Leaf-level Measurements Research Articles

Novel methods facilitating the mechanistic interpretation of multiscale optical remote sensing measurements

Plant physiology concentrates on the study of plant internal processes, such as growth, nutrient uptake and photosynthesis. The quantification of photosynthesis regulation is significant in understanding how plants react to the changing climate. Spectral remote sensing methods, using both reflected light in the visible and near infrared wavelengths, as well as chlorophyll fluorescence, are used to gather information about plant physiological variables. These methods have developed rapidly, prompted by the advances in remote sensing platforms and sensors. However, interpretation of remote sensing signals can be challenging. Due to canopy heterogeneity, the signal is affected by various elements, such as scattering, soil background and canopy structural effects. Additionally, open questions remain linked to the underlying mechanistic processes in the leaf modulating the optical signal, such as nutrient contents and leaf photochemistry, and how these processes and the optical signals diverge in response to temporal variation. Through multi-scale measurements, this thesis aims to advance the interpretation of optical remote sensing signals as they are affected by spatial and temporal variation, while promoting the use of novel methods and devices. Results indicate that diurnal and long-term variation of solar induced fluorescence (SIF) is driven by photosynthetic and structural factors, causing possible misinterpretations in SIF data. Additionally, depending on the scale of observation, results show that the capacity of remote sensing to detect changes in foliar nutrients depends on the covariation of nutrients, pigments and canopy structure, underlining the need for both leaf and canopy level measurements. Finally, we advocate for the implementation of a novel miniaturized fluorometer, demonstrating the ability to track the seasonal regulation of photosynthesis using integrated measurements of chlorophyll fluorescence and gas exchange. The results from this thesis underline the need for simultaneous multi-scale measurements of leaf and canopy physiological factors to further our understanding of photosynthesis regulation.

What to Choose for Estimating Leaf Water Status-Spectral Reflectance or Invivo Chlorophyll Fluorescence?

In the context of global climate change and the increasing need to study plant response to drought, there is a demand for easily, rapidly, and remotely measurable parameters that sensitively reflect leaf water status. Parameters with this potential include those derived from leaf spectral reflectance (R) and chlorophyll fluorescence. As each of these methods probes completely different leaf characteristics, their sensitivity to water loss may differ in different plant species and/or under different circumstances, making it difficult to choose the most appropriate method for estimating water status in a given situation. Here, we present a simple comparative analysis to facilitate this choice for leaf-level measurements. Using desiccation of tobacco (Nicotiana tabacum L. cv. Samsun) and barley (Hordeum vulgare L. cv. Bojos) leaves as a model case, we measured parameters of spectral R and chlorophyll fluorescence and then evaluated and compared their applicability by means of introduced coefficients (coefficient of reliability, sensitivity, and inaccuracy). This comparison showed that, in our case, chlorophyll fluorescence was more reliable and universal than spectral R. Nevertheless, it is most appropriate to use both methods simultaneously, as the specific ranking of their parameters according to the coefficient of reliability may indicate a specific scenario of changes in desiccating leaves.

Making the Genotypic Variation Visible: Hyperspectral Phenotyping in Scots Pine Seedlings.

Hyperspectral reflectance contains valuable information about leaf functional traits, which can indicate a plant's physiological status. Therefore, using hyperspectral reflectance for high-throughput phenotyping of foliar traits could be a powerful tool for tree breeders and nursery practitioners to distinguish and select seedlings with desired adaptation potential to local environments. We evaluated the use of 2 nondestructive methods (i.e., leaf and proximal/canopy) measuring hyperspectral reflectance in the 350- to 2,500-nm range for phenotyping on 1,788 individual Scots pine seedlings belonging to lowland and upland ecotypes of 3 different local populations from the Czech Republic. Leaf-level measurements were collected using a spectroradiometer and a contact probe with an internal light source to measure the biconical reflectance factor of a sample of needles placed on a black background in the contact probe field of view. The proximal canopy measurements were collected under natural solar light, using the same spectroradiometer with fiber optical cable to collect data on individual seedlings' hemispherical conical reflectance factor. The latter method was highly susceptible to changes in incoming radiation. Both spectral datasets showed statistically significant differences among Scots pine populations in the whole spectral range. Moreover, using random forest and support vector machine learning algorithms, the proximal data obtained from the top of the seedlings offered up to 83% accuracy in predicting 3 different Scots pine populations. We conclude that both approaches are viable for hyperspectral phenotyping to disentangle the phenotypic and the underlying genetic variation within Scots pine seedlings.

Attributing differences of solar-induced chlorophyll fluorescence (SIF)-gross primary production (GPP) relationships between two C4 crops: corn and miscanthus

There remains limited information to characterize the solar-induced chlorophyll fluorescence (SIF)-gross primary production (GPP) relationship in C4 cropping systems. The annual C4 crop corn and perennial C4 crop miscanthus differ in phenology, canopy structure and leaf physiology. Investigating the SIF-GPP relationships in these species could deepen our understanding of SIF-GPP relationships within C4 crops. Using in situ canopy SIF and GPP measurements for both species along with leaf-level measurements, we found considerable differences in the SIF-GPP relationships between corn and miscanthus, with a stronger SIF-GPP relationship and higher slope of SIF-GPP observed in corn compared to miscanthus. These differences were mainly caused by leaf physiology. For miscanthus, high non-photochemical quenching (NPQ) under high light, temperature and water vapor deficit (VPD) conditions caused a large decline of fluorescence yield (Φ F ), which further led to a SIF midday depression and weakened the SIF-GPP relationship. The larger slope in corn than miscanthus was mainly due to its higher GPP in mid-summer, largely attributed to the higher leaf photosynthesis and less NPQ. Our results demonstrated variation of the SIF-GPP relationship within C4 crops and highlighted the importance of leaf physiology in determining canopy SIF behaviors and SIF-GPP relationships.

Responses of forest carbon and water coupling to thinning treatments from leaf to stand scales in a young montane pine forest

BackgroundWater-use efficiency (WUE) represents the coupling of forest carbon and water. Little is known about the responses of WUE to thinning at multiple spatial scales. The objective of this research was to use field measurements to understand short-term effects of two thinning treatments (T1: 4500 stems ha−1; and T2: 1100 stems ha−1) and the control (NT: 27,000 stems ha−1) on WUE at the three spatial scales (leaf level: the ratio of leaf photosynthesis to leaf transpiration; tree-level: tree growth to tree transpiration; and stand level: net primary production (NPP) to stand transpiration) and intrinsic WUEi (the ratio of leaf photosynthesis to stomatal conductance at leaf-level; and NPP to canopy conductance at stand-level) in a 16-year old natural lodgepole pine forest. Leaf-level measurements were conducted in 2017, while tree- and stand-level measurements were conducted in both 2016 (the normal precipitation year) and 2017 (the drought year).ResultsThe thinning treatments did not significantly affect the tree- and stand-level WUE in the normal year of 2016. However, the thinning significantly affected WUE in the drought year of 2017: T2 exhibited significantly higher tree-level WUE (0.49 mm2 kg−1) than NT (0.08 mm2 kg−1), and compared to NT, the stand-level WUE values in the thinned stands (T1 and T2) were significantly higher, with means of 0.31, 0.56 and 0.70 kg m−3, respectively. However, the leaf-level and stand-level WUEi in the thinned stands in the drought year were significantly lower than those in the unthinned stands. No significant differences in the leaf-level WUE were found among the treatments in 2017. In addition, the thinning did not significantly change the WUE-VPD relationships at any studied spatial scale.ConclusionsThe thinning treatments did not cause significant changes in all studied WUE metrics in a normal year. However, their effects were significantly promoted under the drought conditions probably due to the decrease in soil water availability, demonstrating that thinning can improve WUE and consequently support forests to cope with the drought effects. The inconsistent results on the effects of the thinning on forest carbon and water coupling at the spatial scales and the lack of the consistent WUE metrics constraint across-scale comparison and transferring of WUE.

Biophysically Informed Imaging Acquisition of Plant Water Status

Vegetation controls carbon and water fluxes because of the fundamental tradeoff between carbon dioxide uptake and water loss occurring when stomata are open. Quantifying the rates of this exchange typically requires either intensive gas exchange or destructive harvesting of tissues and mass spectrometry analyses. Recent developments in high-throughput methods have enhanced our capacity to empirically test plant-environmental interactions. The vast integration characterizing satellite remote sensing methods masks organ-level physiological mechanisms limiting the predictive capability of current process models. Hence, more ground truth studies are necessary to determine the amount of mechanistic information needed to improve our understanding of forest, crop, and land management. Imaging methodologies, such as thermal and chlorophyll a fluorescence, are currently used to collect information for relevant traits such as water use, growth, and stress response. We tested these techniques during progressive drought across species with different susceptibility in controlled greenhouse conditions. We chose two highly represented tree species in North America: the gymnosperm Pinus ponderosa and the angiosperm Populus tremuloides. To better explore the whole drought response parameter space, we also tested a crop (Brassica rapa) and desert shrub (Artemisia tridentata). Thermal and fluorescence images of the canopy were coupled with leaf-level measurements as we performed three tests to predict drought response using 1) leaf temperature, 2) chlorophyll a fluorescence, and 3) the combination of the two. At five days of drought, leaf temperature increased 7 and 10%, accounting for 63% and 73% of the variation in stomatal conductance for both tree species, respectively. The fluorescence signal from images decreased ~12% and ~83% in moderately and severely droughted leaves respectively, reaching zero at mortality. Leaf water status was then predicted using a Bayesian approach that incorporated measurements’ uncertainty and parsimony in the analysis of the parameters. Changes in canopy temperature provided confident predictions for the reductions of daily evapotranspiration at the onset of drought. Empirically combining thermal and fluorescence measurements improved predictions (R2 = 0.81) of midday leaf water potential compared to univariate models. Our results represent an important step towards quantifying plant water status during drought using first principles that do not require species-specific information.

Simultaneous leaf-level measurement of trace gas emissions and photosynthesis with a portable photosynthesis system

Abstract. Plants emit considerable quantities of volatile organic compounds (VOCs), the identity and amount of which vary with temperature, light, and other environmental factors. Portable photosynthesis systems are a useful method for simultaneously quantifying in situ leaf-level emissions of VOCs and plant physiology. We present a comprehensive characterization of the LI-6800 portable photosynthesis system's ability to be coupled to trace gas detectors and measure leaf-level trace gas emissions, including limits in flow rates, environmental parameters, and VOC backgrounds. Instrument contaminants from the LI-6800 can be substantial but are dominantly complex molecules such as siloxanes that are structurally dissimilar to biogenic VOCs and thus unlikely to interfere with most leaf-level emissions measurements. We validate the method by comparing CO2 assimilation calculated internally by the portable photosynthesis system to measurements taken with an external CO2 gas analyzer; these assimilation measurements agree within 1 %. We also demonstrate both online and offline measurements of plant trace gas exchange using the LI-6800. Offline measurements by pre-concentration on adsorbent cartridges enable the detection of a broad suite of VOCs, including monoterpenes (e.g., limonene) and aldehydes (e.g., decanal). Online measurements can be more challenging if flow rates require dilution with ultrapure zero air. We use high-resolution time-of-flight chemical ionization mass spectrometry coupled to the LI-6800 to measure the direct plant emission of formic acid.

Effect of elevated CO2 and spectral quality on whole plant gas exchange patterns in tomatoes.

In controlled environment plant production facilities, elevating either light or CO2 levels generally has led to increased biomass and yield due to enhanced canopy photosynthesis. Today, advancements in light-emitting diodes (LEDs) have made this technology a viable option for both supplementary lighting in greenhouses and a sole lighting source in controlled environment chambers. Our study used tomato plants grown under both ambient CO2 (AC) and elevated CO2 (EC) conditions then exposed them to various CO2 and lighting treatments during both whole plant and leaf level measurements. Plants grown under EC reached the first flower developmental stage 8 days sooner and were approximately 15cm taller than those grown under AC. However, under AC plants had more leaf area while their dry weights were similar. Of note, under EC chlorophyll a and b were lower, as were carotenoids per unit leaf area. Whole plant analyses, under all CO2 challenges, showed that plants exposed to high-pressure sodium (HPS), red-blue LED, and red-white LED had similar photosynthesis, respiration, and daily carbon gain. Under different light qualities, day-time transpiration rates were similar among CO2 conditions. Day-time water-use efficiency (WUE) was higher in plants grown and exposed to EC. Similarly, WUE of plants grown under AC but exposed to short-term elevated CO2 conditions was higher than those grown and tested under AC during all light treatments. Under all CO2 conditions, plants exposed to red-white and red-blue LEDs had lower WUE than those exposed to HPS lighting. Assessing alterations due to CO2 and light quality on a whole plant basis, not merely on an individual leaf basis, furthers our understanding of the interactions between these two parameters during controlled environment production. Principle component analyses of both whole plant and leaf data indicates that increasing CO2 supply has a more dramatic effect on photosynthesis and WUE than on transpiration.

Quantitative assessment of disease severity and rating of barley cultivars based on hyperspectral imaging in a non-invasive, automated phenotyping platform

BackgroundPhenotyping is a bottleneck for the development of new plant cultivars. This study introduces a new hyperspectral phenotyping system, which combines the high throughput of canopy scale measurements with the advantages of high spatial resolution and a controlled measurement environment. Furthermore, the measured barley canopies were grown in large containers (called Mini-Plots), which allow plants to develop field-like phenotypes in greenhouse experiments, without being hindered by pot size.ResultsSix barley cultivars have been investigated via hyperspectral imaging up to 30 days after inoculation with powdery mildew. With a high spatial resolution and stable measurement conditions, it was possible to automatically quantify powdery mildew symptoms through a combination of Simplex Volume Maximization and Support Vector Machines. Detection was feasible as soon as the first symptoms were visible for the human eye during manual rating. An accurate assessment of the disease severity for all cultivars at each measurement day over the course of the experiment was realized. Furthermore, powdery mildew resistance based necrosis of one cultivar was detected as well.ConclusionThe hyperspectral phenotyping system combines the advantages of field based canopy level measurement systems (high throughput, automatization, low manual workload) with those of laboratory based leaf level measurement systems (high spatial resolution, controlled environment, stable conditions for time series measurements). This allows an accurate and objective disease severity assessment without the need for trained experts, who perform visual rating, as well as detection of disease symptoms in early stages. Therefore, it is a promising tool for plant resistance breeding.

Leaf and Canopy Level Detection of Fusarium Virguliforme (Sudden Death Syndrome) in Soybean

Pre-visual detection of crop disease is critical for food security. Field-based spectroscopic remote sensing offers a method to enable timely detection, but still requires appropriate instrumentation and testing. Soybean plants were spectrally measured throughout a growing season to assess the capacity of leaf and canopy level spectral measurements to detect non-visual foliage symptoms induced by Fusarium virguliforme (Fv, which causes sudden death syndrome). Canopy reflectance measurements were made using the Piccolo Doppio dual field-of-view, two-spectrometer (400 to 1630 nm) system on a tractor. Leaf level measurements were obtained, in different plots, using a handheld spectrometer (400 to 2500 nm). Partial least squares discriminant analysis (PLSDA) was applied to the spectroscopic data to discriminate between Fv-inoculated and control plants. Canopy and leaf spectral data allowed identification of Fv infection, prior to visual symptoms, with classification accuracy of 88% and 91% for calibration, 79% and 87% for cross-validation, and 82% and 92% for validation, respectively. Differences in wavelengths important to prediction by canopy vs. leaf data confirm that there are different bases for accurate predictions among methods. Partial least square regression (PLSR) was used on a late-stage canopy level data to predict soybean seed yield, with calibration, cross-validation and validation R2 values 0.71, 0.59 and 0.62 (p < 0.01), respectively, and validation root mean square error of 0.31 t·ha−1. Spectral data from the tractor mounted system are thus sensitive to the expression of Fv root infection at canopy scale prior to canopy symptoms, suggesting such systems may be effective for precision agricultural research and management.

Evaporation dominates evapotranspiration on Alaska’s Arctic Coastal Plain

ABSTRACT The dynamics of evapotranspiration (ET), such as the partitioning to evaporation and transpiration, of polygonal ground on the Arctic Coastal Plain are not well understood. We assessed ET dynamics, including evaporation and transpiration partitioning, created by microtopographic features associated with high- and low-centered polygons. Chamber ET and leaf-level transpiration measurements were conducted in one-week field campaigns in two growing seasons with contrasting weather conditions. We found that ET was greater in the drier and warmer sampling period (2013) compared to the colder and wetter one (2014). Evaporation dominated ET, particularly in the wetter and colder sampling period (>90% in 2014 vs. 80% in 2013). In the 2013 sampling period, wetter and warmer conditions increased ET and the contribution of transpiration to ET. If the soils warm with degrading permafrost, ET and the fraction contributed by transpiration may increase to a certain threshold, when moisture must increase with rising temperatures to further increase these fluxes. While the fraction of transpiration may rise with warmer soils, it is unlikely that transpiration will completely dominate ET. This work highlights the complexities of understanding ET in this dynamic environment and the importance of understanding differences across polygonal ground.

Remote Sensing Using Canopy and Leaf Reflectance for Estimating Nitrogen Status in Red-blush Pears

Reflectance measurements at leaf and canopy scales were made in a red-blush pear (Pyrus communis) orchard for two growing seasons. Canopy reflectance measurements were obtained using a multispectral camera flown on board an unmanned aerial vehicle (UAV), and leaf reflectance measurements were undertaken in a laboratory using a portable spectrometer. These measurements were used to compute reflectance indices as surrogates for direct leaf nitrogen (N) concentration measurements. The indices were evaluated against laboratory analysis of leaf N concentration. Regression results for leaf %N on canopy-level measurements with the multispectral camera resulted in the highest R2 value [R2 = 0.67; root mean square error (RMSE) = 0.24%N] with a new index, Modified Canopy Chlorophyll Content Index (M3CI)_710 nm. Regression results for leaf %N on leaf-level measurements in-laboratory resulted in the highest R2 value (R2 = 0.65) with two other indices, Normalized Difference Vegetation Index (NDVI) and Normalized Difference Red-edge Index (NDRE)_720 nm. The corresponding RMSE values were 0.26%N. The results indicate that reflectance indices measured at the leaf level, with a controlled light source and calibration, could be used to estimate leaf %N. An analysis of uncertainty indicated that if leaf %N is estimated from leaf-level reflectance values, 10 or more leaves (from the same tree) should be averaged. The results support the use of a UAV-based assessment for canopy %N using the M3CI_710 nm, which could provide spatial information of leaf N concentration across an orchard.

Isoprene emission potentials from European oak forests derived from canopy flux measurements: an assessment of uncertainties and inter-algorithm variability

Abstract. Biogenic emission algorithms predict that oak forests account for ∼ 70 % of the total European isoprene budget. Yet the isoprene emission potentials (IEPs) that underpin these model estimates are calculated from a very limited number of leaf-level observations and hence are highly uncertain. Increasingly, micrometeorological techniques such as eddy covariance are used to measure whole-canopy fluxes directly, from which isoprene emission potentials can be calculated. Here, we review five observational datasets of isoprene fluxes from a range of oak forests in the UK, Italy and France. We outline procedures to correct the measured net fluxes for losses from deposition and chemical flux divergence, which were found to be on the order of 5–8 and 4–5 %, respectively. The corrected observational data were used to derive isoprene emission potentials at each site in a two-step process. Firstly, six commonly used emission algorithms were inverted to back out time series of isoprene emission potential, and then an average isoprene emission potential was calculated for each site with an associated uncertainty. We used these data to assess how the derived emission potentials change depending upon the specific emission algorithm used and, importantly, on the particular approach adopted to derive an average site-specific emission potential. Our results show that isoprene emission potentials can vary by up to a factor of 4 depending on the specific algorithm used and whether or not it is used in a big-leaf or canopy environment (CE) model format. When using the same algorithm, the calculated average isoprene emission potential was found to vary by as much as 34 % depending on how the average was derived. Using a consistent approach with version 2.1 of the Model for Emissions of Gases and Aerosols from Nature (MEGAN), we derive new ecosystem-scale isoprene emission potentials for the five measurement sites: Alice Holt, UK (10 500 ± 2500 µg m−2 h−1); Bosco Fontana, Italy (1610 ± 420 µg m−2 h−1); Castelporziano, Italy (121 ± 15 µg m−2 h−1); Ispra, Italy (7590 ± 1070 µg m−2 h−1); and the Observatoire de Haute Provence, France (7990 ± 1010 µg m−2 h−1). Ecosystem-scale isoprene emission potentials were then extrapolated to the leaf-level and compared to previous leaf-level measurements for Quercus robur and Quercus pubescens, two species thought to account for 50 % of the total European isoprene budget. The literature values agreed closely with emission potentials calculated using the G93 algorithm, which were 85 ± 75 and 78 ± 25 µg g−1 h−1 for Q. robur and Q. pubescens, respectively. By contrast, emission potentials calculated using the G06 algorithm, the same algorithm used in a previous study to derive the European budget, were significantly lower, which we attribute to the influence of past light and temperature conditions. Adopting these new G06 specific emission potentials for Q. robur (55 ± 24 µg g−1 h−1) and Q. pubescens (47 ± 16 µg g−1 h−1) reduced the projected European budget by ∼ 17 %. Our findings demonstrate that calculated isoprene emission potentials vary considerably depending upon the specific approach used in their calculation. Therefore, it is our recommendation that the community now adopt a standardised approach to the way in which micrometeorological flux measurements are corrected and used to derive isoprene, and other biogenic volatile organic compounds, emission potentials.

Biomass Allocation Patterns Are Linked to Genotypic Differences in Whole-Plant Transpiration Efficiency in Sunflower.

Increased transpiration efficiency (the ratio of biomass to water transpired, TE) could lead to increased drought tolerance under some water deficit scenarios. Intrinsic (i.e., leaf-level) TE is usually considered as the primary source of variation in whole-plant TE, but empirical data usually contradict this assumption. Sunflower has a significant variability in TE, but a better knowledge of the effect of leaf and plant-level traits could be helpful to obtain more efficient genotypes for water use. The objective of this study was, therefore, to assess if genotypic variation in whole-plant TE is better related to leaf- or plant-level traits. Three experiments were conducted, aimed at verifying the existence of variability in whole-plant TE and whole-plant and leaf-level traits, and to assess their correlation. Sunflower public inbred lines and a segregating population of recombinant inbred lines were grown under controlled conditions and subjected to well-watered and water-deficit treatments. Significant genotypic variation was found for TE and related traits. These differences in whole-plant transpiration efficiency, both between genotypes and between plants within each genotype, showed no association to leaf-level traits, but were significantly and negatively correlated to biomass allocation to leaves and to the ratio of leaf area to total biomass. These associations are likely of a physiological origin, and not only a consequence of genetic linkage in the studied population. These results suggest that genotypic variation for biomass allocation could be potentially exploited as a source for increased transpiration efficiency in sunflower breeding programmes. It is also suggested that phenotyping for TE in this species should not be restricted to leaf-level measurements, but also include measurements of plant-level traits, especially those related to biomass allocation between photosynthetic and non-photosynthetic organs.

Assessing the effects of forest health on sun-induced chlorophyll fluorescence using the FluorFLIGHT 3-D radiative transfer model to account for forest structure

Sun-induced fluorescence (SIF) has been proven to serve as a proxy of photosynthesis activity and therefore, as an early indicator of physiological alterations for global monitoring of vegetation. However, the interpretation of SIF over different spatial resolutions is critical to bridge the existing gap between local and global scales. This study provides insight into the influence of scene components, and forest structure and composition on the quantification of the red and far-red fluorescence signal as an early indicator of forest decline. The experiments were conducted over an oak forest (Quercus ilex) affected by water stress and Phytophthora infection in the southwest of Spain. SIF retrievals through the Fraunhofer Line Depth (FLD) principle with three spectral bands F (FLD3) was assessed using high resolution (60cm) hyperspectral imagery extracting sunlit crown, full crown and aggregated pixels. Results showed the link between F (FLD3) extracted from sunlit crown pixels and the tree physiological condition in this context of disease infection, yielding significant relationships (r2=0.57, p<0.01) for midday xylem water potential (ψ), (r2=0.63, p<0.001) for the de-epoxidation state of the xanthophyll cycle (DEPS), and (r2=0.74, p<0.001) for leaf-level measurements of steady-state fluorescence yield (Fs). In contrast, a poor relationship was obtained when using aggregated pixels at 30m spatial resolution, where the relationship between the image-based F (FLD3) and Fs yielded a non-significant relationship (r2=0.25, p>0.05). These results demonstrate the need for methods to accurately retrieve crown SIF from aggregated pixels in heterogeneous forest canopies with large physiological variability among individual trees. This aspect is critical where structural canopy variations and the direct influence of background and shadows affect the SIF amplitude masking the natural variations caused by physiological condition. FluorFLIGHT, a modified version of the three dimensional (3-D) radiative transfer model FLIGHT was developed for this work, enabling the simulation of canopy radiance and reflectance including fluorescence at different spatial resolutions, such as may be derived from proposed satellite missions such as FLEX, and accounting for canopy structure and varying percentage cover. The 3-D modelling approach proposed here significantly improved the relationship between Fs and F (FLD3) extracted from aggregated pixels (r2=0.70, p<0.001), performing better than when aggregation effects were not considered (r2=0.42, p<0.01). The FluorFLIGHT model used in this study improved the retrieval of SIF from aggregated pixels as a function of fractional cover, Leaf Area Index and chlorophyll content yielding significant relationships between Fs ground-data measurements and fluorescence quantum yield estimated with FluorFLIGHT at p<0.01 (r2=0.79). The methodology presented here using FluorFLIGHT also demonstrated its capabilities for mapping SIF at the tree level for single tree assessment of forest physiological condition in the context of early disease detection.

Springtime ecosystem-scale monoterpene fluxes from Mediterranean pine forests across a precipitation gradient

We quantified springtime ecosystem-scale monoterpene fluxes from two similar Aleppo pine (Pinus halepensis Mill.) forests, located in Israel, that differed in the amount of received precipitation: Yatir in the arid south and Birya in the northern part of Israel (291 and 755mm annual average rainfall, respectively). In addition to the lower water availability, during our measurement campaign the Yatir site suffered from a heat wave with temperatures up to 35°C, which made the campaign-average net CO2 assimilation to occur in the morning (1μmolm−2s−1), with the rest of the daytime hours mainly dominated by net release of CO2. The milder conditions at Birya favored a higher net CO2 assimilation during all daytime hours (with average peaks higher than 10μmolm−2s−1). Despite these large differences in ambient conditions and CO2 net assimilation, daytime monoterpene emission capacities at both sites were comparable. While observed monoterpene fluxes were lower at Yatir than at Birya (hourly averages up to 0.4 and 1mgm−2h−1, respectively), the standardized hourly fluxes, after accounting for the differences in light, temperature and stand density between both sites, were comparable (0–1.3mgm−2h−1). The approach typically used by biogenic emission models overestimated monoterpene fluxes at Yatir when temperatures rose during the heat wave. This result, together with complementary leaf-level measurements showing that summertime monoterpene fluxes almost completely ceased at Yatir while being enhanced at Birya, highlight the interaction of water scarcity and high temperatures that drive monoterpene emissions from vegetation in such extreme climate zones and the need to further improve model performance.

Importance of Fluctuations in Light on Plant Photosynthetic Acclimation.

The acclimation of plants to light has been studied extensively, yet little is known about the effect of dynamic fluctuations in light on plant phenotype and acclimatory responses. We mimicked natural fluctuations in light over a diurnal period to examine the effect on the photosynthetic processes and growth of Arabidopsis (Arabidopsis thaliana). High and low light intensities, delivered via a realistic dynamic fluctuating or square wave pattern, were used to grow and assess plants. Plants subjected to square wave light had thicker leaves and greater photosynthetic capacity compared with fluctuating light-grown plants. This, together with elevated levels of proteins associated with electron transport, indicates greater investment in leaf structural components and photosynthetic processes. In contrast, plants grown under fluctuating light had thinner leaves, lower leaf light absorption, but maintained similar photosynthetic rates per unit leaf area to square wave-grown plants. Despite high light use efficiency, plants grown under fluctuating light had a slow growth rate early in development, likely due to the fact that plants grown under fluctuating conditions were not able to fully utilize the light energy absorbed for carbon fixation. Diurnal leaf-level measurements revealed a negative feedback control of photosynthesis, resulting in a decrease in total diurnal carbon assimilated of at least 20%. These findings highlight that growing plants under square wave growth conditions ultimately fails to predict plant performance under realistic light regimes and stress the importance of considering fluctuations in incident light in future experiments that aim to infer plant productivity under natural conditions in the field.

Coupled response of stomatal and mesophyll conductance to light enhances photosynthesis of shade leaves under sunflecks.

Light gradients within tree canopies play a major role in the distribution of plant resources that define the photosynthetic capacity of sun and shade leaves. However, the biochemical and diffusional constraints on gas exchange in sun and shade leaves in response to light remain poorly quantified, but critical for predicting canopy carbon and water exchange. To investigate the CO2 diffusion pathway of sun and shade leaves, leaf gas exchange was coupled with concurrent measurements of carbon isotope discrimination to measure net leaf photosynthesis (An ), stomatal conductance (gs ) and mesophyll conductance (gm ) in Eucalyptus tereticornis trees grown in climate controlled whole-tree chambers. Compared to sun leaves, shade leaves had lower An , gm , leaf nitrogen and photosynthetic capacity (Amax ) but gs was similar. When light intensity was temporarily increased for shade leaves to match that of sun leaves, both gs and gm increased, and An increased to values greater than sun leaves. We show that dynamic physiological responses of shade leaves to altered light environments have implications for up-scaling leaf level measurements and predicting whole canopy carbon gain. Despite exhibiting reduced photosynthetic capacity, the rapid up-regulation of gm with increased light enables shade leaves to respond quickly to sunflecks.

Effects of intra-genotypic variation, variance with height and time of season on BVOC emissions

Biogenic Volatile Organic Compounds (BVOCs) are trace gases other than CO2 and CH4 produced and emitted by the biosphere, where the amounts released depend on climatic factors such as temperature and solar irradiation. However, interpretation of leaf-level measurements is currently hampered by factors such as large within-genotypic variability, measurement height and time in the season. A campaign was performed between June and August in 2013 in Taastrup, Denmark to study these uncertainties. BVOC emissions were measured from leaves and needles at heights of 2 m, 5.5m and 12.5m in the canopy and for seven trees; four Norway spruces (Picea abies) of which two trees had a budburst approximately a week before the other two, two English oaks (Quercus robur) and one European beech (Fagus sylvatica). Differences in chemical composition and emission strength between June and August were observed between the different trees. English oak's main compound isoprene increased from 62-74%of the total emission in June to approximately 97% in August, which is linked to leaf development over the summer season. The total emission from all measured spruce trees decreased from July to August, but without a loss in the diversity of emitted compounds. The trees showed indications of drought stress as there was a period without precipitation lasting 21 days during the study. There were no differences in emission patterns within all of the measured Norway spruces. For measurement height, there was only a significant difference in emission pattern for European beech as the top of the canopy emitted 7-9 times more in relation to lower canopy levels. Our results suggest there was little within-genotype variability and the wide spacing between trees had an influence on the individual emission patterns. These results are important in order to understand the significance of within-genotypic variation, canopy height and seasonal development in relation to the emission patterns of the selected species. Furthermore, it will provide helpful insights for modelers who wish to improve their emission estimates. (Less)

Canopy-scale flux measurements and bottom-up emission estimates of volatile organic compounds from a mixed oak and hornbeam forest in northern Italy

Abstract. This paper reports the fluxes and mixing ratios of biogenically emitted volatile organic compounds (BVOCs) 4 m above a mixed oak and hornbeam forest in northern Italy. Fluxes of methanol, acetaldehyde, isoprene, methyl vinyl ketone + methacrolein, methyl ethyl ketone and monoterpenes were obtained using both a proton-transfer-reaction mass spectrometer (PTR-MS) and a proton-transfer-reaction time-of-flight mass spectrometer (PTR-ToF-MS) together with the methods of virtual disjunct eddy covariance (using PTR-MS) and eddy covariance (using PTR-ToF-MS). Isoprene was the dominant emitted compound with a mean daytime flux of 1.9 mg m−2 h−1. Mixing ratios, recorded 4 m above the canopy, were dominated by methanol with a mean value of 6.2 ppbv over the 28-day measurement period. Comparison of isoprene fluxes calculated using the PTR-MS and PTR-ToF-MS showed very good agreement while comparison of the monoterpene fluxes suggested a slight over estimation of the flux by the PTR-MS. A basal isoprene emission rate for the forest of 1.7 mg m−2 h−1 was calculated using the Model of Emissions of Gases and Aerosols from Nature (MEGAN) isoprene emission algorithms (Guenther et al., 2006). A detailed tree-species distribution map for the site enabled the leaf-level emission of isoprene and monoterpenes recorded using gas-chromatography mass spectrometry (GC–MS) to be scaled up to produce a bottom-up canopy-scale flux. This was compared with the top-down canopy-scale flux obtained by measurements. For monoterpenes, the two estimates were closely correlated and this correlation improved when the plant-species composition in the individual flux footprint was taken into account. However, the bottom-up approach significantly underestimated the isoprene flux, compared with the top-down measurements, suggesting that the leaf-level measurements were not representative of actual emission rates.