobacter sulfurreducens. FEMS Microbiol. Lett. 185: 205– 211.
81. Magnuson, T. S.,, N. Isoyama,, A. L. Hodges-Myerson,, G. Davidson,, M. J. Maroney,, G. G. Geesey, and, D. R. Lovley. 2001. Isolation, characterization and gene sequence analysis of a membrane-associated 89 kDa Fe(III) reducing cytochrome c from Geobacter sulfurreducens. Biochem. J. 359: 147– 152.
82. Malherbe, S., and, T. E. Cloete. 2002. Lignocellulose biodegradation: fundamental and applications. Rev. Environ. Sci. Technol. 1: 105– 114.
83. McCarty, P. L. 1964a. Anaerobic waste treatment fundamentals, part four: process design. Public Works 1964: 94– 99.
84. McCarty, P. L. 1964b. Anaerobic waste treatment fundamentals, part one: chemistry and microbiology. Public Works 1964: 107– 112.
85. McCarty, P. L. 1964c. Anaerobic waste treatment fundamentals, part three: toxic materials and their control. Public Works 1964: 91– 94.
86. McCarty, P. L. 1964d. Anaerobic waste treatment fundamentals, part two: environmental requirements and control. Public Works 1964: 123– 126.
87. McCarty, P. L., and, D. P. Smith. 1986. Anaerobic wastewater treatment. Environ. Sci. Technol. 20: 1200– 1206.
88. McInerney, M. J. 1988. Anaerobic hydrolysis and fermentation of fats and proteins. In A. J. B. Zehnder (ed.), Biology of Anaerobic Microorganisms. John Wiley and Sons, Inc., New York, NY..
89. Miller, D. N., and, V. H. Varel. 2003. Swine manure composition affects the biochemical origins, composition, and accumulation of odorous compounds. J. Anim. Sci. 81: 2131– 2138.
90. Moon, H.,, I. S. Chang, and, B. H. Kim. 2006. Continuous electricity production from artificial wastewater using a mediator-less microbial fuel cell. Bioresour. Technol. 97: 621– 627.
91. Moral, R.,, J. Moreno-Caselles,, M. D. Perez-Murcia,, A. Perez-Espinosa,, B. Rufete, and, C. Paredes. 2005. Characterization of the organic matter pool in manures. Bioresour. Technol. 96: 153– 158.
92. Mosier, N. S.,, R. Hendrickson,, M. Brewer,, N. Ho,, M. Sedlak,, R. Dreshel,, G. Welch,, B. S. Dien,, A. Aden, and, M. R. Ladisch. 2005. Industrial scale-up of pH-controlled liquid hot water pretreatment of corn fiber for fuel ethanol production. Appl. Biochem. Biotechnol. 125: 77– 97.
93. Mulkerrins, D.,, E. O’Connor,, B. Lawlee, P. Barton, and, A. Dobson. 2004. Assessing the feasibility of achieving biological nutrient removal from wastewater at an Irish food processing factory. Bioresour. Technol. 91: 207– 214.
94. Nemerow, N. L., and, A. Desgupta. 1991. Industrial and Hazardous Waste Treatment. Van Nostrand Reinhold, New York, NY..
95. Nevin, K. P., and, D. R. Lovley. 2000. Lack of production of electron-shuttling compounds or solubilization of Fe(III) during reduction of insoluble Fe(III) oxide by Geobacter metallireducens. Appl. Environ. Microbiol. 66: 2248– 2251.
96. Nevin, K. P., and, D. R. Lovley. 2002. Mechanisms for accessing insoluble Fe(III) oxide during dissimilatory Fe(III) reduction by Geothrix fermentans. Appl. Environ. Microbiol. 68: 2294– 2299.
97. Newman, D. K., and, R. Kolter. 2000. A role for excreted quinones in extracellular electron transfer. Nature 405: 94– 97.
98. Nüsslein, B.,, K. J. Chin,, W. Eckert, and, 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.
99. Odelson, D. A., and, J. A. Breznak. 1983. Volatile fatty acid production by the hindgut microbiota of xylophagous termites. Appl. Environ. Microbiol. 45: 1602– 1613.
100. O’Flynn, G.,, R. P. Ross,, G. F. Fitzgerald, and, A. Coffey. 2004. Evaluation of a cocktail of three bacteriophages for biocontrol of Escherichia coli O157:H7. Appl. Environ. Microbiol. 70: 3417– 3424.
101. O’Sullivan, C. A.,, P. C. Burrell,, W. P. Clarke, and, L. L. Blackall. 2005. Structure of a cellulose degrading bacterial community during anaerobic digestion. Biotechnol. Bioeng. 92: 871– 878.
102. Park, D. H., and, J. G. Zeikus. 2000. Electricity generation in microbial fuel cells using neutral red as an electronophore. Appl. Environ. Microbiol. 66: 1292– 1297.
103. Paul, J.,, S. Saxena, and, A. Varma. 1993. Ultrastructural studies of the termite ( Odontotermes obesus) gut microflora and its cellulolytic properties. World J. Microbiol. Biotechnol. 9: 108– 112.
104. Petersen, S. P., and, B. K. Ahring. 1992. The influence of sulfate on substrate utilization in a thermophilic sewage sludge digester. Appl. Microbiol. Biotechnol. 36: 805– 809.
105. Pynaert, K.,, B. F. Smets,, S. Wyffels,, D. Beheydt,, S. D. Siciliano, and, W. Verstraete. 2003. Characterization of an autotrophic nitrogen-removing biofilm from a highly loaded lab-scale rotating biological contactor. Appl. Environ. Microbiol. 69: 3626– 3635.
106. Rabaey, K.,, N. Boon,, S. D. Siciliano,, M. Verhaege, and, W. Verstraete. 2004. Biofuel cells select for microbial consortia that self-mediate electron transfer. Appl. Environ. Microbiol. 70: 5373– 5382.
107. Rabaey, K.,, G. Lissens,, S. D. Siciliano, and, W. Verstraete. 2003. A microbial fuel cell capable of converting glucose to electricity at high rate and efficiency. Biotechnol. Lett. 25: 1531– 1535.
108. Ramey, D. E., and, Environmental. Energy, Inc. May. 1998. Continuous two stage, dual path anaerobic fermentation of butanol and other organic solvents using two different strains of bacteria. U.S. patent 5,753,474.
109. Rao, K.,, V. Chaudhari,, S. Varanasi, and, D.-S. Kim. 2007. Enhanced ethanol fermentation of brewery wastewater using the genetically modified strain E. coli KO11. Appl. Microbiol. Biotechnol. 74: 50– 60.
110. Raphael, L.,, M. Ely,, M.-Y. Orly, and, A. B. Edward. 1991. Cellulosome-like entities in Bacteroides cellulosolvens. Curr. Microbiol. 22: 27.
111. Reguera, G.,, K. D. McCarthy,, T. Mehta,, J. S. Nicoll,, M. T. Tuominen, and, D. R. Lovley. 2005. Extracellular electron transfer via microbial nanowires. Nature 435: 1098– 1101.
112. Rhoads, A.,, H. Beyenal, and, Z. Lewandowski. 2005. Microbial fuel cell using anaerobic respiration and biomineralization manganese as a cathodic reactant. Environ. Sci. Technol. 39: 4666– 4671.
113. Ringeisen, B. R.,, E. Henderson,, P. K. Wu,, J. Peietron,, R. Ray,, B. Little,, J. C. Biffinger, and, J. M. Jones-Meehan. 2006. High power density from a miniature microbial fuel cell using Shewanella oneidensis DSP10. Environ. Sci. Technol. 40: 2629– 2634.
114. Rittmann, B. E., and, P. L. McCarty. 2001. Environmental Biotechnology. McGraw Hill, Boston, MA.
115. Rodriguez, J.,, R. Kleerebezem,, J. M. Lema, and, M. C. M. van Loosdrecht. 2006. Modeling product formation in anaerobic mixed culture fermentations. Biotechnol. Bioeng. 93: 592– 606.
116. Rodriguez-Martinez, J.,, S. Y. Martinez-Amador, and, Y. Garza-Garcia. 2005. Comparative anaerobic treatment of wastewater from pharmaceutical, brewery, paper and amino acid industries. J. Ind. Microbiol. Biotechnol. 32: 691– 696.
117. Rozendal, R. A.,, H. V. M. Hamelers,, G. J. W. Euverink,, S. J. Metz, and, C. J. N. Buisman. 2006. Principle and perspectives of hydrogen production through biocatalyzed electrolysis. Int. J. Hydrogen Energy 31: 1632– 1640.
118. Russ, W., and, R. Meyer-Pittroff. 2004. Utilizing waste products from the food production and processing industries. Crit. Rev. Food Sci. Nutr. 44: 57– 62.
119. Sayler, G. S., and, S. Ripp. 2000. Field applications of genetically engineered microorganisms for bioremediation processes. Curr. Opin. Biotechnol. 11: 286.
120. Schink, B. 1992. Syntrophism among prokaryotes, p. 276– 299. In A. Balows,, H. G. Trüper,, M. Dworkin,, W. Harder, and, K. H. Schleifer (ed.), The Prokaryotes. Springer Verlag, New York, NY..
121. Schmidt, J. E., and, B. K. Ahring. 1993. Effects of hydrogen and formate on the degradation of propionate and butyrate in thermophilic granules from an upflow anaerobic sludge blanket reactor. Appl. Environ. Microbiol. 59: 2546– 2551.
122. Schnürer, A.,, F. P. Houwen, and, B. H. Svensson. 1994. Mesophilic syntrophic acetate oxidation during methane formation by a tri-culture at high ammonia concentration. Arch. Microbiol. 162: 70– 74.
123. Schnürer, A.,, B. Schink, and, B. H. 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.
124. Schnürer, A.,, B. H. Svensson, and, B. Schink. 1997. Enzyme activities in and energetics of acetate metabolism by the mesophilic syntrophically acetate-oxidizing anaerobe Clostridium ultunense . FEMS Microbiol. Lett. 154: 331– 336.
125. Schnürer, A.,, G. Zellner, and, B. H. Svensson. 1999. Mesophilic syntrophic acetate oxidation during methane formation in biogas reactors. FEMS Microbiol. Ecol. 29: 249– 261.
126. Shoemaker, N. B.,, H. Vlamakis,, K. Hayes, and, A. A. Salyers. 2001. Evidence for extensive resistance gene transfer among Bacteroidesspp. and among Bacteroides and other genera in the human colon. Appl. Environ. Microbiol. 67: 561– 568.
127. Siso, M. I. G. 1996. The biotechnological utilization of cheese whey: a review. Bioresour. Technol. 57: 1– 11.
128. Speece, R. E. 1996. Anaerobic Biotechnology for Industrial Waste-waters. Archaea Press, Nashville, TN.
129. Stams, A. J. M. 1994. Metabolic interactions between anaerobic bacteria in methanogenic environments. Antonie Leeuwenhoek 66: 271– 294.
130. Stanton, T. B., and, E. Canale-Parola. 1980. Treponema bryantii sp. nov., a rumen spirochete that interacts with cellulolytic bacteria. Arch. Microbiol. 127: 145.
131. Sutcliffe, R., and, J. N. Saddler. 1986. The role of lignin in the adsorption of cellulases during enzymatic treatment of lignocellulosic material. Biotechnol. Bioeng. Symp. 17: 749– 762.
132. Taghavi, S.,, T. Barac,, B. Greenberg,, B. Borremans,, J. Vangronsveld, and, D. van der Lelie. 2005. Horizontal gene transfer to endogenous endophytic bacteria from poplar improves phytoremediation of toluene. Appl. Environ. Microbiol. 71: 8500– 8505.
133. Tashiro, Y.,, K. Takeda,, G. Kobayashi,, K. Sonomoto,, A. Ishizaki, and, S. Yoshino. 2004. High butanol production by Clostridium saccharoperbutylacetonicum N1-4 in fed-batch culture with pH-stat continuous butyric acid and glucose feeding method. J. Biosci. Bioeng. 98: 263– 268.
134. Tchobanoglous, G.,, F. L. Burton, and, H. D. Stensel. 2003. Waste-water Engineering, Treatment and Reuse, 4th ed. Metcalf & Eddy, McGraw Hill, New York, NY..
135. Thanakoses, P.,, A. S. Black, and, M. T. Holtzapple. 2003a. Fermentation of corn stover to carboxylic acids. Biotechnol. Bioeng. 83: 191– 200.
136. Thanakoses, P.,, N. A. Mostafa, and, M. T. Holtzapple. 2003b. Conversion of sugarcane bagasse to carboxylic acids using a mixed culture of mesophilic microorganisms. Appl. Biochem. Biotechnol. 105–108: 523– 546.
137. Thauer, R. K.,, K. Jungermann, and, K. Decker. 1977. Energy conservation in chemotrophic anaerobic bacteria. Bacteriol. Rev. 41: 100– 180.
138. Thomas, J. A.,, J. A. Soddell, and, D. I. Kurtböke. 2002. Fighting foam with phages? Water Sci. Technol. 46: 511– 518.
139. Turnbaugh, P. J.,, R. E. Ley,, M. A. Mahowald,, V. Magrini,, E. R. Mardis, and, J. I. Gordon. 2006. An obesity-associated gut micro-biome with increased capacity for energy harvest. Nature 444: 1027– 1031.
140. Vandevoorde, L., and, W. Verstraete. 1987. Anaerobic solid state fermentation of cellulosic substrates with possible application to cellulase production. Appl. Microbiol. Biotechnol. V26: 479.
141. Verthe, K.,, S. Possemiers,, N. Boon,, M. Vaneechoutte, and, W. Verstraete. 2004. Stability and activity of an Enterobacter aerogenes-specific bacteriophage under simulated gastro-intestinal conditions. Appl. Microbiol. Biotechnol. 65: 465– 472.
142. Vijayaraghavan, K.,, D. Ahmad, and, R. Lesa. 2006. Electrolytic treatment of beer brewery wastewater. Ind. Eng. Chem. Res. 45: 6854– 6859.
143. Weiland, P. 2006. Biomass digestion in agriculture: a successful pathway for the energy production and waste treatment in Germany. Eng. Life Sci. 6: 302– 309.
144. Wenzel, M.,, R. Radek,, G. Brugerolle, and, H. Konig. 2003. Identification of the ectosymbiotic bacteria of Mixotricha paradoxa involved in movement symbiosis. Eur. J. Protistol. 39: 11– 23.
145. Whang, L.-M., C.-J. Hsiao, and, S.-S. Cheng. 2006. A dual-substrate steady-state model for biological hydrogen production in an anaerobic hydrogen fermentation process. Biotechnol. Bioeng. 95: 492– 500.
146. Yang, B., and, C. E. Wyman. 2006. BSA treatment to enhance enzymatic hydrolysis of cellulose in lignin containing substrates. Biotechnol. Bioeng. 94: 611– 617.
147. Yu, H. Q., and, H. H. P. Fang. 2003. Acidogenesis of gelatin-rich wastewater in an upflow anaerobic reactor: influence of pH and temperature. Water Res. 37: 55– 66.
148. Yu, H. Q.,, Y. Mu, and, H. H. P. Fang. 2004. Thermodynamic analysis of product formation in mesophilic acidogenesis of lactose. Biotechnol. Bioeng. 87: 813– 822.
149. Yu, Z., and, W. W. Mohn. 2001. Bacterial diversity and community structure in an aerated lagoon revealed by ribosomal intergenic spacer analyses and 16S ribosomal DNA sequencing. Appl. Environ. Microbiol. 67: 1565– 1574.
150. Zhang, R.,, Z. Zhang, and, The. Regents of the University of California. January. 2002. Biogasification of solid waste with an anaerobic-phased solids digester system. U.S. patent 6,342,378.
151. Zhang, T.,, H. Liu, and, H. H. Fang. 2003. Biohydrogen production from starch in wastewater under thermophilic condition. J. Environ. Manage. 69: 149– 156.
152. Zinder, S. H. 1994. Syntrophic acetate oxidation and “reversible acetogenesis,” p. 386– 415. In H. L. Drake (ed.), Acetogenesis. Chapman and Hall, New york, NY..
153. Zinder, S. H., and, M. Koch. 1984. Non-aceticlastic methanogenesis from acetate: acetate oxidation by a thermophilic syntrophic coculture. Arch. Microbiol. 138: 263– 272.
154. Zverlov, V. V.,, O. Berezina,, G. A. Velikodvorskaya, and, W. H. Schwarz. 2006. Bacterial acetone and butanol production by industrial fermentation in the Soviet Union: use of hydrolyzed agricultural waste for biorefinery. Appl. Microbiol. Biotechnol. 71: 587– 597.

References: V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V.