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Like many organisms, plants have evolved a genetic network, the circadian clock, to coordinate processes with day/night cycles. In plants, the clock is a pervasive regulator of development and modulates many aspects of physiology. Clock-regulated processes range from the correct timing of growth and cell division to interactions with the root microbiome. Recently developed techniques, such as single-cell time-lapse microscopy and single-cell RNA-seq, are beginning to revolutionize our understanding of this clock regulation, revealing a surprising degree of organ, tissue, and cell-type specificity. In this review, we highlight recent advances in our spatial view of the clock across the plant, both in terms of how it is regulated and how it regulates a diversity of output processes. We outline how understanding these spatially specific functions will help reveal the range of ways that the clock provides a fitness benefit for the plant.

The circadian clock is a genetic circuit that allows organisms to anticipate daily events caused by the rotation of the Earth. The plant clock regulates physiology at multiple scales, from cell division to ecosystem-scale interactions. It is becoming clear that rather than being a single perfectly synchronised timer throughout the plant, the clock can be sensitive to different cues, run at different speeds, and drive distinct processes in different cell types and tissues. This flexibility may help the plant clock to regulate such a range of developmental and physiological processes. In this review, using examples from the literature, we describe how the clock regulates development at multiple scales and discuss how the clock might allow local flexibility in regulation whilst remaining coordinated across the plant.

The A. thaliana circadian clock is an example of a gene network that generates rich temporal and spatial dynamics. Bioluminescent imaging has proven a powerful method to help dissect the genetic mechanisms that generate oscillations of gene expression over the course of the day. However, its use for the study of spatial regulation is often limited by resolution. Here, we describe a modified luciferase imaging method for the study of the Arabidopsis circadian clock across the plant at sub-tissue-level resolution.

The A. thaliana circadian clock is an example of a gene network that generates rich temporal and spatial dynamics. Bioluminescent imaging has proven a powerful method to help dissect the genetic mechanisms that generate oscillations of gene expression over the course of the day. However, its use for the study of spatial regulation is often limited by resolution. Here, we describe a modified luciferase imaging method for the study of the Arabidopsis circadian clock across the plant at sub-tissue-level resolution.

The responses of plants to their environment often hinge on the spatiotemporal dynamics of transcriptional regulation. While live-imaging tools have been used extensively to quantitatively capture rapid transcriptional dynamics in living animal cells, lack of implementation of these technologies in plants has limited concomitant quantitative studies. Here, we applied the PP7 and MS2 RNA-labeling technologies for the quantitative imaging of RNA polymerase II activity dynamics in single cells of living plants as they respond to experimental treatments. Using this technology, we count nascent RNA transcripts in real-time in Nicotiana benthamiana (tobacco) and Arabidopsis thaliana (Arabidopsis). Examination of heat shock reporters revealed that plant tissues respond to external signals by modulating the number of cells engaged in transcription rather than the transcription rate of active cells. This switch-like behavior, combined with cell-to-cell variability in transcription rate, results in mRNA production variability spanning three orders of magnitude. We determined that cellular heterogeneity stems mainly from the stochasticity intrinsic to individual alleles. Taken together, our results demonstrate that it is now possible to quantitatively study the dynamics of transcriptional programs in single cells of living plants.

Funder: FP7 Ideas: European Research Council (FP7 Ideas); Id: http://dx.doi.org/10.13039/100011199; Grant(s): 338060, Genetically identical individuals in bacterial populations can display significant phenotypic variability. This variability can be functional, for example by allowing a fraction of stress prepared cells to survive an otherwise lethal stress. The optimal fraction of stress prepared cells depends on environmental conditions. However, how bacterial populations modulate their level of phenotypic variability remains unclear. Here we show that the alternative sigma factor σV circuit in Bacillus subtilis generates functional phenotypic variability that can be tuned by stress level, environmental history and genetic perturbations. Using single‐cell time‐lapse microscopy and microfluidics, we find the fraction of cells that immediately activate σV under lysozyme stress depends on stress level and on a transcriptional memory of previous stress. Iteration between model and experiment reveals that this tunability can be explained by the autoregulatory feedback structure of the sigV operon. As predicted by the model, genetic perturbations to the operon also modulate the response variability. The conserved sigma‐anti‐sigma autoregulation motif is thus a simple mechanism for bacterial populations to modulate their heterogeneity based on their environment.

Genetically identical plants growing in the same conditions can display heterogeneous phenotypes. Here we use Arabidopsis seed germination time as a model system to examine phenotypic variability and its underlying mechanisms. We show extensive variation in seed germination time variability between Arabidopsis accessions and use a multiparent recombinant inbred population to identify two genetic loci involved in this trait. Both loci include genes implicated in modulating abscisic acid (ABA) sensitivity. Mutually antagonistic regulation between ABA, which represses germination, and gibberellic acid (GA), which promotes germination, underlies the decision to germinate and can act as a bistable switch. A simple stochastic model of the ABA-GA network shows that modulating ABA sensitivity can generate the range of germination time distributions we observe experimentally. We validate the model by testing its predictions on the effects of exogenous hormone addition. Our work provides a foundation for understanding the mechanism and functional role of phenotypic variability in germination time.

A major bottleneck in the modelling of biological networks is the parameter explosion problem – the exponential increase in the number of parameters that need to be optimised to data as the size of the model increases. Here, we address this problem in the context of the plant circadian clock by applying the method of distributed delays. We show that using this approach, the system architecture can be simplified efficiently – reducing the number of parameters – whilst still preserving the core mechanistic dynamics of the gene regulatory network. Compared to models with discrete time-delays, which are governed by functional differential equations, the distributed delay models can be converted into sets of equivalent ordinary differential equations, enabling the use of standard methods for numerical integration, and for stability and bifurcation analyses. We demonstrate the efficiency of our modelling approach by applying it to three exemplar mathematical models of the Arabidopsis circadian clock of varying complexity, obtaining significant reductions in complexity in each case. Moreover, we revise one of the most up-to-date Arabidopsis models, updating the regulation of the PRR9 and PRR7 genes by LHY in accordance with recent experimental data. The revised model more accurately reproduces the LHY-induction experiments of core clock genes, compared with the original model. Our work thus shows that the method of distributed delays facilitates the optimisation and reformulation of genetic network models.

During development, cells gain positional information through the interpretation of dynamic morphogen gradients. A proposed mechanism for interpreting opposing morphogen gradients is mutual inhibition of downstream transcription factors, but isolating the role of this specific motif within a natural network remains a challenge. Here, we engineer a synthetic morphogen-induced mutual inhibition circuit in E. coli populations and show that mutual inhibition alone is sufficient to produce stable domains of gene expression in response to dynamic morphogen gradients, provided the spatial average of the morphogens falls within the region of bistability at the single cell level. When we add sender devices, the resulting patterning circuit produces theoretically predicted self-organised gene expression domains in response to a single gradient. We develop computational models of our synthetic circuits parameterised to timecourse fluorescence data, providing both a theoretical and experimental framework for engineering morphogen-induced spatial patterning in cell populations., Morphogen gradients can be dynamic and transient yet give rise to stable cellular patterns. Here the authors show that a synthetic morphogen-induced mutual inhibition circuit produces stable boundaries when the spatial average of morphogens falls within the region of bistability.

International audience; Gene expression in individual cells can be surprisingly noisy. In unicellular organisms this noise can be functional; for example, by allowing a subfraction of the population to prepare for environmental stress. The role of gene expression noise in multicellular organisms has, however, remained unclear. In this review, we discuss how new techniques are revealing an unexpected level of variability in gene expression between and within genetically identical plants. We describe recent progress as well as speculate on the function of transcriptional noise as a mechanism for generating functional phenotypic diversity in plants.

Individual plant cells possess a genetic network, the circadian clock, that times internal processes to the day-night cycle. Mathematical models of the clock network have driven a mechanistic understanding of the clock in plants. However, these models are typically either ‘whole plant’ models that ignore tissue or cell type specific clock behavior, or ‘phase only’ models that do not include clock network components explicitly. It is increasingly clear that in order to reveal the design principles of the plant circadian clock, clock network models must address spatial differences. This is because complex spatial behaviours have been observed in tissues and cells in plants, including period and phase differences between cells and spatial waves of gene expression between organs. Here, we implement an up to date clock network model on a spatial template of the plant. In our model, the sensitivity to light inputs varies across the plant, and cells communicate their clock timing locally via the levels of core clock mRNA levels by cell-to-cell coupling. We found that differences in sensitivities to environmental input in the model can explain the experimentally observed differences in clock periods in different organs, and we show using the model that a plausible coupling mechanism can generate the experimentally observed waves in clock gene expression across the plant. We then examined what features of the plant circadian system allow it to keep time under noisy light-dark (LD) cycles. We found that differences in sensitivity to light can allow regional flexibility in phase even under LD cycles, whilst local cell-to-cell coupling minimized variability in clock rhythms in neighboring cells. Thus, local sensitivity to environmental inputs combined with cell-to-cell coupling allows for flexible yet robust circadian timing under noisy environments.

Genetically identical plants growing in the same conditions can display heterogeneous phenotypes. Whether this phenotypic variability is functional and the mechanisms behind it are unclear. Here we use Arabidopsis seed germination time as a model system to examine phenotypic variability. We show extensive variation in seed germination time variability between Arabidopsis accessions, and use a multi-parent recombinant inbred population to identify two loci involved in this trait. Both loci include genes implicated in ABA signalling that could contribute to seed germination variability. Modelling reveals that the GA/ABA bistable switch underlying germination can amplify variability and account for the effects of these two loci on germination distributions. The model predicts the effects of modulating ABA and GA levels, which we validate genetically and by exogenous addition of hormones. We confirm that germination variability could act as a bet hedging strategy, by allowing a fraction of seeds to survive lethal stress.

The shoot apical meristem (SAM) is responsible for the generation of all of the aerial parts of plants. Given its critical role, dynamical changes in SAM activity should play a central role in the adaptation of plant architecture to the environment. Using quantitative microscopy, grafting experiments and genetic perturbations, we connect the plant environment to the SAM, by describing the molecular mechanism by which cytokinins signal the level of nutrient availability to the SAM. We show that a systemic signal of cytokinin precursors mediates the adaptation of SAM size and organogenesis rate to the availability of mineral nutrients by modulating the expression of WUSCHEL, a key regulator of stem cell homeostasis. In time- lapse experiments, we further show that this mechanism allows meristems to adapt to rapid changes in nitrate concentration, and thereby modulate their rate of organ production to the availability of mineral nutrients within a few days. Our work sheds new light on the role of the stem cell regulatory network, by showing that it does not only maintain meristem homeostasis but also allows plants to adapt to rapid changes in the environment.

Summary Circadian clocks are important to much of life on Earth and are of inherent interest to humanity, implicated in fields ranging from agriculture and ecology to developmental biology and medicine. New techniques show that it is not simply the presence of clocks, but coordination between them that is critical for complex physiological processes across the kingdoms of life. Recent years have also seen impressive advances in synthetic biology to the point where parallels can be drawn between synthetic biological and circadian oscillators. This review will emphasise theoretical and experimental studies that have revealed a fascinating dichotomy, of coupling and heterogeneity, among circadian clocks. We will also consolidate the fields of chronobiology and synthetic biology, discussing key design principles of their respective oscillators.

A fundamental question in biology is how gene expression is regulated to give rise to a phenotype. However, transcriptional variability is rarely considered although it could influence the relationship between genotype and phenotype. It is known in unicellular organisms that gene expression is often noisy rather than uniform, and this has been proposed to be beneficial when environmental conditions are unpredictable. However, little is known about inter-individual transcriptional variability in multicellular organisms. Using transcriptomic approaches, we analysed gene expression variability between individual Arabidopsis thaliana plants growing in identical conditions over a 24-h time course. We identified hundreds of genes that exhibit high inter-individual variability and found that many are involved in environmental responses, with different classes of genes variable between the day and night. We also identified factors that might facilitate gene expression variability, such as gene length, the number of transcription factors regulating the genes and the chromatin environment. These results shed new light on the impact of transcriptional variability in gene expression regulation in plants.

Gene expression can be noisy, as can the growth of single cells. Such cell-to-cell variation has been implicated in survival strategies for bacterial populations. However, it remains unclear how single cells couple gene expression with growth to implement these strategies. Here, we show how noisy expression of a key stress-response regulator, RpoS, allows E. coli to modulate its growth dynamics to survive future adverse environments. We reveal a dynamic positive feedback loop between RpoS and growth rate that produces multi-generation RpoS pulses. We do so experimentally using single-cell, time-lapse microscopy and microfluidics and theoretically with a stochastic model. Next, we demonstrate that E. coli prepares for sudden stress by entering prolonged periods of slow growth mediated by RpoS. This dynamic phenotype is captured by the RpoS-growth feedback model. Our synthesis of noisy gene expression, growth, and survival paves the way for further exploration of functional phenotypic variability., Noisy gene expression leading to phenotypic variability can help organisms to survive in changing environments. Here, Patange et al. show that noisy expression of a stress response regulator, RpoS, allows E. coli cells to modulate their growth rates to survive future adverse environments.

Steel slag is a byproduct of the steel industry that can be used as a liming agent, but also has a high mineral nutrient content. While micronutrients are present in steel slag, it is not known if the mineral form of the micronutrients would render them available for plant uptake. The objective of this research was to determine if steel slag could be used as the sole micronutrient source for container-grown nursery crops. Butterfly bush (Buddleja davidii ‘Pink Delight’) and rose (Rosa ‘Radrazz’) were grown in #3 (3 gal) containers in a base substrate composed of pine bark and peatmoss (80:20, by vol). The base substrate was amended with the following treatments: with a complete controlled release fertilizer (CRF) including micronutrients (C-control), a substrate amended with a different CRF containing only N, P, and K along with a granular micronutrient package (M-control), and three additional treatments amended with the CRF (N, P, and K only) and either 1.2, 2.4, or 4.8 kg·m−3 (2, 4, and 8 lb·yd−3) of steel slag. Plants were harvested at 2 and 4 months after potting (MAP). None of the plants displayed any sign of nutrient deficiency or toxicity throughout the experiment. However, plants grown in the substrate amended with the highest slag rate [4.8 kg·m−3 (8 lb·yd−3)] had lower shoot dry weight (SDW) than both control groups. Substrate pH increased with increasing slag rate, which may have affected micronutrient availability in those substrates. Among the micronutrients analyzed, only Copper (Cu) was consistently deficient in both the substrate and foliar tissue of slag-amended treatments. Steel slag either does not provide a sufficient quantity of Cu or the concomitant increase in pH with increasing rates of steel slag renders Cu unavailable for plant uptake. Steel slag should not be used as the sole source of micronutrients for shrubs grown in pine bark-based substrates.

Background Discussions of phenotypic robustness often consider scenarios where invariant phenotypes are optimal and assume that developmental mechanisms have evolved to buffer the phenotypes of specific traits against stochastic and environmental perturbations. However, plastic plant phenotypes that vary between environments or variable phenotypes that vary stochastically within an environment may also be advantageous in some scenarios. Scope Here the conditions under which invariant, plastic and variable phenotypes of specific traits may confer a selective advantage in plants are examined. Drawing on work from microbes and multicellular organisms, the mechanisms that may give rise to each type of phenotype are discussed. Conclusion In contrast to the view of robustness as being the ability of a genotype to produce a single, invariant phenotype, changes in a phenotype in response to the environment, or phenotypic variability within an environment, may also be delivered consistently (i.e. robustly). Thus, for some plant traits, mechanisms have probably evolved to produce plasticity or variability in a reliable manner.

The Arabidopsis circadian clock orchestrates gene regulation across the day/night cycle. Although a multiple feedback loop circuit has been shown to generate the 24h rhythm, it remains unclear how robust the clock is in individual cells, or how clock timing is coordinated across the plant. Here we examine clock activity at the single cell level across Arabidopsis seedlings over several days. Our data reveal robust single cell oscillations, albeit desynchronised. In particular, we observe two waves of clock activity; one going down, and one up the root. We also find evidence of cell-to-cell coupling of the clock, especially in the root tip. A simple model shows that cell-to-cell coupling and our measured period differences between cells can generate the observed waves. Our results reveal the spatial structure of the plant circadian clock and suggest that unlike the centralised mammalian clock, the clock has multiple points of coordination in Arabidopsis.

Gene expression can be noisy1,2, as can the growth of single cells3,4. Such cell-to-cell variation has been implicated in survival strategies for bacterial populations5–7. However, it remains unclear how single cells couple gene expression with growth to implement these survival strategies. Here we show how noisy expression of a key stress response regulator,rpoS8, allows E. coli to modulate its growth dynamics to survive future adverse environments. First, we demonstrate thatrpoShas a long-tailed distribution of expression in an unstressed population of cells. We next reveal how a dynamic positive feedback loop betweenrpoSand growth rate produces multi-generationrpoSpulses, which are responsible for therpoSheterogeneity. We do so experimentally with single-cell, time-lapse microscopy9and microfluidics10and theoretically with a stochastic model11,22. Finally, we demonstrate the function of the coupling of heterogeneousrpoSactivity and growth. It enablesE. colito survive oxidative attack by causing prolonged periods of slow growth. This dynamic phenotype is captured by therpoS-growth feedback model. Our synthesis of noisy gene expression, growth, and survival paves the way for further exploration of functional phenotypic variability.

The shoot apical meristem (SAM) is responsible for the generation of all the aerial parts of plants. Given its critical role, dynamical changes in SAM activity should play a central role in the adaptation of plant architecture to the environment. Using quantitative microscopy, grafting experiments, and genetic perturbations, we connect the plant environment to the SAM by describing the molecular mechanism by which cytokinins signal the level of nutrient availability to the SAM. We show that a systemic signal of cytokinin precursors mediates the adaptation of SAM size and organogenesis rate to the availability of mineral nutrients by modulating the expression of

Physical review / X 8(2), 021035 (2018). doi:10.1103/PhysRevX.8.021035, Published by APS, College Park, Md.

SUMMARY In cells, specific regulators often compete for limited amounts of a core enzymatic resource. It is typically assumed that competition leads to partitioning of core enzyme molecules among regulators at constant levels. Alternatively, however, different regulatory species could time share, or take turns utilizing, the core resource. Using quantitative time-lapse microscopy, we analyzed sigma factor activity dynamics, and their competition for RNA polymerase, in individual Bacillus subtilis cells under energy stress. Multiple alternative sigma factors were activated in ~1-hr pulses in stochastic and repetitive fashion. Pairwise analysis revealed that two sigma factors rarely pulse simultaneously and that some pairs are anti-correlated, indicating that RNAP utilization alternates among different sigma factors. Mathematical modeling revealed how stochastic time-sharing dynamics can emerge from pulse-generating sigma factor regulatory circuits actively competing for RNAP. Time sharing provides a mechanism for cells to dynamically control the distribution of cell states within a population. Since core molecular components are limiting in many other systems, time sharing may represent a general mode of regulation., In Brief Cellular regulatory factors often compete for limited amounts of core enzymes. Sharing is typically assumed to involve statically partitioning core enzyme molecules. In contrast, using time-lapse movies, we find that Bacillus subtilis alternative sigma factors, which compete for core RNA polymerase, activate dynamically in stochastic, repetitive, hour-long pulses. Using mathematical modeling, we show how such pulsatile competitive circuits can effectively time share, or take turns using, core polymerase under similar conditions. Time-sharing represents an alternative mode of resource sharing in cells.

Steel slag (SS) is a fertilizer amendment with a high concentration of calcium oxide, and thus capable of raising substrate pH similar to dolomitic lime (DL). Steel slag, however, contains higher concentrations of some nutrients, such as iron, manganese, and silicon, compared to DL. The objective of this research was to determine the effect of SS rate on pH in a substrate composed of 80 pine bark:20 sphagnum peatmoss (v:v), as well as growth and nutrient concentration of butterfly bush (Buddleja davidii ‘Pink Delight’ Franch.). The base substrate was amended with either DL or SS at rates of 0, 0.6, 2.4, 4.8, 9.5, or 14.3 kg·m−3. Substrates were placed into 12-L nursery containers and potted with a single butterfly bush per container. Dolomitic lime amendment resulted in higher substrate pH at rates from 0.6 to 4.8 kg·m−3 while the SS amendment caused a greater increase in pH at rates higher than 4.8 kg·m−3. Butterfly bush responded well to all but the highest SS rate applied. As the rate of SS increased to 14.3 kg·m−3, decreased Mg availability may have reduced shoot growth. Based on the results of this experiment, SS could be used as an alternative to DL. However, incorporation rates would need to be adjusted slightly higher for SS compared to DL to achieve a desired pH in the range of 6 to 6.5.

SummaryPlant development is highly responsive to ambient temperature, and this trait has been linked to the ability of plants to adapt to climate change [1]. The mechanisms by which natural populations modulate their thermoresponsiveness are not known [2]. To address this, we surveyed Arabidopsis accessions for variation in thermal responsiveness of elongation growth and mapped the corresponding loci. We find that the transcriptional regulator EARLY FLOWERING3 (ELF3) controls elongation growth in response to temperature. Through a combination of modeling and experiments, we show that high temperature relieves the gating of growth at night, highlighting the importance of temperature-dependent repressors of growth. ELF3 gating of transcriptional targets responds rapidly and reversibly to changes in temperature. We show that the binding of ELF3 to target promoters is temperature dependent, suggesting a mechanism where temperature directly controls ELF3 activity.

Significance When and at what size to divide are critical decisions, requiring cells to integrate internal and external cues. While it is known that the 24-h circadian clock and the environment modulate division timings across organisms, how these signals combine to set the size at which cells divide is not understood. Iterating between modeling and experiments, we show that, in both constant and light−dark conditions, the cyanobacterial clock produces distinctly sized and timed subpopulations. These arise from continuous coupling of the clock to the cell cycle, which, in light−dark cycles, steers cell divisions away from dawn and dusk. Stochastic modeling allows us to predict how these effects emerge from the complex interactions between the environment, clock, and cell size control., How cells maintain their size has been extensively studied under constant conditions. In the wild, however, cells rarely experience constant environments. Here, we examine how the 24-h circadian clock and environmental cycles modulate cell size control and division timings in the cyanobacterium Synechococcus elongatus using single-cell time-lapse microscopy. Under constant light, wild-type cells follow an apparent sizer-like principle. Closer inspection reveals that the clock generates two subpopulations, with cells born in the subjective day following different division rules from cells born in subjective night. A stochastic model explains how this behavior emerges from the interaction of cell size control with the clock. We demonstrate that the clock continuously modulates the probability of cell division throughout day and night, rather than solely applying an on−off gate to division, as previously proposed. Iterating between modeling and experiments, we go on to identify an effective coupling of the division rate to time of day through the combined effects of the environment and the clock on cell division. Under naturally graded light−dark cycles, this coupling narrows the time window of cell divisions and shifts divisions away from when light levels are low and cell growth is reduced. Our analysis allows us to disentangle, and predict the effects of, the complex interactions between the environment, clock, and cell size control.

Multicellular development produces patterns of specialized cell types. Yet, it is often unclear how individual cells within a field of identical cells initiate the patterning process. Using live imaging, quantitative image analyses and modeling, we show that during Arabidopsis thaliana sepal development, fluctuations in the concentration of the transcription factor ATML1 pattern a field of identical epidermal cells to differentiate into giant cells interspersed between smaller cells. We find that ATML1 is expressed in all epidermal cells. However, its level fluctuates in each of these cells. If ATML1 levels surpass a threshold during the G2 phase of the cell cycle, the cell will likely enter a state of endoreduplication and become giant. Otherwise, the cell divides. Our results demonstrate a fluctuation-driven patterning mechanism for how cell fate decisions can be initiated through a random yet tightly regulated process.

Organisms use circadian clocks to generate 24‐h rhythms in gene expression. However, the clock can interact with other pathways to generate shorter period oscillations. It remains unclear how these different frequencies are generated. Here, we examine this problem by studying the coupling of the clock to the alternative sigma factor sigC in the cyanobacterium Synechococcus elongatus. Using single‐cell microscopy, we find that psbAI, a key photosynthesis gene regulated by both sigC and the clock, is activated with two peaks of gene expression every circadian cycle under constant low light. This two‐peak oscillation is dependent on sigC, without which psbAI rhythms revert to one oscillatory peak per day. We also observe two circadian peaks of elongation rate, which are dependent on sigC, suggesting a role for the frequency doubling in modulating growth. We propose that the two‐peak rhythm in psbAI expression is generated by an incoherent feedforward loop between the clock, sigC and psbAI. Modelling and experiments suggest that this could be a general network motif to allow frequency doubling of outputs.

Combining heat and light responses Plants integrate a variety of environmental signals to regulate growth patterns. Legris et al. and Jung et al. analyzed how the quality of light is interpreted through ambient temperature to regulate transcription and growth (see the Perspective by Halliday and Davis). The phytochromes responsible for reading the ratio of red to far-red light were also responsive to the small shifts in temperature that occur when dusk falls or when shade from neighboring plants cools the soil. Science , this issue p. 897 , p. 886 ; see also p. 832

Individual plant cells have a genetic circuit, the circadian clock, that times key processes to the day-night cycle. These clocks are aligned to the day-night cycle by multiple environmental signals that vary across the plant. How does the plant integrate clock rhythms, both within and between organs, to ensure coordinated timing? To address this question, we examined the clock at the sub-tissue level across Arabidopsis thaliana seedlings under multiple environmental conditions and genetic backgrounds. Our results show that the clock runs at different speeds (periods) in each organ, which causes the clock to peak at different times across the plant in both constant environmental conditions and light-dark (LD) cycles. Closer examination reveals that spatial waves of clock gene expression propagate both within and between organs. Using a combination of modeling and experiment, we reveal that these spatial waves are the result of the period differences between organs and local coupling, rather than long-distance signaling. With further experiments we show that the endogenous period differences, and thus the spatial waves, can be generated by the organ specificity of inputs into the clock. We demonstrate this by modulating periods using light and metabolic signals, as well as with genetic perturbations. Our results reveal that plant clocks can be set locally by organ-specific inputs but coordinated globally via spatial waves of clock gene expression., Computational modeling and experiments with Arabidopsis thaliana reveal a new mechanism for the coordination of circadian timing across an organism, acting through a combination of organ-specific sensitivity to environmental inputs and local cell-cell coupling.

A series of column studies were conducted to determine the influence of three different biochar types on nitrate, phosphate, and potassium retention and leaching in a typical greenhouse soilless substrate. A commercial substrate composed of 85 sphagnum peatmoss : 15 perlite (v:v) was amended with 10% by volume of three different biochar types including: gasified rice hull biochar (GRHB), sawdust biochar (SDB), and a bark and wood biochar (BWB). The non-amended control substrate, along with substrates amended with one of three biochar materials, were each packed into three columns. Columns were drenched with nutrient solution and leached to determine the impact of biochar on nutrient retention and leaching. Nitrate release curves were exponential and peaked lower, at later leaching events, and had higher residual nitrate release over time with each biochar amendment. The impact of biochar amendment on phosphate retention and release was more variable within and across the two experiments. In both experiments, the GRHB was a net source of phosphate, providing more phosphate to the system than the fertilizer application and hence obscuring any retention and release effect it might have. Potassium release varied by amendment type within each experiment, but within each amendment type was relatively consistent across the two experiments. All biochar types were a source of potassium, with GRHB providing more than SDB, but both providing far more potassium than the fertilizer event. The BWB amendment resulted in more leached potassium than the control substrate, but relatively little compared with GRHB and SDB amendments.

Multicellular development produces patterns of specialized cell types. Yet, it is often unclear how individual cells within a field of identical cells initiate the patterning process. Using live imaging, quantitative image analyses and modeling, we show that during Arabidopsis thaliana sepal development, fluctuations in the concentration of the transcription factor ATML1 pattern a field of identical epidermal cells to differentiate into giant cells interspersed between smaller cells. We find that ATML1 is expressed in all epidermal cells. However, its level fluctuates in each of these cells. If ATML1 levels surpass a threshold during the G2 phase of the cell cycle, the cell will likely enter a state of endoreduplication and become giant. Otherwise, the cell divides. Our results demonstrate a fluctuation-driven patterning mechanism for how cell fate decisions can be initiated through a random yet tightly regulated process. DOI: http://dx.doi.org/10.7554/eLife.19131.001, eLife digest Plant and animal organs contain several types of cells that perform different roles. As a plant or animal develops, these different cell types can form intricate patterns. To start the pattern, a few cells within a group of identical cells must somehow become different from their neighbors. Some patterns of cells are very well organized and easily reproduced. However, sometimes cells spontaneously become different from their neighbors, producing a less ordered pattern. In a plant called Arabidopsis (commonly known as Thale cress), a scattered pattern of giant cells and small cells spontaneously forms within a part of the developing flower called the sepal. A protein called ATML1 is a key regulator in the formation of giant cells, but because it is found in both giant cells and small cells, it is not clear how this regulation works. Mathematical models of this process suggest that identical cells could initially acquire subtle differences, potentially from random fluctuations in the activity of key regulatory molecules, to start the patterning process. Meyer, Teles, Formosa-Jordan et al. used a combination of microscopy, image analysis and mathematical modeling to investigate how the level of ATML1 fluctuates in cells to give rise to the pattern within the sepal. The experiments show that early in the development of the sepal, the levels of ATML1 fluctuate up and down in every sepal cell. If ATML1 reaches a high level specifically when a cell is preparing to divide, that cell will decide to become a giant cell, whereas if the level of ATML1 is low at this point, then the cell will divide and remain small. Overall, the findings of Meyer, Teles, Formosa-Jordan et al. demonstrate that fluctuations of key regulators while cells are preparing to divide are important for creating patterns during development. A future challenge is to examine whether other tissues in plants, or tissues in other organisms, use a similar mechanism to generate patterns of cells. DOI: http://dx.doi.org/10.7554/eLife.19131.002

Byproducts of pyrolysis, known collectively as biochar, are becoming more common and readily available as ventures into alternative energy generation are explored. Little is known about how these materials affect greenhouse container substrates. The objective of this research was to determine the effect of one form of biochar on the nutrient retention and release in a typical commercial greenhouse container substrate. Glass columns filled with 85:15 sphagnum peatmoss:perlite (v:v) and amended with 0%, 1%, 5%, or 10% biochar were drenched with nutrient solution and leached to determine the impact of biochar on nutrient retention and leaching. Nitrate release curves were exponential and peaked lower, at later leaching events, and had higher residual nitrate release over time with increasing biochar amendment rate. This suggests that biochar might be effective in moderating extreme fluctuations of nitrate levels in container substrates over time. Peak phosphate concentration decreased with increasing biochar amendment rate, whereas time of peak release, girth of the peak curve, and final residual phosphate release all increased with increasing biochar amendment. Additional phosphate levels in leachates from biochar-amended substrates, in addition to the higher phosphate concentrations present in later leaching events, suggest this form of biochar as a modest source of phosphate for ornamental plant production. Although there was not sufficient potassium (K) from biochar to adequately replace all fertilizer K in plant production, increasing levels of this form of biochar will add a substantial quantity of K to the substrate and should be accounted for in fertility programs.

Quantitative single-cell time-lapse microscopy is a powerful method for analyzing gene circuit dynamics and heterogeneous cell behavior. We describe the application of this method to imaging bacteria by using an automated microscopy system. This protocol has been used to analyze sporulation and competence differentiation in Bacillus subtilis, and to quantify gene regulation and its fluctuations in individual Escherichia coli cells. The protocol involves seeding and growing bacteria on small agarose pads and imaging the resulting microcolonies. Images are then reviewed and analyzed using our laboratory's custom MATLAB analysis code, which segments and tracks cells in a frame-to-frame method. This process yields quantitative expression data on cell lineages, which can illustrate dynamic expression profiles and facilitate mathematical models of gene circuits. With fast-growing bacteria, such as E. coli or B. subtilis, image acquisition can be completed in 1 d, with an additional 1–2 d for progressing through the analysis procedure.

Nitrogen (N) fertilization recommendations to achieve optimum growth are well established for many floriculture crops. Although it has been shown that plant functions can recover from N deficiency in other crops, little research has investigated the threshold beyond which a bedding plant crop is recoverable. The objective of this research was to determine the effect of N deficiency on geranium chlorophyll content and growth and then to document the degree of recovery and recovery time from N deprivation. This was determined in two experiments by monitoring chlorophyll content and growth of seedlings grown in hydroponic culture in which the N source was removed and then restored after differing lengths of time. Summarizing across both experiments, chlorophyll and foliar N levels were shown to rebound quickly after N deprivation; however, growth was reduced after just 4 days compared with plants fed constantly. Geraniums grown without N for 4 to 12 days resulted in smaller, more compact plants with lower shoot–to-root ratios. Although foliar chlorophyll and N concentration recovered from longer periods in N growth solution, geranium growth was reduced and failed to completely recover for any plant receiving more than 2 days of N-free solution.

Gene regulatory circuits can use dynamic, and even stochastic, strategies to respond to environmental conditions. We examined activation of the general stress response mediated by the alternative sigma factor, σ(B), in individual Bacillus subtilis cells. We observed that energy stress activates σ(B) in discrete stochastic pulses, with increasing levels of stress leading to higher pulse frequencies. By perturbing and rewiring the endogenous system, we found that this behavior results from three key features of the σ(B) circuit: an ultrasensitive phosphorylation switch; stochasticity ("noise"), which activates that switch; and a mixed (positive and negative) transcriptional feedback, which can both amplify a pulse and switch it off. Together, these results show how prokaryotes encode signals using stochastic pulse frequency modulation through a compact regulatory architecture.

The circadian clock is a fundamental feature of eukaryotic gene regulation that is emerging as an exemplar genetic sub-network for systems biology. The circadian system in Arabidopsis plants is complex, in part due to its phototransduction pathways, which are themselves under circadian control. We therefore analysed two simpler experimental systems. Etiolated seedlings entrained by temperature cycles showed circadian rhythms in the expression of genes that are important for the clock mechanism, but only a restricted set of downstream target genes were rhythmic in microarray assays. Clock control of phototransduction pathways remained robust across a range of light inputs, despite the arrhythmic transcription of light-signalling genes. Circadian interactions with light signalling were then analysed using a single active photoreceptor. Phytochrome A (phyA) is expected to be the only active photoreceptor that can mediate far-red (FR) light input to the circadian clock. Surprisingly, rhythmic gene expression was profoundly altered under constant FR light, in a phyA-dependent manner, resulting in high expression of evening genes and low expression of morning genes. Dark intervals were required to allow high-amplitude rhythms across the transcriptome. Clock genes involved in this response were identified by mutant analysis, showing that the EARLY FLOWERING 4 gene is a likely target and mediator of the FR effects. Both experimental systems illustrate how profoundly the light input pathways affect the plant circadian clock, and provide strong experimental manipulations to understand critical steps in the plant clock mechanism.

SummaryThe 24-hour rhythms of the circadian clock [1] allow an organism to anticipate daily environmental cycles, giving it a competitive advantage [2, 3]. Although clock components show little protein sequence homology across phyla, multiple feedback loops and light inputs are universal features of clock networks [4, 5]. Why have circadian systems evolved such a complex structure? All biological clocks entrain a set of regulatory genes to the environmental cycle, in order to correctly time the expression of many downstream processes. Thus the question becomes: What aspects of the environment, and of the desired downstream regulation, are demanding the observed complexity? To answer this, we have evolved gene regulatory networks in silico, selecting for networks that correctly predict particular phases of the day under light/dark cycles. Gradually increasing the realism of the environmental cycles, we have tested the networks for the minimal characteristics of clocks observed in nature: oscillation under constant conditions, entrainment to light signals, and the presence of multiple feedback loops and light inputs. Realistic circadian gene networks are found to require a nontrivial combination of conditions, with seasonal differences in photoperiod as a necessary but not sufficient component.