Stephanie L. Shaw

Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation

The marine unicellular cyanobacterium Prochlorococcus is the smallest-known oxygen-evolving autotroph. It numerically dominates the phytoplankton in the tropical and subtropical oceans, and is responsible for a significant fraction of global photosynthesis. Here we compare the genomes of two Prochlorococcus strains that span the largest evolutionary distance within the Prochlorococcus lineage and that have different minimum, maximum and optimal light intensities for growth. The high-light-adapted ecotype has the smallest genome (1,657,990 base pairs, 1,716 genes) of any known oxygenic phototroph, whereas the genome of its low-light-adapted counterpart is significantly larger, at 2,410,873 base pairs (2,275 genes). The comparative architectures of these two strains reveal dynamic genomes that are constantly changing in response to myriad selection pressures. Although the two strains have 1,350 genes in common, a significant number are not shared, and these have been differentially retained from the common ancestor, or acquired through duplication or lateral transfer. Some of these genes have obvious roles in determining the relative fitness of the ecotypes in response to key environmental variables, and hence in regulating their distribution and abundance in the oceans.

Isoprene Epoxydiols as Precursors to Secondary Organic Aerosol Formation: Acid-Catalyzed Reactive Uptake Studies with Authentic Compounds

Isoprene epoxydiols (IEPOX), formed from the photooxidation of isoprene under low-NO(x) conditions, have recently been proposed as precursors of secondary organic aerosol (SOA) on the basis of mass spectrometric evidence. In the present study, IEPOX isomers were synthesized in high purity (>99%) to investigate their potential to form SOA via reactive uptake in a series of controlled dark chamber studies followed by reaction product analyses. IEPOX-derived SOA was substantially observed only in the presence of acidic aerosols, with conservative lower-bound yields of 4.7-6.4% for β-IEPOX and 3.4-5.5% for δ-IEPOX, providing direct evidence for IEPOX isomers as precursors to isoprene SOA. These chamber studies demonstrate that IEPOX uptake explains the formation of known isoprene SOA tracers found in ambient aerosols, including 2-methyltetrols, C(5)-alkene triols, dimers, and IEPOX-derived organosulfates. Additionally, we show reactive uptake on the acidified sulfate aerosols supports a previously unreported acid-catalyzed intramolecular rearrangement of IEPOX to cis- and trans-3-methyltetrahydrofuran-3,4-diols (3-MeTHF-3,4-diols) in the particle phase. Analysis of these novel tracer compounds by aerosol mass spectrometry (AMS) suggests that they contribute to a unique factor resolved from positive matrix factorization (PMF) of AMS organic aerosol spectra collected from low-NO(x), isoprene-dominated regions influenced by the presence of acidic aerosols.

Real-Time Continuous Characterization of Secondary Organic Aerosol Derived from Isoprene Epoxydiols in Downtown Atlanta, Georgia, Using the Aerodyne Aerosol Chemical Speciation Monitor

Real-time continuous chemical measurements of fine aerosol were made using an Aerodyne Aerosol Chemical Speciation Monitor (ACSM) during summer and fall 2011 in downtown Atlanta, Georgia. Organic mass spectra measured by the ACSM were analyzed by positive matrix factorization (PMF), yielding three conventional factors: hydrocarbon-like organic aerosol (HOA), semivolatile oxygenated organic aerosol (SV-OOA), and low-volatility oxygenated organic aerosol (LV-OOA). An additional OOA factor that contributed to 33 ± 10% of the organic mass was resolved in summer. This factor had a mass spectrum that strongly correlated (r(2) = 0.74) to that obtained from laboratory-generated secondary organic aerosol (SOA) derived from synthetic isoprene epoxydiols (IEPOX). Time series of this additional factor is also well correlated (r(2) = 0.59) with IEPOX-derived SOA tracers from filters collected in Atlanta but less correlated (r(2) < 0.3) with a methacrylic acid epoxide (MAE)-derived SOA tracer, α-pinene SOA tracers, and a biomass burning tracer (i.e., levoglucosan), and primary emissions. Our analyses suggest IEPOX as the source of this additional factor, which has some correlation with aerosol acidity (r(2) = 0.3), measured as H(+) (nmol m(-3)), and sulfate mass loading (r(2) = 0.48), consistent with prior work showing that these two parameters promote heterogeneous chemistry of IEPOX to form SOA.

Characterization and Quantification of Isoprene-Derived Epoxydiols in Ambient Aerosol in the Southeastern United States

Isoprene-derived epoxydiols (IEPOX) are identified in ambient aerosol samples for the first time, together with other previously identified isoprene tracers (i.e., 2-methyltetrols, 2-methylglyceric acid, C(5)-alkenetriols, and organosulfate derivatives of 2-methyltetrols). Fine ambient aerosol collected in downtown Atlanta, GA and rural Yorkville, GA during the 2008 August Mini-Intensive Gas and Aerosol Study (AMIGAS) was analyzed using both gas chromatography/quadrupole mass spectrometry (GC/MS) and gas chromatography/time-of-flight mass spectrometry (GC/TOFMS) with prior trimethylsilylation. Mass concentrations of IEPOX ranged from approximately 1 to 24 ng m(-3) in the aerosol collected from the two sites. Detection of particle-phase IEPOX in the AMIGAS samples supports recent laboratory results that gas-phase IEPOX produced from the photooxidation of isoprene under low-NO(x) conditions is a key precursor of ambient isoprene secondary organic aerosol (SOA) formation. On average, the sum of the mass concentrations of IEPOX and the measured isoprene SOA tracers accounted for about 3% of the organic carbon, demonstrating the significance of isoprene oxidation to the formation of ambient aerosol in this region.

Isoprene production by Prochlorococcus, a marine cyanobacterium, and other phytoplankton

Abstract The oceans are a small source of light (C2–C6) non-methane hydrocarbons (NMHC), which influence the photo-oxidant chemistry of the remote marine atmosphere. Previous work has shown that water column sources of alkenes include photochemical processes, and that various phytoplankton species can produce isoprene. However, only a few phytoplankton species have been studied, and no assessment has been performed of the effects of other pelagic microorganisms on NMHC cycling. The dependence of phytoplanktonic isoprene production on light, temperature, and organism size has also not been investigated. In this work, laboratory cultures of five different marine phytoplankton species (Prochlorococcus, Synechococcus, Micromonas pusilla, Pelagomonas calceolata, and Emiliania huxleyi) were examined for NMHC production capabilities. All species were found to produce isoprene at constant rates during the balanced exponential growth phase; rates ranged from 1×10−21 to 4×10−19 mol cell−1 day−1 over all cell species and growth conditions tested. No other NMHC was consistently produced or consumed by these cells. The presence of heterotrophic bacteria in phytoplankton cultures had no effect on isoprene production rates per phytoplankton cell. A positive allometric relationship was observed between isoprene production rate and cell volume; highest production rates were found for the largest cell, E. huxleyi, and lowest rates for Prochlorococcus, the smallest cell. Isoprene production was a function of light intensity and temperature in Prochlorococcus, with patterns that were similar to those between growth rate and these environmental variables. The maximum production with light intensity occurred in the photoinhibited regime, and the maximum with temperature was at the maximum of growth rate for this species, near 23 °C. Nanoflagellate grazing by Cafeteria roenbergensis on, and phage infection of, Prochlorococcus controlled total isoprene produced in the flask by controlling cell abundances. Phage infection also decreased the isoprene production rate per cell during latent period of infection as compared to healthy cells. With certain assumptions, combining the measured laboratory isoprene production rates with observed water column phytoplankton abundances resulted in a maximum estimated sea-to-air flux of isoprene that was on the same order of magnitude as previously reported values determined using in situ measured seawater and atmospheric measurements.

Nitrogen Isotopic Composition of Coal-Fired Power Plant NOx: Influence of Emission Controls and Implications for Global Emission Inventories

Despite the potential use of δ(15)N as a tracer of NO(x) source contributions, prior documentation of δ(15)N of various NO(x) emission sources is exceedingly limited. This manuscript presents the first measurements of the nitrogen isotopic composition of NO(x) (δ(15)N-NO(x)) emitted from coal-fired power plants in the U.S. at typical operating conditions with and without the presence of selective catalytic reduction (SCR) and selective noncatalytic reduction (SNCR) technology. To accomplish this, a novel method for collection and isotopic analysis of coal-fired stack NO(x) emission samples was developed based on modifications of a historic U.S. EPA stack sampling method. At the power plants included in this study, large differences exist in the isotopic composition of NO(x) emitted with and without SCRs and SNCRs; further the isotopic composition of power plant NO(x) is higher than that of other measured NO(x) emission sources confirming its use as an environmental tracer. These findings indicate that gradual implementation of SCRs at power plants will result in an industry-wide increase in δ(15)N values of NO(x) and NO(y) oxidation products from this emission source.

Production and Emissions of Marine Isoprene and Monoterpenes: A Review

Terrestrial and marine photosynthetic organisms emit trace gases, including isoprene and monoterpenes. The resulting emissions can impact the atmosphere through oxidative chemistry and formation of secondary organic aerosol. Large uncertainty exists as to the magnitude of the marine sources of these compounds, their controlling factors, and contribution to marine aerosol. In recent years, the number of relevant studies has increased substantially, necessitating the review of this topic. Isoprene emissions vary with plankton species, chlorophyll concentration, light, and other factors. Remote marine boundary layer isoprene mixing ratios can reach >300 pptv, and extrapolated global ocean fluxes range from 10 Tg C year−1. Modeling studies using surface chlorophyll concentration as an isoprene emissions proxy suggest variable atmospheric impacts. More information is needed, including emission fluxes of isoprene and monoterpenes from various biogeographical areas, the effects of species and nutrient limitation on emissions, and the aerosol yields via condensation and nucleation, in order to better quantify the atmospheric impacts of marine isoprene and monoterpenes.

Characterizing the isotopic composition of atmospheric ammonia emission sources using passive samplers and a combined oxidation‐bacterial denitrifier approach

RATIONALE Ammonia (NH3) emissions are a substantial source of nitrogen pollution to sensitive terrestrial, aquatic, and marine ecosystems and dependable quantification of NH3 sources is of growing importance due to recently observed increases in ammonium (NH4(+)) deposition rates. While determination of the nitrogen isotopic composition of NH3 (δ(15)N-NH3) can aid in the quantification of NH3 emission sources, existing methods have precluded a comprehensive assessment of δ(15)N-NH3 values from major emission sources. METHODS We report an approach for the δ(15)N-NH4(+) analysis of low concentration NH4(+) samples that couples the bromate oxidation of NH4(+) to NO2(-) and the microbial denitrifier method for δ(15)N-NO2(-) analysis. This approach reduces the required sample mass by 50-fold relative to standard elemental analysis (EA) procedures, is capable of high throughput, and eliminates toxic chemicals used in a prior method for the analysis of low concentration samples. Using this approach, we report a comprehensive inventory of δ(15)N-NH3 values from major emission sources (including livestock operations, marine sources, vehicles, fertilized cornfields) collected using passive sampling devices. RESULTS The δ(15)N-NH4(+) analysis approach developed has a standard deviation of ±0.7‰ and was used to analyze passively collected NH3 emissions with a wide range of ambient NH3 concentrations (0.2 to 165.6 µg/m(3)). The δ(15)N-NH3 values reveal that the NH3 emitted from volatilized livestock waste and fertilizer has relatively low δ(15)N values (-56 to -23‰), allowing it to be differentiated from NH3 emitted from fossil fuel sources that are characterized by relatively high δ(15)N values (-15 to +2‰). CONCLUSIONS The isotopic source signatures presented in this emission inventory can be used as an additional tool in identifying NH3 emission sources and tracing their transport across localized landscapes and regions. The insight into the transport of NH3 emissions provided by isotopic investigation is an important step in devising strategies to reduce future NH3 emissions, a mounting concern for air quality scientists, epidemiologists, and policy-makers.

Assessing the impact of anthropogenic pollution on isoprene-derived secondary organic aerosol formation in PM2.5 collected from the Birmingham, Alabama, ground site during the 2013 Southern Oxidant and Aerosol Study

In the southeastern US, substantial emissions of isoprene from deciduous trees undergo atmospheric oxidation to form secondary organic aerosol (SOA) that contributes to fine particulate matter (PM2.5). Laboratory studies have revealed that anthropogenic pollutants, such as sulfur dioxide (SO2), oxides of nitrogen (NOx), and aerosol acidity, can enhance SOA formation from the hydroxyl radical (OH)-initiated oxidation of isoprene; however, the mechanisms by which specific pollutants enhance isoprene SOA in ambient PM2.5 remain unclear. As one aspect of an investigation to examine how anthropogenic pollutants influence isoprene-derived SOA formation, high-volume PM2.5 filter samples were collected at the Birmingham, Alabama (BHM), ground site during the 2013 Southern Oxidant and Aerosol Study (SOAS). Sample extracts were analyzed by gas chromatography-electron ionization-mass spectrometry (GC/EI-MS) with prior trimethylsilylation and ultra performance liquid chromatography coupled to electrospray ionization high-resolution quadrupole time-of-flight mass spectrometry (UPLC/ESI-HR-QTOFMS) to identify known isoprene SOA tracers. Tracers quantified using both surrogate and authentic standards were compared with collocated gas- and particle-phase data as well as meteorological data provided by the Southeastern Aerosol Research and Characterization (SEARCH) network to assess the impact of anthropogenic pollution on isoprene-derived SOA formation. Results of this study reveal that isoprene-derived SOA tracers contribute a substantial mass fraction of organic matter (OM) (~ 7 to ~ 20 %). Isoprene-derived SOA tracers correlated with sulfate (SO42−) (r2 = 0.34, n = 117) but not with NOx. Moderate correlations between methacrylic acid epoxide and hydroxymethyl-methyl-α-lactone (together abbreviated MAE/HMML)-derived SOA tracers with nitrate radical production (P[NO3]) (r2 = 0.57, n = 40) were observed during nighttime, suggesting a potential role of the NO3 radical in forming this SOA type. However, the nighttime correlation of these tracers with nitrogen dioxide (NO2) (r2 = 0.26, n = 40) was weaker. Ozone (O3) correlated strongly with MAE/HMML-derived tracers (r2 = 0.72, n = 30) and moderately with 2-methyltetrols (r2 = 0.34, n = 15) during daytime only, suggesting that a fraction of SOA formation could occur from isoprene ozonolysis in urban areas. No correlation was observed between aerosol pH and isoprene-derived SOA. Lack of correlation between aerosol acidity and isoprene-derived SOA is consistent with the observation that acidity is not a limiting factor for isoprene SOA formation at the BHM site as aerosols were acidic enough to promote multiphase chemistry of isoprene-derived epoxides throughout the duration of the study. All in all, these results confirm previous studies suggesting that anthropogenic pollutants enhance isoprene-derived SOA formation.

Secondary organic aerosol formation from methacrolein photooxidation: roles of NOx level, relative humidity and aerosol acidity

Environmental context Secondary organic aerosols formed from the oxidation of volatile organic compounds make a significant contribution to atmospheric particulate matter, which in turn affects both global climate change and human health. We investigate the mechanisms of formation and the chemical properties of secondary organic aerosols derived from isoprene, the most abundant non-methane-based, volatile organic compound emitted into the Earth’s atmosphere. However, the exact manner in which these aerosols are formed, and how they are affected by environmental conditions, remains unclear. Abstract Secondary organic aerosol (SOA) formation from the photooxidation of methacrolein (MACR) was examined in a dual outdoor smog chamber under varied initial nitric oxide (NO) levels, relative humidities (RHs) and seed aerosol acidities. Aerosol sizing measurements and off-line chemical analyses by gas chromatography/mass spectrometry and ultra performance liquid chromatography/electrospray ionisation high-resolution quadrupole time-of-flight mass spectrometry (UPLC/ESI-HR-Q-TOFMS) were used to characterise MACR SOA formation. Results indicate that both SOA mass and chemical composition largely depend on the initial MACR/NO ratio and RH conditions. Specifically, at lower initial NO levels (MACR/NO = ~2.7) more substantial SOA is formed under dry conditions (5–20 % RH) compared to wet conditions (30–80 % RH). However, at higher initial NO levels (MACR/NO = ~0.9), the maximum SOA formation was marginally higher under wet conditions. Furthermore, UPLC/ESI-HR-Q-TOFMS data suggest that most particle-phase oligomers, which have been previously observed to form from the oxidation of methacryloylperoxynitrate, were enhanced under dry conditions. In addition to 2-methylglyceric acid and organosulfates derived from MACR oxidation, a nitrogen-containing organic tracer compound was found to form substantially in both chamber-generated and ambient aerosol samples collected from downtown Atlanta, GA, during the 2008 August Mini-Intensive Gas and Aerosol Study (AMIGAS). Moreover, increasing aerosol acidity because of additional sulfuric acid appears to have a negligible effect on both SOA mass and most SOA constituents. Nevertheless, increased RH and aerosol acidity were both observed to enhance organosulfate formation; however, elevating RH mediates organosulfate formation, suggesting that wet sulfate aerosols are necessary to form organosulfates in atmospheric aerosols.