Advanced search
Publication Cover
Critical Reviews in Environmental Science and Technology Volume 43, 2013 - Issue 21
Submit an article Journal homepage
2,043
Views
64
CrossRef citations to date
0
Altmetric
Original Articles

Pathways and Organisms Involved in Ammonia Oxidation and Nitrous Oxide Emission

Jianhua Guo School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin, China; Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering, Beijing University of Technology, Beijing, China
,
Yongzhen Peng School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin, China; Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering, Beijing University of Technology, Beijing, China
,
Shuying Wang Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering, Beijing University of Technology, Beijing, China
,
Bin Ma School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin, China
,
Shijian Ge Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering, Beijing University of Technology, Beijing, China
,
Zhongwei Wang Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering, Beijing University of Technology, Beijing, China
,
Huijun Huang Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering, Beijing University of Technology, Beijing, China
,
Jingrong Zhang Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering, Beijing University of Technology, Beijing, China
&
Liang Zhang School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin, China
 show all
Pages 2213-2296 | Published online: 15 Oct 2013

REFERENCES

  • Aakra , A. , Utaker , J. B. and Nes , I. F. 2001 . Comparative phylogeny of the ammonia monooxygenase subunit A and 16S rRNA genes of ammonia-oxidizing bacteria . FEMS Microbiol. Lett. , 205 : 237 – 242 .
  • Abeliovich , A. and Vonshak , A. 1992 . Anaerobic metabolisms of Nitrosomonas europaea . Arch. Microbiol. , 158 : 267 – 270 .
  • Abma , W. R. , Driessen , W. , Haarhuis , R. and van Loosdrecht , M. C. M. 2010 . Upgrading of sewage treatment plant by sustainable and cost-effective separate treatment of industrial wastewater . Water Sci. Technol. , 61 : 1715 – 1722 .
  • Abma , W. R. , Schultz , C. E. , Mulder , J. W. , van Loosdrecht , M. C. M. , van der Star , W. R. L. , Strous , M. and Tokutomi , T. 2007 . The advance of anammox . Water , 21 : 36 – 37 .
  • Adair , K. L. and Schwartz , E. 2008 . Evidence that ammonia-oxidizing archaea are more abundant than ammonia-oxidizing bacteria in semiarid soils of northern Arizona, USA . Microb. Ecol. , 56 : 420 – 426 .
  • Agogue , H. , Brink , M. , Dinasquet , J. and Herndl , G. J. 2008 . Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic . Nature , 456 : 788 – 792 .
  • Ahmad , N. , Xu , H. , Chen , L. , Liu , Z. and Liu , S. 2008a . Enhanced biological nutrient removal by the alliance of a heterotrophic nitrifying strain with a nitrogen removing ecosystem . J. Environ. Sci.-China. , 20 : 216 – 223 .
  • Ahmad , N. , Xu , H. Y. , Chen , L. P. , Liu , Z. P. and Liu , S. J. 2008b . Enhanced biological nutrient removal by the alliance of a heterotrophic nitrifying strain with a nitrogen removing ecosystem . J. Environ. Sci.–China. , 20 : 216 – 223 .
  • Ahn , Y.-H. 2006 . Sustainable nitrogen elimination biotechnologies: A review . Process Biochem. , 41 : 1709 – 1721 .
  • Altmann , D. , Stief , P. , Amann , R. , de Beer , D. and Schramm , A. 2003 . In situ distribution and activity of nitrifying bacteria in freshwater sediment . Environ. Microbiol. , 5 : 798 – 803 .
  • Alzerreca , J. J. , Norton , J. M. and Klotz , M. G. 1999 . The amo operon in marine, ammonia-oxidizing gamma-proteobacteria . FEMS Microbiol. Lett. , 180 : 21 – 29 .
  • Amano , T. , Yoshinaga , I. , Okada , K. , Yamagishi , T. , Ueda , S. , Obuchi , A. , Sako , Y. and Suwa , Y. 2007 . Detection of anammox activity and diversity of anammox bacteria-related 16S rRNA genes in coastal marine sediment in japan . Microbes and Environments , 22 : 232 – 242 .
  • An , S. M. and Gardner , W. S. 2002 . Dissimilatory nitrate reduction to ammonium (DNRA) as a nitrogen link, versus denitrification as a sink in a shallow estuary (Laguna Madre/Baffin Bay, Texas) . Mar. Ecol.–Prog. Ser. , 237 : 41 – 50 .
  • Anderson , I. C. , Poth , M. , Homstead , J. and Burdige , D. 1993 . A comparison of NO and N2O production by the autotrophic nitrifier nitrosomonas-europaea and the heterotrophic nitrifier alcaligenes-faecalis . Appl. Environ. Microb. , 59 : 3525 – 3533 .
  • Andersson , K. K. , Lipscomb , J. D. , Valentine , M. , Munck , E. and Hooper , A. B. 1986 . Tetraheme cytochrome C-554 from nitrosomonas-europaea-heme-heme interactions and ligand-binding . J. Biol. Chem. , 261 : 1126 – 1138 .
  • Ando , Y. , Nakagawa , T. , Takahashi , R. , Yoshihara , K. and Tokuyama , T. 2009 . Seasonal changes in abundance of ammonia-oxidizing archaea and ammonia-oxidizing bacteria and their nitrification in sand of an eelgrass zone . Microbes. Environ. , 24 : 21 – 27 .
  • Anthonisen , A. C. , Loehr , R. C. , Prakasam , T. B. S. and Srinath , E. G. 1976 . Inhibition of nitrification by ammonia and nitrous-acid . J. Water. Pollut. Con. F. , 48 : 835 – 852 .
  • Arp , D. J. and Stein , L. Y. 2003 . Metabolism of inorganic N compounds by ammonia-oxidizing bacteria . Crit. Rev. Biochem. Mol. Biol. , 38 : 471 – 495 .
  • Aslan , S. , Miller , L. and Dahab , M. 2009 . Ammonium oxidation via nitrite accumulation under limited oxygen concentration in sequencing batch reactors . Bioresour. Technol. , 100 : 659 – 664 .
  • Bae , H. , Chung , Y. C. and Jung , J. Y. 2010 . Microbial community structure and occurrence of diverse autotrophic ammonium oxidizing microorganisms in the anammox process . Water Sci. Technol. , 61 : 2723 – 2732 .
  • Barraclough , D. and Puri , G. 1995 . The use of 15N pool dilution and enrichment to separate the heterotrophic and autotrophic pathways of nitrification . Soil Biol. Biochem. , 27 : 17 – 22 .
  • Bates , S. T. , Berg-Lyons , D. , Caporaso , J. G. , Walters , W. A. , Knight , R. and Fierer , N. 2011 . Examining the global distribution of dominant archaeal populations in soil . ISME J. , 5 : 908 – 917 .
  • Bauhus , J. , Meyer , A. C. and Brumme , R. 1996 . Effect of the inhibitors nitrapyrin and sodium chlorate on nitrification and N2O formation in an acid forest soil . Biol. Fert. Soils , 22 : 318 – 325 .
  • Beman , J. M. and Francis , C. A. 2006 . Diversity of ammonia-oxidizing archaea and bacteria in the sediments of a hypernutrified subtropical estuary: Bahia del Tobari, Mexico . Appl. Environ. Microb. , 72 : 7767 – 7777 .
  • Beman , J. M. , Popp , B. N. and Francis , C. A. 2008 . Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California . ISME J. , 2 : 429 – 441 .
  • Bergmann , D. J. and Hooper , A. B. 1994a . The primary structure of cytochrome P460 of Nitrosomonas europaea: Presence of a c-heme binding motif . FEBS Lett. , 353 : 324 – 326 .
  • Bergmann , D. J. and Hooper , A. B. 1994b . Sequence of the gene, amoB, for the 43-kDa polypeptide of ammonia monooxygenase of Nitrosomonas europaea . Biochem. Bioph. Res. Co. , 204 : 759 – 762 .
  • Bergmann , D. J. , Hooper , A. B. and Klotz , M. G. 2005 . Structure and sequence conservation of hao cluster genes of autotrophic ammonia-oxidizing bacteria: Evidence for their evolutionary history . Appl. Environ. Microb. , 71 : 5371 – 5382 .
  • Bernhard , A. E. , Landry , Z. C. , Blevins , A. , de la Torre , J. R. , Giblin , A. E. and Stahl , D. A. 2010 . Abundance of ammonia-oxidizing archaea and bacteria along an estuarine salinity gradient in relation to potential nitrification rates . Appl. Environ. Microb. , 76 : 1285 – 1289 .
  • Blackburne , R. , Yuan , Z. Q. and Keller , J. 2008a . Demonstration of nitrogen removal via nitrite in a sequencing batch reactor treating domestic wastewater . Water Res. , 42 : 2166 – 2176 .
  • Blackburne , R. , Yuan , Z. G. and Keller , J. 2008b . Partial nitrification to nitrite using low dissolved oxygen concentration as the main selection factor . Biodegradation , 19 : 303 – 312 .
  • Blagodatsky , S. A. , Kesik , M. , Papen , H. and Butterbach-Bahl , K. 2006 . Production of NO and N2O by the heterotrophic nitrifier Alcaligenes faecalis parafaecalis under varying conditions of oxygen saturation . Geomicrobiol. J. , 23 : 165 – 176 .
  • Bock , E. , Schmidt , I. , Stuven , R. and Zart , D. 1995 . Nitrogen loss caused by denitrifying Nitrosomonas cells using ammonium or hydrogen as electron-donors and nitrite as electron-acceptor . Arch. Microbiol. , 163 : 16 – 20 .
  • Bothe , H. , Jost , G. , Schloter , M. , Ward , B. B. and Witzel , K. P. 2000 . Molecular analysis of ammonia oxidation and denitrification in natural environments . FEMS Microbiol. Rev. , 24 : 673 – 690 .
  • Bougard , D. , Bernet , N. , Chèneby , D. and Delgenès , J. P. 2006 . Nitrification of a high-strength wastewater in an inverse turbulent bed reactor: Effect of temperature on nitrite accumulation . Process Biochem. , 41 : 106 – 113 .
  • Boumann , H. A. , Longo , M. L. , Stroeve , P. , Poolman , B. , Hopmans , E. C. , Stuart , M. C. A. , Sinninghe Damsté , J. S. and Schouten , S. 2009a . Biophysical properties of membrane lipids of anammox bacteria: I. Ladderane phospholipids form highly organized fluid membranes . Biochim. Biophys. Acta , 1788 : 1444 – 1451 .
  • Boumann , H. A. , Stroeve , P. , Longo , M. L. , Poolman , B. , Kuiper , J. M. , Hopmans , E. C. , Jetten , M. S. M. , Sinninghe Damst? Jaap , S. and Schouten , S. 2009b . Biophysical properties of membrane lipids of anammox bacteria: II. Impact of temperature and bacteriohopanoids . Biochim. Biophys. Acta , 1788 : 1452 – 1457 .
  • Boyd , E. S. , Lange , R. K. , Mitchell , A. C. , Havig , J. R. , Hamilton , T. L. , Lafreniere , M. J. , Shock , E. L. , Peters , J. W. and Skidmore , M. 2011 . Diversity, abundance, and potential activity of nitrifying and nitrate-reducing microbial assemblages in a subglacial ecosystem . Appl. Environ. Microb. , 77 : 4778 – 4787 .
  • Boyle-Yarwood , S. A. , Bottomley , P. J. and Myrold , D. D. 2008 . Community composition of ammonia-oxidizing bacteria and archaea in soils under stands of red alder and Douglas fir in Oregon . Environ. Microbiol. , 10 : 2956 – 2965 .
  • Brierley , E. D. R. and Wood , M. 2001 . Heterotrophic nitrification in an acid forest soil: isolation and characterisation of a nitrifying bacterium . Soil Biol. Biochem. , 33 : 1403 – 1409 .
  • Brochier-Armanet , C. , Boussau , B. , Gribaldo , S. and Forterre , P. 2008 . Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota . Nat. Rev. Microbiol. , 6 : 245 – 252 .
  • Broda , E. 1977 . Two kinds of lithotrophs missing in nature . Z Allg Mikrobiol , 17 : 491 – 493 .
  • Cabello , P. , Roldan , M. D. and Moreno-Vivian , C. 2004 . Nitrate reduction and the nitrogen cycle in archaea . Microbiol.–SGM , 150 : 3527 – 3546 .
  • Caffrey , J. M. , Bano , N. , Kalanetra , K. and Hollibaugh , J. T. 2007 . Ammonia oxidation and ammonia-oxidizing bacteria and archaea from estuaries with differing histories of hypoxia . ISME J. , 1 : 660 – 662 .
  • Caffrey , J. M. , Hollibaugh , J. T. , Bano , N. and Haskins , J. 2010 . Effects of upwelling on short-term variability in microbial and biogeochemical processes in estuarine sediments from Elkhorn Slough, California, USA . Aquat. Microb. Ecol. , 58 : 261 – 271 .
  • Cai , J. , Jiang , J. X. and Zheng , P. 2010a . Isolation and identification of bacteria responsible for simultaneous anaerobic ammonium and sulfate removal . Sci. China Chem. , 53 : 645 – 650 .
  • Cai , Y. J. , Ding , W. X. , Zhang , X. L. , Yu , H. Y. and Wang , L. F. 2010b . Contribution of heterotrophic nitrification to nitrous oxide production in a long-term N-fertilized arable black soil . Commun. Soil Sci. Plant Anal. , 41 : 2264 – 2278 .
  • Calvó , L. and Garcia-Gil , L. J. 2004 . Use of amoB as a new molecular marker for ammonia-oxidizing bacteria . J. Microbiol. Meth. , 57 : 69 – 78 .
  • Canfield , D. E. , Glazer , A. N. and Falkowski , P. G. 2010 . The Evolution and future of earth's nitrogen cycle . Science , 330 : 192 – 196 .
  • Chen , G. Y. , Qiu , S. L. and Zhou , Y. Y. 2009a . Diversity and abundance of ammonia-oxidizing bacteria in eutrophic and oligotrophic basins of a shallow Chinese lake (Lake Donghu) . Res. Microbiol. , 160 : 173 – 178 .
  • Chen , H. , Liu , S. , Yang , F. , Xue , Y. and Wang , T. 2009b . The development of simultaneous partial nitrification, ANAMMOX and denitrification (SNAD) process in a single reactor for nitrogen removal . Bioresour. Technol. , 100 : 1548 – 1554 .
  • Chen , X. , Zhang , L. M. , Shen , J. P. , Xu , Z. H. and He , J. Z. 2010 . Soil type determines the abundance and community structure of ammonia-oxidizing bacteria and archaea in flooded paddy soils . J. Soil Sediment , 10 : 1510 – 1516 .
  • Chen , X. P. , Zhu , Y. G. , Xia , Y. , Shen , J. P. and He , J. Z. 2008 . Ammonia-oxidizing archaea: important players in paddy rhizosphere soil? . Environ. Microbiol. , 10 : 1978 – 1987 .
  • Choi , O. and Hu , Z. Q. 2008 . Size dependent and reactive oxygen species related nanosilver toxicity to nitrifying bacteria . Environ. Sci. Technol. , 42 : 4583 – 4588 .
  • Chung , J. , Bae , W. , Lee , Y.-W. and Rittmann , B. E. 2007 . Shortcut biological nitrogen removal in hybrid biofilm/suspended growth reactors . Process Biochem. , 42 : 320 – 328 .
  • Church , M. J. , Wai , B. , Karl , D. M. and DeLong , E. F. 2010 . Abundances of crenarchaeal amoA genes and transcripts in the Pacific Ocean . Environ. Microbiol. , 12 : 679 – 688 .
  • Cirpus , I. E. Y. , de Been , M. , Op den Camp , H. J. M. , Strous , M. , Le Paslier , D. , Kuenen , G. J. and Jetten , M. S. M. 2005 . A new soluble 10 kDa monoheme cytochrome c-552 from the anammox bacterium Candidatus “Kuenenia stuttgartiensis . FEMS Microbiol. Lett. , 252 : 273 – 278 .
  • Colliver , B. B. and Stephenson , T. 2000 . Production of nitrogen oxide and dinitrogen oxide by autotrophic nitrifiers . Biotechnol. Adv. , 18 : 219 – 232 .
  • Conrad , R. 1996 . Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O, and NO) . Microbiol. Rev. , 60 : 609 – 640 .
  • Coolen , M. J. L. , Abbas , B. , van Bleijswijk , J. , Hopmans , E. C. , Kuypers , M. M. M. , Wakeham , S. G. and Damste , J. S. S. 2007 . Putative ammonia-oxidizing Crenarchaeota in suboxic waters of the Black Sea: a basin-wide ecological study using 16S ribosomal and functional genes and membrane lipids . Environ. Microbiol. , 9 : 1001 – 1016 .
  • Crossman , L. C. , Moir , J. W. B. , Enticknap , J. J. , Richardson , D. J. and Spiro , S. 1997 . Heterologous expression of heterotrophic nitrification genes . Microbiology , 143 : 3775 – 3783 .
  • Cua , L. S. and Stein , L. Y. 2011 . Effects of nitrite on ammonia-oxidizing activity and gene regulation in three ammonia-oxidizing bacteria . FEMS Microbiol. Lett. , 319 : 169 – 175 .
  • Cui , Y. W. , Pang , Y. Z. , Peng , C. Y. , Gan , X. Q. and Ye , L. 2006 . Achieving biological nitrogen removal via nitrite by salt inhibition . Water Sci. Technol. , 53 : 115 – 122 .
  • Daims , H. , Lücker , S. , Mussmann , M. , Brito , I. , Spieck , E. , Head , I. M. , Paslier , D. L. and Wagner , M. 2009 . Ammonia-oxidizing Archaea and nitrite-oxidizing Nitrospira in wastewater treatment plants: New insights based on molecular tools and environmental genomics Aalborg , , Denmark IWA-Specialized Conference on Microbial Population Dynamics in Biological Wastewater Treatment ASPD 5, May 24–27, 2009
  • Daims , H. , Ramsing , N. B. , Schleifer , K. H. and Wagner , M. 2001 . Cultivation-independent, semiautomatic determination of absolute bacterial cell numbers in environmental samples by fluorescence in situ hybridization . Appl. Environ. Microb. , 67 : 5810 – 5818 .
  • Daims , H. , Taylor , M. W. and Wagner , M. 2006 . Wastewater treatment: a model system for microbial ecology . Trends Biotechnol. , 24 : 483 – 489 .
  • Dale , O. R. , Tobias , C. R. and Song , B. K. 2009 . Biogeographical distribution of diverse anaerobic ammonium oxidizing (anammox) bacteria in Cape Fear River Estuary . Environ. Microbiol. , 11 : 1194 – 1207 .
  • Dalsgaard , T. and Thamdrup , B. 2002 . Factors controlling anaerobic ammonium oxidation with nitrite in marine sediments . Appl. Environ. Microb. , 68 : 3802 – 3808 .
  • Dalsgaard , T. , Thamdrup , B. and Canfield , D. E. 2005 . Anaerobic ammonium oxidation (anammox) in the marine environment . Res. Microbiol. , 156 : 457 – 464 .
  • Damste , J. S. S. , Rijpstra , W. I. C. , Geenevasen , J. A. J. , Strous , M. and Jetten , M. S. M. 2005 . Structural identification of ladderane and other membrane lipids of planctomycetes capable of anaerobic ammonium oxidation (anammox) . FEBS J. , 272 : 4270 – 4283 .
  • Damste , J. S. S. , Strous , M. , Rijpstra , W. I. C. , Hopmans , E. C. , Geenevasen , J. A. J. , van Duin , A. C. T. , van Niftrik , L. A. and Jetten , M. S. M. 2002 . Linearly concatenated cyclobutane lipids form a dense bacterial membrane . Nature , 419 : 708 – 712 .
  • Dang , H. Y. , Zhang , X. X. , Sun , J. , Li , T. G. , Zhang , Z. N. and Yang , G. P. 2008 . Diversity and spatial distribution of sediment ammonia-oxidizing crenarchaeota in response to estuarine and environmental gradients in the Changjiang Estuary and East China Sea . Microbiol.–SGM , 154 : 2084 – 2095 .
  • Dang , H. Y. , Luan , X. W. , Chen , R. P. , Zhang , X. X. , Guo , L. Z. and Klotz , M. G. 2010 . Diversity, abundance and distribution of amoA-encoding archaea in deep-sea methane seep sediments of the Okhotsk Sea . FEMS Microbiol. Ecol. , 72 : 370 – 385 .
  • Daniel , L. M. C. , Pozzi , E. , Foresti , E. and Chinalia , F. A. 2009 . Removal of ammonium via simultaneous nitrification-denitrification nitrite-shortcut in a single packed-bed batch reactor . Bioresour. Technol. , 100 : 1100 – 1107 .
  • Dapena-Mora , A. , Fernandez , I. , Campos , J. L. , Mosquera-Corral , A. , Mendez , R. and Jetten , M. S. M. 2007 . Evaluation of activity and inhibition effects on Anammox process by batch tests based on the nitrogen gas production . Enzyme Microb. Technol. , 40 : 859 – 865 .
  • Dapena-Mora , A. , Vazquez-Padin , J. R. , Campos , J. L. , Mosquera-Corral , A. , Jetten , M. S. M. and Mendez , R. 2010 . Monitoring the stability of an Anammox reactor under high salinity conditions . Biochem. Eng. J. , 51 : 167 – 171 .
  • Daum , M. , Zimmer , W. , Papen , H. , Kloos , K. , Nawrath , K. and Bothe , H. 1998 . Physiological and molecular biological characterization of ammonia oxidation of the heterotrophic nitrifier Pseudomonas putida . Curr. Microbiol. , 37 : 281 – 288 .
  • De Boer , W. and Kowalchuk , G. A. 2001 . Nitrification in acid soils: micro-organisms and mechanisms . Soil Biol. Biochem. , 33 : 853 – 866 .
  • de la Torre , J. R. , Walker , C. B. , Ingalls , A. E. , Konneke , M. and Stahl , D. A. 2008 . Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol . Environ. Microbiol. , 10 : 810 – 818 .
  • de Vet , W. W. J. M. , Dinkla , I. J. T. , Muyzer , G. , Rietveld , L. C. and van Loosdrecht , M. C. M. 2009 . Molecular characterization of microbial populations in groundwater sources and sand filters for drinking water production . Water Res. , 43 : 182 – 194 .
  • de Vet , W. W. J. M. , Kleerebezem , R. , van der Wielen , P. , Rietveld , L. C. and van Loosdrecht , M. C. M. 2011 . Assessment of nitrification in groundwater filters for drinking water production by qPCR and activity measurement . Water Res. , 45 : 4008 – 4018 .
  • Dendooven , L. , Bonhomme , E. , Merckx , R. and Vlassak , K. 1998 . N dynamics and sources of N2O production following pig slurry application to a loamy soil . Biol. Fert. Soils , 26 : 224 – 228 .
  • Di , H. J. , Cameron , K. C. , Shen , J. P. , Winefield , C. S. , O’Callaghan , M. , Bowatte , S. and He , J. Z. 2009 . Nitrification driven by bacteria and not archaea in nitrogen-rich grassland soils . Nature Geoscience , 2 : 621 – 624 .
  • Di , H. J. , Cameron , K. C. , Shen , J. P. , Winefield , C. S. , O’Callaghan , M. , Bowatte , S. and He , J. Z. 2010b . Ammonia-oxidizing bacteria and archaea grow under contrasting soil nitrogen conditions . FEMS Microbiol. Ecol. , 72 : 386 – 394 .
  • Di , H. J. , Cameron , K. C. , Sherlock , R. R. , Shen , J. P. , He , J. Z. and Winefield , C. S. 2010a . Nitrous oxide emissions from grazed grassland as affected by a nitrification inhibitor, dicyandiamide, and relationships with ammonia-oxidizing bacteria and archaea . J. Soil Sediment , 10 : 943 – 954 .
  • Dodsworth , J. A. , Hungate , B. A. and Hedlund , B. P. 2011 . Ammonia oxidation, denitrification and dissimilatory nitrate reduction to ammonium in two US Great Basin hot springs with abundant ammonia-oxidizing archaea . Environ. Microbiol. , 13 : 2371 – 2386 .
  • Dosta , J. , Fernandez , I. , Vazquez-Padin , J. R. , Mosquera-Corral , A. , Campos , J. L. , Mata-Alvarez , J. and Mendez , R. 2008 . Short- and long-term effects of temperature on the Anammox process . J. Hazard. Mater. , 154 : 688 – 693 .
  • Dundee , L. and Hopkins , D. W. 2001 . Different sensitivities to oxygen of nitrous oxide production by Nitrosomonas europaea and Nitrosolobus multiformis . Soil Biol. Biochem. , 33 : 1563 – 1565 .
  • Dytczak , M. A. , Londry , K. L. and Oleszkiewicz , J. A. 2008 . Activated sludge operational regime has significant impact on the type of nitrifying community and its nitrification rates . Water Res. , 42 : 2320 – 2328 .
  • Egli , K. , Fanger , U. , Alvarez , P. J. J. , Siegrist , H. , van der Meer , J. R. and Zehnder , A. J. B. 2001 . Enrichment and characterization of an anammox bacterium from a rotating biological contactor treating ammonium-rich leachate . Arch. Microbiol. , 175 : 198 – 207 .
  • Engstrom , P. , Dalsgaard , T. , Hulth , S. and Aller , R. C. 2005 . Anaerobic ammonium oxidation by nitrite (anammox): Implications for N-2 production in coastal marine sediments . Geochim. Cosmochim. Acta , 69 : 2057 – 2065 .
  • Erguder , T. H. , Boon , N. , Wittebolle , L. , Marzorati , M. and Verstraete , W. 2009 . Environmental factors shaping the ecological niches of ammonia-oxidizing archaea . FEMS Microbiol. Rev. , 33 : 855 – 869 .
  • Ettwig , K. F. , Butler , M. K. , Le Paslier , D. , Pelletier , E. , Mangenot , S. , Kuypers , M. M. M. , Schreiber , F. , Dutilh , B. E. , Zedelius , J. , de Beer , D. , Gloerich , J. , Wessels , H. , van Alen , T. , Luesken , F. , Wu , M. L. , van de Pas-Schoonen , K. T. , den Camp , H. , Janssen-Megens , E. M. , Francoijs , K. J. , Stunnenberg , H. , Weissenbach , J. , Jetten , M. S. M. and Strous , M. 2010 . Nitrite-driven anaerobic methane oxidation by oxygenic bacteria . Nature , 464 543-+
  • Farías , L. , Castro-Gonzalez , M. , Cornejo , M. , Charpentier , J. , Faundez , J. , Boontanon , N. and Yoshida , N. 2009 . Denitrification and nitrous oxide cycling within the upper oxycline of the eastern tropical South Pacific oxygen minimum zone . Limnol. Oceanogr. , 54 : 132 – 144 .
  • Farías , L. and Cornejo , M. 2007 . Effect of seasonal changes in bottom water oxygenation on sediment N oxides and N2O cycling in the coastal upwelling regime off central Chile (36.5°C) . Prog. Oceanogr. , 75 : 561 – 575 .
  • Ferguson , S. J. 1998 . Nitrogen cycle enzymology . Curr. Opin. Chem. Biol. , 2 : 182 – 193 .
  • Foesel , B. U. , Gieseke , A. , Schwermer , C. , Stief , P. , Koch , L. , Cytryn , E. , de la Torre , J. R. , van Rijn , J. , Minz , D. , Drake , H. L. and Schramm , A. 2008 . Nitrosomonas Nm143-like ammonia oxidizers and Nitrospira marina-like nitrite oxidizers dominate the nitrifier community in a marine aquaculture biofilm . FEMS Microbiol. Ecol. , 63 : 192 – 204 .
  • Francis , C. A. , Beman , J. M. and Kuypers , M. M. M. 2007 . New processes and players in the nitrogen cycle: The microbial ecology of anaerobic and archaeal ammonia oxidation . ISME J. , 1 : 19 – 27 .
  • Francis , C. A. , Roberts , K. J. , Beman , J. M. , Santoro , A. E. and Oakley , B. B. 2005 . Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean . Proc. Natl. Acad. Sci. USA , 102 : 14683 – 14688 .
  • Frijlink , M. J. , Abee , T. , Laanbroek , H. J. , Deboer , W. and Konings , W. N. 1992 . The bioenergetics of ammonia and hydroxylamine oxidation in Nitrosomonas europaea at acid and alkaline pH . Arch. Microbiol. , 157 : 194 – 199 .
  • Fuerst , J. A. 2005 . Intracellular compartmentation in planctomycetes . Annu. Rev. Microbiol. , 59 : 299 – 328 .
  • Fujii , C. , Nakagawa , T. , Onodera , Y. , Matsutani , N. , Sasada , K. , Takahashi , R. and Tokuyama , T. 2010 . Succession and community composition of ammonia-oxidizing archaea and bacteria in bulk soil of a Japanese paddy field . Soil Sci. Plant Nutr. , 56 : 212 – 219 .
  • Ganigué , R. , López , H. , Balaguer , M. D. and Colprim , J. 2007 . Partial ammonium oxidation to nitrite of high ammonium content urban land fill leachates . Water Res. , 41 : 3317 – 3326 .
  • Garrity , G. M. and Boone , D. R. 2001 . “ The Archaea and the deeply branching and phototrophic bacteria ” . In Bergey's manual of systematic bacteriology , Edited by: Boone , D. R. , Garrity , G. M. and Castenholz , R. W. Vol. 1 , New York : Springer .
  • Geraats , S. G. M. , Hooijmans , C. M. , Van Niel , E. W. J. , Robertson , L. A. , Heijnen , J. J. , Luyben , K. C. A. M. and Kuenen , J. G. 1990 . The use of a metabolically structured model in the study of growth, nitrification, and denitrification by Thiosphaera pantotropha . Biotechnol. Bioeng. , 36 : 921 – 930 .
  • Gilch , S. , Meyer , O. and Schmidt , I. 2009 . A soluble form of ammonia monooxygenase in Nitrosomonas europaea . Biological Chemistry , 390 : 863 – 873 .
  • Gilch , S. , Meyer , O. and Schmidt , I. 2010 . Electron paramagnetic studies of the copper and iron containing soluble ammonia monooxygenase from Nitrosomonas europaea . BioMetals , 23 : 613 – 622 .
  • Goreau , T. J. , Kaplan , W. A. , Wofsy , S. C. , McElroy , M. B. , Valois , F. W. and Watson , S. W. 1980 . Production of NO2 and N2O by nitrifying bacteria at reduced concentrations of oxygen . Appl. Environ. Microb. , 40 : 526 – 532 .
  • Guo , J. H. , Peng , Y. Z. , Wang , S. , Zheng , Y. , Huang , H. and Wang , Z. 2009a . Long-term effect of dissolved oxygen on partial nitrification performance and microbial community structure . Bioresour. Technol. , 100 : 2796 – 2802 .
  • Guo , J. H. , Peng , Y. Z. , Wang , S. Y. , Zheng , Y. N. , Huang , H. J. and Ge , S. J. 2009b . Effective and robust partial nitrification to nitrite by real-time aeration duration control in an SBR treating domestic wastewater . Process Biochem. , 44 : 979 – 985 .
  • Guo , J. H. , Peng , Y. Z. , Huang , H. J. , Wang , S. Y. , Ge , S. J. , Zhang , J. R. and Wang , Z. W. 2010 . Short- and long-term effects of temperature on partial nitrification in a sequencing batch reactor treating domestic wastewater . J. Hazard. Mater. , 179 : 471 – 479 .
  • Guo , J. H. , Yang , Q. , Peng , Y. Z. , Yang , A. M. and Wang , S. Y. 2007 . Biological nitrogen removal with real-time control using step-feed SBR technology . Enzyme Microb. Technol. , 40 : 1564 – 1569 .
  • Gupta , S. K. and Kshirsagar , M. 2000 . Quantitative estimation of Thiosphaera pantotropha from aerobic mixed culture . Water Res. , 34 : 3765 – 3768 .
  • Güven , D. , Dapena , A. , Kartal , B. , Schmid , M. C. , Maas , B. , van de Pas-Schoonen , K. , Sozen , S. , Mendez , R. , Op den Camp , H. J. M. , Jetten , M. S. M. , Strous , M. and Schmidt , I. 2005 . Propionate oxidation by and methanol inhibition of anaerobic ammonium-oxidizing bacteria . Appl. Environ. Microb. , 71 : 1066 – 1071 .
  • Hallam , S. J. , Konstantinidis , K. T. , Putnam , N. , Schleper , C. , Watanabe , Y. , Sugahara , J. , Preston , C. , de la Torre , J. , Richardson , P. M. and DeLong , E. F. 2006b . Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum . Proc. Natl. Acad. Sci. USA , 103 : 18296 – 18301 .
  • Hallam , S. J. , Mincer , T. J. , Schleper , C. , Preston , C. M. , Roberts , K. , Richardson , P. M. and DeLong , E. F. 2006a . Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota . PLOS Biol. , 4 : 520 – 536 .
  • Hallin , S. , Jones , C. M. , Schloter , M. and Philippot , L. 2009 . Relationship between N-cycling communities and ecosystem functioning in a 50-year-old fertilization experiment . ISME J. , 3 : 597 – 605 .
  • Hamersley , M. R. , Lavik , G. , Woebken , D. , Rattray , J. E. , Lam , P. , Hopmans , E. C. , Damste , J. S. S. , Kruger , S. , Graco , M. , Gutierrez , D. and Kuypers , M. M. M. 2007 . Anaerobic ammonium oxidation in the Peruvian oxygen minimum zone . Limnol. Oceanogr. , 52 : 923 – 933 .
  • Hansel , C. M. , Fendorf , S. , Jardine , P. M. and Francis , C. A. 2008 . Changes in bacterial and archaeal community structure and functional diversity along a geochemically variable soil profile . Appl. Environ. Microb. , 74 : 1620 – 1633 .
  • Hansman , R. L. , Griffin , S. , Watson , J. T. , Druffel , E. R. M. , Ingalls , A. E. , Pearson , A. and Aluwihare , L. I. 2009 . The radiocarbon signature of microorganisms in the mesopelagic ocean . Proc. Natl. Acad. Sci. USA , 106 : 6513 – 6518 .
  • Hashimoto , S. , Gojo , K. , Hikota , S. , Sendai , N. and Otsuki , A. 1999 . Nitrous oxide emissions from coastal waters in Tokyo Bay . Mar. Environ. Res. , 47 : 213 – 223 .
  • Hatzenpichler , R. , Lebedeva , E. V. , Spieck , E. , Stoecker , K. , Richter , A. , Daims , H. and Wagner , M. 2008 . A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring . Proc. Natl. Acad. Sci. USA , 105 : 2134 – 2139 .
  • Hayatsu , M. , Tago , K. and Saito , M. 2008 . Various players in the nitrogen cycle: Diversity and functions of the microorganisms involved in nitrification and denitrification . Soil Sci. Plant Nutr. , 54 : 33 – 45 .
  • He , J. Z. , Shen , J. P. , Zhang , L. M. , Zhu , Y. G. , Zheng , Y. M. , Xu , M. G. and Di , H. J. 2007 . Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices . Environ. Microbiol. , 9 : 2364 – 2374 .
  • Hellinga , C. , Schellen , A. , Mulder , J. W. , van Loosdrecht , M. C. M. and Heijnen , J. J. 1998 . The SHARON process: An innovative method for nitrogen removal from ammonium-rich waste water . Water Sci. Technol. , 37 : 135 – 142 .
  • Hellinga , C. , van Loosdrecht , M. C. M. and Heijnen , J. J. 1999 . Model based design of a novel process for nitrogen removal from concentrated flows . Math. Comp. Model. Dyn. , 5 : 351 – 371 .
  • Herfort , L. , Kim , J. H. , Coolen , M. J. L. , Abbas , B. , Schouten , S. , Herndl , G. J. and Damste , J. S. S. 2009 . Diversity of Archaea and detection of crenarchaeotal amoA genes in the rivers Rhine and Tet . Aquat. Microb. Ecol. , 55 : 189 – 201 .
  • Herrmann , M. , Saunders , A. M. and Schramm , A. 2008 . Archaea dominate the ammonia-oxidizing community in the rhizosphere of the freshwater macrophyte Littorella uniflora . Appl. Environ. Microb. , 74 : 3279 – 3283 .
  • Hietanen , S. and Kuparinen , J. 2008 . Seasonal and short-term variation in denitrification and anammox at a coastal station on the Gulf of Finland, Baltic Sea . Hydrobiologia , 596 : 67 – 77 .
  • Hinojosa , M. B. , Garcia-Ruiz , R. , Vinegla , B. and Carreira , J. A. 2004 . Microbiological rates and enzyme activities as indicators of functionality in soils affected by the Aznalcollar toxic spill . Soil Biol. Biochem. , 36 : 1637 – 1644 .
  • Hippen , A. , Rosenwinkel , K.-H. , Baumgarten , G. and Seyfried , C. F. 1997 . Aerobic deammonification: A new experience in the treatment of wastewaters . Water Sci. Technol. , 35 : 111 – 120 .
  • Hirsch , M. D. , Long , Z. T. and Song , B. 2011 . Anammox bacterial diversity in various aquatic ecosystems based on the detection of hydrazine oxidase genes (hzoA/hzoB) . Microb. Ecol. , 61 : 264 – 276 .
  • Holmes , A. J. , Costello , A. , Lidstrom , M. E. and Murrell , J. C. 1995 . Evidence that particulate methane monooxygenase and ammonia monooxygenase may be evolutionarily related . FEMS Microbiol. Lett. , 132 : 203 – 208 .
  • Hooper , A. B. and Terry , K. R. 1979 . Hydroxylamine oxidoreductase of Nitrosomonas production of nitric-oxide from hydroxylamine . Biochim. Biophys. Acta , 571 : 12 – 20 .
  • Hozuki , T. , Ohtsuka , T. , Arai , K. , Yoshimatsu , K. , Tanaka , S. and Fujiwara , T. 2010 . Effect of salinity on hydroxylamine oxidation in a marine ammonia-oxidizing gammaproteobacterium, Nitrosococcus oceani strain NS58: Molecular and catalytic properties of tetraheme cytochrome c-554 . Microbes. Environ. , 25 : 95 – 102 .
  • Hu , B. L. , Rush , D. , van der Biezen , E. , Zheng , P. , van Mullekom , M. , Schouten , S. , Damste , J. S. S. , Smolders , A. J. P. , Jetten , M. S. M. and Kartal , B. 2011 . New anaerobic, ammonium-oxidizing community enriched from peat soil . Appl. Environ. Microb. , 77 : 966 – 971 .
  • Hu , S. , Zeng , R. J. , Burow , L. C. , Lant , P. , Keller , J. and Yuan , Z. 2009 . Enrichment of denitrifying anaerobic methane oxidizing microorganisms . Environmental Microbiol. Rep. 1377–1384
  • Hu , T. L. and Kung , K. T. 2000 . Study of heterotrophic nitrifying bacteria from wastewater treatment systems treating acrylonitrile, butadiene and styrene resin wastewater . Water Sci. Technol. , 42 : 315 – 321 .
  • Huang , W. E. , Stoecker , K. , Griffiths , R. , Newbold , L. , Daims , H. , Whiteley , A. S. and Wagner , M. 2007 . Raman-FISH: Combining stable-isotope Raman spectroscopy and fluorescence in situ hybridization for the single cell analysis of identity and function . Environ. Microbiol. , 9 : 1878 – 1889 .
  • Humbert , S. , Tarnawski , S. , Fromin , N. , Mallet , M. P. , Aragno , M. and Zopfi , J. 2010 . Molecular detection of anammox bacteria in terrestrial ecosystems: Distribution and diversity . ISME J. , 4 : 450 – 454 .
  • Huston , W. M. , Harhangi , H. R. , Leech , A. P. , Butler , C. S. , Jetten , M. S. M. , Op den Camp , H. J. M. and Moir , J. W. B. 2007 . Expression and characterisation of a major c-type cytochrome encoded by gene kustc0563 from Kuenenia stuttgartiensis as a recombinant protein in Escherichia coli . Protein Expres. Purif , 51 : 28 – 33 .
  • Hyman , M. R. and Wood , P. M. 1985 . Suicidal inactivation and labeling of ammonia monooxygenase by acetylene . Biochem. J. , 227 : 719 – 725 .
  • Hynes , R. K. and Knowles , R. 1984 . Production of nitrous oxide by nitrosomonas-europaea effects of acetylene, pH and oxygen . Can. J. Microbiol. , 30 : 1397 – 1404 .
  • Igarashi , N. , Moriyama , H. , Fujiwara , T. , Fukumori , Y. and Tanaka , N. 1997 . The 2.8 angstrom structure of hydroxylamine oxidoreductase from a nitrifying chemoautotrophic bacterium, Nitrosomonas europaea . Nat. Struct. Biol. , 4 : 276 – 284 .
  • Inamori , Y. , Wu , X.-L. and Mizuochi , M. 1997 . N2O producing capability of Nitrosomonas europaea, Nitrobacter winogradskyi and Alcaligenes faecalis . Water Sci. Technol. , 36 : 65 – 72 .
  • Ingalls , A. E. , Shah , S. R. , Hansman , R. L. , Aluwihare , L. I. , Santos , G. M. , Druffel , E. R. M. and Pearson , A. 2006 . Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon . Proc. Natl. Acad. Sci. USA , 103 : 6442 – 6447 .
  • Intergovernmental Panel on Climate Change . 2001 . Climate change 2001: The scientific basis , New York : Cambridge University Press .
  • Isaka , K. , Date , Y. , Kimura , Y. , Sumino , T. and Tsuneda , S. 2008 . Nitrogen removal performance using anaerobic ammonium oxidation at low temperatures . FEMS Microbiol. Lett. , 282 : 32 – 38 .
  • Isaka , K. , Sumino , T. and Tsuneda , S. 2007 . High nitrogen removal performance at moderately low temperature utilizing anaerobic ammonium oxidation reactions . J. Biosci. Bioeng. , 103 : 486 – 490 .
  • Islam , A. , Chen , D. and White , R. E. 2007a . Heterotrophic and autotrophic nitrification in two acid pasture soils . Soil Biol. Biochem. , 39 : 972 – 975 .
  • Islam , A. , Chen , D. and White , R. E. 2007b . Developing a technique to quantify heterotrophic and autotrophic nitrification in acidic pasture soils . Commun. Soil Sci. Plant Anal. , 38 : 2309 – 2321 .
  • Jaeschke , A. , den Camp , H. , Harhangi , H. , Klimiuk , A. , Hopmans , E. C. , Jetten , M. S. M. , Schouten , S. and Damste , J. S. S. 2009b . 16S rRNA gene and lipid biomarker evidence for anaerobic ammonium-oxidizing bacteria (anammox) in California and Nevada hot springs . FEMS Microbiol. Ecol. , 67 : 343 – 350 .
  • Jaeschke , A. , Hopmans , E. C. , Wakeham , S. G. , Schouten , S. and Damste , J. S. S. 2007 . The presence of ladderane lipids in the oxygen minimum zone of the Arabian Sea indicates nitrogen loss through anammox . Limnol. Oceanogr. , 52 : 780 – 786 .
  • Jaeschke , A. , Lewan , M. D. , Hopmans , E. C. , Schouten , S. and Damste , J. S. S. 2008 . Thermal stability of ladderane lipids as determined by hydrous pyrolysis . Org. Geochem. , 39 : 1735 – 1741 .
  • Jaeschke , A. , Rooks , C. , Trimmer , M. , Nicholls , J. C. , Hopmans , E. C. , Schouten , S. and Damste , J. S. S. 2009a . Comparison of ladderane phospholipid and core lipids as indicators for anaerobic ammonium oxidation (anammox) in marine sediments . Geochim. Cosmochim. Acta , 73 : 2077 – 2088 .
  • Jetten , M. S. M. 2001 . New pathways for ammonia conversion in soil and aquatic systems . Plant Soil , 230 : 9 – 19 .
  • Jetten , M. S. M. , deBruijn , P. and Kuenen , J. G. 1997b . Hydroxylamine metabolism in Pseudomonas PB16: Involvement of a novel hydroxylamine oxidoreductase . Antonie Van Leeuwenhoek , 71 : 69 – 74 .
  • Jetten , M. S. M. , Logemann , S. and Muyzer , G. 1997a . Novel principles in the microbial conversion of nitrogen compounds . Antonie van Leeuwenhoek , 71 : 75 – 93 .
  • Jetten , M. S. M. , Logemann , S. , Muyzer , G. , Robertson , L. A. , de Vries , S. , van Loosdrecht , M. C. M. and Kuenen , J. G. 1997c . Novel principles in the microbial conversion of nitrogen compounds . Antonie van Leeuwenhoek , 71 : 75 – 93 .
  • Jetten , M. S. M. , Strous , M. , van de Pas-Schoonen , K. T. , Schalk , J. , van Dongen , U. , van de Graaf , A. A. , Logemann , S. , Muyzer , G. , van Loosdrecht , M. C. M. and Kuenen , J. G. 1998 . The anaerobic oxidation of ammonium . FEMS Microbiol. Rev. , 22 : 421 – 437 .
  • Jetten , M. S. M. , Strous , M. , van de Pas-Schoonen , K. T. , Schalk , J. , van Dongen , U. , van de Graaf , A. A. , Logemann , S. , Muyzer , G. , van Loosdrecht , M. C. M. and Kuenen , J. G. 1999 . The anaerobic oxidation of ammonium . FEMS Microbiol. Rev. , 22 : 421 – 437 .
  • Jetten , M. S. M. , van Niftrik , L. , Strous , M. , Kartal , B. , Keltjens , J. T. and Op den Camp , H. J. M. 2009 . Biochemistry and molecular biology of anammox bacteria . Crit. Rev. Biochem. Mol. , 44 : 65 – 84 .
  • Jetten , M. S. M. , Wagner , M. , Fuerst , J. , van Loosdrecht , M. , Kuenen , G. and Strous , M. 2001 . Microbiology and application of the anaerobic ammonium oxidation (‘anammox’) process . Curr. Opin. Biotechnol. , 12 : 283 – 288 .
  • Jia , Z. J. and Conrad , R. 2009 . Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil . Environ. Microbiol. , 11 : 1658 – 1671 .
  • Jiang , H. C. , Dong , H. L. , Yu , B. S. , Lv , G. , Deng , S. C. , Berzins , N. and Dai , M. H. 2009 . Diversity and abundance of ammonia-oxidizing Archaea and bacteria in Qinghai Lake, Northwestern China . Geomicrobiol. J. , 26 : 199 – 211 .
  • Jiang , Q. Q. and Bakken , L. R. 1999 . Nitrous oxide production and methane oxidation by different ammonia-oxidizing bacteria . Appl. Environ. Microb. , 65 : 2679 – 2684 .
  • Jiang , X. , Ma , Y. , Yuan , J. , Wright , A. L. and Li , H. 2011 . Soil particle surface electrochemical property effects on abundance of ammonia-oxidizing bacteria and ammonia-oxidizing archaea, NH4 + activity, and net nitrification in an acid soil . Soil Biol. Biochem. , 43 : 2215 – 2221 .
  • Jin , T. , Zhang , T. and Yan , Q. M. 2010 . Characterization and quantification of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in a nitrogen-removing reactor using T-RFLP and qPCR . Appl. Microbiol. Biotechnol. , 87 : 1167 – 1176 .
  • Johnsrud , S. C. 1978 . Heterotrophic nitrification in add forest soils . Ecography , 1 : 27 – 30 .
  • Joo , H. S. , Hirai , M. and Shoda , M. 2005 . Characteristics of ammonium removal by heterotrophic nitrification-aerobic denitrification by Alcaligenes faecalis No. 4 . J. Biosci. Bioeng. , 100 : 184 – 191 .
  • Joo , H. S. , Hirai , M. and Shoda , M. 2006 . Piggery wastewater treatment using Alcaligenes faecalis strain No. 4 with heterotrophic nitrification and aerobic denitrification . Water Res. , 40 : 3029 – 3036 .
  • Joo , H. S. , Hirai , M. and Shoda , M. 2007 . Improvement in ammonium removal efficiency in wastewater treatment by mixed culture of Alcaligenes faecalis no. 4 and L1 . J. Biosci. Bioeng. , 103 : 66 – 73 .
  • Joss , A. , Salzgeber , D. , Eugster , J. , König , R. , Rottermann , K. , Burger , S. , Fabijan , P. , Leumann , S. , Mohn , J. and Siegrist , H. 2009 . Full-Scale nitrogen removal from digester liquid with partial nitritation and anammox in one SBR . Environ. Sci. Technol. , 43 : 5301 – 5306 .
  • Jung , J. , Yeom , J. , Kim , J. , Han , J. , Lim , H. S. , Park , H. , Hyun , S. and Park , W. 2011 . Change in gene abundance in the nitrogen biogeochemical cycle with temperature and nitrogen addition in Antarctic soils . Res. Microbiol. , 162 : 1018 – 1026 .
  • Junier , P. , Molina , V. , Dorador , C. , Hadas , O. , Kim , O. S. , Junier , T. , Witzel , K. P. and Imhoff , J. F. 2010 . Phylogenetic and functional marker genes to study ammonia-oxidizing microorganisms (AOM) in the environment . Appl. Microbiol. Biotechnol. , 85 : 425 – 440 .
  • Könneke , M. , Bernhard , A. E. , de la Torre , J. R. , Walker , C. B. , Waterbury , J. B. and Stahl , D. A. 2005 . Isolation of an autotrophic ammonia-oxidizing marine archaeon . Nature , 437 : 543 – 546 .
  • Kalanetra , K. M. , Bano , N. and Hollibaugh , J. T. 2009 . Ammonia-oxidizing Archaea in the Arctic Ocean and Antarctic coastal waters . Environ. Microbiol. , 11 : 2434 – 2445 .
  • Kampschreur , M. J. , Picioreanu , C. , Tan , N. , Kleerebezem , R. , Jetten , M. S. M. and van Loosdrecht , M. C. M. 2007 . Unraveling the source of nitric oxide emission during nitrification . Water Environ. Res. , 79 : 2499 – 2509 .
  • Kampschreur , M. J. , Tan , N. C. G. , Kleerebezem , R. , Picioreanu , C. , Jetten , M. S. M. and Loosdrecht , M. C. M. 2008 . Effect of dynamic process conditions on nitrogen oxides emission from a nitrifying culture . Environ. Sci. Technol. , 42 : 429 – 435 .
  • Kampschreur , M. J. , Tan , N. C. G. , Picioreanu , C. , Jetten , M. S. M. , Schmidt , I. and van Loosdrecht , M. C. M. 2006 . Role of nitrogen oxides in the metabolism of ammonia-oxidizing bacteria Vol. 34 , 179 – 181 . Biochem. Soc. Trans.
  • Kampschreur , M. J. , Temmink , H. , Kleerebezem , R. , Jetten , M. S. M. and van Loosdrecht , M. C. M. 2009 . Nitrous oxide emission during wastewater treatment . Water Res. , 43 : 4093 – 4103 .
  • Karlsson , R. , Karlsson , A. , Backman , O. , Johansson , B. R. and Hulth , S. 2009 . Identification of key proteins involved in the anammox reaction . FEMS Microbiol. Lett. , 297 : 87 – 94 .
  • Kartal , B. , Koleva , M. , Arsov , R. , van der Star , W. , Jetten , M. S. M. and Strous , M. 2006 . Adaptation of a freshwater anammox population to high salinity wastewater . J. Biotechnol. , 126 : 546 – 553 .
  • Kartal , B. , Kuenen , J. G. and van Loosdrecht , M. C. M. 2010 . Sewage treatment with anammox . Science , 328 : 702 – 703 .
  • Kartal , B. , Kuypers , M. M. M. , Lavik , G. , Schalk , J. , den Camp , H. , Jetten , M. S. M. and Strous , M. 2007a . Anammox bacteria disguised as denitrifiers: nitrate reduction to dinitrogen gas via nitrite and ammonium . Environ. Microbiol. , 9 : 635 – 642 .
  • Kartal , B. , Rattray , J. , van Niftrik , L. A. , van de Vossenberg , J. , Schmid , M. C. , Webb , R. I. , Schouten , S. , Fuerst , J. A. , Damste , J. S. S. , Jetten , M. S. M. and Strous , M. 2007b . Candidatus “Anammoxoglobus propionicus” a new propionate oxidizing species of anaerobic ammonium oxidizing bacteria . Syst. Appl. Microbiol. , 30 : 39 – 49 .
  • Kartal , B. , van Niftrik , L. , Rattray , J. , de Vossenberg , J. , Schmid , M. C. , Damste , J. S. S. , Jetten , M. S. M. and Strous , M. 2008 . Candidatus ‘Brocadia fulgida’: an autofluorescent anaerobic ammonium oxidizing bacterium . FEMS Microbiol. Ecol. , 63 : 46 – 55 .
  • Kasuga , I. , Nakagaki , H. , Kurisu , F. and Furumai , H. 2010 . Abundance and diversity of ammonia-oxidizing archaea and bacteria on biological activated carbon in a pilot-scale drinking water treatment plant with different treatment processes . Water Sci. Technol. , 61 : 3070 – 3077 .
  • Kayee , P. , Sonthiphand , P. , Rongsayamanont , C. and Limpiyakorn , T. 2011 . Archaeal amoA genes outnumber bacterial amoA genes in municipal wastewater treatment plants in Bangkok . Microb. Ecol. , 62 : 776 – 788 .
  • Keller , J. , Subramaniam , K. , Gosswein , J. and Greenfield , P. F. 1997 . Nutrient removal from industrial wastewater using single tank sequencing batch reactors . Water Sci. Technol. , 35 : 137 – 144 .
  • Kesik , M. , Blagodatsky , S. , Papen , H. and Butterbach-Bahl , K. 2006 . Effect of pH, temperature and substrate on N2O, NO and CO2 production by Alcaligenes faecalis p . J. Appl. Microbiol. , 101 : 655 – 667 .
  • Kester , R. A. , deBoer , W. and Laanbroek , H. J. 1997 . Production of NO and N2O by pure cultures of nitrifying and denitrifying bacteria during changes in aeration . Appl. Environ. Microb. , 63 : 3872 – 3877 .
  • Killham , K. 1987 . A new perfusion system for measurement and characterization of potential rates of soil nitrification . Plant Soil , 97 : 267 – 272 .
  • Kim , H. J. , Zatsman , A. , Upadhyay , A. K. , Whittaker , M. , Bergmann , D. , Hendrich , M. P. and Hooper , A. B. 2008a . Membrane tetraheme cytochrome c(m552) of the ammonia-oxidizing Nitrosomonas europaea: A ubiquinone reductase . Biochemistry–U.S. , 47 : 6539 – 6551 .
  • Kim , J.-H. , Guo , X. and Park , H.-S. 2008b . Comparison study of the effects of temperature and free ammonia concentration on nitrification and nitrite accumulation . Process Biochem. , 43 : 154 – 160 .
  • Kim , J. K. , Park , K. J. , Cho , K. S. , Nam , S. W. , Park , T. J. and Bajpai , R. 2005 . Aerobic nitrification-denitrification by heterotrophic Bacillus strains . Bioresour. Technol. , 96 : 1897 – 1906 .
  • Kim , M. , Jeong , S. Y. , Yoon , S. J. , Cho , S. J. , Kim , Y. H. , Kim , M. J. , Ryu , E. Y. and Lee , S. J. 2008c . Aerobic denitrification of Pseudomonas putida AD-21 at different C/N ratios . J. Biosci. Bioeng. , 106 : 498 – 502 .
  • Kirkpatrick , J. , Oakley , B. , Fuchsman , C. , Srinivasan , S. , Staley , J. T. and Murray , J. W. 2006 . Diversity and distribution of Planctomycetes and related bacteria in the suboxic zone of the Black Sea . Appl. Environ. Microb. , 72 : 3079 – 3083 .
  • Kleineidam , K. , Kosmrlj , K. , Kublik , S. , Palmer , I. , Pfab , H. , Ruser , R. , Fiedler , S. and Schloter , M. 2011 . Influence of the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) on ammonia-oxidizing bacteria and archaea in rhizosphere and bulk soil . Chemosphere , 84 : 182 – 186 .
  • Klemedtsson , L. , Svensson , B. H. and Rosswall , T. 1988 . A method of selective inhibition to distinguish between nitrification and denitrification as sources of nitrous oxide in soil . Biol. Fert. Soils , 6 : 112 – 119 .
  • Klotz , M. G. , Alzerreca , J. and Norton , J. M. 1997 . A gene encoding a membrane protein exists upstream of the amoA/amoB genes in ammonia oxidizing bacteria: A third member of the amo operon? . FEMS Microbiol. Lett. , 150 : 65 – 73 .
  • Koops , H. P. and Pommerening-Röser , A. 2001 . Distribution and ecophysiology of the nitrifying bacteria emphasizing cultured species . FEMS Microbiol. Ecol. , 37 : 1 – 9 .
  • Kowalchuk , G. A. and Stephen , J. R. 2001 . Ammonia-oxidizing bacteria: A model for molecular microbial ecology . Annu. Rev. Microbiol. , 55 : 485 – 529 .
  • Kowalchuk , G. A. , Stephen , J. R. , DeBoer , W. , Prosser , J. I. , Embley , T. M. and Woldendorp , J. W. 1997 . Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments . Appl. Environ. Microb. , 63 : 1489 – 1497 .
  • Kristina , S. , Andreas , F. , Sven , L. , Anja , K. , Holger , H. , Soren , T.-B. , Shilpi , S. , Berndt-Michael , W. , Michael , M. , Kornelia , S. , Jean Charles , M. , Wulf , A. , Martin , K. , Michael , S. and Christa , S. 2009 . Dynamics and functional relevance of ammonia-oxidizing archaea in two agricultural soils . Environ. Microbiol. , 11 : 446 – 456 .
  • Kuenen , J. G. 2008 . Anammox bacteria: From discovery to application . Nat. Rev. Microbiol. , 6 : 320 – 326 .
  • Kuenen , J. G. and Robertson , L. A. 1994 . Combined nitrification-denitrification processes . FEMS Microbiol. Rev. , 15 : 109 – 117 .
  • Kuypers , M. M. M. , Lavik , G. , Woebken , D. , Schmid , M. , Fuchs , B. M. , Amann , R. , Jorgensen , B. B. and Jetten , M. S. M. 2005 . Massive nitrogen loss from the Benguela upwelling system through anaerobic ammonium oxidation . Proc. Natl. Acad. Sci. USA , 102 : 6478 – 6483 .
  • Kuypers , M. M. M. , Sliekers , A. O. , Lavik , G. , Schmid , M. , Jorgensen , B. B. , Kuenen , J. G. , Damste , J. S. S. , Strous , M. and Jetten , M. S. M. 2003 . Anaerobic ammonium oxidation by anammox bacteria in the Black Sea . Nature , 422 : 608 – 611 .
  • Laanbroek , H. J. , Bodelier , P. L. E. and Gerards , S. 1994 . Oxygen consumption kinetics of Nitrosomonas europaea and Nitrobacter hamburgensis grown in mixed continuous cultures at different oxygen concentrations . Arch. Microbiol. , 161 : 156 – 162 .
  • Laanbroek , H. J. and Gerards , S. 1993 . Competition for limiting amounts of oxygen between Nitrosomonas europaea and Nitrobacter winogradskyi grown in mixed continuous cultures . Arch. Microbiol. , 159 : 453 – 459 .
  • Lam , P. , Jensen , M. M. , Lavik , G. , McGinnis , D. F. , Muller , B. , Schubert , C. J. , Amann , R. , Thamdrup , B. and Kuypers , M. M. M. 2007 . Linking crenarchaeal and bacterial nitrification to anammox in the Black Sea . Proc. Natl. Acad. Sci. USA , 104 : 7104 – 7109 .
  • Lam , P. , Lavik , G. , Jensen , M. M. , van de Vossenberg , J. , Schmid , M. , Woebken , D. , Dimitri , G. , Amann , R. , Jetten , M. S. M. and Kuypers , M. M. M. 2009 . Revising the nitrogen cycle in the Peruvian oxygen minimum zone . Proc. Natl. Acad. Sci. USA , 106 : 4752 – 4757 .
  • Lang , E. and Jagnow , G. 1986 . Fungi of a forest soil nitrifying at low pH values . FEMS Microbiol. Lett. , 38 : 257 – 265 .
  • Laughlin , R. J. , Rütting , T. , Müller , C. , Watson , C. J. and Stevens , R. J. 2009 . Effect of acetate on soil respiration, N2O emissions and gross N transformations related to fungi and bacteria in a grassland soil . Appl. Soil Ecol. , 42 : 25 – 30 .
  • Lehtovirta-Morley , L. E. , Stoecker , K. , Vilcinskas , A. , Prosser , J. I. and Nicol , G. W. 2011 . Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil . Proc. Natl. Acad. Sci. USA , 108 : 15892 – 15897 .
  • Leininger , S. , Urich , T. , Schloter , M. , Schwark , L. , Qi , J. , Nicol , G. W. , Prosser , J. I. , Schuster , S. C. and Schleper , C. 2006 . Archaea predominate among ammonia-oxidizing prokaryotes in soils . Nature , 442 : 806 – 809 .
  • Li , M. , Ford , T. , Li , X. and Gu , J.-D. 2011 . Cytochrome cd1-containing nitrite reductase encoding gene nirS as a new functional biomarker for detection of anaerobic ammonium oxidizing (Anammox) bacteria . Environ. Sci. Technol. , 45 : 3547 – 3553 .
  • Li , M. , Hong , Y. , Klotz , M. G. and Gu , J.-D. 2010 . A comparison of primer sets for detecting 16S rRNA and hydrazine oxidoreductase genes of anaerobic ammonium-oxidizing bacteria in marine sediments . Appl. Microbiol. Biotechnol. , 86 : 781 – 790 .
  • Li , T. , Wu , T. D. , Mazeas , L. , Toffin , L. , Guerquin-Kern , J. L. , Leblon , G. and Bouchez , T. 2008 . Simultaneous analysis of microbial identity and function using NanoSIMS . Environ. Microbiol. , 10 : 580 – 588 .
  • Li , T. W. , Peng , Y. Z. , Wang , Y. Y. , Zhu , G. B. , Chi , W. Q. and Gu , G. W. 2003 . Experimental study on sequencing batch biofilm reactor with biological filtration (SBBR-BF) for wastewater treatment . Water Sci. Technol. , 48 : 299 – 307 .
  • Li , X. F. , Zhu , Y. G. , Cavagnaro , T. R. , Chen , M. M. , Sun , J. W. , Chen , X. P. and Qiao , M. 2009 . Do ammonia-oxidizing archaea respond to soil Cu contamination similarly asammonia-oxidizing bacteria? . Plant Soil , 324 : 209 – 217 .
  • Limpiyakorn , T. , Kurisu , F. , Sakamoto , Y. and Yagi , O. 2007 . Effects of ammonium and nitrite on communities and populations of ammonia-oxidizing bacteria in laboratory-scale continuous-flow reactors . FEMS Microbiol. Ecol. , 60 : 501 – 512 .
  • Limpiyakorn , T. , Shinohara , Y. , Kurisu , F. and Yagi , O. 2005 . Communities of ammonia-oxidizing bacteria in activated sludge of various sewage treatment plants in Tokyo . FEMS Microbiol. Ecol. , 54 : 205 – 217 .
  • Limpiyakorn , T. , Sonthiphand , P. , Rongsayamanont , C. and Polprasert , C. 2011 . Abundance of amoA genes of ammonia-oxidizing archaea and bacteria in activated sludge of full-scale wastewater treatment plants . Bioresour. Technol. , 102 : 3694 – 3701 .
  • Lindsay , E. A. , Colloff , M. J. , Gibb , N. L. and Wakelin , S. A. 2010 . The abundance of microbial functional genes in grassy woodlands is influenced more by soil nutrient enrichment than by recent weed invasion or livestock exclusion . Appl. Environ. Microb. , 76 : 5547 – 5555 .
  • Lindsay , M. R. , Webb , R. I. , Strous , M. , Jetten , M. S. , Butler , M. K. , Forde , R. J. and Fuerst , J. A. 2001 . Cell compartmentalisation in planctomycetes: Novel types of structural organisation for the bacterial cell . Arch. Microbiol. , 175 : 413 – 429 .
  • Liu , S. T. , Yang , F. L. , Gong , Z. , Meng , F. G. , Chen , H. H. , Xue , Y. and Furukawa , K. J. 2008b . Application of anaerobic ammonium-oxidizing consortium to achieve completely autotrophic ammonium and sulfate removal . Bioresour. Technol. , 99 : 6817 – 6825 .
  • Liu , S. T. , Yang , F. L. , Gong , Z. and Su , Z. C. 2008a . Assessment of the positive effect of salinity on the nitrogen removal performance and microbial composition during the start-up of CANON process . Appl. Microbiol. Biotechnol. , 80 : 339 – 348 .
  • Liu , X. H. , Peng , Y. Z. , Ma , T. , Shang , H. L. and Wu , C. Y. 2007 . Influence of nitrification type on N2O production in nitrogen removal treating domestic wastewater . China Environ. Sci. , 27 : 633 – 637 .
  • Liu , X. H. , Peng , Y. , Wu , C. Y. , Akio , T. and Peng , Y. Z. 2008c . Nitrous oxide production during nitrogen removal from domestic wastewater in lab-scale sequencing batch reactor . J. Environ. Sci.–China. , 20 : 641 – 645 .
  • Liu , Y. R. , Zheng , Y. M. , Shen , J. P. , Zhang , L. M. and He , J. Z. 2010 . Effects of mercury on the activity and community composition of soil ammonia oxidizers . Environ. Sci. Pollut. Res. , 17 : 1237 – 1244 .
  • Liu , Z. P. , Wu , J. F. , Liu , Z. H. and Liu , S. J. 2006 . Pseudonocardia ammonioxydans sp nov., isolated from coastal sediment . Int. J. System. Evolut. Microbiol. , 56 : 555 – 558 .
  • Luesken , F. A. , Sanchez , J. , van Alen , T. A. , Sanabria , J. , Op den Camp , H. J. M. , Jetten , M. S. M. and Kartal , B. 2011 . Simultaneous nitrite-dependent anaerobic methane and ammonium oxidation processes . Appl. Environ. Microbiol. , 77 : 6802 – 6807 .
  • Ma , Y. , Wang , L. and Qian , L. 2008 . Community structure of β-Proteobacterial ammonia-oxidizing bacteria in prawn farm sediment . Prog. Nat. Sci. , 18 : 679 – 684 .
  • Magalhães , C. M. , Machado , A. , Matos , P. and Bordalo , A. A. 2011 . Impact of copper on the diversity, abundance and transcription of nitrite and nitrous oxide reductase genes in an urban European estuary . FEMS Microbiol. Ecol. , 77 : 274 – 284 .
  • Martens-Habbena , W. , Berube , P. M. , Urakawa , H. , de la Torre , J. R. and Stahl , D. A. 2009 . Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and bacteria . Nature , 461 : 976 – 979 .
  • Matsuzaka , E. , Nomura , N. , Nakajima-Kambe , T. , Okada , N. and Nakahara , T. 2003 . A simple screening procedure for heterotrophic nitrifying bacteria with oxygen-tolerant denitrification activity . J. Biosci. Bioeng. , 95 : 409 – 411 .
  • McLain , J. E. T. and Martens , D. A. 2006 . N2O production by heterotrophic N transformations in a semiarid soil . Appl. Soil Ecol. , 32 : 253 – 263 .
  • McTavish , H. , Fuchs , J. A. and Hooper , A. B. 1993a . Sequence of the gene coding for ammonia monooxygenase in Nitrosomonas europaea . J. Bacteriol. , 175 : 2436 – 2444 .
  • McTavish , H. , Laquier , F. , Arciero , D. , Logan , M. , Mundfrom , G. , Fuchs , J. and Hooper , A. B. 1993b . Multiple copies of genes-coding for electron-transport proteins in the bacterium Nitrosomonas-europaea . J. Bacteriol. , 175 : 2445 – 2447 .
  • Mertens , J. , Broos , K. , Wakelin , S. A. , Kowalchuk , G. A. , Springael , D. and Smolders , E. 2009 . Bacteria, not archaea, restore nitrification in a zinc-contaminated soil . ISME J. , 3 : 916 – 923 .
  • Mevel , G. and Prieur , D. 1998 . Thermophilic heterotrophic nitrifiers isolated from Mid-Atlantic Ridge deep-sea hydrothermal vents . Can. J. Microbiol. , 44 : 723 – 733 .
  • Mevel , G. and Prieur , D. 2000 . Heterotrophic nitrification by a thermophilic Bacillus species as influenced by different culture conditions . Can. J. Microbiol. , 46 : 465 – 473 .
  • Meyer , R. L. , Risgaard-Petersen , N. and Allen , D. E. 2005 . Correlation between anammox activity and microscale distribution of nitrite in a subtropical mangrove sediment . Appl. Environ. Microb. , 71 : 6142 – 6149 .
  • Michaud , L. , Blancheton , J. P. , Bruni , V. and Piedrahita , R. 2006 . Effect of particulate organic carbon on heterotrophic bacterial populations and nitrification efficiency in biological filters . Aquacult. Eng. , 34 : 224 – 233 .
  • Mincer , T. J. , Church , M. J. , Taylor , L. T. , Preston , C. , Kar , D. M. and DeLong , E. F. 2007 . Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre . Environ. Microbiol. , 9 : 1162 – 1175 .
  • Mkhabela , M. S. , Gordon , R. , Burton , D. , Madani , A. and Hart , W. 2006 . Effect of lime, dicyandiamide and soil water content on ammonia and nitrous oxide emissions following application of liquid hog manure to a marshland soil . Plant Soil , 284 : 351 – 361 .
  • Moir , J. W. B. , Crossman , L. C. , Spiro , S. and Richardson , D. J. 1996b . The purification of ammonia monooxygenase from Paracoccus denitrficans . FEBS Lett. , 387 : 71 – 74 .
  • Moir , J. W. B. , Wehrfritz , J. M. , Spiro , S. and Richardson , D. J. 1996a . The biochemical characterization of a novel non-haem-iron hydroxylamine oxidase from Paracoccus denitrificans GB17 . Biochem. J. , 319 : 823 – 827 .
  • Molina , V. , Belmar , L. and Ulloa , O. 2010 . High diversity of ammonia-oxidizing archaea in permanent and seasonal oxygen-deficient waters of the eastern South Pacific . Environ. Microbiol. , 12 : 2450 – 2465 .
  • Morimoto , S. , Hayatsu , M. , Hoshino , Y. T. , Nagaoka , K. , Yamazaki , M. , Karasawa , T. , Takenaka , M. and Akiyama , H. 2011 . Quantitative analyses of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in fields with different soil types . Microbes. Environ. , 26 : 248 – 253 .
  • Morley , N. and Baggs , E. M. 2010 . Carbon and oxygen controls on N2O and N2 production during nitrate reduction . Soil Biol. Biochem. , 42 : 1864 – 1871 .
  • Mosier , A. C. and Francis , C. A. 2008 . Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary . Environ. Microbiol. , 10 : 3002 – 3016 .
  • Mulder , A. , van de Graaf , A. A. , Robertson , L. A. and Kuenen , J. G. 1995 . Anaerobic ammonium oxidation discovered in a denitrifying fluidized bed reactor . FEMS Microbiol. Ecol. , 16 : 177 – 183 .
  • Nakagawa , T. , Mori , K. , Kato , C. , Takahashi , R. and Tokuyama , T. 2007 . Distribution of cold-adapted ammonia-oxidizing microorganisms in the deep-ocean of the northeastern Japan Sea . Microbes. Environ. , 22 : 365 – 372 .
  • Nemergut , D. R. and Schmidt , S. K. 2002 . Disruption of narH, narJ, and moaE inhibits heterotrophic nitrification in Pseudomonas strain M19 . Appl. Environ. Microb. , 68 : 6462 – 6465 .
  • Nevison , C. , Butler , J. H. and Elkins , J. W. 2003 . Global distribution of N2O and the Delta N2O-AOU yield in the subsurface ocean . Global Biogeochem. Cycles , : 17
  • Nevison , C. D. , Lueker , T. J. and Weiss , R. F. 2004 . Quantifying the nitrous oxide source from coastal upwelling . Global Biogeochem. Cycles , : 18
  • Nicholls , J. C. and Trimmer , M. 2009 . Widespread occurrence of the anammox reaction in estuarine sediments . Aquat. Microb. Ecol. , 55 : 105 – 113 .
  • Nicol , G. W. , Leininger , S. , Schleper , C. and Prosser , J. I. 2008 . The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria . Environ. Microbiol. , 10 : 2966 – 2978 .
  • Nicolaisen , M. H. and Ramsing , N. B. 2002 . Denaturing gradient gel electrophoresis (DGGE) approaches to study the diversity of ammonia-oxidizing bacteria . J. Microbiol. Meth. , 50 : 189 – 203 .
  • Nishio , T. , Yoshikura , T. , Mishima , H. , Inouye , Z. and Itoh , H. 1998 . Conditions for nitrification and denitrification by an immobilized heterotrophic nitrifying bacterium Alcaligenes faecalis OKK17 . J. Ferment. Bioeng. , 86 : 351 – 356 .
  • Nold , S. C. , Zhou , J. Z. , Devol , A. H. and Tiedje , J. M. 2000 . Pacific northwest marine sediments contain ammonia-oxidizing bacteria in the beta subdivision of the Proteobacteria . Appl. Environ. Microb. , 66 : 4532 – 4535 .
  • O’Mullan , G. D. and Ward , B. B. 2005 . Relationship of temporal and spatial variabilities of ammonia-oxidizing bacteria to nitrification rates in Monterey Bay, California . Appl. Environ. Microb. , 71 : 697 – 705 .
  • Odu , C. T. I. and Adeoye , K. B. 1970 . Heterotrophic nitrification in soils-a preliminary investigation . Soil Biol. Biochem. , 2 : 41 – 45 .
  • Offre , P. , Prosser , J. I. and Nicol , G. W. 2009 . Growth of ammonia-oxidizing archaea in soil microcosms is inhibited by acetylene . FEMS Microbiol. Ecol. , 70 : 99 – 108 .
  • Onodera , Y. , Nakagawa , T. , Takahashi , R. and Tokuyama , T. 2010 . Seasonal change in vertical distribution of ammonia-oxidizing archaea and bacteria and their nitrification in temperate forest soil . Microbes. Environ. , 25 : 28 – 35 .
  • Otte , S. , Grobben , N. G. , Robertson , L. A. , Jetten , M. S. M. and Kuenen , J. G. 1996 . Nitrous oxide production by Alcaligenes faecalis under transient and dynamic aerobic and anaerobic conditions . Appl. Environ. Microb. , 62 : 2421 – 2426 .
  • Painter , H. A. 1970 . A review of literature on inorganic nitrogen metabolism in microorganisms . Water Res. , 4 : 393 – 450 .
  • Park , H. D. , Wells , G. F. , Bae , H. , Criddle , C. S. and Francis , C. A. 2006 . Occurrence of ammonia-oxidizing archaea in wastewater treatment plant bioreactors . Appl. Environ. Microb. , 72 : 5643 – 5647 .
  • Park , S. and Bae , W. 2009 . Modeling kinetics of ammonium oxidation and nitrite oxidation under simultaneous inhibition by free ammonia and free nitrous acid . Process Biochem. , 44 : 631 – 640 .
  • Park , S. J. , Park , B. J. and Rhee , S. K. 2008 . Comparative analysis of archaeal 16S rRNA and amoA genes to estimate the abundance and diversity of ammonia-oxidizing archaea in marine sediments . Extremophiles , 12 : 605 – 615 .
  • Patureau , D. , Delgenes , J. , Moletta , R. and Bernet , N. 2000 . Effect of dissolved oxygen and carbon-nitrogen loads on denitrification by an aerobic consortium . Appl. Microbiol. Biotechnol. , 54 : 535 – 542 .
  • Paulmier , A. , Ruiz-Pino , D. and Garcon , V. 2008 . The oxygen minimum zone (OMZ) off Chile as intense source of CO2 and N2O . Continental Shelf Res. , 28 : 2746 – 2756 .
  • Pearson , A. R. , Elmore , B. O. , Yang , C. , Ferrara , J. D. , Hooper , A. B. and Wilmot , C. M. 2007 . The crystal structure of cytochrome P460 of Nitrosomonas europaea reveals a novel cytochrome fold and heme-protein cross-link . Biochemistry , 46 : 8340 – 8349 .
  • Pedersen , H. , Dunkin , K. and Firestone , M. 1999 . The relative importance of autotrophic and heterotrophic nitrification in a conifer forest soil as measured by 15N tracer and pool dilution techniques . Biogeochemistry , 44 : 135 – 150 .
  • Peng , Y. Z. , Chen , Y. , Peng , C. Y. , Liu , M. , Wang , S. Y. , Song , X. Q. and Cui , Y. W. 2004b . Nitrite accumulation by aeration controlled in sequencing batch reactors treating domestic wastewater . Water Sci. Technol. , 50 : 35 – 43 .
  • Peng , Y. Z. , Li , Y. Z. , Peng , C. Y. and Wang , S. Y. 2004a . Nitrogen removal from pharmaceutical manufacturing wastewater with high concentration of ammonia and free ammonia via partial nitrification and denitrification . Water Sci. Technol. , 50 : 25 – 30 .
  • Peng , Y. Z. , Zhang , S. J. , Zeng , W. , Zheng , S. W. , Mino , T. and Satoh , H. 2008 . Organic removal by denitritation and methanogenesis and nitrogen removal by nitritation from landfill leachate . Water Res. , 42 : 883 – 892 .
  • Peng , Y. Z. and Zhu , G. B. 2006 . Biological nitrogen removal with nitrification and denitrification via nitrite pathway . Appl. Microbiol. Biotechnol. , 73 : 15 – 26 .
  • Pennington , P. I. and Ellis , R. C. 1993 . Autotrophic and heterotrophic nitrification in acidic forest and native grassland soils . Soil Biol. Biochem. , 25 : 1399 – 1408 .
  • Penton , C. R. , Devol , A. H. and Tiedje , J. M. 2006 . Molecular evidence for the broad distribution of anaerobic ammonium-oxidizing bacteria in freshwater and marine sediments . Appl. Environ. Microb. , 72 : 6829 – 6832 .
  • Pommerening-Röser , A. and Koops , H. P. 2005 . Environmental pH as an important factor for the distribution of urease positive ammonia-oxidizing bacteria . Microbiol. Res. , 160 : 27 – 35 .
  • Poth , M. and Focht , D. D. 1985 . 15N kinetic analysis of N2O production by Nitrosomonas europaea: An examination of nitrifier denitrification . Appl. Environ. Microb. , 49 : 1134 – 1141 .
  • Quan , Z. X. , Rhee , S. K. , Zuo , J. E. , Yang , Y. , Bae , J. W. , Park , J. R. , Lee , S. T. and Park , Y. H. 2008 . Diversity of ammonium-oxidizing bacteria in a granular sludge anaerobic ammonium-oxidizing (anammox) reactor . Environ. Microbiol. , 10 : 3130 – 3139 .
  • Radniecki , T. S. , Semprini , L. and Dolan , M. E. 2009 . Expression of merA, amoA and hao in continuously cultured Nitrosomonas europaea cells exposed to zinc chloride additions . Biotechnol. Bioeng. , 102 : 546 – 553 .
  • Raghoebarsing , A. A. , Pol , A. , van de Pas-Schoonen , K. T. , Smolders , A. J. P. , Ettwig , K. F. , Rijpstra , W. I. C. , Schouten , S. , Damste , J. S. S. , Op den Camp , H. J. M. , Jetten , M. S. M. and Strous , M. 2006 . A microbial consortium couples anaerobic methane oxidation to denitrification . Nature , 440 : 918 – 921 .
  • Rattray , J. E. , Strous , M. , den Camp , H. , Schouten , S. , Jetten , M. S. and Damste , J. S. S. 2009 . A comparative genomics study of genetic products potentially encoding ladderane lipid biosynthesis . Biol. Direct , 4 : 16
  • Rattray , J. E. , van de Vossenberg , J. , Hopmans , E. C. , Kartal , B. , van Niftrik , L. , Rijpstra , W. I. C. , Strous , M. , Jetten , M. S. M. , Schouten , S. and Damste , J. S. S. 2008 . Ladderane lipid distribution in four genera of anammox bacteria . Arch. Microbiol. , 190 : 51 – 66 .
  • Reed , D. W. , Smith , J. M. , Francis , C. A. and Fujita , Y. 2010 . Response of ammonia-oxidizing bacterial and archaeal populations to organic nitrogen amendments in low-nutrient groundwater . Appl. Environ. Microbiol. , 76 : 2517 – 2523 .
  • Reigstad , L. J. , Richter , A. , Daims , H. , Urich , T. , Schwark , L. and Schleper , C. 2008 . Nitrification in terrestrial hot springs of Iceland and Kamchatka . FEMS Microbiol. Ecol. , 64 : 167 – 174 .
  • Rezic , T. , Santek , B. , Novak , S. and Maric , V. 2006 . Comparison between the heterotrophic cultivation of Paracoccus denitrificans in continuous stirred tank reactor and horizontal rotating tubular bioreactor . Process Biochem. , 41 : 2024 – 2028 .
  • Rich , J. J. , Dale , O. R. , Song , B. and Ward , B. B. 2008 . Anaerobic ammonium oxidation (Anammox) in Chesapeake Bay sediments . Microb. Ecol. , 55 : 311 – 320 .
  • Risgaard-Petersen , N. , Meyer , R. L. , Schmid , M. , Jetten , M. S. M. , Enrich-Prast , A. , Rysgaard , S. and Revsbech , N. P. 2004 . Anaerobic ammonium oxidation in an estuarine sediment . Aquat. Microb. Ecol. , 36 : 293 – 304 .
  • Risgaard-Petersen , N. , Nielsen , L. P. , Rysgaard , S. , Dalsgaard , T. and Meyer , R. L. 2003 . Application of the isotope pairing technique in sediments where anammox and denitrification coexist . Limnol. Oceanogr. , 1 : 63 – 73 .
  • Robertson , G. P. and Tiedje , J. M. 1987 . Nitrous oxide sources in aerobic soils: Nitrification, denitrification and other biological processes . Soil Biol. Biochem. , 19 : 187 – 193 .
  • Robertson , L. A. and Kuenen , J. G. 1988 . Heterotrophic nitrification in Thiosphaera pantotropha: Oxygen uptake and enzyme studies . J. Gen. Microbiol. , 134 : 857 – 863 .
  • Robertson , L. A. and Kuenen , J. G. 1990 . Combined heterotrophic nitrification and aerobic denitrification in Thiosphaera pantotropha and other bacteria . Antonie van Leeuwenhoek , 57 : 139 – 152 .
  • Robertson , L. A. , van Niel , E. W. J. , Torremans , R. A. M. and Kuenen , J. G. 1988 . Simultaneous nitrification and denitrification in aerobic chemostat cultures of Thiosphaera pantotropha . Appl. Environ. Microbiol. , 54 : 2812 – 2818 .
  • Rotthauwe , J. H. , Deboer , W. and Liesack , W. 1995 . Comparative analysis of gene-sequences encoding ammonia monooxygenase of Nitrosospira sp AHB1 and Nitrosolobus multiformis C-71 . FEMS Microbiol. Lett. , 133 : 131 – 135 .
  • Rotthauwe , J. H. , Witzel , K. P. and Liesack , W. 1997 . The ammonia monooxygenase structural gene amoA as a functional marker: Molecular fine-scale analysis of natural ammonia-oxidizing populations . Appl. Environ. Microb. , 63 : 4704 – 4712 .
  • Rowan , A. K. , Snape , J. R. , Fearnside , D. , Barer , M. R. , Curtis , T. P. and Head , I. M. 2003 . Composition and diversity of ammonia-oxidising bacterial communities in wastewater treatment reactors of different designtreating identical wastewater . FEMS Microbiol. Ecol. , 43 : 195 – 206 .
  • Ruiz , G. , Jeison , D. , Rubilar , O. , Ciudad , G. and Chamy , R. 2006 . Nitrification-denitrification via nitrite accumulation for nitrogen removal from wastewaters . Bioresour. Technol. , 97 : 330 – 335 .
  • Ruyters , S. , Mertens , J. , Springael , D. and Smolders , E. 2010 . Stimulated activity of the soil nitrifying community accelerates community adaptation to Zn stress . Soil Biol. Biochem. , 42 : 766 – 772 .
  • Rysgaard , S. and Glud , R. N. 2004 . Anaerobic N-2 production in Arctic sea ice . Limnol. Oceanogr. , 49 : 86 – 94 .
  • Rysgaard , S. , Glud , R. N. , Risgaard-Petersen , N. and Dalsgaard , T. 2004 . Denitrification and anammox activity in Arctic marine sediments . Limnol. Oceanogr. , 49 : 1493 – 1502 .
  • Sahan , E. and Muyzer , G. 2008 . Diversity and spatio-temporal distribution of ammonia-oxidizing Archaea and Bacteria in sediments of the Westerschelde estuary . FEMS Microbiol. Ecol. , 64 : 175 – 186 .
  • Santoro , A. E. , Buchwald , C. , McIlvin , M. R. and Casciotti , K. L. 2011 . Isotopic signature of N2O produced by marine ammonia-oxidizing archaea . Science , 333 : 1282 – 1285 .
  • Santoro , A. E. , Casciotti , K. L. and Francis , C. A. 2010 . Activity, abundance and diversity of nitrifying archaea and bacteria in the central California Current . Environ. Microbiol. , 12 : 1989 – 2006 .
  • Santoro , A. E. , Francis , C. A. , de Sieyes , N. R. and Boehm , A. B. 2008 . Shifts in the relative abundance of ammonia-oxidizing bacteria and archaea across physicochemical gradients in a subterranean estuary . Environ. Microbiol. , 10 : 1068 – 1079 .
  • Schalk-Otte , S. , Seviour , R. J. , Kuenen , J. G. and Jetten , M. S. M. 2000 . Nitrous oxide (N2O) production by Alcaligenes faecalis during feast and famine regimes . Water Res. , 34 : 2080 – 2088 .
  • Schalk , J. , de Vries , S. , Kuenen , J. G. and Jetten , M. S. M. 2000 . Involvement of a novel hydroxylamine oxidoreductase in anaerobic ammonium oxidation . Biochemistry–U.S. , 39 : 5405 – 5412 .
  • Schauss , K. , Focks , A. , Leininger , S. , Kotzerke , A. , Heuer , H. , Thiele-Bruhn , S. , Sharma , S. , Wilke , B. M. , Matthies , M. , Smalla , K. , Munch , J. C. , Amelung , W. , Kaupenjohann , M. , Schloter , M. and Schleper , C. 2009 . Dynamics and functional relevance of ammonia-oxidizing archaea in two agricultural soils . Environ. Microbiol. , 11 : 446 – 456 .
  • Schimel , J. P. , Firestone , M. K. and Killham , K. S. 1984 . Identification of heterotrophic nitrification in a Sierran forest soi . Appl. Environ. Microb. , 48 : 802 – 804 .
  • Schleper , C. , Jurgens , G. and Jonuscheit , M. 2005 . Genomic studies of uncultivated archaea . Nat. Rev. Microbiol. , 3 : 479 – 488 .
  • Schmid , M. , Schmitz-Esser , S. , Jetten , M. and Wagner , M. 2001 . 16S-23S rDNA intergenic spacer and 23S rDNA of anaerobic ammonium-oxidizing bacteria: Implications for phylogeny and in situ detection . Environ. Microbiol. , 3 : 450 – 459 .
  • Schmid , M. , Twachtmann , U. , Klein , M. , Strous , M. , Juretschko , S. , Jetten , M. , Metzger , J. W. , Schleifer , K. H. and Wagner , M. 2000 . Molecular evidence for genus level diversity of bacteria capable of catalyzing anaerobic ammonium oxidation . Syst. Appl. Microbiol. , 23 : 93 – 106 .
  • Schmid , M. , Walsh , K. , Webb , R. , Rijpstra , W. I. C. , van de Pas-Schoonen , K. , Verbruggen , M. J. , Hill , T. , Moffett , B. , Fuerst , J. , Schouten , S. , Damste , J. S. S. , Harris , J. , Shaw , P. , Jetten , M. and Strous , M. 2003 . Candidatus “Scalindua brodae”, sp nov., Candidatus “Scalindua wagneri”, sp nov., two new species of anaerobic ammonium oxidizing bacteria . Syst. Appl. Microbiol. , 26 : 529 – 538 .
  • Schmid , M. C. , Risgaard-Petersen , N. , van de Vossenberg , J. , Kuypers , M. M. M. , Lavik , G. , Petersen , J. , Hulth , S. , Thamdrup , B. , Canfield , D. , Dalsgaard , T. , Rysgaard , S. , Sejr , M. K. , Strous , M. , den Camp , H. and Jetten , M. S. M. 2007 . Anaerobic ammonium-oxidizing bacteria in marine environments: Widespread occurrence but low diversity . Environ. Microbiol. , 9 : 1476 – 1484 .
  • Schmidt , I. and Bock , E. 1997 . Anaerobic ammonia oxidation with nitrogen dioxide by Nitrosomonas eutropha . Arch. Microbiol. , 167 : 106 – 111 .
  • Schmidt , I. and Bock , E. 1998 . Anaerobic ammonia oxidation by cell-free extracts of Nitrosomonas eutropha . Antonie Van Leeuwenhoek , 73 : 271 – 278 .
  • Schmidt , I. , Sliekers , O. , Schmid , M. , Bock , E. , Fuerst , J. , Kuenen , J. G. , Jetten , M. S. M. and Strous , M. 2003 . New concepts of microbial treatment processes for the nitrogen removal in wastewater . FEMS Microbiol. Rev. , 27 : 481 – 492 .
  • Schmidt , I. , van Spanning , R. J. M. and Jetten , M. S. M. 2004 . Denitrification and ammonia oxidation by Nitrosomonas europaea wild-type, and NirK- and NorB-deficient mutants . Microbiol.–SGM , 150 : 4107 – 4114 .
  • Schmidt , I. , Zart , D. and Bock , E. 2001 . Gaseous NO2 as a regulator for ammonia oxidation of Nitrosomonas eutropha . Antonie van Leeuwenhoek , 79 : 311 – 318 .
  • Schmit , C. G. , Jahan , K. , Schmit , K. H. , Debik , E. and Pattarkine , V. 2010 . Activated Sludge and Other Aerobic Suspended Culture Processes . Water Environ. Res. , 82 : 1073 – 1123 .
  • Schouten , S. , Strous , M. , Kuypers , M. M. M. , Rijpstra , W. I. C. , Baas , M. , Schubert , C. J. , Jetten , M. S. M. and Damste , J. S. S. 2004 . Stable carbon isotopic fractionations associated with inorganic carbon fixation by anaerobic ammonium-oxidizing bacteria . Appl. Environ. Microb. , 70 : 3785 – 3788 .
  • Schubert , C. J. , Durisch-Kaiser , E. , Wehrli , B. , Thamdrup , B. , Lam , P. and Kuypers , M. M. M. 2006 . Anaerobic ammonium oxidation in a tropical freshwater system (Lake Tanganyika) . Environ. Microbiol. , 8 : 1857 – 1863 .
  • Semrau , J. D. , Christoserdov , A. , Lebron , J. , Costello , A. , Davagnino , J. , Kenna , E. , Holmes , A. J. , Finch , R. , Murrell , J. C. and Lidstrom , M. E. 1995 . Particulate methane monooxygenase genes in methanotrophs . J. Bacteriol. , 177 : 3071 – 3079 .
  • Shaw , L. J. , Nicol , G. W. , Smith , Z. , Fear , J. , Prosser , J. I. and Baggs , E. M. 2006 . Nitrosospira spp. can produce nitrous oxide via a nitrifier denitrification pathway . Environ. Microbiol. , 8 : 214 – 222 .
  • Shen , J. P. , Zhang , L. M. , Zhu , Y. G. , Zhang , J. B. and He , J. Z. 2008 . Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam . Environ. Microbiol. , 10 : 1601 – 1611 .
  • Shen , X. Y. , Zhang , L. M. , Shen , J. P. , Li , L. H. , Yuan , C. L. and He , J. Z. 2011 . Nitrogen loading levels affect abundance and composition of soil ammonia oxidizing prokaryotes in semiarid temperate grassland . Journal of Soils and Sediments , 11 : 1243 – 1252 .
  • Shimamura , M. , Nishiyama , T. , Shigetomo , H. , Toyomoto , T. , Kawahara , Y. , Furukawa , K. and Fujii , T. 2007 . Isolation of a multiheme protein with features of a hydrazine-oxidizing enzyme from an anaerobic ammonium-oxidizing enrichment culture . Appl. Environ. Microb. , 73 : 1065 – 1072 .
  • Shimamura , M. , Nishiyama , T. , Shinya , K. , Kawahara , Y. , Furukawa , K. and Fujii , T. 2008 . Another multiheme protein, hydroxylamine oxidoreductase, abundantly produced in an anammox bacterium besides the hydrazine-oxidizing enzyme . J. Biosci. Bioeng. , 105 : 243 – 248 .
  • Siegrist , H. , Reithaar , S. and Lais , P. 1998 . Nitrogen loss in a nitrifying rotating contactor treating ammonium rich leachate without organic carbon . Water Sci. Technol. , 37 : 589 – 591 .
  • Sin , G. , Kaelin , D. , Kampschreur , M. J. , Takacs , I. , Wett , B. , Gernaey , K. V. , Rieger , L. , Siegrist , H. and van Loosdrecht , M. C. M. 2008 . Modelling nitrite in wastewater treatment systems: a discussion of different modelling concepts . Water Sci. Technol. , 58 : 1155 – 1171 .
  • Singurindy , O. , Molodovskaya , M. , Richards , B. K. and Steenhuis , T. S. 2009 . Nitrous oxide emission at low temperatures from manure-amended soils under corn (Zea mays L.) . Agr. Ecosyst. Environ. , 132 : 74 – 81 .
  • Solomon , S. 2007 . Climate change 2007: The physical science basis , Cambridge , , England : Cambridge University Press .
  • Sonthiphand , P. and Limpiyakorn , T. 2011 . Change in ammonia-oxidizing microorganisms in enriched nitrifying activated sludge . Appl. Microbiol. Biotechnol. , 89 : 843 – 853 .
  • Spear , J. R. , Barton , H. A. , Robertson , C. E. , Francis , C. A. and Pace , N. R. 2007 . Microbial community biofabrics in a geothermal mine adit . Appl. Environ. Microb. , 73 : 6172 – 6180 .
  • Stein , L. Y. and Arp , D. J. 1998 . Loss of ammonia monooxygenase activity in Nitrosomonas europaea upon exposure to nitrite . Appl. Environ. Microb. , 64 : 4098 – 4102 .
  • Stephen , J. R. , Chang , Y. J. , Macnaughton , S. J. , Kowalchuk , G. A. , Leung , K. T. , Flemming , C. A. and White , D. C. 1999 . Effect of toxic metals on indigenous soil p-subgroup proteobacterium ammonia oxidizer community structure and protection against toxicity by inoculated metal-resistant bacteria . Appl. Environ. Microb. , 65 : 95 – 101 .
  • Stephen , J. R. , McCaig , A. E. , Smith , Z. , Prosser , J. I. and Embley , T. M. 1996 . Molecular diversity of soil and marine 16S rRNA gene sequences related to beta-subgroup ammonia-oxidizing bacteria . Appl. Environ. Microb. , 62 : 4147 – 4154 .
  • Stroo , H. F. , Klein , T. M. and Alexander , M. 1986 . Heterotrophic nitrification in an acid forest soil and by an acid-tolerant fungus . Appl. Environ. Microb. , 52 : 1107 – 1114 .
  • Strous , M. , Fuerst , J. A. , Kramer , E. H. M. , Logemann , S. , Muyzer , G. , van de Pas-Schoonen , K. T. , Webb , R. , Kuenen , J. G. and Jetten , M. S. M. 1999b . Missing lithotroph identified as new planctomycete . Nature , 400 : 446 – 449 .
  • Strous , M. , Heijnen , J. J. , Kuenen , J. G. and Jetten , M. S. M. 1998 . The sequencing batch reactor as a powerful tool for the study of slowly growing anaerobic ammonium-oxidizing microorganisms . Appl. Microbiol. Biotechnol. , 50 : 589 – 596 .
  • Strous , M. , Kuenen , J. G. and Jetten , M. S. M. 1999a . Key physiology of anaerobic ammonium oxidation . Appl. Environ. Microb. , 65 : 3248 – 3250 .
  • Strous , M. , Pelletier , E. , Mangenot , S. , Rattei , T. , Lehner , A. , Taylor , M. W. , Horn , M. , Daims , H. , Bartol-Mavel , D. , Wincker , P. , Barbe , V. , Fonknechten , N. , Vallenet , D. , Segurens , B. , Schenowitz-Truong , C. , Medigue , C. , Collingro , A. , Snel , B. , Dutilh , B. E. , Op den Camp , H. J. M. , van der Drift , C. , Cirpus , I. , van de Pas-Schoonen , K. T. , Harhangi , H. R. , van Niftrik , L. , Schmid , M. , Keltjens , J. , van de Vossenberg , J. , Kartal , B. , Meier , H. , Frishman , D. , Huynen , M. A. , Mewes , H. W. , Weissenbach , J. , Jetten , M. S. M. , Wagner , M. and Le Paslier , D. 2006 . Deciphering the evolution and metabolism of an anammox bacterium from a community genome . Nature , 440 : 790 – 794 .
  • Strous , M. , VanGerven , E. , Kuenen , J. G. and Jetten , M. 1997a . Effects of aerobic and microaerobic conditions on anaerobic ammonium-oxidizing (Anammox) sludge . Appl. Environ. Microb. , 63 : 2446 – 2448 .
  • Strous , M. , VanGerven , E. , Zheng , P. , Kuenen , J. G. and Jetten , M. S. M. 1997b . Ammonium removal from concentrated waste streams with the anaerobic ammonium oxidation (anammox) process in different reactor configurations . Water Res. , 31 : 1955 – 1962 .
  • Stüven , R. , Vollmer , M. and Bock , E. 1992 . The impact of organic matter on nitric oxide formation by Nitrosomonas europaea . Arch. Microbiol. , 158 : 439 – 443 .
  • Suzuki , I. , Dular , U. and Kwok , S. C. 1974 . Ammonia and ammonium ion as substrate for oxidation by Nitrosomonas cells and extracts . J. Bacteriol. , 120 : 556 – 558 .
  • Szukics , U. , Abell , G. C. J. , Hodl , V. , Mitter , B. , Sessitsch , A. , Hackl , E. and Zechmeister-Boltenstern , S. 2010 . Nitrifiers and denitrifiers respond rapidly to changed moisture and increasing temperature in a pristine forest soil . FEMS Microbiol. Ecol. , 72 : 395 – 406 .
  • Tal , Y. , Watts , J. E. M. and Schreier , H. J. 2005 . Anaerobic ammonia-oxidizing bacteria and related activity in Baltimore inner Harbor sediment . Appl. Environ. Microb. , 71 : 1816 – 1821 .
  • Tallec , G. , Garnier , J. , Billen , G. and Gousailles , M. 2006 . Nitrous oxide emissions from secondary activated sludge in nitrifying conditions of urban wastewater treatment plants: Effect of oxygenation level . Water Res. , 40 : 2972 – 2980 .
  • Tan , N. C. G. , Kampschreur , M. J. , Wanders , W. , van der Pol , W. L. J. , van de Vossenberg , J. , Kleerebezem , R. , van Loosdrecht , M. C. M. and Jetten , M. S. M. 2008 . Physiological and phylogenetic study of an ammonium-oxidizing culture at high nitrite concentrations . Syst. Appl. Microbiol. , 31 : 114 – 125 .
  • Teira , E. , van Aken , H. , Veth , C. and Herndl , G. J. 2006 . Archaeal uptake of enantiomeric amino acids in the meso- and bathypelagic waters of the North Atlantic . Limnol. Oceanogr. , 51 : 60 – 69 .
  • Thamdrup , B. and Dalsgaard , T. 2002 . Production of N-2 through anaerobic ammonium oxidation coupled to nitrate reduction in marine sediments . Appl. Environ. Microb. , 68 : 1312 – 1318 .
  • Thamdrup , B. , Dalsgaard , T. , Jensen , M. M. , Ulloa , O. , Farias , L. and Escribano , R. 2006 . Anaerobic ammonium oxidation in the oxygen-deficient waters off northern Chile . Limnol. Oceanogr. , 51 : 2145 – 2156 .
  • Third , K. A. , Burnett , N. and Cord-Ruwisch , R. 2003 . Simultaneous nitrification and denitrification using stored substrate (PHB) as the electron donor in an SBR . Biotechnol. Bioeng. , 83 : 706 – 720 .
  • Timberlake , D. L. , Strand , S. E. and Williamson , K. J. 1988 . Combined aerobic heterotrophic oxidation, nitrification and denitrification in a permeable-support biofilm . Water Res. , 22 : 1513 – 1517 .
  • Tortoso , A. C. and Hutchinson , G. L. 1990 . Contributions of autotrophic and heterotrophic nitrifiers to soil NO and N2O emissions . Appl. Environ. Microb. , 56 : 1799 – 1805 .
  • Tourna , M. , Freitag , T. E. , Nicol , G. W. and Prosser , J. I. 2008 . Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms . Environ. Microbiol. , 10 : 1357 – 1364 .
  • Tourna , M. , Stieglmeier , M. , Spang , A. , Konneke , M. , Schintlmeister , A. , Urich , T. , Engel , M. , Schloter , M. , Wagner , M. , Richter , A. and Schleper , C. 2011 . Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil . Proc. Natl. Acad. Sci. USA , 108 : 8420 – 8425 .
  • Trap , J. , Bureau , F. , Vinceslas-Akpa , M. , Chevalier , R. and Aubert , M. 2009 . Changes in soil N mineralization and nitrification pathways along a mixed forest chronosequence . Forest. Ecol. Manag. , 258 : 1284 – 1292 .
  • Treusch , A. H. , Leininger , S. , Kletzin , A. , Schuster , S. C. , Klenk , H. P. and Schleper , C. 2005 . Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling . Environ. Microbiol. , 7 : 1985 – 1995 .
  • Trimmer , M. , Nicholls , J. C. and Deflandre , B. 2003 . Anaerobic ammonium oxidation measured in sediments along the Thames estuary, United Kingdom . Appl. Environ. Microb. , 69 : 6447 – 6454 .
  • Trimmer , M. , Nicholls , J. C. , Morley , N. , Davies , C. A. and Aldridge , J. 2005 . Biphasic behavior of anammox regulated by nitrite and nitrate in an estuarine sediment . Appl. Environ. Microb. , 71 : 1923 – 1930 .
  • Tsushima , I. , Kindaichi , T. and Okabe , S. 2007 . Quantification of anaerobic ammonium-oxidizing bacteria in enrichment cultures by real-time PCR . Water Res. , 41 : 785 – 794 .
  • Turk , O. and Mavinic , D. S. 1989 . Maintaining nitrite buildup in a system acclimated to free ammonia . Water Res. , 23 : 1383 – 1388 .
  • Urakawa , H. , Tajima , Y. , Numata , Y. and Tsuneda , S. 2008 . Low temperature decreases the phylogenetic diversity of ammonia-oxidizing archaea and bacteria in aquarium biofiltration systems . Appl. Environ. Microb. , 74 : 894 – 900 .
  • Vadivelu , V. M. , Keller , J. and Yuan , Z. G. 2006 . Effect of free ammonia and free nitrous acid concentration on the anabolic and catabolic processes of an enriched Nitrosomonas culture . Biotechnol. Bioeng. , 95 : 830 – 839 .
  • Vadivelu , V. M. , Keller , J. and Yuan , Z. 2007 . Free ammonia and free nitrous acid inhibition on the anabolic and catabolic processes of Nitrosomonas and Nitrobacter . Water Sci. Technol. , 56 : 89 – 97 .
  • Valentine , D. L. 2007 . Adaptations to energy stress dictate the ecology and evolution of the Archaea . Nat. Rev. Microbiol. , 5 : 316 – 323 .
  • Vallejo , A. , Garcia-Torres , L. , Diez , J. A. , Arce , A. and Lopez-Fernandez , S. 2005 . Comparison of N losses (NO3 −, N2O, NO) from surface applied, injected or amended (DCD) pig slurry of an irrigated soil in a Mediterranean climate . Plant Soil , 272 : 313 – 325 .
  • van de Graaf , A. A. , de Bruijn , P. , Robertson , L. A. , Jetten , M. S. M. and Kuenen , J. G. 1997 . Metabolic pathway of anaerobic ammonium oxidation on the basis of N-15 studies in a fluidized bed reactor . Microbiology–UK , 143 : 2415 – 2421 .
  • van de Graaf , A. A. , Mulder , A. , Debruijn , P. , Jetten , M. S. M. , Robertson , L. A. and Kuenen , J. G. 1995 . Anaerobic oxidation of ammonium is a biologically mediated process . Appl. Environ. Microb. , 61 : 1246 – 1251 .
  • van de Vossenberg , J. , Rattray , J. E. , Geerts , W. , Kartal , B. , van Niftrik , L. , van Donselaar , E. G. , Damste , J. S. S. , Strous , M. and Jetten , M. S. M. 2008 . Enrichment and characterization of marine anammox bacteria associated with global nitrogen gas production . Environ. Microbiol. , 10 : 3120 – 3129 .
  • van der Star , W. R. L. , Abma , W. R. , Blommers , D. , Mulder , J.-W. , Tokutomi , T. , Strous , M. , Picioreanu , C. and van Loosdrecht , M. C. M. 2007 . Startup of reactors for anoxic ammonium oxidation: Experiences from the first full-scale anammox reactor in Rotterdam . Water Res. , 41 : 4149 – 4163 .
  • van der Star , W. R. L. , Miclea , A. I. , van Dongen , U. , Muyzer , G. , Picioreanu , C. and van Loosdrecht , M. C. M. 2008 . The membrane bioreactor: A novel tool to grow anammox bacteria as free cells . Biotechnol. Bioeng. , 101 : 286 – 294 .
  • van der Wielen , P. , Voost , S. and van der Kooij , D. 2009 . Ammonia-oxidizing bacteria and archaea in groundwater treatment and drinking water distribution Systems . Appl. Environ. Microb. , 75 : 4687 – 4695 .
  • Van Hulle , S. W. H. , Vandeweyer , H. J. P. , Meesschaert , B. D. , Vanrolleghem , P. A. , Dejans , P. and Dumoulin , A. 2010 . Engineering aspects and practical application of autotrophic nitrogen removal from nitrogen rich streams . Chem. Eng. J. , 162 : 1 – 20 .
  • van Niel , E. J. W. , Arts , P. A. M. , Wesselink , B. J. , Robertson , L. A. and Kuenen , J. G. 1993 . Competition between heterotrophic and autotrophic nitrifiers for ammonia in chemostat cultures . FEMS Microbiol. Ecol. , 102 : 109 – 118 .
  • van Niel , E. J. W. , Braber , K. J. , Robertson , L. A. and Kuenen , J. G. 1992 . Heterotrophic nitrification and aerobic denitrification in Alcaligenes faecalis strain TUD . Antonie van Leeuwenhoek , 62 : 231 – 237 .
  • van Niftrik , L. A. , Fuerst , J. A. , Damsté , J. S. S. , Kuenen , J. G. , Jetten , M. S. M. and Strous , M. 2004 . The anammoxosome: an intracytoplasmic compartment in anammox bacteria . FEMS Microbiol. Lett. , 233 : 7 – 13 .
  • van Niftrik , L. , Geerts , W. J. C. , van Donselaar , E. G. , Humbel , B. M. , Yakushevska , A. , Verkleij , A. J. , Jetten , M. S. M. and Strous , M. 2008a . Combined structural and chemical analysis of the anammoxosome: A membrane-bounded intracytoplasmic compartment in anammox bacteria . J. Struct. Biol. , 161 : 401 – 410 .
  • van Niftrik , L , Geerts , W. J. C. , van Donselaar , E. G. , Humbel , B. M. , Webb , R. I. , Fuerst , J. A. , Verkleij , A. J. , Jetten , M. S. M. and Strous , M. 2008b . Linking ultrastructure and function in four genera of anaerobic ammonium-oxidizing bacteria: Cell plan, glycogen storage, and localization of cytochrome c proteins . J. Bacteriol. , 190 : 708 – 717 .
  • van Niftrik , L. , van Helden , M. , Kirchen , S. , van Donselaar , E. G. , Harhangi , H. R. , Webb , R. I. , Fuerst , J. A. , Op den Camp , H. J. M. , Jetten , M. S. M. and Strous , M. 2010 . Intracellular localization of membrane-bound ATPases in the compartmentalized anammox bacterium ‘Candidatus Kuenenia stuttgartiensis’ . Mol. Microbiol. , 77 : 701 – 715 .
  • Varela , M. M. , van Aken , H. M. , Sintes , E. and Herndl , G. J. 2008 . Latitudinal trends of crenarchaeota and bacteria in the meso- and bathypelagic water masses of the Eastern North Atlantic . Environ. Microbiol. , 10 : 110 – 124 .
  • Varela , M. M. , van Aken , H. M. , Sintes , E. , Reinthaler , T. and Herndl , G. J. 2011 . Contribution of crenarchaeota and bacteria to autotrophy in the North Atlantic interior . Environ. Microbiol. , 13 : 1524 – 1533 .
  • Venter , J. C. , Remington , K. , Heidelberg , J. F. , Halpern , A. L. , Rusch , D. , Eisen , J. A. , Wu , D. Y. , Paulsen , I. , Nelson , K. E. , Nelson , W. , Fouts , D. E. , Levy , S. , Knap , A. H. , Lomas , M. W. , Nealson , K. , White , O. , Peterson , J. , Hoffman , J. , Parsons , R. , Baden-Tillson , H. , Pfannkoch , C. , Rogers , Y. H. and Smith , H. O. 2004 . Environmental genome shotgun sequencing of the Sargasso Sea . Science , 304 : 66 – 74 .
  • Villaverde , S. , García-Encina , P. A. and Fdz-Polanco , F. 1997 . Influence of pH over nitrifying biofilm activity in submerged biofilters . Water Res. , 31 : 1180 – 1186 .
  • Walker , C. B. , de la Torre , J. R. , Klotz , M. G. , Urakawa , H. , Pinel , N. , Arp , D. J. , Brochier-Armanet , C. , Chain , P. S. G. , Chan , P. P. , Gollabgir , A. , Hemp , J. , Hugler , M. , Karr , E. A. , Konneke , M. , Shin , M. , Lawton , T. J. , Lowe , T. , Martens-Habbena , W. , Sayavedra-Soto , L. A. , Lang , D. , Sievert , S. M. , Rosenzweig , A. C. , Manning , G. and Stahl , D. A. 2010 . Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea . Proc. Natl. Acad. Sci. USA , 107 : 8818 – 8823 .
  • Wang , L. Q. and Yu , Q. L. 2010 . Study on characteristics of a strain of Penicillium sp capable of heterotrophic ammonium oxidation . Agr. Sci. China , 9 : 1816 – 1820 .
  • Wang , S. , Xiao , X. , Jiang , L. , Peng , X. , Zhou , H. , Meng , J. and Wang , F. 2009a . Diversity and abundance of ammonia-oxidizing archaea in hydrothermal vent chimneys of the Juan de Fuca Ridge . Appl. Environ. Microb. , 75 : 4216 – 4220 .
  • Wang , S. Y. , Wang , Y. , Feng , X. J. , Zhai , L. M. and Zhu , G. B. 2011 . Quantitative analyses of ammonia-oxidizing archaea and bacteria in the sediments of four nitrogen-rich wetlands in China . Appl. Microbiol. Biotechnol. , 90 : 779 – 787 .
  • Wang , X. and Wen , X. 2008 . Communities of ammonia oxidizing bacteria in activated sludge of various wastewater treatment plants in Beijing . J. Biotechnol. , 136 : S610 – S610 .
  • Wang , Y. , Ke , X. , Wu , L. and Lu , Y. 2009b . Community composition of ammonia-oxidizing bacteria and archaea in rice field soil as affected by nitrogen fertilization . Syst. Appl. Microbiol. , 32 : 27 – 36 .
  • Ward , B. B. , Voytek , M. A. and Witzel , R. P. 1997 . Phylogenetic diversity of natural populations of ammonia oxidizers investigated by specific PCR amplification . Microb. Ecol. , 33 : 87 – 96 .
  • Wehrfritz , J.-M. , Reilly , A. , Spiro , S. and Richardson , D. J. 1993 . Purification of hydroxylamine oxidase from Thiosphaera pantotropha . FEBS. Lett. , 335 : 246 – 250 .
  • Weidler , G. W. , Dornmayr-Pfaffenhuemer , M. , Gerbl , F. W. , Heinen , W. and Stan-Lotter , H. 2007 . Communities of archaea and bacteria in a subsurface radioactive thermal spring in the Austrian Central Alps, and evidence of ammonia-oxidizing crenarchaeota . Appl. Environ. Microbiol. , 73 : 259 – 270 .
  • Weidler , G. W. , Gerbl , F. W. and Stan-Lotter , H. 2008 . Crenarchaeota and their role in the nitrogen cycle in a subsurface radioactive thermal spring in the Austrian central Alps . Appl. Environ. Microb. , 74 : 5934 – 5942 .
  • Wells , G. F. , Park , H. D. , Yeung , C. H. , Eggleston , B. , Francis , C. A. and Criddle , C. S. 2009 . Ammonia-oxidizing communities in a highly aerated full-scale activated sludge bioreactor: betaproteobacterial dynamics and low relative abundance of Crenarchaea . Environ. Microbiol. , 11 : 2310 – 2328 .
  • Wessén , E. , Nyberg , K. , Jansson , J. K. and Hallin , S. 2010 . Responses of bacterial and archaeal ammonia oxidizers to soil organic and fertilizer amendments under long-term management . Appl. Soil Ecol. , 45 : 193 – 200 .
  • Wessén , E. , Nyberg , K. , Jansson , J. K. and Hallin , S. 2010 . Responses of bacterial and archaeal ammonia oxidizers to soil organic and fertilizer amendments under long-term management . Appl. Soil Ecol. , 45 : 193 – 200 .
  • Wett , B. 2006 . Solved upscaling problems for implementing deammonification of rejection water . Water Sci. Technol. , 53 : 121 – 129 .
  • Whitby , C. B. , Saunders , J. R. , Rodriguez , J. , Pickup , R. W. and McCarthy , A. 1999 . Phylogenetic differentiation of two closely related Nitrosomonas spp. that inhabit different sediment environments in an oligotrophic freshwater lake . Appl. Environ. Microb. , 65 : 4855 – 4862 .
  • Wittebolle , L. , van Vooren , N. , Verstraete , W. and Boon , N. 2009 . High reproducibility of ammonia-oxidizing bacterial communities in parallel sequential batch reactors . J. Appl. Microbiol. , 107 : 385 – 394 .
  • Witzel , K. and Overbeck , H. 1979 . Heterotrophic nitrification by Arthrobacter sp.(strain 9006) as influenced by different cultural conditions, growth state and acetate metabolism . Arch Microbio , 122 : 137 – 143 .
  • Woebken , D. , Lam , P. , Kuypers , M. M. M. , Naqvi , S. W. A. , Kartal , B. , Strous , M. , Jetten , M. S. M. , Fuchs , B. M. and Amann , R. 2008 . A microdiversity study of anammox bacteria reveals a novel Candidatus Scalindua phylotype in marine oxygen minimum zones . Environ. Microbiol. , 10 : 3106 – 3119 .
  • Wolf , I. and Brumme , R. 2002 . Contribution of nitrification and denitrification sources for seasonal N2O emissions in an acid German forest soil . Soil Biol. Biochem. , 34 : 741 – 744 .
  • Woods , D. D. 1938 . The reduction of nitrate to ammonium by Clostridium welchii . Biochem. J. , 32 : 2000 – 2012 .
  • Wrage , N. , Velthof , G. L. , Oenema , O. and Laanbroek , H. J. 2004 . Acetylene and oxygen as inhibitors of nitrous oxide production in Nitrosomonas europaea and Nitrosospira briensis: a cautionary tale . FEMS Microbiol. Ecol. , 47 : 13 – 18 .
  • Wu , Y. C. , Lu , L. , Wang , B. Z. , Lin , X. G. , Zhu , J. G. , Cai , Z. C. , Yan , X. Y. and Jia , Z. J. 2011 . Long-term field fertilization significantly alters community structure of ammonia-oxidizing bacteria rather than archaea in a paddy soil . Soil Sci. Soc. Am. J. , 75 : 1431 – 1439 .
  • Wuchter , C. , Abbas , B. , Coolen , M. J. L. , Herfort , L. , van Bleijswijk , J. , Timmers , P. , Strous , M. , Teira , E. , Herndl , G. J. , Middelburg , J. J. , Schouten , S. and Damste , J. S. S. 2006 . Archaeal nitrification in the ocean . Proc. Natl. Acad. Sci. USA , 103 : 12317 – 12322 .
  • Xue , Y. , Yang , F. L. , Liu , S. T. and Fu , Z. M. 2009 . The influence of controlling factors on the start-up and operation for partial nitrification in membrane bioreactor . Bioresour. Technol. , 100 : 1055 – 1060 .
  • Yamanaka , T. and Shinra , M. 1974 . Cytochrome c-552 and cytochrome c-554 derived from Nitrosomonas europaea. Purification, properties, and their function in hydroxylamine oxidation . J. Biochem. , 75 : 1265 – 1273 .
  • Yang , Q. , Peng , Y. Z. , Liu , X. H. , Zeng , W. , Mino , T. and Satoh , H. 2007 . Nitrogen removal via nitrite from municipal wastewater at low temperatures using real-time control to optimize nitrifying communities . Environ. Sci. Technol. , 41 : 8159 – 8164 .
  • Yang , X. P. , Wang , S. M. , Zhang , D. W. and Zhou , L. X. 2011 . Isolation and nitrogen removal characteristics of an aerobic heterotrophic nitrifying-denitrifying bacterium, Bacillus subtilis A1 . Bioresour. Technol. , 102 : 854 – 862 .
  • Yao , H. , Gao , Y. , Nicol , G. W. , Campbell , C. D. , Prosser , J. I. , Zhang , L. , Han , W. and Singh , B. K. 2011 . Links between ammonia oxidizer community structure, abundance, and nitrification potential in acidic soils . Appl. Environ. Microb. , 77 : 4618 – 4625 .
  • Yasuda , T. , Kuroda , K. , Hanajima , D. , Fukumoto , Y. , Waki , M. and Suzuki , K. 2010 . Characteristics of the microbial community associated with ammonia oxidation in a full-scale rockwool biofilter treating malodors from livestock manure composting . Microbes. Environ. , 25 : 111 – 119 .
  • Ye , L. , Tang , B. , Zhao , K. F. , Pijuan , M. and Peng , Y. Z. 2009 . Nitrogen removal via nitrite in domestic wastewater treatment using combined salt inhibition and on-line process control . Water Sci. Technol. , 60 : 1633 – 1639 .
  • Ye , L. and Zhang , T. 2011 . Ammonia-oxidizing bacteria dominates over ammonia-oxidizing archaea in a saline nitrification reactor under low DO and high nitrogen loading . Biotechnol. Bioeng. , 108 : 2544 – 2552 .
  • Ying , J. Y. , Zhang , L. M. and He , J. Z. 2010 . Putative ammonia-oxidizing bacteria and archaea in an acidic red soil with different land utilization patterns . Environ. Microbiol. Reports , 2 : 304 – 312 .
  • Yuan , Z. G. , Oehmen , A. , Peng , Y. Z. , Ma , Y. and Keller , J. 2008 . Sludge population optimisation in biological nutrient removal wastewater treatment systems through on-line process control: a re/view . Rev. Environ. Sci. Biotechnol. , 7 : 243 – 254 .
  • Zahn , J. A. , Arciero , D. M. , Hooper , A. B. and DiSpirito , A. A. 1996 . Evidence for an iron center in the ammonia monooxygenase from Nitrosomonas europaea . FEBS. Lett. , 397 : 35 – 38 .
  • Zart , D. , Schmidt , I. and Bock , E. 2000 . Significance of gaseous NO for ammonia oxidation by Nitrosomonas eutropha . Antonie Van Leeuwenhoek , 77 : 49 – 55 .
  • Zhang , G. L. , Zhang , J. , Xu , J. and Zhang , F. 2006 . Distributions, sources and atmospheric fluxes of nitrous oxide in Jiaozhou Bay . Estuar. Coast. Shelf. S , 68 : 557 – 566 .
  • Zhang , L. M. , Wang , M. , Prosser , J. I. , Zheng , Y. M. and He , J. Z. 2009a . Altitude ammonia-oxidizing bacteria and archaea in soils of Mount Everest . FEMS Microbiol. Ecol. , 70 : 208 – 217 .
  • Zhang , T. , Jin , T. , Yan , Q. , Shao , M. , Wells , G. , Criddle , C. and Fang , H. H. P. 2009b . Occurrence of ammonia-oxidizing Archaea in activated sludges of a laboratory scale reactor and two wastewater treatment plants . J. Appl. Microbiol. , 107 : 970 – 977 .
  • Zhang , T. , Ye , L. , Tong , A. H. Y. , Shao , M. F. and Lok , S. 2011 . Ammonia-oxidizing archaea and ammonia-oxidizing bacteria in six full-scale wastewater treatment bioreactors . Appl. Microbiol. Biotechnol. , 91 : 1215 – 1225 .
  • Zhao , B. , He , Y. L. , Hughes , J. and Zhang , X. F. 2010 . Heterotrophic nitrogen removal by a newly isolated Acinetobacter calcoaceticus HNR . Bioresour. Technol. , 101 : 5194 – 5200 .
  • Zheng , H. , Hanaki , K. and Matsuo , T. 1994 . Production of nitrous-oxide gas during nitrification of waste-water . Water Sci. Technol. , 30 : 133 – 141 .
  • Zhou , Y. , Oehmen , A. , Lim , M. , Vadivelu , V. and Ng , W. J. 2011 . The role of nitrite and free nitrous acid (FNA) in wastewater treatment plants . Water Res. , 45 : 4672 – 4682 .
  • Zhou , Y. , Pijuan , M. , Zeng , R. J. and Yuan , Z. G. 2008 . Free nitrous acid inhibition on nitrous oxide reduction by a denitrifying-enhanced biological phosphorus removal sludge . Environ. Sci. Technol. , 42 : 8260 – 8265 .
  • Zhu , G. B. , Peng , Y. Z. , Li , B. K. , Guo , J. H. , Yang , Q. and Wang , S. Y. 2008 . Biological removal of nitrogen from wastewater . Rev. Environ. Contam. T , 192 : 159 – 195 .
  • Zhu , G. B. , Peng , Y. Z. , Zhai , L. M. , Wang , Y. and Wang , S. Y. 2009 . Performance and optimization of biological nitrogen removal process enhanced by anoxic/oxic step feeding . Biochem. Eng. J. , 43 : 280 – 287 .
  • Zopfi , A. , Humbert , S. , Bagnoud , A. , Tarnawski , S. , Conen , F. and Seth , B. 2009 . Anammox in terrestrial ecosystems: Distribution, diversity and activity . Geochim. Cosmochim. Acta , 73 : 1538 A

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Order Reprints Request Corporate Permissions

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

Request Academic Permissions

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.

Related research

People also read lists articles that other readers of this article have read.

Recommended articles lists articles that we recommend and is powered by our AI driven recommendation engine.

Cited by lists all citing articles based on Crossref citations.
Articles with the Crossref icon will open in a new tab.