Assessment of bacterial community structure in nitrifying biofilm under inorganic carbon-sufficient and -limited conditions

References

• Kim, D.J.; Lee, D.I.; Keller, J. Effect of temperature and free ammonia on nitrification and nitrite accumulation in landfill leachate and analysis of its nitrifying bacterial community by FISH. Bioresour. Technol. 2006, 97, 459–468.
   PubMed Web of Science ®Google Scholar
• Do, H.; Lim, J.; Shin, S.G.; Wu, Y.J.; Ahn, J.H.; Hwang, S. Simultaneous effect of temperature, cyanide and ammonia-oxidizing bacteria concentrations on ammonia oxidation. J. Ind. Microbiol. Biotechnol. 2008, 35, 1331–1338.
   PubMed Web of Science ®Google Scholar
• Lee, S.; Cho, K.; Lim, J.; Kim, W.; Hwang, S. Acclimation and activity of ammonia-oxidizing bacteria with respect to variations in zinc concentration, temperature, and microbial population. Bioresour. Technol. 2011, 102, 4196–4203.
   PubMed Web of Science ®Google Scholar
• Subrahmanyam, G.; Hu, H.W.; Zheng, Y.M.; Gattupalli, A.; He, J.Z.; Liu, Y.R. Response of ammonia oxidizing microbes to the stresses of arsenic and copper in two acidic alfisols. App. Soil Ecol. 2014, 77, 59–67.
   Web of Science ®Google Scholar
• Wett, B.; Rauch, W. The role of inorganic carbon limitation in biological nitrogen removal of extremely ammonia concentrated wastewater. Water Res. 2003, 37, 1100–1110.
   PubMed Web of Science ®Google Scholar
• Guisasola, A.; Petzet, S.; Baeza, J.A.; Carrera, J.; Lafuente, J. Inorganic carbon limitations on nitrification: Experimental assessment and modelling. Water Res. 2007, 41, 277–286.
   PubMed Web of Science ®Google Scholar
• Villaverde, S.; Garcia-Encina, P.A.; Fdz-Polanco, F. Influence of pH over nitrifying biofilm activity in submerged biofilters. Water Res. 1997, 31, 1180–1186.
   Web of Science ®Google Scholar
• Green, M.; Ruskol, Y.; Tarre, S.; Loewenthal, R.E. Nitrification utilizing CaCO3 as the buffering agent. Environ. Technol. 2002, 23, 303–308.
   PubMed Web of Science ®Google Scholar
• Whang, L.M.; Yang, K.H.; Yang, Y.F.; Han, Y.L.; Chen, Y.J.; Cheng, S.S. Microbial ecology and performance of ammonia oxidizing bacteria (AOB) in biological processes treating petrochemical wastewater with high strength of ammonia: effect of Na2CO3 addition. Water Sci. Technol. 2009, 59, 223–231.
   PubMed Web of Science ®Google Scholar
• Tokutomi, T.; Shibayama, C.; Soda, S.; Ike, M. A novel control method for nitritation: The domination of ammonia-oxidizing bacteria by high concentrations of inorganic carbon in an airlift-fluidized bed reactor. Water Res. 2010, 44, 4195–4203.
   PubMed Web of Science ®Google Scholar
• Fukushima, T.; Whang, L.-M.; Chiang, T.-Y.; Lin, Y.-H.; Chevalier, L.R.; Chen, M.-C.; Wu, Y.-J. Nitrifying bacterial community structures and their nitrification performance under sufficient and limited inorganic carbon conditions. Appl. Microbiol. Biotechnol. 2013, 14, 6613–6523.
   Google Scholar
• Bassin, J.O.P.; Dezotti, M.; Sant’anna, G.L. Jr. Nitrification of industrial and domestic saline wastewaters in moving bed biofilm reactor and sequencing batch reactor. J. Hazard. Mater. 2011, 185, 242–248.
   PubMed Web of Science ®Google Scholar
• Rouse, J.D.; Yazaki, D.; Cheng, Y.; Koyama, T.; Furukawa, K. Swim-bed technology as an innovative attached-growth process for high-rate wastewater treatment. Jpn. J. Water Treat. Biol. 2004, 40, 115–124.
   Google Scholar
• Rusten, B.; Eikebrokk, B.; Ulgenes, Y.; Lygren, E. Design and operations of the Kaldnes moving bed biofilm reactors. Aquacultur. Eng. 2006, 34, 322–331.
   Web of Science ®Google Scholar
• Bai, X.; Ye, Z.F.; Li, Y.F.; Zhou, L.C.; Yang, L.Q. Preparation of crosslinked macroporous PVA foam carrier for immobilization of microorganisms. Proc. Biochem. 2010, 45, 60–66.
   Web of Science ®Google Scholar
• Flemming, H. C.; Wingender, J. The biofilm matrix. Nat. Rev. Microbiol. 2010, 8, 623–633.
   PubMed Web of Science ®Google Scholar
• Kindaichi, T.; Ito, T.; Okabe, S. Ecophysiological interaction between nitrifying bacteria and heterotrophic bacteria in autotrophic nitrifying biofilms as determined by microautoradiography-fluorescence in situ hybridization. Appl. Environ. Microbiol. 2004, 70, 1641–1650.
   PubMed Web of Science ®Google Scholar
• Gieseke, A.; Bjerrum, L.; Wagner, M.; Amann, R. Structure and activity of multiple nitrifying bacterial populations co-existing in a biofilm. Environ. Microbiol. 2003, 5, 355–369.
   PubMed Web of Science ®Google Scholar
• Sakano, Y.; Kerkhof, L. Assessment of changes in microbial community structure during operation of an ammonia biofilter with molecular tools. Appl. Environ. Microbiol. 1998, 64, 4877–4882.
   PubMed Web of Science ®Google Scholar
• Dolinšek, J.; Lagkouvardos, I.; Wanek, W.; Wagner, M.; Daims, H. Interactions of nitrifying bacteria and heterotrophs: identification of a Micavibrio-like putative predator of Nitrospira spp. Appl. Environ. Microbiol. 2013, 79, 2027–2037.
   PubMed Web of Science ®Google Scholar
• Hanaki, K.; Wantawin, C.; Ohgaki, S. Nitrification at low levels of dissolved oxygen with and without organic loading in a suspended-growth reactor. Water Res. 1990, 24, 297–302.
   Web of Science ®Google Scholar
• Ruiz, G.; Jeison, D.; Chamy, R. Nitrification with high nitrite accumulation for the treatment of wastewater with high ammonia concentration. Water Res. 2003, 37, 1371–1377.
   PubMed Web of Science ®Google Scholar
• Chae, K. J.; Kim, S. M.; Oh, S. E.; Ren, X.; Lee, J.; Kim, I. S. Spatial distribution and viability of nitrifying, denitrifying and ANAMMOX bacteria in biofilms of sponge media retrieved from a full-scale biological nutrient removal plant. Bioproc. Biosys. Eng. 2012, 35, 1157–1165.
   PubMed Web of Science ®Google Scholar
• So, M.; Naka, D.; Goel, R.; Yasui, H. Model development of a sponge carrier process using CFD-DEM with permeable particles. J. Water Environ. Tech. 2012, 10, 193–204.
   Google Scholar
• Chandran, K.; Smets, B.F. Single-step nitrification models erroneously describe batch ammonia oxidation profiles when nitrite oxidation becomes rate limiting. Biotech. Bioeng. 2000, 68, 396–406.
   PubMed Web of Science ®Google Scholar
• Bae, H.; Park, J.-H.; Jun, K.-S.; Jung, J.-Y. The community analysis of ammonia-oxidizing bacteria in wastewater treatment plants revealed by the combination of double labeled T-RFLP and sequencing. J. Environ. Sci. Health Part A, 2011, 46, 345–354.
   Web of Science ®Google Scholar
• Limpiyakorn, T.; Shinohara, Y.; Kurisu, F.; Yagi, O. Communities of ammonia-oxidizing bacteria in activated sludge of various sewage treatment plants in Tokyo. FEMS Microbiol. Ecol. 2005, 54, 205–217.
   PubMed Web of Science ®Google Scholar
• Siripong, S.; Rittmann, B.E. Diversity study of nitrifying bacteria in full-scale municipal wastewater treatment plants. Water Res. 2007, 41, 1110–1120.
   PubMed Web of Science ®Google Scholar
• Dionisi, H.M.; Layton, A.C.; Harms, G.; Gregory, I.R.; Robinson, K.G.; Sayler, G.S. Quantification of Nitrosomonas oligotropha-like ammonia-oxidizing bacteria and Nitrospira spp. from full-scale wastewater treatment plants by competitive PCR. Appl. Environ. Microbiol. 2002, 68, 245–253.
   PubMed Web of Science ®Google Scholar
• Gieseke, A.; Purkhold, U.; Wagner, M.; Amann, R.; Schramm, A. Community structure and activity dynamics of nitrifying bacteria in a phosphate-removing biofilm. Appl. Environ. Microbiol. 2001, 67, 1351–1362.
   PubMed Web of Science ®Google Scholar
• Harms, G.; Layton, A.C.; Dionisi, H.M.; Gregory, I.R.; Garrett, V.M.; Hawkins, S.A.; Robinson, K.G.; Sayler, G.S. Real-time PCR quantification of nitrifying bacteria in a municipal wastewater treatment plant. Environ. Sci. Technol. 2003, 37, 343–351.
   PubMed Web of Science ®Google Scholar
• Koops, H.P.; Böttcher, B.; Möller, U.C.; Pommerening-Röser, A.; Stehr, G. Classification of eight new species of ammonia-oxidizing bacteria: Nitrosomonas communis sp. nov., Nitrosomonas ureae sp. nov., Nitrosomonas aestuarii sp. nov., Nitrosomonas marina sp. nov., Nitrosomonas nitrosa sp. nov., Nitrosomonas eutropha sp. nov., Nitrosomonas oligotropha sp. nov. and Nitrosomonas halophila sp. nov.. J. Gen. Microbiol. 1991, 137, 1689–1699.
   Google Scholar
• Koops, H.P.; Purkhold, U.; Pommerening-Röser, A.; Timmermann, G.; Wagner, M. The lithoautotrophic ammonia-oxidizing bacteria. The prokaryotes. 2006, 5, 778–811.
   Google Scholar
• Koops, H.P.; Pommerening-Röser, A. Distribution and ecophysiology of the nitrifying bacteria emphasizing cultured species. FEMS Microbiol. Ecol. 2001, 37, 1–9.
   Web of Science ®Google Scholar
• Friedrich, U.; Prior, K.; Altendorf, K.; Lipski, A. High bacterial diversity of a waste gas-degrading community in an industrial biofilter as shown by a 16S rDNA clone library. Environ. Microbiol. 2002, 4, 721–734.
   PubMed Web of Science ®Google Scholar
• Montràs, A.; Pycke, B.; Boon, N.; Gòdia, F.; Mergeay, M.; Hendrickx, L.; Pérez, J. Distribution of Nitrosomonas europaea and Nitrobacter winogradskyi in an autotrophic nitrifying biofilm reactor as depicted by molecular analyses and mathematical modelling. Water Res. 2008, 42, 1700–1714.
   PubMed Web of Science ®Google Scholar
• Schramm, A.; de Beer, D.; van denHeuvel, J.C.; Ottengraf, S.; Amann, R. Microscale distribution of populations and activities of Nitrosospira and Nitrospira spp. along a macroscale gradient in a nitrifying bioreactor: quantification by in situ hybridization and the use of microsensors. Appl. Environ. Microbiol. 1999, 65, 3690–3696.
   PubMed Web of Science ®Google Scholar
• Sangwan, P.; Chen, X.; Hugenholtz, P.; Janssen, P.H. Chthoniobacter flavus gen. nov., sp. nov., the first pure-culture representative of subdivision two, Spartobacteria classis nov., of the phylum Verrucomicrobia. Appl. Environ. Microbiol. 2004, 70, 5875–5881.
   PubMed Web of Science ®Google Scholar
• Flemming, H.C.; Wingender, J. Relevance of microbial extracellular polymeric substances (EPSs)-Part I: Structural and ecological aspects. Water Sci. Technol. 2001, 43, 1–8.
   PubMed Web of Science ®Google Scholar
• Kämpfer, P.; Müller, C.; Mau, M.; Neef, A.; Auling, G.; Busse, H.J.; Osborn, A.M.; Stolz, A. Description of Pseudaminobacter gen. nov. with two new species, Pseudaminobacter salicylatoxidans sp. nov. and Pseudaminobacter defluvii sp. nov.. Int. J. Syst. Bacteriol. 1999, 49, 887–897.
   PubMedGoogle Scholar
• Frølund, B.; Palmgren, R.; Keiding, K.; Nielsen, P.H. Extraction of extracellular polymers from activated sludge using a cation exchange resin. Water Res. 1996, 30, 1749–1758.
   Web of Science ®Google Scholar
• Tago, Y.; Yokota, A. Comamonas badia sp. nov., a floc-forming bacterium isolated from activated sludge. J. Gen. Appl. Microbiol. 2004, 50, 243–248.
   PubMed Web of Science ®Google Scholar
• Biswas, R.; Bagchi, S.; Bihariya, P.; Das, A.; Nandy, T. Stability and microbial community structure of a partial nitrifying fixed-film bioreactor in long run. Bioresour. Technol. 2011, 102, 2487–2494.
   PubMed Web of Science ®Google Scholar
• Sakano, Y.; Kerkhof, L. Assessment of changes in microbial community structure during operation of an ammonia biofilter with molecular tools. Appl. Environ. Microbiol. 1998, 64, 4877–4882.
   PubMed Web of Science ®Google Scholar
• Velázquez, E.; Igual, J.M.; Willems, A.; Fernández, M.P.; Muñoz, E.; Mateos, P.F.; Abril, A.; Toro, N.; Normand, P.; Cervantes, E.; Gillis, M.; Martínez-Molina, E. Mesorhizobium chacoense sp. nov., a novel species that nodulates Prosopis alba in the Chaco Arido region (Argentina). Int. J. Syst. Evol. Microbiol. 2001, 51, 1011–1021.
   PubMed Web of Science ®Google Scholar
• Pal, L.; Kraigher, B.; Brajer-Humar, B.; Levstek, M.; Mandic-Mulec, I. Total bacterial and ammonia-oxidizer community structure in moving bed biofilm reactors treating municipal wastewater and inorganic synthetic wastewater. Bioresour. Technol. 2012, 110, 135–143.
   PubMed Web of Science ®Google Scholar
• Paul, D.; Bridges, S.; Burgess, S.C.; Dandass, Y.; Lawrence, M.L. Genome sequence of the chemolithoautotrophic bacterium Oligotropha carboxidovorans OM5T. J. Bacteriol. 2008, 190, 5531–5532.
   PubMed Web of Science ®Google Scholar
• Vaz-Moreira, I.; Faria, C.; Lopes, A.R.; Svensson, L.A.; Moore, E.R.B.; Nunes, O.C.; Manaia, C.M. Shinella fusca sp. nov., isolated from domestic waste compost. Int. J. Syst. Evol. Microbiol. 2010, 60, 144–148.
   PubMed Web of Science ®Google Scholar
• An, D.S.; Im, W.T.; Yang, H.C.; Lee, S.T. Shinella granuli gen. nov., sp. nov., and proposal of the reclassification of Zoogloea ramigera ATCC 19623 as Shinella zoogloeoides sp. nov.. Int. J. Syst. Evol. Microbiol. 2006, 56, 443–448.
   PubMed Web of Science ®Google Scholar
• Santos, P.; Pinhal, I.; Rainey, F.A.; Empadinhas, N.; Costa, J.; Fields, B.; Benson, R.; Verissimo, A.; da Costa, M.S. Gamma-Proteobacteria Aquicella lusitana gen. nov., sp. nov., and Aquicella siphonis sp. nov. infect Protozoa and require activated charcoal for growth in laboratory media. Appl. Environ. Microbiol. 2003, 69, 6533–6540.
   PubMed Web of Science ®Google Scholar
• Dastager, S.G.; Lee, J.C.; Ju, Y.J.; Park, D.J.; Kim, C.J. Cryobacterium mesophilum sp. nov., a novel mesophilic bacterium. Int. J. Syst. Evol. Microbiol. 2008, 58, 1241–1244.
   PubMed Web of Science ®Google Scholar
• Baytshtok, V.; Kim, S.; Yu, R.; Park, H.; Chandran, K. Molecular and biokinetic characterization of methylotrophic denitrification using nitrate and nitrite as terminal electron acceptors. Water Sci. Technol. 2008, 58, 359–365.
   PubMed Web of Science ®Google Scholar
• Osaka, T.; Ebie, Y.; Tsuneda, S.; Inamori, Y. Identification of the bacterial community involved in methane-dependent denitrification in activated sludge using DNA stable-isotope probing. FEMS Microbiol. Ecol. 2008, 64, 494–506.
   PubMed Web of Science ®Google Scholar
• Zhao, H.W.; Mavinic, D.S.; Oldham, W.K.; Koch, F.A. Controlling factors for simultaneous nitrification and denitrification in a two-stage intermittent aeration process treating domestic sewage. Water Res. 1999, 33, 961–970.
   Web of Science ®Google Scholar
• Takaya, N.; Catalan-Sakairi, M.A.B.; Sakaguchi, Y.; Kato, I.; Zhou, Z.; Shoun, H. Aerobic denitrifying bacteria that produce low levels of nitrous oxide. App. Environ. Microbiol. 2003, 69, 3152–3157.
   PubMed Web of Science ®Google Scholar
• Zhang, D.C.; Liu, H.C.; Xin, Y.H.; Zhou, Y.G.; Schinner, F.; Margesin, R. Luteimonas terricola sp. nov., a psychrophilic bacterium isolated from soil. Int. J. Syst. Evol. Microbiol. 2010, 60, 1581–1584.
   PubMed Web of Science ®Google Scholar