Bacterial nitrate assimilation: gene distribution and regulation

In the context of the global nitrogen cycle, the importance of inorganic nitrate for the nutrition and growth of marine and freshwater autotrophic phytoplankton has long been recognized. In contrast, the utilization of nitrate by heterotrophic bacteria has historically received less attention because the primary role of these organisms has classically been considered to be the decomposition and mineralization of dissolved and particulate organic nitrogen. In the pre-genome sequence era, it was known that some, but not all, heterotrophic bacteria were capable of growth on nitrate as a sole nitrogen source. However, examination of currently available prokaryotic genome sequences suggests that assimilatory nitrate reductase (Nas) systems are widespread phylogenetically in bacterial and archaeal heterotrophs. Until now, regulation of nitrate assimilation has been mainly studied in cyanobacteria. In contrast, in heterotrophic bacterial strains, the study of nitrate assimilation regulation has been limited to Rhodobacter capsulatus, Klebsiella oxytoca, Azotobacter vinelandii and Bacillus subtilis. In Gram-negative bacteria, the nas genes are subjected to dual control: ammonia repression by the general nitrogen regulatory (Ntr) system and specific nitrate or nitrite induction. The Ntr system is widely distributed in bacteria, whereas the nitrate/nitrite-specific control is variable depending on the organism

Shortcut biological nitrogen removal (SBNR) in microbial fuel cells (MFCs)

Microbial Fuel Cells (MFCs) represent nowadays a promising technology for the treatment of industrial wastewater. In this work the Shortcut Nitritation/Denitritation process in H-type MFC was investigated. The cell was fed by sodium acetate and fumaric acid, as organic carbon source, and ammonium sulphate, sodium nitrite and sodium nitrate as nitrogen source. Anaerobic digestion supernatant (digestate) was used as bacterial source. Batch tests were performed at a TOC/N ratio of 0.35, and Total Organic Carbon (TOC), pH and Open Circuit Voltage (OCV) were daily monitored. High organic carbon removal (up to 85%) in short time (within 6 days) were achieved. The nitritation proved to be independent of organic carbon amount and composition: an ammonium content reduction of about 45% was observed. Regarding the denitritation step, an almost quantitative removal of nitrite and nitrate was observed when fumaric acid was used as a carbon source

Poly(3-hydroxybutyrate) hyperproduction by a global nitrogen regulator NtrB mutant strain of Paracoccus denitrificans PD1222

Paracoccus denitrificans PD1222 accumulates short-length polyhydroxyalkanoates, poly(3-hydroxybutyrate), under nitrogen-deficient conditions. Polyhydroxybutyrate metabolism requires the 3-ketoacyl-CoA thiolase PhaA, the acetoacetyl-CoA dehydrogenase/reductase PhaB and the synthase PhaC for polymerization. Additionally, P. denitrificans PD1222 grows aerobically with nitrate as sole nitrogen source. Nitrate assimilation is controlled negatively by ammonium through the two-component NtrBC system. NtrB is a sensor kinase that autophosphorylates a histidine residue under low-nitrogen concentrations and, in turn, transfers a phosphoryl group to an aspartate residue of the response regulator NtrC protein, which acts as a transcriptional activator of the P. denitrificans PD1222 nasABGHC genes. The P. denitrificans PD1222 NtrB mutant was unable to use nitrate efficiently as nitrogen source when compared to the wild-type strain, and it also overproduced poly(3-hydroxybutyrate). Acetyl-CoA concentration in the P. denitrificans PD1222 NtrB mutant strain was higher than in the wild-type strain. The expression of the phaC gene was also increased in the NtrB mutant when compared to the wild-type strain. These results suggest that accumulation of poly(3-hydroxybutyrate) in the NtrB mutant strain of PD1222 responds to the high levels of acetyl-CoA that accumulate in the cytoplasm as consequence of its inability to efficiently use nitrate as nitrogen source

Niche differentiation in nitrogen metabolism among methanotrophs within an operational taxonomic unit

Background: The currently accepted thesis on nitrogenous fertilizer additions on methane oxidation activity assumes niche partitioning among methanotrophic species, with activity responses to changes in nitrogen content being dependent on the in situ methanotrophic community structure Unfortunately, widely applied tools for microbial community assessment only have a limited phylogenetic resolution mostly restricted to genus level diversity, and not to species level as often mistakenly assumed. As a consequence, intragenus or intraspecies metabolic versatility in nitrogen metabolism was never evaluated nor considered among methanotrophic bacteria as a source of differential responses of methane oxidation to nitrogen amendments. Results: We demonstrated that fourteen genotypically different Methylomonas strains, thus distinct below the level at which most techniques assign operational taxonomic units (OTU), show a versatile physiology in their nitrogen metabolism. Differential responses, even among strains with identical 16S rRNA or pmoA gene sequences, were observed for production of nitrite and nitrous oxide from nitrate or ammonium, nitrogen fixation and tolerance to high levels of ammonium, nitrate, and hydroxylamine. Overall, reduction of nitrate to nitrite, nitrogen fixation, higher tolerance to ammonium than nitrate and tolerance and assimilation of nitrite were general features. Conclusions: Differential responses among closely related methanotrophic strains to overcome inhibition and toxicity from high nitrogen loads and assimilation of various nitrogen sources yield competitive fitness advantages to individual methane-oxidizing bacteria. Our observations proved that community structure at the deepest phylogenetic resolution potentially influences in situ functioning

Urea as the Nitrogen source in NIT Hydroponic System

Urea as the source of nitrogen in the nutrient solution in NIT (nutrient film technique) hydroponic system undergoes hydrolysis which results in the release of ammonium in solution. Urea hydrolysis was rapid from the 7th day onwards and ended by the 20th day. At the same time, ammonium concentration in solution increased and reached its maximum on the 20th day. Nitrification occurred simultaneously and peaked also on the 20th day. Plant dry matter weight at harvest was similar for both urea and nitrate treatments. Ammonium concentration in leaves and roots was higher in urea than in nitrate treatments. Nitrate concentration in leaves and roots was similarfor both treatments. The study showed that urea can be substituted for nitrate as the nitrogen source in the NIT hydroponic system

Enrichment and characterization of a bacteria consortium capable of heterotrophic nitrification and aerobic denitrification at low temperature

Nitrogen removal in wastewater treatment plants is usually severely inhibited under cold temperature. The present study proposes bioaugmentation using psychrotolerant heterotrophic nitrification-aerobic denitrification consortium to enhance nitrogen removal at low temperature. A functional consortium has been successfully enriched by stepped increase in DO concentration. Using this consortium, the specific removal rates of ammonia and nitrate at 10 degrees C reached as high as 3.1 mg N/(g SS h) and 9.6 mg N/ (g SS h), respectively. PCR-DGGE and clone library analysis both indicated a significant reduction in bacterial diversity during enrichment. Phylogenetic analysis based on nearly full-length 16S rRNA genes showed that Alphaproteobacteria. Deltaproteobacteria and particularly Bacteroidetes declined while Gammaproteobacteria (all clustered into Pseudomonas sp.) and Betaproteobacteria (mainly Rhodoferax ferrireducens) became dominant in the enriched consortium. It is likely that Pseudomonas spp. played a major role in nitrification and denitrification, while R. ferrireducens and its relatives utilized nitrate as both electron acceptor and nitrogen source. Crown Copyright (C) 2012 Published by Elsevier Ltd. All rights reserved.http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000312926400021&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=8e1609b174ce4e31116a60747a720701Agricultural EngineeringBiotechnology & Applied MicrobiologyEnergy & FuelsSCI(E)EIPubMed31ARTICLE151-15712

Anthropogenic signals recorded in an ice core from Eclipse Icefield, Yukon Territory, Canada

Trends in the annual flux of sulfate and nitrate in a new ice core collected at an elevation of 3017 m on Eclipse Icefield, 45 km northeast of Mt. Logan were examined to determine the effect of anthropogenic activity on precipitation chemistry in the remote northwest North America mid-troposphere. The annual flux of both sulfate and nitrate at Eclipse began increasing in the 1940s, demonstrating, for the first time, the anthropogenic sulfate and nitrate pollution of the northwest North American Arctic in an ice core from this region. Comparison of the Eclipse record with regional emission estimates for total sulfur and nitrogen oxides suggests that Eurasia is the dominant source of pollutants reaching Eclipse. The available data does not permit a confident assessment of the relative importance of European versus Soviet emissions in producing the observed trends in sulfate and nitrate at Eclipse

Dynamic Optimization of Nitrogen Use in Agriculture

Agricultural production is highly dependent on inorganic substances including fertilizers. High-yielding crop varieties, such as corn, require large amounts of primary nutrients including nitrogen, phosphorus and potassium. Farmers often add a surplus of nutrients to crops to maximize yields. Utilization of primary nutrients has increased by more than 300% while that of nitrogen alone has increased by more than 600% between 1960 and 2007 (USDA, 2009). From 1964 to 2007, the use of nitrogen in the corn sector alone increased from 1,623,000 to 5,714,000 nutrient tons (USDA, 2009). While increasing production, increased fertilizer use can potentially create negative externalities in the form of nitrate-nitrogen contamination in groundwater. Groundwater is the source of drinking water for about half the total U.S. population and nearly all of the rural population, and it provides over 50 billion gallons per day for agricultural needs (USGS, 2009). In the U.S. the main source of nitrate pollution in the groundwater results from the actions of farmers through the use of fertilizers and other chemicals (Haller, et al. 2009). Nitrogen-nitrate contamination can have adverse human affects including methemoglobinemia or ―blue-baby‖ syndrome (Majumdar, 2003). The potential for nitrate contamination in corn production is especially problematic as corn alone accounts for over 90% of feed grains produced in the U.S. (USDA, 2009). The USDA estimates that approximately 80 million acres of land is planted to corn, with the majority in the Heartland region (the Midwest) of the U.S. (2009). The Heartland region is primarily rural and much of the population there derives its drinking water from groundwater. Therefore, the potential for groundwater contamination is greatly increased in this region.Environmental Economics, Nitrogen/Nitrate Contamination, Dynamic Optimization, Agriculture, Agricultural and Food Policy, Demand and Price Analysis, Environmental Economics and Policy, C61, C63, Q10, Q51, Q53,

Tracing nitrate nitrogen input-output dynamics at the Padež stream watershed

The sensitivity of ecosystems to changes in the amounts of nitrogen in the environment is large. In order to protect them against overloads of nutrients and to allow their healthy development, the knowledge of the nitrogen mass balance is crucial. Differences in the amount of nitrogen occur because of increasing inputs from anthropogenic sources, but they are also due to meteorological, hydrological, geological and biological factors or, in other words, to biogeochemical circulation between the biotope and organisms. The data on stream water nitrate concentrations and nitrate concentrations in precipitation together with measurements of precipitations and Padež stream discharge were used to analyze nitrate-nitrogen input-output dynamics. The analysis is presented as a difference between inputs and outputs of nitrate-nitrogen per hectare of catchment area. The impact of seasonality could be observed. Watershed behaves as a sink or as a source of nitrate-nitrogen depending on the hydrological conditions and the amount of potentially available nitrate-nitrogen in soil which is flushed towards the stream and its concentrations in precipitation

Nitrogen Oxyanion-dependent Dissociation of a Two-component Complex That Regulates Bacterial Nitrate Assimilation

Nitrogen is an essential nutrient for growth and is readily available to microbes in many environments in the form of ammonium and nitrate. Both ions are of environmental significance due to sustained use of inorganic fertilizers on agricultural soils. Diverse species of bacteria that have an assimilatory nitrate/nitrite reductase system (NAS) can use nitrate or nitrite as the sole nitrogen source for growth when ammonium is limited. In Paracoccus denitrificans, the pathway-specific two-component regulator for NAS expression is encoded by the nasT and nasS genes. Here, we show that the putative RNA-binding protein NasT is a positive regulator essential for expression of the nas gene cluster (i.e. nasABGHC). By contrast, a nitrogen oxyanion-binding sensor (NasS) is required for nitrate/nitrite-responsive control of nas gene expression. The NasS and NasT proteins co-purify as a stable heterotetrameric regulatory complex, NasS-NasT. This protein-protein interaction is sensitive to nitrate and nitrite, which cause dissociation of the NasS-NasT complex into monomeric NasS and an oligomeric form of NasT. NasT has been shown to bind the leader RNA for nasA. Thus, upon liberation from the complex, the positive regulator NasT is free to up-regulate nas gene expression