A novel root-to-shoot stomatal response to very high CO2 levels in the soil: electrical, hydraulic and biochemical signalling.

Investigations were undertaken in the context of the potential environmental impact of carbon capture and storage (CCS) transportation in the form of a hypothetical leak of extreme levels of CO2 into the soil environment and subsequent effects on plant physiology. Laboratory studies using purpose built soil chambers, separating and isolating the soil and aerial environments, were used to introduce high levels of CO2 gas exclusively into the rhizosphere. CO2 concentrations greater than 32% in the isolated soil environment revealed a previously unknown whole plant stomatal response. Time course measurements of stomatal conductance (gs ), leaf temperature and leaf abscisic acid (ABA) show strong coupling between all three variables over a specific period (3 h following CO2 gassing) occurring as a result of CO2 -specific detection by roots. The coupling of gs and ABA subsequently breaks down resulting in a rapid and complete loss of turgor in the shoot. Root access to water is severely restricted as evidenced by the inability to counter turgor loss, however, the plant regains some turgor over time. Recovery of full turgor is not achieved over the longer term. Results suggest an immediate perception and whole plant response as changes in measured parameters (leaf temperature, gs and ABA) occur in the shoot, but the response is solely due to detection of very high CO2 concentration at the root/soil interface which results in loss of stomatal regulation and disruption to control over water uptake.

Effects of elevated carbon dioxide on stomatal characteristics and carbon isotope ratio of Arabidopsis thaliana ecotypes originating from an altitudinal gradient.

Stomatal functioning regulates the fluxes of CO2 and water vapor between vegetation and atmosphere and thereby influences plant adaptation to their habitats. Stomatal traits are controlled by external environmental and internal cellular signaling. The objective of this study was to quantify the effects of CO2 enrichment (CE) on stomatal density (SD)-related properties, guard cell length (GCL) and carbon isotope ratio (δ13 C) of a range of Arabidopsis thaliana ecotypes originating from a wide altitudinal range [50-1260 m above sea level (asl)], and grown at 400 and 800 ppm [CO2 ], and thereby elucidate the possible adaptation and acclimation responses controlling stomatal traits and water use efficiency (WUE). There was a highly significant variation among ecotypes in the magnitude and direction of response of stomatal traits namely, SD and stomatal index (SI) and GCL, and δ13 C to CE, which represented a short-term acclimation response. A majority of ecotypes showed increased SD and SI with CE with the response not depending on the altitude of origin. Significant ecotypic variation was shown in all stomatal traits and δ13 C at each [CO2 ]. At 400 ppm, means of SD, SI and GCL for broad altitudinal ranges, i.e. low (<100 m), mid (100-400 m) and high (>400 m), increased with increasing altitude, which represented an adaptation response to decreased availability of CO2 with altitude. δ13 C was negatively correlated to SD and SI at 800 ppm but not at 400 ppm. Our results highlight the diversity in the response of key stomatal characters to CE and altitude within the germplasm of A. thaliana and the need to consider this diversity when using A. thaliana as a model plant.

Reconstructing relative genome size of vascular plants through geological time.

The strong positive relationship evident between cell and genome size in both animals and plants forms the basis of using the size of stomatal guard cells as a proxy to track changes in plant genome size through geological time. We report for the first time a taxonomic fine-scale investigation into changes in stomatal guard-cell length and use these data to infer changes in genome size through the evolutionary history of land plants. Our data suggest that many of the earliest land plants had exceptionally large genome sizes and that a predicted overall trend of increasing genome size within individual lineages through geological time is not supported. However, maximum genome size steadily increases from the Mississippian (c. 360 million yr ago (Ma)) to the present. We hypothesise that the functional relationship between stomatal size, genome size and atmospheric CO2 may contribute to the dichotomy reported between preferential extinction of neopolyploids and the prevalence of palaeopolyploidy observed in DNA sequence data of extant vascular plants.

Does growth under elevated CO2 moderate photoacclimation in rice?

Acclimation of plant photosynthesis to light irradiance (photoacclimation) involves adjustments in levels of pigments and proteins and larger scale changes in leaf morphology. To investigate the impact of rising atmospheric CO2 on crop physiology, we hypothesize that elevated CO2 interacts with photoacclimation in rice (Oryza sativa). Rice was grown under high light (HL: 700 µmol m⁻² s⁻¹), low light (LL: 200 µmol m⁻² s⁻¹), ambient CO2 (400 µl l⁻¹) and elevated CO2 (1000 µl l⁻¹). Leaf six was measured throughout. Obscuring meristem tissue during development did not alter leaf thickness indicating that mature leaves are responsible for sensing light during photoacclimation. Elevated CO2 raised growth chamber photosynthesis and increased tiller formation at both light levels, while it increased leaf length under LL but not under HL. Elevated CO2 always resulted in increased leaf growth rate and tiller production. Changes in leaf thickness, leaf area, Rubisco content, stem and leaf starch, sucrose and fructose content were all dominated by irradiance and unaffected by CO2. However, stomata responded differently; they were significantly smaller in LL grown plants compared to HL but this effect was significantly suppressed under elevated CO2. Stomatal density was lower under LL, but this required elevated CO2 and the magnitude was adaxial or abaxial surface-dependent. We conclude that photoacclimation in rice involves a systemic signal. Furthermore, extra carbohydrate produced under elevated CO2 is utilized in enhancing leaf and tiller growth and does not enhance or inhibit any feature of photoacclimation with the exception of stomatal morphology.

Untangling the Complexities of Processing and Analysis for Untargeted LC-MS Data Using Open-Source Tools.

Untargeted metabolomics is a powerful tool for measuring and understanding complex biological chemistries. However, employment, bioinformatics and downstream analysis of mass spectrometry (MS) data can be daunting for inexperienced users. Numerous open-source and free-to-use data processing and analysis tools exist for various untargeted MS approaches, including liquid chromatography (LC), but choosing the 'correct' pipeline isn't straight-forward. This tutorial, in conjunction with a user-friendly online guide presents a workflow for connecting these tools to process, analyse and annotate various untargeted MS datasets. The workflow is intended to guide exploratory analysis in order to inform decision-making regarding costly and time-consuming downstream targeted MS approaches. We provide practical advice concerning experimental design, organisation of data and downstream analysis, and offer details on sharing and storing valuable MS data for posterity. The workflow is editable and modular, allowing flexibility for updated/changing methodologies and increased clarity and detail as user participation becomes more common. Hence, the authors welcome contributions and improvements to the workflow via the online repository. We believe that this workflow will streamline and condense complex mass-spectrometry approaches into easier, more manageable, analyses thereby generating opportunities for researchers previously discouraged by inaccessible and overly complicated software.

Environmental metabolomics links genotype to phenotype and predicts genotype abundance in wild plant populations.

'The Holy Grail' of plant ecology is to uncover rules that associate species and traits with environmental constraints, community composition and subsequent ecosystem functioning. These aims have been crystallized in recent years within the context of global climate change and environmental pollution, increasing the urgency of the need to predict how vegetation will respond across spatial scales. We investigated whether genetic diversity is associated with the way in which phenotypic plasticity within plant populations is realized and whether this is related to genotype abundance. We used environmental metabolomics to demonstrate biochemical variation between co-occurring genotypes of Carex caryophyllea L. A novel combined metabolomic/functional trait analysis was used to test the functionality of this variation in governing plasticity to variation in edaphic conditions, with particular reference to metabolic pathways that play important roles in growth-related traits. We show that genetic diversity within a wild C. caryophyllea population relates to differences in metabolic composition and functional traits in response to soil nutrient variation, influencing genotype abundance within a community. Our findings highlight the vital role genetic diversity plays within a population in facilitating plant phenotypic plasticity and the potential usefulness of environmental metabolomics to future ecological studies.

Heavy metals and metalloids concentrations across UK urban horticultural soils and the factors influencing their bioavailability to food crops.

Urban horticulture (UH) has been proposed as a solution to increase urban sustainability, but the potential risks to human health due to potentially elevated soil heavy metals and metalloids (HM) concentrations represent a major constraint for UH expansion. Here we provide the first UK-wide assessment of soil HM concentrations (total and bioavailable) in UH soils and the factors influencing their bioavailability to crops. Soils from 200 allotments across ten cities in the UK were collected and analysed for HM concentrations, black carbon (BC) and organic carbon (OC) concentrations, pH and texture. We found that although HM are widespread across UK UH soils, most concentrations fell below the respective UK soil screening values (C4SLs): 99 % Cr; 98 % As, Cd, Ni; 95 % Cu; 52 % Zn. However, 83 % of Pb concentrations exceeded C4SL, but only 3.5 % were above Pb national background concentration of 820 mg kg-1. The bioavailable HM concentrations represent a small fraction (0.01-1.8 %) of the total concentrations even for those soils that exceeded C4SLs. There was a significant positive relationship between both total and bioavailable HM and soil BC and OC concentrations. This suggest that while contributing to the accumulation of HM concentrations in UH soils, BC and OC may also provide a biding surface for the bioavailable HM concentrations contributing to their immobilisation. These findings have implications for both management of the risk to human health associated with UH growing in urban soils and with management of UH soil. There is a clear need to understand the mechanisms driving soil-to-crop HM transfer in UH to improve potentially restrictive C4SL (e.g. Pb) especially as public demand for UH land is growing. In addition, the UH community would benefit from education programs promoting soil management practices that reduce the risk of HM exposure - particularly in those plots where C4SLs were exceeded.

The nucleotidase/phosphatase SAL1 is a negative regulator of drought tolerance in Arabidopsis.

An Arabidopsis thaliana drought-tolerant mutant, altered expression of APX2 (alx8), has constitutively increased abscisic acid (ABA) content, increased expression of genes responsive to high light stress and is reported to be drought tolerant. We have identified alx8 as a mutation in SAL1, an enzyme that can dephosphorylate dinucleotide phosphates or inositol phosphates. Previously identified mutations in SAL1, including fiery (fry1-1), were reported as being more sensitive to drought imposed by detachment of rosettes. Here we demonstrate that alx8, fry1-1 and a T-DNA insertional knockout allele all have markedly increased resistance to drought when water is withheld from soil-grown intact plants. Microarray analysis revealed constitutively altered expression of more than 1800 genes in both alx8 and fry1-1. The up-regulated genes included some characterized stress response genes, but few are inducible by ABA. Metabolomic analysis revealed that both mutants exhibit a similar, dramatic reprogramming of metabolism, including increased levels of the polyamine putrescine implicated in stress tolerance, and the accumulation of a number of unknown, potential osmoprotectant carbohydrate derivatives. Under well-watered conditions, there was no substantial difference between alx8 and Col-0 in biomass at maturity; plant water use efficiency (WUE) as measured by carbon isotope discrimination; or stomatal index, morphology or aperture. Thus, SAL1 acts as a negative regulator of predominantly ABA-independent and also ABA-dependent stress response pathways, such that its inactivation results in altered osmoprotectants, higher leaf relative water content and maintenance of viable tissues during prolonged water stress.

Genome size as a predictor of guard cell length in Arabidopsis thaliana is independent of environmental conditions.

The recent discovery of a strong positive relationship between angiosperm genome size and stomatal guard cell length (GCL) opens the possibility of using plant fossil guard cell size as a proxy for changes in angiosperm genome size over periods of environmental change. The responses of GCL to environmental stimuli are currently unknown and may obscure this predictive relationship. Here, we investigated the effects of environmental variables (atmospheric CO2, drought, relative humidity, irradiance, ultraviolet radiation and pathogen attack) on GCL in the model plant Arabidopsis thaliana to quantify environmentally induced variation. GCL responded to all variables tested, but the changes incurred did not significantly impinge on the predictive capability of the relationship.

Metabolomic and physiological responses reveal multi-phasic acclimation of Arabidopsis thaliana to chronic UV radiation.

Biochemical changes in vivo and pathway interactions were investigated using integrated physiological and metabolic responses of Arabidopsis thaliana L. to ultraviolet (UV) radiation (280-400 nm) at 9.96 kJ m(-2) d(-1) over the entire life cycle from seed to seed (8 weeks). Columbia-0 (Col-0) and a UV-B sensitive accession (fah-1) showed significant (P < 0.001) reductions in leaf growth after 6 weeks. Col-0 recovered growth after 8 weeks, with recovery corresponding to a switch from production of phenylpropanoids to flavonoids. fah-1 failed to recover, indicating that sinapate production is an essential component of recovery. Epidermal features show that UV radiation caused significant (P < 0.001) increases in trichome density, which may act as a structural defence response. Stomatal indices showed a significant (P < 0.0001) reduction in Col-0 and a significant (P < 0.001) increase in fah-1. Epidermal cell density was significantly increased under UV radiation on the abaxial leaf surface, suggesting that that a fully functioning phenylpropanoid pathway is a requirement for cell expansion and leaf development. Despite wild-type acclimation, the costs of adaptation lead to reduced plant fitness by decreasing flower numbers and total seed biomass. A multi-phasic acclimation to UV radiation and the induction of specific metabolites link stress-induced biochemical responses to enhanced acclimation.

Long-distance CO(2) signalling in plants.

Stomatal numbers are tightly controlled by environmental signals including light intensity and atmospheric CO(2) partial pressure. This requires control of epidermal cell development during the early phase of leaf growth and involves changes in both the density of cells on the leaf surface and the proportion of cells that adopt a stomatal fate. This paper reviews the current understanding of how stomata develop and describes recent advances that have given insights into the regulatory mechanisms involved using mutant Arabidopsis plants that implicates a role for long-chain fatty acids in cell-to-cell communication. Evidence is presented which indicates that long-distance signalling from mature to newly developing leaves forms part of the mechanism by which stomatal development responds to environmental cues. Analysis of mutant plants suggests that the plant hormones abscisic acid, ethylene and jasmonates are implicated in the long-distance signalling pathway and that the action may be mediated by reactive oxygen species.