Selected Publications :

From Nitrification Network investigators, suggested reading and general interest.

Stahl DA, de la Torre JR. Physiology and diversity of ammonia-oxidizing archaea. Annu Rev Microbiol. 2012 Oct 13;66:83-101.

Bouskill NJ, Eveillard D, Chien D, Jayakumar A, Ward BB. Environmental factors determining ammonia-oxidizing organism distribution and diversity in marine environments. Environ Microbiol. 2012 Mar;14(3):714-29. doi: 10.1111/j.1462-2920.2011.02623.x. Epub 2011 Nov 3.

Suwa Y, Norton JM, Bollmann A, Klotz MG, Stein LY, Laanbroek HJ, Arp DJ, Goodwin LA, Chertkov O, Held B, Bruce D, Detter JC, Detter JC, Tapia R, Han CS.Genome sequence of Nitrosomonas sp. strain AL212, an ammonia-oxidizing bacterium sensitive to high levels of ammonia. J Bacteriol. 2011 Sep;193(18):5047-8.

Klotz MG. Methods in Enzymology. Research on Nitrification and Related Processes, Part A. Methods in Enzymlogy 2011; v 486.

Stein LY and Klotz MG. Methods in Enzymology. Research on Nitrification and Related Processes, Part B. vMethods in Enzymlogy 2011; v 496.

Walker CB, de la Torre JR, Klotz MG, Urakawa H, Pinel N, Arp DJ, Brochier-Armanet C, Chain PS, Chan PP, Gollabgir A, Hemp J, Hügler M, Karr EA, Könneke M, Shin M, Lawton TJ, Lowe T, Martens-Habbena W, Sayavedra-Soto LA, Lang D, Sievert SM, Rosenzweig AC, Manning G, Stahl DA.Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea.Proc Natl Acad Sci U S A. 2010 May 11;107(19):8818-23.

Norton JM, Klotz MG, Stein LY, Arp DJ, Bottomley PJ, Chain PS, Hauser LJ, Land ML, Larimer FW, Shin MW, Starkenburg SR. Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment. Appl Environ Microbiol. 2008 Jun;74(11):3559-72.

Steger D, Ettinger-Epstein P, Whalan S, Hentschel U, de Nys R, Wagner M, Taylor MW.Diversity and mode of transmission of ammonia-oxidizing archaea in marine sponges. Environ Microbiol. 2008 Apr;10(4):1087-94.

de la Torre JR, Walker CB, Ingalls AE, Könneke M, Stahl DA. Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol.Environ Microbiol. 2008 Mar;10(3):810-8.

Starkenburg SR, Larimer FW, Stein LY, Klotz MG, Chain PS, Sayavedra-Soto LA, Poret-Peterson AT, Gentry ME, Arp DJ, Ward B, Bottomley PJ. The complete genome sequence of Nitrobacter hamburgensis X14 and a comparative genomic analysis of species within the Genus Nitrobacter. Appl Environ Microbiol. 2008 Mar 7.

Tourna M, Freitag TE, Nicol GW, Prosser JI. Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms. Environ Microbiol. 2008 Feb 27.

Hatzenpichler R, Lebedeva EV, Spieck E, Stoecker K, Richter A, Daims H, Wagner M. A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. Proc Natl Acad Sci U S A. 2008 Feb 12;105(6):2134-9.

Rich JJ, Dale OR, Song B, Ward BB. Anaerobic ammonium oxidation (anammox) in Chesapeake Bay sediments. Microb Ecol. 2008 Feb;55(2):311-20.

Schouten S, Hopmans EC, Baas M, Boumann H, Standfest S, Könneke M, Stahl DA, Sinninghe Damsté JS. Intact membrane lipids of Candidatus "Nitrosopumilus maritimus", a cultivated representative of the cosmopolitan mesophilic Group I Crenarchaeota. Appl Environ Microbiol. 2008 Feb 22;

Sievert SM, Scott KM, Klotz MG, Chain PS, Hauser LJ, Hemp J, Hügler M, Land M, Lapidus A, Larimer FW, Lucas S, Malfatti SA, Meyer F, Paulsen IT, Ren Q, Simon J; USF Genomics Class. Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans. Appl Environ Microbiol. 2008 Feb;74(4):1145-56.

de la Torre JR, Walker CB, Ingalls AE, Könneke M, Stahl DA. Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environ Microbiol. 2008 Mar;10(3):810-8.

Stein LY, Arp DJ, Berube PM, Chain PS, Hauser L, Jetten MS, Klotz MG, Larimer FW, Norton JM, Op den Camp HJ, Shin M, Wei X.Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation. Environ Microbiol. 2007 Dec;9(12):2993-3007. Link to download the tables of orthologue groupings.

Klotz MG, Stein LY. Nitrifier genomics and evolution of the nitrogen cycle. FEMS Microbiol Lett. 2007 Nov 20.

Bess B. Ward, Damien Eveillard, Julie D. Kirshtein, Joshua D. Nelson, Mary A. Voytek, George A. Jackson. Ammonia-oxidizing bacterial community composition in estuarine and oceanic environments assessed using a functional gene microarray. Environ Microbiol October 2007 9(10):2522-2538.

Gvakharia BO, Permina EA, Gelfand MS, Bottomley PJ, Sayavedra-Soto LA, Arp DJ. Global transcriptional response of Nitrosomonas europaea to chloroform and chloromethane. Appl Environ Microbiol. 2007 May;73(10):3440-5.

Arp DJ, Chain PS, Klotz MG . The Impact of Genome Analyses on Our Understanding of Ammonia-Oxidizing Bacteria. Annu Rev Microbiol. 2006 Aug 16.

Klotz MG, Arp DJ, Chain PS, El-Sheikh AF, Hauser LJ, Hommes NG, Larimer FW, Malfatti SA, Norton JM, Poret-Peterson AT, Vergez LM, Ward BB. Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707. Appl Environ Microbiol. 2006 Sep;72(9):6299-315.

Starkenburg SR, Chain PS, Sayavedra-Soto LA, Hauser L, Land ML, Larimer FW, Malfatti SA, Klotz MG, Bottomley PJ, Arp DJ, Hickey WJ. Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255. Appl Environ Microbiol. 2006 Mar;72(3):2050-63. [top]

Wei X, Yan T, Hommes NG, Liu X, Wu L, McAlvin C, Klotz MG, Sayavedra-Soto LA, Zhou J, Arp DJ. Transcript profiles of Nitrosomonas europaea during growth and upon deprivation of ammonia and carbonate. FEMS Microbiol Lett. 2006 Apr;257(1):76-83. [top]

Bergmann DJ, Hooper AB, Klotz MG. Structure and sequence conservation of hao cluster genes of autotrophic ammonia-oxidizing bacteria: evidence for their evolutionary history. Appl Environ Microbiol. 2005 Sep;71(9):5371-82. [top]

Burton EO, Read HW, Pellitteri MC, Hickey WJ. Identification of acyl-homoserine lactone signal molecules produced by Nitrosomonas europaea strain Schmidt. Appl Environ Microbiol. 2005 Aug;71(8):4906-9. [top]

Ward BB, O'Mullan GD. Community level analysis: genetic and biogeochemical approaches to investigate community composition and function in aerobic ammonia oxidation. Methods Enzymol. 2005;397:395-413. [top]

Casciotti KL, Ward BB. Phylogenetic analysis of nitric oxide reductase gene homologues from aerobic ammonia-oxidizing bacteria. FEMS Microbiol Ecol. 2005 Apr 1;52(2):197-205. Epub 2004 Dec 8. [top]

Koper TE, El-Sheikh AF, Norton JM, Klotz MG. Urease-encoding genes in ammonia-oxidizing bacteria. Appl Environ Microbiol. 2004 Apr;70(4):2342-8. [top]

Arp DJ, Stein LY. Metabolism of inorganic N compounds by ammonia-oxidizing bacteria. Crit Rev Biochem Mol Biol. 2003;38(6):471-95. Review. [top]

Chain P, Lamerdin J, Larimer F, Regala W, Lao V, Land M, Hauser L, Hooper A, Klotz M, Norton J, Sayavedra-Soto L, Arciero D, Hommes N, Whittaker M, Arp D. Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea. J Bacteriol. 2003 May;185(9):2759-73. Erratum in: J Bacteriol. 2003 Nov;185(21):6496. [top]



Suggested reading: [top]

Author: Editors: Bess B. Ward, Daniel J. Arp, and Martin G. Klotz. Nitrification; Book ISBN or Item Number: 978-1-55581-481-6[top]

Johan Rockström et al.A safe operating space for humanity.Nature 461, 472-475 (24 September 2009)[top]

Adair KL, Schwartz E. Evidence that ammonia-oxidizing Archaea are more abundant than ammonia-oxidizing bacteria in semiarid soils of Northern Arizona, USA. Microb Ecol. 2008 Jan 19.[top]

Christopher A Francis, J Michael Beman and Marcel M M Kuypers. New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation. Mini-Review; The ISME Journal (2007) 1, 19-27.[top]

Kartal B, Kuypers MM, Lavik G, Schalk J, Op den Camp HJ, Jetten MS, Strous M. Anammox bacteria disguised as denitrifiers: nitrate reduction to dinitrogen gas via nitrite and ammonium. Environ Microbiol. 2007 Mar;9(3):635-42.[top]

Douglas G. Capone and Angela N. Knapp. Oceanography: A marine nitrogen cycle fix?. Nature 445, 159-160 (11 January 2007).[top]

Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JI, Schuster SC, Schleper C. Archaea predominate among ammonia-oxidizing prokaryotes in soils.. Nature. 2006 Aug 17;442(7104):806-9.[top]

Prosser JI, Embley TM. Cultivation-based and molecular approaches to characterisation of terrestrial and aquatic nitrifiers. Antonie Van Leeuwenhoek. 2002 Aug;81(1-4):165-79.[top]

Kaiser J. Environmental policy. The other global pollutant: nitrogen proves tough to curb. Science. 2001 Nov 9;294(5545):1268-9. [top]

Arp DJ, Sayavedra-Soto LA, Hommes NG. Molecular biology and biochemistry of ammonia oxidation by Nitrosomonas europaea. Arch Microbiol. 2002 Oct;178(4):250-5. Epub 2002 Jun 27. Review. [top]

Bothe H, Jost G, Schloter M, Ward BB, Witzel K. Molecular analysis of ammonia oxidation and denitrification in natural environments. FEMS Microbiol Rev. 2000 Dec;24(5):673-90. Review. [top]

Zwolinski, Harris RF, Hickey WJ. Microbial consortia involved in the anaerobic degradation of hydrocarbons. Biodegradation. 2000;11(2-3):141-58. Review.[top]

Frink CR, Waggoner PE, Ausubel JH. Nitrogen fertilizer: retrospect and prospect. Proc Natl Acad Sci U S A. 1999 Feb 16;96(4):1175-80.[top]



General interest: [top]

Céline Brochier-Armanet, Bastien Boussau, Simonetta Gribaldo and Patrick Forterre. Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota Nature Reviews Microbiology 6, 245-252 (March 2008)[top]