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  • Adair KL & Schwartz E (2008) Evidence that ammonia-oxidizing archaea are more abundant than ammonia-oxidizing bacteria in semiarid soils of Northern Arizona, USA. Microbiol Ecol 56: 420426.
  • Agogue H, Maaike B, Dinasquet J & Herndl GJ (2008) Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic. Nature 456: 788791.
  • Beman JM & Francis CA (2006) Diversity of ammonia-oxidizing archaea and bacteria in the sediments of a hypernutrified subtropical estuary: Bahia del Tobari, Mexico. Appl Environ Microb 72: 77677777.
  • Beman JM, Roberts KJ, Wegley L, Rohwer F & Francis CA (2007) Distribution and diversity of archaeal ammonia monooxygenase genes associated with corals. Appl Environ Microb 73: 56425647.
  • Beman JM, Popp BN & Francis CA (2008) Molecular and biogeochemical evidence for ammonia oxidation by marine crenarchaeota in the Gulf of California. ISME J 2: 429441.
  • Bowker RPG (2000) Biological odour control by diffusion into activated sludge basins. Water Sci Technol 41: 127132.
  • Boyle-Yarwood SA, Bottomley PJ & Myrold DD (2008) Community composition of ammonia-oxidizing bacteria and archaea in soils under stands of red alder and Douglas fir in Oregon. Environ Microbiol 10: 29562965.
  • Buisman CJN, Geraats BG, Ijspeert P & Lettinga G (1990) Optimization of sulphur production in a biotechnological sulphide-removing reactor. Biotechnol Bioeng 35: 5056.
  • Caffrey JM, Sloth NP, Kaspar HF & Blackburn TH (1993) Effect of organic loading on nitrification and denitrification in a marine sediment microcosm. FEMS Microbiol Ecol 12: 159167.
  • Caffrey JM, Bano N, Kalanetra K & Hollibaugh JT (2007) Ammonia oxidation and ammonia-oxidizing bacteria and archaea from estuaries with differing histories of hypoxia. ISME J 1: 660662.
  • Chanton JP, Martens CS & Goldhaber MB (1987) Biogeochemical cycling in an organic-rich coastal marine basin. 7. Sulfur mass balance, oxygen-uptake and sulfide retention. Geochim Cosmochim Ac 51: 11871199.
  • Chen XP, Zhu YG, Xia Y, Shen JP & He JZ (2008) Ammonia-oxidizing archaea: important players in paddy rhizosphere soil? Environ Microbiol 10: 19781987.
  • Chung YC, Lin YY & Tseng CP (2005) Removal of high concentration of NH3 and coexistent H2S by biological activated carbon (BAC) biotrickling filter. Bioresource Technol 96: 18121820.
  • Coolen MJL, Abbas B, Van Bleijswijk J, Hopmans EC, Kuypers MMM, Wakeham SG & Sinninghe Damste JS (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: 10011016.
  • Dapena-Mora A, Fernández I, Campos JL, Mosquera-Corral A, Méndez R & Jetten MSM (2007) Evaluation of activity and inhibition effects on Anammox process by batch tests based on the nitrogen gas production. Enzyme Microb Technol 40: 859865.
  • De Boer W & Kowalchuk GA (2001) Nitrification in acid soils: micro-organisms and mechanisms. Soil Biol Biochem 33: 853866.
  • De La Torre JR, Walker CB, Ingalls AE, Könneke M & Stahl DA (2008) Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environ Microbiol 10: 810818.
  • De Smul A & Verstraete W (1999) The phenomenology and the mathematical modeling of the silicone-supported chemical oxidation of aqueous sulfide to elemental sulfur by ferric sulphate. J Chem Technol Biotechnol 74: 456466.
  • De Vet WWJM, Dinkla IJT, Muyzer G, Rietveld LC & Van Loosdrecht MCM (2009) Molecular characterization of microbial populations in groundwater sources and sand filters for drinking water production. Water Res 43: 182194.
  • Elshahed MS, Senko JM, Najar FZ, Kenton SM, Roe BA, Dewers TA, Spear JR & Krumholz LR (2003) Bacterial diversity and sulfur cycling in a mesophilic sulfide-rich spring. Appl Environ 69: 56095621.
  • Elshahed MS, Youssef NH, Luo QW, Najar FZ, Roe BA, Sisk TM, Bühring SI, Hinrichs KU & Krumholz LR (2007) Phylogenetic and metabolic diversity of planctomycetes from anaerobic, sulfide- and sulfur-rich Zodletone Spring, Oklahoma. Appl Environ Microb 73: 47074716.
  • Fdz-Polanco F, Fdz-Polanco M, Fernandez N, Uruena MA, Garcia PA & Villaverde S (2001) New process for simultaneous removal of nitrogen and sulphur under anaerobic conditions. Water Res 35: 11111114.
  • Francis CA, Roberts KJ, Beman JM, Santoro AE & Oakley BB (2005) Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. P Natl Acad Sci USA 102: 1468314688.
  • Francis CA, Beman JM & Kuypers MMM (2007) New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation. ISME J 1: 1927.
  • Gadekar S, Nemati M & Hill GA (2006) Batch and continuous biooxidation of sulphide by Thiomicrospira sp. CVO: reaction kinetics and stoichiometry. Water Res 40: 24362446.
  • Gardner WS, Seitzinger SP & Malczyk JM (1991) The effects of sea salts on the forms of nitrogen released from estuarine and freshwater sediments: does ion pairing affect ammonium flux? Estuaries 14: 157166.
  • Goldhaber MB & Kaplan IR (1975) Controls and consequences of sulfate reduction rates in recent marine sediments. Soil Sci 119: 4255.
  • Hallam SJ, Konstantinidis KT, Putnam N, Schleper C, Watanabe Y, Sugahara J, Preston C, De La Torre J, Richardson PM & Delong EF (2006a) Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. P Natl Acad Sci USA 103: 1829618301.
  • Hallam SJ, Mincer TJ, Schleper C, Preston C, Roberts K & Richardson PM (2006b) Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine crenarchaeota. PLoS Biology 4: 520536.
  • Hansel CM, Fendorf S, Jardine PM & Francis CA (2008) Changes in bacterial and archaeal community structure and functional diversity along a geochemically variable soil profile. Appl Environ Microb 74: 16201633.
  • Hatzenpichler R, Lebecleva EV, Spieck E, Stoecker K, Richter A, Daims H & Wagner M (2008) A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. P Natl Acad Sci USA 105: 21342139.
  • He JZ, Shen JP, Zhang LM, Zhu YG, Zheng YM, Xu MG & Di H (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: 23642374.
  • Herfort L, Schouten S & Abbas B (2007) Variations in spatial and temporal distribution of Archaea in the North Sea in relation to environmental variables. FEMS Microbiol Ecol 62: 242257.
  • Herrmann M, Saunders AM & Schramm A (2008) Archaea dominate the ammonia-oxidizing community in the rhizosphere of the freshwater macrophyte Littorella uniflora. Appl Environ Microb 74: 32793283.
  • Hooper AB & Terry KR (1973) Specific inhibitors of ammonia oxidation in Nitrosomonas. J Bacteriol 115: 480485.
  • Janssen AJH, Sleyster R, Van Der Kaa C, Jochemsen A, Bontsema J & Lettinga G (1995) Biological sulphide oxidation in a fed-batch reactor. Biotechnol Bioeng 47: 327333.
  • Jørgensen BB (1990) The sulfur cycle of freshwater sediments: role of thiosulfate. Limnol Oceanogr 35: 13291342.
  • Jørgensen BB, Revsbech NP, Blackburn TH & Cohen Y (1979) Diurnal cycle of oxygen and sulfide microgradients and microbial photosynthesis in a cyanobacterial mat sediment. Appl Environ Microb 38: 4658.
  • Joye SB & Hollibaugh JT (1995) Influence of sulfide inhibition of nitrification on nitrogen regeneration in sediments. Science 270: 623625.
  • Kalyuzhnyi S, Gladchenko M, Mulder A & Versprille B (2006) DEAMOX-New biological nitrogen removal process based on anaerobic ammonia oxidation coupled to sulphide-driven conversion of nitrate into nitrite. Water Res 40: 36373645.
  • Kemp WM, Sampou P, Caffrey J, Mayer M, Hendriksen K & Boynton WR (1990) Ammonium recycling versus denitrification in Chesapeake Bay sediments. Limnol Oceanogr 35: 15451563.
  • Koch M, Rudolph C, Moissl C & Huber R (2006) A cold-loving crenarchaeon is a substantial part of a novel microbial community in cold sulphidic marsh water. FEMS Microbiol Ecol 57: 5566.
  • Könneke M, Bernhard AE, De La Torre JR, Walker CB, Waterburry JB & Stahl DA (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437: 543546.
  • Kuypers MMM, Sliekers AO, Lavik G, Schmid M, Jørgensen BB, Kuenen JG, Sinninghe Damste JS, Strous M & Jetten MSM (2003) Anaerobic ammonium oxidation by anammox bacteria in the Black Sea. Nature 442: 608611.
  • Kuypers MMM, Lavik G, Woebken D, Schmid M, Fuchs BM, Amann R, Jørgensen BB & Jetten MSM (2005) Massive nitrogen loss from the Benguela upwelling system through anaerobic ammonium oxidation. P Natl Acad Sci USA 102: 64786483.
  • Lam P, Jensen MM, Lavik G, McGinnis DF, Müler B, Schubert CJ, Amann R, Thamdrup B & Kuypers MMM (2007) Linking crenarchaeal and bacterial nitrification to anammox in the Black Sea. P Natl Acad Sci USA 104: 71047109.
  • Langner HW, Jackson CR, Mcdermott TR & Inskeep WP (2001) Rapid oxidation of arsenite in a hot spring ecosystem, Yellowstone National Park. Environ Sci Technol 35: 33023309.
  • Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JL, Schuster SC & Schleper C (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442: 806809.
  • Lens PM, De Poorte MP, Cronenberg CC & Verstraete WH (1995) Sulfate reducing and methane producing bacteria in aerobic wastewater treatment systems. Water Res 29: 871880.
  • Le Roux X, Poly F, Currey P, Cammeaux C, Hai B, Nicol GW, Prosser JI, Schloter M, Attard E & Klumpp K (2008) Effects of aboveground grazing on coupling among nitrifier activity, abundance and community structure. ISME J 2: 221232.
  • Madigon MT & Martinko JM (2006) Brock, Biology of Microorganisms. 11th edn. Pearson Education Inc., Pearson Prentice Hall, Upper Saddle River, NJ.
  • McCarty GW (1999) Modes of action of nitrification inhibitors. Biol Fertil Soils 29: 19.
  • Mincer TJ, Church MJ, Taylor LT, Preston C, Karl DM & Delong EF (2007) Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre. Environ Microbiol 9: 11621175.
  • Mørkved PT, Dörsch P & Bakken LR (2007) The N2O production ratio of nitrification and its dependence on long-term changes in soil pH. Soil Biology Biochem 39: 20482057.
  • Mosier AC & Francis CA (2008) Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary. Environ Microbiol 10: 30023016.
  • Mulder A (2006) Process for the biological denitrification of ammonium containing wastewater. International Patent Application, WO 2006/022539.
  • Mulder A, Van de Graaf AA, Robertson LA & Kuenen JG (1995) Anaerobic ammonium oxidation discovered in a denitrifying fluidized bed reactor. FEMS Microbiol Ecol 16: 177183.
  • Nakagawa T, Mori K, Kato C, Takahashi R & Tokuyama T (2007) Distribution of cold-adapted ammonia-oxidizing microorganisms in the deep-ocean of the northeastern Japan Sea. Microbes Environ 22: 365372.
  • Nicol GW & Schleper C (2006) Ammonia-oxidising Crenarchaeota: important players in the nitrogen cycle? Trends Microbiol 14: 207212.
  • Nicol GW, Leininger S, Schleper C & Prosser JI (2008) The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environ Microbiol 10: 29662978.
  • Nielsen AH, Vollertsen J & Hvitved-Jacobsen T (2004) Chemical sulfide oxidation of wastewater-effects of pH and temperature. Water Sci Technol 50: 185192.
  • Nugroho RA, Röling WFM, Laverman AM & Verhoef HA (2006) Low nitrification rates in acid Scots pine forest soils are due to pH-related factors. Microbial Ecol 38: 11661171.
  • Okabe S, Ito T, Sugita K & Satoh H (2005) Succession of internal sulfur cycles and sulfur-oxidizing bacterial communities in microaerophilic wastewater biofilms. Appl Environ Microb 71: 25202529.
  • Park HD, Wells GF, Bae H, Criddle CS & Francis CA (2006) Occurrence of ammonia-oxidizing archaea in wastewater treatment plant bioreactors. Appl Environ Microb 72: 56435647.
  • Park SJ, Park BJ & Rhee SK (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: 605615.
  • Prokopenko MG, Hammond DE, Berelson WM, Bernhard JM, Stott L & Douglas R (2006) Nitrogen cycling in the sediments of Santa Barbara basin and Eastern Subtropical North Pacific: nitrogen isotopes, diagenesis and possible chemosymbiosis between two lithotrophs (Thioploca and Anammox)-‘riding on a glider’. Earth Planet Sc Lett 242: 186204.
  • Prosser JL & Nicol GW (2008) Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment. Environ Microbiol 10: 29312941.
  • Reigstad LJ, Richter A, Daims H, Urich T, Schwark L & Schleper C (2008) Nitrification in terrestrial hot springs of Iceland and Kamchatka. FEMS Microbiol Ecol 64: 167174.
  • Rempel CL, Evitts RW & Nemati M (2006) Dynamics of corrosion rates associated with nitrite or nitrate mediated control of souring under biological conditions simulating an oil reservoir. J Ind Microbiol Biot 33: 878886.
  • Sahan E & Muyzer G (2008) Diversity and spatio-temporal distribution of ammonia-oxidizing Archaea and Bacteria in sediments of the Westerschelde estuary. FEMS Microbiol Ecol 64: 175186.
  • Santoro AE, Francis CA, De Sieyes NR & Boehm AB (2008) Shifts in the relative abundance of ammonia-oxidizing bacteria and archaea across physicochemical gradients in a subterranean estuary. Environ Microbiol 10: 10681079.
  • Schmidt CS, Hultman KA, Robinson D, Killham K & Prosser JI (2007) PCR profiling of ammonia-oxidizer communities in acidic soils subjected to nitrogen and sulphur deposition. FEMS Microbiol Ecol 61: 305316.
  • Sears K, Alleman JE, Barnard JL & Oleszkiewicz JA (2004) Impacts of reduced sulfur components on active and resting ammonia oxidizers. J Industrial Microbiol Biot 31: 369378.
  • Seitzinger SP (1988) Denitrification in freshwater sediments and coastal marine ecosystems: ecological and geochemical significance. Limnol Oceanogr 33: 702724.
  • Shen JP, Zhang LM, Zhu YG, Zhang JB & He JZ (2008) Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam. Environ Microbiol 10: 16011611.
  • Siboni N, Ben-Dov E, Sivan A & Kushmaro A (2008) Global distribution and diversity of coral-associated Archaea and their possible role in the coral holobiont nitrogen cycle. Environ Microbiol 10: 29792990.
  • Sinninghe Damste JS, Rijpstra WIC, Hopmans EC, Prahl FG, Wakeham SG & Schouten S (2002) Distribution of membrane lipids of planktonic crenarchaeota in the Arabian sea. Appl Environ Microb 68: 29973002.
  • Sørensen J (1978) Occurrence of nitric and nitrous oxides in a coastal marine sediment. Appl Environ Microb 36: 809813.
  • Sørensen J, Tiedhe JM & Firestone RB (1980) Inhibition by sulfide of nitric and nitrous oxides reduction by denitrifying Pseudomonas fluorescens. Appl Environ Microb 39: 105108.
  • Spear JR, Barton HA, Robertson CE, Francis CA & Pace NR (2007) Microbial community biofabrics in a geothermal mine adit. Appl Environ Microb 73: 61726180.
  • Srna FR & Baggaley A (1975) Kinetic response of perturbed marine nitrification systems. J Water Pollut Cont F 47: 472486.
  • Tourna M, Freitag TE, Nicol GW & Prosser JI (2008) Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms. Environ Microbiol 10: 13571364.
  • Treusch AH, Leininger S, Kletzin A, Schuster SC, Klenk HP & 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: 19851995.
  • Urakawa H, Tajima Y, Numata Y & Tsuneda S (2008) Low temperature decreases the phylogenetic diversity of ammonia-oxidizing archaea and bacteria in aquarium biofiltration systems. Appl Environ Microb 74: 894900.
  • Valentine DL (2007) Adaptations to energy stress dictate the ecology and evolution of the Archaea. Nature Rev Microbiol 5: 316323.
  • Van de Graaf AA, DeBruijn P & Robertson LA (1996) Autotrophic growth of anaerobic ammonium-oxidizing micro-organisms in a fluidized bed reactor. Microbiology 142: 21872196.
  • Venter JC, Remington K, Heidelberg JF et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 6674.
  • Weidler GW, Dornmayr-Pfaffenhuemer M, Gerbl FW, Heinen W & 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 Microb 73: 259270.
  • Wuchter C, Abbas B, Coolen MJL et al. (2006) Archaeal nitrification in the ocean. P Natl Acad Sci USA 103: 1231712322.