Nitrate-limited Conditions Research Articles

Genome-wide systematic characterization of the NRT2 gene family and its expression profile in wheat (Triticum aestivum L.) during plant growth and in response to nitrate deficiency

BackgroundWheat (Triticum aestivum L.) is a major cereal crop that is grown worldwide, and it is highly dependent on sufficient N supply. The molecular mechanisms associated with nitrate uptake and assimilation are still poorly understood in wheat. In plants, NRT2 family proteins play a crucial role in NO3– acquisition and translocation under nitrate limited conditions. However, the biological functions of these genes in wheat are still unclear, especially their roles in NO3– uptake and assimilation.ResultsIn this study, a comprehensive analysis of wheat TaNRT2 genes was conducted using bioinformatics and molecular biology methods, and 49 TaNRT2 genes were identified. A phylogenetic analysis clustered the TaNRT2 genes into three clades. The genes that clustered on the same phylogenetic branch had similar gene structures and nitrate assimilation functions. The identified genes were further mapped onto the 13 wheat chromosomes, and the results showed that a large duplication event had occurred on chromosome 6. To explore the TaNRT2 gene expression profiles in wheat, we performed transcriptome sequencing after low nitrate treatment for three days. Transcriptome analysis revealed the expression levels of all TaNRT2 genes in shoots and roots, and based on the expression profiles, three highly expressed genes (TaNRT2-6A.2, TaNRT2-6A.6, and TaNRT2-6B.4) were selected for qPCR analysis in two different wheat cultivars (‘Mianmai367’ and ‘Nanmai660’) under nitrate-limited and normal conditions. All three genes were upregulated under nitrate-limited conditions and highly expressed in the high nitrogen use efficiency (NUE) wheat ‘Mianmai367’ under low nitrate conditions.ConclusionWe systematically identified 49 NRT2 genes in wheat and analysed the transcript levels of all TaNRT2s under nitrate deficient conditions and over the whole growth period. The results suggest that these genes play important roles in nitrate absorption, distribution, and accumulation. This study provides valuable information and key candidate genes for further studies on the function of TaNRT2s in wheat.

Interactive effects of CO2 , temperature, irradiance, and nutrient limitation on the growth and physiology of the marine cyanobacterium Synechococcus (Cyanophyceae).

The marine cyanobacterium Synechococcus elongatus was grown in a continuous culture system to study the interactive effects of temperature, irradiance, nutrient limitation, and the partial pressure of CO2 (pCO2) on its growth and physiological characteristics. Cells were grown on a 14:10 h light:dark cycle at all combinations of low and high irradiance (50 and 300 μmol photons ⋅ m-2 ⋅ s-1 , respectively), low and high pCO2 (400 and 1000 ppmv, respectively), nutrient limitation (nitrate-limited and nutrient-replete conditions), and temperatures of 20-45°C in 5°C increments. The maximum growth rate was ~4.5 · d-1 at 30-35°C. Under nutrient-replete conditions, growth rates at most temperatures and irradiances were about 8% slower at a pCO2 of 1000 ppmv versus 400 ppmv. The single exception was 45°C and high irradiance. Under those conditions, growth rates were ~45% higher at 1000 ppmv. Cellular carbon:nitrogen ratios were independent of temperature at a fixed relative growth rate but higher at high irradiance than at low irradiance. Initial slopes of photosynthesis-irradiance curves were higher at all temperatures under nutrient-replete versus nitrate-limited conditions; they were similar at all temperatures under high and low irradiance, except at 20°C, when they were suppressed at high irradiance. A model of phytoplankton growth in which cellular carbon was allocated to structure, storage, or the light or dark reactions of photosynthesis accounted for the general patterns of cell composition and growth rate. Allocation of carbon to the light reactions of photosynthesis was consistently higher at low versus high light and under nutrient-replete versus nitrate-limited conditions.

Antarctic meltwater-induced dynamical changes in phytoplankton in the Southern Ocean

It has been suggested that the freshwater flux due to the recent melting of the Antarctic ice-sheet/shelf will suppress ventilation in the Southern Ocean (SO). In this study, we performed idealized earth-system simulations to examine the impacts of Antarctic meltwater on the biomass of surface phytoplankton in the Antarctic Ocean. The enhanced stratification due to the meltwater leads to a decrease in surface nitrate concentration, but an increase in the surface concentration of dissolved iron. These changes are associated with the reduced upwelling of nitrate-rich deep water and the trapped iron exported from terrestrial sediment. Because of the limited iron availability in the SO, the trapped iron in surface water enhances the chlorophyll concentration in the open ocean. However, in the marginal sea along the Antarctic coastline where the iron is relatively sufficient, a nitrate reduction induces a chlorophyll decrease, indicating a regime shift from iron-limited to nitrate-limited conditions.

Interactive Effects of CO2, Temperature, Irradiance, and Nutrient Limitation on the Growth and Physiology of the Marine Diatom Thalassiosira pseudonana (Coscinodiscophyceae)

The marine diatom Thalassiosira pseudonana was grown in continuous culture systems to study the interactive effects of temperature, irradiance, nutrient limitation, and the partial pressure of CO2 (pCO2 ) on its growth and physiological characteristics. The cells were able to grow at all combinations of low and high irradiance (50 and 300μmolphotons·m-2 ·s-1 , respectively, of visible light), low and high pCO2 (400 and 1,000μatm, respectively), nutrient limitation (nitrate-limited and nutrient-replete conditions), and temperatures of 10-32°C. Under nutrient-replete conditions, there was no adverse effect of high pCO2 on growth rates at temperatures of 10-25°C. The response of the cells to high pCO2 was similar at low and high irradiance. At supraoptimal temperatures of 30°C or higher, high pCO2 depressed growth rates at both low and high irradiance. Under nitrate-limited conditions, cells were grown at 38±2.4% of their nutrient-saturated rates at the same temperature, irradiance, and pCO2 . Dark respiration rates consistently removed a higher percentage of production under nitrate-limited versus nutrient-replete conditions. The percentages of production lost to dark respiration were positively correlated with temperature under nitrate-limited conditions, but there was no analogous correlation under nutrient-replete conditions. The results suggest that warmer temperatures and associated more intense thermal stratification of ocean surface waters could lower net photosynthetic rates if the stratification leads to a reduction in the relative growth rates of marine phytoplankton, and at truly supraoptimal temperatures there would likely be a synergistic interaction between the stresses from temperature and high pCO2 (lower pH).

Phosphorylation at Ser28 stabilizes the Arabidopsis nitrate transporter NRT2.1 in response to nitrate limitation.

Nitrate is one of the main inorganic nitrogen sources for plants. Nitrate absorption from soils is achieved through the combined activities of specific nitrate transporters. Nitrate transporter 2.1 (NRT2.1) is the major component of the root high-affinity nitrate transport system in Arabidopsis thaliana. Studies to date have mainly focused on transcriptional control of NRT2.1. Here, we show that NRT2.1 protein stability is also regulated in response to nitrogen nutrition availability. When seedlings were transferred to nitrate-limited conditions, the apparent half-life of NRT2.1 in roots increased from 3 to 9 h. This stabilization of NRT2.1 protein occurred rapidly, even prior to the transcriptional stimulation of NRT2.1. Furthermore, we revealed that phosphorylation at serine 28 (Ser28) of NRT2.1 is involved in regulating the stability of this protein. Substitution of Ser28 by alanine resulted in unstable NRT2.1, and this loss-of-phosphorylation mutant (NRT2.1S28A ) failed to complement the growth-restricted phenotype of the nrt2.1 mutant when a low concentration of nitrate was the sole nitrogen source. These results demonstrate that phosphorylation at Ser28 is crucial for NRT2.1 protein stabilization and accumulation in response to nitrate limitation.

Identification and Expression Analyses of the Nitrate Transporter Gene (NRT2) Family Among Skeletonema species (Bacillariophyceae).

High-affinity nitrate transporters are considered to be the major transporter system for nitrate uptake in diatoms. In the diatom genus Skeletonema, three forms of genes encoding high-affinity nitrate transporters (NRT2) were newly identified from transcriptomes generated as part of the marine microbial eukaryote transcriptome sequencing project. To examine the expression of each form of NRT2 under different nitrogen environments, laboratory experiments were conducted under nitrate-sufficient, ammonium-sufficient, and nitrate-limited conditions using three ecologically important Skeletonema species: S.dohrnii, S.menzelii, and S.marinoi. Primers were developed for each NRT2 form and species and Q-RT-PCR was performed. For each NRT2 form, the three Skeletonema species had similar transcriptional patterns. The transcript levels of NRT2:1 were significantly elevated under nitrogen-limited conditions, but strongly repressed in the presence of ammonium. The transcript levels of NRT2:2 were also repressed by ammonium, but increased 5- to 10-fold under nitrate-sufficient and nitrogen-limited conditions. Finally, the transcript levels of NRT2:3 did not vary significantly under various nitrogen conditions, and behaved more like a constitutively expressed gene. Based on the observed transcript variation among NRT2 forms, we propose a revised model describing nitrate uptake kinetics regulated by multiple forms of nitrate transporter genes in response to various nitrogen conditions in Skeletonema. The differential NRT2 transcriptional responses among species suggest that species-specific adaptive strategies exist within this genus to cope with environmental changes.

The ratio of single-turnover to multiple-turnover fluorescence varies predictably with growth rate and cellular chlorophyll in the green alga Dunaliella tertiolecta.

Marine phytoplankton experience a wide range of nutrient and light conditions in nature and respond to these conditions through changes in growth rate, chlorophyll concentration, and other physiological properties. Chlorophyll fluorescence is a non-invasive and efficient tool for characterizing changes in these physiological properties. In particular, the introduction of fast repetition rate fluorometry (FRRf) into studies of phytoplankton physiology has enabled detailed studies of photosynthetic components and kinetics. One property retrieved with an FRRf is the 'single-turnover' maximum fluorescence (FmST) when the primary electron acceptor, Qa, is reduced but the plastoquinone (PQ) pool is oxidized. A second retrieved property is the 'multiple-turnover' fluorescence (FMT) when both Qa and PQ are reduced. Here, variations in FmST and FMT were measured in the green alga Dunaliella tertiolecta grown under nitrate-limited, light-limited, and replete conditions. The ratio of FmST to FMT (ST/MT) showed a consistent relationship with cellular chlorophyll in D. tertiolecta across all growth conditions. However, the ST/MT ratio decreased with growth rate under nitrate-limited conditions but increased with growth rate under light-limited conditions. In addition, cells from light-limited conditions showed a high accumulation of Qb-nonreducing centers, while cells from nitrate-limited conditions showed little to none. We propose that these findings reflect differences in the reduction and oxidation rates of plastoquinone due to the unique impacts of light and nitrate limitation on the stoichiometry of light-harvesting components and downstream electron acceptors.

Long-term performance evaluation of an anoxic sulfur oxidizing moving bed biofilm reactor under nitrate limited conditions

An anoxic sulfur-oxidizing moving bed biofilm reactor (MBBR) treating sulfur and nitrate-contaminated synthetic wastewater was monitored for 306 days under feed nitrogen-to-sulfur (N/S) molar ratios of 0.5, 0.3 and 0.1.

Performance of full-scale woodchip bioreactors treating effluents from commercial RAS

The aquaculture industry needs new cost-effective solutions for removing effluent nitrogen to reduce their environmental impact. Recent studies have shown that laboratory and pilot-scale woodchip bioreactors can remove nitrate from aquaculture effluent. Encouraged by these results, several Danish fish farmers recently constructed commercial scale woodchip bioreactors prior to- or integrated into existing free water surface constructed wetlands without knowing the effects of design and upscaling on removal performance. The objective of the current study was to monitor initial performance (first 28–52 weeks of operation) of three such custom-designed denitrifying woodchip bioreactors installed in full-scale (350, 650, and 1250 m3 woodchips) for effluent treatment at three commercial recirculated rainbow trout (Oncorhynchus mykiss) farms.All three woodchip bioreactors removed nitrogen (essentially nitrate-nitrogen) continuously from the start and at relatively stable rates (5.3–8.5 g N/m3/d; 4.5–7.8 g NO3-N/m3/d) during the investigation period. Leaching of dissolved organic matter continued for up to half a year whereas there was no similar leaching of dissolved phosphorus. A net production of dissolved organic matter was observed under nitrate-limited conditions in one of the bioreactors characterized by a loading of 5.5 compared to 16.4–16.8 g NO3-N/m3/d at the other sites, and an empty bed contact time (EBCT) of 26 h compared to 15–16 h at the other sites. An increase in water level difference between inlet and outlet indicated that accumulation of particulate organic matter and associated bacterial growth may lead to head loss potentially reducing the long-term performance of the bioreactors. In conclusion, the study confirms that woodchip bioreactors can be applied at full-scale for removing NO3-N from fish farm effluent. Woodchip bioreactors should be designed to minimize head loss and the risk of clogging, and loading and retention time should ensure that denitrifiers do not become nitrate-limited.

Diatom performance in a future ocean: interactions between nitrogen limitation, temperature, and CO2-induced seawater acidification

Abstract Phytoplankton cells living in the surface waters of oceans are experiencing alterations in environmental conditions associated with global change. Given their importance in global primary productivity, it is of considerable concern to know how these organisms will perform physiologically under the changing levels of pH, temperatures, and nutrients predicted for future oceanic ecosystems. Here we show that the model diatom, Thalassiosira pseudonana, when grown at different temperatures (20 or 24 °C), pCO2 (400 or 1000 µatm), and nitrate concentrations (2.5 or 102.5 µmol l−1), displayed contrasting performance in its physiology. Elevated pCO2 (and hence seawater acidification) under the nitrate-limited conditions led to decreases in specific growth rate, cell size, pigment content, photochemical quantum yield of PSII, and photosynthetic carbon fixation. Furthermore, increasing the temperature exacerbated the negative effects of the seawater acidification associated with elevated pCO2 on specific growth rate and chlorophyll content under the N-limited conditions. These results imply that a reduced upward transport of nutrients due to enhanced stratification associated with ocean warming might act synergistically to reduce growth and carbon fixation by diatoms under progressive ocean acidification, with important ramifications for ocean productivity and the strength of the biological CO2 pump.

Arabidopsis plastidial folylpolyglutamate synthetase is required for nitrogen metabolism under nitrate-limited condition in darkness

Folates play an important role in plant metabolism. Here we report a T-DNA insertion mutant (atdfb-3) of the plastidial folylpolyglutamate synthetase gene (AtDFB) was defective in folate metabolism and nitrogen metabolism under nitrate-limited conditions in darkness. Exogenous applied 5-formyl-tetrahydrofolate (5-F-THF) completely restored nitrogen content, soluble protein, total amino acids, individual amino acids including Glu, Gln, Asp, Asn, Pro, Arg and Met, nitrate, and endogenous 5-F-THF in atdfb-3 to the wild-type level. At the same time the application of 5-F-THF partially restored the content of Ser and nitrite in the mutant. Taken together, these results indicated that intact folate metabolism was necessary for nitrogen metabolism in Arabidopsis thaliana under nitrate-limited condition in darkness, providing novel insights into function of folate.

Identification of a Cyanobacterial RND-Type Efflux System Involved in Export of Free Fatty Acids.

An RND (resistance-nodulation-division)-type transporter having the capacity to export free fatty acids (FFAs) was identified in the cyanobacterium Synechococcus elongatus strain PCC 7942 during characterization of a mutant strain engineered to produce FFAs. The basic strategy for construction of the FFA-producing mutant was a commonly used one, involving inactivation of the endogenous acyl-acyl carrier protein synthetase gene (aas) and introduction of a foreign thioesterase gene ('tesA), but a nitrate transport mutant NA3 was used as the parental strain to achieve slow, nitrate-limited growth in batch cultures. Also, a nitrogen-regulated promoter PnirA was used to drive 'tesA to maximize thioesterase expression during the nitrate-limited growth. The resulting mutant (dAS2T) was, however, incapable of growth under the conditions of nitrate limitation, presumably due to toxicity associated with FFA overproduction. Incubation of the mutant culture under the non-permissive conditions allowed for isolation of a pseudorevertant (dAS2T-pr1) capable of growth on nitrate. Genome sequence and gene expression analyses of this strain suggested that expression of an RND-type efflux system had rescued growth on nitrate. Targeted inactivation of the RND-type transporter genes in the wild-type strain resulted in loss of tolerance to exogenously added FFAs including capric, lauric, myristic, oleic and linolenic acids. Overexpression of the genes in dAS2T, on the other hand, enhanced FFA excretion and cell growth in nitrate-containing medium, verifying that the genes encode an efflux pump for FFAs. These results demonstrate the importance of the efflux system in efficient FFA production using genetically engineered cyanobacteria.

Nitrate ammonification in mangrove soils: a hidden source of nitrite?

Nitrate reduction is considered to be a minor microbial pathway in the oxidation of mangrove-derived organic matter due to a limited supply of nitrate in mangrove soils. At a limited availability of this electron acceptor compared to the supply of degradable carbon, nitrate ammonification is thought to be the preferential pathway of nitrate reduction. Mangrove forest mutually differ in their productivity, which may lead to different available carbon to nitrate ratios in their soil. Hence, nitrate ammonification is expected to be of more importance in high- compared to low-productive forests. The hypothesis was tested in flow-through reactors that contain undisturbed mangrove soils from high-productive Avicennia germinans and Rhizophora mangle forests in Florida and low-productive Avicennia marina forests in Saudi Arabia. Nitrate was undetectable in the soils from both regions. It was assumed that a legacy of nitrate ammonification would be reflected by a higher ammonium production from these soils upon the addition of nitrate. Unexpectedly, the soils from the low-productive forests in Saudi Arabia produced considerably more ammonium than the soils from the high-productive forests in Florida. Hence, other environmental factors than productivity must govern the selection of nitrate ammonification or denitrification. A rather intriguing observation was the 1:1 production of nitrite and ammonium during the consumption of nitrate, more or less independent from sampling region, location, sampling depth, mangrove species and from the absence or presence of additional degradable carbon. This 1:1 ratio points to a coupled production of ammonium and nitrite by one group of nitrate-reducing microorganisms. Such a production of nitrite will be hidden by the presence of active nitrite-reducing microorganisms under the nitrate-limited conditions of most mangrove forest soils.

Does the 14C method estimate net photosynthesis? Implications from batch and continuous culture studies of marine phytoplankton

We carried out batch culture studies with seven species of marine phytoplankton and chemostat studies with two of the seven species to determine whether and to what extent 14C uptake approximated net photosynthesis. In two of seven cases, Isochrysis galbana and Dunaliella tertiolecta, cells uniformly labeled with 14C lost no activity when they were transferred to a 14C-free medium and allowed to grow in the light. In similar experiments with four other species, uniformly labeled cells lost activity when incubated in the light, but the loss rates were only a few percent per day. Thus these six species appear to respire primarily recently fixed carbon. In the case of the remaining species, Chlorella kessleri, loss rates of 14C in the light from uniformly labeled cells were about 29% per day, the apparent ratio of respiration to net photosynthesis being 0.4. Follow-up chemostat studies with I. galbana and C. kessleri grown under both light- and nitrate-limited conditions produced results consistent with the implications of the batch culture work: uptake of 14C by I. galbana after incubations of 24h yielded estimates of photosynthetic carbon fixation equal to the product of the chemostat dilution rate and the concentration of organic carbon in the growth chamber. Similar experiments with C. kessleri produced 14C-based estimates of photosynthetic carbon fixation that exceeded the net rates of organic carbon production in the growth chamber by roughly 55%. Time-course studies with both species indicated that at high growth rates recently fixed carbon began to enter the respiratory substrate pool after a time lag of several hours, a result consistent with previous work with D. tertiolecta. The lag time appeared to be much shorter at low growth rates. The results with C. kessleri are similar to results previously reported for Chlorella pyrenoidosa and Amphidium carteri. Collectively these results suggest that 14C uptake by species with relatively high ratios of respiration to photosynthesis may tend to substantially overestimate net photosynthesis, perhaps because a substantial percentage of the carbon respired by such species is old carbon.

Resolving the contributions of the membrane-bound and periplasmic nitrate reductase systems to nitric oxide and nitrous oxide production in Salmonella enterica serovar Typhimurium

The production of cytotoxic nitric oxide (NO) and conversion into the neuropharmacological agent and potent greenhouse gas nitrous oxide (N₂O) is linked with anoxic nitrate catabolism by Salmonella enterica serovar Typhimurium. Salmonella can synthesize two types of nitrate reductase: a membrane-bound form (Nar) and a periplasmic form (Nap). Nitrate catabolism was studied under nitrate-rich and nitrate-limited conditions in chemostat cultures following transition from oxic to anoxic conditions. Intracellular NO production was reported qualitatively by assessing transcription of the NO-regulated genes encoding flavohaemoglobin (Hmp), flavorubredoxin (NorV) and hybrid cluster protein (Hcp). A more quantitative analysis of the extent of NO formation was gained by measuring production of N₂O, the end-product of anoxic NO-detoxification. Under nitrate-rich conditions, the nar, nap, hmp, norV and hcp genes were all induced following transition from the oxic to anoxic state, and 20% of nitrate consumed in steady-state was released as N₂O when nitrite had accumulated to millimolar levels. The kinetics of nitrate consumption, nitrite accumulation and N₂O production were similar to those of wild-type in nitrate-sufficient cultures of a nap mutant. In contrast, in a narG mutant, the steady-state rate of N₂O production was ~30-fold lower than that of the wild-type. Under nitrate-limited conditions, nap, but not nar, was up-regulated following transition from oxic to anoxic metabolism and very little N₂O production was observed. Thus a combination of nitrate-sufficiency, nitrite accumulation and an active Nar-type nitrate reductase leads to NO and thence N₂O production, and this can account for up to 20% of the nitrate catabolized.

Nitrogen economics of root foraging: Transitive closure of the nitrate–cytokinin relay and distinct systemic signaling for N supply vs. demand

As sessile organisms, root plasticity enables plants to forage for and acquire nutrients in a fluctuating underground environment. Here, we use genetic and genomic approaches in a "split-root" framework--in which physically isolated root systems of the same plant are challenged with different nitrogen (N) environments--to investigate how systemic signaling affects genome-wide reprogramming and root development. The integration of transcriptome and root phenotypes enables us to identify distinct mechanisms underlying "N economy" (i.e., N supply and demand) of plants as a system. Under nitrate-limited conditions, plant roots adopt an "active-foraging strategy", characterized by lateral root outgrowth and a shared pattern of transcriptome reprogramming, in response to either local or distal nitrate deprivation. By contrast, in nitrate-replete conditions, plant roots adopt a "dormant strategy", characterized by a repression of lateral root outgrowth and a shared pattern of transcriptome reprogramming, in response to either local or distal nitrate supply. Sentinel genes responding to systemic N signaling identified by genome-wide comparisons of heterogeneous vs. homogeneous split-root N treatments were used to probe systemic N responses in Arabidopsis mutants impaired in nitrate reduction and hormone synthesis and also in decapitated plants. This combined analysis identified genetically distinct systemic signaling underlying plant N economy: (i) N supply, corresponding to a long-distance systemic signaling triggered by nitrate sensing; and (ii) N demand, experimental support for the transitive closure of a previously inferred nitrate-cytokinin shoot-root relay system that reports the nitrate demand of the whole plant, promoting a compensatory root growth in nitrate-rich patches of heterogeneous soil.

PHOSPHATE-LIMITED GROWTH OF PAVLOVA LUTHERI (PRYMNESIOPHYCEAE) IN CONTINUOUS CULTURE: DETERMINATION OF GROWTH-RATE-LIMITING SUBSTRATE CONCENTRATIONS WITH A SENSITIVE BIOASSAY PROCEDURE(1).

The relationship between steady-state growth rate and phosphate concentration was studied for the marine prymnesiophyte Pavlova lutheri (Droop) J. C. Green grown in a chemostat at 22°C under continuous irradiance. A bioassay procedure involving short-term uptake of 10 picomolar spikes of (33) P-labeled phosphate was used to estimate the concentration of phosphate in the growth chamber. The relationship between growth rate and phosphate was well described by a simple rectangular hyperbola with a half-saturation constant of 2.6 nM. The cells were able to take up micromolar spikes of phosphate at rates two to three orders of magnitude higher than steady-state uptake rates. The kinetics of short-term uptake displayed Holling type III behavior, suggesting that P. lutheri may have multiple uptake systems with different half-saturation constants. Chl a:C ratios were linearly related to growth rate and similar to values previously reported for P. lutheri under nitrate-limited conditions. C:N ratios, also linearly related to growth rate, were consistently lower than values reported for P. lutheri under nitrate-limited conditions, a result presumably reflecting luxury assimilation of nitrogen under phosphate-limited conditions. C:P ratios were linearly related to growth rate in a manner consistent with the Droop equation for growth rate versus cellular P:C ratio.

Stable isotope (δ 13C carb and org, δ 15N org) and trace element anomalies during the Late Devonian ‘ punctata Event’ in the Western Canada Sedimentary Basin

Late Devonian marine deposits in the Western Canada Sedimentary Basin were analyzed for (1) accumulations of bioproductivity and paleoredox trace element proxies and for (2) variations of δ 13C (carb and org) and δ 15N org in order to understand and interpret the regional history of the global yet short-term ‘ punctata Event’ geochemical perturbation. Statistical correlations suggest that changes in detrital input and associated micronutrient delivery were the main driver of a eutrophication event noted early and possibly also late in the punctata zone around the isolated Miette platform, manifested by increased TOC, positive δ 13C excursions and concurrent enrichments of all elemental proxies. Evaluation of data within a regional sequence stratigraphic perspective revealed a eustatic sea level influence, with proxy accumulations associated mostly with early transgression (IIc1). Deposition and preservation of organic matter-rich facies occurred during conditions of enhanced primary production and facilitated bottom water suboxia–anoxia. Following eutrophication, lower δ 15N org and δ 13C org values predominated and persisted throughout much of the punctata zone before rebounding toward its close, suggesting a time interval of environmental stagnation and lower overall productivity during which N 2-fixing autotrophs may have had an ecological advantage under nitrate-limited conditions. The punctata Event approximately coincided with the advent of archaeopterid forest expansion beginning around mid-Frasnian time, which fundamentally altered the nature of continental weathering through extensive soil formation and increased nutrient delivery to the oceans. This evolutionary event may have amplified the detrital influx, already elevated by sea level lowstand and early transgression and increased denudation of rising mountain ranges in near-equatorial regions.

Spatial variations in denitrification activity in wetland sediments explained by hydrology and denitrifying community structure

We determined spatial variations in potential denitrification activity and the controlling hydrological as well as biochemical processes in the sediments of a Swedish treatment wetland. Hydrological processes, including water residence times, were analyzed using a 2D depth-averaged flow model and the denitrifier community structure was analyzed using denaturing gradient gel electrophoreses (DGGE) of nosZ genes, encoding nitrous oxide reductase. In addition, we provide a theoretical basis for evaluation of denitrification rates useful in nitrate-limited conditions. The results demonstrate that potential denitrification rates differed significantly between the sampling locations (CV=0.34). The variations were best described by concentration of nitrogen in sediments and water residence time. DGGE analyses indicated that a few key populations dominated and that the community diversity increased with decreasing nutrient levels and increasing water residence times. Moreover, we found that denitrification rates in terms of Menten and first-order kinetics can be evaluated by fitting a mathematical expression, comparing denitrification and other nitrogen-transforming processes to measured product formation in nitrate-limited experiments.

Potential contribution of β-carboxylases to photosynthetic carbon isotope fractionation in a marine diatom

N. Cassar and E.A. Laws. 2007. Potential contribution of β-carboxylases to photosynthetic carbon isotope fractionation in a marine diatom. Phycologia 46: 307–314. DOI: 10.2216/06-50.1In vitro activities of phosphoenolpyruvate carboxylase (PEPC) and phosphoenolpyruvate carboxykinase (PEPCK) were measured in chemostat cultures of the marine diatom Phaeodactylum tricornutum grown under either phosphate-or nitrate-limited conditions and at low (1 μmol kg−1) and high (70–100 μmol kg−1) CO2 concentrations. A comparison of in vitro methods for measuring PEPC activity underscored the importance of including glycerol in the reaction mixture because of its ability to stabilize the quaternary structure of PEPC. Assays for total β-carboxylase activity (PEPC + PEPCK) identified the importance of substituting Mn2+ for Mg2+ as an activator for PEPC since Mg2+ is inhibitory to PEPCK activity. Results indicated that PEPC was constitutive, that is, present in a constant ratio relative to the limiting nutrient over a wide range of growth conditions. PEPCK acclimation was greater, and its intracellular concentration was positively correlated with CO2 concentrations. In vitro β-carboxylase activity averaged 13% of in vivo carbon fixation rates. The low percentage of β- carboxylase activity and the positive correlation between PEPCK and CO2 concentration argue against a C4-type pathway in P. tricornutum; that is, β-carboxylase activity appears related to strictly anaplerotic processes. Calculations indicate that β -carboxylase activity reduces the fractionation associated with carbon fixation but by no more than 2‰.