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References

  • de Almeida NM, Maalcke WJ, Keltjens JT, Jetten MSM & Kartal B (2011) Proteins and protein complexes involved in the biochemical reactions of anaerobic ammonium-oxidizing bacteria. Biochem Soc Trans 39: 303308.
  • Andrade SL, Dickmanns A, Ficner R & Einsle O (2005) Crystal structure of the archaeal ammonium transporter Amt-1 from Archaeoglobus fulgidus. P Natl Acad Sci USA 102: 1499414999.
  • Andrews SC, Harrison PM & Guest JR (1991) A molecular analysis of the 53.3 minute region of the Escherichia coli linkage map. J Gen Microbiol 137: 361367.
  • Andrews SC, Berks BC, McClay J, Ambler A, Quail MA, Golby P & Guest JR (1997) A 12-cistron Escherichia coli operon (hyf) encoding a putative proton-translocating formate hydrogenlyase system. Microbiology 143: 36333647.
  • Arcondéguy T, Jack R & Merrick M (2001) PII signal transduction proteins, pivotal players in microbial nitrogen control. Microbiol Mol Biol Rev 65: 80105.
  • Arp DJ, Sayavedra-Soto LA & Hommes NG (2002) Molecular biology and biochemistry of ammonia oxidation by Nitrosomonas europaea. Arch Microbiol 178: 250255.
  • Arrigo KR (2005) Marine microorganisms and global nutrient cycles. Nature 437: 349355.
  • Atack JM & Kelly DJ (2007) Structure, mechanism and physiological roles of bacterial cytochrome c peroxidases. Adv Microb Physiol 52: 73106.
  • Atkinson SJ, Mowat CG, Reid GA & Chapman SK (2007) An octaheme c-type cytochrome from Shewanella oneidensis can reduce nitrite and hydroxylamine. FEBS Lett 581: 38053808.
  • Auclair SM, Bhanu MK & Kendall DA (2012) Signal peptidase I: cleaving the way to mature proteins. Protein Sci 21: 1325.
  • Baker SC, Saunders NF, Willis AC, Ferguson SJ, Hajdu J & Fülöp V (1997) Cytochrome cd1 structure: unusual haem environments in a nitrite reductase and analysis of factors contributing to beta-propeller folds. J Mol Biol 269: 440455.
  • Baumann B, Snozzi M, Zehnder AJ & Van Der Meer JR (1996) Dynamics of denitrification activity of Paracoccus denitrificans in continuous culture during aerobic-anaerobic changes. J Bacteriol 178: 43674374.
  • Baumann B, van der Meer JR, Snozzi M & Zehnder AJ (1997) Inhibition of denitrification activity but not of mRNA induction in Paracoccus denitrificans by nitrite at a suboptimal pH. Antonie Van Leeuwenhoek 72: 183189.
  • Bertero MG, Rothery RA, Palak M, Hou C, Lim D, Blasco F, Weiner JH & Strynadka NC (2003) Insights into the respiratory electron transfer pathway from the structure of nitrate reductase A. Nat Struct Biol 10: 681687.
  • Betlach MR & Tiedje JM (1981) Kinetic explanation for accumulation of nitrite, nitric oxide, and nitrous oxide during bacterial denitrification. Appl Environ Microbiol 42: 10741084.
  • Borisov VB, Gennis RB, Hemp J & Verkhovsky MI (2011) The cytochrome bd respiratory oxygen reductases. Biochim Biophys Acta 1807: 13981413.
  • Boumann HA, Hopmans EC, van de Leemput I, Op den Camp HJM, van de Vossenberg J, Strous M, Jetten MSM, Sinninghe Damsté JS & Schouten S (2006) Ladderane phospholipids in anammox bacteria comprise phosphocholine and phosphoethanolamine headgroups. FEMS Microbiol Lett 258: 297304.
  • Boumann HA, Longo ML, Stroeve P, Poolman B, Hopmans EC, Stuart MC, Sinninghe Damsté JS & Schouten S (2009a) Biophysical properties of membrane lipids of anammox bacteria: I. Ladderane phospholipids form highly organized fluid membranes. Biochim Biophys Acta 1788: 14441451.
  • Boumann HA, Stroeve P, Longo ML, Poolman B, Kuiper JM, Hopmans EC, Jetten MSM, Sinninghe Damsté JS & Schouten S (2009b) Biophysical properties of membrane lipids of anammox bacteria: II. Impact of temperature and bacteriohopanoids. Biochim Biophys Acta 1788: 14521457.
  • Boyington JC, Gladyshev VN, Khangulov SV, Stadtman TC & Sun PD (1997) Crystal structure of formate dehydrogenase H: catalysis involving Mo, molybdopterin, selenocysteine, and an Fe4S4 cluster. Science 275: 13051308.
  • Broda E (1977) Two kinds of lithotrophs missing in nature. Z. Allg. Mikrobiol 17: 491493.
  • Buckel W & Thauer RK (2012) Energy conservation via electron bifurcating ferredoxin reduction and proton/Na+ translocating ferredoxin oxidation. Biochim Biophys Acta. http://dx.doi.org/10.1016/j.bbabio.2012.07.002. [Epub ahead of print].
  • Campbell MA, Nyerges G, Kozlowski JA, Poret-Peterson AT, Stein LY & Klotz MG (2011) Model of the molecular basis for hydroxylamine oxidation and nitrous oxide production in methanotrophic bacteria. FEMS Microbiol Lett 322: 8289.
  • Chance B & Hollunger G (1961) The interaction of energy and electron transfer reactions in mitochondria. I. General properties and nature of the products of succinate-linked reduction of pyridine nucleotide. J Biol Chem 236: 15341543.
  • Cirpus IE, Geerts W, Hermans JH, Op den Camp HJM, Strous M, Kuenen JG & Jetten MSM (2006) Challenging protein purification from anammox bacteria. Int J Biol Macromol 39: 8894.
  • Claus H (2003) Laccases and their occurrence in prokaryotes. Arch Microbiol 179: 145150.
  • Cooley JW (2010) A structural model for across membrane coupling between the Qo and Qi active sites of cytochrome bc1. Biochim Biophys Acta 1797: 18421848.
  • Coulthurst SJ & Palmer T (2008) A new way out: protein localization on the bacterial cell surface via Tat and a novel Type II secretion system. Mol Microbiol 69: 13311335.
  • Crofts AR (2004) The cytochrome bc1 complex: function in the context of structure. Annu Rev Physiol 66: 689733.
  • Crofts AR, Lhee S, Crofts SB, Cheng J & Rose S (2006) Proton pumping in the bc1 complex: a new gating mechanism that prevents short circuits. Biochim Biophys Acta 1757: 10191034.
  • Czyzewski BK & Wang DN (2012) Identification and characterization of a bacterial hydrosulphide ion channel. Nature 483: 494497.
  • Dang H, Chen R, Wang L, Guo L, Chen P, Tang Z, Tian F, Li S & Klotz MG (2010) Environmental factors shape sediment anammox bacterial communities in hypernutrified Jiaozhou Bay, China. Appl Environ Microbiol 76: 70367047.
  • Di Gennaro P, Bargna A & Sello G (2011) Microbial enzymes for aromatic compound hydroxylation. Appl Microbiol Biotechnol 90: 18171827.
  • Dibrova DV, Galperin MY & Mulkidjanian AY (2010) Characterization of the N-ATPase, a distinct, laterally transferred Na+-translocating form of the bacterial F-type membrane ATPase. Bioinformatics 26: 14731476.
  • Efremov RG & Sazanov LA (2011a) Structure of the membrane domain of respiratory complex I. Nature 476: 414420.
  • Efremov RG & Sazanov LA (2011b) Respiratory complex I: ‘steam engine’ of the cell? Curr Opin Struct Biol 21: 532540.
  • Efremov RG & Sazanov LA (2012) The coupling mechanism of respiratory complex I – a structural and evolutionary perspective. Biochim Biophys Acta, http://dx.doi.org/10.1016/j.bbabio.2012.02.015. [Epub ahead of print].
  • Efremov RG, Baradaran R & Sazanov LA (2010) The architecture of respiratory complex I. Nature 465: 441445.
  • Egli K, Fanger U, Alvarez PJ, Siegrist H, van der Meer JR & Zehnder AJ (2001) Enrichment and characterization of an anammox bacterium from a rotating biological contactor treating ammonium-rich leachate. Arch Microbiol 175: 198207.
  • Egli K, Bosshard F, Werlen C, Lais P, Siegrist H, Zehnder AJ & Van der Meer JR (2003) Microbial composition and structure of a rotating biological contactor biofilm treating ammonium-rich wastewater without organic carbon. Microb Ecol 45: 419432.
  • Einsle O, Messerschmidt A, Stach P, Bourenkov GP, Bartunik HD, Huber R & Kroneck PM (1999) Structure of cytochrome c nitrite reductase. Nature 400: 476480.
  • Fairman JW, Noinaj N & Buchanan SK (2011) The structural biology of β-barrel membrane proteins: a summary of recent reports. Curr Opin Struct Biol 21: 523531.
  • Falke D, Schulz K, Doberenz C, Beyer L, Lilie H, Thiemer B & Sawers RG (2010) Unexpected oligomeric structure of the FocA formate channel of Escherichia coli: a paradigm for the formate-nitrite transporter family of integral membrane proteins. FEMS Microbiol Lett 303: 6975.
  • Forchhammer K (2008) PII signal transducers: novel functional and structural insights. Trends Microbiol 16: 6572.
  • Fuerst JA (2005) Intracellular compartmentation in planctomycetes. Annu Rev Microbiol 59: 299328.
  • Fuerst JA & Sagulenko E (2011) Beyond the bacterium: planctomycetes challenge our concepts of microbial structure and function. Nat Rev Microbiol 9: 403413.
  • Fuerst JA, Webb RI, Van Niftrik L, Jetten MSM & Strous M (2006) Complex intracellular structures in prokaryotes, Chapter 10: Anammoxosomes of anaerobic ammonium-oxidizing planctomycetes. Microbiology Monographs, Vol. 2 (Shiveley JM, ed), pp. 259608. Springer-Verlag, Berlin and Heidelberg.
  • Fülöp V, Moir JW, Ferguson SJ & Hajdu J (1995) The anatomy of a bifunctional enzyme: structural basis for reduction of oxygen to water and synthesis of nitric oxide by cytochrome cd1. Cell 81: 369377.
  • Giardina P, Faraco V, Pezzella C, Piscitelli A, Vanhulle S & Sannia G (2010) Laccases: a never-ending story. Cell Mol Life Sci 67: 369385.
  • Goddard AD, Moir JW, Richardson DJ & Ferguson SJ (2008) Interdependence of two NarK domains in a fused nitrate/nitrite transporter. Mol Microbiol 70: 667681.
  • Gori F, Tringe SG, Kartal B, Machiori E & Jetten MSM (2011) The metagenomic basis of anammox metabolism in Candidatus ‘Brocadia fulgida’. Biochem Soc Trans 39: 17991804.
  • Güven D, Dapena A, Kartal B et al. (2005) Propionate oxidation by and methanol inhibition of anaerobic ammonium-oxidizing bacteria. Appl Environ Microbiol 71: 10661071.
  • Haines TH (2001) Do sterols reduce proton and sodium leaks through lipid bilayers? Prog Lipid Res 40: 299324.
  • Hamersley MR, Woebken D, Boehrer B, Schultze M, Lavik G & Kuypers MMM (2009) Water column anammox and denitrification in a temperate permanently stratified lake (Lake Rassnitzer, Germany). Syst Appl Microbiol 32: 571582.
  • Hamm RE & Thompson TG (1941) Dissolved nitrogen in the sea water of the northeast Pacific with notes on the total carbon dioxide and the dissolved oxygen. J Mar Res 4: 1127.
  • Hemp J & Gennis RB (2008) Diversity of the Heme–Copper superfamily in Archaea: insights from genomics and structural modeling. Results Probl Cell Differ 45: 131.
  • Hira D, Toh H, Migita CT, Okubo H, Nishiyama T, Hattori M, Furukawa K & Fujii T (2012) Anammox organism KSU-1 expresses a NirK-type copper-containing nitrite reductase instead of a NirS-type with cytochrome cd1. FEBS Lett 586: 16581663.
  • Hirst J (2009) Towards the molecular mechanism of respiratory complex I. Biochem J 425: 327339.
  • Hong YG, Li M, Cao H & Gu JD (2011a) Residence of habitat-specific anammox bacteria in the deep-sea subsurface sediments of the South China Sea: analyses of marker gene abundance with physical chemical parameters. Microb Ecol 62: 3647.
  • Hong YG, Yin B & Zheng TL (2011b) Diversity and abundance of anammox bacterial community in the deep-ocean surface sediment from equatorial Pacific. Appl Microbiol Biotechnol 89: 12331241.
  • Hooper AB, Vannelli T, Bergmann DJ & Arciero DM (1997) Enzymology of the oxidation of ammonia to nitrite by bacteria. Antonie Van Leeuwenhoek 71: 5967.
  • Hu BL, Rush D, van der Biezen E, Zheng P, van Mullekom M, Schouten S, Sinninghe Damsté JS, Smolders AJ, Jetten MSM & Kartal B (2011) New anaerobic, ammonium-oxidizing community enriched from peat soil. Appl Environ Microbiol 77: 966971.
  • Huang H, Wang S, Moll J & Thauer RK (2012) Electron bifurcation involved in the energy metabolism of the acetogenic bacterium Moorella thermoacetica growing on glucose or H2 plus CO2. J Bacteriol 194: 36893699.
  • Humbert S, Tarnawski S, Fromin N, Mallet MP, Aragno M & Zopfi J (2010) Molecular detection of anammox bacteria in terrestrial ecosystems: distribution and diversity. ISME J 4: 450454.
  • Igarashi N, Moriyama H, Fujiwara T, Fukumori Y & Tanaka N (1997) The 2.8 A structure of hydroxylamine oxidoreductase from a nitrifying chemoautotrophic bacterium, Nitrosomonas europaea. Nat Struct Biol 4: 276284.
  • Imajo U, Tokutomi T & Furukawa K (2004) Granulation of Anammox microorganisms in up-flow reactors. Water Sci Technol 49: 155163.
  • Ize B, Coulthurst SJ, Hatzixanthis K, Caldelari I, Buchanan G, Barclay EC, Richardson DJ, Palmer T & Sargent F (2009) Remnant signal peptides on non-exported enzymes: implications for the evolution of prokaryotic respiratory chains. Microbiology 155: 39924004.
  • Jensen MM, Lam P, Revsbech NP, Nagel B, Gaye B, Jetten MSM & Kuypers MMM (2011) Intensive nitrogen loss over the Omani Shelf due to anammox coupled with dissimilatory nitrite reduction to ammonium. ISME J 5: 16601670.
  • Jetten MSM, Sliekers O, Kuypers M et al. (2003) Anaerobic ammonium oxidation by marine and freshwater planctomycete-like bacteria. Appl Microbiol Biotechnol 63: 107114.
  • Jetten MSM, Cirpus I, Kartal B et al. (2005) 1994–2004: 10 years of research on the anaerobic oxidation of ammonium. Biochem Soc Trans 33: 119123.
  • Jetten MSM, Niftrik L, Strous M, Kartal B, Keltjens JT & Op den Camp HJM (2009) Biochemistry and molecular biology of anammox bacteria. Crit Rev Biochem Mol Biol 44: 6584.
  • Jetten MSM, Op den Camp HJM, Kuenen JG & Strous M (2010) Description of the order Brocadiales. Bergey's Manual of Systematic Bacteriology, Vol 4 (Krieg NR, Ludwig W, Whitman WB, Hedlund BP, Paster BJ, Staley JT, Ward N, Brown D & Parte A, eds), pp. 596603. Springer, Heidelberg.
  • Johnson HA, Pelletier DA & Spormann AM (2001) Isolation and characterization of anaerobic ethylbenzene dehydrogenase, a novel Mo-Fe-S enzyme. J Bacteriol 183: 45364542.
  • Jormakka M, Törnroth S, Byrne B & Iwata S (2002) Molecular basis of proton motiveforce generation: structure of formate dehydrogenase-N. Science 295: 18631868.
  • Jormakka M, Richardson D, Byrne B & Iwata S (2004) Architecture of NarGH reveals a structural classification of Mo-bisMGD enzymes. Structure 12: 95104.
  • Kampschreur MJ, van der Star WR, Wielders HA, Mulder JW, Jetten MSM & van Loosdrecht MC (2008) Dynamics of nitric oxide and nitrous oxide emission during full-scale reject water treatment. Water Res 42: 812826.
  • Kampschreur MJ, Poldermans R, Kleerebezem R, van der Star WR, Haarhuis R, Abma WR, Jetten MSM & van Loosdrecht MC (2009) Emission of nitrous oxide and nitric oxide from a full-scale single-stage nitritation-anammox reactor. Water Sci Technol 60: 32113217.
  • Karlsson R, Karlsson A, Bäckman O, Johansson BR & Hulth S (2009) Identification of key proteins involved in the anammox reaction. FEMS Microbiol Lett 297: 8794.
  • Kartal B, Rattray J, van Niftrik LA et al. (2007a) Candidatus “Anammoxoglobus propionicus” a new propionate oxidizing species of anaerobic ammonium oxidizing bacteria. Syst Appl Microbiol 30: 3949.
  • Kartal B, Kuypers MMM, Lavik G, Schalk J, Op den Camp HJM, Jetten MSM & Strous M (2007b) Anammox bacteria disguised as denitrifiers: nitrate reduction to dinitrogen gas via nitrite and ammonium. Environ Microbiol 9: 635642.
  • Kartal B, van Niftrik L, Rattray J, van de Vossenberg JL, Schmid MC, Sinninghe Damsté J, Jetten MSM & Strous M (2008) Candidatus ‘Brocadia fulgida’: an autofluorescent anaerobic ammonium oxidizing bacterium. FEMS Microbiol Ecol 63: 4655.
  • Kartal B, Kuenen JG & van Loosdrecht MC (2010a) Sewage treatment with anammox. Science 328: 702703.
  • Kartal B, Tan NC, Van de Biezen E, Kampschreur MJ, Van Loosdrecht MC & Jetten MSM (2010b) Effect of nitric oxide on anammox bacteria. Appl Environ Microbiol 76: 63046306.
  • Kartal B, Geerts W & Jetten MSM (2011a) Cultivation, detection, and ecophysiology of anaerobic ammonium-oxidizing bacteria. Methods Enzymol 486: 89108.
  • Kartal B, Maalcke WJ, de Almeida NM et al. (2011b) Molecular mechanism of anaerobic ammonium oxidation. Nature 479: 127130.
  • Kartal B, van Niftrik L, Keltjens JT, Op den Camp HJ & Jetten MS (2012) Anammox–growth physiology, cell biology, and metabolism. Adv Microb Physiol 60: 211262.
  • Kaster AK, Moll J, Parey K & Thauer RK (2011) Coupling of ferredoxin and heterodisulfide reduction via electron bifurcation in hydrogenotrophic methanogenic archaea. P Natl Acad Sci USA 108: 29812986.
  • Kern M & Simon J (2009) Electron transport chains and bioenergetics of respiratory nitrogen metabolism in Wolinella succinogenes and other Epsilonproteobacteria. Biochim Biophys Acta 1787: 646656.
  • Khademi S, O'Connell J 3rd, Remis J, Robles-Colmenares Y, Miercke LJ & Stroud RM (2004) Mechanism of ammonia transport by Amt/MEP/Rh: structure of AmtB at 1.35 A. Science 305: 15871594.
  • Kim HJ, Zatsman A, Upadhyay AK, Whittaker M, Bergmann D, Hendrich MP & Hooper AB (2008) Membrane tetraheme cytochrome cm552 of the ammonia-oxidizing Nitrosomonas europaea: a ubiquinone reductase. Biochemistry 47: 65396551.
  • Kloer DP, Hagel C, Heider J & Schulz GE (2006) Crystal structure of ethylbenzene dehydrogenase from Aromatoleum aromaticum. Structure 14: 13771388.
  • Klotz MG & Stein LY (2008) Nitrifier genomics and evolution of the nitrogen cycle. FEMS Microbiol Lett 278: 146156.
  • Klotz MG, Schmid MC, Strous M, Op den Camp HJM, Jetten MSM & Hooper AB (2008) Evolution of an octahaem cytochrome c protein family that is key to aerobic and anaerobic ammonia oxidation by bacteria. Environ Microbiol 10: 31503163.
  • Kostera J, Youngblut MD, Slosarczyk JM & Pacheco AA (2008) Kinetic and product distribution analysis of NO* reductase activity in Nitrosomonas europaea hydroxylamine oxidoreductase. J Biol Inorg Chem 13: 10731083.
  • Kostera J, McGarry J & Pacheco AA (2010) Enzymatic interconversion of ammonia and nitrite: the right tool for the job. Biochemistry 49: 85468553.
  • Kraft B, Strous M & Tegetmeyer HE (2011) Microbial nitrate respiration-genes, enzymes and environmental distribution. J Biotechnol 155: 104117.
  • Kuenen JG (2008) Anammox bacteria: from discovery to application. Nat Rev Microbiol 6: 320326.
  • Kuypers MMM, Sliekers AO, Lavik G, Schmid M, Jørgensen BB, Kuenen JG, Sinninghe Damsté JS, Strous M & Jetten MSM (2003) Anaerobic ammonium oxidation by anammox bacteria in the Black Sea. Nature 422: 608611.
  • Lam P & Kuypers MMM (2011) Microbial nitrogen cycling processes in oxygen minimum zones. Ann Rev Mar Sci 3: 317345.
  • Law CJ, Maloney PC & Wang DN (2008) Ins and outs of major facilitator superfamily antiporters. Annu Rev Microbiol 62: 289305.
  • Leigh JA & Dodsworth JA (2007) Nitrogen regulation in bacteria and archaea. Annu Rev Microbiol 61: 349377.
  • Li X, Jayachandran S, Nguyen HH & Chan MK (2007) Structure of the Nitrosomonas europaea Rh protein. P Natl Acad Sci USA 104: 1927919284.
  • Li M, Cao H, Hong Y & Gu JD (2011) Spatial distribution and abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in mangrove sediments. Appl Microbiol Biotechnol 89: 12431254.
  • Lindsay MR, Webb RI, Strous M, Jetten MSM, Butler MK, Forde RJ & Fuerst JA (2001) Cell compartmentalisation in planctomycetes: novel types of structural organisation for the bacterial cell. Arch Microbiol 175: 413429.
  • Loschi L, Brokx SJ, Hills TL, Zhang G, Bertero MG, Lovering AL, Weiner JH & Strynadka NC (2004) Structural and biochemical identification of a novel bacterial oxidoreductase. J Biol Chem 279: 5039150400.
  • Lü W, Du J, Wacker T, Gerbig-Smentek E, Andrade SL & Einsle O (2011) pH-dependent gating in a FocA formate channel. Science 332: 352534.
  • Lücker S, Wagner M, Maixner F et al. (2010) A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria. P Natl Acad Sci USA 107: 1347913484.
  • Machczynski MC, Vijgenboom E, Samyn B & Canters GW (2004) Characterization of SLAC: a small laccase from Streptomyces coelicolor with unprecedented activity. Protein Sci 13: 23882397.
  • Martínez-Espinosa RM, Cole JA, Richardson DJ & Watmough NJ (2011) Enzymology and ecology of the nitrogen cycle. Biochem Soc Trans 39: 175178.
  • Medema MH, Zhou M, van Hijum SA, Gloerich J, Wessels HJ, Siezen RJ & Strous M (2010) A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis. BMC Genomics 11: 299.
  • Mitchell P (1975a) Protonmotive redox mechanism of the cytochrome b-c1 complex in the respiratory chain: protonmotive ubiquinone cycle. FEBS Lett 56: 16.
  • Mitchell P (1975b) The protonmotive Q cycle: a general formulation. FEBS Lett 59: 137139.
  • Mohan SB, Schmid M, Jetten MSM & Cole J (2004) Detection and widespread distribution of the nrfA gene encoding nitrite reduction to ammonia, a short circuit in the biological nitrogen cycle that competes with denitrification. FEMS Microbiol Ecol 49: 433443.
  • Moir JW & Wood NJ (2001) Nitrate and nitrite transport in bacteria. Cell Mol Life Sci 58: 215224.
  • Mowat CG & Chapman SK (2005) Multi-heme cytochromes–new structures, new chemistry. Dalton Trans 7: 33813389.
  • Mulkidjanian AY (2010) Activated Q-cycle as a common mechanism for cytochrome bc1 and cytochrome b6f complexes. Biochim Biophys Acta 1797: 18581868.
  • Neumann S, Jetten MSM & van Niftrik L (2011) The ultrastructure of the compartmentalized anaerobic ammonium-oxidizing bacteria is linked to their energy metabolism. Biochem Soc Trans 39: 18051810.
  • Ni BJ, Hu BL, Fang F, Xie WM, Kartal B, Liu XW, Sheng GP, Jetten M, Zheng P & Yu HQ (2010) Microbial and physicochemical characteristics of compact anaerobic ammonium-oxidizing granules in an upflow anaerobic sludge blanket reactor. Appl Environ Microbiol 76: 26522656.
  • Op den Camp HJM, Kartal B, Güven D et al. (2006) Global impact and application of the anaerobic ammonium-oxidizing(anammox) bacteria. Biochem Soc Trans 34: 174178.
  • Oshiki M, Shimokawa M, Fujii N, Satoh H & Okabe S (2011) Physiological characteristics of the anaerobic ammonium-oxidizing bacterium Candidatus ‘Brocadia sinica’. Microbiology 157: 17061713.
  • Osyczka A, Moser CC & Dutton PL (2005) Fixing the Q cycle. Trends Biochem Sci 30: 176182.
  • Otte S, Grobben NG, Robertson LA, Jetten MSM & Kuenen JG (1996) Nitrous oxide production by Alcaligenes faecalis under transient and dynamic aerobic and anaerobic conditions. Appl Environ Microbiol 62: 24212426.
  • Pacheco AA, McGarry J, Kostera J & Corona A (2011) Techniques for investigating hydroxylamine disproportionation by hydroxylamine oxidoreductases. Methods Enzymol 486: 447463.
  • Paetzel M, Karla A, Strynadka NC & Dalbey RE (2002) Signal peptidases. Chem Rev 102: 45494580.
  • Penton CR, Devol AH & Tiedje JM (2006) Molecular evidence for the broad distribution of anaerobic ammonium-oxidizing bacteria in freshwater and marine sediments. Appl Environ Microbiol 72: 68296832.
  • Pierce E, Xie G, Barabote RD et al. (2008) The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum). Environ Microbiol 10: 25502573.
  • Polyakov KM, Boyko KM, Tikhonova TV, Slutsky A, Antipov AN, Zvyagilskaya RA, Popov AN, Bourenkov GP, Lamzin VS & Popov VO (2009) High-resolution structural analysis of a novel octaheme cytochrome c nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio nitratireducens. J Mol Biol 389: 846862.
  • Poulos TL (2010) Thirty years of heme peroxidase structural biology. Arch Biochem Biophys 500: 312.
  • Quan ZX, Rhee SK, Zuo JE, Yang Y, Bae JW, Park JR, Lee ST & Park YH (2008) Diversity of ammonium-oxidizing bacteria in a granular sludge anaerobic ammonium-oxidizing (anammox) reactor. Environ Microbiol 10: 31303139.
  • Ragsdale SW & Pierce E (2008) Acetogenesis and the Wood-Ljungdahl pathway of CO2 fixation. Biochim Biophys Acta 1784: 18731898.
  • Rattray JE, van de Vossenberg J, Hopmans EC, Kartal B, van Niftrik L, Rijpstra WI, Strous M, Jetten MSM, Schouten S & Sinninghe Damsté JS (2008) Ladderane lipid distribution in four genera of anammox bacteria. Arch Microbiol 190: 5166.
  • Rattray JE, van de Vossenberg J, Jaeschke A et al. (2010) Impact of temperature on ladderane lipid distribution in anammox bacteria. Appl Environ Microbiol 76: 15961603.
  • Richards FA (1965) Chemical observations in some anoxic, sulfide-bearing basins and fjords. Advances in Water Pollution Research, Vol. 3 (Pearson EA, ed), pp. 215232. Pergamon Press, Inc., London.
  • Richardson DJ (2000) Bacterial respiration: a flexible process for a changing environment. Microbiology 146: 551571.
  • Richter K, Schicklberger M & Gescher J (2012) Dissimilatory reduction of extracellular electron acceptors in anaerobic respiration. Appl Environ Microbiol 78: 913921.
  • Robinson C, Matos CF, Beck D, Ren C, Lawrence J, Vasisht N & Mendel S (2011) Transport and proofreading of proteins by the twin-arginine translocation (Tat) system in bacteria. Biochim Biophys Acta 1808: 876884.
  • Rothery RA, Workun GJ & Weiner JH (2008) The prokaryotic complex iron-sulfur molybdoenzyme family. Biochim Biophys Acta 1778: 18971929.
  • Saleh-Lakha S, Shannon KE, Henderson SL, Goyer C, Trevors JT, Zebarth BJ & Burton DL (2009) Effect of pH and temperature on denitrification gene expression and activity in Pseudomonas mandelii. Appl Environ Microbiol 75: 39033911.
  • Sànchez-Melsió A, Cáliz J, Balaguer MD, Colprim J & Vila X (2009) Development of batch-culture enrichment coupled to molecular detection for screening of natural and man-made environments in search of anammox bacteria for N-removal bioreactors systems. Chemosphere 75: 169179.
  • Sazanov LA (2007) Respiratory complex I: mechanistic and structural insights provided by the crystal structure of the hydrophilic domain. Biochemistry 46: 22752288.
  • Sazanov LA & Hinchliffe P (2006) Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus. Science 311: 14301436.
  • Schalk J, de Vries S, Kuenen JG & Jetten MSM (2000) Involvement of a novel hydroxylamine oxidoreductase in anaerobic ammonium oxidation. Biochemistry 39: 54055412.
  • Schmid M, Walsh K, Webb R et al. (2003) Candidatus “Scalindua brodae”, sp. nov., Candidatus “Scalindua wagneri”, sp. nov., two new species of anaerobic ammonium oxidizing bacteria. Syst Appl Microbiol 26: 529538.
  • Schmid MC, Maas B, Dapena A et al. (2005) Biomarkers for in situ detection of anaerobic ammonium-oxidizing (anammox) bacteria. Appl Environ Microbiol 71: 16771684.
  • Schmid MC, Risgaard-Petersen N, van de Vossenberg J et al. (2007) Anaerobic ammonium-oxidizing bacteria in marine environments: widespread occurrence but low diversity. Environ Microbiol 9: 14761484.
  • Schmid MC, Hooper AB, Klotz MG, Woebken D, Lam P, Kuypers MMM, Pommerening-Roeser A, Op den Camp HJM & Jetten MSM (2008) Environmental detection of octahaem cytochrome c hydroxylamine/hydrazine oxidoreductase genes of aerobic and anaerobic ammonium-oxidizing bacteria. Environ Microbiol 10: 31403149.
  • Schmidt I (2008) Nitric oxide: interaction with the ammonia monooxygenase and regulation of metabolic activities in ammonia oxidizers. Methods Enzymol 440: 121135.
  • Schmidt I, Look C, Bock E & Jetten MSM (2004a) Ammonium and hydroxylamine uptake and accumulation in Nitrosomonas. Microbiology 150: 14051412.
  • Schmidt JE, Batstone DJ & Angelidaki I (2004b) Improved nitrogen removal in upflow anaerobic sludge blanket (UASB) reactors by incorporation of Anammox bacteria into the granular sludge. Water Sci Technol 49: 6976.
  • Schubert CJ, Durisch-Kaiser E, Wehrli B, Thamdrup B, Lam P & Kuypers MMM (2006) Anaerobic ammonium oxidation in a tropical freshwater system (Lake Tanganyika). Environ Microbiol 8: 18571863.
  • Shi L, Squier TC, Zachara JM & Fredrickson JK (2007) Respiration of metal (hydr)oxides by Shewanella and Geobacter: a key role for multihaem c-type cytochromes. Mol Microbiol 65: 1220.
  • Shimamura M, Nishiyama T, Shigetomo H, Toyomoto T, Kawahara Y, Furukawa K & Fujii T (2007) Isolation of a multiheme protein with features of a hydrazine-oxidizing enzyme from an anaerobic ammonium-oxidizing enrichment culture. Appl Environ Microbiol 73: 10651072.
  • Shimamura M, Nishiyama T, Shinya K, Kawahara Y, Furukawa K & Fujii T (2008) Another multiheme protein, hydroxylamine oxidoreductase, abundantly produced in an anammox bacterium besides the hydrazine-oxidizing enzyme. J Biosci Bioeng 105: 243248.
  • Simon J (2002) Enzymology and bioenergetics of respiratory nitrite ammonification. FEMS Microbiol Rev 26: 285309.
  • Simon J & Klotz MG (2012) Diversity and evolution of bioenergetic systems involved in microbial nitrogen compound transformations. Biochim Biophys Acta. http://dx.doi.org/10.1016/j.bbabio.2012.07.005. [Epub ahead of print].
  • Simon J, van Spanning RJ & Richardson DJ (2008) The organisation of proton motive and non-proton motive redox loops in prokaryotic respiratory systems. Biochim Biophys Acta 1777: 14801490.
  • Sinninghe Damsté JS, Strous M, Rijpstra WI, Hopmans EC, Geenevasen JA, van Duin AC, van Niftrik LA & Jetten MSM (2002) Linearly concatenated cyclobutane lipids form a dense bacterial membrane. Nature 419: 708712.
  • Sinninghe Damsté JS, Rijpstra WI, Geenevasen JA, Strous M & Jetten MSM (2005) Structural identification of ladderane and other membrane lipids of planctomycetes capable of anaerobic ammonium oxidation (anammox). FEBS J 272: 42704283.
  • Sjögren T & Hajdu J (2001) The structure of an alternative form of Paracoccus pantotrophus cytochrome cd1 nitrite reductase. J Biol Chem 276: 2945029455.
  • Skálová T, Dohnálek J, Østergaard LH, Østergaard PR, Kolenko P, Dusková J, Stepánková A & Hasek J (2009) The structure of the small laccase from Streptomyces coelicolor reveals a link between laccases and nitrite reductases. J Mol Biol 385: 11651178.
  • Smith CJ, Nedwell DB, Dong LF & Osborn AM (2007) Diversity and abundance of nitrate reductase genes (narG and napA), nitrite reductase genes (nirS and nrfA), and their transcripts in estuarine sediments. Appl Environ Microbiol 73: 36123622.
  • Speth DR, Hu B, Bosch N, Keltjens JT, Stunnenberg HG & Jetten MS (2012a) Comparative genomics of two independently enriched “Candidatus Kuenenia stuttgartiensis” anammox bacteria. Front Microbiol 3: 307.
  • Speth DR, van Teeseling MC & Jetten MS (2012b) Genomic analysis indicates the presence of an asymmetric bilayer outer membrane in Planctomycetes and Verrucomicrobia. Front Microbiol 3: 304.
  • Stein LY (2011) Surveying N2O-producing pathways in bacteria. Methods Enzymol 486: 131152.
  • Strohm TO, Griffin B, Zumft WG & Schink B (2007) Growth yields in bacterial denitrification and nitrate ammonification. Appl Environ Microbiol 73: 14201424.
  • Strous M, Heijnen JJ, Kuenen JG & Jetten MSM (1998) The sequencing batch reactor as a powerful tool for the study of slowly growing anaerobic ammonium-oxidizing microorganisms. Appl Microbiol Biotechnol 50: 589596.
  • Strous M, Fuerst JA, Kramer EH, Logemann S, Muyzer G, van de Pas-Schoonen KT, Webb R, Kuenen JG & Jetten MSM (1999a) Missing lithotroph identified as new planctomycete. Nature 400: 446449.
  • Strous M, Kuenen JG & Jetten MSM (1999b) Key physiology of anaerobic ammonium oxidation. Appl Environ Microbiol 65: 32483250.
  • Strous M, Pelletier E, Mangenot S et al. (2006) Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature 440: 790794.
  • Suneethi S & Joseph K (2011) Batch culture enrichment of ANAMMOX populations from anaerobic and aerobic seed cultures. Bioresour Technol 102: 585591.
  • Sutter M, Boehringer D, Gutmann S, Günther S, Prangishvili D, Loessner MJ, Stetter KO, Weber-Ban E & Ban N (2008) Structural basis of enzyme encapsulation into a bacterial nanocompartment. Nat Struct Mol Biol 15: 939947.
  • Tavares P, Pereira AS, Moura JJ & Moura I (2006) Metalloenzymes of the denitrification pathway. J Inorg Biochem 100: 20872100.
  • Thauer RK, Kaster AK, Seedorf H, Buckel W & Hedderich R (2008) Methanogenic archaea: ecologically relevant differences in energy conservation. Nat Rev Microbiol 6: 579591.
  • Tsushima I, Ogasawara Y, Kindaichi T, Satoh H & Okabe S (2007a) Development of high-rate anaerobic ammonium-oxidizing (anammox) biofilm reactors. Water Res 41: 16231634.
  • Tsushima I, Ogasawara Y, Shimokawa M, Kindaichi T & Okabe S (2007b) Development of a super high-rate Anammox reactor and in situ analysis of biofilm structure and function. Water Sci Technol 55: 917.
  • Ukita S, Fujii T, Hira D, Nishiyama T, Kawase T, Migita CT & Furukawa K (2010) A heterodimeric cytochrome c complex with a very low redox potential from an anaerobic ammonium-oxidizing enrichment culture. FEMS Microbiol Lett 313: 6167.
  • Van de Graaf AA, Mulder A, de Bruijn P, Jetten MSM, Robertson LA & Kuenen JG (1995) Anaerobic oxidation of ammonium is a biologically mediated process. Appl Environ Microbiol 61: 12461251.
  • Van de Graaf AA, de Bruijn P, Robertson LA, Jetten MSM & Kuenen JG (1996) Autotrophic growth of anaerobic ammonium-oxidizing micro-organisms in a fluidized bed reactor. Microbiology 142: 21872196.
  • Van de Graaf AA, de Bruijn P, Robertson LA, Jetten MSM & Kuenen JG (1997) Metabolic pathway of anaerobic ammonium oxidation on basis of N-15 studies in a fluidized bed reactor. Microbiology 143: 24152421.
  • Van de Vossenberg J, Woebken D, Maalcke WJ et al. (2012) The metagenome of the marine anammox bacterium ‘Candidatus Scalindua profunda’ illustrates the versatility of this globally important nitrogen cycle bacterium. Environ Microbiol. doi:10.1111/j.1462-2920,2012.02774.x. [Epub ahead of print]
  • Van der Star WR, Miclea AI, van Dongen UG, Muyzer G, Picioreanu C & van Loosdrecht MC (2008a) The membrane bioreactor: a novel tool to grow anammox bacteria as free cells. Biotechnol Bioeng 101: 286294.
  • Van der Star WR, van de Graaf MJ, Kartal B, Picioreanu C, Jetten MSM & van Loosdrecht MC (2008b) Response of anaerobic ammonium-oxidizing bacteria to hydroxylamine. Appl Environ Microbiol 74: 44174426.
  • Van der Star WR, Dijkema C, de Waard P, Picioreanu C, Strous M & van Loosdrecht MC (2010) An intracellular pH gradient in the anammox bacterium Kuenenia stuttgartiensis as evaluated by 31P NMR. Appl Microbiol Biotechnol 86: 311317.
  • Van Niftrik L & Jetten MS (2012) Anaerobic ammonium-oxidizing bacteria: unique microorganisms with exceptional properties. Microbiol Mol Biol Rev 76: 585596.
  • Van Niftrik LA, Fuerst JA, Sinninghe Damsté JS, Kuenen JG, Jetten MSM & Strous M (2004) The anammoxosome: an intracytoplasmic compartment in anammox bacteria. FEMS Microbiol Lett 233: 713.
  • Van Niftrik L, Geerts WJ, van Donselaar EG, Humbel BM, Webb RI, Fuerst JA, Verkleij AJ, Jetten MSM & Strous M (2008a) 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: 708717.
  • Van Niftrik L, Geerts WJ, van Donselaar EG, Humbel BM, Yakushevska A, Verkleij AJ, Jetten MSM & Strous M (2008b) Combined structural and chemical analysis of the anammoxosome: a membrane-bounded intracytoplasmic compartment in anammox bacteria. J Struct Biol 161: 401410.
  • Van Niftrik L, van Helden M, Kirchen S, van Donselaar EG, Harhangi HR, Webb RI, Fuerst JA, Op den Camp HJM, Jetten MSM & Strous M (2010) Intracellular localization of membrane-bound ATPases in the compartmentalized anammox bacterium ‘Candidatus Kuenenia stuttgartiensis’. Mol Microbiol 77: 701715.
  • Verkhovsky MI & Bogachev AV (2010) Sodium-translocating NADH:quinone oxidoreductase as a redox-driven ion pump. Biochim Biophys Acta 1797: 738746.
  • Wagner M & Horn M (2006) The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance. Curr Opin Biotechnol 17: 241249.
  • Waight AB, Love J & Wang DN (2010) Structure and mechanism of a pentameric formate channel. Nat Struct Mol Biol 17: 3137.
  • Wang Y, Huang Y, Wang J, Cheng C, Huang W, Lu P, Xu YN, Wang P, Yan N & Shi Y (2009) Structure of the formate transporter FocA reveals a pentameric aquaporin-like channel. Nature 462: 467472.
  • Ward BB, Devol AH, Rich JJ, Chang BX, Bulow SE, Naik H, Pratihary A & Jayakumar A (2009) Denitrification as the dominant nitrogen loss process in the Arabian Sea. Nature 461: 7881.
  • Watmough NJ, Field SJ, Hughes RJ & Richardson DJ (2009) The bacterial respiratory nitric oxide reductase. Biochem Soc Trans 37: 392399.
  • Wilmot CM & Davidson VL (2009) Uncovering novel biochemistry in the mechanism of tryptophan tryptophylquinone cofactor biosynthesis. Curr Opin Chem Biol 13: 469474.
  • Windey K, De Bo I & Verstraete W (2005) Oxygen-limited autotrophic nitrification-denitrification (OLAND) in a rotating biological contactor treating high-salinity wastewater. Water Res 39: 45124520.
  • Woebken D, Lam P, Kuypers MMM, Naqvi SW, Kartal B, Strous M, Jetten MSM, Fuchs BM & Amann R (2008) A microdiversity study of anammox bacteria reveals a novel Candidatus Scalindua phylotype in marine oxygen minimum zones. Environ Microbiol 10: 31063119.
  • Yasuda T, Waki M, Yoshinaga I, Amano T, Suzuki K, Tanaka Y, Yamagishi T & Suwa Y (2011) Evidence of exponential growth of an anammox population in an anaerobic batch culture. Microbes Environ 26: 266269.
  • Yu R & Chandran K (2010) Strategies of Nitrosomonas europaea 19718 to counter low dissolved oxygen and high nitrite concentrations. BMC Microbiol 10: 70.
  • Yuan J, Zweers JC, van Dijl JM & Dalbey RE (2010) Protein transport across and into cell membranes in bacteria and archaea. Cell Mol Life Sci 67: 179199.
  • Zheng L, Kostrewa D, Bernèche S, Winkler FK & Li XD (2004) The mechanism of ammonia transport based on the crystal structure of AmtB of Escherichia coli. P Natl Acad Sci USA 101: 1709017095.