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DOE OSTI2023

Characterization of promoter elements of isoprene‐responsive genes and the ability of isoprene to bind START domain transcription factors

Abstract Isoprene has recently been proposed to be a signaling molecule that can enhance tolerance of both biotic and abiotic stress. Not all plants make isoprene, but all plants tested to date respond to isoprene. We hypothesized that isoprene interacts with existing signaling pathways rather than requiring novel mechanisms for its effect on plants. We analyzed the cis‐regulatory elements (CREs) in promoters of isoprene‐responsive genes and the corresponding transcription factors binding these promoter elements to obtain clues about the transcription factors and other proteins involved in isoprene signaling. Promoter regions of isoprene‐responsive genes were characterized using the Arabidopsis cis‐regulatory element database. CREs bind ARR1, Dof, DPBF, bHLH112, GATA factors, GT‐1, MYB, and WRKY transcription factors, and light‐responsive elements were overrepresented in promoters of isoprene‐responsive genes; CBF‐, HSF‐, WUS‐binding motifs were underrepresented. Transcription factors corresponding to CREs overrepresented in promoters of isoprene‐responsive genes were mainly those important for stress responses: drought‐, salt/osmotic‐, oxidative‐, herbivory/wounding and pathogen‐stress. More than half of the isoprene‐responsive genes contained at least one binding site for TFs of the class IV (homeodomain leucine zipper) HD‐ZIP family, such as GL2, ATML1, PDF2, HDG11, ATHB17. While the HD‐zipper‐loop‐zipper (ZLZ) domain binds to the L1 box of the promoter region, a special domain called the steroidogenic acute regulatory protein‐related lipid transfer, or START domain, can bind ligands such as fatty acids (e.g., linolenic and linoleic acid). We tested whether isoprene might bind in such a START domain. Molecular simulations and modeling to test interactions between isoprene and a class IV HD‐ZIP family START‐domain‐containing protein were carried out. Without membrane penetration by the HDG11 START domain, isoprene within the lipid bilayer was inaccessible to this domain, preventing protein interactions with membrane bound isoprene. The cross‐talk between isoprene‐mediated signaling and other growth regulator and stress signaling pathways, in terms of common CREs and transcription factors could enhance the stability of the isoprene emission trait when it evolves in a plant but so far it has not been possible to say what how isoprene is sensed to initiate signaling responses.

60 APPLIED LIFE SCIENCES↗

NASA NTRS2023

AMORE-Isoprene v1.0: A New Reduced Mechanism for Gas-Phase Isoprene Oxidation

Gas-phase oxidation of isoprene by ozone (O 3 ) and the hydroxyl (OH) and nitrate (NO 3 ) radicals significantly impacts tropospheric oxidant levels and secondary organic aerosol formation. The most comprehensive and up-to-date chemical mechanism for isoprene oxidation consists of several hundred species and over 800 reactions. Therefore, the computational expense of including the entire mechanism in large-scale atmospheric chemical transport models is usually prohibitive, and most models employ reduced isoprene mechanisms ranging in size from ∼ 10 to ∼ 200 species. We have developed a new reduced isoprene oxidation mechanism using a directed-graph path-based automated model reduction approach, with minimal manual adjustment of the output mechanism. The approach takes as inputs a full isoprene oxidation mechanism, the environmental parameter space, and a list of priority species which are protected from elimination during the reduction process. Our reduced mechanism, AMORE-Isoprene (where AMORE stands for Automated Model Reduction), consists of 12 species which are unique to the isoprene mechanism as well as 22 reactions. We demonstrate its performance in a box model in comparison with experimental data from the literature and other current isoprene oxidation mechanisms. AMORE-Isoprene's performance with respect to predicting the time evolution of isoprene oxidation products, including isoprene epoxydiols (IEPOX) and formaldehyde, is favorable compared with other similarly sized mechanisms. When AMORE-Isoprene is included in the Community Regional Atmospheric Chemistry Multiphase Mechanism 1.0 (CRACMM1AMORE) in the Community Multiscale Air Quality Model (CMAQ, v5.3.3), O 3 and formaldehyde agreement with Environmental Protection Agency (EPA) Air Quality System observations is improved. O 3 bias is reduced by 3.4 ppb under daytime conditions for O 3 concentrations over 50 ppb. Formaldehyde bias is reduced by 0.26 ppb on average for all formaldehyde measurements compared with the base CRACMM1. There was no significant change in computation time between CRACMM1AMORE and the base CRACMM. AMORE-Isoprene shows a 35 % improvement in agreement between simulated IEPOX concentrations and chamber data over the base CRACMM1 mechanism when compared in the Framework for 0-D Atmospheric Modeling (F0AM) box model framework. This work demonstrates a new highly reduced isoprene mechanism and shows the potential value of automated model reduction for complex reaction systems.

Automated Model Reduction↗

DOE OSTI2023

AMORE-Isoprene v1.0: a new reduced mechanism for gas-phase isoprene oxidation

Abstract. Gas-phase oxidation of isoprene by ozone (O3) and the hydroxyl (OH) and nitrate (NO3) radicals significantly impacts tropospheric oxidant levels and secondary organic aerosol formation. The most comprehensive and up-to-date chemical mechanism for isoprene oxidation consists of several hundred species and over 800 reactions. Therefore, the computational expense of including the entire mechanism in large-scale atmospheric chemical transport models is usually prohibitive, and most models employ reduced isoprene mechanisms ranging in size from ∼ 10 to ∼ 200 species. We have developed a new reduced isoprene oxidation mechanism using a directed-graph path-based automated model reduction approach, with minimal manual adjustment of the output mechanism. The approach takes as inputs a full isoprene oxidation mechanism, the environmental parameter space, and a list of priority species which are protected from elimination during the reduction process. Our reduced mechanism, AMORE-Isoprene (where AMORE stands for Automated Model Reduction), consists of 12 species which are unique to the isoprene mechanism as well as 22 reactions. We demonstrate its performance in a box model in comparison with experimental data from the literature and other current isoprene oxidation mechanisms. AMORE-Isoprene's performance with respect to predicting the time evolution of isoprene oxidation products, including isoprene epoxydiols (IEPOX) and formaldehyde, is favorable compared with other similarly sized mechanisms. When AMORE-Isoprene is included in the Community Regional Atmospheric Chemistry Multiphase Mechanism 1.0 (CRACMM1AMORE) in the Community Multiscale Air Quality Model (CMAQ, v5.3.3), O3 and formaldehyde agreement with Environmental Protection Agency (EPA) Air Quality System observations is improved. O3 bias is reduced by 3.4 ppb under daytime conditions for O3 concentrations over 50 ppb. Formaldehyde bias is reduced by 0.26 ppb on average for all formaldehyde measurements compared with the base CRACMM1. There was no significant change in computation time between CRACMM1AMORE and the base CRACMM. AMORE-Isoprene shows a 35 % improvement in agreement between simulated IEPOX concentrations and chamber data over the base CRACMM1 mechanism when compared in the Framework for 0-D Atmospheric Modeling (F0AM) box model framework. This work demonstrates a new highly reduced isoprene mechanism and shows the potential value of automated model reduction for complex reaction systems.

58 GEOSCIENCES↗

DOE OSTI2024

Observation-constrained kinetic modeling of isoprene SOA formation in the atmosphere

Isoprene has the largest global non-methane hydrocarbon emission, and the oxidation of isoprene plays a crucial role in the formation of secondary organic aerosol (SOA). Two primary processes are known to contribute to SOA formation from isoprene oxidation: (1) the reactive uptake of isoprene-derived epoxides on acidic or aqueous particle surfaces and (2) the absorptive gas–particle partitioning of low-volatility oxidation products. In this study, we developed a new multiphase condensed isoprene oxidation mechanism that includes these processes with key molecular intermediates and products. The new mechanism was applied to simulate isoprene gas-phase oxidation products and SOA formation from previously published chamber experiments under a variety of conditions and atmospheric observations during the Southern Oxidant and Aerosol Studies (SOAS) field campaign. Our results show that SOA formation from most of the chamber experiments is reasonably reproduced using our mechanism, except when the concentration ratios of initial nitric oxide to isoprene exceed ~ 2, the formed SOA is significantly underpredicted. The SOAS simulations also reasonably agree with the measurements regarding the diurnal pattern and concentrations of different product categories, while the total isoprene SOA remains underestimated. The molecular compositions of the modeled SOA indicate that multifunctional low-volatility products contribute to isoprene SOA more significantly than previously thought, with a median mass contribution of ~ 57 % to the total modeled isoprene SOA. However, this contribution is intricately intertwined with IEPOX-derived SOA (IEPOX: isoprene-derived epoxydiols), posing challenges for their differentiation using bulk aerosol composition analysis (e.g., the aerosol mass spectrometer with positive matrix factorization). Furthermore, the SOA from these pathways may vary greatly, mainly dependent on the volatility estimation and treatment of particle-phase processes (i.e., photolysis and hydrolysis). Our findings emphasize that the various pathways to produce these low-volatility species should be considered in models to more accurately predict isoprene SOA formation. The new condensed isoprene chemical mechanism can be further incorporated into regional-scale air quality models, such as the Community Multiscale Air Quality Modelling System (CMAQ), to assess isoprene SOA formation on a larger scale.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Anaerobic Biohydrogenation of Isoprene by Acetobacterium wieringae Strain Y

Isoprene is a ubiquitously distributed, biogenic, and climate-active organic compound. Microbial isoprene degradation in oxic environments is fairly well understood; however, studies exploring anaerobic isoprene metabolism remain scarce, with no isolates for study available. Here, we obtained an acetogenic isolate, designated Acetobacterium wieringae strain Y, which hydrogenated isoprene to a mixture of methyl-1-butenes at an overall rate of 288.8 ± 20.9 μM day -1 with concomitant acetate production at a rate of 478.4 ± 5.6 μM day -1 . Physiological characterization demonstrated that isoprene was not utilized in a respiratory process; rather, isoprene promoted acetogenesis kinetically. Bioinformatic analysis and proteomics experiments revealed the expression of candidate ene-reductases responsible for isoprene biohydrogenation. Notably, the addition of isoprene to strain Y cultures stimulated the expression of proteins associated with the Wood-Ljungdahl pathway, indicating unresolved impacts of isoprene on carbon cycling and microbial ecology in anoxic environments (e.g., promoting CO 2 plus H 2 reductive acetogenesis while inhibiting methanogenesis). Our new findings advance understanding of microbial transformation of isoprene under anoxic conditions and suggest that anoxic environments are isoprene sinks.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2006

Quantifying the Seasonal and Interannual Variability of North American Isoprene Emissions Using Satellite Observations of the Formaldehyde Column

Quantifying isoprene emissions using satellite observations of the formaldehyde (HCHO) columns is subject to errors involving the column retrieval and the assumed relationship between HCHO columns and isoprene emissions, taken here from the GEOS-CHEM chemical transport model. Here we use a 6-year (1996-2001) HCHO column data set from the Global Ozone Monitoring Experiment (GOME) satellite instrument to (1) quantify these errors, (2) evaluate GOME-derived isoprene emissions with in situ flux measurements and a process-based emission inventory (Model of Emissions of Gases and Aerosols from Nature, MEGAN), and (3) investigate the factors driving the seasonal and interannual variability of North American isoprene emissions. The error in the GOME HCHO column retrieval is estimated to be 40%. We use the Master Chemical Mechanism (MCM) to quantify the time-dependent HCHO production from isoprene, alpha- and beta-pinenes, and methylbutenol and show that only emissions of isoprene are detectable by GOME. The time-dependent HCHO yield from isoprene oxidation calculated by MCM is 20-30% larger than in GEOS-CHEM. GOME-derived isoprene fluxes track the observed seasonal variation of in situ measurements at a Michigan forest site with a -30% bias. The seasonal variation of North American isoprene emissions during 2001 inferred from GOME is similar to MEGAN, with GOME emissions typically 25% higher (lower) at the beginning (end) of the growing season. GOME and MEGAN both show a maximum over the southeastern United States, but they differ in the precise location. The observed interannual variability of this maximum is 20-30%, depending on month. The MEGAN isoprene emission dependence on surface air temperature explains 75% of the month-to-month variability in GOME-derived isoprene emissions over the southeastern United States during May-September 1996-2001.

Palmer, Paul I.↗

DOE OSTI2020

Leaf isoprene and monoterpene emission distribution across hyperdominant tree genera in the Amazon basin

Tropical forests are acknowledged to be the largest global source of isoprene (C 5 H 8 ) and monoterpenes (C 10 H 16 ) emissions, with current synthesis studies suggesting few tropical species emit isoprenoids (20-38%) and do so with highly variable emission capacities, including within the same genera. This apparent lack of a clear phylogenetic thread has created difficulties both in linking isoprenoid function with evolution and for the development of accurate biosphere-atmosphere models. In this work, we present a systematic emission study of "hyperdominant" tree species in the Amazon Basin. Across 162 individuals, distributed among 25 botanical families and 113 species, isoprenoid emissions were widespread among both early and late successional species (isoprene: 61.9% of the species; monoterpenes: 15.0%; both isoprene and monoterpenes: 9.7%). The hyperdominant species (69) across the top five most abundant genera, which make up about 50% of all individuals in the Basin, had a similar abundance of isoprenoid emitters (isoprene: 63.8%; monoterpenes: 17.4%; both 11.6%). Among the abundant genera, only Pouteria had a low frequency of isoprene emitting species (15.8% of 19 species). In contrast, Protium, Licania, Inga, and Eschweilera were rich in isoprene emitting species (83.3% of 12 species, 61.1% of 18 species, 100% of 8 species, and 100% of 12 species, respectively). Light response curves of individuals in each of the five genera showed light-dependent, photosynthesis-linked emission rates of isoprene and monoterpenes. Importantly, in every genus, we observed species with light-dependent isoprene emissions together with monoterpenes including β-ocimene. These observations support the emerging view of the evolution of isoprene synthases from β-ocimene synthases. Our results have important implications for understanding isoprenoid function-evolution relationships and the development of more accurate Earth System Models.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Can Isoprene Oxidation Explain High Concentrations of Atmospheric Formic and Acetic Acid over Forests?

Formic and acetic acid concentrations are particularly high over forested areas of the world. However, the gas-phase mechanisms for producing these acids are poorly understood even for isoprene, the globally dominant biogenic hydrocarbon. We quantified formic and acetic acid production from reactions of hydroxyl radical (OH) (between high and low ranges of nitric oxide (NO) levels) with isoprene, methacrolein (MACR), isoprene epoxydiol (IEPOX), isoprene hydroxy hydroperoxide (ISOPOOH), and α-pinene from the focused isoprene experiments at California Institute of Technology (FIXCIT) laboratory chamber study. We find that (i) OH oxidation of MACR, IEPOX, and ISOPOOH are sources of formic acid, (ii) isoprene peroxy radical isomerization and associated photolysis oxidation products are potentially important sources of organic acids, and (iii) high levels of NO generally suppress organic acid formation from OH oxidation of isoprene. We modified existing chemical mechanisms for isoprene oxidation to account for organic acid production pathways observed in the FIXCIT study. We simulated organic acid production during the Southeastern Oxidant and Aerosol Study using the updated chemical mechanisms and represented acetic acid within a factor of 2 but still underpredicted formic acid by a factor of 6. While we cannot explain ambient formic acid with explicit chemical mechanisms, the FIXCIT results suggest that the oxidation of isoprene could account for as much as 70% of the global annual production of formic acid from gas-phase reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Stimulation of isoprene emissions and electron transport rates are a key mechanism of thermal tolerance in the tropical species Vismia guianensis

Tropical forests absorb large amounts of atmospheric CO 2 through photosynthesis, but high surface temperatures suppress this absorption while promoting isoprene emissions. While mechanistic isoprene emission models predict a tight coupling to photosynthetic electron transport (ETR) as a function of temperature, direct field observations of these phenomenon are lacking in the tropics and are necessary to assess the impact of a warming climate on global isoprene emissions. In this paper, we demonstrate that in the early successional species Vismia guianensis in the central Amazon, ETR rates increased with temperature in concert with isoprene emissions, even as stomatal conductance ($g _s$) and net photosynthetic carbon fixation ($P_n$) declined. We observed the highest temperatures of continually increasing isoprene emissions yet reported (50°C). While $P_n$ showed an optimum value of 32.6 ± 0.4°C, isoprene emissions, ETR, and the oxidation state of PSII reaction centers (q L ) increased with leaf temperature with strong linear correlations for ETR (ρ = 0.98) and q L (ρ= 0.99) with leaf isoprene emissions. In contrast, other photoprotective mechanisms, such as non-photochemical quenching (NPQ), were not activated at elevated temperatures. Inhibition of isoprenoid biosynthesis repressed $P_n$ at high temperatures through a mechanism that was independent of stomatal closure. While extreme warming will decrease $g_s$ and $P_n$ in tropical species, our observations support a thermal tolerance mechanism where the maintenance of high photosynthetic capacity under extreme warming is assisted by the simultaneous stimulation of ETR and metabolic pathways that consume the direct products of ETR including photorespiration and the biosynthesis of thermoprotective isoprenoids. Our results confirm that models which link isoprene emissions to the rate of ETR hold true in tropical species and provide necessary "ground-truthing" for simulations of the large predicted increases in tropical isoprene emissions with climate warming.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2013

Photosynthesis-dependent Isoprene Emission from Leaf to Planet in a Global Carbon-chemistry-climate Model

We describe the implementation of a biochemical model of isoprene emission that depends on the electron requirement for isoprene synthesis into the FarquharBallBerry leaf model of photosynthesis and stomatal conductance that is embedded within a global chemistry-climate simulation framework. The isoprene production is calculated as a function of electron transport-limited photosynthesis, intercellular and atmospheric carbon dioxide concentration, and canopy temperature. The vegetation biophysics module computes the photosynthetic uptake of carbon dioxide coupled with the transpiration of water vapor and the isoprene emission rate at the 30 min physical integration time step of the global chemistry-climate model. In the model, the rate of carbon assimilation provides the dominant control on isoprene emission variability over canopy temperature. A control simulation representative of the present-day climatic state that uses 8 plant functional types (PFTs), prescribed phenology and generic PFT-specific isoprene emission potentials (fraction of electrons available for isoprene synthesis) reproduces 50 of the variability across different ecosystems and seasons in a global database of 28 measured campaign-average fluxes. Compared to time-varying isoprene flux measurements at 9 select sites, the model authentically captures the observed variability in the 30 min average diurnal cycle (R2 6496) and simulates the flux magnitude to within a factor of 2. The control run yields a global isoprene source strength of 451 TgC yr1 that increases by 30 in the artificial absence of plant water stress and by 55 for potential natural vegetation.

photosynthesis↗

DOE OSTI2020

Molecular understanding of the suppression of new-particle formation by isoprene

Nucleation of atmospheric vapours produces more than half of global cloud condensation nuclei and so has an important influence on climate. Recent studies show that monoterpene ( C 10 H 16 ) oxidation yields highly oxygenated products that can nucleate with or without sulfuric acid. Monoterpenes are emitted mainly by trees, frequently together with isoprene ( C 5 H 8 ), which has the highest global emission of all organic vapours. Previous studies have shown that isoprene suppresses new-particle formation from monoterpenes, but the cause of this suppression is under debate. Here, in experiments performed under atmospheric conditions in the CERN CLOUD chamber, we show that isoprene reduces the yield of highly oxygenated dimers with 19 or 20 carbon atoms – which drive particle nucleation and early growth – while increasing the production of dimers with 14 or 15 carbon atoms. The dimers (termed C 20 and C 15 , respectively) are produced by termination reactions between pairs of peroxy radicals ( RO 2 • ) arising from monoterpenes or isoprene. Compared with pure monoterpene conditions, isoprene reduces nucleation rates at 1.7 nm (depending on the isoprene / monoterpene ratio) and approximately halves particle growth rates between 1.3 and 3.2 nm. However, above 3.2 nm, C 15 dimers contribute to secondary organic aerosol, and the growth rates are unaffected by isoprene. We further show that increased hydroxyl radical ( OH • ) reduces particle formation in our chemical system rather than enhances it as previously proposed, since it increases isoprene-derived RO 2 • radicals that reduce C 20 formation. RO 2 • termination emerges as the critical step that determines the highly oxygenated organic molecule (HOM) distribution and the corresponding nucleation capability. Species that reduce the C 20 yield, such as NO, HO 2 and as we show isoprene, can thus effectively reduce biogenic nucleation and early growth. Therefore the formation rate of organic aerosol in a particular region of the atmosphere under study will vary according to the precise ambient conditions.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Effect of iron substitution in cryptomelane on the heterogeneous reaction with isoprene

Biogenic isoprene is an important pollutant for regional air quality. Being ubiquitously distributed on the earth surface, manganese (hydr)oxides should play a vital role in the transformation of isoprene. Cryptomelane is a typical manganese oxide with isomorphous substitution of Fe for Mn, but less attention has been paid to its heterogeneous reaction with isoprene. When Fe 3+ replaces Mn 3+ , K + is depleted and Mn 3+ is oxidized to Mn 4+ . In contrast, oxygen vacancies are formed when Fe 3+ substitutes Mn 4+ . Fe substitution creates weak crystallites and abundant mesopores, resulting in the increase of isoprene adsorption. As found by theoretical calculations, the Mn 4+ –O 2- bonds at the cross sections of the tunnels is more active than that on the outer wall of the tunnels. After the adsorption of isoprene, bridging carboxylate species and hydrogen-bonding water are produced and the surface octahedra are distorted, i.e., Mn 4+ O 6 → Mn 3+ O 6-δ . As the heat facilitates the breakage of Mn 4+ –O 2- , the increase of environmental temperature enhances the oxidation of isoprene. Here the above findings shed light on the effect of Fe substitution in cryptomelane to enhance the oxidation of isoprene, and illustrates that heterogeneous reaction with isoprene impairs the transformation of other environmental substances on cryptomelane.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Source of 12 C in Calvin–Benson cycle intermediates and isoprene emitted from plant leaves fed with 13 CO 2

Feeding 14 CO 2 was crucial to uncovering the path of carbon in photosynthesis. Feeding 13 CO 2 to photosynthesizing leaves emitting isoprene has been used to develop hypotheses about the sources of carbon for the methylerythritol 4-phosphate pathway, which makes the precursors for terpene synthesis in chloroplasts and bacteria. Both photosynthesis and isoprene studies found that products label very quickly (<10 min) up to 80–90% but the last 10–20% of labeling requires hours indicating a source of 12 C during photosynthesis and isoprene emission. Furthermore, studies with isoprene showed that the proportion of slow label could vary significantly. This was interpreted as a variable contribution of carbon from sources other than the Calvin–Benson cycle (CBC) feeding the methylerythritol 4-phosphate pathway. Here, we measured the degree of label in isoprene and photosynthetic metabolites 20 min after beginning to feed 13 CO 2 . Isoprene labeling was the same as labeling of photosynthesis intermediates. High temperature reduced the label in isoprene and photosynthesis intermediates by the same amount indicating no role for alternative carbon sources for isoprene. A model assuming glucose, fructose, and/or sucrose reenters the CBC as ribulose 5-phosphate through a cytosolic shunt involving glucose 6-phosphate dehydrogenase was consistent with the observations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Future changes in isoprene-epoxydiol-derived secondary organic aerosol (IEPOX SOA) under the Shared Socioeconomic Pathways: the importance of physicochemical dependency

Abstract. Secondary organic aerosol (SOA) is a dominant contributor of fine particulate matter in the atmosphere, but the complexity of SOA formation chemistry hinders the accurate representation of SOA in models. Volatility-based SOA parameterizations have been adopted in many recent chemistry modeling studies and have shown a reasonable performance compared to observations. However, assumptions made in these empirical parameterizations can lead to substantial errors when applied to future climatic conditions as they do not include the mechanistic understanding of processes but are rather fitted to laboratory studies of SOA formation. This is particularly the case for SOA derived from isoprene epoxydiols (IEPOX SOA), for which we have a higher level of understanding of the fundamental processes than is currently parameterized in most models. We predict future SOA concentrations using an explicit mechanism and compare the predictions with the empirical parameterization based on the volatility basis set (VBS) approach. We then use the Community Earth System Model 2 (CESM2.1.0) with detailed isoprene chemistry and reactive uptake processes for the middle and end of the 21st century under four Shared Socioeconomic Pathways (SSPs): SSP1–2.6, SSP2–4.5, SSP3–7.0, and SSP5–8.5. With the explicit chemical mechanism, we find that IEPOX SOA is predicted to increase on average under all future SSP scenarios but with some variability in the results depending on regions and the scenario chosen. Isoprene emissions are the main driver of IEPOX SOA changes in the future climate, but the IEPOX SOA yield from isoprene emissions also changes by up to 50 % depending on the SSP scenario, in particular due to different sulfur emissions. We conduct sensitivity simulations with and without CO2 inhibition of isoprene emissions that is highly uncertain, which results in factor of 2 differences in the predicted IEPOX SOA global burden, especially for the high-CO2 scenarios (SSP3–7.0 and SSP5–8.5). Aerosol pH also plays a critical role in the IEPOX SOA formation rate, requiring accurate calculation of aerosol pH in chemistry models. On the other hand, isoprene SOA calculated with the VBS scheme predicts a nearly constant SOA yield from isoprene emissions across all SSP scenarios; as a result, it mostly follows isoprene emissions regardless of region and scenario. This is because the VBS scheme does not consider heterogeneous chemistry; in other words, there is no dependency on aerosol properties. The discrepancy between the explicit mechanism and VBS parameterization in this study is likely to occur for other SOA components as well, which may also have dependencies that cannot be captured by VBS parameterizations. This study highlights the need for more explicit chemistry or for parameterizations that capture the dependence on key physicochemical drivers when predicting SOA concentrations for climate studies.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2020

High productivity in hybrid-poplar plantations without isoprene emission to the atmosphere

Hybrid-poplar tree plantations provide a source for biofuel and biomass, but they also increase forest isoprene emissions. The consequences of increased isoprene emissions include higher rates of tropospheric ozone production, increases in the lifetime of methane, and increases in atmospheric aerosol production, all of which affect the global energy budget and/or lead to the degradation of air quality. Using RNA interference (RNAi) to suppress isoprene emission, we show that this trait, which is thought to be required for the tolerance of abiotic stress, is not required for high rates of photosynthesis and woody biomass production in the agroforest plantation environment, even in areas with high levels of climatic stress. Biomass production over 4 y in plantations in Arizona and Oregon was similar among genetic lines that emitted or did not emit significant amounts of isoprene. Lines that had substantially reduced isoprene emission rates also showed decreases in flavonol pigments, which reduce oxidative damage during extremes of abiotic stress, a pattern that would be expected to amplify metabolic dysfunction in the absence of isoprene production in stress-prone climate regimes. However, compensatory increases in the expression of other proteomic components, especially those associated with the production of protective compounds, such as carotenoids and terpenoids, and the fact that most biomass is produced prior to the hottest and driest part of the growing season explain the observed pattern of high biomass production with low isoprene emission. Our results show that it is possible to reduce the deleterious influences of isoprene on the atmosphere, while sustaining woody biomass production in temperate agroforest plantations.

oxidative stress↗

DOE OSTI2021

Transport and chemistry of isoprene and its oxidation products in deep convective clouds

Deep convective clouds can transport trace gases from the planetary boundary layer into the upper troposphere where subsequent chemistry may impact aerosol particle formation and growth. In this modelling study, we investigate processes that affect isoprene and its oxidation products injected into the upper troposphere by an isolated deep convective cloud in the Amazon. We run a photochemical box model with coupled cloud microphysics along hundreds of individual air parcel trajectories sampled from a cloud-resolving model simulation of a convective event. The box model simulates gas-phase chemical reactions, gas scavenging by liquid and ice hydrometeors, and turbulent dilution inside a deep convective cloud. The results illustrate the potential importance of gas uptake to anvil ice in regulating the intensity of the isoprene oxidation and associated low volatility organic vapour concentrations in the outflow. Isoprene transport and fate also depends on the abundance of lightning-generated nitrogen oxide radicals (NO x = NO + NO 2 ). If gas uptake on ice is efficient and lightning activity is low, around 30% of the boundary layer isoprene will survive to the cloud outflow after approximately one hour of transport, while all the low volatile oxidation products will be scavenged by the cloud hydrometeors. If lightning NO x is abundant and gas uptake by ice is inefficient, then all isoprene will be oxidised during transport or in the immediate outflow region, while several low volatility isoprene oxidation products will have elevated concentrations in the cloud outflow. Reducing uncertainties associated with the uptake of vapours on ice hydrometeors, especially HO 2 and oxygenated organics, is essential to improve predictions of isoprene and its oxidation products in deep convective outflows and their potential contribution to new particle formation and growth.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2015

Formaldehyde Production from Isoprene Oxidation Across NOx Regimes

The chemical link between isoprene and formaldehyde (HCHO) is a strong, non-linear function of NOx (= 27 NO + NO2). This relationship is a linchpin for top-down isoprene emission inventory verification from orbital HCHO column observations. It is also a benchmark for overall mechanism performance with regard to VOC oxidation. Using a comprehensive suite of airborne in situ observations over the Southeast U.S., we quantify HCHO production across the urban-rural spectrum. Analysis of isoprene and its major first-generation oxidation products allows us to define both a "prompt" yield of HCHO (molecules of HCHO produced per molecule of freshly-emitted isoprene) and the background HCHO mixing ratio (from oxidation of longer-lived hydrocarbons). Over the range of observed NOx values (roughly 0.1 - 2 ppbv), the prompt yield increases by a factor of 3 (from 0.3 to 0.9), while background HCHO increases by more than a factor of 2 (from 1.5 to 3.3 ppbv). We apply the same method to evaluate the performance of both a global chemical transport model (AM3) and a measurement-constrained 0-D chemical box model. Both models reproduce the NOx dependence of the prompt HCHO yield, illustrating that models with updated isoprene oxidation mechanisms can adequately capture the link between HCHO and recent isoprene emissions. On the other hand, both models under-estimate background HCHO mixing ratios, suggesting missing HCHO precursors, inadequate representation of later-generation isoprene degradation and/or under-estimated hydroxyl radical concentrations. Moreover, we find that the total organic peroxy radical production rate is essentially independent of NOx, as the increase in oxidizing capacity with NOx is largely balanced by a decrease in VOC reactivity. Thus, the observed NOx dependence of HCHO mainly reflects the changing fate of organic peroxy radicals.

VOC↗

NASA NTRS2017

Impact of Evolving Isoprene Mechanisms on Simulated Formaldehyde: An Inter-comparison Supported by in Situ Observations from SENEX

Isoprene oxidation schemes vary greatly among gas-phase chemical mechanisms, with potentially significant ramifications for air quality modeling and interpretation of satellite observations in biogenic-rich regions. In this study, in situ observations from the 2013 SENEX mission are combined with a constrained O-D photochemical box model to evaluate isoprene chemistry among five commonly used gas-phase chemical mechanisms: CBO5, CB6r2, MCMv3.2, MCMv3.3.1, and a recent version of GEOS-Chem. Mechanisms are evaluated and inter-compared with respect to formaldehyde (HCHO), a high-yield product of isoprene oxidation. Though underestimated by all considered mechanisms, observed HCHO mixing ratios are best reproduced by MCMv3.3.1 (normalized mean bias = -15%), followed by GEOS-Chem (-17%), MCMv3.2 (-25%), CB6r2 (-32%) and CB05 (-33%). Inter-comparison of HCHO production rates reveals that major restructuring of the isoprene oxidation scheme in the Carbon Bond mechanism increases HCHO production by only approx. 5% in CB6r2 relative to CBO5, while further refinement of the complex isoprene scheme in the Master Chemical Mechanism increases HCHO production by approx. 16% in MCMv3.3.1 relative to MCMv3.2. The GEOS-Chem mechanism provides a good approximation of the explicit isoprene chemistry in MCMv3.3.1 and generally reproduces the magnitude and source distribution of HCHO production rates. We analytically derive improvements to the isoprene scheme in CB6r2 and incorporate these changes into a new mechanism called CB6r2-UMD, which is designed to preserve computational efficiency. The CB6r2-UMD mechanism mimics production of HCHO in MCMv3.3.1 and demonstrates good agreement with observed mixing ratios from SENEX (-14%). Improved simulation of HCHO also impacts modeled ozone: at approx. 0.3 ppb NO, the ozone production rate increases approx. 3% between CB6r2 and CB6r2-UMD, and rises another approx. 4% when HCHO is constrained to match observations.

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