Metabolism of inorganic N compounds by ammonia-oxidizing bacteria

Ammonia oxidizing bacteria extract energy for growth from the oxidation of ammonia to nitrite. Ammonia monooxygenase, which initiates ammonia oxidation, remains enigmatic given the lack of purified preparations. Genetic and biochemical studies support a model for the enzyme consisting of three subunits and metal centers of copper and iron. Knowledge of hydroxylamine oxidoreductase, which oxidizes hydroxylamine formed by ammonia monooxygenase to nitrite, is informed by a crystal structure and detailed spectroscopic and catalytic studies. Other inorganic nitrogen compounds, including NO, N2O, NO2, and N2 can be consumed and/or produced by ammonia-oxidizing bacteria. NO and N2O can be produced as byproducts of hydroxylamine oxidation or through nitrite reduction. NO2 can serve as an alternative oxidant in place of O2 in some ammonia-oxidizing strains. Our knowledge of the diversity of inorganic N metabolism by ammonia-oxidizing bacteria continues to grow. Nonetheless, many questions remain regarding the enzymes and genes involved in these processes and the role of these pathways in ammonia oxidizers.     

酸性土壤氨氧化微生物及其影响因素研究进展

自然条件变化和人类活动不仅加剧了土壤酸化,扩大了酸性土壤面积,而且严重影响了土壤氮循环。氨氧化过程作为硝化作用的限速步骤,是全球氮循环的核心环节,受到国内外研究者的广泛关注。探究酸性土壤氨氧化作用及其功能微生物对完善氮循环机制和促进土壤养分循环具有重要意义。本文主要综述了土壤中氨氧化代谢途径,对比了氨氧化细菌(ammoniaoxidizing bacteria, AOB)、氨氧化古菌(ammonia-oxidizing archaea, AOA)和全程硝化菌(complete ammoniaoxidizers,Comammox)对酸性土壤氨氧化作用的相对贡献,分析了微生物内源功能差异及pH、底物浓度等外部环境因素对氨氧化微生物丰度、活性和群落结构的影响,最后对氨氧化微生物研究进行了展望,以期为酸性土壤氨氧化作用研究和微生物修复技术应用与实践提供科学参考。     

Metabolism of Inorganic N Compounds by Ammonia-Oxidizing Bacteria

ABSTRACT

Ammonia oxidizing bacteria extract energy for growth from the oxidation of ammonia to nitrite. Ammonia monooxygenase, which initiates ammonia oxidation, remains enigmatic given the lack of purified preparations. Genetic and biochemical studies support a model for the enzyme consisting of three subunits and metal centers of copper and iron. Knowledge of hydroxylamine oxidoreductase, which oxidizes hydroxylamine formed by ammonia monooxygenase to nitrite, is informed by a crystal structure and detailed spectroscopic and catalytic studies. Other inorganic nitrogen compounds, including NO, N₂O, NO₂, and N₂ can be consumed and/or produced by ammonia-oxidizing bacteria. NO and N₂O can be produced as byproducts of hydroxylamine oxidation or through nitrite reduction. NO₂ can serve as an alternative oxidant in place of O₂ in some ammonia-oxidizing strains. Our knowledge of the diversity of inorganic N metabolism by ammonia-oxidizing bacteria continues to grow. Nonetheless, many questions remain regarding the enzymes and genes involved in these processes and the role of these pathways in ammonia oxidizers.     

从典型硝化细菌到全程氨氧化微生物：发现及研究进展

生物硝化过程在全球氮循环中起关键性作用,被认为由氨氮氧化成亚硝酸盐和亚硝酸盐氧化成硝酸盐两个步骤组成,分别由氨氧化微生物(Ammonia oxidizing microorganisms,AOM)和硝化细菌(Nitrite oxidizing bacteria,NOB)催化完成。AOM包括氨氧化细菌(Ammonia oxidizing bacteria,AOB)和氨氧化古菌(Ammonia oxidizing archaea,AOA),AOB与AOA分布广泛,两者的相对丰度和氨氮浓度密切相关。2015年底,3个硝化螺菌属(Nitrospira)谱系Ⅱ的NOB被证实含有AOM的特征功能酶,包括氨单加氧酶(AMO)和羟胺脱氢酶(HAO),并证明NOB同时具有氨氧化和亚硝酸盐氧化的能力,命名为全程氨氧化微生物(Complete ammonia oxidizer,Comammox)。根据AMO的α亚基基因amoA的相似性将Comammox分为两大分支clade A和clade B。它们广泛分布于自然环境和人工系统,包括土壤(稻田、森林)、淡水(湿地、河流、湖泊沉积物、蓄水层)、污水处理厂和自来水厂等。本文综述了Comammox的发现及其最新的研究进展,并展望了Comammox作为氮循环关键功能菌群的研究方向和应用前景。     

Impact of protozoan grazing on nitrification and the ammonia- and nitrite-oxidizing bacterial communities in activated sludge

In activated sludge, protozoa feed on free-swimming bacteria and suspended particles, inducing flocculation and increasing the turnover rate of nutrients. In this study, the effect of protozoan grazing on nitrification rates under various conditions in municipal activated sludge batch reactors was examined, as was the spatial distribution of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) within the activated sludge. The reactors were monitored for ammonia, nitrite, nitrate, and total nitrogen concentrations, and bacterial numbers in the presence and absence of cycloheximide (a protozoan inhibitor), allylthiourea (an inhibitor of ammonia oxidation), and EDTA (a deflocculating agent). The accumulations of nitrate, nitrite, and ammonia were lower in batches without than with protozoa grazing. Inhibition of ammonia oxidation also decreased the amount of nitrite and nitrate accumulation. Inhibiting protozoan grazing along with ammonia oxidation further decreased the amounts of nitrite and nitrate accumulated. Induction of deflocculation led to high nitrate accumulation, indicating high levels of nitrification; this effect was lessened in the absence of protozoan grazing. Using fluorescent in situ hybridization and confocal laser scanning microscopy, AOB and NOB were found clustered within the floc, and inhibiting the protozoa, inhibiting ammonia oxidation, or inducing flocculation did not appear to lower the number of AOB and NOB present or affect their position within the floc. These results suggest that the AOB and NOB are present but less active in the absence of protozoa.     

亚硝酸盐氧化细菌的生态位以及对海洋环境变化的响应机制

硝酸盐是海洋微生物可利用氮的主要形式,也是限制表层海洋生物生产力的主要营养物质,海洋中的硝酸盐主要由氨和亚硝酸盐的氧化产生。探索亚硝酸盐氧化细菌在海洋生态系统中的生态位以及对环境变化的响应机制,对认识微生物参与的氮循环具有十分重要的意义。本文综述了海洋亚硝酸盐氧化细菌的研究进程及其主要种类,并总结了其主要的生理生态学特征,指出微生物在海洋生态系统变迁中所衍生出的适应对策。基于当前的研究现状,展望亚硝酸盐氧化细菌未来的研究方向,以期更好地了解海洋中亚硝酸盐的氧化过程,为进一步认识氮在生物地球化学中的循环奠定基础。     

抑制剂在氨氧化微生物研究中的应用

在氨氧化微生物的相关研究中经常使用各类抑制剂,包括针对硝化作用的抑制剂和针对微生物生长的抑制剂。自发现氨氧化古菌以来,人们在氨氧化细菌抑制剂的基础上重新筛选和使用不同的抑制剂来满足氨氧化微生物研究的需求。抑制剂既可以加速氨氧化古菌的富集,也可以帮助研究者区分古菌与细菌对硝化作用的贡献以及它们自身合成代谢能力的差别。本文综述了各类抑制剂的使用浓度和抑制效果,包括双氰胺(DCD)、3,4-二甲基吡啶磷酸盐(DMPP)、丙烯基硫脲(ATU)等传统抑制剂,乙炔和辛炔等炔烃类抑制剂,一氧化氮清除剂以及抗生素等对氨氧化微生物的活性和生长有特异性或通用抑制能力的抑制剂。通过对氨氧化微生物抑制剂的归纳总结,可为氨氧化微生物研究过程中抑制剂的选择提供参考。     

Effects of nitrogen addition on the abundance and composition of soil ammonia oxidizers in Inner Mongolia Grassland

Nitrogen accumulation in soil is increasing in Inner Mongolia which is resulted mainly from fertilization accompanied by conversion of large area of grasslands to croplands. Ammonia-oxidation is the key step of nitrification which is driven by ammonia-oxidizing microorganisms, and study on the response of ammonia-oxidizing microorganisms is necessary for understanding the effects of nitrogen fertilization on ecosystem functions. In this study, the abundance and community structure of soil ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) under long-term N addition of different rates (0, 1.75, 5.25, 10.5, 17.5, and 28 g N m^?2 yr^?1) in a typical steppe of the Inner Mongolia Grassland were investigated using quantitative real-time PCR, cloning and sequencing based on amoA gene. In addition, soil potential ammonia oxidation rate was analyzed. Our results demonstrated that, with the increase of nitrogen addition rate, soil pH declined gradually from 6.6 to 4.9, and potential ammonia oxidation rate also declined which was positively correlated with soil pH (P < 0.01), while the copy number of bacterial amoA gene increased and positively (P < 0.01) correlated with ammonia concentration in soil. The archaeal amoA gene copy number did not change a lot with N nitrogen addition rate below 10.5 g N/m², but significantly decreased with addition of 17.5 and 28 g N m^?2 yr^?1. Sequencing of clone libraries of treatments revealed that in the treatment without N addition, AOB was dominated by Cluster 3a1 of Nitrosospira with a proportion of 87%, while in the treatment with N addition of 28 g N m^?2 yr^?1, proportion of Cluster 2 increased significantly to 41%. All archaeal amoA sequences were affiliated with the soil/sediment clade, and no significant variation of community structure was found between the treatments without N addition and with 28 g N m^?2 yr^?1 addition rate. In conclusion, this study demonstrated significant effects of nitrogen addition on potential ammonia oxidation rate and compositions of ammonia-oxidation microorganisms, which may have important implications for evaluating the impacts of N accumulation on ecosystem functioning. Further, the effects of pH and ammonia concentration on the ammonia oxidation rate and compositions of ammonia-oxidation microorganisms were discussed.     

Nitrite Removal Performance and Community Structure of Nitrite-Oxidizing and Heterotrophic Bacteria Suffered with Organic Matter

Altlhough ammonia oxidation and ammonia-oxidizing bacteria (AOB) have been extensively studied, nitrite oxidation and nitrite-oxidizing bacteria (NOB) are still not well understood. In this article, the effect of organic matter on NOB and heterotrophic bacteria was investigated with functional performance analysis and bacterial community shift analysis. The results showed that at low concentrations of initial sodium acetate [initial sodium acetate (ISA) = 0.5 or 1 g/L], the nitrite removal rate was higher than that obtained under autotrophic conditions and the bacteria had a single growth phase, whereas at high ISA concentrations (5 or 10 g/L), continuous aerobic nitrification and denitrification occurred in addition to higher nitrite removal rates, and the bacteria had double growth phases. The community structure of total bacteria strikingly varied with the different concentrations of ISA; the dominant populations shifted from autotrophic and oligotrophic bacteria (NOB, and some strains of Bacteroidetes, Alphaproteobacteria, Actinobacteria, and green nonsulfur bacteria) to heterotrophic and denitrifying bacteria (strains of Gammaproteobacteria, especially Pseudomonas stutzeri and P. nitroreducens). The reasons that nitrite removal rate increased with supplement of organic matters were discussed.     

Enrichment and characterization of ammonia-oxidizing archaea from the open ocean: phylogeny,physiology and stable isotope fractionation

Archaeal genes for ammonia oxidation are widespread in the marine environment, but direct physiological evidence for ammonia oxidation by marine archaea is limited. We report the enrichment and characterization of three strains of pelagic ammonia-oxidizing archaea (AOA) from the North Pacific Ocean that have been maintained in laboratory culture for over 3 years. Phylogenetic analyses indicate the three strains belong to a previously identified clade of water column-associated AOA and possess 16S ribosomal RNA genes and ammonia monooxygenase subunit a (amoA) genes highly similar (98–99% identity) to those recovered in DNA and complementary DNA clone libraries from the open ocean. The strains grow in natural seawater-based liquid medium while stoichiometrically converting ammonia (NH₃) to nitrite (NO₂⁻). Ammonia oxidation by the enrichments is only partially inhibited by allylthiourea at concentrations known to completely inhibit cultivated ammonia-oxidizing bacteria. The three strains were used to determine the nitrogen stable isotope effect (¹⁵ɛ_NH3) during archaeal ammonia oxidation, an important parameter for interpreting stable isotope ratios in the environment. Archaeal ¹⁵ɛ_NH3 ranged from 13‰ to 41‰, within the range of that previously reported for ammonia-oxidizing bacteria. Despite low amino acid identity between the archaeal and bacterial Amo proteins, their functional diversity as captured by ¹⁵ɛ_NH3 is similar.     

氨氧化古菌的生态学研究进展

上百年来细菌一直被认为是地球氨氧化过程的主要驱动者,2005年海洋中分离到迄今唯一的非极端环境泉古菌,发现其氧化氨态氮获得能源生长,是氨氧化古菌。氨氧化古菌和细菌对地球氨氧化过程的相对贡献率,是目前全球氮循环研究最重要的微生物生态学问题之一。已有的证据表明古菌在海洋氨氧化过程中发挥了重要作用,细菌则是土壤氨氧化过程的主要驱动者。本文重点探讨了原位自然环境下氨氧化古菌的生态学研究进展。     

Effects of nitrogen addition on the abundance and composition of soil ammonia oxidizers in Inner Mongolia Grassland

Nitrogen accumulation in soil is increasing in Inner Mongolia which is resulted mainly from fertilization accompanied by conversion of large area of grasslands to croplands. Ammonia-oxidation is the key step of nitrification which is driven by ammonia-oxidizing microorganisms, and study on the response of ammonia-oxidizing microorganisms is necessary for understanding the effects of nitrogen fertilization on ecosystem functions. In this study, the abundance and community structure of soil ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) under long-term N addition of different rates (0, 1.75, 5.25, 10.5, 17.5, and 28 g N m^?2 yr^?1) in a typical steppe of the Inner Mongolia Grassland were investigated using quantitative real-time PCR, cloning and sequencing based on amoA gene. In addition, soil potential ammonia oxidation rate was analyzed. Our results demonstrated that, with the increase of nitrogen addition rate, soil pH declined gradually from 6.6 to 4.9, and potential ammonia oxidation rate also declined which was positively correlated with soil pH (P < 0.01), while the copy number of bacterial amoA gene increased and positively (P < 0.01) correlated with ammonia concentration in soil. The archaeal amoA gene copy number did not change a lot with N nitrogen addition rate below 10.5 g N/m², but significantly decreased with addition of 17.5 and 28 g N m^?2 yr^?1. Sequencing of clone libraries of treatments revealed that in the treatment without N addition, AOB was dominated by Cluster 3a1 of Nitrosospira with a proportion of 87%, while in the treatment with N addition of 28 g N m^?2 yr^?1, proportion of Cluster 2 increased significantly to 41%. All archaeal amoA sequences were affiliated with the soil/sediment clade, and no significant variation of community structure was found between the treatments without N addition and with 28 g N m^?2 yr^?1 addition rate. In conclusion, this study demonstrated significant effects of nitrogen addition on potential ammonia oxidation rate and compositions of ammonia-oxidation microorganisms, which may have important implications for evaluating the impacts of N accumulation on ecosystem functioning. Further, the effects of pH and ammonia concentration on the ammonia oxidation rate and compositions of ammonia-oxidation microorganisms were discussed.     

重庆紫色水稻土中“全程”和“半程”氨氧化微生物的垂直分异

【目的】系统评估全程氨氧化细菌(complete ammonia oxidizing bacteria, Comammox bacteria)、半程氨氧化细菌(AOB)和古菌(AOA)在典型水稻土剖面的垂直分异规律。2015年发现的"全程"氨氧化细菌(Comammox Nitrospira)可将氨分子一步氧化为硝酸盐,实现硝化作用。而经典的"半程"氨氧化细菌(AOB)或古菌(AOA)将氨分子氧化为亚硝酸盐后,再由系统发育完全不同的硝化细菌将其氧化为硝酸盐。全程氨氧化细菌实现了一步硝化全过程,根本改变了学术界对2类微生物分步硝化的经典认知,但相关研究仍处于初步阶段。【方法】选择重庆北碚地区2017年典型水稻土并采集5、10、20和40 cm不同深度土壤(剖面采样点的上下误差不超过1cm),提取水稻土总DNA后,利用标靶功能基因amoA,通过实时荧光定量PCR技术分析全程氨氧化细菌(Comammox)、半程氨氧化细菌(AOB)和古菌(AOA)在水稻土不同深度的数量变异规律。【结果】半程氨氧化细菌AOB和古菌AOA均随土壤深度增加呈显著下降趋势。然而,全程氨氧化细菌的两大类微生物则表现出相反的规律,Comammox Clade A的丰度随着土壤剖面的加深而显著增加(P0.05),但Clade B并未有类似规律。Clade A在水稻土不同层次的土层中均比Clade B高出1个数量级,在5 cm和40 cm处的最低和最高值分别为3.42×10~7、8.46×10~7 copies/g。AOA与AOB的丰度大致相当,5cm剖面处数量最高分别为1.23×10~7、1.83×10~5copies/g,但其平均丰度远低于全程氨氧化细菌,Comammox与AOA、AOB amoA功能基因拷贝数之比为10–2000。【结论】全程氨氧化细菌(Comammox bacteria)广泛分布于水稻土不同土层中,且数量远高于"半程"氨氧化细菌和古菌,意味着Comammox可能在水稻土硝化作用中起重要作用。     

Bacteria dominate the ammonia-oxidizing community in a hydrothermal vent site at the Mid-Atlantic Ridge of the South Atlantic Ocean

Ammonia oxidation is the first and rate-limiting step of nitrification, which is carried out by two groups of microorganisms: ammonia-oxidizing bacteria (AOB) and the recently discovered ammonia-oxidizing archaea (AOA). In this study, diversity and abundance of AOB and AOA were investigated in five rock samples from a deep-sea hydrothermal vent site at the Mid-Atlantic Ridge (MAR) of the South Atlantic Ocean. Both bacterial and archaeal ammonia monooxygenase subunit A (amoA) gene sequences obtained in this study were closely related to the sequences retrieved from deep-sea environments, indicating that AOB and AOA in this hydrothermal vent site showed typical deep ocean features. AOA were more diverse but less abundant than AOB. The ratios of AOA/AOB amoA gene abundance ranged from 1/3893 to 1/242 in all investigate samples, indicating that bacteria may be the major members responding to the aerobic ammonia oxidation in this hydrothermal vent site. Furthermore, diversity and abundance of AOA and AOB were significantly correlated with the contents of total nitrogen and total sulfur in investigated samples, suggesting that these two environmental factors exert strong influences on distribution of ammonia oxidizers in deep-sea hydrothermal vent environment.     

Diversity, Physiology, and Niche Differentiation of Ammonia-Oxidizing Archaea

Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, has been suggested to have been a central part of the global biogeochemical nitrogen cycle since the oxygenation of Earth. The cultivation of several ammonia-oxidizing archaea (AOA) as well as the discovery that archaeal ammonia monooxygenase (amo)-like gene sequences are nearly ubiquitously distributed in the environment and outnumber their bacterial counterparts in many habitats fundamentally revised our understanding of nitrification. Surprising insights into the physiological distinctiveness of AOA are mirrored by the recognition of the phylogenetic uniqueness of these microbes, which fall within a novel archaeal phylum now known as Thaumarchaeota. The relative importance of AOA in nitrification, compared to ammonia-oxidizing bacteria (AOB), is still under debate. This minireview provides a synopsis of our current knowledge of the diversity and physiology of AOA, the factors controlling their ecology, and their role in carbon cycling as well as their potential involvement in the production of the greenhouse gas nitrous oxide. It emphasizes the importance of activity-based analyses in AOA studies and formulates priorities for future research.     

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

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.     

好氧氨氧化过程中的关键酶及N2O排放研究进展

氧化亚氮(nitrous oxide, N₂O)排放量的持续增加对全球生态平衡造成了严重的威胁。微生物N₂O排放占主要来源。其中,好氧氨氧化过程是氨在有氧的条件下氧化为亚硝酸盐,其直接或间接地影响着全球产生N₂O与释放量。氨氧化古菌(ammonia-oxidizing archaea, AOA)、氨氧化细菌(ammonia-oxidizing bacteria, AOB)、全程氨氧化菌(complete ammonia oxidization, Comammox)和异养氨氧化菌(heterotrophic ammonium oxidizing bacteria, HAOB)是氨氧化过程中主要的参与者,明确这四类微生物N₂O产生的机制对缓解全球N₂O排放是必要的。本文综述了AOA、AOB、Comammox和HAOB在好氧氨氧化过程中驱动的N₂O产生途径,并结合酶学分析了一些关键酶在N₂O产生途径中的作用。本文旨在为调控生物N₂O排放提供理论基础。     

高含氮稻田深层土壤的氨氧化古菌和厌氧氨氧化菌共存及对氮循环影响

随着海洋生态系统中的厌氧氨氧化反应和氨氧化古菌的发现,自然生态系统的氮循环过程被重新认识,但是目前尚无在陆地深层的相关报道。结合同位素示踪与分子生物学技术探索了稻田深层土壤中anammox与AOA的存在及特性。结果表明,在沼渣处理废水浇灌的高含氮稻田深层土壤中,anammox与AOA共存。通过构建克隆文库发现,此土壤中厌氧氨氧化菌的生物多样性相对较低,35个克隆序列只分为4个独立操作单元(OTU),代表序列与Genebank数据库中已探明的厌氧氨氧化菌Candidatus 'Kuenenia stuttgartiensis’的同源性超过95%;对氨氧化古菌的分析发现,20个克隆子共得到5个OTU,其与基因库中土壤/沉积物进化分支关系最近,序列的同源性部分超过98%。同位素示踪的初步结果表明,anammox产生的氮气占此土壤总氮气生成量的24.1%-29.8%。AOA与anammox的共存为anammox反应的广泛存在与发生提供了新思路。