湖泊微生物反硝化过程及速率研究进展

湖泊中微生物介导的反硝化过程对于区域乃至全球的气候环境变化有着深远的影响。因此,研究湖泊微生物反硝化过程及速率有助于我们深刻理解湖泊氮元素生物地球化学循环规律,全面认识湖泊生境对全球氮循环的贡献。本文综述了湖泊生境中反硝化过程(包括典型的反硝化过程及与其他物质循环耦合的反硝化过程,如与有机氮耦合的共反硝化作用、与碳循环耦合的硝酸盐/亚硝酸盐依赖型厌氧甲烷氧化、与铁循环耦合的硝酸盐依赖型铁氧化、与硫循环耦合的硝酸盐还原硫氧化)的速率、驱动微生物及其影响因素。最后对湖泊反硝化过程研究现状和未来发展方向提出总结与展望。     

污水脱氮功能微生物的组学研究进展

生物脱氮是污水处理厂的核心,掌握生物脱氮过程相关微生物代谢特性,对于探索微生物资源和提高污水处理厂脱氮性能具有重要意义。近年来,分子生物学方法不断发展和改进,已被广泛应用于揭示脱氮微生物群落多样性、组成结构和潜在功能等方面,大幅提升了研究者们对污水生物脱氮系统中微生物,尤其是不可培养微生物的代谢机理、抑制调控原理及新型生物脱氮工艺途径的认识。本文对流行的分子生物学方法(16S rRNA基因测序、实时荧光定量PCR技术、宏基因组学、宏转录组学、宏蛋白质组学和代谢组学)进行了介绍,综述了其在硝化细菌、反硝化细菌、完全氨氧化细菌、厌氧氨氧化细菌、厌氧铁氨氧化细菌、硫酸盐型厌氧氨氧化细菌及亚硝酸盐/硝酸盐型厌氧甲烷氧化微生物等方面的研究进展,阐明了这些氮素转化微生物在氮循环过程的代谢途径和酶促反应,并从标准测定方法构建、不同方法的联用及跨学科结合和检测方法的简易化这3个方面展望了分子生物学方法的技术突破及其在污水生物处理系统中的应用前景。本综述从系统角度全面认识脱氮微生物群落及其结构,为未来污水处理生物脱氮微生物的研究提供了新方向。     

陆地和淡水生态系统新型微生物氮循环研究进展

氮生物地球化学循环是地球物质循环的重要枢纽,是决定陆地生态系统生产力水平、水资源安全、温室气体生成排放的关键过程。氮循环是由微生物介导的一系列复杂过程,不同形态、价态氮化合物的转化分别由相应的功能微生物驱动完成。随着厌氧氨氧化、完全氨氧化等新型氮转化过程的相继报道和发现更新了人们对氮循环的认识。本文综述了陆地和淡水生态系统中厌氧氨氧化(anammox)、硝酸盐异化还原为铵(DNRA)、完全氨氧化(comammox)等新型氮循环过程的发生机制、热区分布及环境效应,并总结了这三种氮循环的相互关系。     

海洋氮循环过程及基于基因组代谢网络模型的预测

海洋氮循环在地球元素循环中充当着必不可少的角色。海洋氮循环是由一系列氧化还原反应构成的生物化学过程。固氮作用和氮同化作用为生态系统提供了生物可用氮(铵盐)。硝化作用可进一步将铵盐氧化为硝酸盐,硝酸盐又可以通过反硝化作用转化为氮气。整个氮循环实现了海洋中不同含氮无机盐间的转换。微生物是海洋氮循环的重要驱动者,海洋氮循环的研究可以帮助理解海洋生物与地球环境相互作用及协同演化的机制,从而更好地保护地球生态环境。随着氮循环关键微生物基因组尺度代谢网络模型的发表,研究者可以利用代谢网络模型来研究不同氮循环过程的效率、环境因子对氮循环过程的影响以及解析氮循环及生物网络的内在机理等,从而帮助人们更深入地研究海洋氮转化机制。本文主要综述了海洋氮循环过程中各个转化过程的主要微生物,以及基因组尺度代谢网络模型在分析氮循环中的应用。     

厌氧铁氧化菌研究进展

厌氧铁氧化菌(AFOM)是微生物学、地质学和环境学领域的重大发现.研究AFOM对于认识铁地质层形成,促进铁、氮、碳等元素的地球生物化学循环,丰富微生物学内容,开发厌氧铁氧化工艺,以及探索原始地球环境和外星生命现象,均有重要意义.本文综述了AFOM的研究进展,介绍了AFOM的存在生境,探讨了AFOM的物种多样性及其营养特性和代谢特性,阐述了AFOM在地质学、微生物学和环境学领域的潜在作用,并展望了AFOM在新物种发掘、代谢机理揭示以及开发应用等方面的研究方向.     

厌氧铁氧化菌研究进展

厌氧铁氧化菌(AFOM)是微生物学、地质学和环境学领域的重大发现.研究AFOM对于认识铁地质层形成,促进铁、氮、碳等元素的地球生物化学循环,丰富微生物学内容,开发厌氧铁氧化工艺,以及探索原始地球环境和外星生命现象,均有重要意义.本文综述了AFOM的研究进展,介绍了AFOM的存在生境,探讨了AFOM的物种多样性及其营养特性和代谢特性,阐述了AFOM在地质学、微生物学和环境学领域的潜在作用,并展望了AFOM在新物种发掘、代谢机理揭示以及开发应用等方面的研究方向.     

铁矿物强化厌氧氨氧化效能及其微生物机制研究进展

自然界中的氮循环与铁循环相互交联,参与氮循环的厌氧氨氧化（anaerobic ammonium oxidation,anammox）菌的生长代谢及活性发挥也与铁元素紧密关联。自然界广泛存在的铁矿物因具有运行成本低廉、稳定性好、二次污染小等优势,在污水处理领域得到广泛应用。在厌氧氨氧化脱氮系统中引入适量铁矿物,不仅有助于促进anammox菌和铁还原菌的富集,提高功能基因丰度和相关酶活性,还可能通过影响污泥浓度、血红素c含量、胞外聚合物含量和颗粒化程度,改善污泥性能和提高厌氧氨氧化系统的稳定性。同时,铁矿物具有促进体系多种氮素转化途径（如anammox、铁自养反硝化、铁氨氧化、异化硝酸盐还原成铵和反硝化）相耦合的潜能,可以提高anammox污水处理系统的总氮去除率。本文基于铁矿物在促进污水生物脱氮方面的良好性能及其在anammox系统中的变化,从脱氮效能、污泥特性、微生物特征及酶活性等方面,系统综述了铁矿物对厌氧氨氧化系统的强化作用机制,并从anammox菌对铁矿物的利用及铁元素的摄取角度展望了后续的研究方向,以期为铁矿物强化厌氧氨氧化系统的实际应用提供理论和技术指导。     

微生物在近海氮循环过程的贡献与驱动机制

人类活动导致海岸带氮超载而富营养化,进而引起更多的生态环境问题.在全球变化背景下,进一步揭示微生物驱动的氮循环过程的驱动机制及贡献,对评价与预测近海生态系统服务功能变化、管理决策等至关重要.本文介绍了固氮、氨化、硝化、反硝化、硝酸盐铵化、厌氧氨氧化过程在近海多种生境沉积物中的生物地球化学(速率、通量、贡献)与微生物生态学(功能类群丰度)特征及时空变化规律,阐述温度、溶氧、盐度、活性溶解有机碳、无机氮、沉水植物、底栖动物活动等因素对各过程速率的影响及对各竞争性类群或过程(氨氧化细菌/氨氧化古菌,反硝化/硝酸盐铵化/厌氧氨氧化)的调控机制,并简析了海岸带微生物氮循环研究所面临的机遇与挑战.     

微生物厌氧氨氧化耦合铁还原的研究进展及展望

厌氧氨氧化耦合铁还原[ammonium oxidation coupled to Fe(Ⅲ) reduction, Feammox]作为一种连接氮循环和铁循环之间的氮代谢途径,在自然界中氨氮转化过程中起到了重要作用。系统研究Feammox驱动的氮铁的生物地球化学耦合过程及其受控因素,有助于深入理解地球元素循环的微生物机制,也有助于揭示Feammox在缺氧地质历史时期对古海洋氮库演变和含铁矿物形成过程中的作用。本文从Feammox发展历史、相关微生物、影响因素和潜在地质意义等方面综述了Feammox的研究过程和研究内容,并对Feammox的未来研究方向提出展望。     

微生物驱动硝酸盐还原耦合亚铁氧化成矿过程的锌胁迫

【目的】探究中性厌氧条件下,金属锌影响下硝酸盐依赖型铁氧化菌Pseudomonas stutzeri LS-2驱动的硝酸盐还原耦合亚铁氧化成矿过程机制,对深入理解中性厌氧环境中微生物亚铁氧化驱动的反硝化作用及重金属固定机制具有重要意义。【方法】以不同Zn(Ⅱ)浓度构建LS-2驱动的亚铁氧化成矿体系,分析不同体系中亚铁氧化速率、硝酸盐还原速率以及形成矿物的结构变化规律。【结果】LS-2驱动的硝酸盐还原耦合亚铁氧化成矿过程中,共存Zn(Ⅱ)降低该过程中硝酸盐的还原速率和亚铁氧化速率。同时,随着Zn(Ⅱ)浓度提高,抑制作用增强。微生物亚铁氧化形成的矿物通过吸附、共沉淀和离子置换等过程固定Zn(Ⅱ),降低Zn(Ⅱ)活性。Zn(Ⅱ)浓度对形成的矿物结构有较大的影响:低浓度Zn(Ⅱ)体系中,形成的矿物为纤铁矿;随着Zn(Ⅱ)浓度的提高,矿物结构与结晶度都有一定程度的变化,当Zn(Ⅱ)达到4 mmol/L时,形成的矿物主要为铁锌尖晶石。【结论】明确了重金属锌对LS-2菌株反硝化及亚铁氧化过程的抑制规律,同时阐明了Zn(Ⅱ)浓度对形成矿物结构的影响。研究结果有助于深入认识中性厌氧环境中重金属与微生物驱动的铁循环和反硝化过程的耦合作用,为土壤重金属污染防治提供理论支撑。     

Anaerobic ferrous oxidation by heterotrophic denitrifying enriched culture

Heterotrophic denitrifying enriched culture (DEC) from a lab-scale high-rate denitrifying reactor was discovered to perform nitrate-dependent anaerobic ferrous oxidation (NAFO). The DEC was systematically investigated to reveal their denitrification activity, their NAFO activity, and the predominant microbial population. The DEC was capable of heterotrophic denitrification with methanol as the electron donor, and autotrophic denitrification with ferrous salt as the electron donor named NAFO. The conversion ratios of ferrous-Fe and nitrate-N were 87.41 and 98.74 %, and the consumption Fe/N ratio was 2.3:1 (mol/mol). The maximum reaction velocity and half saturation constant of Fe were 412.54 mg/(l h) and 8,276.44 mg/l, and the counterparts of N were 20.87 mg/(l h) and 322.58 mg/l, respectively. The predominant bacteria were Hyphomicrobium, Thauera, and Flavobacterium, and the predominant archaea were Methanomethylovorans, Methanohalophilus, and Methanolobus. The discovery of NAFO by heterotrophic DEC is significant for the development of wastewater treatment and the biogeochemical iron cycle and nitrogen cycle.     

Anaerobic and aerobic oxidation of ferrous iron at neutral pH by chemoheterotrophic nitrate-reducing bacteria

Nine out of ten anaerobic enrichment cultures inoculated with sediment samples from various freshwater, brackish-water, and marine sediments exhibited ferrous iron oxidation in mineral media with nitrate and an organic cosubstrate at pH 7.2 and 30° C. Anaerobic nitrate-dependent ferrous iron oxidation was a biological process. One strain isolated from brackish-water sediment (strain HidR2, a motile, nonsporeforming, gram-negative rod) was chosen for further investigation of ferrous iron oxidation in the presence of acetate as cosubstrate. Strain HidR2 oxidized between 0.7 and 4.9 mM ferrous iron aerobically and anaerobically at pH 7.2 and 30° C in the presence of small amounts of acetate (between 0.2 and 1.1 mM). The strain gained energy for growth from anaerobic ferrous iron oxidation with nitrate, and the ratio of iron oxidized to acetate provided was constant at limiting acetate supply. The ability to oxidize ferrous iron anaerobically with nitrate at approximately pH 7 appears to be a widespread capacity among mesophilic denitrifying bacteria. Since nitrate-dependent iron oxidation closes the iron cycle within the anoxic zone of sediments and aerobic iron oxidation enhances the reoxidation of ferrous to ferric iron in the oxic zone, both processes increase the importance of iron as a transient electron carrier in the turnover of organic matter in natural sediments. Received: 24 April 1997 / Accepted: 22 September 1997     

Anaerobic nitrate-dependent iron(II) bio-oxidation by a novel lithoautotrophic betaproteobacterium, strain 2002

Microbial nitrate-dependent Fe(II) oxidation is known to contribute to iron biogeochemical cycling; however, the microorganisms responsible are virtually unknown. In an effort to elucidate this microbial metabolic process in the context of an environmental system, a 14-cm sediment core was collected from a freshwater lake and geochemically characterized concurrently with the enumeration of the nitrate-dependent Fe(II)-oxidizing microbial community and subsequent isolation of a nitrate-dependent Fe(II)-oxidizing microorganism. Throughout the sediment core, ambient concentrations of Fe(II) and nitrate were observed to coexist. Concomitant most probable number enumeration revealed the presence of an abundant nitrate-dependent Fe(II)-oxidizing microbial community (2.4 x 10(3) to 1.5 x 10(4) cells g(-1) wet sediment) from which a novel anaerobic, lithoautotrophic, Fe(II)-oxidizing bacterium, strain 2002, was isolated. Analysis of the complete 16S rRNA gene sequence revealed that strain 2002 was a member of the beta subclass of the proteobacteria with 94.8% similarity to Chromobacterium violaceum, a bacterium not previously recognized for the ability to oxidize nitrate-dependent Fe(II). Under nongrowth conditions, both strain 2002 and C. violaceum incompletely reduced nitrate to nitrite with Fe(II) as the electron donor, while under growth conditions nitrate was reduced to gaseous end products (N2 and N2O). Lithoautotrophic metabolism under nitrate-dependent Fe(II)-oxidizing conditions was verified by the requirement of CO2 for growth as well as the assimilation of 14C-labeled CO2 into biomass. The isolation of strain 2002 represents the first example of an anaerobic, mesophilic, neutrophilic Fe(II)-oxidizing lithoautotroph isolated from freshwater samples. Our studies further demonstrate the abundance of nitrate-dependent Fe(II) oxidizers in freshwater lake sediments and provide further evidence for the potential of microbially mediated Fe(II) oxidation in anoxic environments.     

Anaerobic Biooxidation of Fe(II) by Dechlorosoma suillum

Anaerobic microbial oxidation of Fe(II) was only recently discovered and very little is known about this metabolism. We recently demonstrated that several dissimilatory perchlorate-reducing bacteria could utilize Fe(II) as an electron donor under anaerobic conditions. Here we report on a more in-depth analysis of Fe(II) oxidation by one of these organisms, Dechlorosoma suillum. Similarly to most known nitrate-dependent Fe(II) oxidizers, D. suillum did not grow heterotrophically or lithoautotrophically by anaerobic Fe(II) oxidation. In the absence of a suitable organic carbon source, cells rapidly lysed even though nitrate-dependent Fe(II) oxidation was still occurring. The coupling of Fe(II) oxidation to a particular electron acceptor was dependent on the growth conditions of cells of D. suillum. As such, anaerobically grown cultures of D. suillum did not mediate Fe(II) oxidation with oxygen as the electron acceptor, while conversely, aerobically grown cultures did not mediate Fe(II) oxidation with nitrate as the electron acceptor. Anaerobic washed cell suspensions of D. suillum rapidly produced an orange/brown precipitate which X-ray diffraction analysis identified as amorphous ferric oxyhydroxide or ferrihydrite. This is similar to all other identified nitrate-dependent Fe(II) oxidizers but is in contrast to what is observed for growth cultures of D. suillum, which produced a mixed-valence Fe(II)-Fe(III) precipitate known as green rust. D. suillum rapidly oxidized the Fe(II) content of natural sediments. Although the form of ferrous iron in these sediments is unknown, it is probably a component of an insoluble mineral, as previous studies indicated that soluble Fe(II) is a relatively minor form of the total Fe(II) content of anoxic environments. The results of this study further enhance our knowledge of a poorly understood form of microbial metabolism and indicate that anaerobic Fe(II) oxidation by D. suillum is significantly different from previously described forms of nitrate-dependent microbial Fe(II) oxidation.     

Characteristics of Nitrate Reduction Using Fe (II) as Electron Donor in Activated Sludge

Static experiments were conducted to investigate the effects of environmental factors on nitrate (NO₃^?-N)-removal efficiency, such as NO₃^?-N loading, pH value, C/N ratio and temperature in activated sludge using Fe (II) as electron donor. The results demonstrated that the average denitrification rate increased from 1.25 to 2.23 mg NO₃^?-N/(L·h) with NO₃^?-N loading increased from 30 to 60 mg/L. When pH increased from 7 to 8, the concentration of NO₃^?-N and nitrite (NO₂^?-N) in effluent were all maintained at quite low levels. C/N ratio had little impact on denitrification process, i.e., inorganic carbon (C) source could still be enough for denitrification process with C/N ratio as low as 5. Temperature had a significant effect on the denitrification efficiency, and NO₃^?-N removal efficiency of 92.03%, 96.77%, 97.67% and 98.23% could be obtained with temperature of 25°C, 30°C, 35°C and 40°C, respectively. SEM, XRD and XRF analysis was used to investigate microscopic surface morphology and chemical composition of the denitrifying activated sludge, and mechanism of the nitrate-dependent anaerobic ferrous oxidation (NAFO) bacterias could be explored with this research.     

Repeated anaerobic microbial redox cycling of iron

Some nitrate- and Fe(III)-reducing microorganisms are capable of oxidizing Fe(II) with nitrate as the electron acceptor. This enzymatic pathway may facilitate the development of anaerobic microbial communities that take advantage of the energy available during Fe-N redox oscillations. We examined this phenomenon in synthetic Fe(III) oxide (nanocrystalline goethite) suspensions inoculated with microflora from freshwater river floodplain sediments. Nitrate and acetate were added at alternate intervals in order to induce repeated cycles of microbial Fe(III) reduction and nitrate-dependent Fe(II) oxidation. Addition of nitrate to reduced, acetate-depleted suspensions resulted in rapid Fe(II) oxidation and accumulation of ammonium. High-resolution transmission electron microscopic analysis of material from Fe redox cycling reactors showed amorphous coatings on the goethite nanocrystals that were not observed in reactors operated under strictly nitrate- or Fe(III)-reducing conditions. Microbial communities associated with N and Fe redox metabolism were assessed using a combination of most-probable-number enumerations and 16S rRNA gene analysis. The nitrate-reducing and Fe(III)-reducing cultures were dominated by denitrifying Betaproteobacteria (e.g., Dechloromonas) and Fe(III)-reducing Deltaproteobacteria (Geobacter), respectively; these same taxa were dominant in the Fe cycling cultures. The combined chemical and microbiological data suggest that both Geobacter and various Betaproteobacteria participated in nitrate-dependent Fe(II) oxidation in the cycling cultures. Microbially driven Fe-N redox cycling may have important consequences for both the fate of N and the abundance and reactivity of Fe(III) oxides in sediments.     

Chemolithotrophic nitrate-dependent Fe(II)-oxidizing nature of actinobacterial subdivision lineage TM3

Anaerobic nitrate-dependent Fe(II) oxidation is widespread in various environments and is known to be performed by both heterotrophic and autotrophic microorganisms. Although Fe(II) oxidation is predominantly biological under acidic conditions, to date most of the studies on nitrate-dependent Fe(II) oxidation were from environments of circumneutral pH. The present study was conducted in Lake Grosse Fuchskuhle, a moderately acidic ecosystem receiving humic acids from an adjacent bog, with the objective of identifying, characterizing and enumerating the microorganisms responsible for this process. The incubations of sediment under chemolithotrophic nitrate-dependent Fe(II)-oxidizing conditions have shown the enrichment of TM3 group of uncultured Actinobacteria. A time-course experiment done on these Actinobacteria showed a consumption of Fe(II) and nitrate in accordance with the expected stoichiometry (1:0.2) required for nitrate-dependent Fe(II) oxidation. Quantifications done by most probable number showed the presence of 1 × 10⁴ autotrophic and 1 × 10⁷ heterotrophic nitrate-dependent Fe(II) oxidizers per gram fresh weight of sediment. The analysis of microbial community by 16S rRNA gene amplicon pyrosequencing showed that these actinobacterial sequences correspond to ∼0.6% of bacterial 16S rRNA gene sequences. Stable isotope probing using ¹³CO₂ was performed with the lake sediment and showed labeling of these Actinobacteria. This indicated that they might be important autotrophs in this environment. Although these Actinobacteria are not dominant members of the sediment microbial community, they could be of functional significance due to their contribution to the regeneration of Fe(III), which has a critical role as an electron acceptor for anaerobic microorganisms mineralizing sediment organic matter. To the best of our knowledge this is the first study to show the autotrophic nitrate-dependent Fe(II)-oxidizing nature of TM3 group of uncultured Actinobacteria.     

Ecophysiology and the energetic benefit of mixotrophic Fe(II) oxidation by various strains of nitrate-reducing bacteria

In order to assess the importance of nitrate-dependent Fe(II) oxidation and its impact on the growth physiology of dominant Fe oxidizers, we counted these bacteria in freshwater lake sediments and studied their growth physiology. Most probable number counts of nitrate-reducing Fe(II)-oxidizing bacteria in the sediment of Lake Constance, a freshwater lake in Southern Germany, yielded about 10⁵ cells mL⁻¹ of the total heterotrophic nitrate-reducing bacteria, with about 1% (10³ cells mL⁻¹) of nitrate-reducing Fe(II) oxidizers. We investigated the growth physiology of Acidovorax sp. strain BoFeN1, a dominant nitrate-reducing mixotrophic Fe(II) oxidizer isolated from this sediment. Strain BoFeN1 uses several organic compounds (but no sugars) as substrates for nitrate reduction. It also reduces nitrite, dinitrogen monoxide, and O₂, but cannot reduce Fe(III). Growth experiments with cultures amended either with acetate plus Fe(II) or with acetate alone demonstrated that the simultaneous oxidation of Fe(II) and acetate enhanced growth yields with acetate alone (12.5 g dry mass mol⁻¹ acetate) by about 1.4 g dry mass mol⁻¹ Fe(II). Also, pure cultures of Pseudomonas stutzeri and Paracoccus denitrificans strains can oxidize Fe(II) with nitrate, whereas Pseudomonas fluorescens and Thiobacillus denitrificans strains did not. Our study demonstrates that nitrate-dependent Fe(II) oxidation contributes to the energy metabolism of these bacteria, and that nitrate-dependent Fe(II) oxidation can essentially contribute to anaerobic iron cycling.