Archaeal diversity in biofilm technologies applied to treat urban and industrial wastewater: Recent advances and future prospects

International Journal of Molecular Sciences

Volumn 14, Issue 9, 2013, Pages 18572-18598

  Calderón, Kadiya ^a,b   González Martínez, Alejandro ^a   Gómez Silván, Cinta ^a   Osorio, Francisco ^a   Rodelas, Belén ^a   González López, Jesús ^a  

^a UNIVERSITY OF GRANADA   (Spain)

^b UNIV BOURGOGNE FRANCHE COMTÉ   (France)

Author keywords

Archaea; Biofilm; Biofouling; Granular sludge; MBR; Membrane bioreactor; Wastewater treatment; WWT

Indexed keywords

ORGANIC MATTER;

AMMONIA OXIDIZING ARCHAEON; ANAEROBIC BIOREACTOR; ARCHAEON; BACTERIAL METABOLISM; BIODEGRADATION; BIOFILM; BIOFOULING; BIOREACTOR; BIOTECHNOLOGICAL PROCEDURES; CHEMICAL COMPOSITION; GRANULAR SLUDGE; MEMBRANE FILTER; METHANOGENIC ARCHAEON; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; NONHUMAN; PROKARYOTE; PYROSEQUENCING; QUORUM SENSING; REVIEW; SLUDGE; TEMPERATURE SENSITIVITY; WASTE WATER MANAGEMENT;

ARCHAEA; BIOFILMS; BIOREACTORS; WASTE DISPOSAL, FLUID; WASTE WATER;

EID: 84883849907     PISSN: 16616596     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms140918572     Document Type: Review

References (137)

1. Woese, C.R.; Fox, G.E. Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Proc. Natl. Acad. Sci. USA 1977, 74, 5088-5090.
2. Gribaldo, S.; Brochier-Armanet, C. The origin and evolution of Archaea: A state of the art. Philos. Trans. R. Soc. Lond. Ser. B 2006, 361, 1007-1022.
3. Fröls, S. Archaeal biofilms: Widespread and complex. Biochem. Soc. Trans. 2013, 41, 393-398.
4. Stahl, D.A.; de la Torre, J.R. Physiology and diversity of ammonia-oxidizing archaea. Annu. Rev. Microbiol. 2012, 66, 83-101.
5. Stoodley, P.; Sauer, K.; Davies, D.G.; Costerton, J.W. Biofilms as complex differentiated communities. Annu. Rev. Microbiol. 2002, 56, 187-209.
6. Van Leewenhoeck, A. An abstract of a letter from Mr. Anthony Leewenhoeck at Delft, Dated Sep. 17. 1683. Containing some microscopical observations, about animals in the scurf of the teeth, the substance call'd worms in the nose, the cuticula consisting of scales. Philos. Trans. R Soc. Lond. Ser. B 1683, 166, 568-574.
7. Hall-Stoodley, L.; Costerton, J.W.; Stoodley, P. Bacterial biofilms: From the natural environment to infectious diseases. Nat. Rev. Microbiol. 2004, 2, 95-108.
8. Watnick, P.; Kolter, R. Biofilm, city of microbes. J. Bacteriol. 2000, 182, 2675-2679.
9. Guo, W.; Ngo, H.-H.; Li, J. A mini-review on membrane fouling. Bioresour. Technol. 2012, 122, 27-34.
10. Harrison, J.J.; Ceri, H.; Turner, R.J. Multimetal resistance and tolerance in microbial biofilms. Nat. Rev. Microbiol. 2007, 5, 928-938.
11. Weidler, G.W.; Gerbl, F.W.; Stan-Lotter, H. Crenarchaeota and their role in the nitrogen cycle in a subsurface radioactive thermal spring in the Austrian Central Alps. Appl. Environ. Microbiol. 2008, 74, 5934-5942.
12. Reysenbach, A.L.; Ehringer, M.; Hershberger, K. Microbial diversity at 83 degrees C in Calcite Springs, Yellowstone National Park: Another environment where the Aquificales and. Korarchaeota. coexist. Extremophiles 2000, 4, 61-67.
13. Jones, D.S.; Albrecht, H.L.; Dawson, K.S.; Schaperdoth, I.; Freeman, K.H.; Pi, Y.; Pearson, A.; Macalady, J.L. Community genomic analysis of an extremely acidophilic sulfur-oxidizing biofilm. ISME J. 2012, 6, 158-170.
14. Sauder, L.A.; Engel, K.; Stearns, J.C.; Masella, A.P.; Pawliszyn, R.; Neufeld, J.D. Aquarium nitrification revisited: Thaumarchaeota are the dominant ammonia oxidizers in freshwater aquarium biofilters. PLoS One 2011, 6, e23281.
15. Edwards, K.J.; Bond, P.L.; Gihring, T.M.; Banfield, J.F. An archaeal iron-oxidizing extreme acidophile important in acid mine drainage. Science 2000, 287, 1796-1799.
16. Gómez-Silván, C.; Molina-Munoz, M.; Poyatos, J.M.; Ramos, A.; Hontoria, E.; Rodelas, B.; González-López, J. Structure of archaeal communities in membrane-bioreactor and submerged-biofilter wastewater treatment plants. Bioresour. Technol. 2010, 101, 2096-2105.
17. Calderon, K.; Rodelas, B.; Cabirol, N.; Gonzalez-Lopez, J.; Noyola, A. Analysis of microbial communities developed on the fouling layers of a membrane-coupled anaerobic bioreactor applied to wastewater treatment. Bioresour. Technol. 2011, 102, 4618-4627.
18. 2S by Sulfolobus metallicus. Biotechnol. Lett. 2011, 33, 2141-2145.
19. Justice, N.B.; Pan, C.; Mueller, R.; Spaulding, S.E.; Shah, V.; Sun, C.L.; Yelton, A.P.; Miller, C.S.; Thomas, B.C.; Shah, M.; et al. Heterotrophic archaea contribute to carbon cycling in low-pH, suboxic biofilm communities. Appl. Environ. Microbiol. 2012, 78, 8321-8330.
20. Cheng, K.-C.; Demirci, A.; Catchmark, J. Advances in biofilm reactors for production of value-added products. Appl. Microbiol. Biotechnol. 2010, 87, 445-456.
21. Gómez-Villalba, B.; Calvo, C.; Vilchez, R.; González-López, J.; Rodelas, B. TGGE analysis of the diversity of ammonia-oxidizing and denitrifying bacteria in submerged filter biofilms for the treatment of urban wastewater. Appl. Microbiol. Biotechnol. 2006, 72, 393-400.
22. Winkler, M.K.; Kleerebezem, R.; de Bruin, L.M.; Verheijen, P.J.; Abbas, B.; Habermacher, J.; Van Loosdrecht, M.C. Microbial diversity differences within aerobic granular sludge and activated sludge flocs. Appl. Microbiol. Biotechnol. 2013, 97, 7447-7458.
23. Wang, J.; Kang, J. The characteristics of anaerobic ammonium oxidation (ANAMMOX) by granular sludge from an EGSB reactor. Process Biochem. 2005, 40, 1973-1978.
24. Lettinga, G. Anaerobic digestion and wastewater treatment systems. Antonie Leeuwenhoek 1995, 67, 3-28.
25. Tiwari, M.K.; Guha, S.; Harendranath, C.S.; Tripathi, S. Influence of extrinsic factors on granulation in UASB reactor. Appl. Microbiol. Biotechnol. 2006, 71, 145-154.
26. Abbasi, T.; Abbasi, S.A. Formation and impact of granules in fostering clean energy production and wastewater treatment in upflow anaerobic sludge blanket (UASB) reactors. Renew. Sustain. Energy Rev. 2012, 16, 1696-1708.
27. Van der Star, W.R.L.; Abma, W.R.; Blommers, D.; Mulder, J.-W.; Tokutomi, T.; Strous, M.; Picioreanu, C.; Van Loosdrecht, M.C.M. Startup of reactors for anoxic ammonium oxidation: Experiences from the first full-scale anammox reactor in Rotterdam. Water Res. 2007, 41, 4149-4163.
28. Skiadas, I.V.; Gavala, H.N.; Schmidt, J.E.; Ahring, B.K. Anaerobic granular sludge and biofilm reactors. Adv. Biochem. Eng. Biotechnol. 2003, 82, 35-67.
29. Adav, S.S.; Lee, D.-J.; Show, K.-Y.; Tay, J.-H. Aerobic granular sludge: Recent advances. Biotechnol. Adv. 2008, 26, 411-423.
30. Angelidaki, I.; Karakashev, D.; Batstone, D.J.; Plugge, C.M.; Stams, A.J.M. Biomethanation and its potential. Methods Enzymol. 2011, 494, 327-351.
31. Liu, Y.; Whitman, W.B. Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea. Ann. N. Y. Acad. Sci. 2008, 1125, 171-189.
32. Sakai, S.; Imachi, H.; Hanada, S.; Ohashi, A.; Harada, H.; Kamagata, Y. Methanocella paludicola gen. nov., sp. nov., a methane-producing archaeon, the first isolate of the lineage. Rice Cluster I., and proposal of the new archaeal order Methanocellales ord. nov. Int. J. Syst. Evol. Microbiol. 2008, 58, 929-936.
33. Rivière, D.; Desvignes, V.; Pelletier, E.; Chaussonnerie, S.; Guermazi, S.; Weissenbach, J.; Li, T.; Camacho, P.; Sghir, A. Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge. ISME J. 2009, 3, 700-714.
34. Narihiro, T.; Sekiguchi, Y. Oligonucleotide primers, probes and molecular methods for the environmental monitoring of methanogenic archaea. Microb. Biotechnol. 2011, 4, 585-602.
35. Leclerc, M.; Delgènes, J.-P.; Godon, J.-J. Diversity of the archaeal community in 44 anaerobic digesters as determined by single strand conformation polymorphism analysis and 16S rDNA sequencing. Environ. Microbiol. 2004, 6, 809-819.
36. Collins, G.; Kavanagh, S.; McHugh, S.; Connaughton, S.; Kearney, A.; Rice, O.; Carrigg, C.; Scully, C.; Bhreathnach, N.; Mahony, T.; et al. Accessing the black box of microbial diversity and ecophysiology: Recent advances through polyphasic experiments. J. Environ. Sci. Health Part A 2006, 41, 897-922.
37. Dang, Y.; Ye, J.; Mu, Y.; Qiu, B.; Sun, D. Effective anaerobic treatment of fresh leachate from MSW incineration plant and dynamic characteristics of microbial community in granular sludge. Appl. Microbiol. Biotechnol. 2013, 1-12.
38. Visser, F.A.; Van Lier, J.B.; Macario, A.J.; Conway de Macario, E. Diversity and population dynamics of methanogenic bacteria in a granular consortium. Appl. Environ. Microbiol. 1991, 57, 1728-1734.
39. Buzzini, A.P.; Sakamoto, I.K.; Varesche, M.B.; Pires, E.C. Evaluation of the microbial diversity in an UASB reactor treating wastewater from an unbleached pulp plant. Process Biochem. 2006, 41, 168-176.
40. Del Nery, V.; Pozzi, E.; Damianovic, M.H.R.Z.; Domingues, M.R.; Zaiat, M. Granules characteristics in the vertical profile of a full-scale upflow anaerobic sludge blanket reactor treating poultry slaughterhouse wastewater. Bioresour. Technol. 2008, 99, 2018-2024.
41. Tabatabaei, M.; Rahim, R.A.; Abdullah, N.; Wright, A.-D.G.; Shirai, Y.; Sakai, K.; Sulaiman, A.; Hassan, M.A. Importance of the methanogenic archaea populations in anaerobic wastewater treatments. Process Biochem. 2010, 45, 1214-1225.
42. Zhang, D.; Li, J.; Guo, P.; Li, P.; Suo, Y.; Wang, X.; Cui, Z. Dynamic transition of microbial communities in response to acidification in fixed-bed anaerobic baffled reactors (FABR) of two different flow directions. Bioresour. Technol. 2011, 102, 4703-4711.
43. Rademacher, A.; Zakrzewski, M.; Schluter, A.; Schonberg, M.; Szczepanowski, R.; Goesmann, A.; Puhler, A.; Klocke, M. Characterization of microbial biofilms in a thermophilic biogas system by high-throughput metagenome sequencing. FEMS Microbiol. Ecol. 2012, 79, 785-799.
44. Pereira, M.A.; Roest, K.; Stams, A.J.; Mota, M.; Alves, M.; Akkermans, A.D. Molecular monitoring of microbial diversity in expanded granular sludge bed (EGSB) reactors treating oleic acid. FEMS Microbiol. Ecol. 2002, 41, 95-103.
45. O'Reilly, J.; Lee, C.; Collins, G.; Chinalia, F.; Mahony, T.; O'Flaherty, V. Quantitative and qualitative analysis of methanogenic communities in mesophilically and psychrophilically cultivated anaerobic granular biofilims. Water Res. 2009, 43, 3365-3374.
46. Li, J.; Wang, J.; Luan, Z.; Deng, Y.; Chen, L. Evaluation of performance and microbial community in a two-stage UASB reactor pretreating acrylic fiber manufacturing wastewater. Bioresour. Technol. 2011, 102, 5709-5716.
47. Khemkhao, M.; Nuntakumjorn, B.; Techkarnjanaruk, S.; Phalakornkule, C. UASB performance and microbial adaptation during a transition from mesophilic to thermophilic treatment of palm oil mill effluent. J. Environ. Manag. 2012, 103, 74-82.
48. Nelson, M.C.; Morrison, M.; Schanbacher, F.; Yu, Z. Shifts in microbial community structure of granular and liquid biomass in response to changes to infeed and digester design in anaerobic digesters receiving food-processing wastes. Bioresour. Technol. 2012, 107, 135-143.
49. Xing, W.; Zuo, J.E.; Dai, N.; Cheng, J.; Li, J. Reactor performance and microbial community of an EGSB reactor operated at 20 and 15 °C. J. Appl. Microbiol. 2009, 107, 848-857.
50. McHugh, S.; Carton, M.; Mahony, T.; O'Flaherty, V. Methanogenic population structure in a variety of anaerobic bioreactors. FEMS Microbiol. Lett. 2003, 219, 297-304.
51. Liu, Y.; Xu, H.-L.; Yang, S.-F.; Tay, J.-H. Mechanisms and models for anaerobic granulation in upflow anaerobic sludge blanket reactor. Water Res. 2003, 37, 661-673.
52. Sasaki, K.; Morita, M.; Hirano, S.; Ohmura, N.; Igarashi, Y. Effect of adding carbon fiber textiles to methanogenic bioreactors used to treat an artificial garbage slurry. J. Biosci. Bioeng. 2009, 108, 130-135.
53. Najafpour, G.D.; Zinatizadeh, A.A.L.; Mohamed, A.R.; Hasnain Isa, M.; Nasrollahzadeh, H. High-rate anaerobic digestion of palm oil mill effluent in an upflow anaerobic sludge-fixed film bioreactor. Process Biochem. 2006, 41, 370-379.
54. Patel, P.; Patel, C.; Madamwar, D. Anaerobic upflow fixed-film bioreactor for biomethanation of salty cheese whey. Appl. Biochem. Biotechnol. 1999, 76, 193-201.
55. Acharya, B.K.; Mohana, S.; Madamwar, D. Anaerobic treatment of distillery spent wash-A study on upflow anaerobic fixed film bioreactor. Bioresour. Technol. 2008, 99, 4621-4626.
56. Sasaki, K.; Haruta, S.; Tatara, M.; Yamazawa, A.; Ueno, Y.; Ishii, M.; Igarashi, Y. Microbial community in methanogenic packed-bed reactor successfully operating at short hydraulic retention time. J. Biosci. Bioeng. 2006, 101, 271-273.
57. Sasaki, K.; Haruta, S.; Ueno, Y.; Ishii, M.; Igarashi, Y. Archaeal population on supporting material in methanogenic packed-bed reactor. J. Biosci. Bioeng. 2006, 102, 244-246.
58. Sekiguchi, Y.; Kamagata, Y.; Syutsubo, K.; Ohashi, A.; Harada, H.; Nakamura, K. Phylogenetic diversity of mesophilic and thermophilic granular sludges determined by 16S rRNA gene analysis. J. Microbiol. 1998, 144, 2655-2665.
59. McHugh, S.; Carton, M.; Collins, G.; O'Flaherty, V. Reactor performance and microbial community dynamics during anaerobic biological treatment of wastewaters at 16-37 degrees C. FEMS Microbiol. Ecol. 2004, 48, 369-378.
60. Connaughton, S.; Collins, G.; O'Flaherty, V. Development of microbial community structure and actvity in a high-rate anaerobic bioreactor at 18 °C. Water Res. 2006, 40, 1009-1017.
61. Bandara, W.M.K.R.T.W.; Kindaichi, T.; Satoh, H.; Sasakawa, M.; Nakahara, Y.; Takahashi, M.; Okabe, S. Anaerobic treatment of municipal wastewater at ambient temperature: Analysis of archaeal community structure and recovery of dissolved methane. Water Res. 2012, 46, 5756-5764.
62. Zhang, G.; Zhang, F.; Ding, G.; Li, J.; Guo, X.; Zhu, J.; Zhou, L.; Cai, S.; Liu, X.; Luo, Y.; et al. Acyl homoserine lactone-based quorum sensing in a methanogenic archaeon. ISME J. 2012, 6, 1336-1344.
63. Siggins, A.; Enright, A.M.; O'Flaherty, V. Methanogenic community development in anaerobic granular bioreactors treating trichloroethylene (TCE)-contaminated wastewater at 37 degrees C and 15 degrees C. Water Res. 2011, 45, 2452-2462.
64. Hirasawa, J.S.; Sarti, A.; Del Aguila, N.K.; Varesche, M.B. Application of molecular techniques to evaluate the methanogenic archaea and anaerobic bacteria in the presence of oxygen with different COD: Sulfate ratios in a UASB reactor. Anaerobe 2008, 14, 209-218.
65. Kobayashi, T.; Yan, F.; Takahashi, S.; Li, Y.Y. Effect of starch addition on the biological conversion and microbial community in a methanol-fed UASB reactor during long-term continuous operation. Bioresour. Technol. 2011, 102, 7713-7719.
66. Sallis, P.J.; Uyanik, S. Granule development in a split-feed anaerobic baffled reactor. Bioresour. Technol. 2003, 89, 255-265.
67. Song, M.; Shin, S.G.; Hwang, S. Methanogenic population dynamics assessed by real-time quantitative PCR in sludge granule in upflow anaerobic sludge blanket treating swine wastewater. Bioresour. Technol. 2010, 101, S23-S28.
68. Angenent, L.T.; Sung, S.; Raskin, L. Formation of granules and Methanosaeta fibres in an anaerobic migrating blanket reactor (AMBR). Environ. Microbiol. 2004, 6, 315-322.
69. Fernandez, N.; Sierra-Alvarez, R.; Amils, R.; Field, J.A.; Sanz, J.L. Compared microbiology of granular sludge under autotrophic, mixotrophic and heterotrophic denitrification conditions. Water Sci. Technol. 2009, 59, 1227-1236.
70. Zheng, D.; Angenent, L.T.; Raskin, L. Monitoring granule formation in anaerobic upflow bioreactors using oligonucleotide hybridization probes. Biotechnol. Bioeng. 2006, 94, 458-472.
71. Weber, S.D.; Ludwig, W.; Schleifer, K.H.; Fried, J. Microbial composition and structure of aerobic granular sewage biofilms. Appl. Environ. Microbiol. 2007, 73, 6233-6240.
72. Czepiel, P.M.; Crill, P.M.; Harriss, R.C. Methane emissions from municipal wastewater treatment processes. Environ. Sci. Technol. 1993, 27, 2472-2477.
73. Daelman, M.R.J.; Van Voorthuizen, E.M.; Van Dongen, U.G.J.M.; Volcke, E.I.P.; Van Loosdrecht, M.C.M. Methane emission during municipal wastewater treatment. Water Res. 2012, 46, 3657-3670.
74. Gray, N.D.; Miskin, I.P.; Kornilova, O.; Curtis, T.P.; Head, I.M. Occurrence and activity of Archaea in aerated activated sludge wastewater treatment plants. Environ. Microbiol. 2002, 4, 158-168.
75. Lens, P.N.; De Poorter, M.P.; Cronenberg, C.C.; Verstraete, W.H. Sulfate reducing and methane producing bacteria in aerobic wastewater treatment systems. Water Res. 1995, 29, 871-880.
76. Ren, Y.; Wang, J.; Li, H.; Zhang, J.; Qi, P.; Hu, Z. Nitrous oxide and methane emissions from different treatment processes in full-scale municipal wastewater treatment plants. Environ. Technol. 2012, doi:10.1080/09593330.2012.696717.
77. Treusch, A.H.; Leininger, S.; Kletzin, A.; Schuster, S.C.; Klenk, H.P.; Schleper, C. Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environ. Microbiol. 2005, 7, 1985-1995.
78. Könneke, M.; Bernhard, A.E.; De La Torre, J.R.; Walker, C.B.; Waterbury, J.B.; Stahl, D.A. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 2005, 437, 543-546.
79. Tourna, M.; Stieglmeier, M.; Spang, A.; Konneke, M.; Schintlmeister, A.; Urich, T.; Engel, M.; Schloter, M.; Wagner, M.; Richter, A.; et al. Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. Proc. Natl. Acad. Sci. USA 2011, 108, 8420-8425.
80. Beman, J.M.; Francis, C.A. Diversity of ammonia-oxidizing archaea and bacteria in the sediments of a hypernutrified subtropical estuary: Bahia del Tobari, Mexico. Appl. Environ. Microbiol. 2006, 72, 7767-7777.
81. Dang, H.; Li, J.; Zhang, X.; Li, T.; Tian, F.; Jin, W. Diversity and spatial distribution of amoA-encoding archaea in the deep-sea sediments of the tropical West Pacific Continental Margin. J. Appl. Microbiol. 2009, 106, 1482-1493.
82. Hatzenpichler, R. Diversity, physiology, and niche differentiation of ammonia-oxidizing Archaea. Appl. Environ. Microbiol. 2012, 78, 7501-7510.
83. Limpiyakorn, T.; Fürhacker, M.; Haberl, R.; Chodanon, T.; Srithep, P.; Sonthiphand, P. amoA-encoding archaea in wastewater treatment plants: A review. Appl. Microbiol. Biotechnol. 2013, 97, 1425-1439.
84. Brochier-Armanet, C.; Boussau, B.; Gribaldo, S.; Forterre, P. Mesophilic crenarchaeota: Proposal for a third archaeal phylum, the Thaumarchaeota. Nat. Rev. Microbiol. 2008, 6, 245-252.
85. Spang, A.; Hatzenpichler, R.; Brochier-Armanet, C.; Rattei, T.; Tischler, P.; Spieck, E.; Streit, W.; Stahl, D.A.; Wagner, M.; Schleper, C. Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota. Trends Microbiol. 2010, 18, 331-340.
86. Park, S.J.; Kim, J.G.; Jung, M.Y.; Kim, S.J.; Cha, I.T.; Kwon, K.; Lee, J.H.; Rhee, S.K. Draft genome sequence of an ammonia-oxidizing archaeon,. Candidatus Nitrosopumilus koreensis. AR1, from marine sediment. J. Bacteriol. 2012, 194, 6940-6941.
87. Mosier, A.C.; Allen, E.E.; Kim, M.; Ferriera, S.; Francis, C.A. Genome sequence of. Candidatus Nitrosopumilus salaria. BD31, an ammonia-oxidizing archaeon from the San Francisco Bay estuary. J. Bacteriol. 2012, 194, 2121-2122.
88. Park, S.J.; Kim, J.G.; Jung, M.Y.; Kim, S.J.; Cha, I.T.; Ghai, R.; Martin-Cuadrado, A.B.; Rodriguez-Valera, F.; Rhee, S.K. Draft genome sequence of an ammonia-oxidizing archaeon,. Candidatus Nitrosopumilus sediminis. AR2, from Svalbard in the Arctic Circle. J. Bacteriol. 2012, 194, 6948-6949.
89. Kim, B.K.; Jung, M.Y.; Yu, D.S.; Park, S.J.; Oh, T.K.; Rhee, S.K.; Kim, J.F. Genome sequence of an ammonia-oxidizing soil archaeon,. Candidatus Nitrosoarchaeum koreensis. MY1. J. Bacteriol. 2011, 193, 5539-5540.
90. Ren, Y.; Wang, J.; Li, H.; Zhang, J.; Qi, P.; Hu, Z. Nitrous oxide and methane emissions from different treatment processes in full-scale municipal wastewater treatment plants. Environ. Technol. 2012, doi:10.1080/09593330.2012.696717.
91. Treusch, A.H.; Leininger, S.; Kletzin, A.; Schuster, S.C.; Klenk, H.P.; Schleper, C. Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environ. Microbiol. 2005, 7, 1985-1995.
92. Könneke, M.; Bernhard, A.E.; De La Torre, J.R.; Walker, C.B.; Waterbury, J.B.; Stahl, D.A. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 2005, 437, 543-546.
93. Tourna, M.; Stieglmeier, M.; Spang, A.; Konneke, M.; Schintlmeister, A.; Urich, T.; Engel, M.; Schloter, M.; Wagner, M.; Richter, A.; et al. Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. Proc. Natl. Acad. Sci. USA 2011, 108, 8420-8425.
94. Beman, J.M.; Francis, C.A. Diversity of ammonia-oxidizing archaea and bacteria in the sediments of a hypernutrified subtropical estuary: Bahia del Tobari, Mexico. Appl. Environ. Microbiol. 2006, 72, 7767-7777.
95. Dang, H.; Li, J.; Zhang, X.; Li, T.; Tian, F.; Jin, W. Diversity and spatial distribution of amoA-encoding archaea in the deep-sea sediments of the tropical West Pacific Continental Margin. J. Appl. Microbiol. 2009, 106, 1482-1493.
96. Hatzenpichler, R. Diversity, physiology, and niche differentiation of ammonia-oxidizing Archaea. Appl. Environ. Microbiol. 2012, 78, 7501-7510.
97. Limpiyakorn, T.; Fürhacker, M.; Haberl, R.; Chodanon, T.; Srithep, P.; Sonthiphand, P. amoA-encoding archaea in wastewater treatment plants: A review. Appl. Microbiol. Biotechnol. 2013, 97, 1425-1439.
98. Brochier-Armanet, C.; Boussau, B.; Gribaldo, S.; Forterre, P. Mesophilic crenarchaeota: Proposal for a third archaeal phylum, the Thaumarchaeota. Nat. Rev. Microbiol. 2008, 6, 245-252.
99. Spang, A.; Hatzenpichler, R.; Brochier-Armanet, C.; Rattei, T.; Tischler, P.; Spieck, E.; Streit, W.; Stahl, D.A.; Wagner, M.; Schleper, C. Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota. Trends Microbiol. 2010, 18, 331-340.
100. Park, S.J.; Kim, J.G.; Jung, M.Y.; Kim, S.J.; Cha, I.T.; Kwon, K.; Lee, J.H.; Rhee, S.K. Draft genome sequence of an ammonia-oxidizing archaeon,. Candidatus Nitrosopumilus koreensis. AR1, from marine sediment. J. Bacteriol. 2012, 194, 6940-6941.
101. Mosier, A.C.; Allen, E.E.; Kim, M.; Ferriera, S.; Francis, C.A. Genome sequence of. Candidatus Nitrosopumilus salaria. BD31, an ammonia-oxidizing archaeon from the San Francisco Bay estuary. J. Bacteriol. 2012, 194, 2121-2122.
102. Park, S.J.; Kim, J.G.; Jung, M.Y.; Kim, S.J.; Cha, I.T.; Ghai, R.; Martin-Cuadrado, A.B.; Rodriguez-Valera, F.; Rhee, S.K. Draft genome sequence of an ammonia-oxidizing archaeon,. Candidatus Nitrosopumilus sediminis. AR2, from Svalbard in the Arctic Circle. J. Bacteriol. 2012, 194, 6948-6949.
103. Kim, B.K.; Jung, M.Y.; Yu, D.S.; Park, S.J.; Oh, T.K.; Rhee, S.K.; Kim, J.F. Genome sequence of an ammonia-oxidizing soil archaeon,. Candidatus Nitrosoarchaeum koreensis. MY1. J. Bacteriol. 2011, 193, 5539-5540.
104. Sauder, L.A.; Peterse, F.; Schouten, S.; Neufeld, J.D. Low-ammonia niche of ammonia-oxidizing archaea in rotating biological contactors of a municipal wastewater treatment plant. Environ. Microbiol. 2012, 14, 2589-2600.
105. Limpiyakorn, T.; Sonthiphand, P.; Rongsayamanont, C.; Polprasert, C. Abundance of amoA genes of ammonia-oxidizing archaea and bacteria in activated sludge of full-scale wastewater treatment plants. Bioresour. Technol. 2011, 102, 3694-3701.
106. Yu, T.; Li, D.; Qi, R.; Li, S.T.; Xu, S.W.; Yang, M. Structure and dynamics of nitrifier populations in a full-scale submerged membrane bioreactor during start-up. Appl. Microbiol. Biotechnol. 2011, 90, 369-376.
107. Adair, K.; Schwartz, E. Evidence that ammonia-oxidizing archaea are more abundant than ammonia-oxidizing bacteria in semiarid soils of northern Arizona, USA. Microb. Ecol. 2008, 56, 420-426.
108. Prosser, J.I.; Nicol, G.W. Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment. Environ. Microbiol. 2008, 10, 2931-2941.
109. Witzig, R.; Manz, W.; Rosenbergerb, S.; Krugerb, U.; Kraumeb, M.; Szewzyk, U. Microbiological aspects of a bioreactor with submerged membranes for aerobic treatment of municipal wastewater. Water Res. 2002, 36, 394-402.
110. Ye, L.; Zhang, T. Bacterial communities in different sections of a municipal wastewater treatment plant revealed by 16S rDNA 454 pyrosequencing. Appl. Microbiol. Biotechnol. 2013, 97, 2681-2690.
111. Judd, S. The status of membrane bioreactor technology. Trends Biotechnol. 2008, 26, 109-116.
112. Le-Clech, P. Membrane bioreactors and their uses in wastewater treatments. Appl. Microbiol. Biotechnol. 2010, 88, 1253-1260.
113. LaPara, T.M.; Klatt, C.G.; Chen, R. Adaptations in bacterial catabolic enzyme activity and community structure in membrane-coupled bioreactors fed simple synthetic wastewater. J. Biotechnol. 2006, 121, 368-380.
114. He, S.B.; Xue, G.; Wang, B.Z. Factors affecting simultaneous nitrification and de-nitrification (SND) and its kinetics model in membrane bioreactor. J. Hazard Mater. 2009, 168, 704-710.
115. Santegoeds, C.M.; Damgaard, L.R.; Hesselink, G.; Zopfi, J.; Lens, P.; Muyzer, G.; De Beer, D. Distribution of sulfate-reducing and methanogenic bacteria in anaerobic aggregates determined by microsensor and molecular analyses. Appl. Environ. Microbiol. 1999, 65, 4618-4629.
116. Ridgway, H.F.; Flemming, H.-C. Biofouling of Membranes. In Water Treatment Membrane Processes, 1st ed.; Mallevialle, J., Odendaal, P.E., Eds.; McGraw-Hill: New York, NY, USA, 1996; pp. 6.1-6.62.
117. Herrera-Robledo, M.; Morgan-Sagastume, J.M.; Noyola, A. Biofouling and pollutant removal during long-term operation of an anaerobic membrane bioreactor treating municipal wastewater. Biofouling 2010, 26, 23-30.
118. Ivnitsky, H.; Katz, I.; Minz, D.; Volvovic, G.; Shimoni, E.; Kesselman, E.; Semiat, R.; Dosoretz, C.G. Bacterial community composition and structure of biofilms developing on nanofiltration membranes applied to wastewater treatment. Water Res. 2007, 41, 3924-3935.
119. Rosenberger, S.; Evenblij, H.; Te Poele, S.; Wintgens, T.; Laabs, C. The importance of liquid phase analyses to understand fouling in membrane assisted activated sludge processes-Six case studies of different European research groups. J. Membr. Sci. 2005, 263, 113-126.
120. Ramesh, A.; Lee, D.J.; Wang, M.L.; Hsu, J.P.; Juang, R.S.; Hwang, K.J.; Liu, J.C.; Tseng, S.J. Biofouling in membrane bioreactor. Sep. Sci. Technol. 2006, 41, 1345-1370.
121. Ramesh, A.; Lee, D.J.; Lai, J.Y. Membrane biofouling by extracellular polymeric substances or soluble microbial products from membrane bioreactor sludge. Appl. Microbiol. Biotechnol. 2007, 74, 699-707.
122. Miura, Y.; Watanabe, Y.; Okabe, S. Membrane biofouling in pilot-scale membrane bioreactors (MBRs) treating municipal wastewater: Impact of biofilm formation. Environ. Sci. Technol. 2007, 41, 632-638.
123. Gao, D.-W.; Zhang, T.; Tang, C.-Y.Y.; Wu, W.-M.; Wong, C.-Y.; Lee, Y.H.; Yeh, D.H.; Criddle, C.S. Membrane fouling in an anaerobic membrane bioreactor: Differences in relative abundance of bacterial species in the membrane foulant layer and in suspension. J. Membr. Sci. 2010, 364, 331-338.
124. Lin, H.; Liao, B.-Q.; Chen, J.; Gao, W.; Wang, L.; Wang, F.; Lu, X. New insights into membrane fouling in a submerged anaerobic membrane bioreactor based on characterization of cake sludge and bulk sludge. Bioresour. Technol. 2011, 102, 2373-2379.
125. Chang, I.; Le Clech, P.; Jefferson, B.; Judd, S. Membrane fouling in membrane bioreactors for wastewater treatment. J. Environ. Eng. 2002, 128, 1018-1029.
126. Yeon, K.M.; Cheong, W.S.; Oh, H.S.; Lee, W.N.; Hwang, B.K.; Lee, C.H.; Beyenal, H.; Lewandowski, Z. Quorum sensing: A new biofouling control paradigm in a membrane bioreactor for advanced wastewater treatment. Environ. Sci. Technol. 2009, 43, 380-385.
127. Leininger, S.; Urich, T.; Schloter, M.; Schwark, L.; Qi, J.; Nicol, G.W.; Prosser, J.I.; Schuster, S.C.; Schleper, C. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 2006, 442, 806-809.
128. Wuchter, C.; Abbas, B.; Coolen, M.J.; Herfort, L.; Van Bleijswijk, J.; Timmers, P.; Strous, M.; Teira, E.; Herndl, G.J.; Middelburg, J.J. Archaeal nitrification in the ocean. Proc. Natl. Acad. Sci. USA 2006, 103, 12317-12322.
129. Erguder, T.H.; Boon, N.; Wittebolle, L.; Marzorati, M.; Verstraete, W. Environmental factors shaping the ecological niches of ammonia-oxidizing archaea. FEMS Microbiol. Rev. 2009, 33, 855-869.
130. Lequette, Y.; Boels, G.; Clarisse, M.; Faille, C. Using enzymes to remove biofilms of bacterial isolates sampled in the food-industry. Biofouling 2010, 26, 421-431.
131. Fernandez, N.; Diaz, E.E.; Amils, R.; Sanz, J.L. Analysis of microbial community during biofilm development in an anaerobic wastewater treatment reactor. Microb. Ecol. 2008, 56, 121-132.
132. Mathai, J.C.; Sprott, G.D.; Zeidel, M.L. Molecular mechanisms of water and solute transport across archaebacterial lipid membranes. J. Biol. Chem. 2001, 276, 27266-27271.
133. Xun, L.Y.; Mah, R.A.; Boone, D.R. Isolation and characterization of disaggregatase from Methanosarcina mazei LYC. Appl. Environ. Microbiol. 1990, 56, 3693-3698.
134. Osumi, N.; Kakehashi, Y.; Matsumoto, S.; Nagaoka, K.; Sakai, J.; Miyashita, K.; Kimura, M.; Asakawa, S. Identification of the gene for disaggregatase from Methanosarcina mazei. Archaea 2008, 2, 185-191.
135. Orell, A.; Peeters, E.; Vassen, V.; Jachlewski, S.; Schalles, S.; Siebers, B.; Albers, S.V. Lrs14 transcriptional regulators influence biofilm formation and cell motility of Crenarchaea. ISME J. 2013, doi:10.1038/ismej.2013.68.
136. Bernal, P.; Llamas, M.A. Promising biotechnological applications of antibiofilm exopolysaccharides. Microb. Biotechnol. 2012, 5, 670-673.
137. Xiong, Y.; Liu, Y. Biological control of microbial attachment: A promising alternative for mitigating membrane biofouling. Appl. Microbiol. Biotechnol. 2010, 86, 825-837.