Function Of Nitrate Concentration Research Articles

Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution.

Comprehensive sampling of natural genetic diversity with metagenomics enables highly resolved insights into the interplay between ecology and evolution. However, resolving adaptive, neutral, or purifying processes of evolution from intrapopulation genomic variation remains a challenge, partly due to the sole reliance on gene sequences to interpret variants. Here, we describe an approach to analyze genetic variation in the context of predicted protein structures and apply it to a marine microbial population within the SAR11 subclade 1a.3.V, which dominates low-latitude surface oceans. Our analyses reveal a tight association between genetic variation and protein structure. In a central gene in nitrogen metabolism, we observe decreased occurrence of nonsynonymous variants from ligand-binding sites as a function of nitrate concentrations, revealing genetic targets of distinct evolutionary pressures maintained by nutrient availability. Our work yields insights into the governing principles of evolution and enables structure-aware investigations of microbial population genetics.

Growth rates and nitrate uptake of co-occurring red-tide dinoflagellates <italic>Alexandrium affine</italic> and <italic>A. fraterculus</italic> as a function of nitrate concentration under light-dark and continuous light conditions

Growth rates and nitrate uptake of co-occurring red-tide dinoflagellates <italic>Alexandrium affine</italic> and <italic>A. fraterculus</italic> as a function of nitrate concentration under light-dark and continuous light conditions

Linking Solution Structures and Energetics: Thorium Nitrate Complexes.

Seeking predictive insights into how metal-ion speciation impacts solution chemistry as well as the composition and structure of solid-precipitates, thorium correlations, with both solvent and other solute ions, were quantitatively probed in a series of acidic, nitrate/perchlorate solutions held at constant ionic strength. Difference pair-distribution functions (dPDF), obtained from high-energy X-ray scattering (HEXS) data, provide unprecedented structural information on the number of Th ligating ions in solution and how they change with increasing nitrate concentration. A fit of the end member solution, Th (4 m perchloric acid and no nitrate), reveals a homoleptic Th aqua ion with 10 waters in its first coordination shell. Analyses of the acidic solutions containing nitrate reveal exclusively bidentate NO3- complexation with Th, consistent with published solid-state MIV nitrate structures, where MIV = Ce, Th, U, Np, Pu. Metrical fits of Th coordination as a function of nitrate concentration are used to calculate Th-NO3 stability constants, information important to a molecular-scale description of reaction energetics. The coordination environments of Th in solution were compared with single-crystal structures obtained from their precipitates, Th(NO3)4(H2O)4 and Th(NO3)4(H2O)3·(H2O)2. Relative stabilities of the solid-state compounds, assessed based on the results of molecular quantum chemical calculations, reveal the importance of including an accurate description of complexed waters when predicting relative energetics of dissolved ions in aqueous solution.

Facultative nitrate reduction by electrode-respiring Geobacter metallireducens biofilms as a competitive reaction to electrode reduction in a bioelectrochemical system.

Alternative metabolic options of exoelectrogenic biofilms in bioelectrochemical systems (BESs) are important not only to explain the fundamental ecology and performance of these systems but also to develop reliable integrated nutrient removal strategies in BESs, which potentially involve substrates or intermediates that support/induce those alternative metabolisms. This research focused on dissimilatory nitrate reduction as an alternative metabolism to dissimilatory anode reduction. Using the exoelectrogenic nitrate reducer Geobacter metallireducens, the critical conditions controlling those alternative metabolisms were investigated in two-chamber, potentiostatically controlled BESs at various anode potentials and biofilm thicknesses and challenged over a range of nitrate concentrations. Results showed that anode-reducing biofilms facultatively reduced nitrate at all tested anode potentials (-150 to +900 mV vs Standard Hydrogen Electrode) with a rapid metabolic shift. The critical nitrate concentration that triggered a significant decrease in BES performance was a function of anode biofilm thickness but not anode potential. This indicates that these alternative metabolisms were controlled by the availability of nitrate, which is a function of nitrate concentration in bulk solution and its diffusion into an anode-reducing biofilm. Coulombic recovery decreased as a function of nitrate dose due to electron-acceptor substrate competition, and nitrate-induced suspended biomass growth decreased the effluent quality.

Anthropogenic land-use signals propagate through stream food webs in a California, USA, watershed

Human development of watersheds can change aquatic ecosystems via multiple pathways. For instance, human rural development may add nutrients to ecosystems. We used naturally occurring stable isotopes in stream food webs to investigate how land use affects stream ecosystems across a gradient of land development in the San Lorenzo watershed, California. Road density was used as a proxy for land development. We found that streams in watersheds with higher road densities had elevated concentrations of phosphate and nitrate. Furthermore, algal δ15N values increased as a function of nitrate concentration, but saturated at approximately 6‰. This saturating pattern was consistent with a two-source mixing model with anthropogenic and watershed sources, fit using Bayesian model fitting. In sites that had >2.6 km roads km−2, anthropogenic sources of N were estimated to represent >90% of the N pool. This anthropogenic N signal was propagated to stream consumers: rainbow trout (Oncorhynchus mykiss), signal crayfish (Pacifasticus leniusculus), and benthic invertebrate δ15N were positively correlated with algal δ15N. Even relatively low density rural human land use may have substantial impacts on nutrient cycling of stream ecosystems.

The kinetics of denitrification in permeable sediments

Permeable sediments comprise the majority of shelf sediments, yet the rates of denitrification remain highly uncertain in these environments. Computational models are increasingly being used to understand the dynamics of denitrification in permeable sediments, which are complex environments to study experimentally. The realistic implementation of such models requires reliable experimentally derived data on the kinetics of denitrification. Here we undertook measurements of denitrification kinetics as a function of nitrate concentration in carefully controlled flow through reactor experiments on sediments taken from six shallow coastal sites in Port Phillip Bay, Victoria, Australia. The results showed that denitrification commenced rapidly (within 30 min) after the onset of anoxia and the kinetics could be well described by Michaelis–Menten kinetics with half saturation constants (apparent Km) ranging between 1.5 and 19.8 μM, and maximum denitrification rate (Vmax) were in the range of 0.9–7.5 nmol mL−1 h−1. The production of N2 through anaerobic ammonium oxidation (anammox) was generally found to be less than 10 % of denitrification. Vmax were in the same range as previously reported in cohesive sediments despite organic carbon contents one order of magnitude lower for the sediments studied here. The ratio of sediment O2 consumption to Vmax was in the range of 0.02–0.09, and was on average much lower than the theoretical ratio of 0.8. As a consequence, models implemented with the theoretical ratio of 0.8 are likely to overestimate denitrification by a factor of ~3. The most likely explanation for this is that the microbial community is not able to instantaneously shift or optimally use a particular electron acceptor in the highly dynamic redox environment experienced in permeable sediments. In contrast to previous studies, we did not observe any significant rates of oxic denitrification.

Localized Corrosion of Stainless Steel in a Nuclear Waste Cooling Water System—Part 4: Artificial Pit Investigation of Nitrate Inhibition

A nuclear waste cooling water system, constructed from an austenitic stainless steel, is known to be susceptible to localized corrosion because of the combined presence of low concentrations of chloride (Cl−) ions in the water (<10 mg/L) and oxidants produced by water radiolysis. Corrosion propagates in the system as pitting corrosion, and inspections of accessible components indicated that large pit cavities could form. To investigate possible inhibition options, an artificial pit, termed the wire-electrode artificial pit, was developed and shown to be capable of sustaining corrosion under representative conditions. Tests carried out using this artificial pit to investigate the effect of sodium nitrate (NaNO3) added to the bulk water are reported here. The results showed that nitrate (NO3−) was capable of affecting inhibition at 60°C, although large concentrations and long times were required, e.g., inhibition took up to 20 days at 60,000 mg/L NO3−. Complimentary polarization tests were also carried out in a range of artificial pit solutions as a function of nitrate concentration to aid interpretation of the wire-electrode tests. The existence of a threshold molar NO3−/Cl− ratio for passivation to occur was identified but not clearly defined.

Nitrate uptake rate in anoxic profundal sediments from a eutrophic reservoir

There is renewed interest in the use of nitrate to treat the profundal zone of lakes to inhibit anaerobic biogeochemical processes that result in the degradation of bottom water quality (e.g., sediment phosphorus release, mercury methylation). In this study we used experimental sediment–water interface chambers to quantify the rate of sediment nitrate uptake (SNU) in profundal sediments from Lake Perris, a eutrophic raw water reservoir in Southern California. Deoxygenated chamber water was spiked with nitrate, and nitrate concentration was monitored over time under quiescent conditions, followed by mixed conditions with average water velocities of 1 cm/s. Key findings included: (1) SNU decreased with decreasing nitrate concentration, (2) SNU was higher under mixed versus quiescent conditions by nearly 50%, and (3) nitrate uptake as a function of nitrate concentration followed a conventional sediment oxygen demand model in which nitrate uptake was proportional to the square root of nitrate concentration. The probable mechanism for elevated SNU under mixed conditions was an increased diffusional concentration gradient combined with a decrease in the diffusional boundary layer at the sediment–water interface, both of which enhanced the flux of nitrate from overlaying water into sediment. Managers planning to implement lake nitrate addition should account for induced nitrate demand when determining dosing rates. For example, based on our modeling efforts from this data set, SNU in Lake Perris could range by an order of magnitude, from around 12 mg N/m2/d under quiescent, low nitrate conditions (0.1 mg N/l) to around 120 mg N/m2/d under mixed, high nitrate conditions (5 mg N/l).

Nutrient controls on new production in the Bodega Bay, California, coastal upwelling plume

Abstract A theoretical framework for the time-dependent processes leading to the high rates of new production in eastern boundary upwelling systems has been assembled from a series of past upwelling studies. As part of the CoOP WEST (Wind Events and Shelf Transport) study, new production in the Bodega Bay upwelling area and it's control by ambient nitrate and ammonium concentrations and the advective wind regime are described. Data and analyses are focused primarily on the WEST 2001 cruise (May–June 2001) when the two legs differed greatly in wind regimes but not nutrient concentrations. Elevated concentrations of ammonium in upwelled water with high nitrate were observed in both legs. Nitrate uptake by phytoplankton as a function of nitrate concentration was linear rather than Michaelis–Menten-like, modulated by inhibitory levels of ammonium, yielding coefficients that enable the specific nitrate uptake element of new production to be estimated from nutrient concentrations. The range of specific nitrate uptake rates for the two legs of WEST 2001 were similar, essentially a physiological response to nutrient conditions. However, the low “realization” of new production i.e. incorporation of biomass as particulate nitrogen that occurred in this system compared to the theoretical maximum possible was determined by the strong advective and turbulent conditions that dominated the second leg of the WEST 2001 study. These data are compared with other upwelling areas using a physiological shift-up model [Dugdale, R.C., Wilkerson, F.P., Morel, A. 1990. Realization of new production in coastal upwelling areas: a means to compare relative performance. Limnology and Oceanography 35, 822–829].

Photochemical Production and Release of Gaseous NO2 from Nitrate-Doped Water Ice

Temperature-programmed NO2 emissions from frozen aqueous NaNO3 solutions irradiated at 313 nm were monitored as function of nitrate concentration and heating rate, H, above -30 degrees C. Emissions increase nonmonotonically with temperature, displaying transitions suggestive of underlying metamorphic transformations. Thus, NO2 emissions surge at ca. -8 degrees C in frozen [NO3-] > 200 microM samples warmed at H = 0.70 degrees C min(-1) under continuous irradiation, and also in the dark from samples that had been photolyzed at -30 degrees C. The amounts of NO2 released in individual thermograms, SigmaN, increase less than linearly with [NO3-] or the duration of experiments, revealing the significant loss of photogenerated NO2. The actual SigmaN proportional, variant [NO3-]1/2 dependence (at constant H) is consistent with NO2 hydrolysis: 2NO2 + H2O --> NO3- + NO2- + 2H+, overtaking NO2 desorption, even below the eutectic point (-18 degrees C for aqueous NaNO3). The increasingly larger NO2 losses detected in longer experiments (at constant [NO3-]) are ascribed to secondary photolysis of trapped NO2. The relevance of present results to the interpretation of polar NO2 measurements is briefly analyzed.

Reduction of Nitrates by Means of Immobilized Microorganisms

Continuous denitrification of a model solution was carried out in a honeycombed gel bioreactor using immobilized Paracoccus pantotrophus DSM 65 over a period of seven weeks. Supply of nitrate was varied during operation to determine the nitrate degradation rate as a function of nitrate concentration. The experiments have shown that by entrapping living microorganisms into a monolithic block of κ‐Carrageen gel a delicate biological system can gently be transformed into a rugged apparatus.

Nitrate photosensitized degradation of atrazine during UV water treatment

Increasingly, ultraviolet radiation (UV) is being used to treat chemical contaminants in waste and drinking water. To understand the significance of indirect photolysis during such processes, the effect of nitrate on UV treatment of atrazine (ATZ) was investigated at pH 7 in phosphate buffer and solutions containing Suwannee River natural organic matter (NOM). With a medium-pressure mercury lamp, environmentally relevant levels of nitrate (0.7–7 mg-N L–1) lead to initial rates of ATZ removal that are enhanced compared to those without nitrate, and comparison of the product distributions obtained with nitrate and with hydrogen peroxide indicates that this can be attributed to hydroxyl radical (•OH) production from nitrate absorption below 250 nm. Consistent with this, the observed rates decrease as the reaction progresses, presumably due to •OH scavenging by photochemically generated nitrite. In solutions containing NOM, this effect is not observed, and the addition of nitrate leads to lower rates of ATZ removal, albeit higher than predicted on the basis of light-screening by nitrate alone. In order to model this effect, the •OH quantum yield from nitrate photolysis below 250 nm was determined by two methods, competition kinetics between ATZ and 1-octanol and formaldehyde production by reaction of •OH with methanol, and it was found to lie in the range 0.09 to 0.14. This is the first report of the quantum yield at these wavelengths, and this information allows the photolysis rates to be modeled as a function of nitrate concentration and water quality.

Controls on phytoplankton production in the Australasian sector of the subtropical convergence

This paper describes the interaction of physics, chemistry and biology in controlling phytoplankton biomass and production for a region along 152°E between 40°S and 50°30′S in summer 1990. The physical structure in the upper 500 m included a warm core eddy in the north, a cold core feature at 46°30′S, and two major fronts, the Subtropical Convergence and the Subantarctic Front, between 49°S and 50°30′S. In the region between the warm core eddy and the southern fronts, Subantarctic Mode Water was capped by a high salinity layer with a subsurface salinity maximum. Surface nitrate increased from zero in the north to more than 15 μM in the south in a series of steps across surface fronts associated with mesoscale features. Phytoplankton column biomass, estimated column production (based on P vs I incubations) and estimated mixed layer growth rates were moderate throughout the transect (typically 30 mg Chl. a m -2, 300 mgC m -2 d -1, and 0.27 d -1, respectively). Surface nitrate seems unlikely to be seasonally depleted south of 46°30′S, and this region shows characteristics similar to other high nutrient but low chlorophyll regions. Episodic wind mixing appears to play an important role in summer resupply of nitrate to the mixed layer in the central third of the transect. Over the southern half of the transect, changes in surface pH and derived pCO 2 as a function of nitrate concentrations were consistent with DIC uptake at Redfield ratios. The derived surface pCO 2 values showed undersaturation by 50–100 μatm throughout the transect./

The nitrite reductase gene of Pseudomonas aeruginosa: effect of growth conditions on the expression and construction of a mutant by gene disruption.

The expression of nitrite reductase has been tested in a wild-type strain of Pseudomonas aeruginosa (Pao1) as a function of nitrate concentration under anaerobic and aerobic conditions. Very low levels of basal expression are shown under non-denitrifying conditions (i.e. absence of nitrate, in both aerobic and anaerobic conditions); anaerobiosis is not required for high levels of enzyme production in the presence of nitrate. A Pseudomonas aeruginosa strain, mutated in the nitrite reductase gene, has been obtained by gene replacement. This mutant, the first of this species described up to now, is unable to grow under anaerobic conditions in the presence of nitrate. The anaerobic growth can be restored by complementation with the wild-type gene.

The nitrite reductase gene of Pseudomonas aeruginosa: Effect of growth conditions on the expression and construction of a mutant by gene disruption

The expression of nitrite reductase has been tested in a wild-type strain of Pseudomonas aeruginosa (Pao1) as a function of nitrate concentration under anaerobic and aerobic conditions. Very low levels of basal expression are shown under non-denitrifying conditions (i.e. absence of nitrate, in both aerobic and anaerobic conditions); anaerobiosis is not required for high levels of enzyme production in the presence of nitrate. A Pseudomonas aeruginosa strain, mutated in the nitrite reductase gene, has been obtained by gene replacement. This mutant, the first of this species described up to now, is unable to grow under anaerobic conditions in the presence of nitrate. The anaerobic growth can be restored by complementation with the wild-type gene.

Bioelectrocatalysed reduction of nitrate utilizing polythiophene bipyridinium enzyme electrodes

Enzyme electrodes in several configurations including the enzyme nitrate reductase are applied in the bioelectrocatalysed reduction of nitrate to nitrite. One enzyme electrode configuration includes the physical immobilization of nitrate reductase in a polythiophene-bipyridinium matrix formed by electropolymerization of 1-methyl-1′-(3-thiophene-3-yl)-pentyl-4,4′-bipyridinium-bis-hexafluorophosphate. The bipyridinium units of the polymer act as electron mediators between the electrode and the enzyme. The concentration of bioelectrogenerated nitrite depends on the concentration of nitrate in the electrolyte solution. A calibration curve representing the rate of nitrite formation as a function of nitrate concentration in the electrolysis cell allows quantitative analysis of nitrate in aqueous solutions. Two other enzyme-electrode configurations include copolymerization of thiophene-bipyridinium and thiophene-3-acetic acid, onto a gold electrode and layered deposition of two polymers composed of thiophene-bipyridinium and thiophene-3-acetic acid onto the electrode. Covalent linkage of the enzyme nitrate reductase to the carboxylic acid residues of the different polymer matrices results in active enzyme electrodes for bioelectrocatalysed reduction of nitrate to nitrite.

Effect of nitrate and ammonium concentration on nitrate reductase activity in five species of mycorrhizal fungi

The nitrate reducing capacity of pure cultures of Cenococcum geophilum (Sow.) Ferd. & Winge, Paxillus involutes (Batsch: Fr.) Fr. (strains 1 and 2), Piloderma croceum Erikss. & Hjortst., Suillus variegatus (Fr.) O. Kuntze (strains 1 and 2) and an ectendomycorrhizal (E‐strain) fungus was measured using an in vivo nitrate reductase (EC 1.6.6.3) assay. Differences between species and strains were established. The nitrate concentration of the culture medium influenced the nitrate reductase activities of the E‐strain fungus and one strain of S. variegatus. The nitrate reductase activity of certain species and strains was a function of nitrate concentration. Addition of ammonium to the growth medium did not have any significant effect on the in vivo or in vitro nitrate reductase activity. The in vivo nitrate reductase activity in the mycelia of C. geophilum and the E‐strain fungus decreased during 28 day growth in modified Melin‐Norkrans medium. For mycelia of Paxillus involutus, Piloderma croceum and S. variegatus grown on agar the in vitro assays showed higher nitrate reductase activity than the in vivo assays.

SIMULATION OF DENITRIFICATION LOSSES OF NITRATE FERTILIZER APPLIED TO UNCROPPED, CROPPED, AND MANURE-AMENDED FIELD PLOTS

We simulated losses of nitrate fertilizer via denitrification, using a mathematical model that included transport and plant uptake of water and nitrogen in soil. The denitrification rate was considered to be a function of nitrate concentration, water-extractable organic carbon concentration, degree of soil-water saturation, and temperature. Water-extractable organic carbon concentrations were calculated from initial amounts of soil carbon and additions of plant residues or animal manure. We assumed that the consumption of added carbon in the soil system would occur in two or three stages and assigned different rate coefficients for each stage and carbon source. A Q10 value of 2 was used in correcting the rate coefficients for denitrification and carbon consumption at two temperatures. Model simulations for denitrification were compared with measured N2 and N2O gas fluxes at the soil surface during nitrate leaching in field plots of Yolo soil maintained at different soil-water contents and soil temperatures and that received various carbon additions and irrigation frequencies. We found reasonable agreement between measured rates and total amounts of denitrification and those calculated by the model using a single denitrification rate coefficient for all cropped field plots and another rate coefficient for all uncropped field plots.

The coupling of anaerobic steroid dehydrogenation to nitrate reduction in Pseudomonas N.C.I.B. 10590 and Clostridium paraputrificum.

Pseudomonas spp. capable of using sodium deoxycholate as the sole carbon source were isolated from faeces, sewage and soil by enrichment culture in a defined medium. An isolate, designated Pseudomonas N.C.I.B. 10590, oxidized deoxycholic acid during aerobic growth to yield metabolites with the 1,4-diene3-one structure; this oxidation also occurred anaerobically if nitrate was present. The nuclear dehydrogenation reactions carried out by Clostridiumparaputri$cum are of interest in the aetiology of colon cancer (Hill, 1974), but have been studied little because of the complex nutritional requirements of this organism; since the pseudomonad carries out similar reactions in a defmed medium it is more amenable to study. Steroid oxidation by the Pseudomonas was studied as a function ofnitrate concentration to demonstrate thecoupling ofthe dehydrogenation to nitrate reduction in the absence of molecular oxygen. The properties of steroid oxidation in Pseudomonas N.C.I.B. 10590 and CI. paraputriJicum were compared. Anaerobic metabolism of steroids by Pseudomonas spp. was carried out in a buffered mineral salts medium containing the required quantities of KNO, or other electron acceptor and dispensed to fill screw-capped bottles. Washed bacterial cells were added (ha1 density 5 . 0 ~ 10' cells/ml), the caps screwed tightly to exclude air and the cultures incubated at 25°C for 6 days. After acidification to pH4, the steroids were extracted into redistilled ethyl acetate, the solvent was removed by evaporation and the E244 in methanol determined. Nitrite concentrations were determined by a modified Griess-Ilosvay reaction (Pearson, 1973). Steroid products were separated by t.1.c. on silica gel GF254 by the use of two solvent systems and those with the 1,4-diene-3-one structure detected under U.V. light; other products were detected by their colour with anisaldehyde reagent (Kritchevsky et al., 1963).

The nitrate- and nitrite-dependent O2-evolution in N2 by Ankistrodesmus braunii

O2-evolution in N2 by young cells of synchronous Ankistrodesmus braunii was measured manometrically in the presence and in the absence of nitrate or nitrite. Nitrate-starved cells produce O2 as a function of nitrate concentration with an optimum at 10 mM nitrate. The optimum rates are strongly dependent upon the pH of the medium culminating at pH 8.0.