Arctic ozone loss due to denitrification

Climate change favours large seasonal loss of Arctic ozone

Chemical loss of Arctic ozone due to anthropogenic halogens is driven by temperature, with more loss occurring during cold winters favourable for formation of polar stratospheric clouds (PSCs). We show that a positive, statistically significant rise in the local maxima of PSC formation potential (PFP^LM) for cold winters is apparent in meteorological data collected over the past half century. Output from numerous General Circulation Models (GCMs) also exhibits positive trends in PFP^LM over 1950 to 2100, with highest values occurring at end of century, for simulations driven by a large rise in the radiative forcing of climate from greenhouse gases (GHGs). We combine projections of stratospheric halogen loading and humidity with GCM-based forecasts of temperature to suggest that conditions favourable for large, seasonal loss of Arctic column O₃ could persist or even worsen until the end of this century, if future abundances of GHGs continue to steeply rise.

Relative stabilities of HCl•H2SO4•HNO3 aggregates in polar stratospheric clouds

Strong acids such as HCl (C), HNO3 (N) and H2SO4 (S) acquire relevance in Polar Stratospheric Clouds (PSCs) and aerosols in which nucleation processes occur. Ab initio quantum chemical studies of aggregates were performed for these strong acids. Structures were calculated using DFT methods with the B3LYP hybrid functional and aug-cc-pVTZ basis set. As an initial constraint, an H2SO4 moiety was placed in all candidate structures. A total of 11 optimized structures was found: a global minimum (CSN-a) plus ten local minima on the Potential Energy Surface (PES). The global minimum aggregate gave four hydrogen bonds, yielding a hexagonal ring in its structure. HNO3 acts as proton donor in all clusters; nevertheless, using trans-H2SO4 as the proton donor yielded the most stable structures, whereas HCl acts mainly as a proton donor/acceptor. Real harmonic frequencies, IR spectra, and inter-monomeric parameters were obtained. CSN-a symmetric stretching modes were shifted to 2805.56 cm(-1) and 3520.00 cm(-1) for H-Cl modes, while O-H modes shifted to 3256.87 cm(-1) and 3362.47 cm(-1). On the other hand, relative stabilities improved for 5 of the 11 aggregates when the temperature decreased from 298 K to 210 K, 195 K and 188 K. The aggregate CSN-f remained unstable only at 210 K. Moreover, the relative Gibbs free energy, ΔG(0-298K) was -9.26 kcalmol(-1) with respect to CSN-a; relative reaction Gibbs free energy [Δ(ΔG)] values ranged from 0.0 at 298 K, to -6.9 kcalmol(-1) at 188 K. It seems that CSN aggregates remain slightly more stable than CNS aggregates with a HNO3 moiety when the temperature decreases from 298 to 188 K. Five structures remained relatively stable under both study conditions.

Genome analysis coupled with physiological studies reveals a diverse nitrogen metabolism in Methylocystis sp. strain SC2

BACKGROUND

Methylocystis sp. strain SC2 can adapt to a wide range of methane concentrations. This is due to the presence of two isozymes of particulate methane monooxygenase exhibiting different methane oxidation kinetics. To gain insight into the underlying genetic information, its genome was sequenced and found to comprise a 3.77 Mb chromosome and two large plasmids.

PRINCIPAL FINDINGS

We report important features of the strain SC2 genome. Its sequence is compared with those of seven other methanotroph genomes, comprising members of the Alphaproteobacteria, Gammaproteobacteria, and Verrucomicrobia. While the pan-genome of all eight methanotroph genomes totals 19,358 CDS, only 154 CDS are shared. The number of core genes increased with phylogenetic relatedness: 328 CDS for proteobacterial methanotrophs and 1,853 CDS for the three alphaproteobacterial Methylocystaceae members, Methylocystis sp. strain SC2 and strain Rockwell, and Methylosinus trichosporium OB3b. The comparative study was coupled with physiological experiments to verify that strain SC2 has diverse nitrogen metabolism capabilities. In correspondence to a full complement of 34 genes involved in N2 fixation, strain SC2 was found to grow with atmospheric N2 as the sole nitrogen source, preferably at low oxygen concentrations. Denitrification-mediated accumulation of 0.7 nmol (30)N2/hr/mg dry weight of cells under anoxic conditions was detected by tracer analysis. N2 production is related to the activities of plasmid-borne nitric oxide and nitrous oxide reductases.

CONCLUSIONS/PERSPECTIVES

Presence of a complete denitrification pathway in strain SC2, including the plasmid-encoded nosRZDFYX operon, is unique among known methanotrophs. However, the exact ecophysiological role of this pathway still needs to be elucidated. Detoxification of toxic nitrogen compounds and energy conservation under oxygen-limiting conditions are among the possible roles. Relevant features that may stimulate further research are, for example, absence of CRISPR/Cas systems in strain SC2, high number of iron acquisition systems in strain OB3b, and large number of transposases in strain Rockwell.

Sunlight effects on the Osmotrophic uptake of DMSP-sulfur and leucine by polar phytoplankton

Even though the uptake and assimilation of organic compounds by phytoplankton has been long recognized, very little is still known about its potential ecological role in natural marine communities and whether it varies depending on the light regimes the algae experience. We combined measurements of size-fractionated assimilation of trace additions of ³H-leucine and ³⁵S-dimethylsulfoniopropionate (DMSP) with microautoradiography to assess the extent and relevance of osmoheterotrophy in summer phytoplankton assemblages from Arctic and Antarctic waters, and the role of solar radiation on it was further investigated by exposing samples to different radiation spectra. Significant assimilation of both substrates occurred in the size fraction containing most phytoplankton (>5 µm), sunlight exposure generally increasing ³⁵S-DMSP-sulfur assimilation and decreasing ³H-leucine assimilation. Microautoradiography revealed that the capacity to take up both organic substrates seemed widespread among different polar algal phyla, particularly in pennate and centric diatoms, and photosynthetic dinoflagellates. Image analysis of the microautoradiograms showed for the first time interspecific variability in the uptakes of ³⁵S-DMSP and ³H-leucine by phytoplankton depending on the solar spectrum. Overall, these results suggest that the role of polar phytoplankton in the utilization of labile dissolved organic matter may be significant under certain conditions and further confirm the relevance of solar radiation in regulating heterotrophy in the pelagic ocean.

Visualization and direct counting of individual denitrifying bacterial cells in soil by nirK-targeted direct in situ PCR

The abundance of denitrifying bacteria in soil has been determined primarily by the conventional most probable number (MPN) method. We have developed a single-cell identification technique that is culture-independent, direct in situ PCR, to enumerate denitrifying bacteria in soils. The specificity of this method was evaluated with six species of denitrifying bacteria using nirK as the target gene; Escherichia coli was used as a negative control. Almost all (97.3%-100%) of the nirK-type denitrifying bacteria (Agromonas oligotrophica, Alcaligenes faecalis, Achromobacter denitrificans, Bradyrhizobium japonicum, and Pseudomonas chlororaphis) were detected by direct in situ PCR, whereas no E. coli cells and only a few cells (2.4%) of nirS-type denitrifying bacteria (Pseudomonas aeruginosa) were detected. Numbers of denitrifying bacteria in upland and paddy soil samples quantified by this method were 3.3 × 10(8) to 2.6 × 10(9) cells g(-1) dry soil. These values are approximately 1,000 to 300,000 times higher than those estimated by the MPN method. These results suggest that direct in situ PCR is a better tool for quantifying denitrifying bacteria in soil than the conventional MPN method.

Effect of pH and temperature on denitrification gene expression and activity in Pseudomonas mandelii

Pseudomonas mandelii liquid cultures were studied to determine the effect of pH and temperature on denitrification gene expression, which was quantified by quantitative reverse transcription-PCR. Denitrification was measured by the accumulation of nitrous oxide (N(2)O) in the headspace in the presence of acetylene. Levels of gene expression of nirS and cnorB at pH 5 were 539-fold and 6,190-fold lower, respectively, than the levels of gene expression for cells grown at pH 6, 7, and 8 between 4 h and 8 h. Cumulative denitrification levels were 28 micromol, 63 micromol, and 22 micromol at pH 6, 7, and 8, respectively, at 8 h, whereas negligible denitrification was measured at pH 5. P. mandelii cells grown at 20 degrees C and 30 degrees C exhibited 9-fold and 94-fold increases in levels of cnorB expression between 0 h and 2 h, respectively, and an average 17-fold increase in levels of nirS gene expression. In contrast, induction of cnorB and nirS gene expression for P. mandelii cells grown at 10 degrees C did not occur in the first 4 h. Levels of cumulative denitrification at 10 h were 6.6 micromol for P. mandelii cells grown at 10 degrees C and 20 degrees C and 30 micromol for cells grown at 30 degrees C. Overall, levels of cnorB and nirS expression were relatively insensitive to pH values over the range of pH 6 to 8 but were substantially reduced at pH 5, whereas gene expression was sensitive to temperature, with induction and time to achieve maximum gene expression delayed as the temperature decreased from 30 degrees C. Low pH and temperature negatively affected denitrification activity.

Nitric oxide reductase gene expression and nitrous oxide production in nitrate-grown Pseudomonas mandelii

Pure cultures of Pseudomonas mandelii were incubated with or without nitrate, which acts as a substrate and an electron acceptor for denitrification. Nitric oxide reductase (cnorB) gene expression was measured using a quantitative reverse transcription-PCR, and nitrous oxide emissions were measured by gas chromatography. P. mandelii cells in either the presence or absence of nitrate demonstrated an increase in cnorB gene expression during the first 3 h of growth. The level of expression of cnorB in nitrate-amended cells remained high (average, 2.06 x 10(8) transcripts/microg of RNA), while in untreated cells it decreased to an average of 3.63 x 10(6) transcripts/microg of RNA from 4 to 6 h. Nitrous oxide accumulation in the headspace was detected at 2 h, and cumulative emissions continued to increase over a 24-h period to 101 mumol in nitrate-amended cells. P. mandelii cnorB gene expression was not detected under aerobic conditions. These results demonstrate that P. mandelii cnorB gene expression was induced 203-fold at 4 h when nitrate was present in the medium. Accumulations of N(2)O indicated that the cNorB enzyme was synthesized and active.

Combined effects of cadmium and ultraviolet radiation on mortality and mineral content in common frog (Rana temporaria) larvae

The combined effects of UV with Cd(2 +) exposure on the mortality and mineral content of common frog larvae was investigated. Tadpoles were raised in increasing concentrations of Cd(2 +) (0-2000 microg x L(-1)). Additionally the larvae were exposed to biologically effective doses of UV-A (0.24 kJ x m(- 2)) and UV-B (2.71 kJ x m(- 2)). Parallel groups were grown in the same ionic concentrations in the absence of UV. In the second experiment larvae were exposed to sublethal doses of Cd(2 +) (1000 microg x L(-1)) for 3 days. Then the larvae were submitted to 4 weeks of recovery in clean water. Cd, Cu, Zn, Ca, Mg, Fe, Na, K contents and Na/K ratio were measured. In tadpoles exposed exclusively to Cd(2 +) the 96 h LC50 = 3155 microg x L(-1). By contrast in tadpoles exposed to Cd(2 +) and UV for 96 hours the LC50 = 710 microg x L(-1). More cadmium was accumulated in UV-exposed tadpoles. On the other hand tadpoles exposed to UV radiation removed cadmium more efficiently than non-irradiated larvae. Cu, Na, and K were positively correlated with Cd content while Mg was negatively correlated with Cd. Animals exposed to combined stressors had lower Mg, Fe, Ca, Na, Zn contents, lower Na/K ratio and higher Cu and K contents than animals exposed exclusively to cadmium. Our studies indicate that cadmium ions combined with UV significantly increase mortality of common frog tadpoles. This may be related to higher cadmium uptake, disturbances in the content of essential metals and ionic imbalance.

Infrared Detection of HO2 and HO3 Radicals in Water Ice

Infrared spectroscopy has been used to detect HO(2) and HO(3) radicals in H(2)O + O(2) ice mixtures irradiated with 0.8 MeV protons. In these experiments, HO(2) was formed by the addition of an H atom to O(2) and HO(3) was formed by a similar addition of H to O(3). The band positions observed for HO(2) and HO(3) in H(2)O-ice are 1142 and 1259 cm(-1), respectively, and these assignments were confirmed with (18)O(2). HO(2) and HO(3) were also observed in irradiated H(2)O + O(3) ice mixtures, as well as in irradiated H(2)O(2) ice. The astronomical relevance of these laboratory measurements is discussed.

Atmospheric Aerosols: Composition, Transformation, Climate and Health Effects

Aerosols are of central importance for atmospheric chemistry and physics, the biosphere, climate, and public health. The airborne solid and liquid particles in the nanometer to micrometer size range influence the energy balance of the Earth, the hydrological cycle, atmospheric circulation, and the abundance of greenhouse and reactive trace gases. Moreover, they play important roles in the reproduction of biological organisms and can cause or enhance diseases. The primary parameters that determine the environmental and health effects of aerosol particles are their concentration, size, structure, and chemical composition. These parameters, however, are spatially and temporally highly variable. The quantification and identification of biological particles and carbonaceous components of fine particulate matter in the air (organic compounds and black or elemental carbon, respectively) represent demanding analytical challenges. This Review outlines the current state of knowledge, major open questions, and research perspectives on the properties and interactions of atmospheric aerosols and their effects on climate and human health.

Complete conversion of nitrate into dinitrogen gas in co-cultures of denitrifying bacteria

In the past 10 years many molecular aspects of microbial nitrate reduction have been elucidated, but the ecophysiology of this process is hardly understood. In this contribution, our efforts to study the complex microbial communities and interactions involved in the reduction of nitrate to dinitrogen gas are summarized. The initial work concentrated on emission of the greenhouse gas nitrous oxide during incomplete denitrification by Alcaligenes faecalis. As more research methods became available, the fitness of A. faecalis could be tested in mixed cultures with other denitrifying bacteria, most notably with the nitrate-reducing bacterium Pseudomonas G9. Finally, the advancement of molecular diagnostic tools made it possible to survey complex microbial communities using specific primer sets for/and antibodies raised against the various NO(x) reductases. Given the enormous complexity of substrates and environmental conditions, it is evident that mixed cultures rather than single species are responsible for denitrification in man-made and natural ecosystems. However, it is surprising that even for the breakdown of a single compound, such as acetate, mixed cultures are responsible, and that the consecutive denitrification steps are commonly performed by mutualistic co-operating species. Our observations also indicate that we seldom know the identity of the major key players in the nitrogen cycle of these ecosystems.

Tracking nitrate reducers and denitrifiers in the environment

The ability to respire nitrate when oxygen is limited has been described in taxonomically diverse microorganisms including members of the α-, β-, γ- and ε-proteobacteria, high and low GC Gram-positive bacteria and even Archaea. Respiratory nitrate reduction is the first step of the denitrification pathway, which is important since it is the main biological process responsible for the return of fixed nitrogen to the atmosphere, thus completing the nitrogen cycle. During the last decade, considerable knowledge has been accumulated on the biochemistry and genetics of the nitrate reductases. In this paper, we summarize the recent progress in molecular approaches for studying the ecology of the nitrate-reducing community in the environment.

Dynamical variability in the modelling of chemistry–climate interactions

We have used a version of the Met Office's climate model, into which we have introduced schemes for atmospheric chemistry, to study chemistry-dynamics-climate interactions. We have considered the variability of the stratospheric polar vortex, whose behaviour influences stratospheric ozone loss and will affect ozone recovery. In particular, we analyse the dynamical control of high latitude ozone in a model version which includes an assimilation of the equatorial quasi-biennial oscillation (QBO), demonstrating the stability of the linear relation between vortex strength and high latitude ozone. We discuss the effect of interactive model ozone on polar stratospheric cloud (PSC) area/volume and winter-spring stratospheric ozone loss in the northern hemisphere. In general we find larger polar ozone losses calculated in those model integrations in which modelled ozone is used interactively in the radiation scheme, even though we underestimate the slope of the ozone loss per PSC volume relation derived from observations. We have also looked at the influence of changing stratosphere-to-troposphere exchange on the tropospheric oxidizing capacity and, in particular, have considered the variability of tropospheric composition under different climate regimes (El Niño/La Niña, etc.). Focusing on the UT/LS, we show the response of ozone to El Niño in two different model set-ups (tropospheric/ stratospheric). In the stratospheric model set-up we find a distinct signal in the lower tropical stratosphere, which shows an anti-correlation between the Niño 3 index and the ozone column amount. In contrast ozone generally increases in the upper troposphere of the tropospheric model set-up after an El Niño. Understanding future trends in stratospheric ozone and tropospheric oxidizing capacity requires an understanding of natural variability, which we explore here.

Immunological method for direct assessment of the functionality of a denitrifying strain of Pseudomonas fluorescens in soil

This work describes an immunological method for detection and quantification in complex environments of the dissimilative nitrate reductase (NRA) responsible for the reduction of nitrate to nitrite, which plays an important role in ecosystem functioning. The alpha-catalytic subunit of the enzyme was purified from the denitrifying strain Pseudomonas fluorescens YT101 and used for the production of polyclonal antibodies. These antibodies were used to detect and quantify the NRA by a chemifluorescence technique on Western blots after separation of total proteins from pure cultures and soil samples. The specificity, detection threshold and reproducibility of the proposed method were evaluated. A soil experiment showed that our method can be applied to complex environmental samples.

Design and characterization of the balloon-borne Michelson Interferometer for Passive Atmospheric Sounding (MIPAS-B2)

MIPAS-B2 is a balloon-borne limb-emission sounder for atmospheric research. The heart of the instrument is a Fourier spectrometer that covers the mid-infrared spectral range (4-14 microns) and operates at cryogenic temperatures. Essential for this application is the sophisticated line-of-sight stabilization system, which is based on an inertial navigation system and is supplemented with an additional star reference system. The major scientific benefit of the instrument is the simultaneous detection of complete trace gas families in the stratosphere without restrictions concerning the time of day and viewing directions. The specifications, the design considerations, the actual realization of the instrument, and the results of characterization measurements that have been performed are described.

Aquatic ecosystems: effects of solar ultraviolet radiation and interactions with other climatic change factors

Aquatic ecosystems are a key component of the Earth's biosphere. A large number of studies document substantial impact of solar UV radiation on individual species, yet considerable uncertainty remains with respect to assessing impacts on ecosystems. Several studies indicate that the impact of increased UV radiation appears relatively low when considering overall ecosystem response, while, in contrast, effects on individual species show considerable responses. Ecosystem response to climate variability incorporates both synergistic and antagonistic processes with respect to UV-related effects, significantly complicating understanding and prediction at the ecosystem level. The impact of climate variability on UV-related effects often becomes manifest via indirect effects such as reduction in sea ice, changes in water column bio-optical characteristics, changes in cloud cover and shifts in oceanographic biogeochemical provinces.

Denitrifying genes in bacterial and Archaeal genomes

Denitrification, the reduction of nitrate or nitrite to nitrous oxide or dinitrogen, is the major mechanism by which fixed nitrogen returns to the atmosphere from soil and water. Although the denitrifying ability has been found in microorganisms belonging to numerous groups of bacteria and Archaea, the genes encoding the denitrifying reductases have been studied in only few species. Recent investigations have led to the identification of new classes of denitrifying reductases, indicating a more complex genetic basis of this process than previously recognized. The increasing number of genome sequencing projects has opened a new way to study the genetics of the denitrifying process in bacteria and Archaea. In this review, we summarized the current knowledge on denitrifying genes and compared their genetic organizations by using new sequences resulting from the analysis of finished and unfinished microbial genomes with a special attention paid to the clustering of genes encoding different classes of reductases. In addition, some evolutionary relationships between the structural genes are presented.

Arctic "ozone hole" in a cold volcanic stratosphere

Optical depth records indicate that volcanic aerosols from major eruptions often produce clouds that have greater surface area than typical Arctic polar stratospheric clouds (PSCs). A trajectory cloud-chemistry model is used to study how volcanic aerosols could affect springtime Arctic ozone loss processes, such as chlorine activation and denitrification, in a cold winter within the current range of natural variability. Several studies indicate that severe denitrification can increase Arctic ozone loss by up to 30%. We show large PSC particles that cause denitrification in a nonvolcanic stratosphere cannot efficiently form in a volcanic environment. However, volcanic aerosols, when present at low altitudes, where Arctic PSCs cannot form, can extend the vertical range of chemical ozone loss in the lower stratosphere. Chemical processing on volcanic aerosols over a 10-km altitude range could increase the current levels of springtime column ozone loss by up to 70% independent of denitrification. Climate models predict that the lower stratosphere is cooling as a result of greenhouse gas built-up in the troposphere. The magnitude of column ozone loss calculated here for the 1999--2000 Arctic winter, in an assumed volcanic state, is similar to that projected for a colder future nonvolcanic stratosphere in the 2010 decade.