An insight into spectral composition of light available for photosynthesis via remotely assessed absorption coefficient at leaf and canopy levels

Non-invasive comparative analysis of the spectral composition of energy absorbed by crop species at leaf and plant levels was carried out using the absorption coefficient retrieved from leaf and plant reflectance as an informative metric. In leaves of three species with contrasting leaf structures and photosynthetic pathways (maize, soybean, and rice), the blue, green, and red fractions of leaf absorption coefficients were 48, 20, and 32%, respectively. The fraction of green light in the total budget of light absorbed at the plant level was higher than at the leaf level approaching the size of the red fraction (24% green vs. 25.5% red) and surpassing it inside the canopy. The plant absorption coefficient in the far-red region (700-750 nm) was significant reaching 7-10% of the absorption coefficient in green or red regions. The spectral composition of the absorbed light in the three species was virtually the same. Fractions of light in absorbed PAR remained almost invariant during growing season over a wide range of plant chlorophyll content. Fractions of absorption coefficient in the green, red, and far-red were in accord with published results of quantum yield for CO2 fixation on an absorbed light basis. The role of green and far-red light in photosynthesis was demonstrated in simple experiments in natural conditions. The results show the potential for using leaf and plant absorption coefficients retrieved from reflectance to quantify photosynthesis in each spectral range.

Foliar absorption coefficient derived from reflectance spectra: A gauge of the efficiency of in situ light-capture by different pigment groups

The absorption of Photosynthetically Active Radiation (PAR) by different foliar pigments defines the amount of energy available for photosynthesis and also the need for photoprotection. Both characteristics reveal essential information about productivity, development, and stress acclimation of plants. Here we present an approach for the estimation of the efficiency by three foliar pigment groups (chlorophylls, carotenoids, and anthocyanins) at capturing light, via the absorption coefficient derived from leaf reflectance spectra. The absorption coefficient (and hence light capture efficiency) of the pigment is quantitatively related to the ratio of light absorbed by each pigment group over the total amount of light absorbed by the leaf. The proposed approach allows discerning the contribution of pigment groups to the overall light absorption, despite the strong interference by other pigments with overlapping absorption spectra. For photosynthetic pigments, like chlorophylls, this is indicative of the energy captured for photosynthesis and hence of potential plant productivity. For photoprotective pigments, like anthocyanins or secondary carotenoids, it gives information about the spectral ranges where their optical screening works best and their screening capacity. In addition, the approach allows the selection of optimal spectral bands where different pigments operate. Such information improves our understanding of the phenological, physiological and photosynthetic dynamics of plants over space and through time, useful for developing better monitoring and management strategies.

Towards a generic approach to remote non-invasive estimation of foliar carotenoid-to-chlorophyll ratio

Changes of chlorophyll (Chl) and carotenoid (Car) contents and their ratio (Car/Chl) represent a sensitive indicator of vegetation photosynthetic activity, developmental changes, and stress responses. The goal of this study was to design methods for estimating Car/Chl in plants across species, seasonal changes and ontogenetic phases requiring no species-specific parameterization. Four tree species (maple, chestnut, beech, and elm), wild vine shrub, and two crops species (maize and soybean) featuring contrasting leaf structure and photosynthetic pathways, a wide variation of pigment content and composition were studied. Two models based on leaf pigment absorption coefficients retrieved from reflectance spectra were proposed and tested. The first model uses the ratio of absorption coefficients at 500 and 700 nm and the second one-the difference between absorption coefficients at 500 and 660 nm. Both models accurately described Car/Chl changes in the range from 0.15 to 0.6 with determination coefficients R² of 0.87 for the first model and 0.82 for the second; algorithms for Car/Chl estimation did not require parameterization for each species accurately assessing Car/Chl with normalized root mean square error below 11 % and 14 %, respectively. The findings of a close relationship between leaf absorption coefficients, retrieved from reflectance, and Car/Chl present the first step towards accurate generic quantification of pigment composition and hence the progression of developmental stages, impact of stresses, and potential photosynthetic activity.

The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data

The FLUXNET2015 dataset provides ecosystem-scale data on CO₂, water, and energy exchange between the biosphere and the atmosphere, and other meteorological and biological measurements, from 212 sites around the globe (over 1500 site-years, up to and including year 2014). These sites, independently managed and operated, voluntarily contributed their data to create global datasets. Data were quality controlled and processed using uniform methods, to improve consistency and intercomparability across sites. The dataset is already being used in a number of applications, including ecophysiology studies, remote sensing studies, and development of ecosystem and Earth system models. FLUXNET2015 includes derived-data products, such as gap-filled time series, ecosystem respiration and photosynthetic uptake estimates, estimation of uncertainties, and metadata about the measurements, presented for the first time in this paper. In addition, 206 of these sites are for the first time distributed under a Creative Commons (CC-BY 4.0) license. This paper details this enhanced dataset and the processing methods, now made available as open-source codes, making the dataset more accessible, transparent, and reproducible.

Measurement(s)	net ecosystem exchange • carbon dioxide • water • energy
Technology Type(s)	eddy covariance • measurement device
Sample Characteristic - Environment	terrestrial biome • atmosphere
Sample Characteristic - Location	Earth (planet)

Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12295910

Non-invasive quantification of foliar pigments: Possibilities and limitations of reflectance- and absorbance-based approaches

Established reflectance-based approaches for estimation of foliar pigment contents assume close relationship between leaf absorbance and reflectance. Complex organization and high pigment content of leaves may lead to violation of the essential assumptions under Kubleka-Munk theory relating reflectance and absorbance. We compared relationships of absorbance and reciprocal reflectance vs. pigment content in leaves collected across species, developmental stages and physiological states. As a result, limitations of reflectance-based spectroscopy for pigment quantification were revealed. We deduced in situ absorbance of foliar chlorophylls, carotenoids, and flavonoids (including red-colored anthocyanins) and introduced a concept of specific spectral response of the optical properties to each pigment group. Quantitative criteria of spectral range selection for the absorbance- and reflectance-based techniques yielding effect of each pigment on the background of other pigment absorption were suggested and validated. We argue that absorbance- and reflectance-based approaches to pigment estimation complement each other and can be used synergistically in advanced models for accurate estimating foliar pigments. The study provides a deeper insight into interception of light by photosynthetic and photoprotective pigments as function of physiological condition and developmental stage, which is important for plant biology as well as knowledge-driven selection of spectral bands for noninvasive pigment estimation models.

In situ optical properties of foliar flavonoids: Implication for non-destructive estimation of flavonoid content

Flavonoids are a ubiquitous multifunctional group of phenolics of paramount importance for the terrestrial plants involved in protection from biotic and abiotic stresses, color and chemical signaling and other functions. Deciphering of in situ absorption of foliar Flv is important but was thought to be impossible due to a strong overlap with other pigments, complex in situ chemistry of Flv and sophisticated leaf optics. We deduced in situ absorbance of foliar Flv and introduced a concept of specific absorbance spectrum indicative of each pigment group contribution to light absorption and provided a rationale for the choice of spectral bands for non-destructive assessment of Flv in leaves with variable content of other pigments including anthocyanins. Only a narrow band 400-430nm was suitable for Flv assessment, however the effect of other pigments remained substantial, so subtraction of their contribution was necessary. The devised leaf absorbance-based algorithm allowed estimating Flv with error below 21%. Absorption by Flv in plant tissues might extend into the blue and can be commensurate to that of chlorophylls and carotenoids. The potential capacity of Flv to shield the cell in situ from the visible light might be essential for assessments of high light stress tolerance of plants.

Simple and robust methods for remote sensing of canopy chlorophyll content: a comparative analysis of hyperspectral data for different types of vegetation

Canopy chlorophyll content (CCC) is an essential ecophysiological variable for photosynthetic functioning. Remote sensing of CCC is vital for a wide range of ecological and agricultural applications. The objectives of this study were to explore simple and robust algorithms for spectral assessment of CCC. Hyperspectral datasets for six vegetation types (rice, wheat, corn, soybean, sugar beet and natural grass) acquired in four locations (Japan, France, Italy and USA) were analysed. To explore the best predictive model, spectral index approaches using the entire wavebands and multivariable regression approaches were employed. The comprehensive analysis elucidated the accuracy, linearity, sensitivity and applicability of various spectral models. Multivariable regression models using many wavebands proved inferior in applicability to different datasets. A simple model using the ratio spectral index (RSI; R815, R704) with the reflectance at 815 and 704 nm showed the highest accuracy and applicability. Simulation analysis using a physically based reflectance model suggested the biophysical soundness of the results. The model would work as a robust algorithm for canopy-chlorophyll-metre and/or remote sensing of CCC in ecosystem and regional scales. The predictive-ability maps using hyperspectral data allow not only evaluation of the relative significance of wavebands in various sensors but also selection of the optimal wavelengths and effective bandwidths.

Estimation of vegetation photosynthetic capacity from space-based measurements of chlorophyll fluorescence for terrestrial biosphere models

Photosynthesis simulations by terrestrial biosphere models are usually based on the Farquhar's model, in which the maximum rate of carboxylation (Vcmax ) is a key control parameter of photosynthetic capacity. Even though Vcmax is known to vary substantially in space and time in response to environmental controls, it is typically parameterized in models with tabulated values associated to plant functional types. Remote sensing can be used to produce a spatially continuous and temporally resolved view on photosynthetic efficiency, but traditional vegetation observations based on spectral reflectance lack a direct link to plant photochemical processes. Alternatively, recent space-borne measurements of sun-induced chlorophyll fluorescence (SIF) can offer an observational constraint on photosynthesis simulations. Here, we show that top-of-canopy SIF measurements from space are sensitive to Vcmax at the ecosystem level, and present an approach to invert Vcmax from SIF data. We use the Soil-Canopy Observation of Photosynthesis and Energy (SCOPE) balance model to derive empirical relationships between seasonal Vcmax and SIF which are used to solve the inverse problem. We evaluate our Vcmax estimation method at six agricultural flux tower sites in the midwestern US using spaced-based SIF retrievals. Our Vcmax estimates agree well with literature values for corn and soybean plants (average values of 37 and 101 μmol m(-2)  s(-1) , respectively) and show plausible seasonal patterns. The effect of the updated seasonally varying Vcmax parameterization on simulated gross primary productivity (GPP) is tested by comparing to simulations with fixed Vcmax values. Validation against flux tower observations demonstrate that simulations of GPP and light use efficiency improve significantly when our time-resolved Vcmax estimates from SIF are used, with R(2) for GPP comparisons increasing from 0.85 to 0.93, and for light use efficiency from 0.44 to 0.83. Our results support the use of space-based SIF data as a proxy for photosynthetic capacity and suggest the potential for global, time-resolved estimates of Vcmax .

Photic Volume in Photobioreactors Supporting Ultrahigh Population Densities of the Photoautotroph Spirulina platensis

Characterization of the photic zone and light penetration depth in cultures with ultrahigh cell densities represents a major issue in mass cultures of phytoautotrophic microorganisms grown in enclosed photobioreactors. In a study of the effect of underwater optical properties on the penetration depth of photosynthetically active radiation, the inherent optical properties of algal suspensions, i.e., absorption and scattering coefficients, as well as their apparent optical properties, i.e., the reflectance and the vertical attenuation coefficient of downwelling irradiance, were determined by using high-spectral-resolution radiometric measurements. The vertical attenuation coefficient was used to estimate quantitatively the depth of light penetration into a reactor containing an ultrahigh cell density (chlorophyll concentration, up to 300,000 mg m(sup-3)). For such a high cell density, the photic volume in the reactor was found to be extremely small; nevertheless, it differed between the blue and red light (less than 0.06 mm) and the green light (about 0.5 mm). This suggests a singular role for green light under the unique circumstances existing in ultrahigh-cell-density cultures of photoautotrophs.

Non-destructive determination of maize leaf and canopy chlorophyll content

The objective of this study was to develop a rapid non-destructive technique to estimate total chlorophyll (Chl) content in a maize canopy using Chl content in a single leaf. The approach was (1) to calibrate and validate a reflectance-based non-destructive technique to estimate leaf Chl in maize; (2) to quantify the relative contribution of each leaf Chl to the total Chl in the canopy; and (3) to establish a relationship between leaf Chl content and total Chl in a maize canopy. The Red Edge Chlorophyll Index CI(red edge)=(R(NIR)/R(red edge))-1 based on reflectances, R, in the red edge (720-730nm) and near infrared (770-800nm) was found to be an accurate measure of maize leaf Chl. It was able to predict leaf Chl ranging from 10 to 805mgChlm(-2) with root mean-square error less than 38mgChlm(-2). Relationships between Chl content in each maize leaf and total canopy Chl content were established and showed that Chl in the collar leaf before silking or ear leaves explained more than 80% and 87% of the variation in total Chl in a maize canopy, respectively. Thus, non-destructive measurements of both reflectance and area of a single leaf (either collar or ear) can be used to accurately estimate total Chl content in a maize canopy.

Optical characteristics of the phototroph Thiocapsa roseopersicina and implications for real-time monitoring of the bacteriochlorophyll concentration

Optical characteristics of a Thiocapsa roseopersicina culture and environmental samples containing T. roseopersicina were investigated in the spectral range of 400 to 1,100 nm (absorption coefficient, diffuse attenuation coefficient, and reflectance). Specific absorption coefficients of T. roseopersicina at wavelengths of 480, 520, 550, 580, 805, 860, and 880 nm were determined. It is suggested that the optical properties of T. roseopersicina in the near-infrared range of 800 to 930 nm, confirmed in this study, may be used for development of remote sensing techniques for real-time monitoring of T. roseopersicina and other bacteriochlorophyll a-containing microbes.