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Accumulation and metabolic profile of phenolic compounds (PheCs; serving as UV-screening pigments and antioxidants) as well as carbon fixation rate (An) and plant growth are sensitive to irradiance and temperature. Since these factors are naturally co-acting in the environment, it is worthy to study the combined effects of these environmental factors to assess their possible physiological consequences. We investigated how low and high irradiance in combination with different temperatures modify the metabolic profile of PheCs and expression of genes involved in the antioxidative enzyme and PheCs biosynthesis, in relation to photosynthetic activity and availability of non-structural carbohydrates (NSC) in spring barley seedlings. High irradiance positively affected An, NSC, PheCs content, and antioxidant activity (AOX). High temperature led to decreased An, NSC, and increased dark respiration, whilst low temperature was accompanied by reduction of UV-A shielding but increase of PheCs content and AOX. Besides that, irradiance and temperature caused changes in the metabolic profile of PheCs, particularly alteration in homoorientin/isovitexin derivatives ratio, possibly related to demands on AOX-based protection. Moreover, we also observed changes in the ratio of sinapoyl-/feruloyl- acylated flavonoids, the function of which is not yet known. The data also strongly suggested that the NSC content may support the PheCs production.

Plant miRNAs are powerful regulators of gene expression at the post-transcriptional level, which was repeatedly proved in several model plant species. miRNAs are considered to be key regulators of many developmental, homeostatic, and immune processes in plants. However, our understanding of plant miRNAs is still limited, despite the fact that an increasing number of studies have appeared. This systematic review aims to summarize our current knowledge about miRNAs in spring barley (Hordeum vulgare), which is an important agronomical crop worldwide and serves as a common monocot model for studying abiotic stress responses as well. This can help us to understand the connection between plant miRNAs and (not only) abiotic stresses in general. In the end, some future perspectives and open questions are summarized.

The aim of this study was to evaluate the effects of different in situ light regimen on ecophysiological parameters of Luzula sylvatica leaves. Plants of L. sylvatica grown under natural sunny and shade conditions in arcto-alpine tundra were analyzed with respect to their leaf anatomy, content of photosynthetic pigments, UV absorbing compounds and phenanthrenoid compounds. Relationship between chlorophyll concentrations (Chla+b) and SPAD values was determined for sun and shade leaves measured repeatedly within summer and autumn seasons 2019 and 2020. Pooled data showed curvilinear Chla+b to SPAD relationship with the highest Chla+b and SPAD values found for shade leaves. Sun leaves had higher UV-B absorbing compounds contents than shade ones. The HPLC-DAD analysis revealed significant amount of soluble flavonoids in Luzula sylvatica leaves, amongst others the flavone-luteolin and its derivatives (e.g. tentatively identified luteolin-methyl-glucoside and luteolin-glucoside). The accumulation of luteolin based compounds in sun acclimated leaves is also plausible explanation for the higher antioxidant activity determined in sun leaf extraxts. Such response of flavonoid metabolism may help L.S. to cope with excessive-light stress through UV-attenuation mechanism and ROS scavanging. Additionally, phenanthrenoid compounds contents in L. sylvatica leaves were determined. Altogether, 9 phenanthrenoid compounds were identified by HPLC-HRMS. Their content was markedly different (up to the factor of 5) between sun and shade leaves of L.sylvatica.

The acclimation of higher plants to different light intensities is associated with a reorganization of the photosynthetic apparatus. These modifications, namely, changes in the amount of peripheral antenna (LHCII) of photosystem (PS) II and changes in PSII/PSI stoichiometry, typically lead to an altered chlorophyll (Chl) a/b ratio. However, our previous studies show that in spruce, this ratio is not affected by changes in growth light intensity. The evolutionary loss of PSII antenna proteins LHCB3 and LHCB6 in the Pinaceae family is another indication that the light acclimation strategy in spruce could be different. Here we show that, unlike Arabidopsis, spruce does not modify its PSII/PSI ratio and PSII antenna size to maximize its photosynthetic performance during light acclimation. Its large PSII antenna consists of many weakly bound LHCIIs, which form effective quenching centers, even at relatively low light. This, together with sensitive photosynthetic control on the level of cytochrome b

SARS-CoV-2 is a novel positive-sense single-stranded RNA virus from the Coronaviridae family (genus Betacoronavirus), which has been established as causing the COVID-19 pandemic. The genome of SARS-CoV-2 is one of the largest among known RNA viruses, comprising of at least 26 known protein-coding loci. Studies thus far have outlined the coding capacity of the positive-sense strand of the SARS-CoV-2 genome, which can be used directly for protein translation. However, it has been recently shown that transcribed negative-sense viral RNA intermediates that arise during viral genome replication from positive-sense viruses can also code for proteins. No studies have yet explored the potential for negative-sense SARS-CoV-2 RNA intermediates to contain protein-coding loci. Thus, using sequence and structure-based bioinformatics methodologies, we have investigated the presence and validity of putative negative-sense ORFs (nsORFs) in the SARS-CoV-2 genome. Nine nsORFs were discovered to contain strong eukaryotic translation initiation signals and high codon adaptability scores, and several of the nsORFs were predicted to interact with RNA-binding proteins. Evolutionary conservation analyses indicated that some of the nsORFs are deeply conserved among related coronaviruses. Three-dimensional protein modeling revealed the presence of higher order folding among all putative SARS-CoV-2 nsORFs, and subsequent structural mimicry analyses suggest similarity of the nsORFs to DNA/RNA-binding proteins and proteins involved in immune signaling pathways. Altogether, these results suggest the potential existence of still undescribed SARS-CoV-2 proteins, which may play an important role in the viral lifecycle and COVID-19 pathogenesis.

Photosynthetically active radiation (PAR) is an important environmental cue inducing the production of many secondary metabolites involved in plant oxidative stress avoidance and tolerance. To examine the complex role of PAR irradiance and specific spectral components on the accumulation of phenolic compounds (PheCs), we acclimated spring barley (Hordeum vulgare) to different spectral qualities (white, blue, green, red) at three irradiances (100, 200, 400 µmol m−2 s−1). We confirmed that blue light irradiance is essential for the accumulation of PheCs in secondary barley leaves (in UV-lacking conditions), which underpins the importance of photoreceptor signals (especially cryptochrome). Increasing blue light irradiance most effectively induced the accumulation of B-dihydroxylated flavonoids, probably due to the significantly enhanced expression of the F3′H gene. These changes in PheC metabolism led to a steeper increase in antioxidant activity than epidermal UV-A shielding in leaf extracts containing PheCs. In addition, we examined the possible role of miRNAs in the complex regulation of gene expression related to PheC biosynthesis.

The 'standard' fluid-mosaic membrane model can provide a framework for the operation of the photosynthetic and respiratory electron transport systems, the generation of the proton motive force (pmf) and its utilization for ATP synthesis according to the chemiosmotic theory. However, this model, with the bilayer organization of all lipid molecules, assigns no function to non-bilayer lipids - while in recent years it became clear that the two fundamental energy transducing membranes of the biosphere, chloroplast thylakoid membranes (TMs) and inner mitochondrial membranes (IMMs), contain large amounts of non-bilayer (non-lamellar) lipid phases. In this review, we summarize our understanding on the role of non-lamellar phases in TMs and IMMs: (i) We propose that for these membrane vesicles the dynamic exchange model (DEM) provides a more suitable framework than the 'standard' model; DEM complements the 'standard' model by assuming the co-existence of bilayer and non-bilayer phases and their interactions, which contribute to the structural dynamics of the membrane systems and safe-guard the membranes' high protein:lipid ratios. (ii) Non-bilayer phases play pivotal roles in membrane fusion and intermembrane lipid exchanges - essential processes in the self-assembly of these highly folded intricate membranes. (iii) The photoprotective, lipocalin-like lumenal enzyme, violaxanthin de-epoxidase, in its active state requires the presence of non-bilayer lipid phase. (iv) Cardiotoxins, water-soluble polypeptides, induce non-bilayer phases in mitochondria. (v) ATP synthesis, in mammalian heart IMMs, is positively correlated with the amount of non-bilayer packed lipids with restricted mobility. (vi) The hypothesized sub-compartments, due to non-lamellar phases, are proposed to enhance the utilization of pmf and might contribute to the recently documented functional independence of individual cristae within the same mitochondrion. Further research is needed to identify and characterize the structural entities associated with the observed non-bilayer phases; and albeit fundamental questions remain to be elucidated, non-lamellar lipid phases should be considered on a par with the bilayer phase, with which they co-exist in functional TMs and IMMs.

Barley (Hordeum vulgare) accumulates phenolic compounds (PhCs), which play a key role in plant defense against environmental stressors as antioxidants or UV screening compounds. The influence of light and atmospheric CO2 concentration ([CO2]) on the accumulation and localization of PhCs in barley leaves was examined for two varieties with different tolerances to oxidative stress. PhC localization was visualized in vivo using fluorescence microscopy. Close relationships were found between fluorescence-determined localization of PhCs in barley leaves and PhC content estimated using liquid chromatography coupled with mass spectroscopy detection. Light intensity had the strongest effect on the accumulation of PhCs, but the total PhC content was similar at elevated [CO2], minimizing the differences between high and low light. PhCs localized preferentially near the surfaces of leaves, but under low light, an increasing allocation of PhCs in deeper mesophyll layers was observed. The PhC profile was significantly different between barley varieties. The relatively tolerant variety accumulated significantly more hydroxycinnamic acids, indicating that these PhCs may play a more prominent role in oxidative stress prevention. Our research presents novel evidence that [CO2] modulates the accumulation of PhCs in barley leaves. Mesophyll cells, rather than epidermal cells, were most responsive to environmental stimuli in terms of PhC accumulation.

Barley (Hordeum vulgare) accumulates phenolic compounds (PhCs), which play a key role in plant defense against environmental stressors as antioxidants or UV screening compounds. The influence of light and atmospheric CO2 concentration ([CO2]) on the accumulation and localization of PhCs in barley leaves was examined for two varieties with different tolerances to oxidative stress. PhC localization was visualized in vivo using fluorescence microscopy. Close relationships were found between fluorescence-determined localization of PhCs in barley leaves and PhC content estimated using liquid chromatography coupled with mass spectroscopy detection. Light intensity had the strongest effect on the accumulation of PhCs, but the total PhC content was similar at elevated [CO2], minimizing the differences between high and low light. PhCs localized preferentially near the surfaces of leaves, but under low light, an increasing allocation of PhCs in deeper mesophyll layers was observed. The PhC profile was significantly different between barley varieties. The relatively tolerant variety accumulated significantly more hydroxycinnamic acids, indicating that these PhCs may play a more prominent role in oxidative stress prevention. Our research presents novel evidence that [CO2] modulates the accumulation of PhCs in barley leaves. Mesophyll cells, rather than epidermal cells, were most responsive to environmental stimuli in terms of PhC accumulation.

SARS-CoV-2 is an intensively investigated virus from the order Nidovirales (Coronaviridae family) that causes COVID-19 disease in humans. Through enormous scientific effort, thousands of viral strains have been sequenced to date, thereby creating a strong background for deep bioinformatics studies of the SARS-CoV-2 genome. In this study, we inspected high-frequency mutations of SARS-CoV-2 and carried out systematic analyses of their overlay with inverted repeat (IR) loci and CpG islands. The main conclusion of our study is that SARS-CoV-2 hot-spot mutations are significantly enriched within both IRs and CpG island loci. This points to their role in genomic instability and may predict further mutational drive of the SARS-CoV-2 genome. Moreover, CpG islands are strongly enriched upstream from viral ORFs and thus could play important roles in transcription and the viral life cycle. We hypothesize that hypermethylation of these loci will decrease the transcription of viral ORFs and could therefore limit the progression of the disease.

SARS-CoV-2 is a novel positive-sense single-stranded RNA virus from the Coronaviridae family (genus Betacoronavirus), which has been established as causing the COVID-19 pandemic. The genome of SARS-CoV-2 is one of the largest among known RNA viruses, comprising of at least 26 known protein-coding loci. Studies thus far have outlined the coding capacity of the positive-sense strand of the SARS-CoV-2 genome, which can be used directly for protein translation. However, it has been recently shown that transcribed negative-sense viral RNA intermediates that arise during viral genome replication from positive-sense viruses can also code for proteins. No studies have yet explored the potential for negative-sense SARS-CoV-2 RNA intermediates to contain protein coding-loci. Thus, using sequence and structure-based bioinformatics methodologies, we have investigated the presence and validity of putative negative-sense ORFs (nsORFs) in the SARS-CoV-2 genome. Nine nsORFs were discovered to contain strong eukaryotic translation initiation signals and high codon adaptability scores, and several of the nsORFs were predicted to interact with RNA-binding proteins. Evolutionary conservation analyses indicated that some of the nsORFs are deeply conserved among related coronaviruses. Three-dimensional protein modelling revealed the presence of higher order folding among all putative SARS-CoV-2 nsORFs, and subsequent structural mimicry analyses suggest similarity of the nsORFs to DNA/RNA-binding proteins and proteins involved in immune signaling pathways. Altogether, these results suggest the potential existence of still undescribed SARS-CoV-2 proteins, which may play an important role in the viral lifecycle and COVID-19 pathogenesis.Contactpetr.pecinka@osu.cz; tlb20@cam.ac.uk

Barley (Hordeum vulgare) accumulates phenolic compounds (PhCs), which play a key role in tolerance to environmental stress. The influence of irradiance and atmospheric CO2 concentration ([CO2]) on the accumulation and localization of PhCs in barley leaves was examined for two varieties with different tolerances to oxidative stress. PhC localization was visualized using Naturstoff reagent A and fluorescence microscopy. Close relationships were found between fluorescence-determined localization of PhCs in barley leaves and PhC content estimated using liquid chromatography coupled with mass spectroscopy detection. High intensity light had the strongest effect on the accumulation of PhCs, but total PhC content converged at elevated [CO2], minimizing the differences between high and low irradiance. PhCs localized preferentially near the surfaces of leaves, but under low light, increasing allocation of PhCs deeper mesophyll layers was observed. The PhC profile was very different between barley varieties. Our research presents novel evidence that [CO2] modulates the accumulation of PhCs accumulation in barley leaves. Mesophyll cells, rather than epidermal cells, were most responsive to environmental stimuli in terms of PhC accumulation. The relatively tolerant variety accumulated significantly more hydroxycinnamic acids, indicating these PhCs may play a more prominent role in oxidative stress prevention.

The role of non-bilayer lipids and non-lamellar lipid phases in biological membranes is an enigmatic problem of membrane biology. Non-bilayer lipids are present in large amounts in all membranes; in energy-converting membranes they constitute about half of their total lipid content—yet their functional state is a bilayer. In vitro experiments revealed that the functioning of the water-soluble violaxanthin de-epoxidase (VDE) enzyme of plant thylakoids requires the presence of a non-bilayer lipid phase. 31P-NMR spectroscopy has provided evidence on lipid polymorphism in functional thylakoid membranes. Here we reveal reversible pH- and temperature-dependent changes of the lipid-phase behaviour, particularly the flexibility of isotropic non-lamellar phases, of isolated spinach thylakoids. These reorganizations are accompanied by changes in the permeability and thermodynamic parameters of the membranes and appear to control the activity of VDE and the photoprotective mechanism of non-photochemical quenching of chlorophyll-a fluorescence. The data demonstrate, for the first time in native membranes, the modulation of the activity of a water-soluble enzyme by a non-bilayer lipid phase.

Plants have developed many ways to protect reaction centres of photosystems against overexcitation. One of the mechanisms involves reduction of the leaf absorption cross-section by light-induced chloroplast avoidance reaction. Decrease in the probability of photon absorption by the pigments bound within photosystem II (PSII) complexes leads to the increase in quantum yield of PSII photochemistry (ΦPSII). On the other hand, the decrease of PSII excitation probability causes reduction of chlorophyll a fluorescence intensity which is manifested as the apparent increase of determined quantum yield of regulated light-induced non-photochemical quenching (ΦNPQ). Absorption of different light intensity by phototropins led to the different chloroplast distribution within barley leaves, estimated by measurement of the leaf transmittance. Due to a weak blue light used for transmittance measurements, leaves exposed to actinic light with wavelengths longer than 520 nm undergo chloroplast accumulation reaction, in contrast with leaves exposed to light with shorter wavelengths, that showed a different extent of chloroplast avoidance reaction. Based on the ΦNPQ action spectra measured simultaneously with the transmittance, the influence of different chloroplast distribution on ΦNPQ was assessed. The analysis of results showed that decrease in the leaf absorption cross-section due to increasing part of chloroplasts reaching profile position significantly affected the partitioning of excitation energy within PSII and such rearrangement also distorted measured ΦNPQ and cannot be neglected in its interpretation. When the majority of chloroplasts reached profile position, the photoprotective effect appeared to be the most prominent for strong blue light that has the highest absorption in the upper leaf layers in comparison with green or red ones.

Photosystem II (PSII) catalyses the photoinduced oxygen evolution and, by producing reducing equivalents drives, in concert with PSI, the conversion of carbon dioxide to sugars. Our knowledge about the architecture of the reaction centre (RC) complex and the mechanisms of charge separation and stabilisation is well advanced. However, our understanding of the processes associated with the functioning of RC is incomplete: the photochemical activity of PSII is routinely monitored by chlorophyll-a fluorescence induction but the presently available data are not free of controversy. In this work, we examined the nature of gradual fluorescence rise of PSII elicited by trains of single-turnover saturating flashes (STSFs) in the presence of a PSII inhibitor, permitting only one stable charge separation. We show that a substantial part of the fluorescence rise originates from light-induced processes that occur after the stabilisation of charge separation, induced by the first STSF; the temperature-dependent relaxation characteristics suggest the involvement of conformational changes in the additional rise. In experiments using double flashes with variable waiting times (∆τ) between them, we found that no rise could be induced with zero or short ∆τ, the value of which depended on the temperature - revealing a previously unknown rate-limiting step in PSII.

Measurement of Pulse-Amplitude-Modulated (PAM) chlorophyll a fluorescence is widely used method for obtaining information on the functional state of photosystem II (PSII). Recently, it has been shown that some of long-established fluorescence parameters must be interpreted with caution, when the light-induced chloroplast movements occur. In our work we have analyzed the effect of chloroplast movements on these parameters. We have derived new parameters that are independent of the change in PSII absorption occurring during measurement. To verify whether there is a need for new parameters or the difference between the parameters commonly used and the newly derived ones is insignificant, we conducted an experiment with Arabidopsis thaliana wild type plants and its phot1 phot2 mutant defective in chloroplast movement. Plants were exposed to light of different qualities (450, 470, 550 or 660 nm) and quantities (100, 400 or 1200 μmol m−2 s−1) for up to 40 min. Since the blue light-induced chloroplast avoidance reaction is a photoprotective mechanism, we expected that phot1 phot2 mutant will compensate the lack of this mechanism by increasing non-photochemical quenching. However, using the light at both 450 and 470 nm, the calculation of commonly used parameter, ΦNPQ (quantum yield of regulated light-induced thermal energy dissipation in PSII) based on Hendrickson et al. [L. Hendrickson, R.T. Furbank, W.S. Chow, Photosynth. Res. 82 (2004) 73–81] showed the opposite. On the other hand, the results obtained using our newly proposed formulae to determine quantum yield of PSII thermal energy dissipation were in line with our assumption. Thus, the experimental data showed that some formulae of fluorescence parameters are dependent on the change in PSII absorption and need to be interpreted carefully. On the contrary, the formulae introduced by us can remove the effect of changes in PSII absorption that occur during measurement, without additional measurements, and give the real estimate of light-induced non-photochemical quenching.

G-quadruplexes have long been perceived as rare and physiologically unimportant nucleic acid structures. However, several studies have revealed their importance in molecular processes, suggesting their possible role in replication and gene expression regulation. Pathways involving G-quadruplexes are intensively studied, especially in the context of human diseases, while their involvement in gene expression regulation in plants remains largely unexplored. Here, we conducted a bioinformatic study and performed a complex circular dichroism measurement to identify a stable G-quadruplex in the gene RPB1, coding for the RNA polymerase II large subunit. We found that this G-quadruplex-forming locus is highly evolutionarily conserved amongst plants sensu lato (Archaeplastida) that share a common ancestor more than one billion years old. Finally, we discussed a new hypothesis regarding G-quadruplexes interacting with UV light in plants to potentially form an additional layer of the regulatory network.

We examined the dynamics of phenolic compounds (PheCs) and carotenoids (Cars) in the leaves of wild type (WT) spring barley (Hordeum vulgare L.) and its mutant lacking chlorophyll b Chlorina f2 (Clo f2) grown from seeds at high irradiance (8 d at 1 000 μmol m-2 s-1; HI) during 9 d of acclimation to low irradiance (50 μmol m-2 s-1; LI). Our results show that a leaf epidermal flavonoid UV-shielding index remained rather constant after transfer of plants from HIto LIconditions and that it was significantly lower in Clo f2 compared to WTplants. This suggests that HIpretreated plants can be well protected against excessive UVfor at least 9 d, as supported also by the constant absorbance of leaf PheCs extracts in the UV-A region (at 335 nm). In contrast, absorbance in the UV-B region (at 270 nm) was reduced, particularly during the initial days of LItreatment, indicating specific changes in PheC profile. High-performance liquid chromatography of soluble PheCs revealed stable content of the major PheC saponarin during LIacclimation, whereas luteolin and feruloylquinic acid content decreased, particularly in WTplants. We also observed a pronounced decrease in Car relative content, particularly a reduction in the xanthophyll cycle pigments (violaxanthin, antheraxanthin, and zeaxanthin, VAZ) pool and diminution of their de-epoxidation state (DEPS) in dark-adapted leaves. As both VAZ and DEPS were higher in HI-acclimated Clo f2 plants than they were in WTplants, the presence of a significant VAZ pool within the lipid phase of thylakoid membrane is indicated. That can contribute to antioxidant capacity particularly in Clo f2 plants. We can therefore conclude that there is a tendency to retain the PheCs responsible for UVshielding during LIacclimation. Meanwhile, the accumulation of both PheCs and zeaxanthin serving as effective antioxidants is considerably downregulated within 9 d.

Earlier experiments, using 31 P-NMR and time-resolved merocyanine fluorescence spectroscopy, have shown that isolated intact, fully functional plant thylakoid membranes, in addition to the bilayer phase, contain three non-bilayer (or non-lamellar) lipid phases. It has also been shown that the lipid polymorphism of thylakoid membranes can be characterized by remarkable plasticity, i.e. by significant variations in 31 P-NMR signatures. However, changes in the lipid-phase behaviour of thylakoids could not be assigned to changes in the overall membrane organization and the photosynthetic activity, as tested by circular dichroism and 77 K fluorescence emission spectroscopy and the magnitude of the variable fluorescence of photosystem II, which all showed only marginal variations. In this work, we investigated in more detail the temporal stability of the different lipid phases by recording 31 P-NMR spectra on isolated thylakoid membranes that were suspended in sorbitol- or NaCl-based media. We observed, at 5°C during 8 h in the dark, substantial gradual enhancement of the isotropic lipid phases and diminishment of the bilayer phase in the sorbitol-based medium. These changes compared well with the gradually increasing membrane permeability, as testified by the gradual acceleration of the decay of flash-induced electrochromic absorption changes and characteristic changes in the kinetics of fast chlorophyll a-fluorescence transients; all variations were much less pronounced in the NaCl-based medium. These observations suggest that non-bilayer lipids and non-lamellar lipid phases play significant roles in the structural dynamics and functional plasticity of thylakoid membranes.

We investigated the effect of leaf ontogeny and barley genotype on the accumulation of phenolic compounds (PhCs) induced by ultraviolet (UV) and photosynthetically active radiation (PAR). We hypothesized that different groups of PhCs are induced in leaves differing in ontogeny, and that this has consequences for protective functions and the need for other protection mechanisms. Generally, lower constitutive contents of PhCs (under conditions of UV exclusion and reduced PAR) were found in a UV-sensitive genotype (Barke) compared to a tolerant genotype (Bonus). However, UV and PAR induced accumulation of PhCs exceeded the constitutive amounts several fold. Specifically, lutonarin, 3-feruloylquinic acid, unidentified hydroxycinnamic acid and luteolin derivatives were markedly enhanced by high PAR and UV irradiances. Leaves developed during UV and PAR treatments had higher PhCs contents than mature leaves already fully developed at the onset of the UV and PAR treatment. UV and PAR treatments had, however, a minor effect on saponarin and unidentified apigenin derivatives which occur particularly in mature leaves of the tolerant genotype Bonus. In addition, high UV and PAR intensities increased the total content of xanthophylls (VAZ), while chlorophyll content was reduced, particularly in developing leaves. A redundancy analysis revealed positive associations between most of PhCs and VAZ and a negative association between total chlorophylls and carotenoids. Non-linear relationships between VAZ and lutonarin and other PhCs indicate that VAZ accumulation can compensate for the insufficient efficiency of anti-oxidative protection mediated by PhCs. Accordingly, we conclude that UV and PAR-induced accumulation of PhCs is affected by leaf ontogeny, however, this effect is compound-specific.

A database containing 10 min means of solar irradiance measured on a horizontal plane in several ultraviolet and visible bands from July 2014 to December 2016 at three stations in the area of the city of Ostrava (Czech Republic) is presented. The database contains time series of 10 min average irradiances or photosynthetic photon flux densities measured in the following spectral bands: 280–315 nm (UVB); 315–380 nm (UVA); and 400–700 nm (photosynthetically active radiation, PAR); 510–700 nm; 600–700 nm; 610–680 nm; 690–780 nm; 400–1100 nm. A series of meteorological variables including relative air humidity and air temperature at surface is also provided at the same 10 min time step at all three stations, and precipitation is provided for two stations. Air pressure, wind speed, wind direction, and concentrations of air pollutants PM10, SO2, NOx, NO, NO2 were measured at the 1 h time step at the fourth station owned by the Public Health Institute of Ostrava. The details of the experimental sites and instruments used for the measurements are given. Special attention is given to the data quality, and the original approach to the data quality which was established is described in detail. About 130 000 records for each of the three stations are available in the database. This database offers a unique ensemble of variables having a high temporal resolution and it is a reliable source for radiation in relation to environment and vegetation in highly polluted areas of industrial cities in the of northern mid-latitudes. The database has been placed on the PANGAEA repository (https://doi.org/10.1594/PANGAEA.879722) and contains individual data files for each station.

We examined the acclimation response of the photosynthetic apparatus of barley (Hordeum vulgare L.) to a combination of UV-A and UV-B radiation (UVAB) and to UV-B radiation alone. Our aim was to evaluate whether UV-A radiation prevents UV-B-induced damage to the photosynthetic apparatus and whether UV-A pre-acclimation is required to mitigate the negative influence of UV-B radiation. Barley plants were grown from seeds under low photosynthetically active radiation (50 μmol m(-2) s(-1)) either in the absence or presence of UV-A radiation (UVA- and UVA+ plants, respectively). After 8 days of development, plants were exposed simultaneously to UV-A and UV-B radiation for the next 6 days. Additionally, UVA- plants were exposed to UV-B radiation alone. The UVA+ plants had a higher CO2 assimilation rate near the light-saturation region (A(N)) and a higher content of both total chlorophylls (Chls) and total carotenoids than the UVA- plants. Chls content, A(N), the potential quantum yield of photosystem II (PSII) photochemistry (F(V)/F(M)), the capacity of light-induced thermal energy dissipation and the efficiency of excitation energy transfer within PSII remained the same or even increased in both UVA+ and UVA- plants after UVAB treatment. On the contrary, exposure of UVA- plants to UV-B radiation itself led to a reduction in all these characteristics. We revealed that the presence of UV-A radiation during UVAB treatment not only mitigated but completely eliminated the negative effect of UV-B radiation on the functioning of the photosynthetic apparatus and that UV-A pre-acclimation was not crucial for development of this UV-A-induced resistance against UV-B irradiation.

This research paper focuses on with the effects of air pollutants PM10, NOx, and SO2 on the blue (400–510 nm), green (510–600 nm), and red (600–700 nm) spectral regions of photosynthetically active radiation (PAR). The measurements of solar radiation incident on a horizontal surface were taken at two locations in the city of Ostrava (Czech Republic) that differed in the source of air pollution. Linear regression models, with two explanatory variables (solar elevation angle and logarithm of individual pollutant concentration), were used as statistical tools for revealing the effect of air pollutants on incident solar radiation. The effect of air pollution on the Blue/PAR spectral ratio was ambiguous. There was a significant decrease in the Green/PAR spectral ratio, whereas there was a significant enhancement in the Red/PAR spectral ratio caused by the increasing air pollutant concentrations. The effects of air pollutants on these spectral ratios were significant from a statistical point of view with p-values smaller than 0.05, but the magnitude of the effect that the air pollutants had on the Blue/PAR and Red/PAR was small. In comparison to the above mentioned, the pollutants had a dominating effect on the Green/PAR spectral ratio. Pollution did not induce homogenous reduction of all PAR spectral regions, instead each pollutant had a specific effect on the contributions of blue, green, and red spectral regions to PAR irradiance. Possible causes of these effects are discussed.

A dedicated field experiment was conducted to investigate the response of a green reflectance continuum removal-based optical index, called area under the curve normalized to maximal band depth between 511 nm and 557 nm (ANMB511-557), to light-induced transformations in xanthophyll cycle pigments of Norway spruce [Picea abies (L.) Karst] needles. The performance of ANMB511-557 was compared with the photochemical reflectance index (PRI) computed from the same leaf reflectance measurements. Needles of four crown whorls (fifth, eighth, 10th, and 15th counted from the top) were sampled from a 27-year-old spruce tree throughout a cloudy and a sunny day. Needle optical properties were measured together with the composition of the photosynthetic pigments to investigate their influence on both optical indices. Analyses of pigments showed that the needles of the examined whorls varied significantly in chlorophyll content and also in related pigment characteristics, such as the chlorophyll/carotenoid ratio. The investigation of the ANMB511-557 diurnal behaviour revealed that the index is able to follow the dynamic changes in the xanthophyll cycle independently of the actual content of foliar pigments. Nevertheless, ANMB511-557 lost the ability to predict the xanthophyll cycle behaviour during noon on the sunny day, when the needles were exposed to irradiance exceeding 1000 µmol m(-2) s(-1). Despite this, ANMB511-557 rendered a better performance for tracking xanthophyll cycle reactions than PRI. Although declining PRI values generally responded to excessive solar irradiance, they were not able to predict the actual de-epoxidation state in the needles examined.

Chloroplast thylakoid membranes contain virtually all components of the energy-converting photosynthetic machinery. Their energized state, driving ATP synthesis, is enabled by the bilayer organization of the membrane. However, their most abundant lipid species is a non-bilayer-forming lipid, monogalactosyl-diacylglycerol; the role of lipid polymorphism in these membranes is poorly understood. Earlier 31P-NMR experiments revealed the coexistence of a bilayer and a non-bilayer, isotropic lipid phase in spinach thylakoids. Packing of lipid molecules, tested by fluorescence spectroscopy of the lipophilic dye, merocyanine-540 (MC540), also displayed heterogeneity. Now, our 31P-NMR experiments on spinach thylakoids uncover the presence of a bilayer and three non-bilayer lipid phases; time-resolved fluorescence spectroscopy of MC540 also reveals the presence of multiple lipidic environments. It is also shown by 31P-NMR that: (i) some lipid phases are sensitive to the osmolarity and ionic strength of the medium, (ii) a lipid phase can be modulated by catalytic hydrogenation of fatty acids and (iii) a marked increase of one of the non-bilayer phases upon lowering the pH of the medium is observed. These data provide additional experimental evidence for the polymorphism of lipid phases in thylakoids and suggest that non-bilayer phases play an active role in the structural dynamics of thylakoid membranes.

Light quality is an important environmental factor affecting the biosynthesis of photosynthetic pigments whose production seems to be affected not only quantitatively but also qualitatively. In this work, we set out to identify unusual pigment detected in leaves of barley ( Hordeum vulgare L.) and explain its presence in plants grown under monochromatic green light (GL; 500–590 nm). The chromatographic analysis (HPLC-DAD) revealed that a peak belonging to this unknown pigment is eluted between chlorophyll (Chl) a and b . This pigment exhibited the same absorption spectrum and fluorescence excitation and emission spectra as Chl a . It was negligible in control plants cultivated under white light of the same irradiance (photosynthetic photon flux density of 240 μmol m −2 s −1 ). Mass spectrometry analysis of this pigment (ions m/z = 889 [M−H] − ; m/z = 949 [M+acetic acid-H] - ) indicates that it is Chl a with a tetrahydrogengeranylgeraniol side chain (containing two double bonds in a phytyl side chain; Chl a THGG ), which is an intermediate in Chl a synthesis. In plants grown under GL, the proportion of Chl a THGG to total Chl content rose to approximately 8% and 16% after 7 and 14 days of cultivation, respectively. Surprisingly, plants cultivated under GL exhibited drastically increased concentration of the enzyme geranylgeranyl reductase, which is responsible for the reduction of phytyl chain double bonds in the Chl synthesis pathway. This indicates impaired activity of this enzyme in GL-grown plants. A similar effect of GL on Chl synthesis was observed for distinct higher plant species.

The interactive effects of photosynthetically active radiation (PAR) on plants’ acclimation to ultraviolet (UV) radiation were examined under field conditions in two barley varieties (Barke, Bonus). Plants, pre-treated under UV exclusion and low PAR intensities, were subsequently exposed to four radiation treatments representing the combination of low [−] and high [+] UV and PAR intensities. Selective UV and PAR filters were used for UV exclusion and reduction of PAR to ca 25% of ambient irradiance. A system of modulated lamps was used to enhance UV to ca 200% of ambient. Changes in flavonol and chlorophyll content, chlorophyll fluorescence, gas-exchange and leaf hyperspectral reflectance were studied during seven days of acclimation to the new treatments. At the end of this period morphological analysis of aboveground biomass was carried out. The [UV+PAR−] treatment significantly reduced the photosynthetic activity of barley leaves; the reduction was more pronounced in old than young leaves and greater in the variety Barke than Bonus. Whereas, [PAR+] treatment triggered photoprotective mechanisms which partially ameliorated the UV effects on photochemistry and carbon assimilation. The [PAR+] treatment induced accumulation of flavonols, mainly in young leaves, whereas in old leaves UV-induced accumulation was more pronounced. An inverse proportion was found between flavonol content and specific leaf area irrespective of barley variety and UV/PAR treatment. Enhanced UV radiation reduced the final leaf length, particularly in [PAR−] plants, in young leaves and in variety Barke. However, [PAR+] mitigated the morphological effects induced by the [UV+] treatment, particularly changes in SLA.

Summary 1. Cloud cover affects carbon exchange between biota and the atmosphere. Recent studies have demonstrated that an increase in the diffuse radiation fraction enhances the photosynthetic efficiency of canopies. Although the exact mechanism behind this effect is not clear, a more even distribution of light among leaves across the vertical profile of the canopy is considered to be the most important cause of this difference. 2. To test this hypothesis, the net ecosystem production (NEP) of a Norway spruce forest (30-year-old) was measured under cloudy and sunny skies by the eddy covariance method. In parallel, measurements of the diurnal courses of gas exchange and chlorophyll fluorescence parameters were made in the upper sun (5th whorl; 1-year-old needles), middle (8th and 10th whorl; 1- and 2-year-old needles) and lower shade (15th whorl; >2-year-old needles) shoots. 3. The higher diffuse radiation fraction during cloudy days resulted in significantly higher ecosystem carbon uptake than at corresponding incident photosynthetic photon flux density on sunny days. Our shoot-level data show that shoots from deep within the canopy contribute substantially to the overall carbon balance during cloudy days. But, although shade-adapted shoots had a markedly positive carbon balance over a 24-h period on cloudy days, their performance was impaired on sunny days contributing only a marginal or even negative carbon balance from the middle and shaded parts of the canopy. The uppermost sun shoots contributed 78% of the total carbon assimilated during a sunny day, but only 43% during a cloudy day. 4. In addition, afternoon depression of canopy NEP and CO2 assimilation rates of the uppermost shoots (5th and 8th whorl) occurred in response to irradiance on sunny days, characterized by significant decreases in CO2 uptake and apparent quantum yield; however, this depression did not occur under cloudy conditions. Stomatal and non-stomatal regulations of carbon assimilation in the afternoon are discussed.

The present study was conducted to examine changes in photosynthetic pigment composition and functional state of the thylakoid membranes during the individual steps of preparation of samples that are intended for a separation of pigmentprotein complexes by nondenaturing polyacrylamide gel electrophoresis. The thylakoid membranes were isolated from barley leaves (Hordeum vulgare L.) grown under low irradiance (50 μmol m−2 s−1). Functional state of the thylakoid membrane preparations was evaluated by determination of the maximal photochemical efficiency of photosystem (PS) II (FV/FM) and by analysis of excitation and emission spectra of chlorophyll a (Chl a) fluorescence at 77 K. All measurements were done at three phases of preparation of the samples: (1) in the suspensions of osmotically-shocked broken chloroplasts, (2) thylakoid membranes in extraction buffer containing Tris, glycine, and glycerol and (3) thylakoid membranes solubilized with a detergent decyl-β-D-maltosid. FV/FM was reduced from 0.815 in the first step to 0.723 in the second step and to values close to zero in solubilized membranes. Pigment composition was not pronouncedly changed during preparation of the thylakoid membrane samples. Isolation of thylakoid membranes affected the efficiency of excitation energy transfer within PSII complexes only slightly. Emission and excitation fluorescence spectra of the solubilized membranes resemble spectra of trimers of PSII light-harvesting complexes (LHCII). Despite a disrupted excitation energy transfer from LHCII to PSII antenna core in solubilized membranes, energy transfer from Chl b and carotenoids to emission forms of Chl a within LHCII trimers remained effective.

Diurnal courses of photosynthetic gas exchange parameters, chlorophyll a fluorescence characteristics and the de-epoxidation state of the xanthophyll cycle pigments (DEPS) were measured during the gradual acclimation of 4-year-old Norway spruce seedlings to different photosynthetic photon flux density (PPFD) and air temperature (T(air)) regimes, simulating cloudy days with moderate T(air) (LI, maximum PPFD 300 micromol m(-2)s(-1), T(air) range 15-25 degrees C), sunny days with moderate T(air) (HI, maximum PPFD 1000 micromol m(-2)s(-1), T(air) range 15-25 degrees C) and hot sunny days (HI-HT, maximum PPFD 1000 micromol m(-2)s(-1), T(air) range 20-35 degrees C). The plants were acclimated inside a growth chamber and each acclimation regime lasted for 13d. Acclimation to HI conditions led to a strong depression of the net CO(2) assimilation rates (A(N)), particularly during noon and afternoon periods. Exposure to the HI-HT regime led to a further decrease of A(N) even during the morning period. Insufficient stomatal conductance was found to be the main reason for depressed A(N) under HI and HI-HT conditions. Only slight changes of the maximum photosystem II (PSII) photochemical efficiency (F(V)/F(M)), in the range of 0.78-0.82, supported the resistance of the Norway spruce photosynthetic apparatus against PSII photoinhibition during acclimation to both HI and HI-HT conditions. The HI plants showed increased content of xanthophyll cycle pigments (VAZ) and enhanced efficiency of thermal energy dissipation within PSII (D) that closely correlated with the increased DEPS. In contrast, acclimation to the HI-HT regime resulted in a slight reduction of VAZ content and significantly diminished D and DEPS values during the entire day in comparison with HI plants. These results indicate a minor role of the xanthophyll cycle-mediated thermal dissipation in PSII photoprotection under elevated temperatures. The different contributions of the thermal dissipation and non-assimilatory electron transport pathways in PSII photoprotection during acclimation of the Norway spruce photosynthetic apparatus to excess irradiance and heat stresses are discussed.

The hypothesis that elevated CO2 leads to a faster induction of photosynthesis was tested using 7–8-year-old seedlings of broadleaved Fagus sylvatica and coniferous Picea abies exposed for three growing seasons to ambient (385 μmol mol−1; AC) and elevated CO2 (700 μmol mol−1; EC). Since the photosynthetic induction is primarily determined by light modulations of Rubisco activity and stomata opening, the hypothesis was based on the following presumptions: (1) EC reduces the content of Rubisco in leaves, (2) decreases stomatal conductance, and (3) has no effect on the rates of stomatal opening and Rubisco activation upon illumination. Thus, reduced maxima of Rubisco activity and stomatal conductance should be reached faster in EC compared to AC plants after leaf transition from dark to light. The initial presumptions were confirmed, since reductions of Rubisco content (up to 28% and 48%) and light-saturated stomatal conductance (GSmax; up to 40% and 50%) were observed in EC treated F. sylvatica and P. abies as compared to AC ones. However, the presumption of constant induction rates was not confirmed. A slight decrease of the time constant for Rubisco activation (14–27%) was observed as the result of EC treatment in both tree species, whereas stomatal opening rates significantly decreased in F. sylvatica (up to 48%) and remained almost unchanged in P. abies. Thus, EC treatment led to the stimulation of the initial phase of photosynthetic induction. This was demonstrated by higher values of the induction state 60 s after leaf illumination (IS60), determined in both F. sylvatica (up to 129%) and P. abies (up to 108%) as compared to AC treatment. In contrast, the stimulation of the secondary phase of photosynthetic induction, reflecting mainly stomatal opening and described by the time required to reach 90% of maximum steady-state photosynthesis (T90(A)), was only 5–15% in F. sylvatica (non-significant) and 21–28% in P. abies (significant). The reduced rates of stomatal opening by EC treatment thus may limit the general validity of the hypothesis.

The wild-type barley (WT; Hordeum vulgare L.) and its chlorophyll (Chl) b -less mutant chlorina f2 ( clo f2 ) grown under shaded conditions in a greenhouse were transferred to outdoor conditions in early June with predominantly bright sunny days. During 6 days following transfer of plants we monitored the content of photosynthetic pigments, functional state of photosystem II (PSII) by means of Chl fluorescence induction kinetics and epidermal UV-shielding efficiency using Chl fluorescence imaging technique. Clo f2 mutant was more sensitive to exposure to an enhanced natural solar irradiance than WT barley. Nevertheless, clo f2 as well as WT were able to cope with stressful outdoor conditions, as was documented by the recovery of Chl a content and the maximal photochemical efficiency of PSII ( F V / F M ) after an initial decline. This was due to the immediate carotenoid-mediated photoprotection, reflected by strongly increased total carotenoids content and thermal energy dissipation localized within light-harvesting complexes of PSII (assessed by non-photochemical quenching of minimal fluorescence level). The positive acclimation response was further documented by an enhanced light-saturated electron transport rate through PSII (ETR). Based on the ratios of blue- to UV-excited Chl fluorescence we found that for both WT and clo f2 epidermal UV-shielding increased clearly after transfer to outdoor conditions and reached a saturation level after 3 days. In comparison with WT, clo f2 exhibited lower ability to induce UV-shielding. The kinetics of UV-shielding development during the outdoor treatment was different for the particular leaf regions. We suggest that this is related to the different age and developmental stage of the tissue along the leaf blade. The complementarity of carotenoid-mediated photoprotection and UV-shielding in acclimation of the assimilatory apparatus to increased visible and UV radiation is discussed.

Summary The response of Norway spruce saplings ( Picea abies [L.] Karst.) was monitored continuously during short-term exposure (10 days) to high irradiance (HI; 1000 μmol m −2 s −1 ). Compared with plants acclimated to low irradiance (100 μmol m −2 s −1 ), plants after HI exposure were characterized by a significantly reduced CO 2 assimilation rate throughout the light response curve. Pigment contents varied only slightly during HI exposure, but a rapid and strong response was observed in xanthophyll cycle activity, particularly within the first 3 days of the HI treatment. Both violaxanthin convertibility under HI and the amount of zeaxanthin pool sustained in darkness increased markedly under HI conditions. These changes were accompanied by an enhanced non-radiative dissipation of absorbed light energy (NRD) and the acceleration of induction of both NRD and de-epoxidation of the xanthophyll cycle pigments. We found a strong negative linear correlation between the amount of sustained de-epoxidized xanthophylls and the photosystem II (PSII) photochemical efficiency ( F V / F M ), indicating photoprotective down-regulation of the PSII function. Recovery of F V / F M at the end of the HI treatment revealed that Norway spruce was able to cope with a 10-fold elevated irradiance due particularly to an efficient NRD within the PSII antenna that was associated with enhanced violaxanthin convertibility and a light-induced accumulation of zeaxanthin that persisted in darkness.

Recently, we have found that thermal stability of photosystem II (PSII) photochemistry in spruce needles is higher than in other plants (barley, beech) cultivated under the same temperatures. In this work, temperature dependences of various characteristics of PSII organization were studied in order to obtain complex information on the thermal stability of PSII function and organization in spruce. Temperature dependency of circular dichroism spectra revealed by about 6 °C higher thermal stability of macrodomain organization in spruce thylakoid membranes in comparison with Arabidopsis and barley ones; however, thermal disintegration of light-harvesting complex of PSII did not significantly differ among the species studied. These results thus indicate that thermal stability of PSII macro-organization in spruce thylakoid membranes is enhanced to a similar extent as thermal stability of PSII photochemistry. Clear-native polyacrylamide gel electrophoresis of preheated thylakoids demonstrated that among the separated pigment-protein complexes, only PSII supercomplexes (SCs) revealed considerably higher thermal stability in spruce thylakoids as compared to Arabidopsis and barley ones. Hence we suggest that higher thermal stability of PSII macro-organization of spruce is influenced by the maintenance of PSII SCs in the thylakoid membrane. In addition, we discuss possible effects of different PSII organizations and lipid compositions on the thermal stability of spruce thylakoid membranes.

Temperature responses of carbon assimilation processes were studied in four dominant species from mountain grassland ecosystem, i.e. Holcus mollis (L.), Hypericum maculatum (Cr.), Festuca rubra (L.), and Nardus stricta (L.), using the gas exchange technique. Leaf temperature (T L) of all species was adjusted within the range 13–30 °C using the Peltier thermoelectric cooler. The temperature responses of metabolic processes were subsequently modelled using the Arrhenius exponential function involving the temperature coefficient Q 10. The expected increase of global temperature led to a significant increase of dark respiration rate (R D; Q 10 = 2.0±0.5), maximum carboxylation rate (V Cmax; Q 10 = 2.2±0.6), and maximum electron transport rate (J max; Q 10 = 1.6±0.4) in dominant species of mountain grassland ecosystems. Contrariwise, the ratio between J max and V Cmax linearly decreased with T L [y = −0.884 T L + 5.24; r 2 = 0.78]. Hence temperature did not control the ratio between intercellular and ambient CO2 concentration, apparent quantum efficiency, and photon-saturated CO2 assimilation rate (P max). P max primarily correlated with maximum stomatal conductance irrespective of T L. Water use efficiency tended to decrease with T L [y = −0.21 T L + 8.1; r 2 = 0.87].

The spectral composition of photosynthetically active radiation (PAR) during clear and overcast days was studied above the canopy (U) and at two layers of a dense Norway spruce stand [Picea abies (L.) Karst.] characterized with an average LAI = 7.3 ± 0.8 (middle layer: M) and 12.3 ± 0.7 (lower layer: L). Whereas the spectral composition of PAR incoming on the canopy surface during cloudy days (characterized by diffuse index DI > 0.7) was almost independent of the solar elevation angle, the proportion of the blue-green spectral region of PAR was significantly reduced at low elevation angles during days with prevailing direct radiation (DI < 0.3). The PAR spectrum at both M and L levels was only slightly enriched in the green spectral region (more pronounced for DI < 0.3). The penetration of diffuse radiation into the canopy resulted in a slight (approx. 5%) reduction of the blue region proportion that remained stable during the day. On the contrary, under clear sky conditions the penetration of blue and red radiation was dependent on the solar elevation in an opposite manner in comparison with the spectral composition of PAR incident on canopy, giving almost twofold proportion of the blue part of the spectrum at a low elevation angle at M layer. We suggest that the blue enhancement of the spectrum within the Norway spruce canopy during clear days is due to a specific spatial arrangement of the assimilatory apparatus of a coniferous stand. Further, the possible consequences of the observed dynamics of the PAR spectrum inside the canopy during clear days on the efficiency of PAR absorption of the needles located within the canopy are discussed.

Cloud cover increases the proportion of diffuse radiation reaching the Earth’s surface and affects many microclimatic factors such as temperature, vapour pressure deficit and precipitation. We compared the relative efficiencies of canopy photosynthesis to diffuse and direct photosynthetic photon flux density (PPFD) for a Norway spruce forest (25year-old, leaf area index 11 m 2 m � 2 ) during two successive 7-day periods in August. The comparison was based on the response of net ecosystem exchange (NEE) of CO2 to PPFD. NEE and stomatal conductance at the canopy level (Gcanopy) was estimated from halfhourly eddy-covariance measurements of CO2 and H2O fluxes. In addition, daily courses of CO2 assimilation rate (AN) and stomatal conductance (Gs) at shoot level were measured using a gas-exchange technique applied to branches of trees. The extent of spectral changes in incident solar radiation was assessed using a spectroradiometer. We found significantly higher NEE (up to 150%) during the cloudy periods compared with the sunny periods at corresponding PPFDs. Prevailing diffuse radiation under the cloudy days resulted in a significantly lower compensation irradiance (by ca. 50% and 70%), while apparent quantum yield was slightly higher (by ca. 7%) at canopy level and significantly higher (by ca. 530%) in sun-acclimated shoots. The main reasons for these differences appear to be (1) more favourable microclimatic conditions during cloudy periods, (2) stimulation of photochemical reactions and stomatal opening via an increase of blue/red light ratio, and (3) increased penetration of light into the canopy and thus a more equitable distribution of light between leaves. Our analyses identified the most important reason of enhanced NEE under cloudy sky conditions to be the effective penetration of diffuse radiation to lower depths of the canopy. This subsequently led to the significantly higher solar equivalent leaf area compared with the direct radiation. Most of the leaves in such dense canopy are in deep shade, with marginal or negative carbon balances during sunny days. These findings show that the energy of diffuse, compared with direct, solar radiation is used more efficiently in assimilation processes at both leaf and canopy levels.