1887

Chapter 3 : Diversity and Environmental Distribution of Ammonia-Oxidizing Bacteria

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
Zoomout

Diversity and Environmental Distribution of Ammonia-Oxidizing Bacteria, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817145/9781555814816_Chap03-1.gif /docserver/preview/fulltext/10.1128/9781555817145/9781555814816_Chap03-2.gif

Abstract:

This chapter discusses archaeal ammonia oxidation and anaerobic ammonia oxidation processes that have important roles in the global nitrogen cycle. It reviews the diversity, distribution, and biogeography of a subset of the ammonia-oxidizing prokaryotes, the aerobic chemolithotrophic ammonia-oxidizing bacteria (AOB). The terrestrial AOB are generally restricted to the , while the marine organisms are found both in the and the . Phylogeny inference based on the current data set does not support that all nitrosomonads are more closely related to each other than to members of the lineage; especially problematic is the placement of and sp. Stable clusters based on 16S rRNA phylogeny are problematic within because of the overall high levels of identity of the 16S rRNA (>97%). Soils are often dominated by spp., while marine and freshwater systems often have mixtures of the genera of AOB present. During secondary succession, microbial communities develop on the soils that are often depleted in the number and diversity of microorganisms. In marine habitats, , , and coexist with ammonia-oxidizing archaea; their relative contributions and diversity are only beginning to be delineated. The functional cohort of AOB, ammonia-oxidizing archaea, and the nitrite-oxidizing prokaryotes will persist as important model organisms for linking the process of nitrification to microbial diversity and biogeography.

Citation: Norton J. 2011. Diversity and Environmental Distribution of Ammonia-Oxidizing Bacteria, p 39-55. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch3

Key Concept Ranking

16s rRNA Sequencing
0.49600124
Nitrosomonas oligotropha
0.4368473
0.49600124
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of FIGURE 1
FIGURE 1

Two 16S ribosomal RNA guide trees for the clusters of beta-proteobacterial (top) and gamma-proteobacterial (bottom) AOB based on high-quality sequences (>1,200 bp) from isolates. Sequence data retrieval and analysis was preformed with RDP version 10 database functions ( ). Several 16S rRNA gene sequences were from ongoing genomic sequencing projects (M. G. Klotz, personal communication). The scale is substitution per site. Strain selection and cluster designations are based on those of ), , and .

Citation: Norton J. 2011. Diversity and Environmental Distribution of Ammonia-Oxidizing Bacteria, p 39-55. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch3
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2
FIGURE 2

Pairwise comparisons of 493 16S rRNA gene sequences of spp. for genetic distance (percentage of divergence) and geographic distance (m) between sources. Sequence data retrieval and analysis was performed with RDP version 10 database functions ( ). Geographic distances calculated in ArcGIS (version 9.1; Environmental Systems Research Institute, Redlands, CA) were transformed into four categories, as displayed. Statistical analysis on the untransformed geographic and sequence distance matrices was performed with the Mantel r test (Ade4 version 1.4-11 ( ) and indicated that DNA distance increased as geographic distance increased ( = 0.22, = 0.001).

Citation: Norton J. 2011. Diversity and Environmental Distribution of Ammonia-Oxidizing Bacteria, p 39-55. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch3
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555817145.ch03
1. Aakra, A.,, J. B. Utaker,, A. Pommerening-Roser,, H. P. Koops, and, I. F. Nes. 2001. Detailed phylogeny of ammonia-oxidizing bacteria determined by rDNA sequences and DNA homology values. Int. J. Syst. Evol. Microbiol. 51:20212030.
2. Alzerreca, J. J.,, J. M. Norton, and, M. G. Klotz. 1999. The amo operon in marine, ammonia-oxidizing gamma-proteobacteria. FEMS Microbiol. Lett. 180:2129.
3. Avrahami, S.,, and B. J. A. 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. Avrahami, S.,, and R. Conrad. 2005. Cold-temperate climate: a factor for selection of ammonia oxidizers in upland soil? Can. J. Microbiol. 51:709714.
5. Avrahami, S.,, W. Liesack, and, R. Conrad. 2003. Effects of temperature and fertilizer on activity and community structure of soil ammonia oxidizers. Environ. Microbiol. 5:691705.
6. Bano, N.,, and J. T. Hollibaugh. 2000. Diversity and distribution of DNA sequences with affinity to ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in the Arctic Ocean. Appl. Environ. Microbiol. 66:19601969.
7. 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.
8. 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.
9. Bock, E.,, H. P. Koops, and, H. Harms. 1986. Cell biology of nitrifying bacteria, p. 17–38. in J. I. Prosser (ed.), Nitrification. IRL Press, Oxford, United Kingdom.
10. Bollmann, A.,, and H. J. Laanbroek. 2002. Influence of oxygen partial pressure and salinity on the community composition of ammonia-oxidizing bacteria in the Schelde Estuary. Aquat. Microbiol. Ecol. 28:239247.
11. Bruns, M. A.,, J. R. Stephen,, G. A. Kowalchuk,, J. I. Prosser, and, E.A . Paul. 1999. Comparative diversity of ammonia oxidizer 16S rRNA gene sequences in native, tilled, and successional soils. Appl. Environ. Microbiol. 65:29943000.
12. Caffrey, J. M.,, N. Harrington,, I. Solem, and, B. B. Ward. 2003. Biogeochemical processes in a small California estuary. 2. Nitrification activity, community structure and role in nitrogen budgets. Mar. Ecol. Prog. Ser. 248:2740.
13. Cantera, J. J. L.,, and L. Y. Stein. 2007. Molecular diversity of nitrite reductase genes (nirK) in nitrifying bacteria. Environ. Microbiol. 9:765776.
14. 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.
15. Cebron, A.,, M. Coci,, J. Garnier, and, H. J. Laanbroek. 2004. Denaturing gradient gel electrophoretic analysis of ammonia-oxidizing bacterial community structure in the lower Seine River: impact of Paris wastewater effluents. Appl. Environ. Microbiol. 70:67266737.
16. Chain, P.,, J. Lamerdin,, F. Larimer,, W. Regala,, V. Lao,, M. Land,, L. Hauser,, A. Hooper,, M. Klotz,, J. Norton,, L. Sayavedra-Soto,, D. Arciero,, N. Hommes,, M. Whittaker, and, D. Arp. 2003. Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea. J. Bacteriol. 185:27592773.
17. Chapin, F. S.,, P. A. Matson, and, H. A. Mooney. 2002. Principles of Terrestrial Ecosystem Ecology. Springer, New York, NY.
18. Coci, M.,, D. Riechmann,, P. L. E. Bodelier,, S. Stefani,, G. Zwart, and, H. J. Laanbroek. 2005. Effect of salinity on temporal and spatial dynamics of ammonia-oxidising bacteria from intertidal freshwater sediment. FEMS Microbiol. Ecol. 53:359368.
19. Coci, M.,, P. L. E. Bodelier, and, H. J. Laanbroek. 2008. Epiphyton as a niche for ammonia-oxidizing bacteria: detailed comparison with benthic and pelagic compartments in shallow freshwater lakes. Appl. Environ. Microbiol. 74:19631971.
20. Cole, J. R.,, Q. Wang,, E. Cardenas,, J. Fish,, B. Chai,, R. J. Farris,, A. S. Kulam-Syed-Mohideen,, D. M. McGarrell,, T. Marsh,, G. M. Garrity, and, J. M. Tiedje. 2009. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucl. Acids Res. 37:D141D145.
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. Aquat. Microbiol. Ecol. 23:225236.
22. De Boer, W.,, and G. A. Kowalchuk. 2001. Nitrification in acid soils: micro-organisms and mechanisms. Soil Biol. Biochem. 33:853866.
23. De Boer, W.,, P. Gunnewiek,, M. Veenhuis,, E. Bock, and, H. J. Laanbroek. 1991. Nitrification at low pH by aggregated chemolithotrophic bacteria. Appl. Environ. Microbiol. 57:36003604.
24. Dell, E. A.,, D. Bowman,, T. Rufty, and, W. Shi. 2008. Intensive management affects composition of betaproteobacterial ammonia oxidizers in turfgrass systems. Microb. Ecol. 56:178190.
25. Dray, S.,, and A. B. Dufour. 2007. The ade4 package: implementing the duality diagram for ecologists. J. Stat. Softw. 22:120.
26. Euzeby, J. P., and B. J. Tindall. 2004. Status of strains that contravene Rules 27(3) and 30 of the Bacteriological Code. Request for an Opinion. Int. J. Syst. Evol. Microbiol. 54:293301.
27. Fierer, N.,, and R. B. Jackson. 2006. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. USA 103:626631.
28. Fierer, N.,, K. M. Carney,, M. C. Horner-Devine, and, J. P. Megonigal. 2009. The biogeography of ammonia-oxidizing bacterial communities in soil. Microbiol. Ecol. 58:435445.
29. 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.
30. Francis, C. A.,, J. M. Beman, and, M. M. Kuypers. 2007. New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation. ISME J. 1:1927.
31. Freitag, T. E.,, and J. I. Prosser. 2004. Differences between betaproteobacterial ammonia-oxidizing communities in marine sediments and those in overlying water. Appl. Environ. Microbiol. 70:37893793.
32. Freitag, T. E.,, L. Chang, and, J. I. Prosser. 2006. Changes in the community structure and activity of betaproteobacterial ammonia-oxidizing sediment bacteria along a freshwater-marine gradient. Environ. Microbiol. 8:684696.
33. Garbeva, P.,, E. M. Baggs, and, J. I. Prosser. 2007. Phylogeny of nitrite reductase (nirK) and nitric oxide reductase (norB) genes from Nitrosospira species isolated from soil. FEMS Microbiol. Lett. 266:8389.
34. Gomez-Alvarez, V.,, G. M. King, and, K. Nusslein. 2007. Comparative bacterial diversity in recent Hawaiian volcanic deposits of different ages. FEMS Microbiol. Ecol. 60:6073.
35. Gorra, R.,, M. Coci,, R. Ambrosoli, and, H. J. Laanbroek. 2007. Effects of substratum on the diversity and stability of ammonia-oxidizing communities in a constructed wetland used for wastewater treatment. J. Appl. Microbiol. 103:14421452.
36. Green, J. L.,, B. J. M. Bohannan, and, R. J. Whitaker. 2008. Microbial biogeography: from taxonomy to traits. Science 320:10391043.
37. Harms, H.,, H. P. Koops, and, H. Wehrmann. 1976. An ammonia-oxidizing bacterium, Nitrosovibrio tenuis nov. gen. nov. sp. Arch. Microbiol. 108:105111.
38. Hastings, R. C.,, J. R. Saunders,, G. H. Hall,, R. W. Pickup, and, A. J. McCarthy. 1998. Application of molecular biological techniques to a seasonal study of ammonia oxidation in a eutrophic freshwater lake. Appl. Environ. Microbiol. 64:36743682.
39. Hatzenpichler, R.,, E. V. Lebecleva,, 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. Head, I. M.,, W. D. Hiorns,, T. M. Embley,, A. J. McCarthy, and, J. R. Saunders. 1993. The phylogeny of autotrophic ammonia-oxidizing bacteria as determined by analysis of 16S ribosomal-RNA sequences J. Gen. Microbiol. 139:11471153.
41. Horner-Devine, M. C.,, and B. J. M. Bohannan. 2006. Phylogenetic clustering and overdispersion in bacterial communities. Ecology 87:S100S108.
42. Ibekwe, A. M.,, C. M. Grieve, and, S. R. Lyon. 2003. Characterization of microbial communities and composition in constructed dairy wetland wastewater effluent. Appl. Environ. Microbiol. 69:50605069.
43. Ida, T.,, M. Kugimiya,, M. Kogure,, R. Takahashi, and, T. Tokuyama. 2005. Phylogenetic relationships among ammonia-oxidizing bacteria as revealed by gene sequences of glyceraldehyde 3-phosphate dehydrogenase and phosphoglycerate kinase. J. Biosci. Bioeng. 99:569576.
44. Jenny, H. 1941. Factors of Soil Formation; a System of Quantitative Pedology. McGraw Hill, New York, NY.
45. Jiang, Q. Q.,, and L. R. Bakken. 1999. Comparison of Nitrosospira strains isolated from terrestrial environments. FEMS Microbiol. Ecol. 30:171186.
46. Jones, R. D.,, R. Y. Morita,, H. P. Koops, and, S. W. Watson. 1988. A new marine ammonium-oxidizing bacterium, Nitrosomonas cryotolerans sp.-nov. Can. J. Microbiol. 34:11221128.
47. Juretschko, S.,, G. Timmermann,, M. Schmid,, K. H. Schleifer,, A. Pommerening-Roser,, H. P. Koops, and, M. Wagner. 1998. Combined molecular and conventional analyses of nitrifying bacterium diversity in activated sludge: Nitrosococcus mobilis and Nitrospira-like bacteria as dominant populations. Appl. Environ. Microbiol. 64:30423051.
48. Kelly, J. J.,, S. Siripong,, J. McCormack,, L. R. Janus,, H. Urakawa,, S. El Fantroussi,, P. A. Noble,, L. Sappelsa,, B. E. Rittmann, and, D. A. Stahl. 2005. DNA microarray detection of nitrifying bacterial 16S rRNA in wastewater treatment plant samples. Water Res. 39:32293238.
49. King, G. M. 2003. Contributions of atmospheric CO and hydrogen uptake to microbial dynamics on recent Hawaiian volcanic deposits. Appl. Environ. Microbiol. 69:40674075.
50. Kitayama, K. 1996. Soil nitrogen dynamics along a gradient of long-term soil development in a Hawaiian wet montane rainforest. Plant Soil 183:253262.
51. Klotz, M. G.,, and L. Y. Stein. 2007. Nitrifier genomics and evolution of the N-cycle. FEMS Microbiol. Lett. 278:146156.
52. Klotz, M. G.,, D. J. Arp,, P. S. G. Chain,, A. F. El-Sheikh,, L. J. Hauser,, N. G. Hommes,, F. W. Larimer,, S. A. Malfatti,, J. M. Norton,, A. T. Poret-Peterson,, L. M. Vergez, and, B. B. Ward. 2006. Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707. Appl. Environ. Microbiol. 72:62996315.
53. Konneke, 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. Koops, H. P.,, and H. Harms. 1985. Deoxyribonucleic-acid homologies among 96 strains of ammonia-oxidizing bacteria. Arch. Microbiol. 141:214218.
55. Koops, H. P.,, and A. Pommerening-Roser. 2001. Distribution and ecophysiology of the nitrifying bacteria emphasizing cultured species. FEMS Microbiol. Ecol. 37:19.
56. Koops, H. P.,, H. Harms, and, H. Wehrmann. 1976. Isolation of a moderate halophilic ammonia-oxidizing bacterium, Nitrosococcus mobilis nov. sp. Arch. Microbiol. 107:277282.
57. Koops, H. P.,, B. Bottcher,, U. C. Moller,, A. Pommereningroser, and, G. Stehr. 1990. Description of a new species of Nitrosococcus. Arch. Microbiol. 154:244248.
58. Koops, H. P.,, B. Bottcher,, U. C. Moller,, A. Pommerening-Roser, and, G. Stehr. 1991. Classification of eight new species of ammonia-oxidizing bacteria: Nitrosomonas communis sp. nov., Nitrosomonas ureae sp. nov., Nitrosomonas aestuarii sp. nov., Nitrosomonas marina sp. nov., Nitrosomonas nitrosa sp. nov., Nitrosomonas oligotropha sp. nov., Nitrosomonas halophila sp. nov. J. Gen. Microbiol. 137:16891699.
59. Koper, T. E.,, A. F. El-Sheikh,, J. M. Norton, and, M. G. Klotz. 2004. Urease-encoding genes in ammonia-oxidizing bacteria. Appl. Environ. Microbiol. 70:23422348.
60. Kowalchuk, G. A.,, and J. R. Stephen. 2001. Ammonia-oxidizing bacteria: a model for molecular microbial ecology. Annu. Rev. Microbiol. 55:485529.
61. Kowalchuk, G. A.,, J. R. Stephen,, W. DeBoer,, J. I. Prosser,, T. M. Embley, and, J. W. Woldendorp. 1997. Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments. Appl. Environ. Microbiol. 63:14891497.
62. Kowalchuk, G. A.,, A. W. Stienstra,, G. H. J. Heilig,, J. R. Stephen, and, J. W. Woldendorp. 2000a. Changes in the community structure of ammonia-oxidizing bacteria during secondary succession of calcareous grasslands. Environ. Microbiol. 2:99110.
63. Kowalchuk, G. A.,, A. W. Stienstra,, G. H. J. Heilig,, J. R. Stephen, and, J. W. Woldendorp. 2000b. Molecular analysis of ammonia-oxidising bacteria in soil of successional grasslands of the Drentsche A (The Netherlands). FEMS Microbiol. Ecol. 31:207215.
64. Le Roux, X.,, F. Poly,, P. Currey,, C. Commeaux,, B. Hai,, G. W. Nicol,, J. I. Prosser,, M. Schloter,, E. Attard, and, K. Klumpp. 2008. Effects of above-ground grazing on coupling among nitrifier activity, abundance and community structure. ISME J. 2:221232.
65. 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.
66. Martiny, J. B. H.,, B. J. M. Bohannan,, J. H. Brown,, R. K. Colwell,, J. A. Fuhrman,, J. L. Green,, M. C. Horner-Devine,, M. Kane,, J. A. Krumins,, C. R. Kuske,, P. J. Morin,, S. Naeem,, L. Ovreas,, A. L. Reysenbach,, V. H. Smith, and, J. T. Staley. 2006. Microbial biogeography: putting microorganisms on the map. Nat. Rev. Microbiol. 4:102112.
67. Mendum, T. A.,, and P. R. Hirsch. 2002. Changes in the population structure of beta-group autotrophic ammonia oxidising bacteria in arable soils in response to agricultural practice. Soil Biol. Biochem. 34:14791485.
68. Mendum, T. A.,, R. E. Sockett, and, P. R. Hirsch. 1999. Use of molecular and isotopic techniques to monitor the response of autotrophic ammonia-oxidizing populations of the beta subdivision of the class Proteobacteria in arable soils to nitrogen fertilizer. Appl. Environ. Microbiol. 65:41554162.
69. Merila, P.,, A. Smolander, and, R. Strommer. 2002. Soil nitrogen transformations along a primary succession transect on the land-uplift coast in western Finland. Soil Biol. Biochem. 34:373385.
70. Mertens, J.,, D. Springael,, I. De Troyer,, K. Cheyns,, P. Wattiau, and, E. Smolders. 2006. Long-term exposure to elevated zinc concentrations induced structural changes and zinc tolerance of the nitrifying community in soil. Environ. Microbiol. 8:21702178.
71. Miteva, V.,, T. Sowers, and, J. Brenchley. 2007. Production of N2O by ammonia oxidizing bacteria at subfreezing temperatures as a model for assessing the N2O anomalies in the vostok ice core. Geomicrobiol. J. 24:451459.
72. Nejidat, A. 2005. Nitrification and occurrence of salt-tolerant nitrifying bacteria in the Negev desert soils. FEMS Microbiol. Ecol. 52:2129.
73. Nemergut, D. R.,, S. P. Anderson,, C. C. Cleveland,, A. P. Martin,, A. E. Miller,, A. Seimon, and, S. K. Schmidt. 2007. Microbial community succession in an unvegetated, recently deglaciated soil. Microb. Ecol. 53:110122.
74. Norton, J. M. 2008. Nitrification in agricultural soils, p. 173–199. In J. S. Schepers and, W. R. Raun (ed.), Nitrogen in Agricultural Systems. American Society of Agronomy, Inc.; Crop Science Society of America, Inc.; Soil Science Society of America, Inc., Madison, WI.
75. Norton, J. M.,, J. J. Alzerreca,, Y. Suwa, and, M. G. Klotz. 2002. Diversity of ammonia monooxygenase operon in autotrophic ammonia-oxidizing bacteria. Arch. Microbiol. 177:139149.
76. Norton, J. M.,, M. G. Klotz,, L. Y. Stein,, D. J. Arp,, P. J. Bottomley,, P. S. G. Chain,, L. J. Hauser,, M. L. Land,, F. W. Larimer,, M. W. Shin, and, S. R. Starkenburg. 2008. Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment. Appl. Environ. Microbiol. 74:35593572.
77. Nugroho, R. A.,, W. F. M. Roling,, A. M. Laverman, and, H. A. Verhoef. 2007. Low nitrification rates in acid scots pine forest soils are due to pH-related factors. Microbiol. Ecol. 53:8997.
78. 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.
79. Oved, T.,, A. Shaviv,, T. Goldrath,, R. T. Mandelbaum, and, D. Minz. 2001. Influence of effluent irrigation on community composition and function of ammonia-oxidizing bacteria in soil. Appl. Environ. Microbiol. 67:34263433.
80. Park, H. D.,, J. M. Regan, and, D. R. Noguera. 2002. Molecular analysis of ammonia-oxidizing bacterial populations in aerated-anoxic Orbal processes. Water Sci. Tech. 46:273280.
81. Park, H. D.,, G. F. Wells,, H. Bae,, C. S. Criddle, and, C. A. Francis. 2006. Occurrence of ammonia-oxidizing archaea in wastewater treatment plant bioreactors. Appl. Environ. Microbiol. 72:56435647.
82. Phillips, C. J.,, Z. Smith,, T. M. Embley, and, J. I. Prosser. 1999. Phylogenetic differences between particle-associated and planktonic ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in the northwestern Mediterranean Sea. Appl. Environ. Microbiol. 65:779786.
83. Phillips, C. J.,, D. Harris,, S. L. Dollhopf,, K. L. Gross,, J. I. Prosser, and, E. A. Paul. 2000. Effects of agronomic treatments on structure and function of ammonia-oxidizing communities. Appl. Environ. Microbiol. 66:54105418.
84. Polymenakou, P. N.,, M. Mandalakis,, E. G. Stephanou, and, A. Tselepides. 2008. Particle size distribution of airborne microorganisms and pathogens during an intense African dust event in the eastern Mediterranean. Environ. Health Perspect. 116:292296.
85. Pommerening-Roser, A.,, and H. P. Koops. 2005. Environmental pH as an important factor for the distribution of urease positive ammonia-oxidizing bacteria. Microbiol. Res. 160:2735.
86. Pommerening-Roser, A.,, G. Rath, and, H. P. Koops. 1996. Phylogenetic diversity within the genus Nitrosomonas. Syst. Appl. Microbiol. 19:344351.
87. Prosser, J. I.,, and T. M. Embley. 2002. Cultivation-based and molecular approaches to characterisation of terrestrial and aquatic nitrifiers. Antonie Van Leewenhoek Int. J. Gen. Mol. Microbiol. 81:165179.
88. Purkhold, U.,, A. Pommerening-Roser,, S. Juretschko,, M. C. Schmid,, H. P. Koops, and, M. Wagner. 2000. Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: Implications for molecular diversity surveys. Appl. Environ. Microbiol. 66:53685382.
89. Purkhold, U.,, M. Wagner,, G. Timmermann,, A. Pommerening-Roser, and, H. P. Koops. 2003. 16S rRNA and amo A-based phylogeny of 12 novel betaproteobacterial ammonia-oxidizing isolates: extension of the dataset and proposal of a new lineage within the nitrosomonads. Int. J. Syst. Evol. Microbiol. 53:14851494.
90. Ramette, A.,, and J. M. Tiedje. 2007a. Biogeography: An emerging cornerstone for understanding prokaryotic diversity, ecology, and evolution. Microbiol. Ecol. 53:197207.
91. Ramette, A.,, and J. M. Tiedje. 2007b. Multiscale responses of microbial life to spatial distance and environmental heterogeneity in a patchy ecosystem. Proc. Natl. Acad. Sci. USA 104:27612766.
92. Rotthauwe, J. H.,, W. de Boer, and, W. Liesak. 1995. Comparative analysis of gene sequences encoding for ammonia monooxygenase of Nitrosospira sp. AHB1 and Nitrosolobus multiformis C-71. FEMS Microbiol. Lett. 133:133135.
93. Ruiz-Rueda, O.,, S. Hallin, and, L. Baneras. 2009. Structure and function of denitrifying and nitrifying bacterial communities in relation to the plant species in a constructed wetland. FEMS Microbiol. Ecol. 67:308319.
94. Sigler, W. V.,, and J. Zeyer. 2002. Microbial diversity and activity along the forefields of two receding glaciers. Microbiol. Ecol. 43:397407.
95. Siripong, S.,, and B. E. Rittmann. 2007. Diversity study of nitrifying bacteria in full-scale municipal wastewater treatment plants. Water Res. 41:11101120.
96. Smithwick, E. A. H.,, M. G. Turner,, M. C. Mack, and, F. S. Chapin. 2005. Postfire soil N cycling in northern conifer forests affected by severe, stand-replacing wildfires. Ecosystems 8:163181.
97. Song, Y. N.,, P. Marschner,, L. Li,, X. G. Bao,, J. H. Sun, and, F. S. Zhang. 2007. Community composition of ammonia-oxidizing bacteria in the rhizosphere of intercropped wheat (Triticum aestivum L.), maize (Zea mays L.), and faba bean (Vicia faba L.). Biol. Fertil. Soils 44:307314.
98. Sorokin, D.,, T. Tourova,, M. C. Schmid,, M. Wagner,, H. P. Koops,, J. G. Kuenen, and, M. Jetten. 2001. Isolation and properties of obligately chemolithoautotrophic and extremely alkali-tolerant ammonia-oxidizing bacteria from Mongolian soda lakes. Arch. Microbiol. 176:170177.
99. Stein, L. Y.,, D. J. Arp,, P. M. Berube,, P. S. G. Chain,, L. Hauser,, M. S. M. Jetten,, M. G. Klotz,, F. W. Larimer,, J. M. Norton,, H. J. M. O. d. Camp,, M. Shin, and, X. Wei. 2007. Whole-genome analysis of the ammonia-oxidzing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation. Environ. Microbiol. 9:29933007.
100. Stephen, J. R.,, A. E. McCaig,, Z. Smith,, J. I. Prosser, and, T. M. Embley. 1996. Molecular diversity of soil and marine 16S rRNA gene sequences related to beta-subgroup ammonia-oxidizing bacteria. Appl. Environ. Microbiol. 62:41474154.
101. Suwa, Y.,, Y. Imamura,, T. Suzuki,, T. Tashiro, and, Y. Urushigawa. 1994. Ammonia-oxidizing bacteria with different sensitivities to (NH4)2SO4 in activated sludges. Water Res. 28:15231532.
102. Teske, A.,, E. Alm,, J. M. Regan,, S. Toze,, B. E. Rittmann, and, D. A. Stahl. 1994. Evolutionary relationships among ammonia-oxidizing and nitrite-oxidizing bacteria. J. Bacteriol. 176:66236630.
103. 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.
104. Turner, M. G.,, E. A. H. Smithwick,, K. L. Metzger,, D. B. Tinker, and, W. H. Romme. 2007. Inorganic nitrogen availability after severe stand-replacing fire in the Greater Yellowstone Ecosystem. Proc. Natl. Acad. Sci. USA 104:47824789.
105. Utaker, J. B.,, L. Bakken,, L. J. Jiang, and, I. F. Nes. 1995. Phylogenetic analysis of seven new isolates of ammonia-oxidizing bacteria based on 16S rRNA gene sequences. Syst. Appl. Microbiol. 18:549559.
106. Viessman, W.,, and M. J. Hammer. 2004. Water Supply and Pollution Control. Pearson Prentice Hall, Upper Saddle River, NJ.
107. Vitousek, P. M.,, P. A. Matson, and, K. Vancleve. 1989. Nitrogen availability and nitrification during succession-primary, secondary and old-field seres. Plant Soil 115:229239.
108. Voytek, M. A.,, J. C. Priscu, and, B. B. Ward. 1999. The distribution and relative abundance of ammonia-oxidizing bacteria in lakes of the McMurdo Dry Valley, Antarctica. Hydrobiologia 401:113130.
109. Wagner, M.,, G. Rath,, H. P. Koops,, J. Flood, and, R. Amann. 1996. In situ analysis of nitrifying bacteria in sewage treatment plants. Water Sci. Tech. 34:237244.
110. Ward, B. B.,, and G. D. O’Mullan. 2002. Worldwide distribution of Nitrosococcus oceani, a marine ammonia-oxidizing gamma-proteobacterium, detected by PCR and sequencing of 16S rRNA and amo A genes. Appl. Environ. Microbiol. 68:41534157.
111. Ward, B. B.,, M. A. Voytek, and, R. P. Witzel. 1997. Phylogenetic diversity of natural populations of ammonia oxidizers investigated by specific PCR amplification. Microbiol. Ecol. 33:8796.
112. Ward, B. B.,, D. Eveillard,, J. D. Kirshtein,, J. D. Nelson,, M. A. Voytek, and, G. A. Jackson. 2007. Ammonia-oxidizing bacterial community composition in estuarine and oceanic environments assessed using a functional gene microarray. Environ. Microbiol. 9:25222538.
113. Watson, S. W. 1965. Characteristics of a marine nitrifying bacterium, Nitrosocystis oceanus sp. nov. Limnol. Oceanogr. 10:R247R289.
114. Watson, S. W. 1971a. Reisolation of Nitrosospira briensis S. Winogradsky and H. Winogradsky 1933. Arch Mikrobiol 75:179188.
115. Watson, S. W. 1971b. Taxonomic considerations of the family Nitrobacteraceae Buchanan. Int. J. Syst. Bacteriol. 21:254270.
116. Watson, S. W.,, L. B. Graham,, C. C. Remsen, and, F. W. Valois. 1971. A lobular, ammonia-oxidizing bacterium, Nitrosolobus multiuformis nov. gen. nov. sp. Arch. Microbiol. 76:183203.
117. Webster, G.,, T. M. Embley, and, J. I. Prosser. 2002. Grassland management regimens reduce small-scale heterogeneity and species diversity of beta-proteobacterial ammonia oxidizer populations. Appl. Environ. Microbiol. 68:2030.
118. Webster, G.,, T. M. Embley,, T. E. Freitag,, Z. Smith, and, J. I. Prosser. 2005. Links between ammonia oxidizer species composition, functional diversity and nitrification kinetics in grassland soils. Environ. Microbiol. 7:676684.
119. 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.
120. Whitby, C. B.,, J. R. Saunders,, R. W. Pickup, and, A. J. McCarthy. 2001. A comparison of ammonia-oxidiser populations in eutrophic and oligotrophic basins of a large freshwater lake. Antonie Van Leewenhoek Int. J. Gen. Mol. Microbiol. 79:179188.
121. Winogradsky, S. 1892. Contributions a la morphologie des organismes de la nitrification. Arch. Sci. Biol. St. Peterburg. 1:86137
122. Woese, C. R.,, W. G. Weisburg,, B. J. Paster,, C. M. Hahn,, R. S. Tanner,, N. R. Krieg,, H. P. Koops,, H. Harms, and, E. Stackebrandt. 1984. The phylogeny of the purple bacteria—the Beta-subdivision. Syst. Appl. Microbiol. 5:327336.
123. Woese, C. R.,, W. G. Weisburg,, C. M. Hahn,, B. J. Paster,, L. B. Zablen,, B. J. Lewis,, T. J. Macke,, W. Ludwig, and, E. Stackebrandt. 1985. The phylogeny of the purple bacteria-the Gamma-subdivision. Syst. Appl. Microbiol. 6:2533.
124. 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.
125. Yergeau, E.,, S. Kang,, Z. He,, J. Zhou, and, G. A. Kowalchuk. 2007. Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect. ISME J. 1:163179.
126. Zhang, C. L.,, Q. Ye,, Z. Y. Huang,, W. J. Li,, J. Q. Chen,, Z. Q. Song,, W. D. 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.
127. Zhang, T.,, T. Jin,, Q. Yan,, M. Shao,, G. Wells,, C. Criddle, and, H. H. P. Fang. 2009. Occurrence of ammonia-oxidizing Archaea in activated sludges of a laboratory scale reactor and two wastewater treatment plants. J. Appl. Microbiol. 107:970977.

Tables

Generic image for table
TABLE 1

Outline of the taxonomy of chemolithotrophic AOB for selected pure culture isolates and strains

Citation: Norton J. 2011. Diversity and Environmental Distribution of Ammonia-Oxidizing Bacteria, p 39-55. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch3

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