Enrichment and genome sequence of the group I.1a ammonia-oxidizing archaeon "Ca. Nitrosotenuis uzonensis" representing a clade globally distributed in thermal habitats

PLoS ONE

Volumn 8, Issue 11, 2013, Pages

  Lebedeva, Elena V ^a   Hatzenpichler, Roland ^b,f   Pelletier, Eric ^c,d,e   Schuster, Nathalie ^b   Hauzmayer, Sandra ^b   Bulaev, Aleksandr ^a   Grigor'eva, Nadezhda V ^a   Galushko, Alexander ^b   Schmid, Markus ^b   Palatinszky, Marton ^b   Le Paslier, Denis ^c,d,e   Daims, Holger ^b   Wagner, Michael ^b  

^a WINOGRADSKY INSTITUTE OF MICROBIOLOGY   (Russian Federation)

^b UNIVERSITY OF VIENNA   (Austria)

^c CENTRE NATIONAL DE SÉQUENÇAGE   (France)

^d CNRS   (France)

^e UNIVERSITÉ D EVRY VAL D ESSONNE   (France)

^f CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMMONIA OXIDATION; AMMONIA OXIDIZING ARCHAEON; ARCHAEAL GENOME; ARTICLE; CARBON FIXATION; CHEMOLITHOAUTOTROPH; CHEMOTAXIS; CLADISTICS; CONTROLLED STUDY; ECOLOGICAL NICHE; ENRICHMENT CULTURE; FLAGELLUM; GENE SEQUENCE; NEW GENUS; NEW SPECIES; NITROSOTENUIS UZONENSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; OXIDATION; RUSSIAN FEDERATION; THAUMARCHAEOTA; THERMAL SPRING; THERMOPHILIC ARCHAEON; ARCHAEON; CELL DIVISION; CLASSIFICATION; CYTOLOGY; ECOSYSTEM; GENETICS; METABOLISM; OXIDATION REDUCTION REACTION; PHYLOGENY; TRANSPORT AT THE CELLULAR LEVEL; ULTRASTRUCTURE;

AMMONIA; CARBON; NITRITE; RNA 16S;

AMMONIA; ARCHAEA; BASE SEQUENCE; BIOLOGICAL TRANSPORT; CARBON; CELL DIVISION; CHEMOTAXIS; ECOSYSTEM; FLAGELLA; GENOME, ARCHAEAL; NITRITES; OXIDATION-REDUCTION; PHYLOGENY; RNA, RIBOSOMAL, 16S; RUSSIA;

EID: 84894268023     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0080835     Document Type: Article

References (83)

1. Hatzenpichler R (2012) Diversity, physiology, and niche differentiation of ammonia-oxidizing archaea. Appl Environ Microbiol 78: 7501-7510. doi:10.1128/AEM.01960-12. PubMed: 22923400.
2. Schleper C, Nicol GW (2010) Ammonia-oxidising archaea - physiology, ecology and evolution. Adv Microb Physiol 57: 1-41. doi:10.1016/B978-0-12- 381045-8.00001-1. PubMed: 21078440.
3. Stahl DA, de la Torre JR (2012) Physiology and diversity of ammonia-oxidizing archaea. Annu Rev Microbiol 66: 83-101. doi:10.1146/annurev- micro-092611-150128. PubMed: 22994489.
4. Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P (2008) Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat Rev Microbiol 6: 245-252. doi:10.1038/nrmicro1852. PubMed: 18274537. (Pubitemid 351256319)
5. Spang A, Hatzenpichler R, Brochier-Armanet C, Rattei T, Tischler P et al. (2010) Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota. Trends Microbiol 18: 331-340. doi:10.1016/j.tim.2010.06.003. PubMed: 20598889.
6. Mußmann M, Brito I, Pitcher A, Damste JSS, Hatzenpichler R et al. (2011) Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers. Proc Natl Acad Sci U S A 108: 16771-16776. doi:10.1073/pnas.1106427108. PubMed: 21930919.
7. Koops HP, Pommerening-Röser A (2001) Distribution and ecophysiology of the nitrifying bacteria emphasizing cultured species. FEMS Microbiol Ecol 37: 1-9. doi:10.1111/j.1574-6941.2001.tb00847.x.
8. Koops HP, Purkhold U, Pommerening-Röser A, Timmermann G, Wagner M (2003) The lithoautotrophic ammonia-oxidizing bacteria. In: D Mea. The Procaryotes: An Evolving Electronic Resource for the Microbiological Community. Third edition. New York: Springer.
9. Adair KL, Schwartz E (2008) Evidence that ammonia-oxidizing archaea are more abundant than ammonia-oxidizing bacteria in semiarid soils of Northern Arizona, USA. Microb Ecol 56: 420-426. doi:10.1007/s00248-007-9360-9. PubMed: 18204798.
10. He JZ, Shen JP, Zhang LM, Zhu YG, Zheng YM et al. (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: 2364-2374. doi:10.1111/j.1462- 2920.2007.01358.x. PubMed: 17686032.
11. Leininger S, Urich T, Schloter M, Schwark L, Qi J et al. (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442: 806-809. doi:10.1038/nature04983. PubMed: 16915287. (Pubitemid 44258909)
12. Shen JP, Zhang LM, Zhu YG, Zhang JB, He JZ (2008) Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam. Environ Microbiol 10: 1601-1611. doi:10.1111/j.1462-2920.2008.01578.x. PubMed: 18336563.
13. Beman JM, Popp BN, Francis CA (2008) Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California. ISME J 2: 429-441. doi:10.1038/ismej.2007.118. PubMed: 18200070. (Pubitemid 351518401)
14. Nakagawa T, Mori K, Kato C, Takahashi R, Tokuyama T (2007) Distribution of cold-adapted ammonia-oxidizing microorganisms in the deep-ocean of the Northeastern Japan Sea. Microbes Environ 22: 365-372. doi:10.1264/jsme2.22.365.
15. Wuchter C, Abbas B, Coolen MJ, Herfort L, van Bleijswijk J et al. (2006) Archaeal nitrification in the ocean. Proc Natl Acad Sci U S A 103: 12317-12322. doi:10.1073/pnas.0600756103. PubMed: 16894176. (Pubitemid 44267257)
16. Caffrey JM, Bano N, Kalanetra K, Hollibaugh JT (2007) Ammonia oxidation and ammonia-oxidizing bacteria and archaea from estuaries with differing histories of hypoxia. ISME J 1: 660-662. doi:10.1038/ismej.2007.79. PubMed: 18043673. (Pubitemid 350076523)
17. Park SJ, Park BJ, Rhee SK (2008) Comparative analysis of archaeal 16S rRNA and amoA genes to estimate the abundance and diversity of ammonia-oxidizing archaea in marine sediments. Extremophiles 12: 605-615. doi:10.1007/s00792-008- 0165-7. PubMed: 18465082.
18. de la Torre JR, Walker CB, Ingalls AE, Könneke M, Stahl DA (2008) Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environ Microbiol 10: 810-818. doi:10.1111/j.1462-2920.2007.01506. x. PubMed: 18205821.
19. Jiang H, Huang Q, Dong H, Wang P, Wang F et al. (2010) RNA-based investigation of ammonia-oxidizing archaea in hot springs of Yunnan Province, China. Appl Environ Microbiol 76: 4538-4541. doi:10.1128/AEM.00143-10. PubMed: 20435758.
20. Reigstad LJ, Richter A, Daims H, Urich T, Schwark L et al. (2008) Nitrification in terrestrial hot springs of Iceland and Kamchatka. FEMS Microbiol Ecol 64: 167-174. doi:10.1111/j.1574-6941.2008.00466.x. PubMed: 18355293. (Pubitemid 351533426)
21. Dodsworth JA, McDonald AI, Hedlund BP (2012) Calculation of total free energy yield as an alternative approach for predicting the importance of potential chemolithotrophic reactions in geothermal springs. FEMS Microbiol Ecol 81: 446-454. doi:10.1111/j.1574-6941.2012.01369.x. PubMed: 22443686.
22. Hatzenpichler R, Lebedeva EV, Spieck E, Stoecker K, Richter A et al. (2008) A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. Proc Natl Acad Sci U S A 105: 2134-2139. doi:10.1073/pnas.0708857105. PubMed: 18250313. (Pubitemid 351439477)
23. Spear JR, Barton HA, Robertson CE, Francis CA, Pace NR (2007) Microbial community biofabrics in a geothermal mine adit. Appl Environ Microbiol 73: 6172-6180. doi:10.1128/AEM.00393-07. PubMed: 17693567. (Pubitemid 47548027)
24. Weidler GW, Gerbl FW, Stan-Lotter H (2008) Crenarchaeota and their role in the nitrogen cycle in a subsurface radioactive thermal spring in the Austrian Central Alps. Appl Environ Microbiol 74: 5934-5942. doi:10.1128/AEM.02602-07. PubMed: 18723663.
25. Zhang T, Jin T, Yan Q, Shao M, Wells G et al. (2009) Occurrence of ammonia-oxidizing archaea in activated sludges of a laboratory scale reactor and two wastewater treatment plants. J Appl Microbiol 107: 970-977. doi:10.1111/j.1365-2672.2009.04283.x. PubMed: 19486399.
26. Zhao W, Song Z, Jiang H, Li W, Mou X et al. (2011) Ammonia-oxidzing archaea in Kamchatka hot springs. Geomicrobiol J 28: 149-159. doi:10.1080/01490451003753076.
27. Dodsworth JA, Hungate BA, Hedlund BP (2011) Ammonia oxidation, denitrification and dissimilatory nitrate reduction to ammonium in two US Great Basin hot springs with abundant ammonia-oxidizing archaea. Environ Microbiol 13: 2371-2386. doi:10.1111/j.1462-2920.2011.02508.x. PubMed: 21631688.
28. Wang F, Zhou H, Meng J, Peng X, Jiang L et al. (2009) GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent. Proc Natl Acad Sci U S A 106: 4840-4845. doi:10.1073/pnas.0810418106. PubMed: 19273854.
29. Wang S, Xiao X, Jiang L, Peng X, Zhou H et al. (2009) Diversity and abundance of ammonia-oxidizing archaea in hydrothermal vent chimneys of the juan de fuca ridge. Appl Environ Microbiol 75: 4216-4220. doi:10.1128/AEM.01761-08. PubMed: 19395559.
30. Zhang CL, Ye Q, Huang ZY, Li WJ, Chen JQ et al. (2008) Global occurrence of archaeal amoA genes in terrestrial hot springs. Appl Environ Microbiol 74: 6417-6426. doi:10.1128/AEM.00843-08. PubMed: 18676703.
31. Pitcher A, Hopmans EC, Mosier AC, Park S-J, Rhee S-K et al. (2011) Core and intact polar glycerol dibiphytanyl glycerol tetraether lipids of ammonia-oxidizing archaea enriched from marine and estuarine sediments. Appl Environ Microbiol 77: 3468-3477. doi:10.1128/AEM.02758-10. PubMed: 21441324.
32. Schouten S, Hopmans EC, Baas M, Boumann H, Standfest S et al. (2008) Intact membrane lipids of Candidatus "Nitrosopumilus maritimus", a cultivated representative of the cosmopolitan mesophilic Group I Crenarchaeota. Appl Environ Microbiol 74: 2433-2440. doi:10.1128/AEM.01709-07. PubMed: 18296531. (Pubitemid 351555455)
33. Pitcher A, Rychlik N, Hopmans EC, Spieck E, Rijpstra WI, et al. (2009) Crenarchaeol dominates the membrane lipids of Candidatus Nitrososphaera gargensis, a thermophilic Group I.1b Archaeon. ISME J 4: 542-552.
34. Pearson A, Pi YD, Zhao WD, Li WJ, Li YL et al. (2008) Factors controlling the distribution of archaeal tetraethers in terrestrial hot springs. Appl Environ Microbiol 74: 3523-3532. doi:10.1128/AEM.02450-07. PubMed: 18390673. (Pubitemid 351812807)
35. Pearson A, Huang Z, Ingalls AE, Romanek CS, Wiegel J et al. (2004) Nonmarine crenarchaeol in Nevada hot springs. Appl Environ Microbiol 70: 5229-5237. doi:10.1128/AEM.70.9.5229-5237.2004. PubMed: 15345404. (Pubitemid 39279594)
36. Pitcher A, Schouten S, Damste JSS (2009) In situ production of crenarchaeol in two California hot springs. Appl Environ Microbiol 75: 4443-4451. doi:10.1128/AEM.02591-08. PubMed: 19411420.
37. Schouten S, van der Meer MT, Hopmans EC, Rijpstra WI, Reysenbach AL et al. (2007) Archaeal and bacterial glycerol dialkyl glycerol tetraether lipids in hot springs of Yellowstone National Park (USA). Appl Environ Microbiol 73: 6181-6191. doi:10.1128/AEM.00630-07. PubMed: 17693566. (Pubitemid 47548028)
38. Blainey PC, Mosier AC, Potanina A, Francis CA, Quake SR (2011) Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis. PLOS ONE 6: e16626. doi:10.1371/journal.pone.0016626. PubMed: 21364937.
39. French E, Kozlowski JA, Mukherjee M, Bullerjahn G, Bollmann A (2012) Ecophysiological characterization of ammonia-oxidizing archaea and bacteria from freshwater. Appl Environ Microbiol 78: 5773-6780. doi:10.1128/AEM.00432-12. PubMed: 22685142.
40. Jung MY, Park SJ, Min D, Kim JS, Rijpstra WI et al. (2011) Enrichment and characterization of an autotrophic ammonia-oxidizing archaeon of mesophilic crenarchaeal group I.1a from an agricultural soil. Appl Environ Microbiol 77: 8635-8647. doi:10.1128/AEM.05787-11. PubMed: 22003023.
41. Könneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB et al. (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437: 543-546. doi:10.1038/nature03911. PubMed: 16177789. (Pubitemid 41613550)
42. Lehtovirta-Morley LE, Stoecker K, Vilcinskas A, Prosser JI, Nicol GW (2011) Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil. Proc Natl Acad Sci U S A 108: 15892-15897. doi:10.1073/pnas. 1107196108. PubMed: 21896746.
43. Mosier AC, Allen EE, Kim M, Ferriera S, Francis CA (2012) Genome sequence of "Candidatus Nitrosopumilus salaria" BD31, an ammoni-aoxidizing archaeon from the San Francisco Bay estuary. J Bacteriol 194: 2121-2122. doi:10.1128/JB.00013-12. PubMed: 22461555.
44. Tourna M, Stieglmeier M, Spang A, Könneke M, Schintlmeister A et al. (2011) Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. Proc Natl Acad Sci U S A 108: 8420-8425. doi:10.1073/pnas.1013488108. PubMed: 21525411.
45. Lebedeva EV, Off S, Zumbrägel S, Kruse M, Shagzhina A et al. (2011) Isolation and characterization of a moderately thermophilic nitrite-oxidizing bacterium from a geothermal spring. FEMS Microbiol Ecol 75: 195-204. doi:10.1111/j.1574-6941.2010.01006.x. PubMed: 21138449.
46. Ellen AF, Zolghadr B, Driessen AM, Albers SV (2010) Shaping the archaeal cell envelope. Archaea doi:10.1155/2010/608243.
47. Jeanthon C, L'Haridon S, Reysenbach AL, Corre E, Vernet M et al. (1999) Methanococcus vulcanius sp. nov., a novel hyperthermophilic methanogen isolated from East Pacific Rise, and identification of Methanococcus sp. DSM 4213T as Methanococcus fervens sp. nov. Int J Syst Bacteriol 49 2: 583-589. doi:10.1099/00207713-49-2-583. PubMed: 10319479.
48. Pester M, Rattei T, Flechl S, Gröngröft A, Richter A et al. (2012) amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions. Environ Microbiol 14: 525-539. doi:10.1111/j.1462-2920.2011.02666.x. PubMed: 22141924.
49. Weidler GW, Dornmayr-Pfaffenhuemer M, Gerbl FW, Heinen W, Stan-Lotter H (2007) Communities of Archaea and Bacteria in a subsurface radioactive thermal spring in the Austrian central alps, and evidence of ammonia-oxidizing Crenarchaeota. Appl Environ Microbiol 73: 259-270. doi:10.1128/AEM.01570-06. PubMed: 17085711. (Pubitemid 46079958)
50. Berg IA, Kockelkorn D, Buckel W, Fuchs G (2007) A 3-hydroxypropionate/4- hydroxybutyrate autotrophic carbon dioxide assimilation pathway in archaea. Science 318: 1782-1786. doi:10.1126/science.1149976. PubMed: 18079405. (Pubitemid 350274390)
51. Walker CB, de la Torre JR, Klotz MG, Urakawa H, Pinel N et al. (2010) Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. Proc Natl Acad Sci U S A 107: 8818-8823. doi:10.1073/pnas.0913533107. PubMed: 20421470.
52. Kim BK, Jung MY, Yu DS, Park SJ, Oh TK et al. (2011) Genome sequence of an ammonia-oxidizing soil archaeon, "Candidatus Nitrosoarchaeum koreensis" MY1. J Bacteriol 193: 5539-5540. doi:10.1128/JB.05717-11. PubMed: 21914867.
53. Mosier AC, Allen EE, Kim M, Ferriera S, Francis CA (2012) Genome sequence of "Candidatus Nitrosoarchaeum limnia" BG20, a low-salinity ammonia-oxidizing archaeon from the San Francisco Bay estuary. J Bacteriol 194: 2119-2120. doi:10.1128/JB.00007-12. PubMed: 22461554.
54. Spang A, Poehlein A, Offre P, Zumbrägel S, Haider S et al. (2012) The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: Insights into metabolic versatility and environmental adaptations. Environ Microbiol 14: 3122-3145. doi:10.1111/j.1462-2920.2012.02893.x. PubMed: 23057602.
55. Bartossek R, Spang A, Weidler G, Lanzen A, Schleper C (2012) Metagenomic analysis of ammonia-oxidizing archaea affiliated with the soil group. Front Microbiol 3: 208. PubMed: 22723795.
56. Hallam SJ, Mincer TJ, Schleper C, Preston CM, Roberts K et al. (2006) Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. PLoS Biol 4: e95. doi:10.1371/journal.pbio.0040095. PubMed: 16533068.
57. Offre P, Nicol GW, Prosser JI (2011) Community profiling and quantification of putative autotrophic thaumarchaeal communities in environmental samples. Environ Microbiol Rep 3: 245-253. doi:10.1111/j.1758- 2229.2010.00217.x. PubMed: 23761257.
58. 2 fixation by archaea and bacteria in an agricultural soil. Proc Natl Acad Sci U S A 108: 4170-4175. doi:10.1073/pnas.1010981108. PubMed: 21368116.
59. Zhang LM, Offre PR, He JZ, Verhamme DT, Nicol GW et al. (2010) Autotrophic ammonia oxidation by soil thaumarchaea. Proc Natl Acad Sci U S A 107: 17240-17245. doi:10.1073/pnas.1004947107. PubMed: 20855593.
60. 2 fixation pathways. Appl Environ Microbiol 77: 1925-1936. doi: 10.1128/AEM.02473-10. PubMed: 21216907.
61. Yakimov MM, La Cono V, Denaro R (2009) A first insight into the occurrence and expression of functional amoA and accA genes of autotrophic and ammonia oxidizing bathypelagic Crenarchaeota of Tyrrhenian Sea. Deep Sea Res Part II Top Stud Oceanogr 56: 748-754. doi:10.1016/j.dsr2.2008.07.024.
62. Deppenmeier U (2002) Redox-driven proton translocation in methanogenic archaea. Cell Mol Life Sci 59: 1513-1533. doi:10.1007/s00018-002-8526-3. PubMed: 12440773.
63. 420-dependent anti-oxidant defense system. J Biol Chem 285: 19135-19144. doi:10.1074/jbc.M109.074310. PubMed: 20075070.
64. 420-dependent glucose-6-phosphate dehydrogenase from Mycobacterium smegmatis. J Bacteriol 178: 2861-2866. PubMed: 8631674.
65. Reynolds PJ, Colleran E (1987) Evaluation and improvement of methods for coenzyme F420 analysis in anaerobic sludges. Journal of Microbiological Methods 7: 115-130. doi:10.1016/0167-7012(87)90032-7.
66. Francis CA, Roberts KJ, Beman JM, Santoro AE, Oakley BB (2005) Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proc Natl Acad Sci U S A 102: 14683-14688. doi:10.1073/pnas.0506625102. PubMed: 16186488. (Pubitemid 41457116)
67. Labrenz M, Sintes E, Toetzke F, Zumsteg A, Herndl GJ et al. (2010) Relevance of a crenarchaeotal subcluster related to Candidatus Nitrosopumilus maritimus to ammonia oxidation in the suboxic zone of the central Baltic Sea. ISME J 4: 1496-1508. doi:10.1038/ismej.2010.78. PubMed: 20535219.
68. Preston CM, Wu KY, Molinski TF, DeLong EF (1996) A psychrophilic crenarchaeon inhabits a marine sponge: Cenarchaeum symbiosum gen. nov., sp. nov. Proc Natl Acad Sci U S A 93: 6241-6246. doi:10.1073/pnas.93.13.6241. PubMed: 8692799. (Pubitemid 26230289)
69. Lindås AC, Karlsson EA, Lindgren MT, Ettema TJ, Bernander R (2008) A unique cell division machinery in the Archaea. Proc Natl Acad Sci U S A 105: 18942-18946. doi:10.1073/pnas.0809467105. PubMed: 18987308.
70. Pelve EA, Lindås AC, Martens-Habbena W, de la Torre JR, Stahl DA et al. (2011) Cdv-based cell division and cell cycle organization in the thaumarchaeon Nitrosopumilus maritimus. Mol Microbiol 82: 555-566. doi:10.1111/j.1365-2958.2011.07834.x. PubMed: 21923770.
71. Ng K-H, Srinivas V, Srinivasan R, Balasubramanian R (2013) The CdvB, but not FtsZ, assembles into polymers. Archaea 2013. Available: http://dx.doi.org/ 10.1155/2013/104147.
72. Yutin N, Koonin EV (2012) Archaeal origins of tubulin. Biology Direct 7. doi:10.1186/1745-6150-1187-1110.
73. Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106: 19126-19131. doi:10.1073/pnas.0906412106. PubMed: 19855009.
74. Bollmann A, French E, Laanbroek HJ (2011) Isolation, cultivation, and characterization of ammonia-oxidizing bacteria and archaea adapted to low ammonium concentrations. Methods Enzymol 486: 55-88. doi:10.1016/B978-0-12- 381294-0.00003-1. PubMed: 21185431.
75. Lueders T, Manefield M, Friedrich MW (2004) Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients. Environ Microbiol 6: 73-78. PubMed: 14686943. (Pubitemid 38162029)
76. Rotthauwe JH, Witzel KP, Liesack W (1997) The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl Environ Microbiol 63: 4704-4712. PubMed: 9406389. (Pubitemid 27524201)
77. Ludwig W, Strunk O, Westram R, Richter L, Meier H et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363-1371. doi:10.1093/nar/gkh293. PubMed: 14985472. (Pubitemid 38854737)
78. Felsenstein J (1993) PHYLIP (Phylogeny Interference Package) version 3.5c. Department of Genetics, University of Washington, Seattle: distributed by the author
79. Pernthaler A, Pernthaler P, Amann R (2004) Sensitive multi-color flourescence in situ hybridization for the identification of environmental microorganisms. Molecular Microbial Ecology Manual. 2 ed. Boston: Kluwer Academic Publishers. pp. 711-726.
80. Aury JM, Cruaud C, Barbe V, Rogier O, Mangenot S et al. (2008) High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies. BMC Genomics 9: 603. doi:10.1186/1471-2164-9-603. PubMed: 19087275.
81. Lücker S, Wagner M, Maixner F, Pelletier E, Koch H et al. (2010) A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria. Proc Natl Acad Sci U S A 107: 13479-13484. doi:10.1073/pnas.1003860107. PubMed: 20624973.
82. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M et al. (2004) Versatile and open software for comparing large genomes. Genome Biol 5: R12. doi:10.1186/gb-2004-5-6-p12. PubMed: 14759262.
83. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R et al. (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19: 1639-1645. doi:10.1101/gr.092759.109. PubMed: 19541911.