臺灣博碩士論文加值系統

硝化是全球氮循環中不可或缺的部分，而氨氧化則是硝化作用之速率限制步驟。氨氧化早期被認為是氨氧化細菌（ammonia oxidizing bacteria, AOB）所主導，直到近年來由於分子生物技術的進步，許多研究結果顯示，氨氧化古菌（ammonia oxidizing archaea, AOA）在各種環境中廣泛存在，對環境中的氨氧化作用有著重要的貢獻，因此對氨氧化古菌也有越來越多的關注和探討。本研究從淡水魚缸中採集底泥樣本進行氨氧化古菌之富集培養，利用添加抗生素、固態培養基培養、過濾培養以及連續稀釋等方法純化，獲得一株穩定之氨氧化古菌，暫命名為strain THU。經分析strain THU的16S rDNA序列，與已成功培養之氨氧化古菌Nitrososphaera gargensis相似度為97%。strain THU細胞形態呈現球桿狀，具有鞭毛構造以及移動性，大小直徑約為0.35~0.5 µm，長度約為0.75~1.8 µm。其生長環境為中性pH，氧氣為生長時所需之必要物質;培養後期培養液不會混濁，呈現透明狀。該菌株生長溫度範圍為25~55℃，最適生長溫度為45℃。以硫酸銨當作基質利用，其可生長氨氮濃度範圍為0.05~2 mM，最適生長基質濃度為0.05 mM。鹽濃度可生長範圍為0~0.1%，最適生長鹽濃度為0.1%。震盪培養對該菌株氨氧化有輕微抑制效果，光照則會完全抑制，然而，添加有機酸（甲酸鈉、乙酸鈉及丙酮酸鈉）對於培養菌株時，並無明顯刺激生長及氨氧化之作用，其中甲酸鈉反而會有些微抑制。根據本研究結果顯示，Strain THU與目前已知之氨氧化古菌特性不同，可推斷strain THU為Nitrososphaera屬之一株新穎氨氧化古菌，因此，暫時將本研究所分離之氨氧化古菌命名為”Candidatus Nitrososphaera taiwanensis”。

Ammonia oxidation is critical to nitrification and is often thought to be driven only by ammonia-oxidizing bacteria (AOB). However, recent metagenomic studies have revealed the existence of unique ammonia monooxygenase subunit (amoA) genes derived from ammonia-oxidizing archaea (AOA). Discovery of ammonia-oxidizing archaea involving in ammonia oxidation has dramatically changed the perception of the diversity of microbes involved in nitrification. AOA are thought to have advantages over AOB in extreme environments, such as extreme temperature, salinity and pH. Therefore, AOA play more important role than AOB on ammonia oxidation in harsh environments. In this study a novel aerobic, moderately thermophilic ammonia oxidizing archaea was enriched from freshwater aquarium. Phylogenetic analysis of 16S rDNA sequence and amoA gene sequence of the strain showed that the isolate was closely related to Nitrososphaera viennensis and Nitrososphaera gargensis, there for the isolate was tentatively named strain THU. Cells of strain THU were coccobacillus, sized of 0.35~0.5 µm in diameter and 0.75~1.8 µm in length. Cells were motile with monotrichous flagellum. Growth of the isolate occurred in the range of temperature 25~55℃, salinity 0~0.1% and ammonia concentration 0.05~2 mM. Optimal growth conditions was found at 45℃, pH 7.01, salinity at 0.1% and ammonia concentration at 0.05 mM. Ammonia oxidation by the isolate was slightly inhibited by shaking and completely inhibited by white-light. Addition of organic substrates (formate, acetate and pyruvate) did not stimulate the growth and ammonia oxidation. There results suggested that strain THU differed from currently known AOA and was proposed to designate the novel strain as “Candidatus Nitrososphaera taiwanesis”

中文摘要…………………….……………………………………………………….I
英文摘要……………………………………….……………………………………II
第一章 前言…………………………………………………………………………1
1-1 研究動機…………………………………………………………………...1
1-2 研究目的…………………………………………………………………...2
第二章 文獻回顧……………………………………………………………………4
2.1 自然界的氮循環…………………………………………………………...4
2.2 硝化作用…………………………………………………………………...5
2.3氨氧化反應之參與酵素………………….………………………………...6
2.4 氨氧化細菌…………………………………………………………...........7
2.5 氨氧化古菌………………………………………………………….........10
2.5.1 古菌的分類………………………………………………………..10
2.5.1.1 泉古菌門…………………………………………………...10
2.5.1.2 廣古菌門…………………………………………………...11
2.5.1.3 初古菌門…………………………………………………...11
2.5.1.4 納古菌門…………………………………………………...11
2.5.1.5 驚奇古菌門………………………………………………...11
2.5.2 氨氧化古菌之分佈………………………………………………..12
2.5.3 氨氧化古菌之分離………………………………………………..13
2.5.3.1 Nitrosopumlius maritimus…………………………………..13
2.5.3.2 Nitrososphaera viennensis………………………………….13
2.5.3.3 Nitrosocaldus yellowstonii………………………………….15
2.5.3.4 Nitrosoarchaeum koreensis…………………………………15
2.5.3.5 Nitrosotalea devanaterra…………………....………………15
2.5.3.6 Nitrososphaera gargensis……………….......………………16
2.5.3.7 Nitrosotenuis uzonensis…………………....………………...16
2.6 氨氧化古菌之生化機制…………………....……………………………..17
2.7影響氨氧化作用之環境因子……….....………………………………......19
2.7.1溶氧（dissolved oxygen）..……………………………………......19
2.7.2 pH…….... ..………..…………....………………………………......19
2.7.3溫度…….... …………………....………………………….……......20
2.7.4基質（substrate）……………....…………………………………..21
2.7.5碳源（carbon sources）…………………………….…….……......21
2.7.6光源…….... …………………....……………………………….......22
2.8微生物分類…………………... ………….... …………………..................22
2.8.1氨氧化古菌分類……………....………………………………........24
2.9分子生物技術………………....…………………………………….…......25
第三章 實驗設計與方法………….... …………………....………………………..26
3.1實驗流程設計……………....………………………….…………………..26
3.2採樣來源... …………………....……………………………….…………..26
3.3菌株培養... …………….... …………………....…………………………..28
3.3.1菌株分離與純化……………....………………………………..…..30
3.3.1.1固態培養基培養……………....……………...……………..30
3.3.1.2過濾培養…………………....……………………………….31
3.3.1.3連續稀釋培養……………....……………...………………..31
3.4實驗分析項目與方法………....……………...………………………..…..31
3.4.1氨氮…….... …………………....……………...………….......…….31
3.4.2亞硝酸鹽氮………………....……………...……………………….32
3.4.3硝酸鹽氮………………....……………...………………………….32
3.5菌株之生理生化特性探討....……………...……………………...……….33
3.5.1菌相觀察. …………………....……………...…………………..….33
3.5.1.1位相差顯微鏡………………....……………...…….………33
3.5.1.2穿透式電子顯微鏡…………....……………...…….………33
3.5.1.2.1 負染色法………………………………………………..33
3.5.1.2.2 超薄切片…………………………………..……………34
3.5.2溫度與pH之影響…………....……………...………...….……….34
3.5.3鹽濃度之影響………………....……………...…….……………...34
3.5.4基質濃度之影響…………....……………...…………....……....…35
3.5.5有機酸之影響……………....……………...…………....………....35
3.5.6震盪培養之影響…………....……………...………………………35
3.5.7光照培養之影響…………....……………...………………………35
3.5.8 SDS感受性測試…………....……………...………………………36
3.6分子生物技術…………....………………..…………...…….……………36
3.6.1 DNA萃取………………....……………...………………………..36
3.6.2 DNA純度與濃度定量………....……………...…………………..37
3.6.3洋菜膠電泳…………………....……………...……………………38
3.6.4聚合酶連鎖反應……………....……………...……………………39
3.6.5變性梯度凝膠電泳…………....……………...……………………40
3.6.6分子選殖…………………....……………...………………………43
3.6.7序列分析. …………………....……………...…………………..…44
3.6.7.1序列比對（BLAST）....…………………………………...44
3.6.7.2親緣分析………....……………...………….………………44
第四章 結果與討論.... …………………....……………...………………………..45
4.1菌群馴養………....……………...………………………………….......…45
4.2菌株分離與純化....……………...………………………………….......…46
4.2.1添加抗生素...……………...………………………………….....…46
4.2.2固態培養基培養……………...………………………………........47
4.2.3過濾與稀釋……………...…………………………………........…47
4.3生理特性鑑定.……………...…………………………………..............…48
4.3.1菌相觀察...……………...………………………………….....……48
4.4生化特性鑑定…………...…………………………….……………....…..50
4.4.1最適氨氧化溫度…..……...…………………….…………….....…50
4.4.2最適氨氧化pH…………...…………………….…………….....…53
4.4.3最適氨氧化基質濃度……...………………….……………….......55
4.4.4最適氨氧化鹽濃度……...…………………….……………...……58
4.4.5有機酸刺激測試…………...………………….………………...... 60
4.4.6抗生素測試…………...……………………….………….....……..62
4.4.7震盪培養測試…………...………………….……………….....…..64
4.4.8光照培養測試…………...………………….……………….....…..64
4.4.9 SDS感受性測試………...…………………….…………….....…..66
4.5菌株特性整理……...………………………………….…...…...............…66
4.6菌株分類....……………...………………………….…………...….......…66
4.6.1變性梯度凝膠電泳分析…...……………….………………….......66
4.6.2分子選殖…....……………...……………….………………….......69
4.6.3菌群親緣分析……………...……………….………………….......70
第五章 結論與建議……………....……………...……….……………...………...72
5.1結論…....……………...………………………….………................……..72
5.2建議……....……………...……………………….………………........…..73
參考文獻（References）
附錄（Appendix）
 
表目錄
Table 2-1 Classification and characteristics of representative ammonia oxidizing bacteria (AOB)……………………………………………………………9
Table 2-2 Description of currently known ammonia oxidizing archaea……………14
Table 2-3 PCR primers used for amplification of archaeal amoA gene…………….24
Table 3-1 Methods for water quality analysis………………………………………26
Table 3-2 Composition of mineral salt medium for AOA cultivation………………29
Table 3-3 Composition of trace element stock solution…………………………….29
Table 3-4 PCR primers used for amplification of archaeal and bacterial 16S rRNA
and amoA gene…….……………………………………………………..30
Table 3-5 Agarose gel percentage and efficient range of DNA separation………….38
Table 3-6 PCR primers used for amplification of archaeal 16S rRNA and
amoA gene……………………………………………………….……….39
Table 3-7 Reagent and volume for PCR reaction…………………………………...40
Table 3-8 Thermocycling condition for amplification of 16S rRNA and archaeal
amoA gene………………………………………………………………..40
Table 3-9 Polyacrylamide gel concentration and efficient range of DNA fragment separation in DGGE……………………………………………………....42
Table 3-10 Reagent of 6% polyacrylamide gel of DGGE in this study……………..42
Table 3-11 LB medium for host cell growth and solutions in cloning procedures….43
Table 4-1 Characteristic comparison of the ammonia oxidizing archaea strain THU
to currently known AOA………………………………………………….67
 
圖目錄
Fig 2-1 Nitrogen cycle………………..……..………………………………………...4
Fig 2-2 Respiratory pathways for ammonia oxidation in AOB……………………….8
Fig 2-3 Proposed respiratory pathways for ammonia oxidation in AOA……………18
Fig 2-4 Dependence of the ammonia/ammonium ratio as a function of pH………....20
Fig 2-5 Autotrophic 3-hydroxypropionate/4-hydroxybutyrate cycle………………..23
Fig 3-1 Flowchart of experimental design…………………………………………...27
Fig 4-1 Ammonia oxidation and nitrite production in the enrichment culture………45
Fig 4-2 Agarose gel electrophoresis analysis, PCR amplicons of the archaeal amoA genes and archaeal 16S rRNA………………………………………………………..46
Fig 4-3 Influence of antibiotics on ammonia oxidation by enriched culture………...47
Fig 4-4 Photomicrographs of strain THU…...………………………………………..49
Fig 4-5 Effect of temperature on activity of ammonia oxidation by enriched AOA culture. (25~55℃)....…………………………………………………………………51
Fig 4-6 Effect of temperature on activity of ammonia oxidation by enriched AOA culture. (35~50℃)…………………………………………………………………....51
Fig 4-7 Specific ammonia oxidation rates of enriched AOA culture in different temperature between 25℃ and 55℃.....……………………………………………..52
Fig 4-8 Effect of initial pH’s on activity of ammonia oxidation by enriched AOA culture……………….…………………………………………………………….….54
Fig 4-9 Specific ammonia oxidation rates of enriched AOA culture in different pH between pH 5 and pH 8…..……………………………………………………….….54
Fig 4-10 Effect of substrate concentrations on ammonia oxidation by enriched AOA culture. (0.05~40 mM)..........................................…………………………………...56
Fig 4-11 Effect of substrate concentrations on ammonia oxidation by enriched AOA culture. (0.1~8 mM)..............................................…………………………………...56
Fig 4-12 Specific ammonia oxidation rates of enriched AOA culture in different substrate concentrations between 0.05 mM and 2 mM………………………………57
Fig 4-13 Effect of salinity on ammonia oxidation by enriched AOA culture.…………………………………………………………………………….….59
Fig 4-14 Specific ammonia oxidation rates of enriched AOA culture in different salinity between 0.0％ and 0.2％.……………………………………………….….59
Fig 4-15 Effect of different organic acid salts on ammonia oxidation by enriched AOA culture…………………………………………………….…………………….….....61
Fig 4-16 Specific ammonia oxidation rates of enriched AOA culture in different organic acid salts......................………………………………………………………61
Fig 4-17 Effect of different antibiotics on ammonia oxidation by enriched AOA culture…………………………………………………………………………….......63
Fig 4-18 Effect of shaking during growth on ammonia oxidation by enriched AOA culture…………………………………………………………………………….......65
Fig 4-19 Effect of light during growth on ammonia oxidation by enriched AOA culture…………………………………………………………………………….......65
Fig 4-20 Denaturing gradient gel electrophoresis of partial fragments of 16S rRNA amd amoA gene obtained from the enriched AOA culture…………………………...68
Fig 4-21 Agarose gel electrophoresis analysis, the size of colony PCR was according to designs primer (1500 bps)…….……………………………………………….......69
Fig 4-22 Phylogenetic analysis of the archaeal amoA gene sequence (ca. 635 bp)….……………………………………………………………………………........71
Fig 4-23 Phylogenetic analysis of the archaeal 16S rRNA gene sequence (ca. 1500 bp)…….…………………………………………………………………………........71

Alves, R. J. E. (2011). Ammonia-oxidizing archaea from high artic soils. M.Sc. thesis, University of Lisbon, Repository.
Amann, R. I., Ludwig, W. and Schleifer, K. H. (1995). Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59, 143-169.
Arp, D. J., Sayavedra-Soto, L. A. and Hommes, N. G. (2002). Molecular biology and biochemistry of ammonia oxidation by Nitrosomonas europaea. Arch. Microbiol.178, 250-255.
Auguet, J.C., Nomokonova, N., Camarero, L. and Casamayor, E.O. (2011). Seasonal changes of freshwater ammonia-oxidizing archaeal assemblages and nitrogen species in oligotrophic alpine lakes. Appl. Environ. Microbiol. 77, 1937-1945.
Banning, N., Brock, F., Fry, J. C., Parkes, R. J., Hornibrook, E. R. C. and Weightman, A.J. (2005). Investigation of the methanogen population structure and activity in a brackish lake sediment. Environ. Microbiol. 7, 947-960.
Barns, S. M., Delwiche, C. F., Jeffrey, J. D. and Pace, N. R. (1996). Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc. Natl. Acad. Sci. 93, 9188-9193
Barns, S. M., Fundyga, R. E., Jeffries, M. W. and Pace, N. R. (1994). Remark¬able archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc. Natl. Acad. Sci. 91, 1609-1613.
Berg, I. A., Kockelkorn, D., Buckel, W., and Fuchs, G. (2007). A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in archaea. Science 318, 1782-1786.
 
Blöchl, E., Rachel, R., Burggraf, S., Hafenbradl, D., Jannasch, H.W. and Stetter, K.O. (1997). Pyrolobus fumarii, gen. and sp. nov., represents a novel group of archaea, extending the upper temperature limit for life to 113ºC. Exptremeophiles 1, 14-27.
Bodelier, P. L. E., Libochant, J.A., Blom, C. W. P. M. and Laanbroek, H. J. (1996). Dynamics of nitrification and denitrification in rootoxygenated sediments and adaptations of ammoniaoxidizing bacteria to low oxygen or anoxic habitats. Appl. Environ. Microbiol. 62, 4100-4107
Boer, W. and Kowalchuk, G. A. (2001). Nitrification in acid soils: micro-organisms and mechanisms. Soil Biol. Biochem. 33, 853-866.
Bollmann, A., French, E. and Laanbroek, H. J. (2011). Isolation, cultivation, and characterization of ammonia-oxidizing bacteria and archaea adapted to low ammonium concentrations. Methods Enzymol. 486, 55-88.
Brochier-Armanet, C., Boussau, B., Gribaldo, S. and Forterre, P. (2008). Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat. Rev. Microbiol. 6, 245-252.
de la Torre, J. R., Walker, C. B., Ingalls, A. E., Könneke, M. and Stahl, D. A. (2008). Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environ. Microbiol. 10, 810-818.
Delong, E. F. (1992). Archaea in coastal marine environments. Proc. Natl. Acad. Sci. 89, 5685-5689.
Edwards, U., Rogall, T., Blöcker, H., Emde, M. and Böttger, E.C. (1989). Isola¬tion and direct complete nucleotide determination of entire genes: characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res. 17, 7843-7853.
 
Elkins, J.G., Podar, M., Graham, D.E., Makarova, K.S., Wolf, Y. and Randau, L. (2008). A korarchaeal genome reveals insights into the evolution of the archaea. Proc. Natl. Acad. Sci. 105, 8102-8107.
FAO/WHO (1996). Safety evaluation of certain food additives. Food Additives Series 35.
Fischer, S.G. and Lerman, L.S. (1979). Length-independent separation of DNA restriction fragments in two dimensional gel electrophoresis. Cell. 16, 191-200.
Francis, C. A., Roberts, K. J., Beman, J. M., Santoro, A. E. and Oakley, B. B. (2005). Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proc. Natl. Acad. Sci. 102, 14683-14688.
French, E., Kozlowski, J. A., Mukherjee, M., Bullerjahn, G. and Bollmann, A. (2012). Ecophysiological characterization of ammonia-oxidizing archaea and bacteria from freshwater. Appl. Environ. Microbiol.78, 5773-5780
Fuhrman, J. A., McCallum, K. and Davis, A. A. (1992). Novel major archaebacterial group from marine plankton. Nature 356, 148-149.
Gilch, S., Meyer, O. and Schmidt, I. (2009). A soluble form of ammonia monooxygenase from Nitrosomonas europaea. Biol. Chem.
Hatzenpichler, R. (2012). Diversity, physiology, and niche differentiation of ammonia-oxidizing archaea. Appl. Environ. Microbiol. 78, 7501-7510
Hatzenpichler, R., Lebedeva, E. V., Spieck, E., Stoecker, K., Richter, A., Daims, H. and Wagner, M. (2008). A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. Proc. Natl. Acad. Sci. 105, 2134-2139.
Hill, A.R., DeVito, K.J., Campagnolo, S. and Sanmugadas, K. (2000). Subsurface denitrification in a forest riparian zone: interactions between hydrology and supplies of nitrate and organic carbon. Biogeochemistry 51, 193-223.
 
Hommes, N. G., Sayavedra-Soto, L. A. and Arp, D. J. (2001). Transcript analysis of multiple copies of amo (encoding ammonia monooxygenase) and hao (encoding hydroxylamine oxidoreductase) in Nitrosomonas europaea. J Bacteriol 183, 1096-1100.
Hooper, A. B. and Terry, K. R. (1974). Photoinactivation of ammonia oxidation in Nitrosomonas. J Bacteriol 119, 899-906.
Huber, H., Hohn, M.J., Rachel, R., Fuchs, T., Wimmer, V.C. and Stetter, K.O. (2002). A new phylum of archaea represented by a nanosized hyperthermophilic symbiont. Nature 417, 63-67.
Jung, M. Y., Park, S. J., Min, D., Kim, J. S., Rijpstra, W. I., Sinninghe Damsté, J. S., Kim, G. J., Madsen, E. L. and Rhee, S. K. (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.
Kalanetra, K. M., Bano, N. and Hollibaugh, J. T. (2009). Ammonia-oxidizing archaea in the arctic ocean and antarctic coastal waters. Environ. Microbiol. 11, 2434-2445.
Kasten, B. and Reski, R. (1997). β-lactam antibiotics inhibit chloroplast division in a moss (Physcomitrella patens) but not in tomato (Solanum lycopersicum). Plant Physiology 150, 137-140.
Kim, B. K., Jung, M. Y., Yu, D. S., Park, S. J., Oh, T. K., Rhee, S. K. and Kim, J. F. (2011). Genome sequence of an ammonia-oxidizing soil archaeon, ‘Candidatus Nitrosoarchaeum koreensis’ MY1. J Bacteriol. 193, 5539-5540.
Kirschbaum, M. U. (1995). The temperature dependence of soil organic matter decomposition, and the effect of global warming on soil organic C storage. Soil Biol. Biochem. 27, 753-760.
Kobayashi, G., Moriya, S. and Wada, C. (2001). Deficiency of essential GTP binding protein ObgE in Escherichia coli inhibits chromosome partition. Mol Microbiol 41, 1037-1051.
Könneke, M., Berhnard, A. E., de la Torre, J. R., Walker, C. B., Waterbury, J. B., and Stahl, D. A. (2005). Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437, 543-546.
Lane, D. J. (1991). 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics. 115-175.
Lebedeva, E. V., Hatzenpichler, R., Pelletier, E., Schuster, N. and Hauzmayer, S. (2013) 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 8(11)
Lehtovirta-Morley, L. E., Stoecker, K., Vilcinskas, A., Prosser, J. I. and Nicol, G. W. (2011). Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil. Proc. Natl. Acad. Sci. 108, 15892-15897.
Leininger, S., Urich, T., Schloter, M., Schwark, L., Qi, J. and Nicol, G. W. (2006). Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature. 442, 806-809.
Liu, K., Fang, Y., Yu, F., Liu, Q., Li, F. and Peng, S. (2010). Soil acidification in response to acid deposition in three subtropical forests of subtropical China. Pedosphere 20, 399- 408.
 
LlirÓs, M., Gich, F., Plasencia, A., Auguet, J. C., Darchambeau, F., Casamayor, E. O., Descy, J. P. and Borrego, C. (2010). Vertical distribution of ammonia-oxidizing crenarchaeota and methanogens in the epipelagic waters of Lake Kivu (Rwanda- Democratic Republic of the Congo). Appl. Environ. Microbiol. 76, 6853-6863.
Martens-Habbena, W., Berube, P. M., Urakawa, H., de la Torre, J. R. and Stahl, D. A. (2009). Ammonia oxidation kinetics determine niche separation of nitrifying archaea and bacteria. Nature 461, 976-979.
Martens-Habbena, W. and Stahl, D. A. (2011). Nitrogen metabolism and kinetics of ammonia-oxidizing archaea. Methods Enzymol. 496, 465-487.
McCarthy, R. (1999). Phylogenetic differentiation of two closely related Nitrosomonas spp. that inhabit different sediment environments in an oligotrophic freshwater lake. Appl. Environ. Microbiol. 65, 4855-4862.
McTavish, H., J.A. Fuchs and A.B. Hooper. (1993).Sequence of the gene coding for ammonia monooxygenase in Nitrosomonas europaea. J. Bacteriol., 175, 2436-2444
Muyzer, G. (1999). DGGE/TGGE: a method for identifying genes from natural ecosystems. Curr. Opin. Microbiol. 2, 317-322.
Muyzer, G., DE Waal, E.C., and Uitterlinden, A. G. (1993). Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59, 695-700.
Nicol, G.W. and Schleper, C. (2006). Ammonia-oxidising Crenarchaeota: important players in the nitrogen cycle? TRENDS in Microbiology. 14, 207-212.
Norman, J.S. and Barrett J.E. (2014). Substrate and nutrient limitation of ammonia-oxidizing bacteria and archaea in temperate forest soil. Soil Biol. Biochem. 69, 141-146
Offre, P., Prosser, J.I. and Nicol, G.W. (2009). Growth of ammonia-oxidizing archaea in soil microcosms is inhibited by acetylene. FEMS Microbiology Ecology. 70, 99-108.
Olsen, G. J., Lane, D. J., Giovannoni, S. J., Pace, N. R., and Stalh, D. A. (1986). Microbial ecology and evolution: a ribosomal RNA approach. Ann. Rev. Microbiol. 40, 337-365.
Otte, S., Gallegi, P., Hamilton, J., Koopman, B., Jain, R., Holloway, B., Lyberatos, G. and Svoronos, S. A. (1999). Effect of temperature and pH on the effective maximum specific growth rate of nitrifying bacteria. Water Research 24, 97-101
Park, B., Park, S., Yoon, D., Schouten, S., Sinninghe Damste, J. S. and Rhee, S. (2010).Cultivation of autotrophic ammonia-oxidizing archaea from marine sediments in coculture with sulfur-oxidizing bacteria. Appl. Environ. Microbiol. 76, 7575-7587
Pester, M., Schleper, C. and Wagner, M. (2011). The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology. Curr. Opin. Microbiol. 14, 300-306.
Purkhold, U., Pommerening-Roser, A., Juretschko, S., Schmid, M. C., Koops, H. P. and Wagner, M. (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, 5368-5382.
Reigstad, L. J., Richter, A., Daims, H., Urich, T., Schwark, L. and Schleper, C. (2008). Nitrification in terrestrial hot springs of Iceland and Kamchatka. FEMS Microbiology Ecology. 64: 167-174.
 
Rotthauwe, J.H., Witzel, K.P., and 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.
Sambrook, J. and Russell, D. (2001). Molecular Cloning: a Laboratory Manual, 3rd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
Santoro, A. E., Buchwald, C., Mcllvin, M. R. and Casciotti, K. L., (2011). Isotopic signature of N2O produced by marine ammonia-oxidizing archaea. Science.333, 1282-1285.
Schleper, C. and Nicol, G.W. (2010). Ammonia-oxidising archaea- physiology, ecology and evolution. Adv. Microb. Physiol. 57, 1–41.
Schmidt, I., Sliekers, O., Schmid, M., Bock, E., Fuerst, J., Kuenen, J. G., Jetten, M. S. and Strous, M. (2003). New concepts of microbial treatment processes for the nitrogen removal in wastewater. FEMS Microbiology Ecology. 27, 481-492.
Schön, G. H. and H. Engel. (1962). Der einfluss des lichtes auf Nitrosomonas europaea. Arch. Mikrobiol. 42, 415-428.
Shears, J. H. and Wood, P. M. (1985). Spectroscopic evidence for a photosensitive oxygenated state of ammonia monoxygenase. Bio. Chem. J. 226, 499-507
Stahl, D. A. and de la Torre, J. R. (2012). Physiology and diversity of ammonia-oxidizing archaea. Annual Review of Microbiology 83-101.
Strous, M., Kuenen, J. G. and Jetten, M. S. M. (1999). Key physiology of anaerobic ammonium oxidation. Appl. Environ. Microbiol.65, 3248-3250
 
Surampalli, R. Y., Tyagi, R. D. O., Scheible, O. K. and Heidman, J. A. (1997). Nitrification de nitrification and phosphorus removal in sequential batch reactors. Bioresource Technol. 61, 151–157.
Tourna, M., Stieglmeier, M., Spang, A., Koneke, M., Schintlmeister, A. and Urich, T. (2011). Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. Proc. Natl. Acad. Sci.108, 8420-8425.
Treusch, A. H., Leininger, S., Kletzin, A., Schuster, S. C., Klenk, H. P. and Schleper, C. (2005). Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic Crenarchaeota in nitrogen cycling. Environ. Microbiol. 7, 1985-1995.
Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., Fouts, D. E., Levy, S., Knap, A. H., Lomas, M. W., Nealson, K., White, O., Peterson, J., Hoffman, J., Parsons, R., Baden-Tillson, H., Pfannkoch, C., Rogers, Y. H. and Smith, H. O. (2004). Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66–74.
Verhagen, F. J. M. and Laanbroek, H. J. (1991) Competition for ammonium between nitrifying and heterotrophic bacteria in dual energy-limited chemostats. Appl. Environ. Microbiol. 57, 3255-3263.
Waksman, S. A. and Woodruff, H. B. (1942). Streptothricin, a new selective bacteriostatic and bactericidal agent, particularly active against gram-negative bacteria, Proc. Soc. Exptl. Biol. Med., 49, 207-210.
Walton, G. (1951). Survey of literature relating to infant methemoglobinemia due to nitrate-contaminated water. Am. J. Public Health. 41, 986-996.
Watson, S. W. (1965). Characteristics of a marine nitrifying bacterium, Nitrosocystis Oceanus sp. n. Limnol. Oceanogr. 10, 274-289.
Watson, S. W. (1971). Reisolation of Nitrosospira bnensis. Arch. Mikrobiol. 75, 179-188.
Winogradsky, S. (1892). Contributions a` la morphologie des organismes de la nitrification. Arch Sci Biol 1, 88–37.
Winogradsky, S. and Winogradsky, H. (1933). Etudes sur la microbiologie du sol. VII. Nouvelles recherches sur les organismes de la nitrification. Annals de l’lnstitut Pasteur 50, 350-432.
You, J., Das, A., Dolan, E. M. and Hu, Z. (2009). Ammonia-oxidizing archaea involved in nitrogen removal. Water Research. 43, 1801-1809