微生物异化硝酸盐和亚硝酸盐产铵研究进展

异化硝酸盐和亚硝酸盐还原产铵是氮转化附属途径,为生态系统中氮的重复利用提供了依据,已成为近年来的研究热点。据报道,氮源的种类及浓度不同异化还原产铵的发生机制及强度具有差异性,决定着微生物产铵的效率,因此,有必要明确不同氮源异化还原产铵的代谢机制。本文详细论述了参与硝酸盐和亚硝酸盐异化还原产铵过程的相关微生物种类、产铵途径及其机理;系统分析了单一氮源和混合氮源对不同微生物产铵的影响和差异,比较了放线菌与其他微生物产铵的优势,并对未来的研究方向进行了展望,旨在为微生物异化硝酸盐和亚硝酸盐还原产铵提供理论基础。     

Microbial nitrate respiration--genes, enzymes and environmental distribution

Nitrate is a key node in the network of the assimilatory and respiratory nitrogen pathways. As one of the ‘fixed’ forms of nitrogen, nitrate plays an essential role in both nature and industry. For bacteria, it is both a nitrogen source and an electron acceptor. In agriculture and wastewater treatment, nitrate respiration by microorganisms is an important issue with respect to economics, greenhouse gas emission and public health. Several microbial processes compete for nitrate: denitrification, dissimilatory nitrate reduction to ammonium and anaerobic ammonium oxidation. In this review we provide an up to date overview of the organisms, genes and enzymes involved in nitrate respiration. We also address the molecular detection of these processes in nature. We show that despite rapid progress in the experimental and genomic analyses of pure cultures, knowledge on the mechanism of nitrate reduction in natural ecosystems is still largely lacking.     

Anammox bacteria disguised as denitrifiers: nitrate reduction to dinitrogen gas via nitrite and ammonium

Anaerobic ammonium-oxidizing (anammox) bacteria oxidize ammonium with nitrite and produce N(2). They reside in many natural ecosystems and contribute significantly to the cycling of marine nitrogen. Anammox bacteria generally live under ammonium limitation, and it was assumed that in nature anammox bacteria depend on other biochemical processes for ammonium. In this study we investigated the possibility of dissimilatory nitrate reduction to ammonium by anammox bacteria. Physically purified Kuenenia stuttgartiensis cells reduced (15)NO(3) (-) to (15)NH(4) (+) via (15)NO(2) (-) as the intermediate. This was followed by the anaerobic oxidation of the produced ammonium and nitrite. The overall end-product of this metabolism of anammox bacteria was (15)N(15)N dinitrogen gas. The nitrate reduction to nitrite proceeds at a rate of 0.3 +/- 0.02 fmol cell(-1) day(-1) (10% of the 'normal' anammox rate). A calcium-dependent cytochrome c protein with a high (305 mumol min(-1) mg protein(-1)) rate of nitrite reduction to ammonium was partially purified. We present evidence that dissimilatory nitrate reduction to ammonium occurs in Benguela upwelling system at the same site where anammox bacteria were previously detected. This indicates that anammox bacteria could be mediating dissimilatory nitrate reduction to ammonium in natural ecosystems.     

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.     

Interactions between Benthic Copepods,Bacteria and Diatoms Promote Nitrogen Retention in Intertidal Marine Sediments

The present study aims at evaluating the impact of diatoms and copepods on microbial processes mediating nitrate removal in fine-grained intertidal sediments. More specifically, we studied the interactions between copepods, diatoms and bacteria in relation to their effects on nitrate reduction and denitrification. Microcosms containing defaunated marine sediments were subjected to different treatments: an excess of nitrate, copepods, diatoms (Navicula sp.), a combination of copepods and diatoms, and spent medium from copepods. The microcosms were incubated for seven and a half days, after which nutrient concentrations and denitrification potential were measured. Ammonium concentrations were highest in the treatments with copepods or their spent medium, whilst denitrification potential was lowest in these treatments, suggesting that copepods enhance dissimilatory nitrate reduction to ammonium over denitrification. We hypothesize that this is an indirect effect, by providing extra carbon for the bacterial community through the copepods'' excretion products, thus changing the C/N ratio in favour of dissimilatory nitrate reduction. Diatoms alone had no effect on the nitrogen fluxes, but they did enhance the effect of copepods, possibly by influencing the quantity and quality of the copepods'' excretion products. Our results show that small-scale biological interactions between bacteria, copepods and diatoms can have an important impact on denitrification and hence sediment nitrogen fluxes.     

硝态氮异化还原机制及其主导因素研究进展

硝态氮(NO_3~-)异化还原过程通常包含反硝化和异化还原为铵(DNRA)两个方面,是土壤氮素转化的重要途径,其强度大小直接影响着硝态氮的利用和环境效应(如淋溶和氮氧化物气体排放)。反硝化和DNRA过程在反应条件、产物和影响因素等方面常会呈现出协同与竞争的交互作用机制。综述了反硝化和DNRA过程的研究进展及其二者协同竞争的作用机理,并阐述了在NO_3~-、pH、有效C、氧化还原电位(Eh)等环境条件和土壤微生物对其发生强度和产物的影响,提出了今后应在产生机理、土壤环境因素、微生物学过程以及与其他氮素转化过程耦联作用等方面亟需深入研究,以期增进对氮素循环过程的认识以及为加强氮素管理利用提供依据。     

Patterns and drivers of anaerobic nitrogen transformations in sediments of thermokarst lakes

Significant attention has been given to the way in which the soil nitrogen (N) cycle responds to permafrost thaw in recent years, yet little is known about anaerobic N transformations in thermokarst lakes, which account for more than one-third of thermokarst landforms across permafrost regions. Based on the N isotope dilution and tracing technique, combined with qPCR and high-throughput sequencing, we presented large-scale measurements of anaerobic N transformations of sediments across 30 thermokarst lakes over the Tibetan alpine permafrost region. Our results showed that gross N mineralization, ammonium immobilization, and dissimilatory nitrate reduction rates in thermokarst lakes were higher in the eastern part of our study area than in the west. Denitrification dominated in the dissimilatory nitrate reduction processes, being two and one orders of magnitude higher than anaerobic ammonium oxidation (anammox) and dissimilatory nitrate reduction to ammonium (DNRA), respectively. The abundances of the dissimilatory nitrate reduction genes (nirK, nirS, hzsB, and nrfA) exhibited patterns consistent with sediment N transformation rates, while α diversity did not. The inter-lake variability in gross N mineralization and ammonium immobilization was dominantly driven by microbial biomass, while the variability in anammox and DNRA was driven by substrate supply and organic carbon content, respectively. Denitrification was jointly affected by nirS abundance and organic carbon content. Overall, the patterns and drivers of anaerobic N transformation rates detected in this study provide a new perspective on potential N release, retention, and removal upon the formation and development of thermokarst lakes.     

Thermodynamic constraints on the utility of ecological stoichiometry for explaining global biogeochemical patterns

Carbon and nitrogen cycles are coupled through both stoichiometric requirements for microbial biomass and dissimilatory metabolic processes in which microbes catalyse reduction‐oxidation reactions. Here, we integrate stoichiometric theory and thermodynamic principles to explain the commonly observed trade‐off between high nitrate and high organic carbon concentrations, and the even stronger trade‐off between high nitrate and high ammonium concentrations, across a wide range of aquatic ecosystems. Our results suggest these relationships are the emergent properties of both microbial biomass stoichiometry and the availability of terminal electron acceptors. Because elements with multiple oxidation states (i.e. nitrogen, manganese, iron and sulphur) serve as both nutrients and sources of chemical energy in reduced environments, both assimilative demand and dissimilatory uses determine their concentrations across broad spatial gradients. Conceptual and quantitative models that integrate rather than independently examine thermodynamic, stoichiometric and evolutionary controls on biogeochemical cycling are essential for understanding local to global biogeochemical patterns.     

Simultaneous occurrence of denitrification and nitrate ammonification in sediments of the French Mediterranean Coast

Dissimilatory nitrate reductions in coastal marine sediment of Carteau Cove (French Mediterranean Coast) were studied between April 1993 and July 1994. Simultaneous determination of denitrification and dissimilatory nitrate reduction to ammonium was achieved by using a combination of acetylene blockage and 15N techniques. After short incubations (maximum 5 h), a part of 15N labelled nitrate added to the sediment was recovered as ammonium without incorporation in organic matter. The result indicate that a fraction of nitrate was reduced to ammonium by a dissimilatory mechanism instead of denitrifying. Denitrifying and nitrate ammonifying activities ranged from 0 to 19.8 μmol l-1 d-1 and from 2.3 to 83.2 μmol l-1 d-1, respectively. Denitrification rates were highest in early spring whereas nitrate ammonification were highest in fall. The recovery of nitrate reduced as N2O-N plus ammonium was between 40 and 100%, the highest nitrogen losses were recorded in July. Depending on the station and time of year denitrification accounted for between 0 and 43% of the total nitrate reduction whereas dissimilatory nitrate reduction to ammonium (DNRA) accounted for between 18 and 100%. The reduction rate data suggest that the pathway of nitrate reduction to ammonium may be important in coastal sediments. This revised version was published online in July 2006 with corrections to the Cover Date.     

Chemcial aspects of the energy process in nitrate reduction in different representatives of soil microflora

Chemical aspects of dissimilatory nitrate reduction were studied by mass spectrometry in the following soil bacteria: Bacillus filaris, Bacillus polymyxa and Pseudomonas denitrificans. Chemical peculiarity of this process in spore-forming soil bacteria is the simultaneous operation of two energy processes: denitrification and nitrate respiration. The first process is terminated by the formation of molecular nitrogen, the second, by the production of ammonia. The quantitative ratio between these processes demonstrates the advantage of nitrate respiration in the overall energy pathway of nitrate dissimilation. Pseudomonas denitrificans maintains the abilityfor intensive gas production as a result of denitrification upon long storage on artificial media: ca. 34 per cent of the nitrate nitrogen is reduced to gaseous forms of nitrogen.     

红树林生态系统微生物驱动的氮素循环过程研究进展

微生物驱动的氮循环过程在红树林生态系统物质循环、净化外来污染物、维持生态系统平衡等方面起重要作用。相较于其他自然生态系统,因红树林处于沿海陆地交界地带,其氮循环过程及其相关微生物的种类丰富,受交错复杂的环境因素影响与调控。本文梳理了红树林土壤性质及特性,综述了红树林生态系统中由微生物驱动的固氮、氮素矿化、硝化、厌氧氨氧化、反硝化、异化硝酸盐还原为铵等主要的氮循环过程,并讨论了氮循环与其他循环的耦合过程。最后讨论pH、盐度、季节、螃蟹活动、红树林树种等环境因素对氮循环过程及其相关微生物丰度、多样性的影响。本综述以期为红树林湿地生态系统的保护和修复提供理论参考。     

Microbial Nitrogen and Sulfur Cycles at the Gypsum Dunes of White Sands National Monument,New Mexico

The White Sands National Monument from New Mexico (U.S.A) contains one of the largest known gypsum dune fields with unique, rapidly migrating, arid, evaporitic habitats. Deposits from dune sides and interdune areas were collected in order to determine the characteristics of microbial habitat and communities through mineral assemblages, microbial pigments along with investigations of nitrogen and sulfur cycles. The most abundant pigments, scytonemin and carotenoids, were common UV protective pigments. Predominance of nitrite and nitrate over ammonium nitrogen (2.16: 1) implies that nitrification processes might be important in this ecosystem. Ammonium oxidizers from groups of β-, γ-proteobacteria and archaea were detected in all deposits, thereby indicating microbial involvement in nitrification. Additionally, denitrifying organisms with nirS and nirK genes were also present in most of the analyzed samples. The presence of trace carbonate mineral phases in association with biofilm implies possible microbial sulfate reduction. Microbes with metabolic abilities for sulfur cycling (i.e., dissimilatory sulfite reducers, purple sulfur bacteria, green sulfur and non-sulfur bacteria, and organisms with the APS enzyme) were identified in all samples. These particular organisms have the ability to reduce sulfate and to re-oxidize reduced sulfur compounds back to sulfate.     

Anaerobic ammonium oxidation in marine environments: contribution to biogeochemical cycles and biotechnological developments for wastewater treatment

Microbial processes are responsible for most reactions involved in the nitrogen cycle in the oceans, which determine the fluxes of this crucial nutrient in these environments. The present review provides an overview of the contribution of anaerobic ammonium oxidation (Anammox) to marine biogeochemical processes. Besides the conventional Anammox process, anaerobic ammonium oxidation coupled to the microbial reduction of alternative electron acceptors, such as sulfate (Sulfammox), ferric iron (Feammox), and natural organic matter (NOM-dependent Anammox) is also described in the context of global marine biogeochemical cycles. Also, the complex interactions among the oceanic biogeochemical cycles of N, S and Fe are discussed at the light of the new findings available in the literature. The review also underlines the important role of the microbial processes performing the Anammox reaction in the development of wastewater treatment systems for the removal of nitrogen from saline effluents. Strategies to enrich and immobilize Anammox bacteria in different reactor configurations for the treatment of saline wastewaters are also described as well as future directions for novel biotechnological developments based on Anammox.

     

Induction of a dissimilatory reduction pathway of nitrate in Halobacterium of the Dead Sea. A possible role for the 2 Fe-ferredoxin isolated from this organism

The processes involved in nitrate metabolism in Halobacterium of the Dead Sea are part of a dissimilatory pathway operating in these bacteria. The induction of both nitrate and nitrite reductases is shown to depend on the presence of nitrate and of anaerobic conditions. The gas products of the denitrification process were identified as nitrous oxide and nitrogen. Some properties of two of the enzymes involved in this process, nitrate and nitrite reductases, are reported. It is shown that the 2 Feferredoxin, which is present in large quantities in Halobacterium of the Dead Sea, can serve as an electron donor for nitrite reduction by nitrite reductase. It is suggested that the presence of a dissimilatory pathway for the reduction of nitrate in Halobacterium of the Dead Sea can be used as a tool for its classification.     

Anaerobic nitrate reduction to ammonium in two strains isolated from coastal marine sediment: A dissimilatory pathway

Abstract: A total of 28 nitrate-reducing bacteria were isolated from marine sediment (Mediterranean coast of France) in which dissimilatory reduction of nitrate to ammonium (DRNA) was estimated as 80% of the overall nitrate consumption. Thirteen isolates were considered as denitrifiers and ten as dissimilatory ammonium producers. ¹⁵N ammonium production from ¹⁵N nitrate by an Enterobacter sp. and a Vibrio sp., the predominant bacteria involved in nitrate ammonification in marine sediment, was characterized in pure culture studies. For both strains studied, nitrate-limited culture (1 mM) produced ammonium as the main product of nitrate reduction (> 90%) while in the presence of 10 mM nitrate, nitrite was accumulated in the spent media and ammonia production was less efficient. Concomitantly with the dissimilation of nitrate to nitrite and ammonium the molar yield of growth on glucose increased. Metabolic products of glucose were investigated under different growth conditions. Under anaerobic conditions without nitrate, ethanol was formed as the main product; in the presence of nitrate, ethanol disappeared and acetate increased concomitantly with an increased amount of ammonium. These results indicate that nitrite reduction to ammonium allows NAD regeneration and ATP synthesis through acetate formation, instead of ethanol formation which was favoured in the absence of nitrate.     

Microbially facilitated nitrogen cycling in tropical corals

Tropical scleractinian corals support a diverse assemblage of microbial symbionts. This ‘microbiome’ possesses the requisite functional diversity to conduct a range of nitrogen (N) transformations including denitrification, nitrification, nitrogen fixation and dissimilatory nitrate reduction to ammonium (DNRA). Very little direct evidence has been presented to date verifying that these processes are active within tropical corals. Here we use a combination of stable isotope techniques, nutrient uptake calculations and captured metagenomics to quantify rates of nitrogen cycling processes in a selection of tropical scleractinian corals. Denitrification activity was detected in all species, albeit with very low rates, signifying limited importance in holobiont N removal. Relatively greater nitrogen fixation activity confirms that corals are net N importers to reef systems. Low net nitrification activity suggests limited N regeneration capacity; however substantial gross nitrification activity may be concealed through nitrate consumption. Based on nrfA gene abundance and measured inorganic N fluxes, we calculated significant DNRA activity in the studied corals, which has important implications for coral reef N cycling and warrants more targeted investigation. Through the quantification and characterisation of all relevant N-cycling processes, this study provides clarity on the subject of tropical coral-associated biogeochemical N-cycling.Subject terms: Stable isotope analysis, Biogeochemistry, Biogeochemistry, Biogeochemistry, Microbial ecology     

湖泊氮素氧化及脱氮过程研究进展

自然界中氮的生物地球化学循环主要由微生物驱动,由固氮作用、硝化作用、反硝化作用和氨化作用来完成。过去数十年间,随着异养硝化、厌氧氨氧化和古菌氨氧化作用的发现,人们对环境中氮素循环认识逐步深入,提出了多种脱氮途径新假说。对湖泊生态系统中氮素的输入、输出及其在水体、沉积物和水土界面的迁移转化过程进行了概括,对湖泊生态系统中反硝化和厌氧氨氧化脱氮机理及脱氮效率的最新研究进展进行了探讨,并对以后的氮素循环研究进行了展望。     

滨海湿地生态系统微生物驱动的氮循环研究进展

滨海湿地生态系统介于陆地生态系统和海洋生态系统之间,其类型多种多样,环境差异极大,微生物种类丰富。近年来,随着人为氮源的大量输入,造成滨海湿地生态系统富营养化污染问题日趋严重。本文主要总结了滨海湿地生态系统微生物驱动的固氮、硝化、反硝化、厌氧氨氧化、NO_3~-还原成铵等主要氮循环过程,并综述了通过功能基因(如nifH、amoA、hzo、nirS、nirK、nrfA)检测微生物群落多样性及其环境影响因素的相关研究,旨在更好理解微生物驱动氮循环过程以去除氮,以期为减轻富营养化和危害性藻类爆发提供科学依据。     

Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics

Stratified sulfurous lakes are appropriate environments for studying the links between composition and functionality in microbial communities and are potentially modern analogs of anoxic conditions prevailing in the ancient ocean. We explored these aspects in the Lake Banyoles karstic area (NE Spain) through metagenomics and in silico reconstruction of carbon, nitrogen and sulfur metabolic pathways that were tightly coupled through a few bacterial groups. The potential for nitrogen fixation and denitrification was detected in both autotrophs and heterotrophs, with a major role for nitrogen and carbon fixations in Chlorobiaceae. Campylobacterales accounted for a large percentage of denitrification genes, while Gallionellales were putatively involved in denitrification, iron oxidation and carbon fixation and may have a major role in the biogeochemistry of the iron cycle. Bacteroidales were also abundant and showed potential for dissimilatory nitrate reduction to ammonium. The very low abundance of genes for nitrification, the minor presence of anammox genes, the high potential for nitrogen fixation and mineralization and the potential for chemotrophic CO₂ fixation and CO oxidation all provide potential clues on the anoxic zones functioning. We observed higher gene abundance of ammonia-oxidizing bacteria than ammonia-oxidizing archaea that may have a geochemical and evolutionary link related to the dominance of Fe in these environments. Overall, these results offer a more detailed perspective on the microbial ecology of anoxic environments and may help to develop new geochemical proxies to infer biology and chemistry interactions in ancient ecosystems.