Microbial fuel cells and microbial ecology: Applications in ruminant health and production research

Microbial Ecology

Volumn 59, Issue 3, 2010, Pages 415-427

  Bretschger, Orianna ^a   Osterstock, Jason B ^b   Pinchak, William E ^b   Ishii, Shun'ichi ^a   Nelson, Karen E ^a  

^a J CRAIG VENTER INSTITUTE   (United States)

^b TEXAS A AND M UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALIA; BOVIDAE;

HYDROGEN; METHANE;

ANIMAL; ANIMAL FOOD; BIOENERGY; BIOFILM; BIOREMEDIATION; BIOSYNTHESIS; BOVIDS; FERMENTATION; MICROBIOLOGY; OXIDATION REDUCTION REACTION; REVIEW; RUMINANT STOMACH; SEWAGE;

ANIMAL NUTRITIONAL PHYSIOLOGICAL PHENOMENA; ANIMALS; BIODEGRADATION, ENVIRONMENTAL; BIOELECTRIC ENERGY SOURCES; BIOFILMS; FERMENTATION; HYDROGEN; METHANE; OXIDATION-REDUCTION; RUMEN; RUMINANTS; WASTE DISPOSAL, FLUID;

EID: 77952501235     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-009-9623-8     Document Type: Review

References (132)

1. Griffin D (1997) Economic impact associated with respiratory disease in beef cattle. Vet Clin North Am Food Anim Pract 13: 367-377.
2. Aelterman P, Rabaey K, De Schamphelaire L, Clauwaert P, Boon N, Verstraete W (2008) Microbial fuel cells as an engineered ecosystem. In: Wall JD, Harwood CS, Demain AL (eds) Bioenergy. ASM, Washington, DC.
3. Rismani-Yazdi H, Christy AD, Dehority BA, Morrison M, Yu Z, Tuovinen OH (2007) Electricity generation from cellulose by rumen microorganisms in microbial fuel cells. Biotechnol Bioeng 97: 1398-1407.
4. Schröder U (2007) Anodic electron transfer mechanisms in microbial fuel cells and their energy efficiency. Phys Chem Chem Phys 9: 2619-2629.
5. Aelterman P, Freguia S, Keller J, Verstraete W, Rabaey K (2008) The anode potential regulates bacterial activity in microbial fuel cells. Appl Microbiol Biotechnol 78: 409-418.
6. Cheng KY, Ho G, Cord-Ruwisch R (2008) Affinity of microbial fuel cell biofilm for the anodic potential. Environ Sci Technol 42: 3828-3834.
7. Choi Y, Jung E, Park H, Paik SR, Jung S, Kim S (2004) Construction of microbial fuel cells using thermophilic microorganisms, Bacillus licheniformis and Bacillus thermoglucosidasius. Bull Korean Chem Soc 25: 813-818.
8. Clauwaert P, van der Ha D, Verstraete W (2008) Energy recovery from energy rich vegetable products with microbial fuel cells. Biotechnol Lett 30: 1947-1951.
9. Ishii Si, Shimoyama T, Hotta Y, Watanabe K (2008) Characterization of a filamentous biofilm community established in a cellulose-fed microbial fuel cell. BMC Microbiology 8: 6-18.
10. Jung S, Regan J (2007) Comparison of anode bacterial communities and performance in microbial fuel cells with different electron donors. Appl Microbiol Biotechnol 77: 393-402.
11. Kaku N, Yonezawa N, Kodama Y, Watanabe K (2008) Plant/microbe cooperation for electricity generation in a rice paddy field. Appl Microbiol Biotechnol 79: 43-49.
12. Ishii Si, Hotta Y, Watanabe K (2008) Methanogenesis versus electrogenesis: morphological and phylogenetic comparisons of microbial communites. Biosci Biotechnol Biochem 72: 286-294.
13. Prathap P, César IT, Hyung-Sool L, Rosa K-B, Bruce ER (2009) Syntrophic interactions among anode respiring bacteria (ARB) and Non-ARB in a biofilm anode: electron balances. Biotechnol Bioeng 103: 513-523.
14. Lee J, Phung NT, Chang IS, Kim BH, Sung HC (2003) Use of acetate for enrichment of electrochemically active microorganisms and their 16S rDNA analyses. FEMS Microbiol Lett 223: 185.
15. Franks AE, Nevin KP, Jia H, Izallalen M, Woodard TL, Lovley DR (2009) Novel strategy for three-dimensional real-time imaging of microbial fuel cell communities: monitoring the inhibitory effects of proton accumulation within the anode biofilm. Energy and Environmental Science 2: 113-119.
16. Donlan RM, Costerton JW (2002) Biofilms: survival mechanisms of clinically relevant microorganisms. Clin Microbiol Rev 15: 167-193.
17. Boyd A, Chakrabarty AM (1995) Pseudomonas aeruginosa biofilms: role of the alginate exopolysaccharide. J Ind Microbiol 15: 162-168.
18. Costerton JW, Lewandowski Z, Caldwell DE, Korber DR, Lappin-Scott HM (1995) Microbial Biofilms. Annu Rev Microbiol 49: 711-745.
19. Nadell CD, Xavier JB, Foster KR (2009) The sociobiology of biofilms. FEMS Microbiol Rev 33: 206-224.
20. Santegoeds CM, Muyzer G, de Beer D (1998) Biofilm dynamics studied with microsensors and molecular techniques. Water Sci Technol 37: 125-129.
21. Ramos C, Licht TR, Sternberg C, Krogfelt KA, Molin S (2001) Microbial growth in biofilms: part B, special environments and physiochemical aspects. In: Doyle RJ (ed) Methods in enzymology, vol 337. Academic, San Diego, pp 21-42.
22. Stoodley P, Sauer K, Davies DG, Costerton JW (2002) Biofilms as complex differentiated communities. Annu Rev Microbiol 56: 187-209.
23. Wang X, Feng Y, Ren N, Wang H, Lee H, Li N, Zhao Q (2009) Accelerated start-up of two-chambered microbial fuel cells: effect of anodic positive poised potential. Electrochimica Acta 54: 1109-1114.
24. Lovley DR, Phillips EJP, Lonergan DJ (1989) Hydrogen and formate oxidation coupled to dissimilatory reduction of iron and manganese by Alteromonas putrefaciens. Appl Environ Microbiol 55: 700-706.
25. Rabaey K, VandeSompel K, Maignien L, Boon N, Aelterman P, Clauwaert P, DeSchamphelaire L, Pham HT, Vermeulen J, Verhaege M, Lens P, Verstraete W (2006) Microbial fuel cells for sulfide removal. Environ Sci Technol 40: 5218-5224.
26. Gregory KB, Bond DR, Lovley DR (2004) Graphite electrodes as electron donors for anaerobic respiration. Environ Microbiol 6: 596-604.
27. Bergel A, Féron D, Mollica A (2005) Catalysis of oxygen reduction in pem fuel cell by seawater biofilm. Electrochem Commun 7: 900-904.
28. He Z, Angenent Largus T (2006) Application of bacterial biocathodes in microbial fuel cells. Electroanalysis 18: 2009-2015.
29. Clauwaert P, Rabaey K, Aelterman P, DeSchamphelaire L, Pham TH, Boeckx P, Boon N, Verstraete W (2007) Biological denitrification in microbial fuel cells. Environ Sci Technol 41: 3354-3360.
30. Chen G-W, Choi S-J, Lee T-H, Lee G-Y, Cha J-H, Kim C-W (2008) Application of biocathode in microbial fuel cells: cell performance and microbial community. Appl Microbiol Biotechnol 79(3): 379-388.
31. Brock TD, Madigan MT (1991) Biology of microorganisms. Prentice-Hall, Englewood Cliffs.
32. Nealson KH, Belz A, McKee B (2002) Breathing metals as a way of life: geobiology in action. Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology 81: 215-222.
33. Rabaey K, Rodriguez J, Blackall LL, Keller J, Gross P, Batstone D, Verstraete W, Nealson KH (2007) Microbial ecology meets electrochemistry: electricity-driven and driving communities. ISME J 1: 9-18.
34. Rozendal RA, Leone E, Keller J, Rabaey K (2009) Efficient hydrogen peroxide generation from organic matter in a bioelectrochemical system. Electrochem Commun 11: 1752-1755.
35. Rabaey K, Angenent L, Schroder U, Keller J (2009) Bioelectrochemical systems from extracellular electron transfer to biotechnological application. IWA, London.
36. Reimers C, Girguis P, Westall J, Newman D, Stecher H, Howell K, Alleau Y (2005) Using electrochemical methods to study redox processes and harvest energy from marine sediments. Geochim Cosmochim Acta 69: A575-A575.
37. Kim BH, Park HS, Kim HJ, Kim GT, Chang IS, Lee J, Phung NT (2004) Enrichment of microbial community generating electricity using a fuel-cell-type electrochemical cell. Appl Microbiol Biotechnol 63: 672-681.
38. Kim JR, Min B, Logan BE (2005) Evaluation of procedures to acclimate a microbial fuel cell for electricity production. Appl Microbiol Biotechnol 68: 23-30.
39. White HK, Reimers CE, Cordes EE, Dilly GF, Girguis PR (2009) Quantitative population dynamics of microbial communities in plankton-fed microbial fuel cells. ISME J 3: 635-646.
40. Reimers CE, Stecher HA III, Westall JC, Alleau Y, Howell KA, Soule L, White HK, Girguis PR (2007) Substrate degradation kinetics, microbial diversity, and current efficiency of microbial fuel cells supplied with marine plankton. Appl Environ Microbiol 73: 7029-7040.
41. Attwood GT, Kelly WJ, Altermann EH, Moon CD, Leahy S, Cookson AL (2008) Application of rumen microbial genome information to livestock systems in the postgenomic era. Aust J Exp Agric 48: 695-700.
42. Lin C, Raskin L, Stahl DA (1997) Microbial community structure in gastrointestinal tracts of domestic animals: comarative analyses using rRNA-targeted oligonucleotide probes. FEMS Microbiol Ecol 22: 281-294.
43. Kiyoshi T, Takafumi N, Hiroki M, Mutsumi N, Rustam IA (2001) Phylogenetic analysis of archaeal 16S rRNA libraries from the rumen suggests the existence of a novel group of archaea not associated with known methanogens. FEMS Microbiol Lett 200: 67-72.
44. Ziemer CJ, Sharp R, Stern MD, Cotta MA, Whitehead TR, Stahl DA (2000) Comparison of microbial populations in model and natural rumens using 16S ribosomal RNA-targeted probes. Environ Microbiol 2: 632-643.
45. Weimer PJ, Price NPJ, Kroukamp O, Joubert L-M, Wolfaardt GM, van Zyl WH (2006) Studies of the extracellular glycocalyx of the anaerobic cellulolytic bacterium Ruminococcus albus 7. Appl Environ Microbiol 72: 7559-7566.
46. Edwards JE, Huws SA, Kim EJ, Lee MRF, Kingston-Smith AH, Scollan ND (2008) Advances in microbial ecosystem concepts and their consequences for ruminant agriculture. Animal 2: 653-660.
47. Larue R, Yu ZT, Parisi VA, Egan AR, Morrison M (2005) Novel microbial diversity adherent to plant biomass in the herbivore gastrointestinal tract, as revealed by ribosomal intergenic spacer analysis and rrs gene sequencing. Environ Microbiol 7: 530-543.
48. Edwards JE, McEwan NR, Travis AJ, John Wallace R (2004) 16S rDNA library-based analysis of ruminal bacterial diversity. Antonie van Leeuwenhoek 86: 263-281.
49. Whitford MF, Forster RJ, Beard CE, Gong J, Teather RM (1998) Phylogenetic analysis of rumen bacteria by comparative sequence analysis of cloned 16S rRNA genesß. Anaerobe 4: 153-163.
50. Tajima K, Arai S, Ogata K, Nagamine T, Matsui H, Nakamura M, Aminov RI, Benno Y (2000) Rumen bacterial community transition during adaptation to high-grain diet. Anaerobe 6: 273-284.
51. Brulc JM, Antonopoulos DA, Berg Miller ME, Wilson MK, Yannarell AC, Dinsdale EA, Edwards RE, Frank ED, Emerson JB, Wacklin P, Coutinho PM, Henrissat B, Nelson KE, White BA (2009) Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci U S A 106: 1948-1953.
52. Singh B, Gautam SK, Verma V, Kumar M, Singh B (2008) Metagenomics in animal gastrointestinal ecosystem: potential biotechnological prospects. Anaerobe 14: 138-144.
53. Nicholson MJ, Evans PN, Joblin KN (2007) Analysis of methanogen diversity in the rumen using temporal temperature gradient gel electrophoresis: identification of uncultured methanogens. Microb Ecol 54: 141-150.
54. Tajima K, Nagamine T, Matsui H, Nakamura M, Aminov RI (2001) Phylogenetic analysis of archaeal 16S rRNA libraries from the rumen suggests the existence of a novel group of archaea not associated with known methanogens. FEMS Microbiol Lett 200: 67-72.
55. Galbraith EA, Antonopoulos DA, White BA (2004) Suppressive subtractive hybridization as a tool for identifying genetic diversity in an environmental metagenome: the rumen as a model. Environ Microbiol 6: 928-937.
56. Kocherginskaya SA, Aminov RI, White BA (2001) Analysis of the rumen bacterial diversity under two different diet conditions using denaturing gradient gel electrophoresis, random sequencing, and statistical ecology approaches. Anaerobe 7: 119-134.
57. Briesacher SL, May T, Grigsby KN, Kerley MS, Anthony RV, Paterson JA (1992) Use of DNA probes to monitor nutritional effects on ruminal prokaryotes and Fibrobacter succinogenes S85. J Anim Sci 70: 289-295.
58. Flint HJ, Bayer EA, Rincon MT, Lamed R, White BA (2008) Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Nat Rev Microbiol 6: 121-131.
59. Tajima K, Aminov RI, Nagamine T, Matsui H, Nakamura M, Benno Y (2001) Diet-dependent shifts in the bacterial population of the rumen revealed with real-time PCR. Appl Environ Microbiol 67: 2766-2774.
60. Krause DO, Dalrymple BP, Smith WJ, Mackie RI, McSweeney CS (1999) 16S rDNA sequencing of Ruminococcus albus and Ruminococcus flavefaciens: design of a signature probe and its application in adult sheep. Microbiology 145: 1797-1807.
61. Stahl DA, Flesher B, Mansfield HR, Montgomery L (1988) Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology. Appl Environ Microbiol 54: 1079-1084.
62. Guan IL, Nkrumah JD, Basarab JA, Moore SS (2008) Linkage of microbial ecology to phenotype: correlation of rumen microbial ecology to cattle's feed efficiency. FEMS Microbiol Lett 288: 85-91.
63. Rabaey K, Boon N, Siciliano SD, Verhaege M, Verstraete W (2004) Biofuel cells select for microbial consortia that self-mediate electron transfer. Appl Environ Microbiol 70: 5473-5482.
64. Phung NT, Lee J, Kang KH, Chang IS, Gadd GM, Kim BH (2004) Analysis of microbial diversity in oligotrophic microbial fuel cells using 16s rdna sequences. FEMS Microbiol Lett 233: 77.
65. Chung K, Okabe S (2009) Continuous power generation and microbial community structure of the anode biofilms in a three-stage microbial fuel cell system. Appl Microbiol Biotechnol 83: 965-977.
66. Mohan SV, Mohanakrishna G, Sarma PN (2008) Effect of anodic metabolic function on bioelectricity generation and substrate degradation in single chambered microbial fuel cell. Environ Sci Technol 42: 8088-8094.
67. Chae K-J, Choi M-J, Lee J-W, Kim K-Y, Kim IS (2009) Effect of different substrates on the performance, bacterial diversity, and bacterial viability in microbial fuel cells. Bioresour Technol 100: 3518-3525.
68. Liu Z, Li H, Liu J, Su Z (2008) Effects of inoculation strategy and cultivation approach on the performance of microbial fuel cell using marine sediment as bio-matrix. J Appl Microbiol 104: 1163-1170.
69. Freguia S, Rabaey K, Yuan Z, Keller J (2007) Electron and carbon balances in microbial fuel cells reveal temporary bacterial storage behavior during electricity generation. Environ Sci Technol 41: 2915-2921.
70. Virdis B, Rabaey K, Yuan ZG, Rozendal RA, Keller J (2009) Electron fluxes in a microbial fuel cell performing carbon and nitrogen removal. Environ Sci Technol 43: 5144-5149.
71. Back JH, Kim MS, Cho H, Chang IS, Lee J, Kim KS, Kim BH, Park YI, Han YS (2004) Construction of bacterial artificial chromosome library from electrochemical microorganisms. FEMS Microbiol Lett 238: 65.
72. Jia Y-H, Tran H-T, Kim D-H, Oh S-J, Park D-H, Zhang R-H, Ahn D-H (2008) Simultaneous organics removal and bio-electrochemical denitrification in microbial fuel cells. Bioprocess Biosyst Eng 31: 315-321.
73. Aelterman P, Versichele M, Marzorati M, Boon N, Verstraete W (2008) Loading rate and external resistance control the electricity generation of microbial fuel cells with different three-dimensional anodes. Bioresour Technol 99: 8895-8902.
74. Venkata Mohan S, Veer Raghavulu S, Sarma PN (2008) Influence of anodic biofilm growth on bioelectricity production in single chambered mediatorless microbial fuel cell using mixed anaerobic consortia. Biosens Bioelectron 24: 41-47.
75. Wrighton KC, Agbo P, Warnecke F, Weber KA, Brodie EL, DeSantis TZ, Hugenholtz P, Andersen GL, Coates JD (2008) A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells. ISME J 2: 1146-1156.
76. Holmes DE, Bond DR, O'Neil RA, Reimers CE, Tender LR, Lovley DR (2004) Microbial communities associated with electrodes harvesting electricity from a variety of aquatic sediments. Microb Ecol 48: 178-190.
77. Erable B, Roncato MA, Achouak W, Bergel A (2009) Sampling natural biofilms: a new route to build efficient microbial anodes. Environ Sci Technol 43: 3194-3199.
78. Ellis JL, Dijkstra J, Kebreab E, Bannink A, Odongo NE, McBride BW, France J (2008) Aspects of rumen microbiology central to mechanistic modelling of methane production in cattle. Journal of Agricultural Science 146: 213-233.
79. Johnson KA, Johnson DE (1995) Methane emissions from cattle. J Anim Sci 73: 2483-2492.
80. Gill M, Smith P, Wilkinson JM (2009) Mitigating climate change: the role of domestic livestock. Animal. Published online by Cambridge University Press. doi: 10. 1017/S1751731109004662.
81. Janssen PH, Kirs M (2008) Structure of the archaeal community of the rumen. Appl Environ Microbiol 74: 3619-3625.
82. van Soest PJ (1982) Nutritional ecology of the ruminant. O & B, Corvallis.
83. Zhou M, Hernandez-Sanabria E, Guan LL (2009) Assessment of the microbial ecology of ruminal methanogens in cattle with different feed efficiencies. Appl Environ Microbiol 75: 6524-6533.
84. Beauchemin KA, McGinn SM (2005) Methane emissions from feedlot cattle fed barley or corn diets. J Anim Sci 83: 653-661.
85. Beauchemin KA, McGinn SM (2006) Methane emissions from beef cattle: effects of fumaric acid, essential oil, and canola oil. J Anim Sci 84: 1489-1496.
86. DeRamus HA, Clement TC, Giampola DD, Dickison PC (2003) Methane emissions of beef cattle on forages: efficiency of grazing management systems. J Environ Qual 32: 269-277.
87. McGinn SM, Beauchemin KA, Coates T, Colombatto D (2004) Methane emissions from beef cattle: effects of monensin, sunflower oil, enzymes, yeast, and fumaric acid. J Anim Sci 82: 3346-3356.
88. Jordan E, Kenny D, Hawkins M, Malone R, Lovett DK, O'Mara FP (2006) Effect of refined soy oil or whole soybeans on intake, methane output, and performance of young bulls. J Anim Sci 84: 2418-2425.
89. Hegarty RS, Goopy JP, Herd RM, McCorkell B (2007) Cattle selected for lower residual feed intake have reduced daily methane production. J Anim Sci 85: 1479-1486.
90. Nkrumah JD, Okine EK, Mathison GW, Schmid K, Li C, Basarab JA, Price MA, Wang Z, Moore SS (2006) Relationships of feedlot feed efficiency, performance, and feeding behavior with metabolic rate, methane production, and energy partitioning in beef cattle. J Anim Sci 84: 145-153.
91. EPA (2009) Mandatory reporting of greenhouse gasses. Federal Register, Washington.
92. Dargatz D (1999) Feedlot 99, Part III: health management and biosecurity in U. S. Feedlots. United States Department of Agriculture, National Animal Health Monitoring System, Washington, DC.
93. USDA (2007) Dairy 2007. USDA, Animal and Plant Health Inspection Service, Veterinary Services, National Animal Health Monitoring System, Fort Collins.
94. Peterhans E, Jungi TW, Schweizer M (2003) BVDV and innate immunity. Biologicals 31: 107-112.
95. Navarre CB, Belknap EB, Rowe SE (2000) Differentiation of gastrointestinal diseases of calves. Vet Clin North Am Food Anim Pract 16: 37-57.
96. Ngwai YB, Adachi Y, Ogawa Y, Hara H (2006) Characterization of biofilm-forming abilities of antibiotic-resistant Salmonella typhimurium DT104 on hydrophobic abiotic surfaces. J Environ Qual 39: 278-291.
97. Fox LK, Zadoks RN, Gaskins CT (2005) Biofilm production by Staphylococcus aureus associated with intramammary infection. Vet Microbiol 107: 295-299.
98. Melchior MB, Fink-Gremmels J, Gaastra W (2007) Extended antimicrobial susceptibility assay for Staphylococcus aureus isolates from bovine mastitis growing in biofilms. Vet Microbiol 125: 141-149.
99. Melchior MB, Vaarkamp H, Fink-Gremmels J (2006) biofilms: a role in recurrent mastitis infections? Vet J 171: 398-407.
100. Oliveira M, Nunes SF, Carneiro C, Bexiga R, Bernardo F, Vilela CL (2007) Time course of biofilm formation by Staphylococcus aureus and Staphylococcus epidermidis mastitis isolates. Vet Microbiol 124: 187-191.
101. Sela S, Hammer-Muntz O, Krifucks O, Pinto R, Weisblit L, Leitner G (2007) Phenotypic and genotypic characterization of Pseudomonas aeruginosa strains isolated from mastitis outbreaks in dairy herds. J Dairy Res 74: 955-962.
102. Vautor E, Abadie G, Pont A, Thiery R (2008) Evaluation of the presence of the bap gene in Staphylococcus aureus isolates recovered from human and animals species. Vet Microbiol 127: 407-411.
103. Sandal I, Shao JQ, Annadata S, Apicella MA, Boye M, Jensen TK, Saunders GK, Inzana TJ (2009) Histophilus somni biofilm formation in cardiopulmonary tissue of the bovine host following respiratory challenge. Microbes Infect 11: 254-263.
104. Behr MA, Schurr E (2006) Mycobacteria in Crohn's disease: a persistent hypothesis. Inflammatory Bowel Diseases 12: 1000-1004.
105. Behr MA, Kapur V (2008) The evidence for Mycobacterium paratuberculosis in Crohn's disease. Curr Opin Gastroenterol 24: 17-21.
106. El-Zaatari FA, Osato MS, Graham DY (2001) Etiology of Crohn's disease: the role of Mycobacterium avium paratuberculosis. Trends Mol Med 7: 247-252.
107. C-w Wu, Schmoller SK, Bannantine JP, Eckstein TM, Inamine JM, Livesey M, Albrecht R, Talaat AM (2009) A novel cell wall lipopeptide is important for biofilm formation and pathogenicity of Mycobacterium avium subspecies paratuberculosis. Microb Pathog 46: 222-230.
108. Huggett J, Dehda K, Zumla A, Rook G (2004) Crohn's disease and MAP. Lancet 364: 2178-2179.
109. Skandamis PN, Stopforth JD, Ashton LV, Geornaras I, Kendall PA, Sofos JN (2009) Escherichia coli O157: H7 survival, biofilm formation and acid tolerance under simulated slaughter plant moist and dry conditions. Food Microbiol 26: 112-119.
110. Macovei L, Ghosh A, Thomas VC, Hancock LE, Mahmood S, Zurek L (2009) Enterococcus faecalis with the gelatinase phenotype regulated by the fsr operon and with biofilm-forming capacity are common in the agricultural environment. Environ Microbiol 11: 1540-1547.
111. Dumont MG, Murrell JC (2005) Stable isotope probing - linking microbial identity to function. Nat Rev Microbiol 3: 499-504.
112. Madsen EL (2006) The use of stable isotope probing techniques in bioreactor and field studies on bioremediation. Curr Opin Biotechnol 17: 92-97.
113. Kalyuzhnaya MG, Lapidus A, Ivanova N, Copeland AC, McHardy AC, Szeto E, Salamov A, Grigoriev IV, Suciu D, Levine SR, Markowitz VM, Rigoutsos I, Tringe SG, Bruce DC, Richardson PM, Lidstrom ME, Chistoserdova L (2008) High-resolution metagenomics targets specific functional types in complex microbial communities. Nat Biotechnol 26: 1029-1034.
114. Gilbert JA, Field D, Huang Y, Edwards R, Li W, Gilna P, Joing I (2008) Detection of large numbers of novel sequences in the metatranscriptome of complex marine microbial communties. PLoS ONE 3: e3042.
115. Miner JR, Humenik FJ, Overcash MR (2000) Managing livestock wastes to preserve environmental quality. Iowa State University Press, Ames.
116. Clifford E, Rodgers M, de Paor D (2008) Dairy washwater treatment using a horizontal flow biofilm system. Water Sci Technol 58: 1879-1888.
117. Rodgers M, de Paor D, Clifford E (2008) Dairy washwater treatment using a horizontal flow biofilm system. J Environ Manag 86: 114-120.
118. Rittmann BE (2008) Opportunities for renewable bioenergy using microorganisms. Biotechnol Bioeng 100: 203-212.
119. Kim JR, Dec J, Bruns MA, Logan BE (2008) Removal of odors from swine wastewater by using microbial fuel cells. Appl Environ Microbiol 74: 2540-2543.
120. Min B, Kim J, Oh S, Regan JM, Logan BE (2005) Electricity generation from swine wastewater using microbial fuel cells. Water Res 39: 4961.
121. Jung Rae K, Yi Z, John MR, Bruce EL (2008) Analysis of ammonia loss mechanisms in microbial fuel cells treating animal wastewater. Biotechnol Bioeng 99: 1120-1127.
122. Cheng S, Logan BE (2007) Sustainable and efficient biohydrogen production via electrohydrogenesis. Proc Natl Acad Sci U S A 104: 18871-18873.
123. Wagner RC, Regan JM, Oh SE, Zuo Y, Logan BE (2009) Hydrogen and methane production from swine wastewater using microbial electrolysis cells. Water Res 43: 1480-1488.
124. Liu H, Grot S, Logan BE (2005) Electrochemically assisted microbial production of hydrogen from acetate. Environ Sci Technol 39: 4317-4320.
125. Clauwaert P, Verstraete W (2009) Methanogenesis in membraneless microbial electrolysis cells. Appl Microbiol Biotechnol 82: 829-836.
126. McGarvey JA, Miller WG, Zhang R, Ma Y, Mitloehner F (2007) Bacterial population dynamics in dairy waste during aerobic and anaerobic treatment and subsequent storage. Appl Environ Microbiol 73: 193-202.
127. Wang AJ, Liu WZ, Cheng SA, Xing DF, Zhou JH, Logan BE (2009) Source of methane and methods to control its formation in single chamber microbial electrolysis cells. Int J Hydrog Energy 34: 3653-3658.
128. 2 greenhouse gases. National Service Center for Environmental Publications, Washington.
129. FAO (2002) World agriculture: towards 2015/2030. United Nations, Rome.
130. Schmeisser C, Steele H, Streit WR (2007) Metagenomics, biotechnology with non-culturable microbes. Appl Microbiol Biotechnol 75: 955-962.
131. Xu J (2006) Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances. Mol Ecol 15: 1713-1731.
132. Henze M, Harremoes P, JlC J, Arvin E (2002) Wastewater treatment. Springer, Heidelberg.