Carbon partitioning in Arabidopsis thaliana is a dynamic process controlled by the plants metabolic status and its circadian clock

Weaker photosynthetic acclimation to fluctuating than to corresponding steady UVB radiation treatments in grapevines

The effects of transient increases in UVB radiation on plants are not well known; whether cumulative damage dominates or, alternately, an increase in photoprotection and recovery periods ameliorates any negative effects. We investigated photosynthetic capacity and metabolite accumulation of grapevines (Vitis vinifera Cabernet Sauvignon) in response to UVB fluctuations under four treatments: fluctuating UVB (FUV) and steady UVB radiation (SUV) at similar total biologically effective UVB dose (2.12 and 2.23 kJ m-2 day-1), and their two respective no UVB controls. We found a greater decrease in stomatal conductance under SUV than FUV. There was no decrease in maximum yield of photosystem II (Fv/Fm) or its operational efficiency (ɸPSII) under the two UVB treatments, and Fv/Fm was higher under SUV than FUV. Photosynthetic capacity was enhanced under FUV in the light-limited region of rapid light-response curves but enhanced by SUV in the light-saturated region. Flavonol content was similarly increased by both UVB treatments. We conclude that, while both FUV and SUV effectively stimulate acclimation to UVB radiation at realistic doses, FUV confers weaker acclimation than SUV. This implies that recovery periods between transient increases in UVB radiation reduce UVB acclimation, compared to an equivalent dose of UVB provided continuously. Thus, caution is needed in interpreting the findings of experiments using steady UVB radiation treatments to infer effects in natural environments, as the stimulatory effect of steady UVB is greater than that of the equivalent fluctuating UVB.

Coordination of carbon partitioning and photosynthesis by a two-component signaling network in Synechococcus elongatus PCC 7942

Photosynthetic organisms need to balance the rate of photosynthesis with the utilization of photosynthetic products by downstream reactions. While such "source/sink" pathways are well-interrogated in plants, analogous regulatory systems are unknown or poorly studied in single-celled algal and cyanobacterial species. Towards the identification of energy/sugar sensors in cyanobacteria, we utilized an engineered strain of Synechococcus elongatus PCC 7942 that allows experimental manipulation of carbon status. We conducted a screening of all two-component systems (TCS) and serine/threonine kinases (STKs) encoded in S. elongatus PCC 7942 by analyzing phenotypes consistent with sucrose-induced relaxation of sink inhibition. We narrowed the candidate sensor proteins by analyzing changes observed after sucrose feeding. We show that a clustered TCS network containing RpaA, CikB, ManS and NblS are involved in the regulation of genes related to photosynthesis, pigment synthesis, and Rubisco concentration in response to sucrose. Altogether, these results highlight a regulatory TCS group that may play under-appreciated functions in carbon partitioning and energy balancing in cyanobacteria.

Tripogon loliiformis tolerates rapid desiccation after metabolic and transcriptional priming during initial drying

Crop plants and undomesticated resilient species employ different strategies to regulate their energy resources and growth. Most crop species are sensitive to stress and prioritise rapid growth to maximise yield or biomass production. In contrast, resilient plants grow slowly, are small, and allocate their resources for survival in challenging environments. One small group of plants, termed resurrection plants, survive desiccation of their vegetative tissue and regain full metabolic activity upon watering. However, the precise molecular mechanisms underlying this extreme tolerance remain unknown. In this study, we employed a transcriptomics and metabolomics approach, to investigate the mechanisms of desiccation tolerance in Tripogon loliiformis, a modified desiccation-tolerant plant, that survives gradual but not rapid drying. We show that T. loliiformis can survive rapid desiccation if it is gradually dried to 60% relative water content (RWC). Furthermore, the gene expression data showed that T. loliiformis is genetically predisposed for desiccation in the hydrated state, as evidenced by the accumulation of MYB, NAC, bZIP, WRKY transcription factors along with the phytohormones, abscisic acid, salicylic acid, amino acids (e.g., proline) and TCA cycle sugars during initial drying. Through network analysis of co-expressed genes, we observed differential responses to desiccation between T. loliiformis shoots and roots. Dehydrating shoots displayed global transcriptional changes across broad functional categories, although no enrichment was observed during drying. In contrast, dehydrating roots showed distinct network changes with the most significant differences occurring at 40% RWC. The cumulative effects of the early stress responses may indicate the minimum requirements of desiccation tolerance and enable T. loliiformis to survive rapid drying. These findings potentially hold promise for identifying biotechnological solutions aimed at developing drought-tolerant crops without growth and yield penalties.

Assessing the impacts of genetic defects on starch metabolism in Arabidopsis plants using the carbon homeostasis model

Starch serves as an important carbon storage mechanism for many plant species, facilitating their adaptation to the cyclic variations in the light environment, including day-night cycles as well as seasonal changes in photoperiod. By dynamically adjusting starch accumulation and degradation rates, plants maintain carbon homeostasis, enabling continuous growth under fluctuating environmental conditions. To understand dynamic nature of starch metabolism at the molecular level, it is necessary to integrate empirical knowledge from genetic defects in specific regulatory pathways into the dynamical system of starch metabolism. To achieve this, we evaluated the impact of genetic defects in the circadian clock, sugar sensing and starch degradation pathways using the carbon homeostasis model that encompasses the interplay between these pathways. Through the collection of starch metabolism data from 10 Arabidopsis mutants, we effectively fitted the experimental data to the model. The system-level assessment revealed that genetic defects in both circadian clock components and sugar sensing pathway hindered the appropriate adjustment of the starch degradation rate, particularly under long-day conditions. These findings not only confirmed the previous empirical findings but also provide the novel insights into the role of each gene within the gene regulatory network on the emergence of carbon homeostasis.

Growing at the right time: interconnecting the TOR pathway with photoperiod and circadian regulation

Plants can adjust their growth to specific times of the day and season. Different photoperiods result in distinct growth patterns, which correlate with specific carbon-partitioning strategies in source (leaves) and sink (roots) organs. Therefore, external cues such as light, day length, and temperature need to be integrated with intracellular processes controlling overall carbon availability and anabolism. The target of rapamycin (TOR) pathway is a signalling hub where environmental signals, circadian information, and metabolic processes converge to regulate plant growth. TOR complex mutants display altered patterns of root growth and starch levels. Moreover, depletion of TOR or reduction in cellular energy levels affect the pace of the clock by extending the period length, suggesting that this pathway could participate in circadian metabolic entrainment. However, this seems to be a mutual interaction, since the TOR pathway components are also under circadian regulation. These results strengthen the role of this signalling pathway as a master sensor of metabolic status, integrating day length and circadian cues to control anabolic processes in the cell, thus promoting plant growth and development. Expanding this knowledge from Arabidopsis thaliana to crops will improve our understanding of the molecular links connecting environmental perception and growth regulation under field conditions.

Species variation in the hydrogen isotope composition of leaf cellulose is mostly driven by isotopic variation in leaf sucrose

Experimental approaches to isolate drivers of variation in the carbon-bound hydrogen isotope composition (δ² H) of plant cellulose are rare and current models are limited in their application. This is in part due to a lack in understanding of how ² H-fractionations in carbohydrates differ between species. We analysed, for the first time, the δ² H of leaf sucrose along with the δ² H and δ¹⁸ O of leaf cellulose and leaf and xylem water across seven herbaceous species and a starchless mutant of tobacco. The δ² H of sucrose explained 66% of the δ² H variation in cellulose (R²  = 0.66), which was associated with species differences in the ² H enrichment of sucrose above leaf water ( ε sucrose <math altimg="urn:x-wiley:01407791:media:pce14362:pce14362-math-0001" wiley:location="equation/pce14362-math-0001.png" xmlns="http://www.w3.org/1998/Math/MathML"><mrow><msub><mtext>\unicode{x003B5}</mtext><mtext>sucrose</mtext></msub></mrow></math> : -126% to -192‰) rather than by variation in leaf water δ² H itself. ε sucrose <math altimg="urn:x-wiley:01407791:media:pce14362:pce14362-math-0002" wiley:location="equation/pce14362-math-0002.png" xmlns="http://www.w3.org/1998/Math/MathML"><mrow><msub><mtext>\unicode{x003B5}</mtext><mtext>sucrose</mtext></msub></mrow></math> was positively related to dark respiration (R²  = 0.27), and isotopic exchange of hydrogen in sugars was positively related to the turnover time of carbohydrates (R²  = 0.38), but only when ε sucrose <math altimg="urn:x-wiley:01407791:media:pce14362:pce14362-math-0003" wiley:location="equation/pce14362-math-0003.png" xmlns="http://www.w3.org/1998/Math/MathML"><mrow><mrow><msub><mi mathvariant="normal">\unicode{x003B5}</mi><mtext>sucrose</mtext></msub></mrow></mrow></math> was fixed to the literature accepted value of - 171 <math altimg="urn:x-wiley:01407791:media:pce14362:pce14362-math-0004" wiley:location="equation/pce14362-math-0004.png" xmlns="http://www.w3.org/1998/Math/MathML"><mrow><mrow><mo>\unicode{x02212}</mo><mn>171</mn></mrow></mrow></math> ‰. No relation was found between isotopic exchange of hydrogen and oxygen, suggesting large differences in the processes shaping post-photosynthetic fractionation between elements. Our results strongly advocate that for robust applications of the leaf cellulose hydrogen isotope model, parameterization utilizing δ² H of sugars is needed.

Plant growth: An active or passive role for starch reserves?

Starch metabolism is linked to plant growth, yet blocking its biosynthesis has species-specific consequences. In a new study, plastidial phosphoglucomutase is knocked out in aspen trees using CRISPR-Cas9, limiting starch production and altering photosynthesis, but growth, bud break and wood production proceed unaffected.

Role of Circadian Rhythms in Major Plant Metabolic and Signaling Pathways

Plants require an endogenous regulatory network and mechanism to cope with diurnal environmental changes and compensate for their sessile nature. Plants use the circadian clock to anticipate diurnal changes. Circadian rhythm predicts a 24-h cycle with 16 h of light and 8 h of darkness in response to abiotic and biotic factors as well as the appropriate temperature. For a plant's fitness, proper growth, and development, these rhythms synchronize the diurnal photoperiodic changes. Input pathway, central oscillator, and output pathway are the three components that make up the endogenous clock. There are also transcriptional and translational feedback loops (TTFLs) in the clock, which are dependent on the results of gene expression. Several physiological processes, such as stress acclimatization, hormone signaling, morphogenesis, carbon metabolism, and defense response, are currently being investigated for their interactions with the circadian clock using phenotypic, genomic, and metabolic studies. This review examines the role of circadian rhythms in the regulation of plant metabolic pathways, such as photosynthesis and carbon metabolism, as well as developmental and degenerative processes, such as flowering and senescence. Furthermore, we summarized signaling pathways related to circadian rhythms, such as defense response and gene regulatory pathways.

BETA-AMYLASE9 is a plastidial nonenzymatic regulator of leaf starch degradation

β-Amylases (BAMs) are key enzymes of transitory starch degradation in chloroplasts, a process that buffers the availability of photosynthetically fixed carbon over the diel cycle to maintain energy levels and plant growth at night. However, during vascular plant evolution, the BAM gene family diversified, giving rise to isoforms with different compartmentation and biological activities. Here, we characterized BETA-AMYLASE 9 (BAM9) of Arabidopsis (Arabidopsis thaliana). Among the BAMs, BAM9 is most closely related to BAM4 but is more widely conserved in plants. BAM9 and BAM4 share features including their plastidial localization and lack of measurable α-1,4-glucan hydrolyzing capacity. BAM4 is a regulator of starch degradation, and bam4 mutants display a starch-excess phenotype. Although bam9 single mutants resemble the wild-type (WT), genetic experiments reveal that the loss of BAM9 markedly enhances the starch-excess phenotypes of mutants already impaired in starch degradation. Thus, BAM9 also regulates starch breakdown, but in a different way. Interestingly, BAM9 gene expression is responsive to several environmental changes, while that of BAM4 is not. Furthermore, overexpression of BAM9 in the WT reduced leaf starch content, but overexpression in bam4 failed to complement fully that mutant's starch-excess phenotype, suggesting that BAM9 and BAM4 are not redundant. We propose that BAM9 activates starch degradation, helping to manage carbohydrate availability in response to fluctuations in environmental conditions. As such, BAM9 represents an interesting gene target to explore in crop species.

Carbon flux through photosynthesis and central carbon metabolism show distinct patterns between algae, C3 and C4 plants

Photosynthesis-related pathways are regarded as a promising avenue for crop improvement. Whilst empirical studies have shown that photosynthetic efficiency is higher in microalgae than in C3 or C4 crops, the underlying reasons remain unclear. Using a tailor-made microfluidics labelling system to supply 13CO2 at steady state, we investigated in vivo labelling kinetics in intermediates of the Calvin Benson cycle and sugar, starch, organic acid and amino acid synthesis pathways, and in protein and lipids, in Chlamydomonas reinhardtii, Chlorella sorokiniana and Chlorella ohadii, which is the fastest growing green alga on record. We estimated flux patterns in these algae and compared them with published and new data from C3 and C4 plants. Our analyses identify distinct flux patterns supporting faster growth in photosynthetic cells, with some of the algae exhibiting faster ribulose 1,5-bisphosphate regeneration and increased fluxes through the lower glycolysis and anaplerotic pathways towards the tricarboxylic acid cycle, amino acid synthesis and lipid synthesis than in higher plants.

Photosystem I Inhibition, Protection and Signalling: Knowns and Unknowns

Photosynthesis is the process that harnesses, converts and stores light energy in the form of chemical energy in bonds of organic compounds. Oxygenic photosynthetic organisms (i.e., plants, algae and cyanobacteria) employ an efficient apparatus to split water and transport electrons to high-energy electron acceptors. The photosynthetic system must be finely balanced between energy harvesting and energy utilisation, in order to limit generation of dangerous compounds that can damage the integrity of cells. Insight into how the photosynthetic components are protected, regulated, damaged, and repaired during changing environmental conditions is crucial for improving photosynthetic efficiency in crop species. Photosystem I (PSI) is an integral component of the photosynthetic system located at the juncture between energy-harnessing and energy consumption through metabolism. Although the main site of photoinhibition is the photosystem II (PSII), PSI is also known to be inactivated by photosynthetic energy imbalance, with slower reactivation compared to PSII; however, several outstanding questions remain about the mechanisms of damage and repair, and about the impact of PSI photoinhibition on signalling and metabolism. In this review, we address the knowns and unknowns about PSI activity, inhibition, protection, and repair in plants. We also discuss the role of PSI in retrograde signalling pathways and highlight putative signals triggered by the functional status of the PSI pool.

A Satellite-Based Method for National Winter Wheat Yield Estimating in China

Satellite-based models have tremendous potential for monitoring crop production because satellite data can provide temporally and spatially continuous crop growth information at large scale. This study used a satellite-based vegetation production model (i.e., eddy covariance light use efficiency, EC-LUE) to estimate national winter wheat gross primary production, and then combined this model with the harvest index (ratio of aboveground biomass to yield) to convert the estimated winter wheat production to yield. Specifically, considering the spatial differences of the harvest index, we used a cross-validation method to invert the harvest index of winter wheat among counties, municipalities and provinces. Using the field-surveyed and statistical yield data, we evaluated the model performance, and found the model could explain more than 50% of the spatial variations of the yield both in field-surveyed regions and most administrative units. Overall, the mean absolute percentage errors of the yield are less than 20% in most counties, municipalities and provinces, and the mean absolute percentage errors for the production of winter wheat at the national scale is 4.06%. This study demonstrates that a satellite-based model is an alternative method for crop yield estimation on a larger scale.

Field microenvironments regulate crop diel transcript and metabolite rhythms

Most research in plant chronobiology has been done in laboratory conditions. However, laboratories usually fail to mimic natural conditions and their slight fluctuations, highlighting or obfuscating rhythmicity. High-density crops, such as sugarcane (Saccharum hybrid), generate field microenvironments with specific light and temperature regimes resulting from mutual shading. We measured the metabolic and transcriptional rhythms in the leaves of 4-month-old (4 mo) and 9 mo field-grown sugarcane. Most of the assayed rhythms in 9 mo sugarcane peaked >1 h later than in 4 mo sugarcane, including rhythms of the circadian clock gene, LATE ELONGATED HYPOCOTYL (LHY). We hypothesized that older sugarcane perceives dawn later than younger sugarcane as a consequence of self-shading. As a test, we measured LHY rhythms in plants on the east and the west sides of a field. We also tested if a wooden wall built between lines of sugarcane plants changed their rhythms. The LHY peak was delayed in the plants in the west of the field or beyond the wall; both shaded at dawn. We conclude that plants in the same field may have different phases resulting from field microenvironments, impacting important agronomical traits, such as flowering time, stalk weight and number.

Root Carbon Interaction with Soil Minerals Is Dynamic, Leaving a Legacy of Microbially Derived Residues

Minerals preserve the oldest, most persistent soil carbon, and mineral characteristics appear to play a critical role in the formation of soil organic matter (SOM) associations. To test the hypothesis that roots, and differences in carbon source and microbial communities, influence mineral SOM associations over short timescales, we incubated permeable mineral bags in soil microcosms with and without plants, inside a ¹³CO₂ labeling chamber. Mineral bags contained quartz, ferrihydrite, kaolinite, or soil minerals isolated via density separation. Using ¹³C-nuclear magnetic resonance, Fourier transform ion cyclotron resonance mass spectrometry, and lipidomics, we traced carbon deposition onto minerals, characterizing total carbon, ¹³C enrichment, and SOM chemistry over three growth stages of Avena barbata. Carbon accumulation was rapid and mineral-dependent but slowed with time; the accumulated amount was not significantly affected by root presence. However, plant roots strongly shaped the chemistry of mineral-associated SOM. Minerals incubated in a plant rhizosphere were associated with a more diverse array of compounds (with different functional groups-carbonyl, aromatics, carbohydrates, and lipids) than minerals incubated in an unplanted bulk soil control. We also found that many of the lipids that sorbed to minerals were microbially derived, including many fungal lipids. Together, our data suggest that diverse rhizosphere-derived compounds may represent a transient fraction of mineral SOM, rapidly exchanging with mineral surfaces.

The CrRLK1L subfamily: One of the keys to versatility in plants

Catharanthus roseous kinase 1L receptors (CrRLK1Ls) are a subfamily of membrane receptors unique to plant cells that perceive internal and external signals, integrate metabolic, physiological, and molecular processes, and regulate plant development. Recent genomic studies have suggested that this receptor subfamily arose during the emergence of terrestrial plants and has since diversified, preserving its essential functions. Participation of some of these CrRLK1Ls in different processes is presented and discussed herein, as well as the increasing number of interactors necessary for their function. At least five different responses have been detected after activating these receptors, such as physiological changes, formation or disassembly of protein complexes, metabolic responses, modification of gene expression, and modulation of phytohormone activity. To date, a common response mechanism for all processes involving CrRLK1Ls has not been described. In this review, the information available on the different functions of CrRLK1Ls was compiled. Additionally, the physiological and/or molecular mechanisms involved in the signaling processes triggered by these receptors are also discussed. In this review, we propose a possible common signaling mechanism for all processes regulated by CrRLK1Ls and pose questions to be answered in the future.

The sugar-responsive circadian clock regulator bZIP63 modulates plant growth

Adjustment to energy starvation is crucial to ensure growth and survival. In Arabidopsis thaliana (Arabidopsis), this process relies in part on the phosphorylation of the circadian clock regulator bZIP63 by SUCROSE non-fermenting RELATED KINASE1 (SnRK1), a key mediator of responses to low energy. We investigated the effects of mutations in bZIP63 on plant carbon (C) metabolism and growth. Results from phenotypic, transcriptomic and metabolomic analysis of bZIP63 mutants prompted us to investigate the starch accumulation pattern and the expression of genes involved in starch degradation and in the circadian oscillator. bZIP63 mutation impairs growth under light-dark cycles, but not under constant light. The reduced growth likely results from the accentuated C depletion towards the end of the night, which is caused by the accelerated starch degradation of bZIP63 mutants. The diel expression pattern of bZIP63 is dictated by both the circadian clock and energy levels, which could determine the changes in the circadian expression of clock and starch metabolic genes observed in bZIP63 mutants. We conclude that bZIP63 composes a regulatory interface between the metabolic and circadian control of starch breakdown to optimize C usage and plant growth.

Distinct plastid fructose bisphosphate aldolases function in photosynthetic and non-photosynthetic metabolism in Arabidopsis

Plastid metabolism is critical in both photoautotrophic and heterotrophic plant cells. In chloroplasts, fructose-1,6-bisphosphate aldolase (FBA) catalyses the formation of both fructose 1,6-bisphosphate and sedoheptulose 1,7-bisphosphate within the Calvin-Benson cycle. Three Arabidopsis genes, AtFBA1-AtFBA3, encode plastidial isoforms of FBA, but the contribution of each isoform is unknown. Phylogenetic analysis indicates that FBA1 and FBA2 derive from a recently duplicated gene, while FBA3 is a more ancient paralog. fba1 mutants are phenotypically indistinguishable from the wild type, while both fba2 and fba3 have reduced growth. We show that FBA2 is the major isoform in leaves, contributing most of the measurable activity. Partial redundancy with FBA1 allows both single mutants to survive, but combining both mutations is lethal, indicating a block of photoautotrophy. In contrast, FBA3 is expressed predominantly in heterotrophic tissues, especially the leaf and root vasculature, but not in the leaf mesophyll. We show that the loss of FBA3 affects plastidial glycolytic metabolism of the root, potentially limiting the biosynthesis of essential compounds such as amino acids. However, grafting experiments suggest that fba3 is dysfunctional in leaf phloem transport, and we suggest that a block in photoassimilate export from leaves causes the buildup of high carbohydrate concentrations and retarded growth.

Sucrose Utilization for Improved Crop Yields: A Review Article

Photosynthetic carbon converted to sucrose is vital for plant growth. Sucrose acts as a signaling molecule and a primary energy source that coordinates the source and sink development. Alteration in source-sink balance halts the physiological and developmental processes of plants, since plant growth is mostly triggered when the primary assimilates in the source leaf balance with the metabolic needs of the heterotrophic sinks. To measure up with the sink organ's metabolic needs, the improvement of photosynthetic carbon to synthesis sucrose, its remobilization, and utilization at the sink level becomes imperative. However, environmental cues that influence sucrose balance within these plant organs, limiting positive yield prospects, have also been a rising issue over the past few decades. Thus, this review discusses strategies to improve photosynthetic carbon assimilation, the pathways actively involved in the transport of sucrose from source to sink organs, and their utilization at the sink organ. We further emphasize the impact of various environmental cues on sucrose transport and utilization, and the strategic yield improvement approaches under such conditions.

A Palette of Minimally Tagged Sucrose Analogues for Real-Time Raman Imaging of Intracellular Plant Metabolism

Sucrose is the main saccharide used for long-distance transport in plants and plays an essential role in energy metabolism; however, there are no analogues for real-time imaging in live cells. We have optimised a synthetic approach to prepare sucrose analogues including very small (≈50 Da or less) Raman tags in the fructose moiety. Spectroscopic analysis identified the alkyne-tagged compound 6 as a sucrose analogue recognised by endogenous transporters in live cells and with higher Raman intensity than other sucrose derivatives. Herein, we demonstrate the application of compound 6 as the first optical probe to visualise real-time uptake and intracellular localisation of sucrose in live plant cells using Raman microscopy.

A Palette of Minimally Tagged Sucrose Analogues for Real-Time Raman Imaging of Intracellular Plant Metabolism

Sucrose is the main saccharide used for long-distance transport in plants and plays an essential role in energy metabolism; however, there are no analogues for real-time imaging in live cells. We have optimised a synthetic approach to prepare sucrose analogues including very small (≈50 Da or less) Raman tags in the fructose moiety. Spectroscopic analysis identified the alkyne-tagged compound 6 as a sucrose analogue recognised by endogenous transporters in live cells and with higher Raman intensity than other sucrose derivatives. Herein, we demonstrate the application of compound 6 as the first optical probe to visualise real-time uptake and intracellular localisation of sucrose in live plant cells using Raman microscopy.

A temperature regime that disrupts clock-controlled starch mobilization induces transient carbohydrate starvation, resulting in compact growth

In nature plants are usually subjected to a light/temperature regime of warm day and cold night (referred to as +DIF). Compared to growth under +DIF, Arabidopsis plants show compact growth under the same photoperiod, but with an inverse temperature regime (cold day and warm night: -DIF). Here we show that -DIF differentially affects the phase and amplitude of core clock gene expression. Under -DIF the phase of the morning clock gene CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) is delayed, similar to that of plants grown on low sucrose. Indeed, under -DIF carbohydrate (CHO) starvation marker genes are specifically upregulated at the End of the Night (EN) in Arabidopsis rosettes. However, only in inner-rosette tissue (small sink leaves and petioles of older leaves) sucrose levels are lower under -DIF compared to under +DIF, suggesting that sucrose in source leaf blades is not sensed for CHO status and that sucrose transport from source to sink may be impaired at EN. CHO-starvation under -DIF correlated with increased starch breakdown during the night and decreased starch accumulation during the day. Moreover, we demonstrate that different ways of inducing CHO-starvation all link to reduced growth of sink leaves. Practical implications for control of plant growth in horticulture are discussed.

TOC1 in Nicotiana attenuata regulates efficient allocation of nitrogen to defense metabolites under herbivory stress

The circadian clock contextualizes plant responses to environmental signals. Plants use temporal information to respond to herbivory, but many of the functional roles of circadian clock components in these responses, and their contribution to fitness, remain unknown. We investigate the role of the central clock regulator TIMING OF CAB EXPRESSION 1 (TOC1) in Nicotiana attenuata's defense responses to the specialist herbivore Manduca sexta under both field and glasshouse conditions. We utilize 15 N pulse-labeling to quantify nitrogen incorporation into pools of three defense compounds: caffeoylputrescine (CP), dicaffeoyl spermidine (DCS) and nicotine. Nitrogen incorporation was decreased in CP and DCS and increased in nicotine pools in irTOC1 plants compared to empty vector (EV) under control conditions, but these differences were abolished after simulated herbivory. Differences between EV and irTOC1 plants in nicotine, but not phenolamide production, were abolished by treatment with the ethylene agonist 1-methylcyclopropene. Using micrografting, TOC1's effect on nicotine was isolated to the root and did not affect the fitness of heterografts under field conditions. These results suggest that the circadian clock contributes to plant fitness by balancing production of metabolically expensive nitrogen-rich defense compounds and mediating the allocation of resources between vegetative biomass and reproduction.

Circadian Regulation Does Not Optimize Stomatal Behaviour

The circadian clock is a molecular timer of metabolism that affects the diurnal pattern of stomatal conductance (gs), amongst other processes, in a broad array of plant species. The function of circadian gs regulation remains unknown and here, we test whether circadian regulation helps to optimize diurnal variations in stomatal conductance. We subjected bean (Phaseolus vulgaris) and cotton (Gossypium hirsutum) canopies to fixed, continuous environmental conditions of photosynthetically active radiation, temperature, and vapour pressure deficit (free-running conditions) over 48 h. We modelled gs variations in free-running conditions to test for two possible optimizations of stomatal behaviour under circadian regulation: (i) that stomata operate to maintain constant marginal water use efficiency; or (ii) that stomata maximize C net gain minus the costs or risks of hydraulic damage. We observed that both optimization models predicted gs poorly under free-running conditions, indicating that circadian regulation does not directly lead to stomatal optimization. We also demonstrate that failure to account for circadian variation in gs could potentially lead to biased parameter estimates during calibrations of stomatal models. More broadly, our results add to the emerging field of plant circadian ecology, where circadian controls may partially explain leaf-level patterns observed in the field.

Elevated Temperatures Impose Transcriptional Constraints and Elicit Intraspecific Differences Between Coffee Genotypes

The projected impact of global warming on coffee production may require the heat-adapted genotypes in the next decades. To identify cellular strategies in response to warmer temperatures, we compared the effect of elevated temperature on two commercial Coffea arabica L. genotypes exploring leaf physiology, transcriptome, and carbohydrate/protein composition. Growth temperatures were 23/19°C (day/night), as optimal condition (OpT), and 30/26°C (day/night) as a possible warmer scenario (WaT). The cv. Acauã showed lower levels of leaf temperature (Tleaf) under both conditions compared to cv. Catuaí, whereas slightly or no differences for other leaf physiological parameters. Therefore, to explore temperature responsive pathways the leaf transcriptome was examined using RNAseq. Genotypes showed a marked number of differentially-expressed genes (DEGs) under OpT, however DEGs strongly decrease in both at WaT condition indicating a transcriptional constraint. DEGs responsive to WaT revealed shared and genotype-specific genes mostly related to carbohydrate metabolism. Under OpT, leaf starch content was greater in cv. Acauã and, as WaT temperature was imposed, the leaf soluble sugar did not change in contrast to cv. Catuaí, although the levels of leaf starch, sucrose, and leaf protein decreased in both genotypes. These findings revealed intraspecific differences in the underlying transcriptional and metabolic interconnected pathways responsive to warmer temperatures, which is potentially linked to thermotolerance, and thus may be useful as biomarkers in breeding for a changing climate.

The pulse of the tree is under genetic control: eucalyptus as a case study

The pulse of the tree (diurnal cycle of stem radius fluctuations) has been widely studied as a way of analyzing tree responses to the environment, including the phenotypic plasticity of tree-water relationships in particular. However, the genetic basis of this daily phenotype and its interplay with the environment remain largely unexplored. We characterized the genetic and environmental determinants of this response, by monitoring daily stem radius fluctuation (dSRF) on 210 trees from a Eucalyptus urophylla × E. grandis full-sib family over 2 years. The dSRF signal was broken down into hydraulic capacitance, assessed as the daily amplitude of shrinkage (DA), and net growth, estimated as the change in maximum radius between two consecutive days (ΔR). The environmental determinants of these two traits were clearly different: DA was positively correlated with atmospheric variables relating to water demand, while ΔR was associated with soil water content. The heritability for these two traits ranged from low to moderate over time, revealing a time-dependent or environment-dependent complex genetic determinism. We identified 686 and 384 daily quantitative trait loci (QTL) representing 32 and 31 QTL regions for DA and ΔR, respectively. The identification of gene networks underlying the 27 major genomics regions for both traits generated additional hypotheses concerning the biological mechanisms involved in response to water demand and supply. This study highlights that environmentally induced changes in daily stem radius fluctuation are genetically controlled in trees and suggests that these daily responses integrated over time shape the genetic architecture of mature traits.

Transient Carbon Reserves in Barley: Malate, Sucrose and Starch Are the Main Players, Their Quantitative Involvement Being Light Intensity Dependant

Under natural environment plants experience different light intensities which can affect photosynthesis and consequently the availability of carbohydrates for daytime growth and their transient storage to supply night growth. We grew a spring barley cultivar, Propino, under three different light intensities under warm days and nights, and evaluated the spatial and diurnal adjustments occurring in the transient carbon stores. Leaves under high light at the end of the day accumulated mainly sucrose (30%) and malate (35%), with lower content of hexoses (5%), starch (15%) and fructans (15%). Under low light, plants presented reduced photosynthesis, with lower metabolite contents at end of day. The malate represented 51% of the total carbon accumulated at end of the day, at the expense of sucrose (12%), other metabolite contributions remaining similar to high light. The percentage of metabolites consumed at night was similar for all light intensities with around 75% of the sucrose and starch being mobilized whilst malate and fructans were only partially mobilized with 56 and 44%, respectively. Altogether, sucrose and malate were the main contributors of the total carbon used at night by barley plants, sucrose being predominant under high light (35% vs. 27%), but malate being the major metabolite used under low light with 40% of the total carbon consumed. Interestingly, light intensity also influenced the location of the C transient stores, the plants under low light prioritizing the accumulation of the metabolites, mostly malate, in the youngest tissues. Therefore, light influences quantitatively, but also qualitatively and spatially the carbon stores in the spring barley cv. Propino, suggesting a tight regulation of the primary metabolism.

Is triose phosphate utilization involved in the feedback inhibition of photosynthesis in rice under conditions of sink limitation?

This study aimed to understand the physiological basis of rice photosynthetic response to C source-sink imbalances, focusing on the dynamics of the photosynthetic parameter triose phosphate utilization (TPU). Here, rice (Oriza sativa L.) indica cultivar IR64 were grown in controlled environment chambers under current ambient CO2 concentration until heading, and thereafter two CO2 treatments (400 and 800 μmol mol-1) were compared in the presence and absence of a panicle-pruning treatment modifying the C sink. At 2 weeks after heading, photosynthetic parameters derived from CO2 response curves, and non-structural carbohydrate content of flag leaf and internodes were measured three to four times of day. Spikelet number per panicle and flag leaf area on the main culm were recorded. Net C assimilation and TPU decreased progressively after midday in panicle-pruned plants, especially under 800 μmol mol-1 CO2. This TPU reduction was explained by sucrose accumulation in the flag leaf resulting from the sink limitation. Taking together, our findings suggest that TPU is involved in the regulation of photosynthesis in rice under elevated CO2 conditions, and that sink limitation effects should be considered in crop models.

Holobiont chronobiology: mycorrhiza may be a key to linking aboveground and underground rhythms

Circadian clocks are nearly ubiquitous timing mechanisms that can orchestrate rhythmic behavior and gene expression in a wide range of organisms. Clock mechanisms are becoming well understood in fungal, animal, and plant model systems, yet many of these organisms are surrounded by a complex and diverse microbiota which should be taken into account when examining their biology. Of particular interest are the symbiotic relationships between organisms that have coevolved over time, forming a unit called a holobiont. Several studies have now shown linkages between the circadian rhythms of symbiotic partners. Interrelated regulation of holobiont circadian rhythms seems thus important to coordinate shifts in activity over the day for all the partners. Therefore, we suggest that the classical view of "chronobiological individuals" should include "a holobiont" rather than an organism. Unfortunately, mechanisms that may regulate interspecies temporal acclimation and the evolution of the circadian clock in holobionts are far from being understood. For the plant holobiont, our understanding is particularly limited. In this case, the holobiont encompasses two different ecosystems, one above and the other below the ground, with the two potentially receiving timing information from different synchronizing signals (Zeitgebers). The arbuscular mycorrhizal (AM) symbiosis, formed by plant roots and fungi, is one of the oldest and most widespread associations between organisms. By mediating the nutritional flux between the plant and the many microbes in the soil, AM symbiosis constitutes the backbone of the plant holobiont. Even though the importance of the AM symbiosis has been well recognized in agricultural and environmental sciences, its circadian chronobiology remains almost completely unknown. We have begun to study the circadian clock of arbuscular mycorrhizal fungi, and we compile and here discuss the available information on the subject. We propose that analyzing the interrelated temporal organization of the AM symbiosis and determining its underlying mechanisms will advance our understanding of the role and coordination of circadian clocks in holobionts in general.

The Photoperiodic Flowering Time Regulator FKF1 Negatively Regulates Cellulose Biosynthesis

Cellulose synthesis is precisely regulated by internal and external cues, and emerging evidence suggests that light regulates cellulose biosynthesis through specific light receptors. Recently, the blue light receptor CRYPTOCHROME 1 (CRY1) was shown to positively regulate secondary cell wall biosynthesis in Arabidopsis (Arabidopsis thaliana). Here, we characterize the role of FLAVIN-BINDING KELCH REPEAT, F-BOX 1 (FKF1), another blue light receptor and well-known photoperiodic flowering time regulator, in cellulose biosynthesis. A phenotype suppression screen using a cellulose deficient mutant cesa1aegeus,cesa3ixr1-2 (c1,c3), which carries nonlethal point mutations in CELLULOSE SYNTHASE A 1 (CESA1) and CESA3, resulted in identification of the phenotype-restoring large leaf (llf) mutant. Next-generation mapping using the whole genome resequencing method identified the llf locus as FKF1 FKF1 was confirmed as the causal gene through observation of the llf phenotype in an independent triple mutant c1,c3,fkf1-t carrying a FKF1 T-DNA insertion mutant. Moreover, overexpression of FKF1 in llf plants restored the c1,c3 phenotype. The fkf1 mutants showed significant increases in cellulose content and CESA gene expression compared with that in wild-type Columbia-0 plants, suggesting a negative role of FKF1 in cellulose biosynthesis. Using genetic, molecular, and phenocopy and biochemical evidence, we have firmly established the role of FKF1 in regulation of cellulose biosynthesis. In addition, CESA expression analysis showed that diurnal expression patterns of CESAs are FKF1 independent, whereas their circadian expression patterns are FKF1 dependent. Overall, our work establishes a role of FKF1 in the regulation of cell wall biosynthesis in Arabidopsis.

Roots of the Resurrection Plant Tripogon loliiformis Survive Desiccation Without the Activation of Autophagy Pathways by Maintaining Energy Reserves

Being sessile, plants must regulate energy balance, potentially via source-sink relations, to compromise growth with survival in stressful conditions. Crops are sensitive, possibly because they allocate their energy resources toward growth and yield rather than stress tolerance. In contrast, resurrection plants tightly regulate sugar metabolism and use a series of physiological adaptations to suppress cell death in their vegetative tissue to regain full metabolic capacity from a desiccated state within 72 h of watering. Previously, we showed that shoots of the resurrection plant Tripogon loliiformis, initiate autophagy upon dehydration as one strategy to reinstate homeostasis and suppress cell death. Here, we describe the relationship between energy status, sugar metabolism, trehalose-mediated activation of autophagy pathways and investigate whether shoots and roots utilize similar desiccation tolerance strategies. We show that despite containing high levels of trehalose, dehydrated Tripogon roots do not display elevated activation of autophagy pathways. Using targeted and non-targeted metabolomics, transmission electron microscopy (TEM) and transcriptomics we show that T. loliiformis engages a strategy similar to the long-term drought responses of sensitive plants and continues to use the roots as a sink even during sustained stress. Dehydrating T. loliiformis roots contained more sucrose and trehalose-6-phosphate compared to shoots at an equivalent water content. The increased resources in the roots provides sufficient energy to cope with stress and thus autophagy is not required. These results were confirmed by the absence of autophagosomes in roots by TEM. Upregulation of sweet genes in both shoots and roots show transcriptional regulation of sucrose translocation from leaves to roots and within roots during dehydration. Differences in the cell's metabolic status caused starkly different cell death responses between shoots and roots. These findings show how shoots and roots utilize different stress response strategies and may provide candidate targets that can be used as tools for the improvement of stress tolerance in crops.

Influence of starch deficiency on photosynthetic and post-photosynthetic carbon isotope fractionations

Carbon isotope (13C) fractionations occurring during and after photosynthetic CO2 fixation shape the carbon isotope composition (δ13C) of plant material and respired CO2. However, responses of 13C fractionations to diel variation in starch metabolism in the leaf are not fully understood. Here we measured δ13C of organic matter (δ13COM), concentrations and δ13C of potential respiratory substrates, δ13C of dark-respired CO2 (δ13CR), and gas exchange in leaves of starch-deficient plastidial phosphoglucomutase (pgm) mutants and wild-type plants of four species (Arabidopsis thaliana, Mesembryanthemum crystallinum, Nicotiana sylvestris, and Pisum sativum). The strongest δ13C response to the pgm-induced starch deficiency was observed in N. sylvestris, with more negative δ13COM, δ13CR, and δ13C values for assimilates (i.e. sugars and starch) and organic acids (i.e. malate and citrate) in pgm mutants than in wild-type plants during a diel cycle. The genotype differences in δ13C values could be largely explained by differences in leaf gas exchange. In contrast, the PGM-knockout effect on post-photosynthetic 13C fractionations via the plastidic fructose-1,6-bisphosphate aldolase reaction or during respiration was small. Taken together, our results show that the δ13C variations in starch-deficient mutants are primarily explained by photosynthetic 13C fractionations and that the combination of knockout mutants and isotope analyses allows additional insights into plant metabolism.

Alternative Carbon Sources for Isoprene Emission

Isoprene and other plastidial isoprenoids are produced primarily from recently assimilated photosynthates via the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway. However, when environmental conditions limit photosynthesis, a fraction of carbon for MEP pathway can come from extrachloroplastic sources. The flow of extrachloroplastic carbon depends on the species and on leaf developmental and environmental conditions. The exchange of common phosphorylated intermediates between the MEP pathway and other metabolic pathways can occur via plastidic phosphate translocators. C1 and C2 carbon intermediates can contribute to chloroplastic metabolism, including photosynthesis and isoprenoid synthesis. Integration of these metabolic processes provide an example of metabolic flexibility, and results in the synthesis of primary metabolites for plant growth and secondary metabolites for plant defense, allowing effective use of environmental resources under multiple stresses.

Changes in resource partitioning between and within organs support growth adjustment to neighbor proximity in Brassicaceae seedlings

In dense communities, plants compete for light and sense potentially threatening neighbors prior to actual shading. In response to neighbor proximity cues, shade-intolerant plants selectively elongate stem-like structures, thereby enhancing access to unfiltered sunlight. Although key steps in plant proximity sensing and signaling have been identified, we know little about the metabolic adaptations underlying enhanced stem growth. Here, we show that, following the detection of neighbor proximity cues, seedlings allocate more carbon fixed in the cotyledons to the faster elongating hypocotyl. Moreover, we show that sucrose transport and a transcription factor responding to light and metabolic cues control hypocotyl elongation. Collectively, our work provides important insights into the metabolic changes underlying organ-specific growth adaptations to an environmental stress signal.

In shade-intolerant plants, the perception of proximate neighbors rapidly induces architectural changes resulting in elongated stems and reduced leaf size. Sensing and signaling steps triggering this modified growth program have been identified. However, the underlying changes in resource allocation that fuel stem growth remain poorly understood. Through ¹⁴CO₂ pulse labeling of Brassica rapa seedlings, we show that perception of the neighbor detection signal, low ratio of red to far-red light (R:FR), leads to increased carbon allocation from the major site of photosynthesis (cotyledons) to the elongating hypocotyl. While carbon fixation and metabolite levels remain similar in low R:FR, partitioning to all downstream carbon pools within the hypocotyl is increased. Genetic analyses using Arabidopsis thaliana mutants indicate that low-R:FR–induced hypocotyl elongation requires sucrose transport from the cotyledons and is regulated by a PIF7-dependent metabolic response. Moreover, our data suggest that starch metabolism in the hypocotyl has a growth-regulatory function. The results reveal a key mechanism by which metabolic adjustments can support rapid growth adaptation to a changing environment.

The Coumarin Glucoside, Esculin, Reveals Rapid Changes in Phloem-Transport Velocity in Response to Environmental Cues

The study of phloem transport and its vital roles in long-distance communication and carbon allocation have been hampered by a lack of suitable tools that allow high-throughput, real-time studies. Esculin, a fluorescent coumarin glucoside, is recognized by Suc transporters, including AtSUC2, which loads it into the phloem for translocation to sink tissues. These properties make it an ideal tool for use in live-imaging experiments, where it acts as a surrogate for Suc. Here, we show that esculin is translocated with a similar efficiency to Suc and, because of its ease of application and detection, demonstrate that it is an ideal tool for in vivo studies of phloem transport. We used esculin to determine the effect of different environmental cues on the velocity of phloem transport. We provide evidence that fluctuations in cotyledon Suc levels influence phloem velocity rapidly, supporting the pressure-flow model of phloem transport. Under acute changes in light levels, the phloem velocity mirrored changes in the expression of AtSUC2 This observation suggests that under certain environmental conditions, transcriptional regulation may affect the abundance of AtSUC2 and thus regulate the phloem transport velocity.

A pivotal role for starch in the reconfiguration of 14C-partitioning and allocation in Arabidopsis thaliana under short-term abiotic stress

Plant carbon status is optimized for normal growth but is affected by abiotic stress. Here, we used 14C-labeling to provide the first holistic picture of carbon use changes during short-term osmotic, salinity, and cold stress in Arabidopsis thaliana. This could inform on the early mechanisms plants use to survive adverse environment, which is important for efficient agricultural production. We found that carbon allocation from source to sinks, and partitioning into major metabolite pools in the source leaf, sink leaves and roots showed both conserved and divergent responses to the stresses examined. Carbohydrates changed under all abiotic stresses applied; plants re-partitioned 14C to maintain sugar levels under stress, primarily by reducing 14C into the storage compounds in the source leaf, and decreasing 14C into the pools used for growth processes in the roots. Salinity and cold increased 14C-flux into protein, but as the stress progressed, protein degradation increased to produce amino acids, presumably for osmoprotection. Our work also emphasized that stress regulated the carbon channeled into starch, and its metabolic turnover. These stress-induced changes in starch metabolism and sugar export in the source were partly accompanied by transcriptional alteration in the T6P/SnRK1 regulatory pathway that are normally activated by carbon starvation.

Illuminating the translocation stream

This review focuses on the recent development of a suite of fluorescent probes that can be used to trace phloem-transport rates in a range of diverse species. Some of these probes are loaded into the phloem by virtue of optimal physico-chemical properties for ion trapping in the high pH environment of the sieve element. However, others are clearly loaded by carrier-mediated transport, such as the blue-emitting probe, esculin, which is loaded into the Arabidopsis phloem by the sucrose transporter, AtSUC2, allowing it to be used as a surrogate for sucrose in phloem transport studies. We also describe additional chemical groups which, although highly charged (e.g. sulphonates), facilitate entry into the phloem. The addition of such 'mobilophores' to existing chemical groups has allowed us to expand the range of fluorophores that can be loaded into the phloem, and provides clues as to the nature of selectivity for phloem loading of xenobiotic compounds.

Diurnal periodicity of assimilate transport shapes resource allocation and whole-plant carbon balance

Whole-plant carbon balance comprises diurnal fluctuations of photosynthetic carbon gain and respiratory losses, as well as partitioning of assimilates between phototrophic and heterotrophic organs. Because it is difficult to access, the root system is frequently neglected in growth models, or its metabolism is rated based on generalizations from other organs. Here, whole-plant cuvettes were used for investigating total-plant carbon exchange with the environment over full diurnal cycles. Dynamics of primary metabolism and diurnally resolved phloem exudation profiles, as proxy of assimilate transport, were combined to obtain a full picture of resource allocation. This uncovered a strong impact of periodicity of inter-organ transport on the efficiency of carbon gain. While a sinusoidal fluctuation of the transport rate, with minor diel deflections, minimized respiratory losses in Arabidopsis wild-type plants, triangular or rectangular patterns of transport, found in mutants defective in either starch or sucrose metabolism, increased root respiration at the end or beginning of the day, respectively. Power spectral density and cross-correlation analysis revealed that only the rate of starch synthesis was strictly correlated to the rate of net photosynthesis in wild-type, while in a sucrose-phosphate synthase mutant (spsa1), this applied also to carboxylate synthesis, serving as an alternative carbon pool. In the starchless mutant of plastidial phospho-gluco mutase (pgm), none of these rates, but concentrations of sucrose and glucose in the root, followed the pattern of photosynthesis, indicating direct transduction of shoot sugar levels to the root. The results demonstrate that starch metabolism alone is insufficient to buffer diurnal fluctuations of carbon exchange.

Carbon source-sink relationship in Arabidopsis thaliana: the role of sucrose transporters

MAIN CONCLUSION

The regulation of source-to-sink sucrose transport is associated with AtSUC and AtSWEET sucrose transporters' gene expression changes in plants grown hydroponically under different physiological conditions. Source-to-sink transport of sucrose is one of the major determinants of plant growth. Whole-plant carbohydrates' partitioning requires the specific activity of membrane sugar transporters. In Arabidopsis thaliana plants, two families of transporters are involved in sucrose transport: AtSUCs and AtSWEETs. This study is focused on the comparison of sucrose transporter gene expression, soluble sugar and starch levels and long distance sucrose transport, in leaves and sink organs (mainly roots) in different physiological conditions (along the plant life cycle, during a diel cycle, and during an osmotic stress) in plants grown hydroponically. In leaves, the AtSUC2, AtSWEET11, and 12 genes known to be involved in phloem loading were highly expressed when sucrose export was high and reduced during osmotic stress. In roots, AtSUC1 was highly expressed and its expression profile in the different conditions tested suggests that it may play a role in sucrose unloading in roots and in root growth. The SWEET transporter genes AtSWEET12, 13, and 15 were found expressed in all organs at all stages studied, while differential expression was noticed for AtSWEET14 in roots, stems, and siliques and AtSWEET9, 10 expressions were only detected in stems and siliques. A role for these transporters in carbohydrate partitioning in different source-sink status is proposed, with a specific attention on carbon demand in roots. During development, despite trophic competition with others sinks, roots remained a significant sink, but during osmotic stress, the amount of translocated [U-14C]-sucrose decreased for rosettes and roots. Altogether, these results suggest that source-sink relationship may be linked with the regulation of sucrose transporter gene expression.

A "Do-It-Yourself" phenotyping system: measuring growth and morphology throughout the diel cycle in rosette shaped plants

BACKGROUND

Improvements in high-throughput phenotyping technologies are rapidly expanding the scope and capacity of plant biology studies to measure growth traits. Nevertheless, the costs of commercial phenotyping equipment and infrastructure remain prohibitively expensive for wide-scale uptake, while academic solutions can require significant local expertise. Here we present a low-cost methodology for plant biologists to build their own phenotyping system for quantifying growth rates and phenotypic characteristics of Arabidopsis thaliana rosettes throughout the diel cycle.

RESULTS

We constructed an image capture system consisting of a near infra-red (NIR, 940 nm) LED panel with a mounted Raspberry Pi NoIR camera and developed a MatLab-based software module (iDIEL Plant) to characterise rosette expansion. Our software was able to accurately segment and characterise multiple rosettes within an image, regardless of plant arrangement or genotype, and batch process image sets. To further validate our system, wild-type Arabidopsis plants (Col-0) and two mutant lines with reduced Rubisco contents, pale leaves and slow growth phenotypes (1a3b and 1a2b) were grown on a single plant tray. Plants were imaged from 9 to 24 days after germination every 20 min throughout the 24 h light-dark growth cycle (i.e. the diel cycle). The resulting dataset provided a dynamic and uninterrupted characterisation of differences in rosette growth and expansion rates over time for the three lines tested.

CONCLUSION

Our methodology offers a straightforward solution for setting up automated, scalable and low-cost phenotyping facilities in a wide range of lab environments that could greatly increase the processing power and scalability of Arabidopsis soil growth experiments.

Photosynthate partitioning to starch in Arabidopsis thaliana is insensitive to light intensity but sensitive to photoperiod due to a restriction on growth in the light in short photoperiods

Photoperiod duration can be predicted from previous days, but irradiance fluctuates in an unpredictable manner. To investigate how allocation to starch responds to changes in these two environmental variables, Arabidopsis Col-0 was grown in a 6 h and a 12 h photoperiod at three different irradiances. The absolute rate of starch accumulation increased when photoperiod duration was shortened and when irradiance was increased. The proportion of photosynthate allocated to starch increased strongly when photoperiod duration was decreased but only slightly when irradiance was decreased. There was a small increase in the daytime level of sucrose and twofold increases in glucose, fructose and glucose 6-phosphate at a given irradiance in short photoperiods compared to long photoperiods. The rate of starch accumulation correlated strongly with sucrose and glucose levels in the light, irrespective of whether these sugars were responding to a change in photoperiod or irradiance. Whole plant carbon budget modelling revealed a selective restriction of growth in the light period in short photoperiods. It is proposed that photoperiod sensing, possibly related to the duration of the night, restricts growth in the light period in short photoperiods, increasing allocation to starch and providing more carbon reserves to support metabolism and growth in the long night.

Adjustment of the Arabidopsis circadian oscillator by sugar signalling dictates the regulation of starch metabolism

Arabidopsis plants store part of the carbon fixed by photosynthesis as starch to sustain growth at night. Two competing hypotheses have been proposed to explain this diel starch turnover based on either the measurement of starch abundance with respect to circadian time, or the sensing of sugars to feedback to the circadian oscillator to dynamically adjust the timing of starch turnover. We report a phase oscillator model that permitted derivation of the ideal responses of the circadian regulation of starch breakdown to maintain sucrose homeostasis. Testing the model predictions using a sugar-unresponsive mutant of Arabidopsis demonstrated that the dynamics of starch turnover arise from the circadian clock measuring and responding to the rate of change of cellular sucrose. Our theory and experiments suggest that starch turnover is controlled by the circadian clock acting as a dynamic homeostat responding to sucrose signals to maintain carbon homeostasis.

Leaf Starch Turnover Occurs in Long Days and in Falling Light at the End of the Day

We investigated whether starch degradation occurs at the same time as starch synthesis in Arabidopsis (Arabidopsis thaliana) leaves in the light. Starch accumulated in a linear fashion for about 12 h after dawn, then accumulation slowed and content plateaued. Following decreases in light intensity, the rate of accumulation of starch declined in proportion to the decline in photosynthesis if the decrease occurred <10 h after dawn, but accumulation ceased or loss of starch occurred if the same decrease in light intensity was imposed more than 10 h after dawn. These changes in starch accumulation patterns after prolonged periods in the light occurred at both high and low starch contents and were not related to time-dependent changes in either the rate of photosynthesis or the partitioning of assimilate between starch and Suc, as assessed from metabolite measurements and ¹⁴CO₂ pulse experiments. Instead, measurements of incorporation of ¹³C from ¹³CO₂ into starch and of levels of the starch degradation product maltose showed that substantial starch degradation occurred simultaneously with synthesis at time points >14 h after dawn and in response to decreases in light intensity that occurred >10 h after dawn. Starch measurements in circadian clock mutants suggested that the clock influences the timing of onset of degradation. We conclude that the propensity for leaf starch to be degraded increases with time after dawn. The importance of this phenomenon for efficient use of carbon for growth in long days and for prevention of starvation during twilight is discussed.

Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism

BACKGROUND

The circadian clock regulates plant metabolic functions and is an important component in plant health and productivity. Rhizosphere bacteria play critical roles in plant growth, health, and development and are shaped primarily by soil communities. Using Illumina next-generation sequencing and high-resolution mass spectrometry, we characterized bacterial communities of wild-type (Col-0) Arabidopsis thaliana and an acyclic line (OX34) ectopically expressing the circadian clock-associated cca1 transcription factor, relative to a soil control, to determine how cycling dynamics affected the microbial community. Microbial communities associated with Brachypodium distachyon (BD21) were also evaluated.

RESULTS

Significantly different bacterial community structures (P = 0.031) were observed in the rhizosphere of wild-type plants between light and dark cycle samples. Furthermore, 13% of the community showed cycling, with abundances of several families, including Burkholderiaceae, Rhodospirillaceae, Planctomycetaceae, and Gaiellaceae, exhibiting fluctuation in abundances relative to the light cycle. However, limited-to-no cycling was observed in the acyclic CCAox34 line or in soil controls. Significant cycling was also observed, to a lesser extent, in Brachypodium. Functional gene inference revealed that genes involved in carbohydrate metabolism were likely more abundant in near-dawn, dark samples. Additionally, the composition of organic matter in the rhizosphere showed a significant variation between dark and light cycles.

CONCLUSIONS

The results of this study suggest that the rhizosphere bacterial community is regulated, to some extent, by the circadian clock and is likely influenced by, and exerts influences, on plant metabolism and productivity. The timing of bacterial cycling in relation to that of Arabidopsis further suggests that diurnal dynamics influence plant-microbe carbon metabolism and exchange. Equally important, our results suggest that previous studies done without relevance to time of day may need to be reevaluated with regard to the impact of diurnal cycles on the rhizosphere microbial community.

Light quality and quantity regulate aerobic methane emissions from plants

Studies have been mounting in support of the finding that plants release aerobic methane (CH₄ ), and that these emissions are increased by both short-term and long-term environmental stress. It remains unknown whether or not they are affected by variation in light quantity and quality, whether emissions change over time, and whether they are influenced by physiological parameters. Light is the primary energy source of plants, and therefore an important regulator of plant growth and development. Both shade-intolerant sunflower and shade-tolerant chrysanthemum were investigated for the release of aerobic CH₄ emissions, using either low or high light intensity, and varying light quality, including control, low or normal red:far-red ratio (R:FR), and low or high levels of blue, to discern the relationship between light and CH₄ emissions. It was found that low levels of light act as an environmental stress, facilitating CH₄ release from both species. R:FR and blue lights increased emissions under low light, but the results varied with species, providing evidence that both light quantity and quality regulate CH₄ emissions. Emission rates of 6.79-41.13 ng g^-1 DW h^-1 and 18.53-180.25 ng g^-1 DW h^-1 were observed for sunflower and chrysanthemum, respectively. Moreover, emissions decreased with age as plants acclimated to environmental conditions. Since effects were similar in both species, there may be a common trend among a number of shade-tolerant and shade-intolerant species. Light quantity and quality are influenced by factors including cloud covering, so it is important to know how plants will be affected in the context of aerobic CH₄ emissions.

Implications of leaf ontogeny on drought-induced gradients of CAM expression and ABA levels in rosettes of the epiphytic tank bromeliad Guzmania monostachia

Guzmania monostachia is an epiphytic heteroblastic bromeliad that exhibits rosette leaves forming water-holding tanks at maturity. Different portions along its leaf blades can display variable degrees of crassulacean acid metabolism (CAM) up-regulation under drought. Since abscisic acid (ABA) can act as an important long-distance signal, we conducted a joint investigation of ontogenetic and drought impacts on CAM intensity and ABA levels in different leaf groups within the G. monostachia rosette. For this, three groups of leaves were analysed according to their position within the mature-tank rosette (i.e., younger, intermediate, and older leaves) to characterize the general growth patterns and magnitude of drought-modulated CAM expression. CAM activity was evaluated by analysing key molecules in the biochemical machinery of this photosynthetic pathway, while endogenous ABA content was comparatively measured in different portions of each leaf group after seven days under well-watered (control) or drought treatment. The results revealed that G. monostachia shows more uniform morphological characteristics along the leaves when in the atmospheric stage. The drought treatment of mature-tank rosettes generally induced in older leaves a more severe water loss, followed by the lowest CAM activity and a higher increase in ABA levels, while younger leaves showed an opposite response. Therefore, leaf groups at distinct ontogenetic stages within the tank rosette of G. monostachia responded to drought with variable degrees of water loss and CAM expression. ABA seems to participate in this tissue-compartmented response as a long-distance signalling molecule, transmitting the drought-induced signals originated in older leaves towards the younger ones.

Can stable isotope mass spectrometry replace ‎radiolabelled approaches in metabolic studies?

Metabolic pathways and the key regulatory points thereof can be deduced using isotopically labelled substrates. One prerequisite is the accurate measurement of the labeling pattern of targeted metabolites. The subsequent estimation of metabolic fluxes following incubation in radiolabelled substrates has been extensively used. Radiolabelling is a sensitive approach and allows determination of total label uptake since the total radiolabel content is easy to detect. However, the incubation of cells, tissues or the whole plant in a stable isotope enriched environment and the use of either mass spectrometry or nuclear magnetic resonance techniques to determine label incorporation within specific metabolites offers the possibility to readily obtain metabolic information with higher resolution. It additionally also offers an important complement to other post-genomic strategies such as metabolite profiling providing insights into the regulation of the metabolic network and thus allowing a more thorough description of plant cellular function. Thus, although safety concerns mean that stable isotope feeding is generally preferred, the techniques are in truth highly complementary and application of both approaches in tandem currently probably provides the best route towards a comprehensive understanding of plant cellular metabolism.

Regulation of Leaf Starch Degradation by Abscisic Acid Is Important for Osmotic Stress Tolerance in Plants

Starch serves functions that range over a timescale of minutes to years, according to the cell type from which it is derived. In guard cells, starch is rapidly mobilized by the synergistic action of β-AMYLASE1 (BAM1) and α-AMYLASE3 (AMY3) to promote stomatal opening. In the leaves, starch typically accumulates gradually during the day and is degraded at night by BAM3 to support heterotrophic metabolism. During osmotic stress, starch is degraded in the light by stress-activated BAM1 to release sugar and sugar-derived osmolytes. Here, we report that AMY3 is also involved in stress-induced starch degradation. Recently isolated Arabidopsis thaliana amy3 bam1 double mutants are hypersensitive to osmotic stress, showing impaired root growth. amy3 bam1 plants close their stomata under osmotic stress at similar rates as the wild type but fail to mobilize starch in the leaves. (14)C labeling showed that amy3 bam1 plants have reduced carbon export to the root, affecting osmolyte accumulation and root growth during stress. Using genetic approaches, we further demonstrate that abscisic acid controls the activity of BAM1 and AMY3 in leaves under osmotic stress through the AREB/ABF-SnRK2 kinase-signaling pathway. We propose that differential regulation and isoform subfunctionalization define starch-adaptive plasticity, ensuring an optimal carbon supply for continued growth under an ever-changing environment.