硝化作用研究的新发现:单步硝化作用与全程氨氧化微生物

doi:10.13287/j.1001-9332.201701.015

摘要/Abstract

摘要： 硝化作用是氨被微生物氧化为硝酸盐的过程,分别由氨氧化微生物(AOB和AOA)和亚硝酸盐氧化细菌(NOB)主导完成.一个世纪以来,我们把这个分步硝化过程当成唯一的硝化途径来学习和研究.虽然根据动力学理论推测,环境中应该存在单步硝化作用,即由一种微生物单独完成整个硝化过程,将NH₃氧化为NO₃^-,但一直没有研究能直接证明该种微生物的存在.直到2015年底,3个科研团队分别在不同环境中发现了3种不同的经过纯培养的细菌(Candidatus Nitrospira nitrosa、Candidatus Nitrospira nitrificans和Candidatus Nitrospira inopinata)和一种未经过纯培养的细菌(类Nitrospira),它们都具备单独将氨氧化为硝酸盐的能力,这些微生物被定义为全程氨氧化微生物(Comammox).单步硝化作用和全程氨氧化微生物的发现终结了传承百年的理论,并引发了众多关于全球氮素循环的重要科学问题,如这些微生物在环境中的生态位点及其在硝化作用中的相对贡献等.本文就单步硝化作用及全程氨氧化微生物的发现作了简要概述.

关键词: 动力学理论, 氮循环, 硝化螺菌, 氨氧化微生物

Abstract: Nitrification is the process of microbial oxidation of ammonia to nitrate, completed by the ammonia oxidizers (AOB and AOA) and nitrite oxidizing bacteria (NOB), sequentially. For a century, we have been learning and studying the established two-step process as the unique way for nitrification. According to the kinetic theory, there should be a one-step nitrification in the environment, that is, the whole process of nitrification (from NH₃ to NO₃^-) was completed by one microorganism, but no study could give a direct proof for the existence of this microorganism. Until the end of 2015, three different cultivated bacteria (Candidatus Nitrospira nitrosa, Candidatus Nitrospira nitrificans and Candidatus Nitrospira inopinata) and an uncultivated bacterium (Nitrospira-like orga-nism) respectively found in different environments by three research teams, were defined as complete ammonia oxidizing microorganisms (Comammox), because all of them could carry out the complete oxidation of ammonia to nitrate. The discovery of one-step nitrification and Comammox ended the 100-year-old dogma, and triggered many important scientific issues of the global nitrogen cycle, such as the ecological niche of these microorganisms in the environment and their relative contribution in nitrification. This paper made a brief overview of the discovery of one-step nitrification and Comammox.

Key words: ammonia oxidizing microorganism, nitrogen cycle, Nitrospira, kinetic theory

董兴水, 王智慧, 黄学茹, 蒋先军. 硝化作用研究的新发现:单步硝化作用与全程氨氧化微生物[J]. 应用生态学报, 2017, 28(1): 345-352.

DONG Xing-shui, WANG Zhi-hui, HUANG Xue-ru, JIANG Xian-jun. Recent discovery in nitrification: One-step nitrification and complete ammonia oxidizing microorganisms[J]. Chinese Journal of Applied Ecology, 2017, 28(1): 345-352.

参考文献

[1] Winogradsky S. The morphology of the contributions of nitrification system. Archives of Biological Sciences, 1890, 4: 257-275
[2] Könneke M, Bernhard AE, de la Torre JR, et al. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature, 2005, 437: 543-546
[3] Bock E, Wagner M. Oxidation of inorganic nitrogen compounds as an energy source. The Prokaryotes, 1992, 2: 457-495
[4] van Kessel MA, Speth DR, Albertsen M, et al. Complete nitrification by a single microorganism. Nature, 2015, 528: 555-559
[5] Daims H, Lebedeva EV, Pjevac P, et al. Complete nitrification by Nitrospira bacteria. Nature, 2015, 528: 504-509
[6] Pinto AJ, Marcus DN, Ijaz UZ, et al. Metagenomic evidence for the presence of Comammox Nitrospira-like bacteria in a drinking water system. mSphere, 2015, 1(1): e00054-15, doi:10.1128/mSphere.00054-15
[7] Costa E, Pérez J, Kreft JU. Why is metabolic labour divided in nitrification? Trends in Microbiology, 2006, 14: 213-219
[8] Arp DJ, Bottomley PJ. Nitrifiers: More than 100 years from isolation to genome sequences. Microbe, 2006, 1: 229-234
[9] Pfeiffer T, Bonhoeffer S. Evolution of cross-feeding in microbial populations. The American Naturalist, 2004, 163: E126-E135
[10] Heinrich R, Schuster S. The Regulation of Cellular Systems. Berlin: Springer, 1996
[11] Zheng P (郑平), Feng X-S (冯孝善). Biochemical principle of nitrification. Microbiology (微生物学通报), 1999, 26(3): 215-217 (in Chinese)
[12] Chain P, Lamerdin J, Larimer F, et al. Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea. Journal of Bacteriology, 2003, 185: 2759-2773
[13] Aleem MI. Generation of reducing power in chemosynthesis. II. Energy-linked reduction of pyridine nucleotides in the chemoautotroph, Nitrosomonas europaea. Biochimica et Biophysica Acta, 1966, 113: 216-224
[14] Ferguson SJ. Is a proton-pumping cytochrome oxidase essential for energy conservation in Nitrobacter? FEBS Letters, 1982, 146: 239-243
[15] Hagopian DS, Riley JG. A closer look at the bacteriology of nitrification. Aquacultural Engineering, 1998, 18: 223-244
[16] Hooper AB, Vannelli T, Bergmann DJ, et al. Enzymo-logy of the oxidation of ammonia to nitrite by bacteria. Antonie van Leeuwenhoek, 1997, 71: 59-67
[17] Wang W (王薇), Cai Z-C (蔡祖聪), Zhong W-H (钟文辉), et al. Research progress of aerobic denitrification bacteria. Chinese Journal of Applied Ecology (应用生态学报), 2007, 18(11): 2618-2625 (in Chinese)
[18] Freitag A, Rudert M, Bock E. Growth of Nitrobacter by dissimilatoric nitrate reduction. FEMS Microbiology Letters, 1987, 48: 105-109
[19] Smith AJ, Hoare DS. Acetate assimilation by Nitrobacter agilis in relation to its “obligate autotrophy”. Journal of Bacteriology, 1968, 95: 844-855
[20] Spieck E, Bock E. Bergey’s Manual of Systematic Bacteriology. New York: Springer, 2005
[21] Steinmüller W, Bock E. Growth of nitrobacter in the presence of organic matter. II. Chemoorganotrophic growth of Nitrobacter agilis. Archives of Microbiology, 1976, 108: 299-304
[22] Krieg NR, Staley JT, Brown DR, et al. Bergey’s Ma-nual of Systematic Bacteriology. 7th Ed. New York: Springer, 2010
[23] Winkler MK, Bassin JP, Kleerebezem R, et al. Unra-velling the reasons for disproportion in the ratio of AOB and NOB in aerobic granular sludge. Applied Microbiology and Biotechnology, 2012, 94: 1657-1666
[24] Zeng W (曾薇), Zhang L-M (张丽敏), Wang A-Q (王安其), et al. Microbial community structure and dynamic changes of nitrification bacteria in sewage treatment system. China Environmental Science (中国环境科学), 2015, 35(11): 3257-3265 (in Chinese)
[25] Park SN, Lee HJ, Lee KH, et al. In situ distribution and activity of nitrifying bacteria in freshwater sediment. Environmental Microbiology, 2003, 5: 798-803
[26] Zhao H-P (赵海萍), Tao J-H (陶建华), Li Q-X (李清雪). Studies on the ecological environment of nitrification and denitrification in the waters of Bohai Bay. Ocean Technology (海洋技术), 2005, 24(4): 44-49 (in Chinese)
[27] Wu W (伍文), Huang Y-Z (黄益宗), Li M-S (李明顺), et al. Effects of elevated O₃ concentration on the number of ammonia oxidizing bacteria, ammonia oxidizing bacteria and bacteria in the soil of wheat field. Journal of Agro-environment Science (农业环境科学学报), 2012, 31(3): 491-497 (in Chinese)
[28] Crab R, Avnimelech Y, Defoirdt T, et al. Nitrogen removal techniques in aquaculture for a sustainable production. Aquaculture, 2007, 270: 1-14
[29] Albertsen M, Hugenholtz P, Skarshewski A, et al. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nature Biotechnology, 2013, 31: 533-538
[30] Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Procee-dings of the National Academy of Sciences of the United States of America, 2009, 106: 19126-19131
[31] Daims H, Nielsen JL, Nielsen PH, et al. In situ characterization of Nitrospira-like nitrite-oxidizing bacteria active in wastewater treatment plants. Applied and Environmental Microbiology, 2001, 67: 5273-5284
[32] Stoecker K, Bendinger B, Schöning B, et al. Cohn’s Crenothrix is a filamentous methane oxidizer with an unusual methane monooxygenase. Proceedings of the National Academy of Sciences of the United States of America, 2006, 103: 2363-2367
[33] Luesken FA, van Alen TA, van der Biezen E, et al. Diversity and enrichment of nitrite-dependent anaerobic methane oxidizing bacteria from wastewater sludge. Applied Microbiology and Biotechnology, 2011, 92: 845-854
[34] Rotthauwe JH, Witzel KP, Liesack W. The ammonia monooxygenase structural gene amoA as a functional marker: Molecular fine-scale analysis of natural ammonia-oxidizing populations. Applied and Environmental Microbiology, 1997, 63: 4704-4712
[35] Johnson M, Zaretskaya I, Raytselis Y, et al. NCBI BLAST: A better web interface. Nucleic Acids Research, 2008, 36: 5-9
[36] Lücker S, Wagner M, Maixner F, et al. A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria. Proceedings of the National Academy of Sciences of the United States of America, 2010, 107: 13479-13484
[37] Koch H, Lücker S, Albertsen M, et al. Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira. Proceedings of the National Academy of Sciences of the United States of America, 2015, 112: 11371-11376
[38] El Sheikh AF, Poret-Peterson AT, Klotz MG, et al. Characterization of two new genes, amoR and amoD, in the amo operon of the marine ammonia oxidizer Nitrosococcus oceani ATCC 19707. Applied and Environmental Microbiology, 2008, 74: 312-318
[39] Berube PM, Stahl DA. The divergent amoC₃ subunit of ammonia monooxygenase functions as part of a stress response system in Nitrosomonas europaea. Journal of Bacteriology, 2012, 194: 3448-3456
[40] Wagner M, Nielsen PH, Loy A, et al. Linking micro-bial community structure with function: Fluorescence in situ hybridization-microautoradiography and isotope arrays. International Journal of Dermatology, 2006, 17: 83-91
[41] Dong L-H (董莲华), Yang J-S (杨金水), Yuan H-L (袁红莉). Advances in molecular ecology of ammonia oxidizing bacteria. Chinese Journal of Applied Ecology (应用生态学报), 2008, 19(6): 1381-1388 (in Chinese)
[42] Klotz MG, Schmid MC, Strous M, et al. Evolution of an octahaem cytochrome c protein family that is key to aerobic and anaerobic ammonia oxidation by bacteria. Environmental Microbiology, 2008, 10: 3150-3163
[43] Arp DJ, Chain PS, Klotz MG. The impact of genome analyses on our understanding of ammonia-oxidizing bacteria. Annual Review of Microbiology, 2007, 61: 503-528
[44] Radajewski S, Webster G, Reay DS, et al. Identification of active methylotroph populations in an acidic forest soil by stable-isotope probing. Microbiology, 2002, 148: 2331-2342
[45] Ehrich S, Behrens D, Lebedeva E, et al. A new obligately chemolithoautotrophic, nitrite-oxidizing bacte-rium, Nitrospira moscoviensis sp. nov. and its phylogenetic relationship. Archives of Microbiology, 1995, 164: 16-23
[46] Santoro AE. The do-it-all nitrifier. Science, 2016, 351: 342-343
[47] Hyman MR, Arp DJ. ¹⁴C₂H₂- and ¹⁴CO₂-labeling stu-dies of the de novo synthesis of polypeptides by Nitrosomonas europaea during recovery from acetylene and light inactivation of ammonia monooxygenase. Journal of Biological Chemistry, 1992, 267: 1534-1545
[48] Leininger S, Urich T, Schloter M, et al. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature, 2006, 442: 806-809
[49] Zhang LM, Hu HW, Shen JP, et al. Ammonia-oxidizing archaea have more important role than ammonia-oxidizing bacteria in ammonia oxidation of strongly acidic soils. The ISME Journal, 2012, 6: 1032-1045
[50] Xia WW, Zhang CX, Zeng XW, et al. Autotrophic growth of nitrifying community in an agricultural soil. The ISME Journal, 2011, 5: 1226-1236
[51] He JZ, Shen JP, Zhang LM, et al. 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. Environmental Microbiology, 2007, 9: 2364-2374
[52] Yao HY, Gao YM, Nicol GW, et al. Links between ammonia oxidizer community structure, abundance, and nitrification potential in acidic soils. Applied and Environmental Microbiology, 2011, 77: 4618-4625
[53] Yao HY, Campbell CD, Chapman SJ, et al. Multi-factorial drivers of ammonia oxidizer communities: Evidence from a national soil survey. Environmental Microbiology, 2013, 15: 2545-2556
[54] Huang R, Wu YC, Zhang JB, et al. Nitrification activity and putative ammonia-oxidizing archaea in acidic red soils. Journal of Soils and Sediments, 2012, 12: 420-428
[55] Stopnisek N, Gubry-Rangin C, Höfferle Š, et al. Thaumarchaeal ammonia oxidation in an acidic forest peat soil is not influenced by ammonium amendment. Applied and Environmental Microbiology, 2010, 76: 7626-7634
[56] Jia ZJ, Conrad R. Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil. Environmental Microbiology, 2009, 11: 1658-1671
[57] Li SW, Jiang XJ, Wang XL, et al. Tillage effects on soil nitrification and the dynamic changes in nitrifying microorganisms in a subtropical rice-based ecosystem: A long-term field study. Soil and Tillage Research, 2015, 150: 132-138
[58] Hussain Q, Liu YZ, Jin ZJ, et al. Temporal dynamics of ammonia oxidizer (amoA) and denitrifier (nirK) communities in the rhizosphere of a rice ecosystem from Tai Lake region, China. Applied Soil Ecology, 2011, 48: 210-218
[59] Alves RJ, Wanek W, Zappe A, et al. Nitrification rates in Arctic soils are associated with functionally distinct populations of ammonia-oxidizing archaea. The ISME Journal, 2013, 7: 1620-1631
[60] Wrighton KC, Thomas BC, Sharon I, et al. Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science, 2012, 337: 1661-1665
[61] Gruber-Dorninger C, Pester M, Kitzinger K, et al. Functionally relevant diversity of closely related Nitrospira in activated sludge. The ISME Journal, 2015, 9: 643-655
[62] LaPara TM, Wilkinson HK, Strait JM, et al. The bacterial communities of full-scale biologically active, granular activated carbon filters are stable and diverse and potentially contain novel ammonia-oxidizing microorga-nisms. Applied and Environmental Microbiology, 2015, 81: 6864-6872
[63] Palatinszky M, Herbold C, Jehmlich N. Cyanate as an energy source for nitrifiers. Nature, 2015, 524: 105-108
[64] Ma Y (马勇), Peng Y-Z (彭永臻), Chen L-Q (陈伦强), et al. Short-cut/complete nitrification and denitrification in a pilot-scale plant treating actual domestic wastewater. Environmental Science(环境科学), 2006, 27(12): 2477-2482 (in Chinese)
[65] Bock E, Schmidt I, Stüven R, et al. Nitrogen loss caused by denitrifying Nitrosomonas cells using ammo-nium or hydrogen as electron donors and nitrite as electron acceptor. Archives of Microbiology, 1995, 163: 16-20