[1] Canfield D E, Glazer A N, Falkowski P G. The evolution and future of earth's nitrogen cycle[J]. Science, 2010, 330(6001):192-196.
[2] Daims H, Lebedeva E V, Pjevac P, et al. Complete nitrification by Nitrospira bacteria[J]. Nature, 2015, 528(7583):504-509.
[3] Francis C A, Beman J M, Kuypers M M M. New processes and players in the nitrogen cycle:the microbial ecology of anaerobic and archaeal ammonia oxidation[J]. The ISME Journal, 2007, 1(1):19-27.
[4] Klotz M G, Stein L Y. Nitrifier genomics and evolution of the nitrogen cycle[J]. FEMS Microbiology Letters, 2008, 278(2):146-156.
[5] Ward B, Capone D, Zehr J. What's new in the nitrogen cycle?[J]. Oceanography, 2007, 20(2):101-109.
[6] Troelstra S R, Wagenaar R, Boer W D. Nitrification in Dutch heathland soils:I. General soil characteristics and nitrification in undisturbed soil cores[J]. Plant and Soil, 1990, 127(2):179-192.
[7] Winogradsky S. Recherches sur les organisms de la nitrification[J]. Annales de L Institut Pasteur. Microbiology, 1890, 4:213-231.
[8] Bennett K, Sadler N C, Wright A T, et al. Activity-based protein profiling of ammonia monooxygenase in Nitrosomonas europaea[J]. Applied and Environmental Microbiology, 2016, 82(8):2270-2279.
[9] Chain P, Lamerdin J, Larimer F, et al. Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea[J]. Journal of Bacteriology, 2003, 185(9):2759-2773.
[10] Kozlowski J A, Price J, Stein L Y. Revision of N2O-producing pathways in the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC 19718[J]. Applied and Environmental Microbiology, 2014, 80(16):4930-4935.
[11] Rotthauwe J H, Witzel K P, Liesack W. The ammonia monooxygenase structural gene amoA as a functional marker:molecular fine-scale analysis of natural ammonia-oxidizing populations[J]. Applied and Environmental Microbiology, 1997, 63(12):4704-4712.
[12] Campbell M A, Chain P S G, Dang H, et al. Nitrosococcus watsonii sp. Nov., a new species of marine obligate ammonia-oxidizing bacteria that is not omnipresent in the world's oceans:calls to validate the names ‘Nitrosococcus halophilus’ and ‘Nitrosomonas mobilis’[J]. FEMS Microbiology Ecology, 2010, 76(1):39-48.
[13] Monteiro M, Séneca J, Magalhães C. The history of aerobic ammonia oxidizers:from the first discoveries to today[J]. Journal of Microbiology, 2014, 52(7):537-547.
[14] Purkhold U, PommereningRöser A, Juretschko S, et al. Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis:implications for molecular diversity surveys[J]. Applied and Environmental Microbiology, 2000, 66(12):5368-5382.
[15] Urakawa H, Garcia J C, Nielsen J L, et al. Nitrosospira lacus sp. Nov., a psychrotolerant, ammonia-oxidizing bacterium from sandy lake sediment[J]. International Journal of Systematic and Evolutionary Microbiology, 2015, 65(1):242-250.
[16] Lin W, Kent L C, Hongyue D, et al. D1FHS, the type strain of the ammonia-oxidizing bacterium Nitrosococcus wardiae spec. Nov.:enrichment, isolation, phylogenetic, and growth physiological characterization[J]. Frontiers in Microbiology, 2016, 7(512):75.
[17] Ward B B, O'Mullan G D. Worldwide distribution of Nitrosococcus oceani, a marine ammonia-oxidizing γ-proteobacterium, detected by PCR and sequencing of 16S rRNA and amoA genes[J]. Applied and Environmental Microbiology, 2002, 68(8):4153-4157.
[18] Jordan F L, Cantera J J L, Fenn M E, et al. Autotrophic ammonia-oxidizing bacteria contribute minimally to nitrification in a nitrogen-impacted forested ecosystem[J]. Applied and Environmental Microbiology, 2005, 71(1):197-206.
[19] Venter J C, Remington K, Heidelberg J F, et al. Environmental genome shotgun sequencing of the Sargasso Sea[J]. Science, 2004, 304(5667):66-74.
[20] Schleper C, Jurgens G, Jonuscheit M. Genomic studies of uncultivated archaea[J]. Nature Reviews Microbiology, 2005, 3(6):479-488.
[21] Treusch A H, Leininger S, Kletzin A, et al. Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic Crenarchaeota in nitrogen cycling[J]. Environmental Microbiology, 2005, 7(12):1985-1995.
[22] Könneke M, Bernhard A E, de la Torre, José R, et al. Isolation of an autotrophic ammonia-oxidizing marine archaeon[J]. Nature, 2005, 437(7058):543-546.
[23] Mincer T J, Church M J, Taylor L T, et al. Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre[J]. Environmental microbiology, 2007, 9(5):1162-1175.
[24] Wuchter C, Abbas B, Coolen M J L, et al. Archaeal nitrification in the ocean[J]. Proceedings of the National Academy of Sciences of the United States of America, 2006, 103(33):12317-12322.
[25] Martens-Habbena W, Berube P M, Urakawa H, et al. Ammonia oxidation kinetics determine niche separation of nitrifying archaea and bacteria[J]. Nature, 2009, 461(7266):976-979.
[26] DeLong E F. Oceans of archaea[J]. ASM News, 2003, 69(10):503-511.
[27] Delong E F. Everything in moderation:archaea as ‘non-extremophiles’[J]. Current Opinion in Genetics & Development, 1998, 8(6):649-654.
[28] Robertson C E, Harris J K, Spear J R, et al. Phylogenetic diversity and ecology of environmental archaea[J]. Current Opinion in Microbiology, 2005, 8(6):638-642.
[29] Brochier-Armanet C, Boussau B, Gribaldo S, et al. Mesophilic Crenarchaeota:proposal for a third archaeal phylum, the Thaumarchaeota[J]. Nature Reviews Microbiology, 2008, 6(3):245-252.
[30] 张丽梅, 贺纪正. 一个新的古菌类群:奇古菌门(Thaumarchaeota)[J]. 微生物学报, 2012, 52(4):411-421.
[31] Biller S J, Mosier A C, Wells G F, et al. Global biodiversity of aquatic ammonia-oxidizing archaea is partitioned by habitat[J]. Frontiers in Microbiology, 2012, 3:252.
[32] Pester M, Rattei T, Flechl S, et al. amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions[J]. Environmental Microbiology, 2012, 14(2):525-539.
[33] Arp D J, Chain P S, Klotz M G. The impact of genome analyses on our understanding of ammonia-oxidizing bacteria[J]. Annual Review Microbiology, 2007, 61(1):503.
[34] Nicol G W, Schleper C. Ammonia-oxidizing Crenarchaeota:important players in the nitrogen cycle?[J]. Trends in Microbiology, 2006, 14(5):207-212.
[35] Glass J B, Orphan V J. Trace metal requirements for microbial enzymes involved in the production and consumption of methane and nitrous oxide[J]. Frontiers in Microbiology, 2012, 3:61.
[36] Walker C B, de la Torre J R, Klotz M G, et al. Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea[J]. Proceedings of the National Academy of Sciences of the United States of America, 2010, 107(19):8818-8823.
[37] Stahl D A, de la Torre J R. Physiology and diversity of ammonia-oxidizing archaea[J]. Annual Review of Microbiol, 2012, 66(1):83-101.
[38] Vajrala N, Martens-Habbena W, Sayavedra-Soto L A, et al. Hydroxylamine as an intermediate in ammonia oxidation by globally abundant marine archaea[J]. Proceedings of the National Academy of Sciences of the United States of America, 2013, 110(3):1006-1011.
[39] Fuhrman J A, McCallum K, Davis A A. Novel major archaebacterial group from marine plankton[J]. Nature, 1992, 356(6365):148-149.
[40] Delong E F. Archaea in coastal marine environments[J]. Proceedings of the National Academy of Sciences of the United States of America, 1992, 89(12):5685-5689.
[41] Karner M B, Delong E F, Karl D M. Archaeal dominance in the mesopelagic zone of the Pacific ocean[J]. Nature, 2001, 409(6819):507-510.
[42] Teira E, Lebaron P, van Aken H, et al. Distribution and activity of bacteria and archaea in the deep water masses of the North Atlantic[J]. Limnology and Oceanography, 2006, 51(5):2131-2144.
[43] Teira E, Reinthaler T, Pernthaler A, et al. Combining catalyzed reporter deposition-fluorescence in situ hybridization and microautoradiography to detect substrate utilization by bacteria and archaea in the deep ocean[J]. Applied and Environmental Microbiology, 2004, 70(7):4411-4414.
[44] Francis C A, Roberts K J, Beman J M, et al. Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean[J]. Proceedings of the National Academy of Sciences of the United States of America, 2005, 102(41):14683-14688.
[45] Baker B J, Lesniewski R A, Dick G J. Genome-enabled transcriptomics reveals archaeal populations that drive nitrification in a deep-sea hydrothermal plume[J]. The ISME Journal, 2012, 6(12):2269-2279.
[46] Hollibaugh J T, Gifford S, Sharma S, et al. Metatranscriptomic analysis of ammonia-oxidizing organisms in an estuarine bacterioplankton assemblage[J]. The ISME Journal, 2010, 5(5):866-878.
[47] Stewart F J, Ulloa O, DeLong E F. Microbial metatranscriptomics in a permanent marine oxygen minimum zone[J]. Environmental Microbiology, 2012, 14(1):23-40.
[48] Kelly D. Bioenergetics of chemolithotrophic bacteria[M]. London:InCompanion to Microbiology, 1978:363-386.
[49] Blainey P C, Mosier A C, Potanina A, et al. Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis[J]. PLOS ONE, 2011, 6(2):e16626.
[50] Hallam S J, Konstantinidis K T, Putuam N, et al. Genomic analysis of the uncultivated marine crenarchaeote cenarchaeum symbiosum[J]. Proceedings of the National Academy of Sciences of the United States of America, 2006, 103(48):18296-18301.
[51] Spang A, Poehlein A, Offre P, et al. The genome of the ammonia-oxidizing Candidatus nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations[J]. Environmental Microbiology, 2012, 14(12):3122.
[52] Tourna M, Stieglmeier M, Spang A, et al. Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil[J]. Proceedings of the National Academy of Sciences of the United States of America, 2011, 108(20):8420-8425.
[53] Könneke M, Schubert D M, Brown P C, et al. Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation[J]. Proceedings of the National Academy of Sciences of the United States of America, 2014, 111(22):8239-8244.
[54] Bergauer K, Sintes E, van Bleijswijk J, et al. Abundance and distribution of archaeal acetyl-CoA/propionyl-CoA carboxylase genes indicative for putatively chemoautotrophic archaea in the tropical Atlantic's interior[J]. FEMS Microbiology Ecology, 2013, 84(3):461-473.
[55] Hu A, Jiao N, Zhang C L. Community structure and function of planktonic Crenarchaeota: changes with depth in the South China Sea[J]. Microbial Ecology, 2011a, 62(3):549-563.
[56] Hu A, Jiao N, Zhang R, et al. Niche partitioning of marine group Crenarchaeota in the euphotic and upper mesopelagic zones of the east china sea[J]. Applied and Environmental Microbiology, 2011b, 77(21):7469-7478.
[57] Song Z Q, Wang L, Wang F P, et al. Abundance and diversity of archaeal accA gene in hot springs in Yunnan Province, China[J]. Extremophiles, 2013, 17(5):871-879.
[58] Yakimov M M, Cono V L, Denaro R. A first insight into the occurrence and expression of functional amoA and accA genes of autotrophic and ammonia-oxidizing bathypelagic Crenarchaeota, of Tyrrhenian Sea[J]. Deep Sea Research Part II:Topical Studies in Oceanography, 2009, 56(11/12):748-754.
[59] Yakimov M M, Cono V L, Smedile F, et al. Contribution of crenarchaeal autotrophic ammonia oxidizers to the dark primary production in Tyrrhenian deep waters (Central Mediterranean Sea)[J]. The ISME Journal, 2011, 5(6):945-961.
[60] P A del Giorgio, Duarte C M. Respiration in the open ocean[J]. Nature, 2002, 420(6914):379-384.
[61] Carlson C A, Ducklow H W, Michaels A F. Annual flux of dissolved organic carbon from the euphotic zone in the Northwestern Sargasso Sea[J]. Nature, 1994, 371(6496):405-408.
[62] Reinthaler T, van Aken H, Veth C, et al. Prokaryotic respiration and production in the meso-and bathypelagic realm of the eastern and western North Atlantic Basin[J]. Limnology and Oceanography, 2006, 51(3):1262-1273.
[63] Karl D M, Knauer G A, Martin J H, et al. Bacterial chemolithotrophy in the ocean is associated with sinking particles[J]. Nature, 1984, 309(5963):54-56.
[64] Middelburg J J. Chemoautotrophy in the ocean[J]. Geophysical Research Letters, 2011, 38(24):L26404.
[65] Ingalls A E, Shah S R, Hansman R L, et al. Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon[J]. Proceedings of the National Academy of Sciences of the United States of America, 2006, 103(17):6442-6447.
[66] Hansman R L, Griffin S, Watson J T, et al. The radiocarbon signature of microorganisms in the mesopelagic ocean[J]. Proceedings of the National Academy of Sciences of the United States of America, 2009, 106(16):6513-6518.
[67] Herndl G J, Reinthaler T, Teira E, et al. Contribution of archaea to total prokaryotic production in the deep Atlantic ocean[J]. Applied Environmental Microbiology, 2005, 71(5):2303-2309.
[68] Tetu S G, Breakwell K, Elbourne L D H, et al. Life in the dark:metagenomic evidence that a microbial slime community is driven by inorganic nitrogen metabolism[J]. The ISME Journal, 2013, 7(6):1227-1236.
[69] Reinthaler T, van Aken H M, Herndl G J. Major contribution of autotrophy to microbial carbon cycling in the deep North Atlantic Basin[J]. Deep Sea Research Part II:Topical Studies in Oceanography, 2010, 57(16):1572-1580.
[70] Jiao N, Herndl G J, Hansell D A, et al. Microbial production of recalcitrant dissolved organic matter:long-term carbon storage in the global ocean[J]. Nature Reviews Microbiology, 2010, 8(8):593-599.
[71] Jiao N, Herndl G J, Hansell D A, et al. The microbial carbon pump and the oceanic recalcitrant dissolved organic matter pool[J]. Nature Reviews Microbiology, 2011, 9(7):555.
