A Novel Hyperspectral Method to Detect Moldy Core in Apple Fruits.

An innovative low-cost device based on hyperspectral spectroscopy in the near infrared (NIR) spectral region is proposed for the non-invasive detection of moldy core (MC) in apples. The system, based on light collection by an integrating sphere, was tested on 70 apples cultivar (cv) Golden Delicious infected by Alternaria alternata, one of the main pathogens responsible for MC disease. Apples were sampled in vertical and horizontal positions during five measurement rounds in 13 days' time, and 700 spectral signatures were collected. Spectral correlation together with transmittance temporal patterns and ANOVA showed that the spectral region from 863.38 to 877.69 nm was most linked to MC presence. Then, two binary classification models based on Artificial Neural Network Pattern Recognition (ANN-AP) and Bagging Classifier (BC) with decision trees were developed, revealing a better detection capability by ANN-AP, especially in the early stage of infection, where the predictive accuracy was 100% at round 1 and 97.15% at round 2. In subsequent rounds, the classification results were similar in ANN-AP and BC models. The system proposed surpassed previous MC detection methods, needing only one measurement per fruit, while further research is needed to extend it to different cultivars or fruits.

Dynamics of sun-induced chlorophyll fluorescence and reflectance to detect stress-induced variations in canopy photosynthesis.

Passive measurement of sun-induced chlorophyll fluorescence (F) represents the most promising tool to quantify changes in photosynthetic functioning on a large scale. However, the complex relationship between this signal and other photosynthesis-related processes restricts its interpretation under stress conditions. To address this issue, we conducted a field campaign by combining daily airborne and ground-based measurements of F (normalized to photosynthetically active radiation), reflectance and surface temperature and related the observed changes to stress-induced variations in photosynthesis. A lawn carpet was sprayed with different doses of the herbicide Dicuran. Canopy-level measurements of gross primary productivity indicated dosage-dependent inhibition of photosynthesis by the herbicide. Dosage-dependent changes in normalized F were also detected. After spraying, we first observed a rapid increase in normalized F and in the Photochemical Reflectance Index, possibly due to the blockage of electron transport by Dicuran and the resultant impairment of xanthophyll-mediated non-photochemical quenching. This initial increase was followed by a gradual decrease in both signals, which coincided with a decline in pigment-related reflectance indices. In parallel, we also detected a canopy temperature increase after the treatment. These results demonstrate the potential of using F coupled with relevant reflectance indices to estimate stress-induced changes in canopy photosynthesis.

Plants with less chlorophyll: A global change perspective.

The necessary reduction of greenhouse gas (GHG) emissions may lead in the future to an increase in solar irradiance (solar brightening). Anthropogenic aerosols (and their precursors) that cause solar dimming are in fact often co-emitted with GHGs. While the reduction of GHG emissions is expected to slow down the ongoing increase in the greenhouse effect, an increased surface irradiance due to reduced atmospheric aerosol load might occur in the most populated areas of the earth. Increased irradiance may lead to air warming, favour the occurrence of heatwaves and increase the evaporative demand of the atmosphere. This is why effective and sustainable solar radiation management strategies to reflect more light back to space should be designed, tested and implemented together with GHG emission mitigation. Here we propose that new plants (crops, orchards and forests) with low-chlorophyll (Chl) content may provide a realistic, sustainable and relatively simple solution to increase surface reflectance of large geographical areas via changes in surface albedo. This may finally offset all or part of the expected local solar brightening. While high-Chl content provides substantial competitive advantages to plants growing in their natural environment, new plants with low-Chl content may be successfully used in agriculture and silviculture and be as productive as the green wildtypes (or even more). The most appropriate strategies to obtain highly productive and highly reflective plants are discussed in this paper and their mitigation potential is examined together with the challenges associated with their introduction in agriculture.

Leaf and canopy photosynthesis of a chlorophyll deficient soybean mutant.

The photosynthetic, optical, and morphological characteristics of a chlorophyll-deficient (Chl-deficient) "yellow" soybean mutant (MinnGold) were examined in comparison with 2 green varieties (MN0095 and Eiko). Despite the large difference in Chl content, similar leaf photosynthesis rates were maintained in the Chl-deficient mutant by offsetting the reduced absorption of red photons by a small increase in photochemical efficiency and lower non-photochemical quenching. When grown in the field, at full canopy cover, the mutants reflected a significantly larger proportion of incoming shortwave radiation, but the total canopy light absorption was only slightly reduced, most likely due to a deeper penetration of light into the canopy space. As a consequence, canopy-scale gross primary production and ecosystem respiration were comparable between the Chl-deficient mutant and the green variety. However, total biomass production was lower in the mutant, which indicates that processes other than steady state photosynthesis caused a reduction in biomass accumulation over time. Analysis of non-photochemical quenching relaxation and gas exchange in Chl-deficient and green leaves after transitions from high to low light conditions suggested that dynamic photosynthesis might be responsible for the reduced biomass production in the Chl-deficient mutant under field conditions.

Industrial point source CO2 emission strength estimation with aircraft measurements and dispersion modelling.

CO2 remains the greenhouse gas that contributes most to anthropogenic global warming, and the evaluation of its emissions is of major interest to both research and regulatory purposes. Emission inventories generally provide quite reliable estimates of CO2 emissions. However, because of intrinsic uncertainties associated with these estimates, it is of great importance to validate emission inventories against independent estimates. This paper describes an integrated approach combining aircraft measurements and a puff dispersion modelling framework by considering a CO2 industrial point source, located in Biganos, France. CO2 density measurements were obtained by applying the mass balance method, while CO2 emission estimates were derived by implementing the CALMET/CALPUFF model chain. For the latter, three meteorological initializations were used: (i) WRF-modelled outputs initialized by ECMWF reanalyses; (ii) WRF-modelled outputs initialized by CFSR reanalyses and (iii) local in situ observations. Governmental inventorial data were used as reference for all applications. The strengths and weaknesses of the different approaches and how they affect emission estimation uncertainty were investigated. The mass balance based on aircraft measurements was quite succesful in capturing the point source emission strength (at worst with a 16% bias), while the accuracy of the dispersion modelling, markedly when using ECMWF initialization through the WRF model, was only slightly lower (estimation with an 18% bias). The analysis will help in highlighting some methodological best practices that can be used as guidelines for future experiments.

Plant adaptation or acclimation to rising CO2 ? Insight from first multigenerational RNA-Seq transcriptome.

Atmospheric carbon dioxide (CO2 ) directly determines the rate of plant photosynthesis and indirectly effects plant productivity and fitness and may therefore act as a selective pressure driving evolution, but evidence to support this contention is sparse. Using Plantago lanceolata L. seed collected from a naturally high CO2 spring and adjacent ambient CO2 control site, we investigated multigenerational response to future, elevated atmospheric CO2 . Plants were grown in either ambient or elevated CO2 (700 µmol mol-1 ), enabling for the first time, characterization of the functional and population genomics of plant acclimation and adaptation to elevated CO2 . This revealed that spring and control plants differed significantly in phenotypic plasticity for traits underpinning fitness including above-ground biomass, leaf size, epidermal cell size and number and stomatal density and index. Gene expression responses to elevated CO2 (acclimation) were modest [33-131 genes differentially expressed (DE)], whilst those between control and spring plants (adaptation) were considerably larger (689-853 DE genes). In contrast, population genomic analysis showed that genetic differentiation between spring and control plants was close to zero, with no fixed differences, suggesting that plants are adapted to their native CO2 environment at the level of gene expression. An unusual phenotype of increased stomatal index in spring but not control plants in elevated CO2 correlated with altered expression of stomatal patterning genes between spring and control plants for three loci (YODA, CDKB1;1 and SCRM2) and between ambient and elevated CO2 for four loci (ER, YODA, MYB88 and BCA1). We propose that the two positive regulators of stomatal number (SCRM2) and CDKB1;1 when upregulated act as key controllers of stomatal adaptation to elevated CO2 . Combined with significant transcriptome reprogramming of photosynthetic and dark respiration and enhanced growth in spring plants, we have identified the potential basis of plant adaptation to high CO2 likely to occur over coming decades.

Effects of climate extremes on the terrestrial carbon cycle: concepts, processes and potential future impacts.

Extreme droughts, heat waves, frosts, precipitation, wind storms and other climate extremes may impact the structure, composition and functioning of terrestrial ecosystems, and thus carbon cycling and its feedbacks to the climate system. Yet, the interconnected avenues through which climate extremes drive ecological and physiological processes and alter the carbon balance are poorly understood. Here, we review the literature on carbon cycle relevant responses of ecosystems to extreme climatic events. Given that impacts of climate extremes are considered disturbances, we assume the respective general disturbance-induced mechanisms and processes to also operate in an extreme context. The paucity of well-defined studies currently renders a quantitative meta-analysis impossible, but permits us to develop a deductive framework for identifying the main mechanisms (and coupling thereof) through which climate extremes may act on the carbon cycle. We find that ecosystem responses can exceed the duration of the climate impacts via lagged effects on the carbon cycle. The expected regional impacts of future climate extremes will depend on changes in the probability and severity of their occurrence, on the compound effects and timing of different climate extremes, and on the vulnerability of each land-cover type modulated by management. Although processes and sensitivities differ among biomes, based on expert opinion, we expect forests to exhibit the largest net effect of extremes due to their large carbon pools and fluxes, potentially large indirect and lagged impacts, and long recovery time to regain previous stocks. At the global scale, we presume that droughts have the strongest and most widespread effects on terrestrial carbon cycling. Comparing impacts of climate extremes identified via remote sensing vs. ground-based observational case studies reveals that many regions in the (sub-)tropics are understudied. Hence, regional investigations are needed to allow a global upscaling of the impacts of climate extremes on global carbon-climate feedbacks.

Fate of Soil Organic Carbon and Polycyclic Aromatic Hydrocarbons in a Vineyard Soil Treated with Biochar.

The effect of biochar addition on the levels of black carbon (BC) and polcyclic aromatic hydrocarbons (PAHs) in a vineyard soil in central Italy was investigated within a two year period. Hydropyrolysis (HyPy) was used to determine the contents of BC (BCHyPy) in the amended and control soils, while the hydrocarbon composition of the semi-labile (non-BCHyPy) fraction released by HyPy was determined by gas chromatography-mass spectrometry, together with the solvent-extractable PAHs. The concentrations of these three polycyclic aromatic carbon reservoirs changed and impacted differently the soil organic carbon over the period of the trial. The addition of biochar (33 ton dry biochar ha(-1)) gave rise to a sharp increase in soil organic carbon, which could be accounted for by an increase in BCHyPy. Over time, the concentration of BCHyPy decreased significantly from 36 to 23 mg g(-1) and as a carbon percentage from 79% to 61%. No clear time trends were observed for the non-BCHyPy PAHs varying from 39 to 34 µg g(-1) in treated soils, not significantly different from control soils. However, the concentrations of extractable PAHs increased markedly in the amended soils and decreased with time from 153 to 78 ng g(-1) remaining always higher than those in untreated soil. The extent of the BCHyPy loss was more compatible with physical rather than chemical processes.

WhiteRef: a new tower-based hyperspectral system for continuous reflectance measurements.

Proximal sensing is fundamental to monitor the spatial and seasonal dynamics of ecosystems and can be considered as a crucial validation tool to upscale in situ observations to the satellite level. Linking hyperspectral remote sensing with carbon fluxes and biophysical parameters is critical to allow the exploitation of spatial and temporal extensive information for validating model simulations at different scales. In this study, we present the WhiteRef, a new hyperspectral system designed as a direct result of the needs identified during the EUROSPEC ES0903 Cost Action, and developed by Fondazione Edmund Mach and the Institute of Biometeorology, CNR, Italy. The system is based on the ASD FieldSpec Pro spectroradiometer and was designed to acquire continuous radiometric measurements at the Eddy Covariance (EC) towers and to fill a gap in the scientific community: in fact, no system for continuous spectral measurements in the Short Wave Infrared was tested before at the EC sites. The paper illustrates the functioning of the WhiteRef and describes its main advantages and disadvantages. The WhiteRef system, being based on a robust and high quality commercially available instrument, has a clear potential for unattended continuous measurements aiming at the validation of satellites' vegetation products.

Comparing integrated stable isotope and eddy covariance estimates of water-use efficiency on a Mediterranean successional sequence.

Water-use efficiency (WUE), thought to be a relevant trait for productivity and adaptation to water-limited environments, was estimated for three different ecosystems on the Mediterranean island of Pianosa: Mediterranean macchia (SMM), transition (S(TR)) and abandoned agricultural (SAA) ecosystems, representing a successional series. Three independent approaches were used to study WUE: eddy covariance measurements, C isotope composition of ecosystem respired CO2, and C isotope discrimination (Δ) of leaf material (dry matter and soluble sugars). Seasonal variations in C-water relations and energy fluxes, compared in S(MM) and in SAA, were primarily dependent on the specific composition of each plant community. WUE of gross primary productivity was higher in SMM than in SAA at the beginning of the dry season. Both structural and fast-turnover leaf material were, on average, more enriched in (13)C in S(MM) than SAA, indicating relatively higher stomatal control and WUE for the long-lived macchia species. This pattern corresponded to (13)C-enriched respired CO2 in SMM compared to the other ecosystems. Conversely, most of the annual herbaceous SAA species (terophytes) showed a drought-escaping strategy, with relatively high stomatal conductance and low WUE. An ecosystem-integrated Δ value was weighted for each ecosystem on the abundance of different life forms, classified according to Raunkiar's system. Agreement was found between ecosystem WUE calculated using eddy covariance and those estimated using integrated Δ approaches. Comparing the isotopic methods, Δ of leaf soluble sugars provided the most reliable proxy for short-term changes in photosynthetic discrimination and associated shifts in integrated canopy-level WUE along the successional series.

Aircraft mass budgeting to measure CO2 emissions of Rome, Italy.

Aircraft measurements were used to estimate the CO2 emission rates of the city of Rome, assessed against high-resolution inventorial data. Three experimental flights were made, composed of vertical soundings to measure Planetary Boundary Layer (PBL) properties, and circular horizontal transects at various altitudes around the city area. City level emissions and associated uncertainties were computed by means of mass budgeting techniques, obtaining a positive net CO2 flux of 14.7 ± 4.5, 2.5 ± 1.2, and 10.3 ± 1.2 µmol m(-2) s(-1) for the three flights. Inventorial CO2 fluxes at the time of flights were computed by means of spatial and temporal disaggregation of the gross emission inventory, at 10.9 ± 2.5, 9.6 ± 1.3, and 17.4 ± 9.6 µmol m(-2) s(-1). The largest differences between the two dataset are associated with a greater variability of wind speed and direction in the boundary layer during measurements. Uncertainty partitioned into components related to horizontal boundary flows and top surface flow, revealed that the latter dominates total uncertainty in the presence of a wide variability of CO2 concentration in the free troposphere (up to 7 ppm), while it is a minor term with uniform tropospheric concentrations in the study area (within 2 ppm). Overall, we demonstrate how small aircraft may provide city level emission measurements that may integrate and validate emission inventories. Optimal atmospheric conditions and measurement strategies for the deployment of aircraft experimental flights are finally discussed.

Elevated CO2 enrichment induces a differential biomass response in a mixed species temperate forest plantation.

In a free-air carbon dioxide (CO(2)) enrichment study (BangorFACE), Alnus glutinosa, Betula pendula and Fagus sylvatica were planted in areas of one-, two- and three-species mixtures (n = 4). The trees were exposed to ambient or elevated CO(2) (580 µmol mol(-1)) for 4 yr, and aboveground growth characteristics were measured. In monoculture, the mean effect of CO(2) enrichment on aboveground woody biomass was + 29, + 22 and + 16% for A. glutinosa, F. sylvatica and B. pendula, respectively. When the same species were grown in polyculture, the response to CO(2) switched to + 10, + 7 and 0% for A. glutinosa, B. pendula and F. sylvatica, respectively. In ambient atmosphere, our species grown in polyculture increased aboveground woody biomass from 12.9 ± 1.4 to 18.9 ± 1.0 kg m(-2), whereas, in an elevated CO(2) atmosphere, aboveground woody biomass increased from 15.2 ± 0.6 to 20.2 ± 0.6 kg m(-2). The overyielding effect of polyculture was smaller (+ 7%) in elevated CO(2) than in an ambient atmosphere (+ 18%). Our results show that the aboveground response to elevated CO(2) is affected significantly by intra- and interspecific competition, and that the elevated CO(2) response may be reduced in forest communities comprising tree species with contrasting functional traits.

Two decades of fumigation data from the Soybean Free Air Concentration Enrichment facility.

The Soybean Free Air Concentration Enrichment (SoyFACE) facility is the longest running open-air carbon dioxide and ozone enrichment facility in the world. For over two decades, soybean, maize, and other crops have been exposed to the elevated carbon dioxide and ozone concentrations anticipated for late this century. The facility, located in East Central Illinois, USA, exposes crops to different atmospheric concentrations in replicated octagonal ~280 m2 Free Air Concentration Enrichment (FACE) treatment plots. Each FACE plot is paired with an untreated control (ambient) plot. The experiment provides important ground truth data for predicting future crop productivity. Fumigation data from SoyFACE were collected every four seconds throughout each growing season for over two decades. Here, we organize, quality control, and collate 20 years of data to facilitate trend analysis and crop modeling efforts. This paper provides the rationale for and a description of the SoyFACE experiments, along with a summary of the fumigation data and collation process, weather and ambient data collection procedures, and explanations of air pollution metrics and calculations.

Quantification of excess water loss in plant canopies warmed with infrared heating.

Here we investigate the extent to which infrared heating used to warm plant canopies in climate manipulation experiments increases transpiration. Concerns regarding the impact of the infrared heater technique on the water balance have been raised before, but a quantification is lacking. We calculate transpiration rates under infrared heaters and compare these with air warming at constant relative humidity. As infrared heating primarily warms the leaves and not the air, this method increases both the gradient and the conductance for water vapour. Stomatal conductance is determined both independently of vapour pressure differences and as a function thereof, while boundary layer conductance is calculated using several approaches. We argue that none of these approaches is fully accurate, and opt to present results as an interval in which the actual water loss is likely to be found. For typical conditions in a temperate climate, our results suggest a 12-15% increase in transpiration under infrared heaters for a 1 °C warming. This effect decreases when stomatal conductance is allowed to vary with the vapour pressure difference. Importantly, the artefact is less of a concern when simulating heat waves. The higher atmospheric water demand underneath the heaters reflects naturally occurring increases of potential evapotranspiration during heat waves resulting from atmospheric feedback. While air warming encompasses no increases in transpiration, this fully depends on the ability to keep humidity constant, which in the case of greenhouses requires the presence of an air humidification system. As various artefacts have been associated with chamber experiments, we argue that manipulating climate in the field should be prioritized, while striving to limit confounding factors. The excess water loss underneath infrared heaters reported upon here could be compensated by increasing irrigation or applying newly developed techniques for increasing air humidity in the field.

The Optical Response of a Mediterranean Shrubland to Climate Change: Hyperspectral Reflectance Measurements during Spring.

Remote sensing techniques in terms of monitoring plants' responses to environmental constraints have gained much attention during recent decades. Among these constraints, climate change appears to be one of the major challenges in the Mediterranean region. In this study, the main goal was to determine how field spectrometry could improve remote sensing study of a Mediterranean shrubland submitted to climate aridification. We provided the spectral signature of three common plants of the Mediterranean garrigue: Cistus albidus, Quercus coccifera, and Rosmarinus officinalis. The pattern of these spectra changed depending on the presence of a neighboring plant species and water availability. Indeed, the normalized water absorption reflectance (R975/R900) tended to decrease for each species in trispecific associations (11-26%). This clearly indicates that multispecific plant communities will better resist climate aridification compared to monospecific stands. While Q. coccifera seemed to be more sensible to competition for water resources, C. albidus exhibited a facilitation effect on R. officinalis in trispecific assemblage. Among the 17 vegetation indices tested, we found that the pigment pheophytinization index (NPQI) was a relevant parameter to characterize plant-plant coexistence. This work also showed that some vegetation indices known as indicators of water and pigment contents could also discriminate plant associations, namely RGR (Red Green Ratio), WI (Water Index), Red Edge Model, NDWI1240 (Normalized Difference Water Index), and PRI (Photochemical Reflectance Index). The latter was shown to be linearly and negatively correlated to the ratio of R975/R900, an indicator of water status.

Coppicing shifts CO2 stimulation of poplar productivity to above-ground pools: a synthesis of leaf to stand level results from the POP/EUROFACE experiment.

A poplar short rotation coppice (SRC) grown for the production of bioenergy can combine carbon (C) storage with fossil fuel substitution. Here, we summarize the responses of a poplar (Populus) plantation to 6 yr of free air CO(2) enrichment (POP/EUROFACE consisting of two rotation cycles). We show that a poplar plantation growing in nonlimiting light, nutrient and water conditions will significantly increase its productivity in elevated CO(2) concentrations ([CO(2)]). Increased biomass yield resulted from an early growth enhancement and photosynthesis did not acclimate to elevated [CO(2)]. Sufficient nutrient availability, increased nitrogen use efficiency (NUE) and the large sink capacity of poplars contributed to the sustained increase in C uptake over 6 yr. Additional C taken up in high [CO(2)] was mainly invested into woody biomass pools. Coppicing increased yield by 66% and partly shifted the extra C uptake in elevated [CO(2)] to above-ground pools, as fine root biomass declined and its [CO(2)] stimulation disappeared. Mineral soil C increased equally in ambient and elevated [CO(2)] during the 6 yr experiment. However, elevated [CO(2)] increased the stabilization of C in the mineral soil. Increased productivity of a poplar SRC in elevated [CO(2)] may allow shorter rotation cycles, enhancing the viability of SRC for biofuel production.

Changes in the pattern of polycyclic aromatic hydrocarbons in soil treated with biochar from a multiyear field experiment.

The influence of biochar added to an agricultural soil on polycyclic aromatic hydrocarbon (PAH) levels, PAH diagnostic ratios and soil properties was investigated in a five-year field experiment. The experiment was carried out in an Italian vineyard and included two biochar treatments: 16.5 t ha-1 of biochar applied in 2009 (soil B); 16.5 t ha-1 in 2009 and further 16.5 t ha-1 in 2010 (soil BB). A set of 75 samples that included five replicates and a control soil (untreated) was characterized in terms of organic carbon, pH, cation exchange capacity (CEC), bulk density and concentration of PAHs. Biochar addition to soil caused an increase in organic carbon, pH and CEC, and a decrease of bulk density. After almost two years the first application of biochar, PAH concentrations were higher in soil B (56 ng g-1) and BB (153 ng g-1) in comparison to control soil (24 ng g-1). Thereafter, PAH concentrations decreased significantly, but the original PAHs levels were reached only in soil B after five years. The naphthalene/(naphthalene + phenanthrene) ratios were higher in the treated soils in accordance to the dominance of naphthalene in the original biochar. The cross plots naphthalene/(naphthalene + phenanthrene) vs. fluoranthene/(fluoranthene + pyrene) enabled to trace the signature of biochar PAHs up to five years after its first application. Diagnostic ratios can be a useful tool to study the persistence of PAHs introduced in soil by biochar when the pattern of these contaminants in biochar and original soil are different.

Next generation of elevated [CO2] experiments with crops: a critical investment for feeding the future world.

A rising global population and demand for protein-rich diets are increasing pressure to maximize agricultural productivity. Rising atmospheric [CO(2)] is altering global temperature and precipitation patterns, which challenges agricultural productivity. While rising [CO(2)] provides a unique opportunity to increase the productivity of C(3) crops, average yield stimulation observed to date is well below potential gains. Thus, there is room for improving productivity. However, only a fraction of available germplasm of crops has been tested for CO(2) responsiveness. Yield is a complex phenotypic trait determined by the interactions of a genotype with the environment. Selection of promising genotypes and characterization of response mechanisms will only be effective if crop improvement and systems biology approaches are closely linked to production environments, that is, on the farm within major growing regions. Free air CO(2) enrichment (FACE) experiments can provide the platform upon which to conduct genetic screening and elucidate the inheritance and mechanisms that underlie genotypic differences in productivity under elevated [CO(2)]. We propose a new generation of large-scale, low-cost per unit area FACE experiments to identify the most CO(2)-responsive genotypes and provide starting lines for future breeding programmes. This is necessary if we are to realize the potential for yield gains in the future.