应用生态学报 ›› 2020, Vol. 31 ›› Issue (8): 2831-2840.doi: 10.13287/j.1001-9332.202008.032
高复云1,2, 李雅颖2, 姚槐应1,2*
收稿日期:
2019-12-04
修回日期:
2020-05-07
出版日期:
2020-08-15
发布日期:
2021-02-15
通讯作者:
* E-mail: hyyao@iue.ac.cn
作者简介:
高复云, 女, 1994年生, 硕士研究生。主要从事土壤微生物生态学研究。E-mail: gaofy0917@163.com
基金资助:
GAO Fu-yun1,2, LI Ya-ying2, YAO Huai-ying1,2*
Received:
2019-12-04
Revised:
2020-05-07
Online:
2020-08-15
Published:
2021-02-15
Supported by:
摘要: 硝化作用是氮素循环的核心环节,一直是土壤生物化学研究的热点之一。2015年,完全氨氧化菌(Comammox)的发现颠覆了两步硝化的传统观点,丰富了土壤氮素循环的理论体系。完全氨氧化菌能够独立执行整个硝化过程,具有将氨直接氧化成硝酸盐的能力。本文从完全氨氧化菌的定量检测方法、系统发育及组学分析入手对其分子生态学的国内外研究进展进行了系统综述,着重阐述了完全氨氧化菌在土壤中的多样性和分布规律。未来的研究可以针对以下内容开展:1)探索完全氨氧化菌的分子标志物,设计特异性引物,使其具有更高的分子覆盖度,从而完善完全氨氧化菌多样性的研究;2)优化完全氨氧化菌分离培养技术,富集分离得到更多完全氨氧化菌富集物或纯培养,完善完全氨氧化菌生理生化特性的研究;3)对完全氨氧化菌的功能和活性进行原位表征,并解析其对土壤硝化过程的贡献,阐明完全氨氧化菌的生态学特征,为促进土壤氮素良性循环和生态环境保护提供科学依据。
高复云, 李雅颖, 姚槐应. 完全氨氧化菌的分子生态学研究进展[J]. 应用生态学报, 2020, 31(8): 2831-2840.
GAO Fu-yun, LI Ya-ying, YAO Huai-ying. Research progress on primers and molecular ecology of comammox Nitrospira[J]. Chinese Journal of Applied Ecology, 2020, 31(8): 2831-2840.
[1] Chen XP, Zhu YG, Xia Y, et al. Ammonia-oxidizing archaea: Important players in paddy rhizosphere soil? Environmental Microbiology, 2008, 10: 1978-1987 [2] Arp D, Sayavedra-Soto L, Hommes N. Molecular biology and biochemistry of ammonia oxidation by Nitrosomonas europaea. Archives of Microbiology, 2002, 178: 250-255 [3] Daims H, Lucker S, Wagner M. A new perspective on microbes formerly known as nitrite-oxidizing bacteria. Trends in Microbiology, 2016, 24: 699-712 [4] 单晓雨, 张萌, 郑平. Nar与Nxr: 氮素循环中微生物关键酶研究进展. 科技通报, 2016, 32(7): 202-206 [Shan X-Y, Zhang M, Zheng P. Nar and Nxr: Key enzymes in microbiological nitrogen cycle. Bulletin of Science and Technology, 2016, 32(7): 202-206] [5] 张星, 林炜铁, 朱雅楠. 硝化细菌中亚硝酸盐氧化还原酶的研究进展. 微生物学通报, 2008, 35(11): 1806-1810 [Zhang X, Lin W-T, Zhu Y-N. Research progress of nitrite oxidoreductase in nitrobacteria. Microbiology, 2008, 35(11): 1806-1810] [6] Konneke M, Bernhard AE, de la Torre JR, et al. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature, 2005, 437: 543-546 [7] Daims H, Lebedeva EV, Pjevac P, et al. Complete nitrification by Nitrospira bacteria. Nature, 2015, 528: 504-509 [8] van Kessel MA, Speth DR, Albertsen M, et al. Complete nitrification by a single microorganism. Nature, 2015, 528: 555-559 [9] Costa E, Perez J, Kreft JU. Why is metabolic labour divided in nitrification? Trends in Microbiology, 2006, 14: 213-219 [10] Kits KD, Sedlacek CJ, Lebedeva EV, et al. Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle. Nature, 2017, 549: 269-272 [11] Daims H, Wagner M. Nitrospira. Trends in Microbiology, 2018, 26: 462-463 [12] 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 [13] Pinto AJ, Marcus DN, Ijaz UZ, et al. Metagenomic evidence for the presence of comammox Nitrospira-like bacteria in a drinking water system. Applied and Environmental Science, 2016, 1: e00054-15, doi:10.1128/mSphere.00054-15 [14] Chao Y, Mao Y, Yu K, et al. Novel nitrifiers and comammox in a full-scale hybrid biofilm and activated sludge reactor revealed by metagenomic approach. Applied Microbiology and Biotechnology, 2016, 100: 8225-8237 [15] Spieck E, Hartwig C, McCormack I, et al. Selective enrichment and molecular characterization of a previously uncultured Nitrospira-like bacterium from activated sludge. Environmental Microbiology, 2006, 8: 405-415 [16] Maixner F, Noguera DR, Anneser B, et al. Nitrite concentration influences the population structure of Nitrospira-like bacteria. Environmental Microbiology, 2006, 8: 1487-1495 [17] Juretschko S, Timmermann G, Schmid M, et al. Combined molecular and conventional analyses of nitrifying bacterium diversity in activated sludge: Nitrosococcus mobilis and Nitrospira-like bacteria as dominant populations. Applied and Environmental Microbiology, 1998, 64: 3042-3051 [18] Fujitani H, Aoi Y, Tsuneda S. Selective enrichment of two different types of Nitrospira-like nitrite-oxidizing bacteria from a wastewater treatment plant. Microbes and Environments, 2013, 28: 236-243 [19] Bao P, Wang S, Ma B, et al. Achieving partial nitrification by inhibiting the activity of Nitrospira-like bacteria under high-DO conditions in an intermittent aeration reactor. Journal of Environmental Sciences, 2017, 56: 71-78 [20] Pjevac P, Schauberger C, Poghosyan L, et al. AmoA-targeted polymerase chain reaction primers for the specific detection and quantification of comammox Nitrospira in the environment. Frontiers in Microbiology, 2017, 8: 1508, doi: 10.3389/fmicb.2017.01508 [21] Bartelme RP, McLellan SL, Newton RJ. Freshwater recirculating aquaculture system operations drive biofilter bacterial community shifts around a stable nitrifying consortium of ammonia-oxidizing archaea and comammox Nitrospira. Frontiers in Microbiology, 2017, 8: 101, doi: 10.3389/fmicb.2017.00101 [22] Beach NK, Noguera DR. Design and assessment of species-level qPCR primers targeting comammox. Frontiers in Microbiology, 2019, 10: 36, doi: 10.3389/fmicb.2019.00036 [23] Fowler SJ, Palomo A, Dechesne A, et al. Comammox Nitrospira are abundant ammonia oxidizers in diverse groundwater-fed rapid sand filter communities. Environmental Microbiology, 2018, 20: 1002-1015 [24] Wang JG, Xia F, Zeleke J, et al. An improved protocol with a highly degenerate primer targeting copper-containing membrane-bound monooxygenase genes for community analysis of methane- and ammonia-oxidizing bacteria. FEMS Microbiology Ecology, 2017, 93: 244, doi: 10.1093/femsec/fiw244 [25] Wang M, Huang G, Zhao Z, et al. Newly designed primer pair revealed dominant and diverse comammox amoA gene in full-scale wastewater treatment plants. Bioresource Technology, 2018, 270: 580-587 [26] Xia F, Wang JG, Zhu T, et al. Ubiquity and diversity of complete ammonia oxidizers (comammox). Applied and Environmental Microbiology, 2018, 84: 18, doi: 10.1128/AEM.01390-18 [27] Yu C, Hou L, Zheng Y, et al. Evidence for complete nitrification in enrichment culture of tidal sediments and diversity analysis of clade a comammox Nitrospira in natural environments. Applied Microbiology and Biotechnology, 2018, 102: 9363-9377 [28] Zhao Z, Huang G, He S, et al. Abundance and community composition of comammox bacteria in different ecosystems by a universal primer set. Science of the Total Environment, 2019, 691: 146-155 [29] Wang Y, Ma L, Mao Y, et al. Comammox in drinking water systems. Water Research, 2017, 116: 332-341 [30] Roots P, Wang Y, Rosenthal AF, et al. Comammox Nitrospira are the dominant ammonia oxidizers in a mainstream low dissolved oxygen nitrification reactor. Water Research, 2019, 157: 396-405 [31] Zheng MS, Wang MY, Zhao ZR, et al. Transcriptional activity and diversity of comammox bacteria as a pre-viously overlooked ammonia oxidizing prokaryote in full-scale wastewater treatment plants. Science of the Total Environment, 2019, 656: 717-722 [32] Gonzalez-Martinez A, Rodriguez-Sanchez A, van Loosdrecht MCM, et al. Detection of comammox bacteria in full-scale wastewater treatment bioreactors using tag-454-pyrosequencing. Environmental Science and Pollution Research, 2016, 23: 25501-25511 [33] Jiang Q, Xia F, Zhu T, et al. Distribution of comammox and canonical ammonia oxidizing bacteria in tidal flat sediments of the Yangtze River estuary at different depths over four seasons. Journal of Applied Microbiology, 2019, 127: 533-543 [34] 王梅, 王智慧, 石孝均, 等. 长期不同施肥量对全程氨氧化细菌(comammox Nitrospira)丰度的影响. 环境科学, 2018, 39(10): 4727-4734 [Wang M, Wang Z-H, Shi X-J, et al. Long-term fertilization effects on the abundance of complete ammonia oxidizing bacteria(comammox Nitrospira) in a neutral paddy soil. Environmental Science, 2018, 39: 4727-4734] [35] Hu HW, He JZ. Comammox: A newly discovered nitrification process in the terrestrial nitrogen cycle. Journal of Soils and Sediments, 2017, 17: 2709-2717 [36] Gao JF, Fan XY, Pan KL, et al. Diversity, abundance and activity of ammonia-oxidizing microorganisms in fine particulate matter. Scientific Reports, 2016, 6: 38785, doi: 10.1038/srep38785 [37] Stoecker K, Bendinger B, Ning BS, 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 [38] Radajewski S, Webster G, Murrell JC, et al. Identification of active methylotroph populations in an acidic forest soil by stable isotope probing. Microbiology, 2002, 148: 2331-2342 [39] Palomo A, Pedersen AG, Fowler SJ, et al. Comparative genomics sheds light on niche differentiation and the evolutionary history of comammox Nitrospira. The ISME Journal, 2018, 12: 1779-1793 [40] Tatari K, Musovic S, Gulay A, et al. Density and distribution of nitrifying guilds in rapid sand filters for drin-king water production: Dominance of Nitrospira spp. Water Research, 2017, 127: 239-248 [41] Camejo PY, Santo Domingo J, McMahon KD, et al. Genome-enabled insights into the ecophysiology of the comammox bacterium “Candidatus Nitrospira nitrosa”. Applied and Environmental Science, 2017, 2: 17, doi: 10.1128/mSystems.00059-17 [42] Li C, Hu HW, Chen QL, et al. Comammox Nitrospira play an active role in nitrification of agricultural soils amended with nitrogen fertilizers. Soil Biology and Biochemistry, 2019, 138: 107609, doi: 10.1016/j.soilbio.2019.107609 [43] Wang J, Wang J, Rhodes G, et al. Adaptive responses of comammox Nitrospira and canonical ammonia oxidizers to long-term fertilizations: Implications for the relative contributions of different ammonia oxidizers to soil nitrogen cycling. Science of the Total Environment, 2019, 668: 224-233 [44] Wang Z, Cao Y, Zhu-Barker X, et al. Comammox Nitrospira clade B contributes to nitrification in soil. Soil Biology and Biochemistry, 2019, 135: 392-395 [45] Poghosyan L, Koch H, Lavy A, et al. Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface. Environmental Microbiology, 2019, 21: 3627-3637 [46] 杨韦玲. 全程硝化菌的富集培养及优化研究. 硕士论文. 杭州: 浙江大学, 2019 [Yang W-L. Enrichment and Optimization of Complete Ammonia Oxidizer. Master Thesis. Hangzhou: Zhejiang University, 2019] [47] Off S, Alawi M, Spieck E. Enrichment and physiological characterization of a novel Nitrospira-like bacterium obtained from a marine sponge. Applied and Environmental Microbiology, 2010, 76: 4640-4646 [48] Luo X, Han S, Lai S, et al. Long-term straw returning affects Nitrospira-like nitrite oxidizing bacterial community in a rapeseed-rice rotation soil. Journal of Basic Microbiology, 2017, 57: 309-315 [49] 万琪慧, 王书玲, 赵伟烨, 等. 重庆紫色水稻土中“全程”和“半程”氨氧化微生物的垂直分异. 微生物学报, 2019, 59(2): 291-302 [Wan Q-H, Wang S-L, Zhao W-Y, et al. Vertical abundance variations of “incomplete ammonia oxidizers” and “comammox” in purple paddy soil in Chongqing. Acta Microbiologica Sinica, 2019, 59(2): 291-302] [50] 史国帅, 白莉, 周立光, 等. 岸边带生态系统中全程氨氧化细菌以及硝化螺菌属群落结构的研究. 环境科学学报, 2019, doi:10.13671/j.hjkxxb.2019.0083 [Shi G-S, Bai L, Zhou L-G, et al. Comammox bacterium and Nitrospira community structure in riparian zone ecosystems. Acta Scientiae Circumstantiae, 2019, doi:10.13671/j.hjkxxb.2019.0083] [51] Zamanian K, Zarebanadkouki M, Kuzyakov Y. Nitrogen fertilization raises CO2 efflux from inorganic carbon: A global assessment. Global Change Biology, 2018, 24: 2810-2817 [52] Beeckman F, Motte H, Beeckman T. Nitrification in agricultural soils: Impact, actors and mitigation. Current Opinion in Biotechnology, 2018, 50: 166-173 [53] 贺纪正, 张丽梅. 土壤氮素转化的关键微生物过程及机制. 微生物学通报, 2013, 40(1): 98-108 [He J-Z, Zhang L-M. Key processes and microbial mechanisms of soil nitrogen transformation. Microbiology, 2013, 40(1): 98-108] [54] Kits KD, Jung MY, Vierheilig J, et al. Low yield and abiotic origin of N2O formed by the complete nitrifier Nitrospira inopinata. Nature Communications, 2019, 10: 1836, https://doi.org/10.1038/s41467-019-09790-x [55] Liu S, Han P, Hink L, et al. Abiotic conversion of extracellular NH2OH contributes to N2O emission during ammonia oxidation. Environmental Science and Technology, 2017, 51: 13122-13132 [56] Xia L, Lam SK, Chen D, et al. Can knowledge-based N management produce more staple grain with lower greenhouse gas emission and reactive nitrogen pollution? A meta-analysis. Global Change Biology, 2017, 23: 1917-1925 [57] Lu Y, Zhang X, Jiang J, et al. Effects of the biological nitrification inhibitor 1,9-decanediol on nitrification and ammonia oxidizers in three agricultural soils. Soil Biology and Biochemistry, 2019, 129: 48-59 [58] 张昊青, 赵学强, 张玲玉, 等. 石灰和双氰胺对红壤酸化和硝化作用的影响及其机制. 土壤学报, 2020, doi: 10.11766/trxb201908080361 [Zhang H-Q, Zhao X-Q, Zhang L-Y, et al. Effects of liming and dicyandiamide (DCD) application on soil pH and nitrification of acidic red soil. Acta Pedologica Sinica, 2020, doi: 10.11766/trxb201908080361] [59] 毛新伟, 程敏, 徐秋芳, 等. 硝化抑制剂对毛竹林土壤N2O排放和氨氧化微生物的影响. 土壤学报, 2016, 53(6): 1528-1540 [Mao X-W, Cheng M, Xu Q-F, et al. Effects of nitrification inhibitors on soil N2O emission and community structure and abundance of ammonia oxidation microorganism in soil under extensively managed phyllostachys edulis stands. Acta Pedologica Sinica, 2016, 53(6): 1528-1540] [60] 白杨, 杨明, 陈松岭, 等. 掺混氮肥配施抑制剂对土壤氮库的调控作用. 应用生态学报, 2019, 30(11): 3804-3810 [Bai Y, Yang M, Chen S-L, et al. Effects of the blended nitrogen fertilizers combined with inhibitors on soil nitrogen pools. Chinese Journal of Applied Ecology, 2019, 30(11): 3804-3810] [61] 李博, 李巧玲, 范长华, 等. 施用生物炭与硝化抑制剂对菜地综合温室效应的影响. 应用生态学报, 2014, 25(9): 2651-2657 [Li B, Li Q-L, Fan C-H, et al. Effects of biochar and nitrification inhibitor incorporation on global warming potential of a vegetable field in Nanjing, China. Chinese Journal of Applied Ecology, 2014, 25(9): 2651-2657] [62] 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 [63] Dai Y, Di HJ, Cameron KC, et al. Effects of nitrogen application rate and a nitrification inhibitor dicyandiamide on ammonia oxidizers and N2O emissions in a grazed pasture soil. Science of the Total Environment, 2013, 465: 125-135 [64] Li C, Hu HW, Chen QL, et al. Growth of comammox Nitrospira is inhibited by nitrification inhibitors in agricultural soils. Journal of Soils and Sediments, 2020, 20: 621-628 [65] Li YY, Chapman SJ, Nicol GW, et al. Nitrification and nitrifiers in acidic soils. Soil Biology and Biochemistry, 2018, 116: 290-301 [66] Liao HK, Chapman SJ, Li YY, et al. Dynamics of microbial biomass and community composition after short-term water status change in Chinese paddy soils. Environmental Science and Pollution Research, 2018, 25: 2932-2941 [67] Xi R, Long XE, Huang S, et al. pH rather than nitrification and urease inhibitors determines the community of ammonia oxidizers in a vegetable soil. AMB Express, 2017, 7: 129, doi: 10.1186/s13568-017-0426-x |
[1] | 李长青, 纪萌, 马萌萌, 王硕, 刘欢, 孙志梅. 天然增效剂与化学抑制剂复配对小麦/玉米轮作体系产量、氮素利用及氮平衡的影响 [J]. 应用生态学报, 2023, 34(9): 2391-2397. |
[2] | 冯蒙蒙, 林永新, 贺子洋, 刘小飞, 陈仕东, 宛颂, 段春健, 叶桂萍, 贺纪正. 亚热带米槠天然林土壤氨氧化微生物对模拟氮沉降的响应 [J]. 应用生态学报, 2022, 33(6): 1622-1628. |
[3] | 李学红, 李东坡, 武志杰, 崔磊, 肖富容, 李永华, 郑野, 张金明. 脲酶/硝化抑制剂在黑土和褐土中对尿素氮转化的调控效果 [J]. 应用生态学报, 2021, 32(4): 1352-1360. |
[4] | 肖富容, 李东坡, 武志杰, 薛妍, 崔磊, 张可, 李永华, 郑野. 添加生化抑制剂和腐植酸的稳定性增效尿素在黄土中的施用效果 [J]. 应用生态学报, 2021, 32(12): 4419-4428. |
[5] | 崔磊,李东坡,武志杰,薛妍,肖富容,张可,李永华,郑野. 不同硝化抑制剂对红壤氮素硝化作用及玉米产量和氮素利用率的影响 [J]. 应用生态学报, 2021, 32(11): 3953-3960. |
[6] | 攸越, 吴蔡楠, 钟苇杰, 侯之琳, 刘越, 都韶婷, 金崇伟. 速效氮肥配施双氰胺对减控小白菜镉积累的作用 [J]. 应用生态学报, 2020, 31(9): 3093-3100. |
[7] | 崔磊, 李东坡, 武志杰, 李学红, 李永华, 闫增辉, 郑野, 张金明. 高效稳定性硫酸铵氮肥在黑土中的施用效果 [J]. 应用生态学报, 2020, 31(7): 2390-2398. |
[8] | 张英鹏, 李洪杰, 刘兆辉, 孙明, 孙翠平, 井永苹, 罗加法, 李彦. 农田减氮调控施肥对华北潮土区小麦-玉米轮作体系氮素损失的影响 [J]. 应用生态学报, 2019, 30(4): 1179-1187. |
[9] | 油伦成, 李东坡, 武志杰, 崔磊, 闫增辉, 张金明, 崔永坤, 刘裕. 稳定性铵态氮肥在黑土和褐土中的氮素转化特征 [J]. 应用生态学报, 2019, 30(4): 1079-1087. |
[10] | 白杨, 杨明, 陈松岭, 朱晓晴, 蒋一飞, 邹洪涛, 张玉龙. 掺混氮肥配施抑制剂对土壤氮库的调控作用 [J]. 应用生态学报, 2019, 30(11): 3804-3810. |
[11] | 于伟家, 李雪松, 陈竹君, 周建斌. 氮肥对不同无机碳含量土壤二氧化碳释放的影响 [J]. 应用生态学报, 2018, 29(8): 2493-2500. |
[12] | 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. |
[13] | 郭 晨, 徐正伟, 王 斌, 任 涛, 万运帆, 邹家龙, 鲁剑巍, 李小坤. 缓/控释尿素对稻田周年CH4和N2O排放的影响 [J]. 应用生态学报, 2016, 27(5): 1489-1495. |
[14] | 马志雯, 高霄鹏, 桂东伟, 匡文浓, 王西和, 刘骅. 高效氮肥对新疆膜下滴灌棉田土壤氧化亚氮排放的影响 [J]. 应用生态学报, 2016, 27(12): 3961-3968. |
[15] | 李博,李巧玲,范长华,孙丽英,熊正琴**. 施用生物炭与硝化抑制剂对菜地综合温室效应的影响 [J]. 应用生态学报, 2014, 25(9): 2651-2657. |
阅读次数 | ||||||
全文 |
|
|||||
摘要 |
|
|||||