Nitrogen transformations in stratified aquatic microbial ecosystems

New analytical methods such as advanced molecular techniques and microsensors have resulted in new insights about how nitrogen transformations in stratified microbial systems such as sediments and biofilms are regulated at a μm–mm scale. A large and ever-expanding knowledge base about nitrogen fixation, nitrification, denitrification, and dissimilatory reduction of nitrate to ammonium, and about the microorganisms performing the processes, has been produced by use of these techniques. During the last decade the discovery of anammmox bacteria and migrating, nitrate accumulating bacteria performing dissimilatory reduction of nitrate to ammonium have given new dimensions to the understanding of nitrogen cycling in nature, and the occurrence of these organisms and processes in stratified microbial communities will be described in detail.     

Carbon, nitrogen, and phosphorus dynamics during leaf decay in nutrient-enriched stream microecosystems

We investigated the effects of long-term enrichment with nitrate, phosphate, and nitrate+phosphate on the first 5 weeks of leaf detritus processing in laboratory stream microecosystems. Enrichment with nitrate+phosphate accelerated leaf weight loss and increased rates of respiration associated with the leaves. However, whole-system respiration was little changed from that observed in the control stream since respiration in the water was greatly reduced. Enrichment with phosphate alone had little effect except to lower respiration associated with leaf discs. Enrichment with nitrate alone also decreased leaf-disc respiration but resulted in a greatly increased rate of respiration in the water. Net leaching and fragmentation of carbon from the leaves was also increased by nitrate enrichment. Nitrogen and phosphorus levels in leaf material were little affected by enrichment with nitrate or phosphorus alone. Leaves in those streams and in the control stream released nitrogen and phosphorus to the water. In contrast, percent nitrogen and phosphorus increased greatly in the leaves in the stream enriched with both nitrate and phosphate. The leaves in this system immobilized both nitrogen and phosphorus from the water. We also studied the importance of nitrogen fixation as a vector for nitrogen incorporation associated with leaf decomposition in streams. Somewhat surprisingly, fixation by microbes associated with the leaves and by microbes suspended in the water occurred under all three experimental enrichment treatments as well as in the control, casting doubt on the effectiveness of nitrate in inhibiting nitrogenase synthesis in nature. However, N₂-fixation is only a minor source of nitrogen for leaves decaying under the conditions studied.     

Influence of Nitrogen Form and Nitrogen Absence on Utilization of Assimilates for Growth and Maintenance in Tops and Roots of Lolium multiflorum

Utilization of assimilates for growth and maintenance of tops and roots of Lolium multiflorum was determined for plants supplied with either nitrate or ammonium. Carbon dioxide exchange rates were measured continuously for tops and roots separately. Three-day periods were applied for two irradiation levels. On the last day of each three-day period no nitrogen was supplied to the two treatments. In the nitrate treatment, the coefficient of utilization for converting assimilates into constructive growth (Y_G) remained unaffected in absence of nitrate. However, in absence of nitrate the maintenance respiration (M) for both tops and roots was only one third of that in presence of nitrate. In the treatment with ammonium the maintenance respiration of the plants was not influenced by the absence of ammonium. However, especially for the tops Y_G increased in absence of ammonium. In both the treatments, growth respiration of the roots was inefficient compared to that of the tops. Only in the case of absence of nitrate, maintenance respiration of the roots was similar to that of the tops.     

Growth and the efficiency of root respiration of Pisum sativum as dependent on the source of nitrogen

Growth and efficiency of root respiration were investigated in Pisum sativum L. cv. Alaska and cv. Rondo. Plants were grown in culture solutions, either in symbiosis with Rhizobium leguminosanm , or with an abundant supply of nitrate or ammonium and completely lacking nodules. In comparison with plants utilizing nitrate or ammonium, Ni-fixing plants showed lower rates of dry matter and nitrogen accumulation, as well as lower rates of total and cytochrome-mediated root respiration. Rates of shoot dry matter accumulation and root respiration in plants utilizing ammonium were lower than in plants utilizing nitrate. The efficiency of root respiration was high in N₂-fixing plants, as indicated by a low activity of the SHAM-sensitive, alternative, non-phosphorylating pathway. In nitrate and ammonium grown plants of cv. Alaska, the efficiency of root respiration was about the same, and in both cases lower than in N₂-fixing plants. The efficiency of root respiration in non-symbiotically grown pea plants was generally higher than in many non-legumes. Comparison of the ATP costs of synthesis of root dry matter for different N-sources was complicated by large differences in relative growth rate of the root and in shoot to root ratio between N-treatments. A quantitative correction of the ATP production during synthesis of root dry matter for differences in shoot to root ratio and root maintenance respiration has been made. It is concluded that ATP costs of root dry matter production are highest in the case of N₂-fixing plants. In plants utilizing ammonium, ATP costs of synthesis of root dry matter were slightly lower than in plants utilizing nitrate. The physiological significance of the alternative pathway in root metabolism is discussed in relation to the assimilation of different sources of nitrogen.     

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.     

Ammonium and nitrate nutrition inPlantago lanceolata andPlantago major L. ssp.major

P. lanceolata andP. major were grown in culture solutions with nitrate or ammonium as the nitrogen source. Dry matter accumulation in the shoot was faster with nitrate than with ammonium, whilst that of the roots was not affected by the nitrogen source. As a consequence, the shoot-to-root ratio was lower with ammonium than with nitrate. InP. lanceolata, dry matter percentage of shoot and root tissue was lower with nitrate nutrition, suggesting better elongation growth than with ammonium. However, in shoot tissue ofP. major the opposite was found. The rate of root respiration declined with time, and this was almost completely due to a declining activity of the alternative path, which amounted to about 30–60% of total root respiration. Respiration via the cytochrome path was for a part of time slightly increased by ammonium, whereas the activity of the alternative path was strongly enhanced. The concentration of ethanol-soluble carbohydrates (SC) in the roots of both species was higher when nitrate was used, but no difference in the concentration of starch was found. When the plants were transferred from one nitrogen source to the other, many parameters, including the concentration of nitrate and chloride, and the shoot to root ratio, adjusted to the new situation in both species. Grassland Species Research Group, Publication no. 116.     

Preferential Assimilation of Ammonium Ions from Ammonium Nitrate Solutions by Apple Seedlings

Apple seedlings, Pyrus malus L., were grown in complete nutrient solutions containing nitrate, ammonium, or ammonium plus nitrate as the nitrogen source. Uptake of nitrogen was calculated from depletion measurements of the nutrient solutions and by using ¹⁵N labelled nitrate and ammonium salts. If the plants received nitrogen as ammonium only or as nitrate only, the amounts of nitrogen taken up were similar. However, if the seedlings were supplied with ammonium nitrate, the amount of nitrate-nitrogen assimilated was only half that of ammonium. Nevertheless, if ammonium and nitrate were supplied to a plant with a split-root system, with each root half receiving a different ion, the uptakes were similar. The possibility of independent inhibition by ammonium of both nitrate uptake and reduction in the roots is discussed.     

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.     

Nitrogen Use Efficiency of Crop Plants: Physiological Constraints upon Nitrogen Absorption

Current global nitrogen fertilizer use has reached approximately one hundred billion kg per annum. In many agricultural systems, a very substantial portion of this applied nitrogen fertilizer is lost from soil to groundwaters, rivers and oceans. While soil physicochemical properties play a significant part in these losses, there are several characteristic features of plant nitrogen transporter function that facilitate N losses. Nitrate and ammonium efflux from roots result in a reduction of net nitrogen uptake. As external nitrate and ammonium concentrations, respectively, are increased, particularly into the range of concentrations that are typical of agricultural soils, elevated rates of nitrate and ammonium efflux result. The rapid down-regulation of high-affinity influx as plants become nitrogen replete further reduces the root's capacity to acquire external nitrogen; only nitrogen-starved roots absorb with both high capacity and high affinity. The results of studies using molecular biology methods demonstrate that genes encoding nitrate and ammonium transporters are rapidly down-regulated when nitrogen is resupplied to nitrogen-starved plants. Provision of ammonium to roots of plants actively absorbing nitrate imposes a block on nitrate uptake, the extent of which depends on the ammonium concentration, thus further reducing the efficient utilization of soil nitrate. During the daily variation of incoming light and during periods of low incident irradiation (i.e. heavy cloud cover) the expression levels of genes encoding nitrate and ammonium transporters, and rates of nitrate and ammonium uptake, are substantially reduced. Low temperatures reduce growth and nitrogen demand, and appear to discriminate against high-affinity nitrogen influx. In sum, these several factors conspire to limit rates of plant nitrogen uptake to values that are well below capacity. These characteristics of the plant's nitrogen uptake systems facilitate nitrogen losses from soils.     

Factors Controlling Anaerobic Ammonium Oxidation with Nitrite in Marine Sediments

Factors controlling the anaerobic oxidation of ammonium with nitrate and nitrite were explored in a marine sediment from the Skagerrak in the Baltic-North Sea transition. In anoxic incubations with the addition of nitrite, approximately 65% of the nitrogen gas formation was due to anaerobic ammonium oxidation with nitrite, with the remainder being produced by denitrification. Anaerobic ammonium oxidation with nitrite exhibited a biological temperature response, with a rate optimum at 15°C and a maximum temperature of 37°C. The biological nature of the process and a 1:1 stoichiometry for the reaction between nitrite and ammonium indicated that the transformations might be attributed to the anammox process. Attempts to find other anaerobic ammonium-oxidizing processes in this sediment failed. The apparent K_m of nitrite consumption was less than 3 μM, and the relative importance of ammonium oxidation with nitrite and denitrification for the production of nitrogen gas was independent of nitrite concentration. Thus, the quantitative importance of ammonium oxidation with nitrite in the jar incubations at elevated nitrite concentrations probably represents the in situ situation. With the addition of nitrate, the production of nitrite from nitrate was four times faster than its consumption and therefore did not limit the rate of ammonium oxidation. Accordingly, the rate of this process was the same whether nitrate or nitrite was added as electron acceptor. The addition of organic matter did not stimulate denitrification, possibly because it was outcompeted by manganese reduction or because transport limitation was removed due to homogenization of the sediment.     

Transformations of inorganic nitrogen by Azospirillum spp.

Azospirillum spp. participate in all steps of the nitrogen cycle except nitrification. They can fix molecular nitrogen and perform assimilatory nitrate reduction and nitrate respiration. Culture conditions have been defined under which nitrate is used both as terminal respiratory electron acceptor and as nitrogen source for growth. Nitrate and, possibly to a very limited extent, nitrite, but not sulfate, iron or fumarate support anaerobic respiration. Under anaerobic conditions, nitrate can also supply energy for nitrogen fixation but without supporting growth. Nitrate-dependent nitrogenase activity lasts only for 3–4 h until the enzymes of assimilatory nitrate reduction are synthesized. Nitrite accumulates during this period and inhibits nitrogenase activity at concentrations of about 1 mM.     

Nitrate Reduction to Nitrite,Nitric Oxide and Ammonia by Gut Bacteria under Physiological Conditions

The biological nitrogen cycle involves step-wise reduction of nitrogen oxides to ammonium salts and oxidation of ammonia back to nitrites and nitrates by plants and bacteria. Neither process has been thought to have relevance to mammalian physiology; however in recent years the salivary bacterial reduction of nitrate to nitrite has been recognized as an important metabolic conversion in humans. Several enteric bacteria have also shown the ability of catalytic reduction of nitrate to ammonia via nitrite during dissimilatory respiration; however, the importance of this pathway in bacterial species colonizing the human intestine has been little studied. We measured nitrite, nitric oxide (NO) and ammonia formation in cultures of Escherichia coli, Lactobacillus and Bifidobacterium species grown at different sodium nitrate concentrations and oxygen levels. We found that the presence of 5 mM nitrate provided a growth benefit and induced both nitrite and ammonia generation in E.coli and L.plantarum bacteria grown at oxygen concentrations compatible with the content in the gastrointestinal tract. Nitrite and ammonia accumulated in the growth medium when at least 2.5 mM nitrate was present. Time-course curves suggest that nitrate is first converted to nitrite and subsequently to ammonia. Strains of L.rhamnosus, L.acidophilus and B.longum infantis grown with nitrate produced minor changes in nitrite or ammonia levels in the cultures. However, when supplied with exogenous nitrite, NO gas was readily produced independently of added nitrate. Bacterial production of lactic acid causes medium acidification that in turn generates NO by non-enzymatic nitrite reduction. In contrast, nitrite was converted to NO by E.coli cultures even at neutral pH. We suggest that the bacterial nitrate reduction to ammonia, as well as the related NO formation in the gut, could be an important aspect of the overall mammalian nitrate/nitrite/NO metabolism and is yet another way in which the microbiome links diet and health.     

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。     

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。     

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。     

Interactions between nitrate and ammonium during uptake by carob seedlings and the effect of the form of earlier nitrogen nutrition

Seedlings of carob ( Ceratonia siliqua L. cv. Mulata) were used in two sets of experiments in order to evaluate; (1) the reciprocal effects of each nitrogen form on net uptake of nitrate and ammonium, and (2) the effect of earlier nitrogen nutrition on ammonium versus nitrate uptake. In the former group of experiments we studied the kinetics of nitrate and ammonium uptake as well as the interference of each of the two forms with net uptake of ammonium and nitrate by both nitrogen depleted and nitrogen fed carob seedlings. On the whole, nitrogen depletion led to increase in both affinity and V_max of the system for both forms of nitrogen, at the same time as the effects of nitrate on uptake of ammonium and vice versa were concentration dependent. In the second group of experiments the effects of earlier nitrogen nutrition on nitrate and ammonium uptake were characterized, and in this case we observed that: (a) if only one form of N was supplied, ammonium was taken up in greater amounts than nitrate; (b) the presence of ammonium enhanced nitrate uptake; (c) ammonium uptake was inhibited by nitrate; (d) there was a significant effect of the earlier nitrogen nutrition on the response of the plants to a different nitrogen source. The latter was evident mainly as regards ammonium uptake by plants grown in ammonium nitrate. The interactions between nitrate and ammonium uptake systems are discussed on the basis of the adaptation to the nitrogen source during early growth.     

Accelerated Nitrate Uptake in Wheat Seedlings: Effects of Ammonium and Nitrite Pretreatments and of 6-Methylpurine and Puromycin

The experiments reported herein had two objectives. One was to determine if the slow rate of nitrate uptake which occurs upon initial exposure of nitrogen-depleted wheat (Triticum vulgare cv. Knox) plants to nitrate was the result of insufficient reduced nitrogen. The second was to determine the impact of restrictions in ribonucleic acid or protein synthesis on both nitrate uptake and nitrate reduction. Pretreatments of 14-day-old seedlings for a few hours in ammonium or nitrite did not result in an enhancement of the initial slow rate of nitrate uptake. Growth for two additional weeks in ammonium also failed to eliminate the induction period. The evidence indicates that the presence of nitrate, rather than a product of its reduction, was required to initiate development of the accelerated rate of nitrate uptake. Puromycin (400 μg ml^?1) and 6-methylpurine (0.5 mM) prevented development of the accelerated phase of nitrate uptake. With both compounds, the relative restriction of nitrate uptake was greater than that of nitrate reduction as revealed by incorporation of ¹⁵N from labeled nitrate into reduced forms. The proportion of reduction which occurred in the root system under the imposed treatments could not be delineated precisely, preventing an unequivocal determination of the extent to which the two processes are coupled in the root system. The data nevertheless indicate nitrate reduction was closely associated with nitrate uptake. Accumulation of nitrate in the shoots was markedly restricted in presence of 6 methylpurine. This effect most likely was a result of a severe restriction in the translocation of nitrate into the xylem, rather than an increase in the reduction rate in the shoots.     

Ammonium and nitrate nutrition inPlantago lanceolata L. andPlantago major L. ssp.major

With the aims (1) to test whether the different natural occurrence of twoPlantago species in grasslands is explained by a different preference of the species for nitrate or ammonium; (2) to test whether the different occurrence is explained by differences in the flexibility of the species towards changes in the nitrogen form; (3) to find suitable parameters as a tool to study ammonium and nitrate utilization of these species at the natural sites in grasslands, plants ofPlantago lanceolata andP. major ssp.major were grown with an abundant supply of nitrate, ammonium or nitrate+ammonium as the nitrogen source (0.5 mM). The combination of ammonium and nitrate gave a slightly higher final plant weight than nitrate or ammonium alone. Ammonium lowered the shoot to root ratio inP. major. Uptake of nitrate per g root was faster than that of ammonium, but from the mixed source ammonium and nitrate were taken up at the same rate. In vivo nitrate reductase activity (NRA) was present in both shoot and roots of plants receiving nitrate. When ammonium was applied in addition to nitrate, NRA of the shoot was not affected, but in the root the activity decreased. Thus, a larger proportion of total NRA was present in the shoot than with nitrate alone. In vitro glutamate dehydrogenase activity (GDHA) was enhanced by ammonium, both in the shoot and in the roots.In vitro glutamine synthetase activity (GSA) was highest in roots of plants receiving ammonium. Both GDHA and GSA were higher inP. lanceolata than inP. major. The concentration of ammonium in the roots increased with ammonium, but it did not accumulate in the shoot. The concentration of amino acids in the roots was also enhanced by ammonium. Protein concentration was not affected by the form of nitrogen. Nitrate accumulated in both the shoot and the roots of nitrate grown plants. When nitrate in the solution was replaced by ammonium, the nitrate concentration in the roots decreased rapidly. It also decreased in the shoot, but slowly. It is concluded that the nitrogen metabolism of the twoPlantago species shows a similar response to a change in the form of the nitrogen source, and that differences in natural occurrence of these species are not related to a differential adaptation of nitrogen metabolism towards the nitrogen form. Suitable parameters for establishing the nitrogen source in the field are thein vivo NRA, nitrate concentrations in tissues and xylem exudate, and the fraction of total reduced nitrogen in the roots that is in the soluble form, and to some extent thein vitro GDHA and GSA of the roots. Grassland Species Research Group. Publ. no 118.