Chapter 7 : Distribution and Activity of Ammonia-Oxidizing Archaea in Natural Environments

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in

Distribution and Activity of Ammonia-Oxidizing Archaea in Natural Environments, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817145/9781555814816_Chap07-1.gif /docserver/preview/fulltext/10.1128/9781555817145/9781555814816_Chap07-2.gif


One of the major challenges in studying microorganisms from natural habitats is the inability to cultivate many of them in the laboratory. Recently, the complete genome sequence of was determined from a metagenomic library providing further insights into the potential physiological properties of uncultured ammonia-oxidizing archaea (AOA). The genes of ammonia-oxidizing bacteria (AOB) and AOA are distantly related, and molecular approaches to study the distribution and diversity of ammonia oxidizers rely on specific PCR primers that amplify the archaeal A or the bacterial A variant. Nitrification is an important process in sedimentary biogeochemistry and particularly in estuarine sediments, which can be exposed to high loads of nutrients from agricultural runoff. There is now unambiguous evidence for the occurrence of AOA in environments of elevated temperature. The mechanisms by which soil pH influences the growth and activity of many microbial functional groups have been determined through a combination of physiological and soil microcosm studies. With their involvement in ammonia oxidation, the majority of mesophilic crenarchaeota (or thaumarchaeota) are most likely major players in biogeochemical cycling. Most studies that attempted to evaluate the actual activity of AOA (and bacteria) seem to reveal that there could, in fact, be an ecological niche differentiation between AOA and AOB.

Citation: Nicol G, Leininger S, Schleper C. 2011. Distribution and Activity of Ammonia-Oxidizing Archaea in Natural Environments, p 157-178. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch7

Key Concept Ranking

Bacteria and Archaea
Denaturing Gradient Gel Electrophoresis
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


Image of FIGURE 1

Phylogenetic analysis of crenarchaeal 16S rRNA gene sequences recovered from marine and terrestrial environments together with cultivated AOA and hyperthermophiles. Sequence names in bold represent cultivated organisms or genomic fragments containing both 16S rRNA and AMO subunit genes. Lineages with a bold arc represent those known to have associated AMO subunit genes. Dashed lines at multifurcating nodes indicate manual adjustment reflecting low bootstrap support for any relative branching order. The scale bar represents an estimated 0.05 changes per nucleotide position, and numbers at nodes indicate the most conservative value of bootstrap support from three treeing methods.

Citation: Nicol G, Leininger S, Schleper C. 2011. Distribution and Activity of Ammonia-Oxidizing Archaea in Natural Environments, p 157-178. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch7
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2

Phylogenetic analysis showing the diversity of AMO subunit A genes associated with archaea and the environments from which they were obtained. The height and length of each triangle is proportional to the number of taxa included in this analysis and maximum individual branch length, respectively. The scale bars represent an estimated 0.05 changes per nucleotide position, and numbers at nodes indicate the most conservative value of bootstrap support from three treeing methods. (From , with permission.)

Citation: Nicol G, Leininger S, Schleper C. 2011. Distribution and Activity of Ammonia-Oxidizing Archaea in Natural Environments, p 157-178. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch7
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 3

Analysis of a soil depth profile of a sandy ecosystem (Rotböll, Darmstadt, Germany). Absolute numbers of genes of archaea and bacteria quantified by qPCR and phylogenetic analysis illustrating the relatedness of AOA sequences retrieved from two depths (0 to 10 and 60 to 70 cm) are shown. The clustering of sequences from the same depth demonstrates the presence of populations adapted to specific conditions within the soil profile. (Adapted from data obtained by Leininger et al., 806–809, 2006, with permission from Macmillan Publishers, Ltd.)

Citation: Nicol G, Leininger S, Schleper C. 2011. Distribution and Activity of Ammonia-Oxidizing Archaea in Natural Environments, p 157-178. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch7
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 4

Distribution of inorganic nitrogen, ammonia oxidation rates, and archaeal and 16S rRNA genes in a 100 m vertical profile in Guaymas Basin, Gulf of California. Areas of active nitrification and correlation with crenarchaeal/AOA numbers and NH ammonia oxidation rates are highlighted between dotted lines. (From Beman et al., 429–441, 2008, with permission from Macmillan Publishing, Ltd.)

Citation: Nicol G, Leininger S, Schleper C. 2011. Distribution and Activity of Ammonia-Oxidizing Archaea in Natural Environments, p 157-178. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch7
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 5

Growth of acetylene-sensitive AOA in nitrifying soil microcosms. (A) Denaturing gradient gel electrophoresis (DGGE) analysis of AOA communities after PCR amplification of genes. Each lane represents an individual microcosm. The arrow indicates the growth of a specific population of AOA in control microcosms only (no acetylene). (B) Demonstration of complete inhibition of ammonia-oxidizing activity in microcosms with a 10 Pa acetylene headspace partial pressure. (C) qPCR assay specific for the AOA population highlighted in the DGGE profile. Growth of the AOA occurred only in those microcosms with active nitrification. (Adapted from data obtained by Offre et al., 99–108, 2009, with permission.)

Citation: Nicol G, Leininger S, Schleper C. 2011. Distribution and Activity of Ammonia-Oxidizing Archaea in Natural Environments, p 157-178. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch7
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 6

Abundances of AOB and AOA in nitrifying soil mesocosms amended with fertilizer and various amounts of the antibiotic sulfadiazine. genes were quantified by qPCR. Dark gray bars, 0 mg of sulfadiazine (kg of soil) added; light gray bars, 10 mg kg added; open bars, 100 mg kg added. While both AOA and AOB communities increased in size upon fertilization, the AOA population was less sensitive to sulfadiazine and thus was probably responsible for most of the ammonia oxidation measured after antibiotic treatment. Note the large numbers of archaea compared with AOB (different scales in the figure). (From Schauss et al., 446–456, 2009, with permission.)

Citation: Nicol G, Leininger S, Schleper C. 2011. Distribution and Activity of Ammonia-Oxidizing Archaea in Natural Environments, p 157-178. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch7
Permissions and Reprints Request Permissions
Download as Powerpoint


1. Agogue, H.,, M. Brink,, J. Dinasquet, and, G. J. Herndl. 2008. Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic. Nature. 456:788791.
2. Allison, S. M.,, and J. I. Prosser. 2001. Urease activity in neutrophilic autotrophic ammonia-oxidizing bacteria isolated from acid soils. Soil Biol. Biochem. 23:4551.
3. Avrahami, S.,, and B. J. Bohannan. 2007. Response of Nitrosospira sp. strain AF-like ammonia oxidizers to changes in temperature, soil moisture content, and fertilizer concentration. Appl. Environ. Microbiol. 73:11661173.
4. Barns, S. M.,, C. F. Delwiche,, J. D. Palmer, and, N. R. Pace. 1996. Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc. Natl. Acad. Sci. USA 93:91889193.
5. Bartossek, R.,, G. W. Nicol,, A. Lanzen,, H.- P. Klenk, and, C. Schleper. 2010. Homologues of nitrite reductases in ammonia-oxidizing archaea: diversity and genomic context. Environ. Microbiol. 12:10751088.
6. Beja, O.,, M. T. Suzuki,, E. V. Koonin,, L. Aravind,, A. Hadd,, L. P. Nguyen,, R. Villacorta,, M. Amjadi,, C. Garrigues,, S. B. Jovanovich,, R. A. Feldman, and, E. F. DeLong. 2000. Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ. Microbiol. 2:516529.
7. Beja, O.,, E. V. Koonin,, L. Aravind,, L. T. Taylor,, H. Seitz,, J. L. Stein,, D. C. Bensen,, R. A. Feldman,, R. V. Swanson, and, E. F. DeLong. 2002. Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces. Appl. Environ. Microbiol. 68:335345.
8. Beman J. M.,, and C. A. Francis. 2006. Diversity of ammonia oxidizing Archaea and bacteria in the sediments of a hypernutrified subtropical estuary: Bahía del Tóbari, Mexico. Appl. Environ. Microbiol. 72:76777777.
9. Beman, J. M.,, K. J. Roberts,, L. Wegley,, F. Rohwer, and, C. A. Francis. 2007. Distribution and diversity of archaeal ammonia monooxygenase genes associated with corals. Appl. Environ. Microbiol. 73:56425647.
10. Beman, J. M.,, B. N. Popp, and, C. A. Francis. 2008. Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California. ISME J. 2:429441.
11. Berg, I. A.,, D. Kockelkorn,, W. Buckel, and, G. Fuchs. 2007. A 3-hydroxypropionate/4-hydroxy-butyrate autotrophic carbon dioxide assimilation pathway in Archaea. Science 318:17821786.
12. Bernhard, A. E.,, T. Donn,, A. E. Giblin, and, D. A. Stahl. 2005. Loss of diversity of ammonia-oxidizing bacteria correlates with increasing salinity in an estuary system. Environ. Microbiol. 7:12891297.
13. Bernhard, A. E.,, J. Tucker,, A. E. Giblin, and, D. A. Stahl. 2007. Functionally distinct communities of ammonia-oxidizing bacteria along an estuarine salinity gradient. Environ. Microbiol. 9:14391447.
14. Boyle-Yarwood, S. A.,, P. J. Bottomley, and, D. D. Myrold. 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.
15. Brochier-Armanet, C.,, B. Boussau,, S. Gribaldo, and, P. Forterre. 2008. Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat. Rev. Microbiol. 6:245252.
16. Buckley, D. H.,, J. R. Graber, and, T. M. Schmidt. 1998. Phylogenetic analysis of nonthermophilic members of the kingdom crenarchaeota and their diversity and abundance in soils. Appl. Environ. Microbiol. 64:43334339.
17. Cantera, J. J.,, and L. Y. Stein, 2007. Molecular diversity of nitrite reductase genes (nirK) in nitrifying bacteria. Environ. Microbiol. 9:765776.
18. Cebron, A.,, T. Berthe, and, J. Garnier. 2003. Nitrification and nitrifying bacteria in the lower Seine River and estuary (France). Appl. Environ. Microbiol. 69:70917100.
19. Coolen, M. J.,, B. Abbas,, J. van Bleijswijk,, E. C. Hopmans,, M. M. Kuypers,, S. G. Wakeham, and, J. S. Sinninghe Damsté. 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.
20. Corredor, J. E.,, C. R. Wilkinson,, V. P. Vicente,, J. M. Morell, and, E. Otero. 1988. Nitrate release by Caribbean reef sponges. Limnol. Oceanogr. 33:114120.
21. de Bie, M. J. M.,, A. Speksnijder,, G. A. Kowalchuk,, T. Schuurman,, G. Zwart,, J. R. Stephen,, O. E. Diekmann, and, H. J. Laanbroek. 2001. Shifts in the dominant populations of ammonia-oxidizing beta-subclass Proteobacteria along the eutrophic Schelde estuary. Aquatic Microbiol. Ecol. 23:225236.
22. De Boer, W.,, and G. A. Kowalchuk. 2001. Nitrification in acid soils: microorganisms and mechanisms. Soil Biol. Biochem. 33:853866.
23. de la Torre, J. R.,, C. B. Walker,, A. E. Ingalls,, M. Konneke, and, D. A. Stahl. 2008. Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environ. Microbiol. 10:810818.
24. DeLong, E. F. 1992. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 89:56855689.
25. DeLong, E. F. 1998. Everything in moderation: archaea as “non-extremophiles.” Curr. Opin. Genet. Dev. 8:649654.
26. DeLong, E. F.,, L. T. Taylor,, T. L. Marsh, and, C. M. Preston. 1999. Visualization and enumeration of marine planktonic archaea and bacteria by using polyribonucleotide probes and fluorescent in situ hybridization. Appl. Environ. Microbiol. 65:55545563.
27. Di, H. J.,, K. C. Cameron,, J. P. Shen,, C. S. Wine-field,, M. O’Callaghan,, S. Bowatte, and, J. Z. He. 2009. Nitrification driven by bacteria and not archaea in nitrogen-rich grassland soils. Nat. Geosci. 2:621624.
28. Diaz, M. C.,, and B. B. Ward. 1997. Sponge-mediated nitrification in tropical benthic communities. Mar. Ecol. Prog. Ser. 156:97107.
29. Diaz, M. C.,, D. Akob, and, C. S. Cary. 2004. Denaturing gradient gel electrophoresis of nitrifying microbes associated with tropical sponges. Boll. Mus. Ist. Biol. Univ. Genova 68:279289.
30. Galloway, J. N.,, F. J. Dentener,, D. G. Capone,, E. W. Boyer,, R. W. Howarth,, S. P. Seitzinger,, G. P. Asner,, C. C. Cleveland,, P. A. Green,, E. A. Holland,, D. M. Karl,, A. F. Michaels,, J. H. Porter,, A. R. Townsend, and, C. J. Vorosmarty. 2004. Nitrogen cycles: past, present, and future. Biogeochemistry 70:153226.
31. Garcia, J.-L.,, B. K. C. Patel, and, B. Ollivier. 2000. Taxonomic, phylogenetic, and ecological diversity of methanogenic Archaea. Anaerobe 6:205226.
32. Fierer, N.,, and R. B. Jackson. 2006. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. USA 103:626631.
33. Francis, C. A.,, G. D. O’Mullan, and, B. B. Ward. 2003. Diversity of ammonia monooxygenase (amoA) genes across environmental gradients in Chesapeake Bay sediments. Geobiology 1:129140.
34. Francis, C. A.,, K. J. Roberts,, J. M. Beman,, A. E. Santoro, and, B. B. Oakley. 2005. Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proc. Natl. Acad. Sci. USA 102:1468314688.
35. Hallam, S. J.,, K. T. Konstantinidis,, N. Putnam,, C. Schleper,, Y. Watanabe,, J. Sugahara,, C. Preston,, J. de la Torre,, P. M. Richardson, and, E. F. DeLong. 2006a. Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proc. Natl. Acad. Sci. USA 103:1829618301.
36. Hallam, S. J.,, T. J. Mincer,, C. Schleper,, C. M. Preston,, K. Roberts,, P. M. Richardson, and, E. F. DeLong. 2006b. Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. PLoS Biol. 4:e95.
37. Handelsman, J. 2004. Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev. 68:669685.
38. Hansel, C. M.,, S. Fendorf,, P. M. Jardine, and, C. A. Francis. 2008. Changes in bacterial and archaeal community structure and functional diversity along a geochemically variable soil profile. Appl. Environ. Microbiol. 74:16201633.
39. Hatzenpichler, R.,, E. V. Lebedeva,, E. Spieck,, K. Stoecker,, A. Richter,, H. Daims, and, M. Wagner. 2008. A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. Proc. Natl. Acad. Sci. USA 105:21342139.
40. He, J.,, J. Shen,, L. Zhang,, Y. Zhu,, Y. Zheng,, M. Xu, and, H. J. Di. 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.
41. Herfort, L.,, S. Schouten,, B. Abbas,, M. J. Veldhuis,, M. J. Coolen,, C. Wuchter,, J. P. Boon,, G. J. Herndl, and, J. S. Sinninghe Damsté. 2007. Variations in spatial and temporal distribution of Archaea in the North Sea in relation to environmental variables. FEMS Microbiol. Ecol. 62:242257.
42. Herndl, G. J.,, T. Reinthaler,, E. Teira,, H. van Aken,, C. Veth,, A. Pernthaler, and, J. Pernthaler. 2005. Contribution of archaea to total prokaryotic production in the deep Atlantic Ocean. Appl. Environ. Microbiol. 71:23032309.
43. Hoffmann, F.,, R. Radax,, D. Woebken,, M. Holtappels,, G. Lavik,, H. T. Rapp,, M.- L. Schläppy,, C. Schleper, and, M. M. Kuypers. 2010. Complex nitrogen cycling in the sponge Geodia barretti. Environ. Microbiol. 11:22282243.
44. Holmes, B.,, and H. Blanch. 2007. Genus-specific associations of marine sponges with group I crenarchaeotes. Mar. Biol. 150:759772.
45. Ingalls, A. E.,, S. R. Shah,, R. L. Hansman,, L. I. Aluwihare,, G. M. Santos,, E. R. Druffel, and, A. Pearson. 2006. Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon. Proc. Natl. Acad. Sci. USA 103:64426447.
46. Jia, Z.,, and R. Conrad. 2009. Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil. Environ. Microbiol. 11:16581671.
47. Jimenez, E.,, and M. Ribes. 2007. Sponges as a source of dissolved inorganic nitrogen: Nitrification mediated by temperate sponges. Limnol. Oceanogr. 52:948958.
48. Karner, M. B.,, E. F. DeLong, and, D. M. Karl. 2001. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature. 409:507510.
49. Koops, H.-P.,, U. Purkhold,, A. Pommerening-Rösner,, G. Timmermann, and, M. Wagner. 2003. The lithoautotrophic ammonia-oxidizing bacteria, p. 778–811. In M. Dworkin,, S. Falkow,, E. Rosenberg,, K.-H. Schleifer, and, E. Stackebrandt (ed.), The Prokaryotes: an Evolving Electronic Resource for the Microbiological Community, 3rd ed., vol. 5. Springer-Verlag, New York, NY.
50. Konstantinidis, K. T.,, J. Braff,, D. M. Karl, and, E. F. DeLong. 2009. Comparative metagenomic analysis of a microbial community residing at a depth of 4,000 meters at station ALOHA in the North Pacific Subtropical Gyre. Appl. Environ. Microbiol. 75:53455355.
51. Kvist, T.,, A. Mengewein,, S. Manzel,, B. K. Ahring, and, P. Westermann. 2005. Diversity of thermophilic and non-thermophilic crenarchaeota at 80 degrees C. FEMS Microbiol. Lett. 244:6168.
52. Kvist, T.,, B. K. Ahring, and, P. Westermann. 2007. Archaeal diversity in Icelandic hot springs. FEMS Microbiol. Ecol. 59:7180.
53. Könneke, M.,, A. E. Bernhard,, J. R. de la Torre,, C. B. Walker,, J. B. Waterbury, and, D. A. Stahl. 2005. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437:543546.
54. Kuypers, M. M.,, P. Blokker,, J. Erbacher,, H. Kinkel,, R. D. Pancost,, S. Schouten, and, J. S. Sinninghe Damsté. 2001. Massive expansion of marine archaea during a mid-Cretaceous oceanic anoxic event. Science 293:9295.
55. Lam, P.,, M. M. Jensen,, G. Lavik,, D. F. McGinnis,, B. Muller,, C. J. Schubert,, R. Amann,, B. Thamdrup, and, M. M. M. Kuypers. 2007. Linking crenarchaeal and bacterial nitrification to anammox in the Black Sea. Proc. Natl. Acad. Sci. USA 104:71047109.
56. Lebedeva, E. V.,, M. Alawi,, C. Fiencke,, B. Namsaraev,, E. Bock, and, E. Spieck. 2005. Moderately thermophilic nitrifying bacteria from a hot spring of the Baikal rift zone. FEMS Microbiol. Ecol. 54:297306.
57. Leininger, S.,, T. Urich,, M. Schloter,, L. Schwark,, J. Qi,, G. W. Nicol,, J. I. Prosser,, S. C. Schuster, and, C. Schleper. 2006. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442:806809.
58. Lieberman, R. L.,, and A. C. Rosenzweig. 2005. Crystal structure of a membrane-bound metalloenzyme that catalyses the biological oxidation of methane. Nature 434:177182.
59. Lopez-Garcia, P.,, C. Brochier,, D. Moreira, and, F. Rodriguez-Valera. 2004. Comparative analysis of a genome fragment of an uncultivated mesopelagic crenarchaeote reveals multiple horizontal gene transfers. Environ. Microbiol. 6:1934.
60. Mahmood, S.,, and J. I. Prosser. 2006. The influence of synthetic sheep urine on ammonia oxidizing bacterial communities in grassland soil. FEMS Microbiol. Ecol. 56:444454.
61. Martens-Habbena, W.,, P. M. Berube,, H. Urakawa,, J. R. de la Torre, and, D. A. Stahl. 2009. Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature 461:976979.
62. Massana, R.,, A. E. Murray,, C. M. Preston, and, E. F. DeLong. 1997. Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel. Appl. Environ. Microbiol. 63:5056.
63. Mincer, T. J.,, M. J. Church,, L. T. Taylor,, C. Preston,, D. M. Karl, and, E. F. DeLong. 2007. Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre. Environ. Microbiol. 9:11621175.
64. Mosier, A. C.,, and C. A. Francis. 2008. Relative abundance of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary. Environ. Microbiol. 10:30023016.
65. Murray, A. E.,, C. M. Preston,, R. Massana,, L. T. Taylor,, A. Blakis,, K. Wu, and, E. F. DeLong. 1998. Seasonal and spatial variability of bacterial and archaeal assemblages in the coastal waters near Anvers Island, Antarctica. Appl. Environ. Microbiol. 64:25852595.
66. Murray, A. E.,, A. Blakis,, R. Massana,, S. Strawzewski,, U. Passow,, A. Alldredge, and, E. F. DeLong. 1999. A time series assessment of planktonic archaeal variability in the Santa Barbara Channel. Aquat. Microb. Ecol. 20:129145.
67. Nakagawa, T.,, K. Mori,, C. Kato,, R. Takahashi, and, T. Tokuyama. 2007. Distribution of cold-adapted ammonia-oxidizing microorganisms in the deep-ocean of the northeastern Japan Sea. Microbes Environ. 22:365372.
68. Nicol, G. W.,, and C. Schleper. 2006. Ammoniaoxidising Crenarchaeota: important players in the nitrogen cycle? Trends Microbiol. 14:207212.
69. Nicol, G. W.,, L. A. Glover, and, J. I. Prosser. 2003. The impact of grassland management on archaeal community structure in upland pasture rhizosphere soil. Environ. Microbiol. 5:152162.
70. Nicol, G. W.,, G. Webster,, L. A. Glover, and, J. I. Prosser. 2004. Differential response of archaeal and bacterial communities to nitrogen inputs and pH changes in upland pasture rhizosphere soil. Environ. Microbiol. 6:861867.
71. Nicol, G. W.,, D. Tscherko,, T. M. Embley, and, J. I. Prosser. 2005. Primary succession of soil Crenarchaeota across a receding glacier foreland. Environ. Microbiol. 7:337347.
72. Nicol, G. W.,, D. Tscherko,, L. Chang,, U. Hammesfahr, and, J. I. Prosser. 2006. Crenarchaeal community assembly and microdiversity in developing soils at two sites associated with deglaciation. Environ. Microbiol. 8:13821393.
73. Nicol, G. W.,, S. Leininger,, C. Schleper, and, J. I. Prosser. 2008. The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environ. Microbiol. 10:29662978.
74. Ochsenreiter, T.,, D. Selezi,, A. Quaiser,, L. Bonch-Osmolovskaya, and, C. Schleper. 2003. Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time PCR. Environ. Microbiol. 5:787797.
75. Offre, P.,, J. I. Prosser, and, G. W. Nicol. 2009 Growth of ammonia-oxidizing archaea in soil microcosms is inhibited by acetylene. FEMS Microbiol. Ecol. 70:99108.
76. O’Mullan, G. D.,, and B. B. Ward. 2005. Relationship of temporal and spatial variabilities of ammonia-oxidizing bacteria to nitrification rates in Monterey Bay, California. Appl. Environ. Microbiol. 71:697705.
77. Ouverney, C. C.,, and J. A. Fuhrman. 2000. Marine planktonic archaea take up amino acids. Appl. Environ. Microbiol. 66:48294833.
78. Pearson, A.,, A. P. McNichol,, B. C. Benitez-Nelson,, J. M. Hayes, and, T. I. Eglinton. 2001. Origins of lipid biomarkers in Santa Monica Basin surface sediment: A case study using compound-specific Delta C-14 analysis. Geochim. Cosmochim. Acta. 65:31233137.
79. Preston, C. M.,, K. Y. Wu,, T. F. Molinski, and, E. F. DeLong. 1996. A psychrophilic crenarchaeon inhabits a marine sponge: Cenarchaeum symbiosum gen. nov., sp. nov. Proc. Natl. Acad. Sci. USA 93:62416246.
80. Prosser, J. I.,, and G. W. Nichol. 2008. Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment. Environ. Microbiol. 10:29312941.
81. Quaiser, A.,, T. Ochsenreiter,, H. P. Klenk,, A. Kletzin,, A. H. Treusch,, G. Meurer,, J. Eck,, C. W. Sensen, and, C. Schleper. 2002. First insight into the genome of an uncultivated crenarchaeote from soil. Environ. Microbiol. 4:603611.
82. Reigstad, L. J.,, A. Richter,, H. Daims,, T. Urich,, L. Schwark, and, C. Schleper. 2008. Nitrification in terrestrial hot springs of Iceland and Kamchatka. FEMS Microbiol. Ecol. 64:167174.
83. Sandaa, R. A.,, O. Enger, and, V. Torsvik. 1999. Abundance and diversity of Archaea in heavy-metal-contaminated soils. Appl. Environ. Microbiol. 65:32932937.
84. Santoro, A. E.,, C. A. Francis,, N. R. de Sieyes, and, A. B. Boehm. 2008. Shifts in the relative abundance of ammonia-oxidizing bacteria and archaea across physicochemical gradients in a subterranean estuary. Environ. Microbiol. 10:10681079.
85. Schauss, K.,, A. Focks,, S. Leininger,, A. Kotzerke,, H. Heuer,, S. Thiele-Bruhn,, S. Sharma,, B.- M. Wilke,, M. Matthies,, K. Smalla,, J. C. Munch,, W. Amelung,, M. Kaupenjohann,, M. Schloter, and, C. Schleper. 2009. Dynamics and functional relevance of ammonia-oxidizing archaea in two agricultural soils. Environ. Microbiol. 11:446456.
86. Schleper, C.,, R. V. Swanson,, E. J. Mathur, and, E. F. DeLong. 1997. Characterization of a DNA polymerase from the uncultivated psychrophilic archaeon Cenarchaeum symbiosum. J. Bacteriol. 179:78037811.
87. Schleper, C.,, E. F. DeLong,, C. M. Preston,, R. A. Feldman,, K. Y. Wu, and, R. V. Swanson. 1998. Genomic analysis reveals chromosomal variation in natural populations of the uncultured psychrophilic archaeon Cenarchaeum symbiosum. J. Bacteriol. 180:50035009.
88. Schleper, C.,, G. Jurgens, and, M. Jonuscheit. 2005. Genomic studies of uncultivated archaea. Nat. Rev. Microbiol. 3:479488.
89. Seitzinger, S. P. 1988. Denitrification in freshwater and coastal marine ecosystems: ecological and geochemical significance. Limnol. Oceanogr. 33:702724.
90. Seitzinger, S.,, J. A. Harrison,, J. K. hlke,, A. F. Bouwman,, R. Lowrance,, B. Peterson,, C. Tobias, and, G. V. Drecht. 2006. Denitrification across landscapes and waterscapes: a synthesis. Ecol. Appl. 16:20642090.
91. Spang, A.,, R. Hatzenpichler,, C. Brochier-Armanet,, T. Rattei,, P. Tischler,, E. Spieck,, W. Streit,, D. A. Stahl,, M. Wagner, and, C. Schleper. 2010. Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota. Trends Microbiol. 18:331340.
92. Spear, J. R.,, H. A. Barton,, C. E. Robertson,, C. A. Francis, and, N. R. Pace. 2007. Microbial community biofabrics in a geothermal mine adit. Appl. Environ. Microbiol. 73:61726180.
93. Steger, D.,, P. Ettinger-Epstein,, S. Whalan,, U. Hentschel,, R. de Nys,, M. Wagner, and, M. W. Taylor. 2008. Diversity and mode of transmission of ammonia-oxidizing archaea in marine sponges. Environ. Microbiol. 10:10871094.
94. Stein, J. L.,, T. L. Marsh,, K. Y. Wu,, H. Shizuya, and, E. F. DeLong. 1996. Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J. Bacteriol. 178:591599.
95. Taylor, M. W.,, R. Radax,, D. Steger, and, M. Wagner. 2007. Sponge-associated microorganisms: evolution, ecology, and biotechnological potential. Microbiol. Mol. Biol. Rev. 71:295347.
96. Teira, E.,, H. van Aken,, C. Veth, and, G. J. Herndl. 2006a. Archaeal uptake of enantiomeric amino acids in the meso- and bathypelagic waters of the North Atlantic. Limnol. Oceanogr. 51:6069.
97. Teira, E.,, P. Lebaron,, H. van Aken, and, G. J. Herndl. 2006b. Distribution and activity of Bacteria and Archaea in the deep water masses of the North Atlantic. Limnol. Oceanogr. 51:21312144.
98. Treusch, A.,, and C. Schleper. 2005. Environmental genomics: a novel tool to study uncultivated microorganisms, p. 45–58. In C. W. Sensen (ed.), Handbook of Genome Research. Wiley-VCH, Weinheim, Germany.
99. Treusch, A. H.,, A. Kletzin,, G. Raddatz,, T. Ochsenreiter,, A. Quaiser,, G. Meurer,, S. C. Schuster, and, C. Schleper. 2004. Characterization of large-insert DNA libraries from soil for environmental genomic studies of Archaea. Environ. Microbiol. 6:970980.
100. Treusch, A. H.,, S. Leininger,, A. Kletzin,, S. C. Schuster,, H. P. Klenk, and, C. Schleper. 2005. Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environ. Microbiol. 7:19851995.
101. Tourna, M.,, T. E. Freitag,, G. W. Nicol, and, J. I. Prosser. 2008. Growth, activity and temperature responses of ammonia oxidising archaea and bacteria in soil microcosms. Environ. Microbiol. 10:13571364.
102. Valentine, D. L. 2007. Adaptations to energy stress dictate the ecology and evolution of the Archaea. Nat. Rev. Microbiol. 5:316323.
103. Venter, J. C.,, K. Remington,, J. F. Heidelberg,, A. L. Halpern,, D. Rusch,, J. A. Eisen,, D. Wu,, I. Paulsen,, K. E. Nelson,, W. Nelson,, D. E. Fouts,, S. Levy,, A. H. Knap,, M. W. Lomas,, K. Nealson,, O. White,, J. Peterson,, J. Hoffman,, R. Parsons,, H. Baden-Tillson,, C. Pfannkoch,, Y. H. Rogers, and, H. O. Smith. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:6674.
104. Wang, S.,, X. Xiao,, L. Jiang,, X. Peng,, H. Zhou,, J. Meng, and, F. Wang. 2009. Diversity and abundance of ammonia-oxidizing Archaea in hydro-thermal vent chimneys of the Juan de Fuca Ridge. Appl. Environ. Microbiol. 75:42164220.
105. Ward, B. B. 2000. Nitrification and the marine nitrogen cycle, p. 427–453. In D. L. Kirchmann (ed.), Microbial Ecology of the Oceans. Wiley Series, New York, NY.
106. Ward, B. B. 2005. Temporal variability in nitrification rates and related biogeochemical factors in Monterey Bay, California, USA. Mar. Ecol. Prog. Ser. 292:97109.
107. Weidler, G. W.,, F. W. Gerbl, and, H. Stan-Lotter. 2008. Crenarchaeota and their role in the nitrogen cycle in a subsurface radioactive thermal spring in the Austrian central Alps. Appl. Environ. Microbiol. 74:59345942.
108. Wells, G. F.,, H.- D. Park,, C.- H. Yeung,, B. Eggleston,, C. A. Francis, and, C. S. Criddle. 2009. Ammonia-oxidizing communities in a highly aerated full-scale activated sludge bioreactor: betaproteobacterial dynamics and low relative abundance of Crenarchaea. Environ. Microbiol. 11:23102328.
109. Wuchter, C.,, S. Schouten,, H. T. Boschker, and, J. S. Sinninghe Damste. 2003. Bicarbonate uptake by marine Crenarchaeota. FEMS Microbiol. Lett. 219:203207.
110. Wuchter, C.,, B. Abbas,, M. J. L. Coolen,, L. Her-fort,, J. van Bleijswijk,, P. Timmers,, M. Strous,, E. Teira,, G. J. Herndl,, J. J. Middelburg,, S. Schouten, and, J. S. S. Damste. 2006. Archaeal nitrification in the ocean. Proc. Natl. Acad. Sci. USA 103:1231712322.
111. Zhang, C. L.,, Q. Ye,, Z. Huang,, W. Li,, J. Chen,, Z. Song,, W. Zhao,, C. Bagwell,, W. P. Inskeep,, C. Ross,, L. Gao,, J. Wiegel,, C. S. Romanek,, E. L. Shock, and, B. P. Hedlund. 2008. Global occurrence of archaeal amoA genes in terrestrial hot springs. Appl. Environ. Microbiol. 74:64176426.

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error