Significant amounts of ethanol are produced from biofuel crops such as corn and, in the future, likely switchgrass. The atmospheric effects of growing these plant species on a large scale are investigated here by measuring the plant-atmosphere exchange of volatile organic compounds (VOCs). Field grown corn and switchgrass emit VOCs at flux rates of 4.4 nmol(C) m(-2) s(-1) (10(-9) mol carbon per square meter leaf area per second) and 2.4 nmol(C) m(-2) s(-1), respectively. Methanol contributes 60% to the molar flux but small emissions of carbonyls, aromatic compounds and terpenoids are relatively more important for potential air quality impacts. Switchgrass can act as a sink for carbonyls and aromatic compounds with compensation points of a few hundred pptv. In switchgrass moderate drought stress may induce enhanced emissions of monoterpenes, carbonyls and aromatics. Per liter of fuel ethanol produced, the estimated VOC emissions associated with the biomass growth of corn (7.8 g l(-1)) or switchgrass (6.2 g l(-1)) are in the same range as the VOC emissions from the use of one liter gasoline in vehicle engines. VOC emissions from the growing of biofuel crops can therefore be a significant contributor to the VOC emissions in the life cycle of biofuels. The VOC emissions from corn and switchgrass are small compared to those of tree species suggested as biofuel crops. Due to their reactivity with respect to OH the emissions from corn and switchgrass are not likely to have a significant impact on regional ozone formation. (c) 2011 Elsevier Ltd. All rights reserved.

Volatile organic compound (VOC) emissions from elephant grass (Miscanthus gigantus) and black bamboo (Phyllostachys nigra) were measured online in semi-field chamber and plant enclosure experiments during growth and harvest using proton-transfer reaction mass spectrometry (PTR-MS), proton-transfer reaction ion-trap mass spectrometry (PIT-MS) and gas chromatography-mass spectrometry (GC–MS). Both cultivars are being considered for second-generation biofuel production. Before this study, no information was available on their yearly VOC emissions. This exploratory investigation shows that black bamboo is a strong isoprene emitter (daytime 28,516 ng gdwt−1 h−1) and has larger VOC emissions, especially for wound compounds from the hexanal and hexenal families, than elephant grass. Daytime emissions of methanol, acetaldehyde, acetone + propanal and acetic acid of black bamboo were 618, 249, 351, and 1034 ng gdwt−1 h−1, respectively. In addition, it is observed that elephant grass VOC emissions after harvesting strongly depend on the seasonal stage. Not taking VOC emission variations throughout the season for annual and perennial species into account, may lead to an overestimation of the impact on local air quality in dry periods. In addition, our data suggest that the use of perennial grasses for extensive growing for biofuel production have lower emissions than woody species, which might be important for regional atmospheric chemistry.

The mevalonic acid (MVA) and methylerythritol phosphate (MEP) pathways for isoprenoid biosynthesis both culminate in the production of the two-five carbon prenyl diphosphates: dimethylallyl diphosphate (DMAPP) and isopentenyl diphosphate (IPP). These are the building blocks for higher isoprenoids, including many that have industrial and pharmaceutical applications. With growing interest in producing commercial isoprenoids through microbial engineering, reports have appeared of toxicity associated with the accumulation of prenyl diphosphates in Escherichia coli expressing a heterologous MVA pathway. Here we explored whether similar prenyl diphosphate toxicity, related to MEP pathway flux, could also be observed in the bacterium Bacillus subtilis. After genetic and metabolic manipulations of the endogenous MEP pathway in B. subtilis, measurements of cell growth, MEP pathway flux, and DMAPP contents suggested cytotoxicity related to prenyl diphosphate accumulation. These results have implications as to understanding the factors impacting isoprenoid biosynthesis in microbial systems.

Volatile organic compound (VOC) emission rates during the growth and simulated harvest phases were determined for switchgrass (Panicum virgatum) using laboratory chamber measurements. Switchgrass is a candidate for use in second-generation (cellulosic) biofuel production and the acreage dedicated to its growth in the USA has already increased during the past decade. We estimate that the yearly emissions from switchgrass plantations, including both the growth and harvest phases will be on the order of 3 kg C ha(-1) methanol, 1 kg C ha(-1) acetaldehyde, 1 kg C ha(-1) acetone, 0.9 kg C ha(-1) monoterpenes, 0.5 kg C ha(-1) isoprene + another compound, most likely 1-penten-3-ol, 0.2 kg C ha(-1) hexenals, and 0.1 kg C ha(-1) hexenols. These emission rates are much lower than those expected from Eucalyptus or poplar plantations, which are other potential biofuel crops and have significantly higher VOC emissions, suggesting that the choice of species in the production of biofuels could have serious implications for regional air quality. (C) 2011 Elsevier Ltd. All rights reserved.

Volatile organic compound (VOC) mixing ratios were measured with two different instruments at the T1 ground site in Mexico City during the Megacity Initiative: Local and Global Research Observations (MILAGRO) campaign in March of 2006. A gas chromatograph with flame ionization detector (GC-FID) quantified 18 light alkanes, alkenes and acetylene while a proton-transfer-reaction ion-trap mass spectrometer (PIT-MS) quantified 12 VOC species including oxygenated VOCs (OVOCs) and aromatics. A GC separation system was used in conjunction with the PIT-MS (GC-PIT-MS) to evaluate PIT-MS measurements and to aid in the identification of unknown VOCs. The VOC measurements are also compared to simultaneous canister samples and to two independent proton-transfer-reaction mass spectrometers (PTR-MS) deployed on a mobile and an airborne platform during MILAGRO. VOC diurnal cycles demonstrate the large influence of vehicle traffic and liquid propane gas (LPG) emissions during the night and photochemical processing during the afternoon. Emission ratios for VOCs and OVOCs relative to CO are derived from early-morning measurements. Average emission ratios for non-oxygenated species relative to CO are on average a factor of ~2 higher than measured for US cities. Emission ratios for OVOCs are estimated and compared to literature values the northeastern US and to tunnel studies in California. Positive matrix factorization analysis (PMF) is used to provide insight into VOC sources and processing. Three PMF factors were distinguished by the analysis including the emissions from vehicles, the use of liquid propane gas and the production of secondary VOCs + long-lived species. Emission ratios to CO calculated from the results of PMF analysis are compared to emission ratios calculated directly from measurements. The total PIT-MS signal is summed to estimate the fraction of identified versus unidentified VOC species.

We have recently characterized sliding motility in Bacillus subtilis strains that lack functional flagella, and here describe the discovery of inhibitors of colony spreading in these strains as well as the aflagellate pathogen, Bacillus anthracis. Aflagellate B. subtilis strains were used to screen for new types of antibacterials that might inhibit colony spreading on semi-solid media. From a diverse set of organic structures, p-nitrophenylglycerol (NPG), an agent used primarily in clinical laboratories to control Proteus swarming, was found to inhibit colony spreading. The four stereoisomers of NPG were synthesized and tested, and only the 1R,2S-(1R-anti) and 1R,2R-(1R-syn) NPG isomers had significant activity in a quantitative colony spreading assay. Twenty-six NPG analogs and related structures were synthesized and tested to identify more active inhibitors. p-Methylsulfonylphenylglycerol (p-SPG), but not its ortho or meta analogs, was found to be the most effective of these compounds, and synthesis and testing of all four p-SPG stereoisomers showed that the 1R-anti-isomer was the most active with an average IC50 of 16 mu M (3-5 mu g mL (1)). For B. anthracis, the colony-spreading IC50 values for 1R-anti-SPG and 1R-anti-NPG are 12 mu M (2-4 mu g mL (1)) and >150 mu M, respectively. For both Bacillus species tested, 1R-anti-SPG inhibits colony spreading of surface cultures on agar plates, but is not bacteriostatic or bacteriocidal in liquid cultures. Work is in progress to find the cellular target(s) of the NPG/SPG class of compounds, since this could lead to an understanding of the mechanism(s) of colony spreading as well as design and development of more potent inhibitors for the control of B. anthracis surface cultures. (C) 2011 Elsevier Ltd. All rights reserved.

We measured isocyanic acid (HNCO) in laboratory biomass fires at levels up to 600 parts per billion by volume (ppbv), demonstrating that it has a significant source from pyrolysis/combustion of biomass. We also measured HNCO at mixing ratios up to 200 pptv (parts-per-trillion by volume) in ambient air in urban Los Angeles, CA, and in Boulder, CO, during the recent 2010 Fourmile Canyon fire. Further, our measurements of aqueous solubility show that HNCO is highly soluble, as it dissociates at physiological pH. Exposure levels > 1 ppbv provide a direct source of isocyanic acid and cyanate ion (NCO - ) to humans at levels that have recognized health effects: atherosclerosis, cataracts, and rheumatoid arthritis, through the mechanism of protein carbamylation. In addition to the wildland fire and urban sources, we observed HNCO in tobacco smoke, HNCO has been reported from the low-temperature combustion of coal, and as a by-product of urea-selective catalytic reduction (SCR) systems that are being phased-in to control on-road diesel NO x emissions in the United States and the European Union. Given the current levels of exposure in populations that burn biomass or use tobacco, the expected growth in biomass burning emissions with warmer, drier regional climates, and planned increase in diesel SCR controls, it is imperative that we understand the extent and effects of this HNCO exposure.

ABSTRACT Bacteria and fungi are ubiquitous in the atmosphere. The diversity and abundance of airborne microbes may be strongly influenced by atmospheric conditions or even influence atmospheric conditions themselves by acting as ice nucleators. However, few comprehensive studies have described the diversity and dynamics of airborne bacteria and fungi based on culture-independent techniques. We document atmospheric microbial abundance, community composition, and ice nucleation at a high-elevation site in northwestern Colorado. We used a standard small-subunit rRNA gene Sanger sequencing approach for total microbial community analysis and a bacteria-specific 16S rRNA bar-coded pyrosequencing approach (4,864 sequences total). During the 2-week collection period, total microbial abundances were relatively constant, ranging from 9.6 × 10 5 to 6.6 × 10 6 cells m −3 of air, and the diversity and composition of the airborne microbial communities were also relatively static. Bacteria and fungi were nearly equivalent, and members of the proteobacterial groups Burkholderiales and Moraxellaceae (particularly the genus Psychrobacter ) were dominant. These taxa were not always the most abundant in freshly fallen snow samples collected at this site. Although there was minimal variability in microbial abundances and composition within the atmosphere, the number of biological ice nuclei increased significantly during periods of high relative humidity. However, these changes in ice nuclei numbers were not associated with changes in the relative abundances of the most commonly studied ice-nucleating bacteria.

Growing tendrils of aflagellate hag mutants of Bacillus subtilis were found to show an avoidance response when colonizing a semi-solid medium, suggesting a tip-to-tip communication mechanism between colonies. There may be a second sensing mechanism involved in shaping the morphology of tendrils. Tendril growth in B. subtilis was dependent on and possibly shaped by the release of surfactin, a biosurfactant. Transposon mutagenesis yielded two mutants with 'touching' tendrils, and each had a disrupted gspA gene that encodes a putative glycosyltransferase. Tendrils of gspA mutants, unlike the parental strain, were unresponsive to tendril tip growth by surfactin, suggesting disruption of intercellular signaling. Tendril sensing and avoidance could be physiologically relevant in habitats, such as plant roots, where some limiting nutrient might induce this type of multicellular behavior, promoting avoidance of previously explored areas by sibling colonies.

Leaves of Populus deltoides emit acetaldehyde under various conditions, and we have discovered that leaf veins and petioles, seen in this image, contain the enzyme pyruvate decarboxylase (PDC), which produces acetaldehyde as a product. We have purified leaf vein PDC 143-fold, and it appears to act as a high affinity PDC, operating under the semi-aerobic conditions occurring in vascular bundles.

There is considerable interest in modeling isoprene emissions from terrestrial vegetation, because these emissions exert a principal control over the oxidative capacity of the troposphere. We used a unique field experiment that employs a continuous gradient in CO2 concentration from 240 to 520 ppmv to demonstrate that isoprene emissions in Eucalyptus globulus were enhanced at the lowest CO2 concentration, which was similar to the estimated CO2 concentrations during the last Glacial Maximum, compared with 380 ppmv, the current CO2 concentration. Leaves of Liquidambar styraciflua did not show an increase in isoprene emission at the lowest CO2 concentration. However, isoprene emission rates from both species were lower for trees grown at 520 ppmv CO2 compared with trees grown at 380 ppmv CO2. When grown in environmentally controlled chambers, trees of Populus deltoides and Populus tremuloides exhibited a 30-40% reduction in isoprene emission rate when grown at 800 ppmv CO2, compared with 400 ppmv CO2. P. tremuloides exhibited a 33% reduction when grown at 1200 ppmv CO2, compared with 600 ppmv CO2. We used current models of leaf isoprene emission to demonstrate that significant errors occur if the CO2 inhibition of isoprene is not taken into account. In order to alleviate these errors, we present a new model of isoprene emission that describes its response to changes in atmospheric CO2 concentration. The model logic is based on assumed competition between cytosolic and chloroplastic processes for pyruvate, one of the principal substrates of isoprene biosynthesis.

Growing tendrils of aflagellate hag mutants of Bacillus subtilis were found to show an avoidance response when colonizing a semi-solid medium, suggesting a tip-to-tip communication mechanism between colonies. There may be a second sensing mechanism involved in shaping the morphology of tendrils. Tendril growth in B. subtilis was dependent on and possibly shaped by the release of surfactin, a biosurfactant. Transposon mutagenesis yielded two mutants with 'touching' tendrils, and each had a disrupted gspA gene that encodes a putative glycosyltransferase. Tendrils of gspA mutants, unlike the parental strain, were unresponsive to tendril tip growth by surfactin, suggesting disruption of intercellular signaling. Tendril sensing and avoidance could be physiologically relevant in habitats, such as plant roots, where some limiting nutrient might induce this type of multicellular behavior, promoting avoidance of previously explored areas by sibling colonies.

We have developed a negative-ion proton-transfer chemical-ionization mass spectrometry (NI-PT-CIMS) technique for on-line analysis of gaseous organic and inorganic acids. In this detection scheme, acetate ions (CH3C(O)O−) react very selectively with atmospheric trace acids, by proton transfer, to produce unique product ion species. We tested this ion chemistry for 11 species of which only four showed measurable fragmentation. We investigated both the time response of the inlet and humidity dependence for both formic acid and pyruvic acid measurements. A formic acid calibration was performed and found a sensitivity of 21±4.3 counts per second per pptv. Formic acid measurements made during two separate informal ambient air intercomparisons: (1) with a quantum cascade IR laser absorption system (QCL) and (2) a proton-transfer reaction mass spectrometer (PTR-MS) show good agreement validating this measurement technique. The measurements of the NI-PT-CIMS and PTR-MS agree to within 5% with a high degree of correlation (r2>0.93). We have found the NI-PT-CIMS detection limit for formic acid is approximately 80–90pptv for a 1s integration period, and is currently limited by the formate background in the instrument. The fast time response and high sensitivity of the NI-PT-CIMS method make it a promising technique for the measurement of organic acids in ambient conditions.

Coupled surface–atmosphere models are being used with increased frequency to make predictions of tropospheric chemistry on a ‘future’ earth characterized by a warmer climate and elevated atmospheric CO2 concentration. One of the key inputs to these models is the emission of isoprene from forest ecosystems. Most models in current use rely on a scheme by which global change is coupled to changes in terrestrial net primary productivity (NPP) which, in turn, is coupled to changes in the magnitude of isoprene emissions. In this study, we conducted measurements of isoprene emissions at three prominent global change experiments in the United States. Our results showed that growth in an atmosphere of elevated CO2 inhibited the emission of isoprene at levels that completely compensate for possible increases in emission due to increases in aboveground NPP. Exposure to a prolonged drought caused leaves to increase their isoprene emissions despite reductions in photosynthesis, and presumably NPP. Thus, the current generation of models intended to predict the response of isoprene emission to future global change probably contain large errors. A framework is offered as a foundation for constructing new isoprene emission models based on the responses of leaf biochemistry to future climate change and elevated atmospheric CO2 concentrations.

Abstract Background We have recently shown that undomesticated strains of Bacillus subtilis can extensively colonize the surfaces of rich, semi-solid media, by a flagellum-independent mechanism and suggested that sliding motility is responsible for surface migration. Here we have used a flagella-less hag null mutant to examine and confirm sliding motility. Results Using a defined semi-solid medium we determined that a B. subtilis hag mutant colonized the surface in two stages, first as tendril-like clusters of cells followed by a profuse pellicle-like film. We determined the levels of macro- and micro-nutrients required for the tendril-to-film transition. Sufficient levels of each of the macronutrients, glycerol, Na-glutamate, and Na-phosphate, and inorganic nutrients, K+, Mg2+, Fe2+ and Mn2+, were required for robust film formation. The K+ requirement was quantified in more detail, and the thresholds for complete tendril coverage (50 μM KCl) or film coverage (2–3 mM KCl) were determined. In addition, disruption of the genes for the higher affinity K+ transporter (KtrAB), but not the lower affinity K+ transporter (KtrCD), strongly inhibited the formation of both tendrils and films, and could be partially overcome by high levels of KCl. Examination of hag tendrils by confocal scanning laser microscopy revealed that tendrils are multicellular structures, but that the cells are not as highly organized as cells in wild-type B. subtilis pellicles. Conclusion These results suggest that B. subtilis can use sliding motility to colonize surfaces, using a tendril-like growth mode when various macronutrients or micronutrients are limiting. If nutrients are balanced and sufficient, the surfaces between tendrils can be colonized by robust surface films. Sliding motility may represent a strategy for nutrient-deprived cells to colonize surfaces in natural environments, such as plant roots, and the media described here may be useful in investigations of this growth phenotype.