Airborne flux measurements of biogenic isoprene over California

The article of record as published may be located at http://dx.doi.org/10.5194/acp-14-10631-2014The Supplement related to this article is available online at doi:10.5194/acp-14-10631-2014-supplement.Biogenic isoprene fluxes were measured onboard the CIRPAS Twin Otter aircraft as part of the California Airborne Biogenic volatile organic compound (BVOC) Emission Research in Natural Ecosystem Transects (CABERNET) campaign during June 2011. The airborne virtual disjunct eddy covariance (AvDEC) approach used measurements from a proton transfer reaction mass spectrometer (PTR–MS) and a wind radome probe to directly determine fluxes of isoprene over 7400 km of flight paths focusing on areas of California predicted to have the largest emissions. The fast Fourier transform (FFT) approach was used to calculate fluxes of isoprene over long transects of more than 15 km, most commonly between 50 and 150 km. The continuous wavelet transformation (CWT) approach was used over the same transects to also calculate instantaneous isoprene fluxes with localization of both frequency and time independent of non-stationarities. Fluxes were generally measured by flying consistently at 400m±50m (a.g.l.) altitude, and extrapolated to the surface according to the determined flux divergence determined in the racetrack-stacked profiles. The wavelet-derived surface fluxes of isoprene averaged to 2 km spatial resolution showed good correspondence to basal emission factor (BEF) land-cover data sets used to drive BVOC emission models. The surface flux of isoprene was close to zero over Central Valley crops and desert shrublands, but was very high (up to 15 mgm−2 h−1) above oak woodlands, with clear dependence of emissions on temperature and oak density. Isoprene concentrations of up to 8 ppb were observed at aircraft height on the hottest days and over the dominant source regions

Airborne Flux Measurements of BVOCs above Californian Oak Forests: Experimental Investigation of Surface and Entrainment Fluxes, OH Densities, and Damköhler Numbers

The article of record as published may be located at http://dx.doi.org/10.1175/JAS-D-13-054.1Airborne flux measurements of isoprene were performed over the Californian oak belts surrounding the Central Valley. The authors demonstrate for the first time 1) the feasibility of airborne eddy covariance measurements of reactive biogenic volatile organic compounds; 2) the effect of chemistry on the vertical transport of reactive species, such as isoprene; and 3) the applicability of wavelet analysis to estimate regional fluxes of biogenic volatile organic compounds. These flux measurements demonstrate that instrumentation operating at slower response times (e.g., 1–5 s) can still be used to determine eddy covariance fluxes in the mixed layer above land, where typical length scales of 0.5–3km were observed. Flux divergence of isoprene measured in the planetary boundary layer (PBL) is indicative of OH densities in the range of 4–7 3 106 molecules per cubic centimeter and allows extrapolation of airborne fluxes to the surface with Damk€ohler numbers (ratio between the mixing time scale and the chemical time scale) in the range of 0.3–0.9. Most of the isoprene is oxidized in the PBL with entrainment fluxes of about 10% compared to the corresponding surface fluxes. Entrainment velocities of 1–10 cm s21 were measured. The authors present implications for parameterizing PBL schemes of reactive species in regional and global models

Development of PTR-MS selectivity for structural isomers: monoterpenes as a case study

Proton-Transfer-Reaction Mass Spectrometry (PTR-MS) is a very useful tool for high frequency detection and quantification of gas-phase volatile organic compounds (VOCs) but the soft ionization means it is difficult to discriminate structural isomers. For example, to date it has only been possible to measure the sum of monoterpene concentrations, which have been monitored most commonly at m/z 81 and 137 at a constant drift voltage and pressure. We show here that PTR-MS is capable of discriminating individual monoterpenes when operating in the alternating drift voltage (AD) mode. The approach is based on the principle that slightly different energies are required for the fragmentation/clustering of a given monoterpene, so in AD mode each monoterpene has different time points for fragmentation. Therefore from a fragmentation analysis of background-subtracted standards it is possible to calculate the percentage of each monoterpene in an absolute concentration of their sum. Although monoterpenes have been chosen as an example, the method is likely to be effective for other structural isomeric species such as the sesquiterpenes or methyl vinyl ketone/methacrolein (MVK/MACR)

The influence of small-scale variations in isoprene concentrations on atmospheric chemistry over a tropical rainforest

Biogenic volatile organic compounds (BVOCs) such as isoprene constitute a large proportion of the global atmospheric oxidant sink. Their reactions in the atmosphere contribute to processes such as ozone production and secondary organic aerosol formation. However, over the tropical rainforest, where 50 % of the global emissions of BVOCs are believed to occur, atmospheric chemistry models have been unable to simulate concurrently the measured daytime concentration of isoprene and that of its principal oxidant, hydroxyl (OH). One reason for this model-measurement discrepancy may be incomplete mixing of isoprene within the convective boundary layer, leading to patchiness or segregation in isoprene and OH mixing ratios and average concentrations that appear to be incompatible with each other. One way of capturing this effect in models of atmospheric chemistry is to use a reduced effective rate constant for their reaction. Recent studies comparing atmospheric chemistry global/box models with field measurements have suggested that this effective rate reduction may be as large as 50 %; which is at the upper limit of that calculated using large eddy simulation models. To date there has only been one field campaign worldwide that has reported co-located measurements of isoprene and OH at the necessary temporal resolution to calculate the segregation of these compounds. However many campaigns have recorded sufficiently high resolution isoprene measurements to capture the small-scale fluctuations in its concentration. Assuming uniform distributions of other OH production and loss processes, we use a box model of atmospheric chemistry, constrained by the spectrum of isoprene concentrations measured, as a virtual instrument, to estimate the variability in OH at a point and hence, to estimate the segregation intensity of isoprene and OH from high-frequency isoprene time series. The method successfully reproduces the only directly observed segregation, using measurements made in a deciduous forest in Germany. The effective rate constant reduction for the reaction of isoprene and OH over a South-East Asian rainforest is calculated to be typically <15 %. Although there are many unconstrained uncertainties, the likely nature of those processes suggests that this value represents an upper limit. The estimate is not sensitive to heterogeneities in NO at this remote site, unless they are correlated with those of isoprene, or to OH-recycling schemes in the isoprene oxidation mechanism, unless the recycling happens in the first reaction step. Segregation alone is therefore unlikely to be the sole cause of model-measurement discrepancies for isoprene and OH above a rainforest

A global model study of the impact of land-use change in Borneo on atmospheric composition

In this study, we use a high resolution version of the Cambridge p-TOMCAT model, along with data collected during the 2008 NERC-funded Oxidant and Particle Photochemical Processes (OP3) project, to examine the potential impact of the expansion of oil palm in Borneo on air quality and atmospheric composition. Several model emission scenarios are run for the OP3 measurement period, incorporating emissions from both global datasets and local flux measurements. Isoprene fluxes observed at a forest site during OP3 were considerably less than fluxes calculated using the MEGAN model. Incorporating the observed isoprene fluxes into p-TOMCAT substantially improved the comparison between modelled and observed isoprene surface mixing ratios and OH concentrations relative to using the MEGAN emissions. If both observed isoprene fluxes and HOx recycling chemistry were included, the ability of the model to capture diurnal variations in isoprene and OH was further improved. However, a similar improvement was also achieved using a~standard chemical mechanism without HOx recycling, by fixing boundary layer isoprene concentrations over Borneo to follow the OP3 observations. Further model simulations, considering an extreme scenario with all of Borneo converted to oil palm plantation, were run to determine the maximum atmospheric impact of land use change in Borneo. In these simulations, the level of nitrogen oxides was found to be critical. If only isoprene emissions from oil palm are considered, then large scale conversion to oil palm produced a decrease in monthly mean surface ozone of up to ~20%. However, if related changes in NOx emissions from fertilisation, industrial processing and transport are also included then ozone increases of up to ~70% were calculated. Although the largest changes occurred locally, the model also calculated significant regional changes of O3, OH and other species downwind of Borneo and in the free troposphere

Direct ecosystem fluxes of volatile organic compounds from oil palms in South-East Asia

This paper reports the first direct eddy covariance fluxes of reactive biogenic volatile organic compounds (BVOCs) from oil palms to the atmosphere using proton-transfer-reaction mass spectrometry (PTR-MS), measured at a plantation in Malaysian Borneo. At midday, net isoprene flux constituted the largest fraction (84 %) of all emitted BVOCs measured, at up to 30 mg m−2 h−1 over 12 days. By contrast, the sum of its oxidation products methyl vinyl ketone (MVK) and methacrolein (MACR) exhibited clear deposition of 1 mg m−2 h−1, with a small average canopy resistance of 230 s m−1. Approximately 15 % of the resolved BVOC flux from oil palm trees could be attributed to floral emissions, which are thought to be the largest reported biogenic source of estragole and possibly also toluene. Although on average the midday volume mixing ratio of estragole exceeded that of toluene by almost a factor of two, the corresponding fluxes of these two compounds were nearly the same, amounting to 0.81 and 0.76 mg m−2 h−1, respectively. By fitting the canopy temperature and PAR response of the MEGAN emissions algorithm for isoprene and other emitted BVOCs a basal emission rate of isoprene of 7.8 mg m−2 h−1 was derived. We parameterise fluxes of depositing compounds using a resistance approach using direct canopy measurements of deposition. Consistent with Karl et al. (2010), we also propose that it is important to include deposition in flux models, especially for secondary oxidation products, in order to improve flux predictions

Biogenic VOC emissions from rainforest and oil palm plantations in South East Asia (contribution to OP3 and ACES projects)

For the first time in South-East Asia earlier this year canopy-scale measurements of volatile organic compound (VOC) emission from a selectively logged rainforest and from an oil palm plantation were conducted using PTR-MS combined with virtual disjunct eddy covariance. This was done in the multi-team collaborative effort of the OP3 and ACES projects. Both rainforests and oil palm plantations transfer large amounts of reactive organic carbon to the lower atmosphere, resulting inter alia in formation of tropospheric ozone, secondary organic aerosols (SOA) and peroxy radicals. The impact of biogenic VOCs on the depletion of OH radicals is still not fully recognised. Recent studies over Amazon forests proposed that peroxy radical recycling was responsible for sustaining the atmospheric oxidation capacity (Lelieveld et al., 2008). Isoprene and monoterpenes are regarded as the most important biogenic VOCs, whose fluxes were suggested to be significantly different from rainforest than from oil palms. Although the first lab studies predicted potentially high isoprene emissions from oil palms (Wilkinson et al., 2006), measurements reported here have proven this at the ecosystem scale. Overall at the rainforest, the maximum fluxes of isoprene were observed at about 13:00 with an average of 2.5 mg m-2 h-1. Maximum isoprene emissions from oil palms were recorded earlier in the day, at 11:00, with a mean value of 13 mg m-2 h-1. Initial flux results for total monoterpenes indicate that their mass emission ratio with respect to isoprene was about 1:9 at the rainforest and 1:18 at the oil palm plantation. The results are presented with reference to temperature, photosynthetic radiation and meteorological drivers as well as in comparison with CO2 and H2O fluxes. Although the earlier data for isoprene flux from the Amazon forest during the dry season presented by Karl et al. (2007) seemed higher than our fluxes from the Borneo forest, the emission potentials of the vegetation may be similar after accounting for different temperatures. However, the highest fluxes from oil palms, experiencing steeper exponential growth with temperature than rainforest species, indicate that the basal emission rates of oil palms must be much higher than those of the forest species. The consequences for atmospheric chemistry of land use change from rainforest to oil palm plantation can therefore be quite dramatic. Global models predicting atmospheric changes and bottom-up estimates from the tropics must be constrained by direct measurements such as presented here, taking separate account of these major contributions from oil palm plantations and tropical rainforests

Large estragole fluxes from oil palms in Borneo

During two field campaigns (OP3 and ACES), which ran in Borneo in 2008, we measured large emissions of estragole (methyl chavicol; IUPAC systematic name 1-allyl-4-methoxybenzene; CAS number 140-67-0) in ambient air above oil palm canopies (0.81 mg m−2 h−1 and 3.2 ppbv for mean midday fluxes and mixing ratios respectively) and subsequently from flower enclosures. However, we did not detect this compound at a nearby rainforest. Estragole is a known attractant of the African oil palm weevil (Elaeidobius kamerunicus), which pollinates oil palms (Elaeis guineensis). There has been recent interest in the biogenic emissions of estragole but it is normally not included in atmospheric models of biogenic emissions and atmospheric chemistry despite its relatively high potential for secondary organic aerosol formation from photooxidation and high reactivity with OH radical. We report the first direct canopy-scale measurements of estragole fluxes from tropical oil palms by the virtual disjunct eddy covariance technique and compare them with previously reported data for estragole emissions from Ponderosa pine. Flowers, rather than leaves, appear to be the main source of estragole from oil palms; we derive a global estimate of estragole emissions from oil palm plantations of ~0.5 Tg y−1. The observed ecosystem mean fluxes (0.44 mg m−2 h−1) and mean ambient volume mixing ratios (3.0 ppbv) of estragole are the highest reported so far. The value for midday mixing ratios is not much different from the total average as, unlike other VOCs (e.g. isoprene), the main peak occurred in the evening rather than in the middle of the day. Despite this, we show that the estragole flux can be parameterised using a modified G06 algorithm for emission. However, the model underestimates the afternoon peak even though a similar approach works well for isoprene. Our measurements suggest that this biogenic compound may have an impact on regional atmospheric chemistry that previously has not been accounted for in models and could become more important in the future due to expansion of the areas of oil palm plantation

Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigens

International audienceEndosymbiosis of bacteria by eukaryotes is a defining feature of cellular evolution. In addition to well-known bacterial origins for mitochondria and chloroplasts, multiple origins of bacterial endosymbiosis are known within the cells of diverse animals, plants and fungi. Early-diverging lineages of terrestrial fungi harbor endosymbiotic bacteria belonging to the Burkholderiaceae. We sequenced the metagenome of the soil-inhabiting fungus Mortierella elongata and assembled the complete circular chromosome of its endosymbiont, Mycoavidus cysteinexigens, which we place within a lineage of endofungal symbionts that are sister clade to Burkholderia. The genome of M. elongata strain AG77 features a core set of primary metabolic pathways for degradation of simple carbohydrates and lipid biosynthesis, while the M. cysteinexigens (AG77) genome is reduced in size and function. Experiments using antibiotics to cure the endobacterium from the host demonstrate that the fungal host metabolism is highly modulated by presence/absence of M. cysteinexigens. Independent comparative phylogenomic analyses of fungal and bacterial genomes are consistent with an ancient origin for M. elongata - M. cysteinexigens symbiosis, most likely over 350 million years ago and concomitant with the terrestrialization of Earth and diversification of land fungi and plants