Updating and evaluating the NH3 gas-phase chemical mechanism of MOZART-4 in the WRF-Chem model

The accuracy of determining atmospheric chemical mechanisms is a key factor in air pollution prediction, pollution-cause analysis and the development of control schemes based on air quality model simulations. However, the reaction of NH3 and OH to generate NH2 and its subsequent reactions are often ignored in the MOZART-4 chemical mechanism. To solve this problem, the gas-phase chemical mechanism of NH3 was updated in this study. Response surface methodology (RSM), integrated gas-phase reaction rate (IRR) diagnosis and process analysis (PA) were used to quantify the influence of the updated NH3 chemical mechanism on the O3 simulated concentration, the nonlinear response relationship of O3 and its precursors, the chemical reaction rate of O3 generation and the meteorological transport process. The results show that the updated NH3 chemical mechanism can reduce the error between the simulated and observed O3 concentrations and better simulate the O3 concentration. Compared with the Base scenario (original chemical mechanism simulated), the first-order term of NH3 in the Updated scenario (updated NH3 chemical mechanism simulated) in RSM passed the significance test (p < 0.05), indicating that NH3 emissions have an influence on the O3 simulation, and the effects of the updated NH3 chemical mechanism on NOx-VOC-O3 in different cities are different. In addition, the analysis of chemical reaction rate changes showed that NH3 can affect the generation of O3 by affecting the NOx concentration and NOx circulation with radicals of OH and HO2 in the Updated scenario, and the change of pollutant concentration in the atmosphere leads to the change of meteorological transmission, eventually leading to the reduction of O3 concentration in Beijing. In conclusion, this study highlights the importance of atmospheric chemistry for air quality models to model atmospheric pollutants and should attract more research focus.

Effects of chemical boundary conditions on simulated O3 concentrations in China and their chemical mechanisms

Chemical boundary conditions (BCs) are important inputs for regional chemical transport models. In this study, we use the brute-force method (BFM), process analysis (PA) and response surface model (RSM) to quantify the effects of BCs on simulated O₃ concentrations in different regions of China by the weather research and forecasting with chemistry (WRF-Chem) model. We combine the model with an integrated gas-phase reaction rate (IRR) tool to further analyze the changes in the O₃ chemical mechanisms. Our results show that the simulated O₃ concentrations in western cities are significantly affected by the O₃ in the BCs (BC-O₃), which can increase the maximum simulated O₃ concentration, such as in Lanzhou (36.6 μg/m³, 26.3 %), Wuhai (30.1 μg/m³, 25.5 %) and Urumqi (50.7 μg/m³, 41.2 %). In contrast, O₃ generation in the eastern region is dominated by emissions. Subsequently, we compare the reaction rate changes in O₃ generation and consumption under the effects of BC-O₃ in the western city of Urumqi and the eastern city of Beijing. The results show that in Beijing, the O₃ concentration and the related chemical reaction rates undergo little change, while in Urumqi, the concentration and reaction rates have significant differences. The BC-O₃ significantly accelerates the O₃ photochemical reaction process in Urumqi, resulting in increased O₃ generation and consumption reaction rates; additionally, there may be a chemical reaction pathway for the formation of O₃: BC-O₃ + NO → NO₂ + hv → O + O₂ → O₃. BC-O₃ transmission is the main pathway of changes in the simulated O₃ concentration in the study area, and the chemical reactions between BC-O₃ and local pollutants are primarily characterized by O₃ consumption. In conclusion, the study shows the importance of BCs for regional model simulation while providing supporting information for O₃ formation in model studies.

A previously uncharacterized, nonphotosynthetic member of the Chromatiaceae is the primary CO2-fixing constituent in a self-regenerating biocathode

Biocathode extracellular electron transfer (EET) may be exploited for biotechnology applications, including microbially mediated O2 reduction in microbial fuel cells and microbial electrosynthesis. However, biocathode mechanistic studies needed to improve or engineer functionality have been limited to a few select species that form sparse, homogeneous biofilms characterized by little or no growth. Attempts to cultivate isolates from biocathode environmental enrichments often fail due to a lack of some advantage provided by life in a consortium, highlighting the need to study and understand biocathode consortia in situ. Here, we present metagenomic and metaproteomic characterization of a previously described biocathode biofilm (+310 mV versus a standard hydrogen electrode [SHE]) enriched from seawater, reducing O2, and presumably fixing CO2 for biomass generation. Metagenomics identified 16 distinct cluster genomes, 15 of which could be assigned at the family or genus level and whose abundance was roughly divided between Alpha- and Gammaproteobacteria. A total of 644 proteins were identified from shotgun metaproteomics and have been deposited in the the ProteomeXchange with identifier PXD001045. Cluster genomes were used to assign the taxonomic identities of 599 proteins, with Marinobacter, Chromatiaceae, and Labrenzia the most represented. RubisCO and phosphoribulokinase, along with 9 other Calvin-Benson-Bassham cycle proteins, were identified from Chromatiaceae. In addition, proteins similar to those predicted for iron oxidation pathways of known iron-oxidizing bacteria were observed for Chromatiaceae. These findings represent the first description of putative EET and CO2 fixation mechanisms for a self-regenerating, self-sustaining multispecies biocathode, providing potential targets for functional engineering, as well as new insights into biocathode EET pathways using proteomics.

Thunderstorms: an important mechanism in the transport of air pollutants

Acid deposition and photochemical smog are urban air pollution problems, and they remain localized as long as the sulfur, nitrogen, and hydrocarbon pollutants are confined to the lower troposphere (below about 1-kilometer altitude) where they are short-lived. If, however, the contaminants are rapidly transported to the upper troposphere, then their atmospheric residence times grow and their range of influence expands dramatically. Although this vertical transport ameliorates some of the effects of acid rain by diluting atmospheric acids, it exacerbates global tropospheric ozone production by redistributing the necessary nitrogen catalysts. Results of recent computer simulations suggest that thunderstorms are one means of rapid vertical transport. To test this hypothesis, several research aircraft near a midwestern thunderstrom measured carbon monoxide, hydrocarbons, ozone, and reactive nitrogen compounds. Their concentrations were much greater in the outflow region of the storm, up to 11 kilometers in altitude, than in surrounding air. Trace gas measurements can thus be used to track the motion of air in and around a cloud. Thunderstorms may transform local air pollution problems into regional or global atmospheric chemistry problems.

Distribution, diversity and ecology of aerobic CO-oxidizing bacteria

Numerous studies indicate that carbon monoxide (CO) participates in a broader range of processes than any other single molecule, ranging from subcellular to planetary scales. Despite its toxicity to many organisms, a diverse group of bacteria that span multiple phylogenetic lineages metabolize CO. These bacteria are globally distributed and include pathogens, plant symbionts and biogeochemically important lineages in soils and the oceans. New molecular and isolation techniques, as well as genome sequencing, have greatly expanded our knowledge of the diversity of CO oxidizers. Here, we present a newly emerging picture of the distribution, diversity and ecology of aerobic CO-oxidizing bacteria.

Atmospheric depositions around a heavily industrialized area in a seasonally dry tropical environment of India

Clear and through-fall bulk depositions were collected in the downwind of a highly industrialized region in Sonbhadra district of India to estimate the influence of anthropogenic activities on chemical composition of depositions. Significant spatial and temporal variations in depositions of cations and anions were observed. Depositions were higher near the thermal power stations and coal mines as compared to distantly situated site. Seasonally summer samples showed maximum cation and anion depositions followed by winter and minimum in rainy season. The mean pH of the depositions indicates that rainfall in the area is alkaline. Among the anions, maximum deposition was recorded for SO4(2-) followed by NO3- and minimum for Cl-. Among the cations, Ca2+ deposition was maximum followed by NH4+. Na+, K+ and Mg2+ deposition rates showed more or less similar values. The depositions of cations and anions as well as pH were higher in through-fall than clear-fall samples. Results of the present study suggest that atmospheric depositions are strongly modified due to thermal power stations and coal mines in the area.

Trifluoromethoxycarbonyl Peroxynitrate, CF3OC(O)OONO2

The trioxide, CF(3)OC(O)OOOC(O)OCF(3), reacts with NO(2) at 0 degrees C to yield the new peroxynitrate, CF(3)OC(O)OONO(2), which is stable for hours at room temperature. It is spectroscopically characterized and some thermal properties are reported. From the vapor pressure, ln(p/p(0)) = 14.06 - 4565/T, of the liquid above the melting point of -89 degrees C, the extrapolated boiling point is 52 degrees C. CF(3)OC(O)OONO(2) dissociates at higher temperatures and low pressures into the radicals CF(3)OC(O)OO and NO(2) as demonstrated by matrix isolation experiments. The matrix-isolated peroxy radicals consist in a rotameric mixture of trans,trans,trans-CF(3)OC(O)OO and trans,trans,cis-CF(3)OC(O)OO, where trans and cis denote dihedral angles of ca. 180 degrees and 0 degree, respectively, around beta F-C-O-C, beta C-O-C-O, and beta O-C-O-O, with an equilibrium composition dependent on the thermolysis temperature. The radical trans,trans,cis-CF(3)OC(O)OO is found to be ca. 3 kJ mol(-1) higher in enthalpy than trans,trans,trans-CF(3)OC(O)OO. DFT calculations are performed to support the vibrational assignments and to provide structural information about CF(3)OC(O)OONO(2).

Molecular and culture-based analyses of aerobic carbon monoxide oxidizer diversity

Isolates belonging to six genera not previously known to oxidize CO were obtained from enrichments with aquatic and terrestrial plants. DNA from these and other isolates was used in PCR assays of the gene for the large subunit of carbon monoxide dehydrogenase (coxL). CoxL and putative coxL fragments were amplified from known CO oxidizers (e.g., Oligotropha carboxidovorans and Bradyrhizobium japonicum), from novel CO-oxidizing isolates (e.g., Aminobacter sp. strain COX, Burkholderia sp. strain LUP, Mesorhizobium sp. strain NMB1, Stappia strains M4 and M8, Stenotrophomonas sp. strain LUP, and Xanthobacter sp. strain COX), and from several well-known isolates for which the capacity to oxidize CO is reported here for the first time (e.g., Burkholderia fungorum LB400, Mesorhizobium loti, Stappia stellulata, and Stappia aggregata). PCR products from several taxa, e.g., O. carboxidovorans, B. japonicum, and B. fungorum, yielded sequences with a high degree (>99.6%) of identity to those in GenBank or genome databases. Aligned sequences formed two phylogenetically distinct groups. Group OMP contained sequences from previously known CO oxidizers, including O. carboxidovorans and Pseudomonas thermocarboxydovorans, plus a number of closely related sequences. Group BMS was dominated by putative coxL sequences from genera in the Rhizobiaceae and other alpha-PROTEOBACTERIA: PCR analyses revealed that many CO oxidizers contained two coxL sequences, one from each group. CO oxidation by M. loti, for which whole-genome sequencing has revealed a single BMS-group putative coxL gene, strongly supports the notion that BMS sequences represent functional CO dehydrogenase proteins that are related to but distinct from previously characterized aerobic CO dehydrogenases.

Soil-atmosphere CO exchanges and microbial biogeochemistry of CO transformations in a Brazilian agricultural ecosystem

Although anthropogenic land use has major impacts on the exchange of soil and atmosphere gas in general, relatively little is known about its impacts on carbon monoxide. We compared soil-atmosphere CO exchanges as a function of land use, crop type, and tillage treatment on an experimental farm in Parãna, Brazil, that is representative of regionally important agricultural ecosystems. Our results showed that cultivated soils consumed CO at rates between 3 and 6 mg of CO m(-2) day(-1), with no statistically significant effect of tillage method or crop. However, CO exchange for a pasture soil was near zero, and an unmanaged woodlot emitted CO at a rate of 9 mg of CO m(-2) day(-1). Neither nitrite, aluminum sulfate, nor methyl fluoride additions affected CO consumption by tilled or untilled soils from soybean plots, indicating that CO oxidation did not depend on ammonia oxidizers and that CO oxidation patterns differed in part from patterns reported for forest soils. The apparent K(m) for CO uptake, 5 to 11 ppm, was similar to values reported for temperate forest soils; V(max) values, approximately 1 micro g of CO g (dry weight)(-1) h(-1), were comparable for woodlot and cultivated soils in spite of the fact that the latter consumed CO under ambient conditions. Short-term (24-h) exposure to elevated levels of CO (10% CO) partially inhibited uptake at lower concentrations (i.e., 100 ppm), suggesting that the sensitivity to CO of microbial populations that are active in situ differs from that of known carboxydotrophs. Soil-free soybean and corn roots consumed CO when they were incubated with 100-ppm concentrations and produced CO when they were incubated with ambient concentrations. These results document for the first time a role for cultivated plant roots in the dynamics of CO in an agricultural ecosystem.

Enrichment of high-affinity CO oxidizers in Maine forest soil

Carboxydotrophic activity in forest soils was enriched by incubation in a flowthrough system with elevated concentrations of headspace CO (40 to 400 ppm). CO uptake increased substantially over time, while the apparent K(m) ((app)K(m)) for uptake remained similar to that of unenriched soils (<10 to 20 ppm). Carboxydotrophic activity was transferred to and further enriched in sterile sand and forest soil. The (app)K(m)s for secondary and tertiary enrichments remained similar to values for unenriched soils. CO uptake by enriched soil and freshly collected forest soil was inhibited at headspace CO concentrations greater than about 1%. A novel isolate, COX1, obtained from the enrichments was inhibited similarly. However, in contrast to extant carboxydotrophs, COX1 consumed CO with an (app)K(m) of about 15 ppm, a value comparable to that of fresh soils. Phylogenetic analysis based on approximately 1,200 bp of its 16S rRNA gene sequence suggested that the isolate is an alpha-proteobacterium most closely related to the genera Pseudaminobacter, Aminobacter, and Chelatobacter (98.1 to 98.3% sequence identity).

Carbon monoxide production is not enhanced by nitrogenase activity

A diverse group of nitrogen-fixing bacteria and two heme degraders were grown with and without fixed nitrogen sources under oxic and suboxic conditions, with and without addition of heme-containing compounds. Several of the strains produced carbon monoxide (CO) under one or more of these conditions, but nitrogenase activity did not stimulate rates of production relative to controls. Although nitrogenase can reduce CO(2) to CO in vitro in the absence of N(2), this process likely contributes minimally to CO production in soils under in situ conditions. In contrast, myoglobin or hematin addition under oxic conditions significantly stimulated CO production by the heme degraders. However, estimates of CO production from microbial heme turnover suggest that this too is likely to be only a small source of CO in soils in situ.

Attributes of atmospheric carbon monoxide oxidation by Maine forest soils

CO, one of the most important trace gases, regulates tropospheric methane, hydroxyl radical, and ozone contents. Ten to 25% of the estimated global CO flux may be consumed by soils annually. Depth profiles for (14)CO oxidation and CO concentration indicated that CO oxidation occurred primarily in surface soils and that photooxidation of soil organic matter did not necessarily contribute significantly to CO fluxes. Kinetic analyses revealed that the apparent K(m) was about 18 nM (17 ppm) and the V(max) was 6.9 micromol g (fresh weight)(-1) h(-1); the apparent K(m) was similar to the apparent K(m) for atmospheric methane consumption, but the V(max) was more than 100 times higher. Atmospheric CO oxidation responded sensitively to soil water regimes; decreases in water content in initially saturated soils resulted in increased uptake, and optimum uptake occurred at water contents of 30 to 60%. However, extended drying led to decreased uptake and net CO production. Rewetting could restore CO uptake, albeit with a pronounced hysteresis. The responses to changing temperatures indicated that the optimum temperature for net uptake was between 20 and 25 degrees C and that there was a transition to net production at temperatures above 30 degrees C. The responses to methyl fluoride and acetylene indicated that populations other than ammonia oxidizers and methanotrophs must be involved in forest soils. The response to acetylene was notable, since the strong initial inhibition was reversed after 12 h of incubation; in contrast, methyl fluoride did not have an inhibitory effect. Ammonium did not inhibit CO uptake; the level of nitrite inhibition was initially substantial, but nitrite inhibition was reversible over time. Nitrite inhibition appeared to occur through indirect effects based on abiological formation of NO.