Atmospheric nitrogen oxides (NOx), hydrogen sulphide (H2S) and carbon monoxide (CO): Boon or Bane for plant metabolism and development?

Urban air pollution has been a global challenge world-wide. While urban vegetation or forest modelling can be useful in reducing the toxicities of the atmospheric gases by their absorption, the surge in gaseous pollutants negatively affects plant growth, thereby altering photosynthetic efficiency and harvest index. The present review analyses our current understanding of the toxic and beneficial effects of atmospheric nitrogen oxides (NOx), hydrogen sulphide (H2S) and carbon monoxide (CO) on plant growth and metabolism. The atmospheric levels of these gases vary considerably due to urbanization, automobile emission, volcanic eruptions, agricultural practices and other anthropological activities. These gaseous pollutants prevalent in the atmosphere are known for their dual action (toxic or beneficiary) on plant growth, development and metabolism. NO seems to exert a specialized impact by upregulating nitrogen metabolism and reducing tropospheric ozone. High H2S emission in specific areas of geothermal plants, fumarolic soils and wetlands can be a limitation to air quality control. Certain shortcomings associated with the designing of field experiments, sensitivity of detection methods and simulation development are yet to be overcome to analyze the precise levels of NO, H2S and CO in the rhizosphere of diverse agro-climatic regions. Several laboratory-based investigations have been undertaken to assess the roles of atmospheric gases, namely NOx, CO, H2S, and particulate matter (PM). However, in order to enable natural and sustainable mitigation, it is essential to increase the number of field experiments in order to identify the pollutant-tolerant plants and study their interactive impact on plant growth and agriculture.

Dynamic environmental interactions shaped by vegetative plant volatiles

Covering: up to November 2022Plants shape terrestrial ecosystems through physical and chemical interactions. Plant-derived volatile organic compounds in particular influence the behavior and performance of other organisms. In this review, we discuss how vegetative plant volatiles derived from leaves, stems and roots are produced and released into the environment, how their production and release is modified by abiotic and biotic factors, and how they influence other organisms. Vegetative plant volatiles are derived from different biosynthesis and degradation pathways and are released via distinct routes. Both biosynthesis and release are regulated by other organisms as well as abiotic factors. In turn, vegetative plant volatiles modify the physiology and the behavior of a wide range of organisms, from microbes to mammals. Several concepts and frameworks can help to explain and predict the evolution and ecology of vegetative plant volatile emission patterns of specific pathways: multifunctionality of specialized metabolites, chemical communication displays and the information arms race, and volatile physiochemistry. We discuss how these frameworks can be leveraged to understand the evolution and expression patterns of vegetative plant volatiles. The multifaceted roles of vegetative plant volatiles provide fertile grounds to understand ecosystem dynamics and harness their power for sustainable agriculture.

Effects of tillage and cropping sequences on crop production and environmental benefits in the North China Plain

The ever-increasing trend of greenhouse gas (GHG) emissions is accelerating global warming and threatening food security. Environmental benefits and sustainable food production must be pursued locally and globally. Thus, a field experiment was conducted in 2015 to understand how to balance the trade-offs between agronomic productivity and environment quality in the North China Plain (NCP). Eight treatments consisted of two factors, i.e., (1) tillage practices: rotary tillage (RT) and no-till (NT), and (2) cropping sequences (CS): maize-wheat-soybean-wheat (MWSW), soybean-wheat-maize-wheat (SWMW), soybean-wheat (SW), and maize-wheat (MW). The economic and environmental benefits were evaluated by multiple indicators including the carbon footprint (CF), maize equivalent economic yield (MEEY), energy yield (EY), and carbon sustainability index (CSI). Compared with NT, RT increased the EY and MEEY, but emitted 9.4% higher GHGs. Among different CSs, no significant reduction was observed in CF. The lowest (2.0 Mg CO₂-eq ha^-1 year^-1) and the highest (5.6 Mg CO₂-eq ha^-1 year^-1) CF values were observed under MW and SWMW, respectively. However, CSs with soybean enhanced MEEY and the net revenue due to their higher price compared to that of MW. Although the highest CSI was observed under RT-MW, soybean-based crop rotation could offset the decline in CSI under NT when compared to that for RT. These findings suggest that conservation agriculture (CA) could enhance the balance in trade-offs between economic and environmental benefits. Additional research is needed on how to achieve high crop production by establishing a highly efficient CA system in the NCP.

Role of water in unexpectedly large changes in emission flux of volatile organic compounds in soils under dynamic temperature conditions

Understanding the diffusive transport behavior of volatile organic compounds (VOCs) in near-surface soils is important because soil VOC emissions affect atmospheric conditions and climate. Previous studies have suggested that temperature changes affect the transport behavior; however, the effect of these changes are poorly understood. Indeed, under dynamic temperature conditions, the change in VOC flux is much larger than that expected from the temperature dependency of the diffusion coefficient of VOCs in air. However, the mechanism is not well understood, although water in soil has been considered to play an important role. Here, we present the results of experiments for the upward vertical vapor-phase diffusive transport of two VOCs (benzene and tetrachloroethylene) in sandy soil under sinusoidal temperature variations of 20-30 °C, as well as its numerical representation. The results clarify that the unexpectedly large changes in emission flux can occur as a result of changes in the VOC concentration gradient due to VOC release (volatilization) from/trapping (dissolution) into water, and that such flux changes may occur in various environments. This study suggests the importance of a global evaluation of soil VOC emissions by continuous measurements in various soil environments and/or predictions through numerical simulations with thorough consideration of the role of water in dynamic soil environments.

Plant biochemistry influences tropospheric ozone formation, destruction, deposition, and response

Tropospheric ozone (O₃) is among the most damaging air pollutant to plants. Plants alter the atmospheric O₃ concentration in two distinct ways: (i) by the emission of volatile organic compounds (VOCs) that are precursors of O_3; and (ii) by dry deposition, which includes diffusion of O₃ into vegetation through stomata and destruction by nonstomatal pathways. Isoprene, monoterpenes, and higher terpenoids are emitted by plants in quantities that alter tropospheric O₃. Deposition of O₃ into vegetation is related to stomatal conductance, leaf structural traits, and the detoxification capacity of the apoplast. The biochemical fate of O₃ once it enters leaves and reacts with aqueous surfaces is largely unknown, but new techniques for the tracking and identification of initial products have the potential to open the black box.

Monoterpenes from tropical forest and oil palm plantation floor in Malaysian Borneo/Sabah: emission and composition

Regional estimates of VOC fluxes focus largely on emissions from the canopy and omit potential contributions from the forest floor including soil, litter and understorey vegetation. Here, we measured monoterpene emissions every 2 months over 2 years from logged tropical forest and oil palm plantation floor in Malaysian Borneo using static flux chambers. The main emitted monoterpenes were α-pinene, β-pinene and d-limonene. The amount of litter present was the strongest indicator for higher monoterpene fluxes. Mean α-pinene fluxes were around 2.5-3.5 μg C m^-2 h^-1 from the forest floor with occasional fluxes exceeding 100 μg C m^-2 h^-1. Fluxes from the oil palm plantation, where hardly any litter was present, were lower (on average 0.5-2.9 μg C m^-2 h^-1) and only higher when litter was present. All other measured monoterpenes were emitted at lower rates. No seasonal trends could be identified for all monoterpenes and mean fluxes from both forest and plantation floor were ~ 100 times smaller than canopy emission rates reported in the literature. Occasional spikes of higher emissions from the forest floor, however, warrant further investigation in terms of underlying processes and their contribution to regional scale atmospheric fluxes.

Heatwave frequency and seedling death alter stress-specific emissions of volatile organic compounds in Aleppo pine

Biogenic volatile organic compounds (BVOC) play important roles in plant stress responses and can serve as stress indicators. While the impacts of gradual environmental changes on BVOCs have been studied extensively, insights in emission responses to repeated stress and recovery are widely absent. Therefore, we studied the dynamics of shoot gas exchange and BVOC emissions in Pinus halepensis seedlings during an induced moderate drought, two four-day-long heatwaves, and the combination of drought and heatwaves. We found clear stress-specific responses of BVOC emissions. Reductions in acetone emissions with declining soil water content and transpiration stood out as a clear drought indicator. All other measured BVOC emissions responded exponentially to rising temperatures during heat stress (maximum of 43 °C), but monoterpenes and methyl salicylate showed a reduced temperature sensitivity during the second heatwave. We found that these decreases in monoterpene emissions between heatwaves were not reflected by similar declines in their internal storage pools. Because stress intensity was extremely severe, most of the seedlings in the heat-drought treatment died at the end of the second heatwave (dark respiration ceased). Interestingly, BVOC emissions (methanol, monoterpenes, methyl salicylate, and acetaldehyde) differed between dying and surviving seedlings, already well before indications of a reduced vitality became visible in gas exchange dynamics. In summary, we could clearly show that the dynamics of BVOC emissions are sensitive to stress type, stress frequency, and stress severity. Moreover, we found indications that stress-induced seedling mortality was preceded by altered methanol, monoterpene, and acetaldehyde emission dynamics.

Leaf isoprene emission as a trait that mediates the growth-defense tradeoff in the face of climate stress

Plant isoprene emissions are known to contribute to abiotic stress tolerance, especially during episodes of high temperature and drought, and during cellular oxidative stress. Recent studies have shown that genetic transformations to add or remove isoprene emissions cause a cascade of cellular modifications that include known signaling pathways, and interact to remodel adaptive growth-defense tradeoffs. The most compelling evidence for isoprene signaling is found in the shikimate and phenylpropanoid pathways, which produce salicylic acid, alkaloids, tannins, anthocyanins, flavonols and other flavonoids; all of which have roles in stress tolerance and plant defense. Isoprene also influences key gene expression patterns in the terpenoid biosynthetic pathways, and the jasmonic acid, gibberellic acid and cytokinin signaling networks that have important roles in controlling inducible defense responses and influencing plant growth and development, particularly following defoliation. In this synthesis paper, using past studies of transgenic poplar, tobacco and Arabidopsis, we present the evidence for isoprene acting as a metabolite that coordinates aspects of cellular signaling, resulting in enhanced chemical defense during periods of climate stress, while minimizing costs to growth. This perspective represents a major shift in our thinking away from direct effects of isoprene, for example, by changing membrane properties or quenching ROS, to indirect effects, through changes in gene expression and protein abundances. Recognition of isoprene's role in the growth-defense tradeoff provides new perspectives on evolution of the trait, its contribution to plant adaptation and resilience, and the ecological niches in which it is most effective.

Expected Impacts of Mixing European Beech with Silver Fir on Regional Air Quality and Radiation Balance

The anticipated climate change during the next decades is posing crucial challenges to ecosystems. In order to decrease the vulnerability of forests, introducing tree species’ mixtures are a viable strategy, with deep-rooting native Silver fir (Abies alba) being a primary candidate for admixture into current pure stands of European beech (Fagus sylvatica) especially in mountainous areas. Such a change in forest structure also has effects on the regional scale, which, however, have been seldomly quantified. Therefore, we measured and modeled radiative balance and air chemistry impacts of admixing Silver fir to European beech stands, including changes in biogenic volatile organic compound emissions. An increased fraction of Silver fir caused a smaller albedo and a (simulated) larger evapotranspiration, leading to a dryer and warmer forest. While isoprene emission was negligible for both species, sesquiterpene and monoterpene emissions were larger for fir than for beech. From these differences, we derived that ozone concentration as well as secondary organic aerosols and cloud condensation nuclei would increase regionally. Overall, we demonstrated that even a relatively mild scenario of tree species change will alter the energy balance and air quality in a way that could potentially influence the climate on a landscape scale.

Wildfire effects on BVOC emissions from boreal forest floor on permafrost soil in Siberia

One of the effects of climate change on boreal forest will be more frequent forest wildfires and permafrost thawing. These will increase the availability of soil organic matter (SOM) for microorganisms, change the ground vegetation composition and ultimately affect the emissions of biogenic volatile organic compounds (BVOCs), which impact atmospheric chemistry and climate. BVOC emissions from boreal forest floor have been little characterized in southern boreal region, and even less so in permafrost soil, which underlies most of the northern boreal region. Here, we report the long-term effects of wildfire on forest floor BVOC emission rates along a wildfire chronosequence in a Larix gmelinii forest in central Siberia. We determined forest floor BVOC emissions from forests exposed to wildfire 1, 23 and > 100 years ago. We studied how forest wildfires and the subsequent succession of ground vegetation, as well as changes in the availability of SOM along with the deepened and recovered active layer, influence BVOC emission rates. The forest floor acted as source of a large number of BVOCs in all forest age classes. Monoterpenes were the most abundant BVOC group in all age classes. The total BVOC emission rates measured from the 23- and >100-year-old areas were ca. 2.6 times higher than the emissions from the 1-year-old area. Lower emissions were related to a decrease in plant coverage and microbial decomposition of SOM after wildfire. Our results showed that forest wildfires play an important indirect role in regulating the amount and composition of BVOC emissions from post-fire originated boreal forest floor. This could have a substantial effect on BVOC emissions if the frequency of forest wildfires increases in the future as a result of climate warming.

The Atmosphere

The atmosphere is composed of nitrogen, oxygen and argon, a variety of trace gases, and particles or aerosols from a variety of sources. Reactive, trace gases have short mean residence time in the atmosphere and large spatial and temporal variations in concentration. Many trace gases are removed by reaction with hydroxyl radical and deposition in rainfall or dryfall at the Earth's surface. The upper atmosphere, the stratosphere, contains ozone that screens ultraviolet light from the Earth's surface. Chlorofluorocarbons released by humans lead to the loss of stratospheric ozone, which might eventually render the Earth's land surface uninhabitable. Changes in the composition of the atmosphere, especially rising concentrations of CO₂, CH₄, and N₂O, will lead to climatic changes over much of the Earth's surface.

Molecular characterization and kinetics of isoprene degrading bacteria

Isoprene, the highly reactive volatile organic compound, is used as monomer for the synthesis of several useful polymers. Its extensive production and usage leads to contamination of air. Once released, it alters the atmospheric chemistry by reacting with hydroxyl radicals (OH) and nitrogen oxides (NO_x) to generate tropospheric ozone. Its prolonged exposure causes deleterious effects in human and plants. Therefore, its removal from the contaminated environment through biodegradation, provides a promising remedial solution. In the present study, isoprene utilizing bacteria namely, Pseudomonas sp., Arthrobacter sp., Bacillus sp. Sphingobacterium sp., Sphingobium sp., and Pantoea sp. were isolated and characterized from leaf surface of Madhuca latifolia and Tectona grandis, and also from soils under these plants. Their isoprene degrading capability and kinetics were assessed in batch mode. The isoprene degradation study indicated Pseudomonas sp. to be the most efficient isoprene degrader.

Profiles of volatile organic compound emissions from soils amended with organic waste products

Volatile Organic Compounds (VOCs) are reactive compounds essential to atmospheric chemistry. They are mainly emitted by living organisms, and mostly by plants. Soil microbes also contribute to emissions of VOCs. However, these emissions have not yet been characterised in terms of quality and quantity. Furthermore, long-term organic matter amendments are known to affect the microbial content of soils, and hence the quantity and quality of VOC emissions. This study investigates which and how much of these VOCs are emitted from soil amended with organic waste products (OWPs). Four OWPs were investigated: municipal solid waste compost (MSW), green waste and sludge co-compost (GWS), bio-waste compost (BIOW) and farmyard manure (FYM). These OWPs have been amended every two years since 1998 until now at a rate of ~4 tC ha^-1. A soil receiving no organic inputs was used as a reference (CN). VOCs emissions were measured under laboratory conditions using a Proton Transfer Reaction-Quadrupole ion guide Time of Flight-Mass Spectrometry (PTR-QiToF-MS). A laboratory system was set up made of two Pyrex chambers, one for samples and the second empty, to be used as a blank. Our results showed that total VOC emissions were higher in BIOW than in MSW. Further findings outlined that the most emitted compounds were acetone, butanone and acetaldehyde in all treatments, suggesting a common production mechanism for these compounds, meaning they were not affected by the OWP amendment. We isolated 21 VOCs that had statistically different emissions between the treatments and could therefore be considered as good markers of soil biological functioning. Our results suggest that organic matter and pH jointly influenced total VOC emissions. In conclusion, OWPs in soil affect the type of VOC emissions and the total flux also depends on the pH of the soil and the quantity of organic matter.

Structural and Chemical Biology of Terpenoid Cyclases

The year 2017 marks the twentieth anniversary of terpenoid cyclase structural biology: a trio of terpenoid cyclase structures reported together in 1997 were the first to set the foundation for understanding the enzymes largely responsible for the exquisite chemodiversity of more than 80000 terpenoid natural products. Terpenoid cyclases catalyze the most complex chemical reactions in biology, in that more than half of the substrate carbon atoms undergo changes in bonding and hybridization during a single enzyme-catalyzed cyclization reaction. The past two decades have witnessed structural, functional, and computational studies illuminating the modes of substrate activation that initiate the cyclization cascade, the management and manipulation of high-energy carbocation intermediates that propagate the cyclization cascade, and the chemical strategies that terminate the cyclization cascade. The role of the terpenoid cyclase as a template for catalysis is paramount to its function, and protein engineering can be used to reprogram the cyclization cascade to generate alternative and commercially important products. Here, I review key advances in terpenoid cyclase structural and chemical biology, focusing mainly on terpenoid cyclases and related prenyltransferases for which X-ray crystal structures have informed and advanced our understanding of enzyme structure and function.

Monocarbon cationic cluster yields from N2/CH4 mixtures embedded in He nanodroplets and their calculated binding energies

The formation of monocarbon cluster ions has been investigated by electron ionization mass spectrometry of cold helium nanodroplets doped with nitrogen/methane mixtures. Ion yields for two groups of clusters, CHmN2(+) or CHmN4(+), were determined for mixtures with different molecular ratios of CH4. The possible geometrical structures of these clusters were analyzed using electronic structure computations. Little correlation between the ion yields and the associated binding energies has been observed indicating that in most cases kinetic control is more important than thermodynamic control for forming the clusters.

Why only some plants emit isoprene

Isoprene (2-methyl-1,3-butadiene) is emitted from many plants and it appears to have an adaptive role in protecting leaves from abiotic stress. However, only some species emit isoprene. Isoprene emission has appeared and been lost many times independently during the evolution of plants. As an example, our phylogenetic analysis shows that isoprene emission is likely ancestral within the family Fabaceae (= Leguminosae), but that it has been lost at least 16 times and secondarily gained at least 10 times through independent evolutionary events. Within the division Pteridophyta (ferns), we conservatively estimate that isoprene emissions have been gained five times and lost two times through independent evolutionary events. Within the genus Quercus (oaks), isoprene emissions have been lost from one clade, but replaced by a novel type of light-dependent monoterpene emissions that uses the same metabolic pathways and substrates as isoprene emissions. This novel type of monoterpene emissions has appeared at least twice independently within Quercus, and has been lost from 9% of the individuals within a single population of Quercus suber. Gain and loss of gene function for isoprene synthase is possible through relatively few mutations. Thus, this trait appears frequently in lineages; but, once it appears, the time available for evolutionary radiation into environments that select for the trait is short relative to the time required for mutations capable of producing a non-functional isoprene synthase gene. The high frequency of gains and losses of the trait and its heterogeneous taxonomic distribution in plants may be explained by the relatively few mutations necessary to produce or lose the isoprene synthase gene combined with the assumption that isoprene emission is advantageous in a narrow range of environments and phenotypes.

A Laboratory of Extremophiles: Iceland Coordination Action for Research Activities on Life in Extreme Environments (CAREX) Field Campaign

Existence of life in extreme environments has been known for a long time, and their habitants have been investigated by different scientific disciplines for decades. However, reports of multidisciplinary research are uncommon. In this paper, we report an interdisciplinary three-day field campaign conducted in the framework of the Coordination Action for Research Activities on Life in Extreme Environments (CAREX) FP7EU program, with participation of experts in the fields of life and earth sciences. In situ experiments and sampling were performed in a 20 m long hot springs system of different temperature (57 °C to 100 °C) and pH (2 to 4). Abiotic factors were measured to study their influence on the diversity. The CO2 and H2S concentration varied at different sampling locations in the system, but the SO2 remained the same. Four biofilms, mainly composed by four different algae and phototrophic protists, showed differences in photosynthetic activity. Varying temperature of the sampling location affects chlorophyll fluorescence, not only in the microbial mats, but plants (Juncus), indicating selective adaptation to the environmental conditions. Quantitative polymerase chain reaction (PCR), DNA microarray and denaturing gradient gel electrophoresis (DGGE)-based analysis in laboratory showed the presence of a diverse microbial population. Even a short duration (30 h) deployment of a micro colonizer in this hot spring system led to colonization of microorganisms based on ribosomal intergenic spacer (RISA) analysis. Polyphasic analysis of this hot spring system was possible due to the involvement of multidisciplinary approaches.

Evidence for iron-mediated anaerobic methane oxidation in a crude oil-contaminated aquifer

In a methanogenic crude oil contaminated aquifer near Bemidji, Minnesota, the decrease in dissolved CH(4) concentrations along the groundwater flow path, along with the positive shift in δ(13) C(CH) (4) and negative shift in δ(13) C(DIC) , is indicative of microbially mediated CH(4) oxidation. Calculations of electron acceptor transport across the water table, through diffusion, recharge, and the entrapment and release of gas bubbles, suggest that these processes can account for at most 15% of the observed total reduced carbon oxidation, including CH(4) . In the anaerobic plume, the characteristic Fe(III)-reducing genus Geobacter was the most abundant of the microbial groups tested, and depletion of labile sediment iron is observed over time, confirming that reduced carbon oxidation coupled to iron reduction is an important process. Electron mass balance calculations suggest that organic carbon sources in the aquifer, BTEX and non-volatile dissolved organic carbon, are insufficient to account for the loss in sediment Fe(III), implying that CH(4) oxidation may also be related to Fe(III) reduction. The results support a hypothesis of Fe(III)-mediated CH(4) oxidation in the contaminated aquifer.

Modeling the isoprene emission rate from leaves

The leaves of many plants emit isoprene (2-methyl-1,3-butadiene) to the atmosphere, a process which has important ramifications for global and regional atmospheric chemistry. Quantitation of leaf isoprene emission and its response to environmental variation are described by empirically derived equations that replicate observed patterns, but have been linked only in some cases to known biochemical and physiological processes. Furthermore, models have been proposed from several independent laboratories, providing multiple approaches for prediction of emissions, but with little detail provided as to how contrasting models are related. In this review we provide an analysis as to how the most commonly used models have been validated, or not, on the basis of known biochemical and physiological processes. We also discuss the multiple approaches that have been used for modeling isoprene emission rate with an emphasis on identifying commonalities and contrasts among models, we correct some mathematical errors that have been propagated through the models, and we note previously unrecognized covariances within processes of the models. We come to the conclusion that the state of isoprene emission modeling remains highly empirical. Where possible, we identify gaps in our knowledge that have prevented us from achieving a greater mechanistic foundation for the models, and we discuss the insight and data that must be gained to fill those gaps.

Increased thermostability of thylakoid membranes in isoprene-emitting leaves probed with three biophysical techniques

Three biophysical approaches were used to get insight into increased thermostability of thylakoid membranes in isoprene-emittingplants.Arabidopsis (Arabidopsis thaliana) plants genetically modified to make isoprene and Platanus orientalis leaves, in which isoprene emission was chemically inhibited, were used. First, in the circular dichroism spectrum the transition temperature of the main band at 694 nm was higher in the presence of isoprene, indicating that the heat stability of chiral macrodomains of chloroplast membranes, and specifically the stability of ordered arrays of light-harvesting complex II-photosystem II in the stacked region of the thylakoid grana, was improved in the presence of isoprene. Second, the decay of electrochromic absorbance changes resulting from the electric field component of the proton motive force (ΔA₅₁₅) was evaluated following single-turnover saturating flashes. The decay of ΔA₅₁₅ was faster in the absence of isoprene when leaves of Arabidopsis and Platanus were exposed to high temperature, indicating that isoprene protects the thylakoid membranes against leakiness at elevated temperature. Finally, thermoluminescence measurements revealed that S₂Q(B)⁻ charge recombination was shifted to higher temperature in Arabidopsis and Platanus plants in the presence of isoprene, indicating higher activation energy for S₂Q(B)⁻ redox pair, which enables isoprene-emitting plants to perform efficient primary photochemistry of photosystem II even at higher temperatures. The data provide biophysical evidence that isoprene improves the integrity and functionality of the thylakoid membranes at high temperature. These results contribute to our understanding of isoprene mechanism of action in plant protection against environmental stresses.

Structure of isoprene synthase illuminates the chemical mechanism of teragram atmospheric carbon emission

The X-ray crystal structure of recombinant PcISPS (isoprene synthase from gray poplar hybrid Populus×canescens) has been determined at 2.7 Å resolution, and the structure of its complex with three Mg(2+) and the unreactive substrate analogue dimethylallyl-S-thiolodiphosphate has been determined at 2.8 Å resolution. Analysis of these structures suggests that the generation of isoprene from substrate dimethylallyl diphosphate occurs via a syn-periplanar elimination mechanism in which the diphosphate-leaving group serves as a general base. This chemical mechanism is responsible for the annual atmospheric emission of 100 Tg of isoprene by terrestrial plant life. Importantly, the PcISPS structure promises to guide future protein engineering studies, potentially leading to hydrocarbon fuels and products that do not rely on traditional petrochemical sources.

Environmental control of terpene emissions from Cistus monspeliensis L. in natural Mediterranean shrublands

The large amount of volatile organic compound (VOC) emitted by vegetation modifies air quality contributing to both tropospheric ozone and secondary organic aerosol production. A better understanding of the factors controlling VOC emissions by vegetation is mandatory in order to improve emission estimates derived from tropospheric chemistry models. Although the Mediterranean shrublands are particularly abundant and rich in emitting species, their emission potential is poorly known. Focusing on a VOC-emitting shrub species widespread in the Mediterranean area (Cistus monspeliensis L.), we measured and analysed its emissions of terpenes taking into account the age of individuals, the season of sampling and the soil type. Sampling was done under natural environmental conditions. Species of the genus Cistus are frequently reported to be storing species, although we found only one stored monoterpene and three sesquiterpenes in very low amount. Major emitted compounds were alpha-pinene and beta-myrcene. Total terpene emissions were not influenced by plant age but emission of some individual terpenes was positively correlated with age. A strong seasonal effect was evidenced. A larger amount of terpenes was emitted during spring and summer than during fall and winter. Summer emission rates were nearly 70 times higher than winter emission rates. Total and individual terpene emissions were influenced by soil type; emissions on siliceous substrate were ca. seven times higher than those on calcareous substrate. In conclusion, it appears clearly that environmental factors such as soil nature and season should be taken into account in order to achieve improved modelling of terpene emissions by shrub species.

Characterization of marine isoprene-degrading communities

Isoprene is a volatile and climate-altering hydrocarbon with an atmospheric concentration similar to that of methane. It is well established that marine algae produce isoprene; however, until now there was no specific information about marine isoprene sinks. Here we demonstrate isoprene consumption in samples from temperate and tropical marine and coastal environments, and furthermore show that the most rapid degradation of isoprene coincides with the highest rates of isoprene production in estuarine sediments. Isoprene-degrading enrichment cultures, analysed by denaturing gradient gel electrophoresis and 454 pyrosequencing of the 16S rRNA gene and by culturing, were generally dominated by Actinobacteria, but included other groups such as Alphaproteobacteria and Bacteroidetes, previously not known to degrade isoprene. In contrast to specialist methane-oxidizing bacteria, cultivated isoprene degraders were nutritionally versatile, and nearly all of them were able to use n-alkanes as a source of carbon and energy. We therefore tested and showed that the ubiquitous marine hydrocarbon-degrader, Alcanivorax borkumensis, could also degrade isoprene. A mixture of the isolates consumed isoprene emitted from algal cultures, confirming that isoprene can be metabolized at low, environmentally relevant concentrations, and suggesting that, in the absence of spilled petroleum hydrocarbons, algal production of isoprene could maintain viable populations of hydrocarbon-degrading microbes. This discovery of a missing marine sink for isoprene is the first step in obtaining more robust predictions of its flux, and suggests that algal-derived isoprene provides an additional source of carbon for diverse microbes in the oceans.

Isoprene and nitric oxide reduce damages in leaves exposed to oxidative stress

Isoprene and nitric oxide (NO) are two volatile molecules that are produced in leaves. Both compounds were suggested to have an important protective role against stresses. We tested, in two isoprene-emitting species, Populus nigra and Phragmites australis, whether: (1) NO emission outside leaves is measurable and is affected by oxidative stresses; and (2) isoprene and NO protect leaves against oxidative stresses, both singularly and in combination. The emission of NO was undetectable, and the compensation point was very low in control poplar leaves. Both emission and compensation point increased dramatically in stressed leaves. NO emission was inversely associated with stomatal conductance. More NO was emitted in leaves that were isoprene-inhibited, and more isoprene was emitted when NO was reduced by NO scavenger c-PTIO. Both isoprene and NO reduced oxidative damages. Isoprene-emitting leaves which were also fumigated with NO, or treated with NO donor, showed low damage to photosynthesis, a reduced accumulation of H(2)O(2) and a reduced membrane denaturation. We conclude that measurable amounts of NO are only produced and emitted by stressed leaves, that both isoprene and NO are effective antioxidant molecules and that an additional protection is achieved when both molecules are released.

Phylogenetic and functional gene analysis of the bacterial and archaeal communities associated with the surface microlayer of an estuary

The surface microlayer (SML) is the thin biogenic film found at the surface of a water body. The SML is poorly understood but has been shown to be important in biogeochemical cycling and sea-air gas exchange. We sampled the SML of the Blyth estuary at two sites (salinities 21 and 31 psu) using 47 mm polycarbonate membranes. DNA was extracted from the SML and corresponding subsurface water (0.4 m depth) and microbial (bacteria and archaea) community analysis was performed using denaturing gradient gel electrophoresis of 16S rRNA gene PCR amplicons. The diversity of bacterial functional genes that encode enzyme subunits for methane monooxygenase (pmoA and mmoX) and carbon monoxide dehydrogenase (coxL) was assessed using PCR, clone library construction and restriction fragment length polymorphism (RFLP) analysis. Methanotroph genes were present only in low copy numbers and pmoA was detected only in subsurface samples. Diversity of mmoX genes was low and most of the clone sequences detected were similar to those of mmoX from Methylomonas spp. Interestingly, some sequences detected in the SML were different from those detected in the subsurface. RFLP analysis of coxL clone libraries indicated a high diversity of carbon monoxide (CO)-utilizing bacteria in the estuary. The habitats of the closely related coxL sequences suggest that CO-utilizing bacteria in the estuary are recruited from both marine and freshwater/terrestrial inputs. In contrast, methanotroph recruitment appears to occur solely from freshwater input into the estuary.

Regulation of isoprene emission in Populus trichocarpa leaves subjected to changing growth temperature

The hydrocarbon isoprene is emitted in large quantities from numerous plant species, and has a substantial impact on atmospheric chemistry. Temperature affects isoprene emission at several levels: the temperature at which emission is measured, the temperature at which leaves develop, and the temperatures to which a mature leaf is exposed in the days prior to emission measurement. The molecular regulation of the response to the last of these factors was investigated in this study. When plants were grown at 20 degrees C and moved from 20 to 30 degrees C and back, or grown at 30 degrees C and moved from 30 to 20 degrees C and back, their isoprene emission peaked within 3 h of the move and stabilized over the following 3 d. Trees that developed at 20 degrees C and experienced 30 degrees C episodes had higher isoprene emission capacities than did leaves grown exclusively at 20 degrees C, even 2 weeks after the last 30 degrees C episode. The levels and extractable activities of isoprene synthase protein, which catalyses the synthesis of isoprene, and those of dimethylallyl diphosphate (DMADP), its substrate, alone could not explain observed variations in isoprene emission. Therefore, we conclude that control of isoprene emission in mature leaves is shared between isoprene synthase protein and DMADP supply.

The effect of elevated CO2, soil and atmospheric water deficit and seasonal phenology on leaf and ecosystem isoprene emission

Two cottonwood plantations were grown at different CO₂ concentrations at the Biosphere 2 Laboratory in Arizona to investigate the response of isoprene emission to elevated [CO₂] and its interaction with water deficits. We focused on responses due to seasonal variation and variation in the mean climate from one year to the next. In fall and in spring, isoprene emission rate showed a similar inhibition by elevated [CO₂], despite an 8-10°C seasonal difference in mean air temperature. The overall response of isoprene emission to drought was also similar for observations conducted during the spring or fall, and during the fall of two different years with an approximate 5°C difference in mean air temperature. In general, leaf-level isoprene emission rates, measured at constant temperature and photon-flux density, decreased slightly, or remained constant during drought, whereas ecosystem-level isoprene emission rates increased. The uncoupling of ecosystem- and leaf-scale responses is not due to differential dependence on leaf area index (LAI) as LAI increased only slightly, or decreased, during the drought treatments at the same time that ecosystem isoprene emission rate increased greatly. Nor does the difference in isoprene emission rate between leaves and ecosystems appear to be due solely to increases in canopy surface temperature during the drought, though some increase in temperature was observed. It is possible that still further factors, such as increased penetration of PPFD into the canopy as a result of changes in leaf angle, reduced sink strength of the soil for atmospheric isoprene, and decreases in the mean C_i of leaves, combined with the small increases in canopy surface temperature, increased the ecosystem isoprene emission rate. Whatever the causes of the differences in the leaf and ecosystem responses, we conclude that the overall shape of the leaf and ecosystem responses to drought was constant irrespective of season or year.

Isoprene emission from terrestrial ecosystems in response to global change: minding the gap between models and observations

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.

Carbon monoxide uptake kinetics in unamended and long-term nitrogen-amended temperate forest soils

The effect of nitrogen (N) additions on the dynamics of carbon monoxide consumption in temperate forest soils is poorly understood. We measured soil CO profiles, potential rates of CO consumption and uptake kinetics in temperate hardwood and pine control plots and plots amended with 50 and 150 kg N ha-1 year-1 for more than 15 years. Soil profiles of CO concentrations were above atmospheric levels in the high-N plots of both stands, suggesting that in these forest soils the balance between consumption and production may be shifted so that either production is increased or consumption decreased. Highest rates of CO consumption were measured in the organic horizon and decreased with soil depth. In the N-amended plots, CO consumption increased in all but one soil depth of the hardwood stand, but decreased in all soil depths of the pine stand. CO enzyme affinities increased with soil depth in the control plots. However, enzyme affinities in the most active soil depths (organic and 0-5 cm mineral) decreased in response to low levels of N in both stands. In the high-N plots, affinities dramatically-increased in the hardwood stand, but decreased in the organic horizon and increased slightly in the 0-5 cm mineral soil in the pine stand. These findings indicate that long-term N addition either by fertilization or deposition may alter the size, composition and/or physiology of the community of CO consumers so that their ability to act as a sink for atmospheric CO has changed. This change could have a substantial effect on the lifetime of greenhouse gases such as CH4 and therefore the future of Earth's climate.

The interacting effects of elevated atmospheric CO2 concentration, drought and leaf-to-air vapour pressure deficit on ecosystem isoprene fluxes

Isoprene is the most abundant biogenic hydrocarbon released from vegetation and it plays a major role in tropospheric chemistry. Because of its link to climate change, there is interest in understanding the relationship between CO2, water availability and isoprene emission. We explored the effect of atmospheric elevated CO2 concentration and its interaction with vapour pressure deficit (VPD) and water stress, on gross isoprene production (GIP) and net ecosystem exchange of CO2 (NEE) in two Populus deltoides plantations grown at ambient and elevated atmospheric CO2 concentration in the Biosphere 2 Laboratory facility. Although GIP and NEE showed a similar response to light and temperature, their responses to CO2 and VPD were opposite; NEE was stimulated by elevated CO2 and depressed by high VPD, while GIP was inhibited by elevated CO2 and stimulated by high VPD. The difference in response between isoprene production and photosynthesis was also evident during water stress. GIP was stimulated in the short term and declined only when the stress was severe, whereas NEE started to decrease from the beginning of the experiment. This contrasting response led the carbon lost as isoprene in both the ambient and the elevated CO2 treatments to increase as water stress progressed. Our results suggest that water limitation can override the inhibitory effect of elevated CO2 leading to increased global isoprene emissions in a climate change scenario with warmer and drier climate.

Effect of elevated CO2 concentration and vapour pressure deficit on isoprene emission from leaves of Populus deltoides during drought

To further our understanding of the influence of global climate change on isoprene production we studied the effect of elevated [CO₂] and vapour pressure deficit (VPD) on isoprene emission rates from leaves of Populus deltoides Bartr. during drought stress. Trees, grown inside three large bays with atmospheres containing 430, 800, or 1200 μmol mol^-1 CO₂ at the Biosphere 2 facility, were subjected to a period of drought during which VPD was manipulated, switching between low VPD (approximately 1 kPa) and high VPD (approximately 3 kPa) for several days. When trees were not water-stressed, elevated [CO₂] inhibited isoprene emission and stimulated photosynthesis. Isoprene emission was less responsive to drought than photosynthesis. As water-stress increased, the inhibition of isoprene emission disappeared, probably as a result of stomatal closure and the resulting decreases in intercellular [CO₂] (C_i). This assumption was supported by increased isoprene emission under high VPD. Drought and high VPD dramatically increased the proportion of assimilated carbon lost as isoprene. When measured at the same [CO₂], leaves from trees grown at ambient [CO₂] always had higher isoprene emission rates than the leaves of trees grown at elevated [CO₂], demonstrating that CO₂ inhibition is a long-term effect.

CO-sensing mechanisms

Carbon monoxide (CO) has long been known to have dramatic physiological effects on organisms ranging from bacteria to humans, but recently there have a number of suggestions that organisms might have specific sensors for CO. This article reviews the current evidence for a variety of proteins with demonstrated or potential CO-sensing ability. Particular emphasis is placed on the molecular description of CooA, a heme-containing CO sensor from Rhodospirillum rubrum, since its biological role as a CO sensor is clear and we have substantial insight into the basis of its sensing ability.

Isoprenoid emissions of Quercus spp. (Q. suber and Q. ilex) in mixed stands contrasting in interspecific genetic introgression

•  Among oak species, Quercus ilex is classified as a monoterpene emitter and Q. suber is mainly known as a nonisoprenoid emitter. The extent and origin of this diversification is unknown. •  We examined intra- and interspecific emission variability in two mixed stands which differed in their level of hybridization and reciprocal genetic introgression based on variations in cytoplasmic (chloroplast DNA) and nuclear (allozyme) markers. •  At both sites all trees identified as Q. ilex, or as recent descendants from Q. ilex × Q. suber hybrids, emitted monoterpenes. Of Q. suber trees (genetically introgressed or not by Q. ilex), 91% were also monoterpene emitters, and the remainder nonemitters. One tree identified as a Q. canariensis × Q. ilex hybrid emitted both isoprene and monoterpenes. Compared with Q. ilex, the standard emission rate of Q. suber was higher in summer and lower in autumn. Both species emitted the same monoterpenes, proportions of which showed significant intra- and interspecific variability. •  The results suggest that Q. suber populations in the French Mediterranean intrinsically emit monoterpenes, and that gene flow between oak species contributes to diversification of emission signatures.