Identification of genetics and hormonal factors involved in Quercus robur root growth regulation in different cultivation system

Understanding the molecular processes and hormonal signals that govern root growth is of paramount importance for effective forest management. While Arabidopsis studies have shed light on the role of the primary root in root system development, the structure of root systems in trees is considerably more intricate, posing challenges to comprehend taproot growth in acorn-sown and nursery-cultivated seedlings. In this study, we investigated Quercus robur seedlings using rhizotrons, containers, and transplanted containers to rhizotrons, aiming to unravel the impact of forest nursery practices on processes governing taproot growth and root system development. Root samples were subjected to RNA-seq analysis to identify gene expression patterns and perform differential gene expression and phytohormone analysis. Among studied cultivation systems, differentially expressed genes (DEGs) exhibited significant diversity, where the number of co-occurring DEGs among cultivation systems was significantly smaller than the number of unique DEGs in different cultivation systems. Moreover, the results imply that container cultivation triggers the activation of several genes associated with linolenic acid and peptide synthesis in root growth. Upon transplantation from containers to rhizotrons, rapid enhancement in gene expression occurs, followed by gradual reduction as root growth progresses, ultimately reaching a similar expression pattern as observed in the taproot of rhizotron-cultivated seedlings. Phytohormone analysis revealed that taproot growth patterns under different cultivation systems are regulated by the interplay between auxin and cytokinin concentrations. Moreover, the diversification of hormone levels within the root zone and cultivation systems allows for taproot growth inhibition and prompt recovery in transplanted seedlings. Our study highlights the crucial role of hormone interactions during the early stages of taproot elongation, influencing root system formation across.

Molecular identification and functional characterization of an environmental stress responsive glutaredoxin gene ROXY1 in Quercus glauca

Quercus glauca is a valuable natural resource with both economic and ecological values. It is one of the dominant forest tree species widely distributed in Southern China. As a perennial broadleaf plant, Q. glauca inevitably encounters numerous stresses from environment. Glutaredoxins (GRXs) are a kind of small oxidoreductases that play an important role in response to oxidative stress. CC-type GRXs also known as ROXYs are specific to land plants. In this study, we isolated a CC-type GRX gene, QgROXY1, from Q. glauca. Expression of QgROXY1 is induced by a variety of environmental stimuli. QgROXY1 protein localizes to both cytoplasm and nucleus; whereas the nucleus localized QgROXY1 could physically interact with the basic region/leucine zipper motif (bZIP) transcription factor AtTGA2 from Arabidopsis thaliana. Transgenic A. thaliana ectopically expressing QgROXY1 is hypersensitive to exogenously applied salicylic acid. Induction of plant defense gene is significantly impaired in QgROXY1 transgenic plants that results in enhanced susceptibility to infection of Botrytis cinerea pathogen, indicating the evolutionary conserved function among ROXY homologs in weedy and woody plants. This is the first described function for the ROXYs in tree plants. Through this case study, we demonstrated the feasibility and efficacy of molecular technology applied to characterization of gene function in tree species.

Long-term rain exclusion in a Mediterranean forest: response of physiological and physico-chemical traits of Quercus pubescens across seasons

With climate change, an aggravation in summer drought is expected in the Mediterranean region. To assess the impact of such a future scenario, we compared the response of Quercus pubescens, a drought-resistant deciduous oak species, to long-term amplified drought (AD) (partial rain exclusion in natura for 10 years) and natural drought (ND). We studied leaf physiological and physico-chemical trait responses to ND and AD over the seasonal cycle, with a focus on chemical traits including major groups of central (photosynthetic pigments and plastoquinones) and specialized (tocochromanols, phenolic compounds, and cuticular waxes) metabolites. Seasonality was the main driver of all leaf traits, including cuticular triterpenoids, which were highly concentrated in summer, suggesting their importance to cope with drought and thermal stress periods. Under AD, trees not only reduced CO2 assimilation (-42%) in summer and leaf concentrations of some phenolic compounds and photosynthetic pigments (carotenoids from the xanthophyll cycle) but also enhanced the levels of other photosynthetic pigments (chlorophylls, lutein, and neoxanthin) and plastochromanol-8, an antioxidant located in chloroplasts. Overall, the metabolomic adjustments across seasons and drought conditions reinforce the idea that Q. pubescens is highly resistant to drought although significant losses of antioxidant defenses and photoprotection were identified under AD.

Identification of Functional Brassinosteroid Receptor Genes in Oaks and Functional Analysis of QmBRI1

Brassinosteroids (BRs) play important regulatory roles in plant growth and development, with functional BR receptors being crucial for BR recognition or signaling. Although functional BR receptors have been extensively studied in herbaceous plants, they remain largely under-studied in forest tree species. In this study, nine BR receptors were identified in three representative oak species, of which BRI1s and BRL1s were functional BR receptors. Dispersed duplications were a driving force for oak BR receptor expansion, among which the Brassinosteroid-Insensitive-1 (BRI1)-type genes diverged evolutionarily from most rosids. In oak BRI1s, we identified that methionine in the conserved Asn-Gly-Ser-Met (NGSM) motif was replaced by isoleucine and that the amino acid mutation occurred after the divergence of Quercus and Fagus. Compared with QmBRL1, QmBRI1 was relatively highly expressed during BR-induced xylem differentiation and in young leaves, shoots, and the phloem and xylem of young stems of Quercus mongolica. Based on Arabidopsis complementation experiments, we proved the important role of QmBRI1 in oak growth and development, especially in vascular patterning and xylem differentiation. These findings serve as an important supplement to the findings of the structural, functional and evolutionary studies on functional BR receptors in woody plants and provide the first example of natural mutation occurring in the conserved BR-binding region (NGSM motif) of angiosperm BRI1s.

Silver nanoparticles synthesized from Quercus brantii ameliorated ethanol-induced gastric ulcers in rats by decreasing oxidative stress and improving antioxidant systems

Gastric ulcers are caused by an imbalance between aggressive and defensive factors. The green synthesis of silver nanoparticles is becoming a new and promising method in the treatment of gastrointestinal ulcers. This study was conducted to investigate the protective and antioxidant effects of silver nanoparticles synthesized from Quercus brantii extract (NSQBE) on gastric damage induced by alcohol in rats. In this study, silver nanoparticles were produced by the green synthesis method using oak extract. The structure and morphology of nanoparticles were confirmed by various techniques such as UV-Vis spectroscopy, fourier transforms infrared spectrometer (FTIR), scanning electron microscope (SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD), energy-dispersive X-ray analysis (EDX), and dynamic light scattering )DLS(. For the animal studies, 30 male Wistar rats weighing 200 ± 20 g were randomly selected and divided into five groups (the normal, ethanolic, NSQBE treatment (received doses of 20 and 5 mg/kg), and standard (received a dose of 50 mg/kg of ranitidine) groups. After the rats were euthanized, their stomach was removed. A part of the stomach tissue of rats was used for histopathological studies, and the other part was used to study biochemical parameters such as the level of reactive oxygen species (ROS), protein carbonyl oxidation (PCO), malondialdehyde (MDA), catalase (CAT), superoxide dismutase (SOD) and reduced glutathione (GSH) as well as nitric oxide (NO). Our results showed that in the ethanol group, the levels of ROS, MDA, PCO, and serum NO were higher than in the normal group. In addition, reduced GSH, CAT, SOD, tissue NO, gastric mucus, and antioxidant potential were decreased. In rats pretreated with NSQBE and ranitidine, the levels of ROS, MDA, PCO, and serum NO decreased, and the levels of GSH, CAT, SOD, tissue NO, gastric mucus, and antioxidant potential were increased in comparison to the ethanol group. The results of this study showed that silver nanoparticles synthesized using Quercus brantii are a promising approach for the treatment of gastric ulcers.

The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber

Over the last decade, genome-scale metabolic models have been increasingly used to study plant metabolic behaviour at the tissue and multi-tissue level under different environmental conditions. Quercus suber, also known as the cork oak tree, is one of the most important forest communities of the Mediterranean/Iberian region. In this work, we present the genome-scale metabolic model of the Q. suber (iEC7871). The metabolic model comprises 7871 genes, 6231 reactions, and 6481 metabolites across eight compartments. Transcriptomics data was integrated into the model to obtain tissue-specific models for the leaf, inner bark, and phellogen, with specific biomass compositions. The tissue-specific models were merged into a diel multi-tissue metabolic model to predict interactions among the three tissues at the light and dark phases. The metabolic models were also used to analyse the pathways associated with the synthesis of suberin monomers, namely the acyl-lipids, phenylpropanoids, isoprenoids, and flavonoids production. The models developed in this work provide a systematic overview of the metabolism of Q. suber, including its secondary metabolism pathways and cork formation.

The Selective Cytotoxicity of Quercus Brantii Lindl. Galls on A375 and SK-MEL-3 Human Malignant Melanoma Cell Lines

This study aimed to find out the mechanism of cytotoxic effects of galls of Quercus Brantii on A375 and SK-MEL-3 melanoma and AGO-1522 normal human fibroblast cell lines for the first time. Therefore, cell viability and cytotoxic activities were evaluated. Furthermore, ROS formation, lipid peroxidation, and release of cytochrome-c were also assessed. The results revealed that the extract of these galls at a concentration of 0.05 mg/ml significantly (P<0.001) increased cytotoxicity, ROS formation, TBARS formation, and cytochrome-c release in A375 and SK-MEL-3 melanoma cell lines compared to AGO-1522 normal human fibroblast. These results demonstrated that these galls can be considered a promising candidate which acts in synergy with anticancer agents used in the clinical treatment of human malignant melanoma.

Chromosome-scale genome assembly and insights into the metabolome and gene regulation of leaf color transition in an important oak species, Quercus dentata

Quercus dentata Thunb., a dominant forest tree species in northern China, has significant ecological and ornamental value due to its adaptability and beautiful autumn coloration, with color changes from green to yellow into red resulting from the autumnal shifts in leaf pigmentation. However, the key genes and molecular regulatory mechanisms for leaf color transition remain to be investigated. First, we presented a high-quality chromosome-scale assembly for Q. dentata. This 893.54 Mb sized genome (contig N50 = 4.21 Mb, scaffold N50 = 75.55 Mb; 2n = 24) harbors 31 584 protein-coding genes. Second, our metabolome analyses uncovered pelargonidin-3-O-glucoside, cyanidin-3-O-arabinoside, and cyanidin-3-O-glucoside as the main pigments involved in leaf color transition. Third, gene co-expression further identified the MYB-bHLH-WD40 (MBW) transcription activation complex as central to anthocyanin biosynthesis regulation. Notably, transcription factor (TF) QdNAC (QD08G038820) was highly co-expressed with this MBW complex and may regulate anthocyanin accumulation and chlorophyll degradation during leaf senescence through direct interaction with another TF, QdMYB (QD01G020890), as revealed by our further protein-protein and DNA-protein interaction assays. Our high-quality genome assembly, metabolome, and transcriptome resources further enrich Quercus genomics and will facilitate upcoming exploration of ornamental values and environmental adaptability in this important genus.

Protein Tyrosine Phosphatases: Mighty oaks from little acorns grow

In October 2020, we were finally able to gather for a celebration of Eddy Fischer's 100th birthday. As with many other events, COVID had disrupted and restricted preparations for the gathering, which ultimately was held via ZOOM. Nevertheless, it was a wonderful opportunity to share a day with Eddy, an exceptional scientist and true renaissance man, and to appreciate his stellar contributions to science. Eddy Fischer, together with Ed Krebs, was responsible for the discovery of reversible protein phosphorylation, which launched the entire field of signal transduction. The importance of this seminal work is now being felt throughout the biotechnology industry with the development of drugs that target protein kinases, which have transformed the treatment of a wide array of cancers. I was privileged to have worked with Eddy both as a postdoc and a junior faculty member, during which time we laid the foundations for our current understanding of the protein tyrosine phosphatase (PTP) family of enzymes and their importance as critical regulators of signal transduction. This tribute to Eddy is based upon the talk I presented at the event, giving a personal perspective on Eddy's influence on my career, our early research efforts together in this area, and how the field has developed since then.

Genome-wide identification, phylogeny, and gene duplication of the epigenetic regulators in Fagaceae

Epigenetic regulators are proteins involved in controlling gene expression. Information about the epigenetic regulators within the Fagaceae, a relevant family of trees and shrubs of the northern hemisphere ecosystems, is scarce. With the intent to characterize these proteins in Fagaceae, we searched for orthologs of DNA methyltransferases (DNMTs) and demethylases (DDMEs) and Histone modifiers involved in acetylation (HATs), deacetylation (HDACs), methylation (HMTs), and demethylation (HDMTs) in Fagus, Quercus, and Castanea genera. Blast searches were performed in the available genomes, and freely available RNA-seq data were used to de novo assemble transcriptomes. We identified homologs of seven DNMTs, three DDMEs, six HATs, 11 HDACs, 32 HMTs, and 21 HDMTs proteins. Protein analysis showed that most of them have the putative characteristic domains found in these protein families, which suggests their conserved function. Additionally, to elucidate the evolutionary history of these genes within Fagaceae, paralogs were identified, and phylogenetic analyses were performed with DNA and histone modifiers. We detected duplication events in all species analyzed with higher frequency in Quercus and Castanea and discuss the evidence of transposable elements adjacent to paralogs and their involvement in gene duplication. The knowledge gathered from this work is a steppingstone to upcoming studies concerning epigenetic regulation in this economically important family of Fagaceae.

Ectomycorrhizal fungi enhance the tolerance of phytotoxicity and cadmium accumulation in oak (Quercus acutissima Carruth.) seedlings: modulation of growth properties and the antioxidant defense responses

Ectomycorrhizal fungi (EMF), which form symbiotic ectomycorrhiza with tree roots, mediate heavy metal tolerance of host plants. To investigate the roles of EMF in the growth, modulation of oxidative stress, and cadmium (Cd) accumulation and translocation in Quercus acutissima seedlings, ectomycorrhizal seedlings inoculated with Suillus luteus were treated with different Cd concentrations (0.1, and 5 mg kg^-1) for 14 days. EMF accelerated seedling growth and Cd accumulation in roots under the highest Cd concentration of 5 mg kg^-1. Catalase (CAT), ascorbate peroxidase (APX), and glutathione reductase (GR) activities increased in the leaves of ectomycorrhizal seedlings under the highest Cd concentration. Superoxide dismutase (SOD) trended to increase under both Cd concentrations. Although reduced glutathione (GSH) increased after inoculation of EMF under both Cd concentrations, the release of malondialdehyde increased in the leaves and roots under the highest Cd concentration, indicating that the defense role of EMF in Q. acutissima depends on the Cd concentration. These results indicate that EMF mitigate Cd stress by promoting plant growth and nutrient uptake while modulating the antioxidant system to reduce oxidative stress.

Efflux and assimilation of xylem-transported CO2 in stems and leaves of tree species with different wood anatomy

Determining the fate of CO₂ respired in woody tissues is necessary to understand plant respiratory physiology and to evaluate CO₂ recycling mechanisms. An aqueous ¹³ C-enriched CO₂ solution was infused into the stem of 3-4 m tall trees to estimate efflux and assimilation of xylem-transported CO₂ via cavity ring-down laser spectroscopy and isotope ratio mass spectrometry, respectively. Different tree locations (lower stem, upper stem and leafy shoots) and tissues (xylem, bark and leaves) were monitored in species with tracheid, diffuse- and ring-porous wood anatomy (cedar, maple and oak, respectively). Radial xylem CO₂ diffusivity and xylem [CO₂ ] were lower in cedar relative to maple and oak trees, thereby limiting label diffusion. Part of the labeled ¹³ CO₂ was assimilated in cedar (8.7%) and oak (20.6%) trees, mostly in xylem and bark tissues of the stem, while limited solution uptake in maple trees hindered the detection of label assimilation. Little label reached foliar tissues, suggesting substantial label loss along the stem-branch transition following reductions in the radial diffusive pathway. Differences in respiration rates and radial xylem CO₂ diffusivity (lower in conifer relative to angiosperm species) might reconcile discrepancies in efflux and assimilation of xylem-transported CO₂ so far observed between taxonomic clades.

The rainbow protocol: A sequential method for quantifying pigments, sugars, free amino acids, phenolics, flavonoids and MDA from a small amount of sample

The elucidation of plant health status requires quantifying multiple molecular metabolism markers. Until now, the extraction of these biomarkers is performed independently, with different extractions and protocols. This approach is inefficient, since it increases laboratory time, amount of sample, and could introduce biases or difficulties when comparing data. To limit these drawbacks, we introduce a versatile protocol for quantifying seven of the most commonly analysed biomarkers (photosynthetic pigments, free amino acids, soluble sugars, starch, phenolic compounds, flavonoids and malondialdehyde) covering substantial parts of plant metabolism, requiring only a minimum sample amount and common laboratory instrumentation. The procedures of this protocol rely on classic methods that have been updated to allow their sequential use, increasing reproducibility, sensibility and easiness to obtain quantitative results. Our method has been tested and validated over an extended diversity of organisms (Arabidopsis thaliana, Solanum lycopersicum, Olea europaea, Quercus ilex, Pinus pinaster and Chlamydomonas reinhardtii), tissues (leaves, roots and seeds) and stresses (cold, drought, heat, ultraviolet B and nutrient deficiency). Its application will allow increasing the number of parameters that can be monitored at once while decreasing sample handling and consequently, increasing the capacity of the laboratory.

Spectral effect of streetlamps on urban trees: A simulated study on tissue water, nitrogen, and carbohydrate contents in maple and oak

Streetlamps enforce night lighting on urban forest trees, but scarce information is available concerning the ecophysiological performance of street trees under these conditions. In this study, maple (Acer truncatum Bunge) and oak (Quercus mongolica Fisch. ex Ledeb.) seedlings were cultured with simulated exposure to streetlamp spectra in white (red/green/blue, 7.7:1.0:2.2) and red plus blue (RB; red/green/blue, 4.6:0.0:1.0) lights with photosynthetic photon flux rate of 80 μmol m^-2 s^-1 in a 18-h photoperiod. Nitrogen (N) was loaded through 15 weekly applications to an amount of 80 mg N plant^-1 to mimic the mineral N deposition to landscape trees. Variables of biomass, carbohydrate accumulation, N and water contents were rarely found difference between the two LED-spectra treatments for both species. Compared to the un-lighted control, the RB spectrum lowered N concentration in oak seedlings and water content in maple seedlings. The white light spectrum resulted in an increase of starch concentration. Carbohydrate concentration had a positive relationship with biomass and N content across two species but a negative relationship with water content in maple seedlings. Overall, streetlamp-lights imposed effects on tree growth by a prolonged photoperiod instead of specific spectrum. Maple had a strong response of water uptake to streetlamp lighting at the cost of carbohydrate consumption, but oak had scarce demand of water-use for growth.

Evolutionary relationships between drought-related traits and climate shape large hydraulic safety margins in western North American oaks

Quantitative knowledge of xylem physical tolerance limits to dehydration is essential to understanding plant drought tolerance but is lacking in many long-vessel angiosperms. We examine the hypothesis that a fundamental association between sustained xylem water transport and downstream tissue function should select for xylem that avoids embolism in long-vessel trees by quantifying xylem capacity to withstand air entry of western North American oaks (Quercus spp.). Optical visualization showed that 50% of embolism occurs at water potentials below -2.7 MPa in all 19 species, and -6.6 MPa in the most resistant species. By mapping the evolution of xylem vulnerability to embolism onto a fossil-dated phylogeny of the western North American oaks, we found large differences between clades (sections) while closely related species within each clade vary little in their capacity to withstand air entry. Phylogenetic conservatism in xylem physical tolerance, together with a significant correlation between species distributions along rainfall gradients and their dehydration tolerance, suggests that closely related species occupy similar climatic niches and that species' geographic ranges may have shifted along aridity gradients in accordance with their physical tolerance. Such trends, coupled with evolutionary associations between capacity to withstand xylem embolism and other hydraulic-related traits, yield wide margins of safety against embolism in oaks from diverse habitats. Evolved responses of the vascular system to aridity support the embolism avoidance hypothesis and reveal the importance of quantifying plant capacity to withstand xylem embolism for understanding function and biogeography of some of the Northern Hemisphere's most ecologically and economically important plants.

Mass spectrometry-based forest tree metabolomics

Research in forest tree species has advanced slowly when compared with other agricultural crops and model organisms, mainly due to the long-life cycles, large genome sizes, and lack of genomic tools. Additionally, trees are complex matrices, and the presence of interferents (e.g., oleoresins and cellulose) challenges the analysis of tree tissues with mass spectrometry (MS)-based analytical platforms. In this review, advances in MS-based forest tree metabolomics are discussed. Given their economic and ecological significance, particular focus is given to Pinus, Quercus, and Eucalyptus forest tree species to better understand their metabolite responses to abiotic and biotic stresses in the current climate change scenario. Furthermore, MS-based metabolomics technologies produce large and complex datasets that require expertize to adequately manage, process, analyze, and store the data in dedicated repositories. To ensure that the full potential of forest tree metabolomics data are translated into new knowledge, these data should comply with the FAIR principles (i.e., Findable, Accessible, Interoperable, and Re-usable). It is essential that adequate standards are implemented to annotate metadata from forest tree metabolomics studies as is already required by many science and governmental agencies and some major scientific publishers. © 2019 John Wiley & Sons Ltd. Mass Spec Rev 40:126-157, 2021.

Coupled plant traits adapted to wetting/drying cycles of substrates co-define niche multidimensionality

Theories attempting to explain species coexistence in plant communities have argued in favour of species' capacities to occupy a multidimensional niche with spatial, temporal and biotic axes. We used the concept of hydrological niche segregation to learn how ecological niches are structured both spatially and temporally and whether small scale humidity gradients between adjacent niches are the main factor explaining water partitioning among tree species in a highly water-limited semiarid forest ecosystem. By combining geophysical methods, isotopic ecology, plant ecophysiology and anatomical measurements, we show how coexisting pine and oak species share, use and temporally switch between diverse spatially distinct niches by employing a set of functionally coupled plant traits in response to changing environmental signals. We identified four geospatial niches that turned into nine, when considering the temporal dynamics of the wetting/drying cycles in the substrate and the particular plant species adaptations to garner, transfer, store and use water. Under water scarcity, pine and oak exhibited water use segregation from different niches, yet under maximum drought when oak trees crossed physiological thresholds, niche overlap occurred. The identification of niches and mechanistic understanding of when and how species use them will help unify theories of plant coexistence and competition.

Roles of metabolic regulation in developing Quercus variabilis acorns at contrasting geologically-derived phosphorus sites in subtropical China

BACKGROUND

Phosphorus (P) -rich soils develop in phosphorite residing areas while P-deficient soils are ubiquitous in subtropical regions. Little has been reported that how metabolites participate in the seed development and the processes involved in their coping with contrasting-nutrient environments.

RESULTS

Here we quantified the metabolites of Quercus variabilis acorns in the early (July), middle (August), late (September) development stages, and determined element (C, H, O, N, P, K, Ca, Mg, S, Fe, Al, Mn, Na, Zn, and Cu) concentrations of acorns in the late stage, at geologically-derived contrasting-P sites in subtropical China. The primary metabolic pathways included sugar metabolism, the TCA cycle, and amino acid metabolism. Most metabolites (especially C- and N-containing metabolites) increased and then decreased from July to September. Acorns between the two sites were significantly discriminated at the three stages, respectively, by metabolites (predominantly sugars and organic acids). Concentrations of P, orthophosphoric acid and most sugars were higher; erythrose was lower in late-stage acorns at P-rich sites than those at P-deficient sites. No significant differences existed in the size and dry mass of individual acorns between oak populations at the two sites.

CONCLUSIONS

Oak acorns at the two sites formed distinct metabolic phenotypes related to their distinct geologically-derived soil conditions, and the late-stage acorns tended to increase P-use-efficiency in the material synthesis process at P-deficient sites, relative to those at P-rich sites.

Leaf Carbon Export and Nonstructural Carbohydrates in Relation to Diurnal Water Dynamics in Mature Oak Trees

Trees typically experience large diurnal depressions in water potential, which may impede carbon export from leaves during the day because the xylem is the source of water for the phloem. As water potential becomes more negative, higher phloem osmotic concentrations are needed to draw water in from the xylem. Generating this high concentration of sugar in the phloem is particularly an issue for the ∼50% of trees that exhibit passive loading. These ideas motivate the hypothesis that carbon export in woody plants occurs predominantly at night, with sugars that accumulate during the day assisting in mesophyll turgor maintenance or being converted to starch. To test this, diurnal and seasonal patterns of leaf nonstructural carbohydrates, photosynthesis, solute, and water potential were measured, and carbon export was estimated in leaves of five mature (>20 m tall) red oak (Quercus rubra) trees, a species characterized as a passive loader. Export occurred throughout the day at equal or higher rates than at night despite a decrease in water potential to -1.8 MPa at midday. Suc and starch accumulated over the course of the day, with Suc contributing ∼50% of the 0.4 MPa diurnal osmotic adjustment. As a result of this diurnal osmotic adjustment, estimates of midday turgor were always >0.7 MPa. These findings illustrate the robustness of phloem functioning despite diurnal fluctuations in leaf water potential and the role of nonstructural carbohydrates in leaf turgor maintenance.

Epiphyte associations and canopy soil volume: nutrient capital and factors influencing soil retention in the canopy

Canopy soil (CS) volume reflect epiphyte community maturity, but little is known about the factors that retain CS or species succession within it. Humus fern species (e.g. Phlebodium areolatum) appear capable of retaining CS. In ten Quercus spp. we sampled 987 epiphyte mats to examine the role of the common epiphyte species and crown traits determining CS volume, in order to infer successional stages and identify pioneer and late successional species. Branch traits (height, diameter and slope), CS volume and cover of the epiphyte species were determined for each mat. Nutrient content was determined in CS random samples of 12 epiphyte associations and sizes (one sample from each size quintile). A total of 60% of the mats lack CS. Cover of P. areolatum was the main variable explaining CS volume, and this species was present in 46.8% of those with CS. Epiphyte composition was highly variable, but pioneer (species appearing in monospecific mats, without CS) and late successional species could be identified. Canopy soil nutrient content was similar among the associations of epiphytes. Magnesium, Ca and pH decreased with CS volume, while P and N increased. Phlebodium areolatum is associated with high CS volumes and could act as a key species in its retention. Monospecific mats of pioneer species lack CS or have low volumes, while CS is much higher in mats with late successional species, but the mechanisms of CS formation and nutrient retention in response to interactions between epiphyte species remain to be tested.

Two coastal Pacific evergreens, Arbutus menziesii, Pursh. and Quercus agrifolia, Née show little water stress during California's exceptional drought

California's coastal climate is characterized by rainy winters followed by a dry summer season that is supplemented by frequent fog. While rising temperatures and drought caused massive tree mortality in central California during the 2011–2015 extreme drought, dying trees were less common in the central coast region. We hypothesized that cooler, maritime-ameliorated temperatures reduced the effects of drought stress on coastal vegetation. To test this, weekly measurements of water potential and stomatal conductance were made on two coast evergreen tree species, Arbutus menziesii and Quercus agrifolia, throughout the summer 2014 dry season. Water potential remained generally constant during this period but stomatal conductance declined in both species as the dry season progressed. Species' resistance to embolism was determined using the centrifuge method, and showed Q. agrifolia to be more vulnerable to embolism than A. menziesii. The stem vulnerability curves were consistent with species' seasonal water relations as well as their anatomy; the ring-porous Q. agrifolia had substantially larger conduits than the diffuse-porous A. menziesii. Leaf turgor loss points differed significantly as did other pressure-volume parameters but these data were consistent with the trees' seasonal water relations. Overall, the two species appear to employ differing water use strategies; A. menziesii is more profligate in its water use, while Q. agrifolia is more conservative, with a narrower safety margin against drought-induced loss of xylem transport capacity. Despite the extended drought, these species exhibited neither branch die-back nor any obvious symptoms of pronounced water-stress during the study period, implying that the maritime climate of California's central coast may buffer the local vegetation against the severe effects of prolonged drought.

Acorn Isotopic Composition: A New Promising Tool for Authenticity Maps of Montado's High-Value Food Products

It is often overlooked that even food production is linked to the ecology of plants and animals. Living organisms respond to environmental short-and long-term variability: acknowledging this may help in the ultimate goal of valorizing a territory/product. We investigated acorns of the two main Quercus species of the Portuguese Montado, a main feed of the renown black Iberian pig. We tested their responses to an aridity gradient by morphological parameters and isotopic signature. Q. rotundifolia and Q. suber acorns did not differ morphologically, even if a higher variability in all parameters was observed in acorns of Q. suber. According to the site-specific Aridity Index, correlations are indicative to higher weight and length only in Q. suber acorns from more arid sites. As for isotopic composition, there were no differences in nitrogen or carbon (δ15N and δ13C) between the two species. However, combining the samples and testing for association with the Aridity Index, we found that more arid sites lead to a 15N enrichment. This result, combined with the positive correlation between AI and acorns length, support the use of acorns as a tool, their isoscapes of nitrogen being a stepping stone for the provenance of the black Iberian pig.

Insights of carbon assimilation and allocation in young cork oak (Quercus suber L.) plants using Carbon-14

¹⁴ C methods were applied to young, woody, branched and well-watered cork oak (Quercus suber L.) plants to determine carbon assimilation and its distribution among plant organs. Carbon assimilation rates by attached leaves clamped in a foliar ¹⁴ CO₂ assimilation chamber containing 3.7 × 10⁴  Bq of a portable ventilated diffusion porometer were measured at different ¹⁴ CO₂ pulse-labeling periods (15, 30, 45, 60 and 120 s) in summer. Allocation of recently fixed C by attached leaves within plants was evaluated 7 days after a 60-min of 5.6 MBq of ¹⁴ CO₂ pulse-labeling in late winter. ¹⁴ CO₂ pulse-labeling was separately induced on leaves of a lower branch, two opposite branches at the same lower level, a middle branch and a top branch. ¹⁴ C activity incorporated into the plants was measured by liquid scintillation and autoradiography. Our results show the optimum ¹⁴ CO₂ pulse-labeling period is between 15 and 30 s, which corresponds to 9.81 ± 0.15 and 9.16 ± 0.12 µmol m^-2 s^-1 C assimilation rates in summer, respectively. The investment of current assimilates ranged from 18 to 29% in leaves, 1 to 7% in lateral branches, 0 to 3% in the stem and over 65% in roots, in late winter. Roots displayed the greatest sink strength for the total ¹⁴ C recovered by whole-plants. These results were expected because the trial was done in winter, when cork oak does not produce their leaves. Our results highlight the contribution of current assimilates for growth and maintenance of roots, in young woody plants under Mediterranean climate.

Transcriptome profiles of Quercus rubra responding to increased O3 stress

BACKGROUND

Climate plays an essential role in forest health, and climate change may increase forest productivity losses due to abiotic and biotic stress. Increased temperature leads to the increased formation of ozone (O3). Ozone is formed by the interaction of sunlight, molecular oxygen and by the reactions of chemicals commonly found in industrial and automobile emissions such as nitrogen oxides and volatile organic compounds. Although it is well known that productivity of Northern red oak (Quercus rubra) (NRO), an ecologically and economically important species in the forests of eastern North America, is reduced by exposure to O3, limited information is available on its responses to exogenous stimuli at the level of gene expression.

RESULTS

RNA sequencing yielded more than 323 million high-quality raw sequence reads. De novo assembly generated 52,662 unigenes, of which more than 42,000 sequences could be annotated through homology-based searches. A total of 4140 differential expressed genes (DEGs) were detected in response to O3 stress, as compared to their respective controls. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of the O3-response DEGs revealed perturbation of several biological pathways including energy, lipid, amino acid, carbohydrate and terpenoid metabolism as well as plant-pathogen interaction.

CONCLUSION

This study provides the first reference transcriptome for NRO and initial insights into the genomic responses of NRO to O3. Gene expression profiling reveals altered primary and secondary metabolism of NRO seedlings, including known defense responses such as terpenoid biosynthesis.

Changes in oak (Quercus robur) photosynthesis after winter moth (Operophtera brumata) herbivory are not explained by changes in chemical or structural leaf traits

Insect herbivores have the potential to change both physical and chemical traits of their host plant. Although the impacts of herbivores on their hosts have been widely studied, experiments assessing changes in multiple leaf traits or functions simultaneously are still rare. We experimentally tested whether herbivory by winter moth (Operophtera brumata) caterpillars and mechanical leaf wounding changed leaf mass per area, leaf area, leaf carbon and nitrogen content, and the concentrations of 27 polyphenol compounds on oak (Quercus robur) leaves. To investigate how potential changes in the studied traits affect leaf functioning, we related the traits to the rates of leaf photosynthesis and respiration. Overall, we did not detect any clear effects of herbivory or mechanical leaf damage on the chemical or physical leaf traits, despite clear effect of herbivory on photosynthesis. Rather, the trait variation was primarily driven by variation between individual trees. Only leaf nitrogen content and a subset of the studied polyphenol compounds correlated with photosynthesis and leaf respiration. Our results suggest that in our study system, abiotic conditions related to the growth location, variation between tree individuals, and seasonal trends in plant physiology are more important than herbivory in determining the distribution and composition of leaf chemical and structural traits.

A Pipeline for Metabolic Pathway Reconstruction in Plant Orphan Species

In the era of high-throughput biology, it is necessary to develop a simple pipeline for metabolic pathway reconstruction in plant orphan species. However, obtaining a global picture of the plant metabolism may be challenging, especially in nonmodel species. Moreover, the use of bioinformatics tools and statistical analyses is required. This chapter describes how to use different software and online tools for the reconstruction of metabolic pathways of plant species using existing pathway knowledge. In particular, Quercus ilex omics data is employed to develop the present pipeline.

Effects of soil rewatering on mesophyll and stomatal conductance and the associated mechanisms involving leaf anatomy and some physiological activities in Manchurian ash and Mongolian oak in the Changbai Mountains

The recoveries of mesophyll (g_m) and stomatal conductance to CO₂ (g_sc) after soil rewatering have received considerable attention in recent years, but the recovery mechanisms involving leaf anatomy and physiological activities are poorly understood. Moreover, it is also unclear whether leaf gas-phase conductance (g_ias) or liquid-phase conductance (g_liq) is the main factor promoting g_m recovery. By simultaneously using gas exchange and chlorophyll fluorescence, we measured the recoveries of g_m and g_sc in saplings of Manchurian ash (Fraxinus mandshurica Rupr.) and Mongolian oak (Quercus mongolica Fish. ex Ledeb) exposed to two initial water stress (medium water stress, MW, and severe water stress, SW) and following rewatering. Furthermore, leaf anatomical characteristics and the activities of aquaporin (AQP) and carbonic anhydrase (CA) were measured to explain the mechanisms of g_m and g_sc recoveries. The results showed that (i) both g_m and g_sc were partly recovered after rewatering, and the recoveries decreased with initial water stress in both species. (ii) The g_m recovery was much greater in Mongolian oak than in Manchurian ash, while the g_sc recovery was much greater in Manchurian ash. Consequently, the photosynthesis recovery in Manchurian ash was mostly affected by g_sc recovery, while that in Mongolian oak was mostly affected by g_m recovery. (iii) The g_m recovery mainly resulted from the great increase in leaf g_liq after rewatering rather than that in g_ias, as g_ias had a negative effect on g_m recovery. The stomatal opening status improved after rewatering, as the stomatal pore size (SS) increased, greatly promoting g_sc recovery. In addition, the activities of both AQP and CA increased after rewatering, which improved CO₂ transmembrane transports and greatly promoted g_m and g_sc recoveries.

Two-Source δ18O Method to Validate the CO18O-Photosynthetic Discrimination Model: Implications for Mesophyll Conductance

Theoretical models of photosynthetic isotopic discrimination of CO2 (13C and 18O) are commonly used to estimate mesophyll conductance (g m). This requires making simplifying assumptions and assigning parameter values so that g m can be solved for as the residual term. Uncertainties in g m estimation occur due to measurement noise and assumptions not holding, including parameter uncertainty and model parametrization. Uncertainties in the 13C model have been explored previously, but there has been little testing undertaken to determine the reliability of g m estimates from the 18O model (g m18). In this study, we exploited the action of carbonic anhydrase in equilibrating CO2 with leaf water and manipulated the observed photosynthetic discrimination (Δ18O) by changing the oxygen isotopic composition of the source gas CO2 and water vapor. We developed a two-source δ18O method, whereby two measurements of Δ18O were obtained for a leaf with its gas-exchange characteristics otherwise unchanged. Measurements were performed in broad bean (Vicia faba) and Algerian oak (Quercus canariensis) in response to light and vapor pressure deficit. Despite manipulating the Δ18O by over 100‰, in most cases we observed consistency in the calculated g m18, providing confidence in the measurements and model theory. Where there were differences in g m18 estimates between source-gas measurements, we explored uncertainty associated with two model assumptions (the isotopic composition of water at the sites of CO2-water exchange, and the humidity of the leaf internal airspace) and found evidence for both. Finally, we provide experimental guidelines to minimize the sensitivity of g m18 estimates to measurement errors. The two-source δ18O method offers a flexible tool for model parameterization and provides an opportunity to refine our understanding of leaf water and CO2 fluxes.

The leaf lipid composition of ectomycorrhizal oak plants shows a drought-tolerance signature

Ectomycorrhizas have been reported to increase plant tolerance to drought. However, the mechanisms involved are not yet fully understood. Membranes are the first targets of degradation during drought, and growing evidences support a role for membrane lipids in plant tolerance and adaptation to drought. We have previously shown that improved tolerance of ectomycorrhizal oak plants to drought could be related to leaf membrane lipid metabolism, namely through an increased ability to sustain fatty acid content and composition, indicative of a higher membrane stability under stress. Here, we analysed in deeper detail the modulation of leaf lipid metabolism in oak plants mycorrhized with Pisolithus tinctorius and subjected to drought stress. Results show that mycorrhizal plants show patterns associated with water deficit tolerance, like a higher content of chloroplast lipids, whose levels are maintained upon drought stress. Likewise, mycorrhizal plants show increased levels of unsaturated fatty acids in the chloroplast phosphatidylglycerol lipid fraction. As a common response to drought, the digalactosyldiacyloglycerol/monogalactosyldiacyloglycerol ratio increased in the non-mycorrhizal plants, but not in the mycorrhizal plants, associated to smaller alterations in the expression of galactolipid metabolism genes, indicative of a higher drought tolerance. Under drought, inoculated plants showed increased expression of genes involved in neutral lipids biosynthesis, which could be related to an increased ability to tolerate drought stress. Overall, results from this study provide evidences of the involvement of lipid metabolism in the response of ectomycorrhizal plants to water deficit and point to an increased ability to maintain a stable chloroplast membrane functional integrity under stress.

Potassium supply reduces cesium uptake in Konara oak not by an alteration of uptake mechanism, but by the uptake competition between the ions

Radiocesium contamination of forests has been a severe problem after the Fukushima Daiichi Nuclear Power Plant accident in 2011. Bed logs of Konara oak (Quercus serrata Murray), used for mushroom cultivation, were an economically important product from the forests prior to their contamination. One of the potential countermeasures to reduce radiocesium content in trees is potassium fertilization, but the evidence for the effect of K⁺ in reducing Cs⁺ uptake has not been obtained yet in the woody plant. Therefore, we investigated the ability of rhizospheric K⁺ to suppress uptake and translocation of Cs⁺ in Konara oak seedlings through hydroponic experiments in order to clarify the effect of K⁺. Elemental analysis showed that the seedlings cultivated for 4 weeks under low-K (K⁺ = 50 μM) contained higher amount of Cs comparing to the seedlings cultivated under high-K (K⁺ = 3 mM). Then, the uptake rate of Cs⁺ and K⁺ in the seedlings from the solution having 50 μM K⁺ and 0.1 μM Cs⁺ was calculated using radioactive ¹³⁷Cs⁺ and ⁴²K⁺ to evaluate the effect of growth condition on the ion uptake mechanism. The interference between Cs⁺ and K⁺ at the site of root uptake was also evaluated based on the Cs⁺ and K⁺ uptake rates at K⁺ concentrations of 50 μM, 200 μM, and 3 mM in the seedlings grown under the medium-K (K⁺ = 200 μM) condition. As a result, the Cs⁺ uptake rate at 50 μM K⁺ was not influenced by the growth condition, whereas Cs⁺ uptake decreased when the uptake solution itself was supplemented with 3 mM K⁺. In addition, the Cs/K ratio in the seedlings was found to rise to exceed the Cs/K ratio in the culture solution as the rhizospheric K⁺ concentration increased, which was in contrast with previous findings in herbaceous plants. Our experiments demonstrated the first direct evidence for woody plants that a high K⁺ concentration can suppress Cs accumulation in Konara oak and that it was derived from competition for uptake between K⁺ and Cs⁺ in the rhizosphere, not from the growth K⁺ condition.

The "one-point method" for estimating maximum carboxylation capacity of photosynthesis: A cautionary tale

The maximum carboxylation capacity of Rubisco, V_c,max , is an important photosynthetic parameter that is key to accurate estimation of carbon assimilation. The gold-standard technique for determining V_c,max is to derive V_c,max from the initial slope of an A-C_i curve (the response of photosynthesis, A, to intercellular CO₂ concentration, C_i ). Accurate estimates of V_c,max derived from an alternative and rapid "one-point" measurement of photosynthesis could greatly accelerate data collection and model parameterization. We evaluated the practical application of the one-point method in six species measured under standard conditions (saturating irradiance and 400 μmol CO₂ mol^-1 ) and under conditions that would increase the likelihood for successful estimation of V_c,max : (a) ensuring Rubisco-limited A by measuring at 300 μmol CO₂ mol^-1 and (b) allowing time for acclimation to saturating irradiance prior to measurement. The one-point method significantly underestimated V_c,max in four of the six species, providing estimates 21%-32% below fitted values. We identified ribulose-1,5-bisphosphate-limited A, light acclimation, and the use of an assumed respiration rate as factors that limited the effective use of the one-point method to accurately estimate V_c,max . We conclude that the one-point method requires a species-specific understanding of its application, is often unsuccessful, and must be used with caution.

Pretreatment and enzymatic saccharification of oak at high solids loadings to obtain high titers and high yields of sugars

Production of high-titer sugar from lignocellulose is important in terms of process economics of bio-based product industry. In this study, to obtain high titers and yields of sugars, we combined pretreatment and saccharification steps, both at high solids loadings. First, pretreatment of oak was optimized at a 30% (w/w) solids loading. The whole slurry of the pretreated oak was subjected to a fed-batch saccharification step at the final solids loading of 30%, to minimize loss of fermentable sugars and simplify the processes. As a result, high-titer sugars (157.5 g/L) consisting of 120.2 g/L of glucose and 37.3 g/L of xylose were obtained at 75.9% and 58.6%, respectively, of theoretical maximum yields, based on the initial glucan and xylan contents. Thus, through proper optimization processes of oak, the combination of pretreatment and saccharification at high solids loadings was effective in obtaining both high titers and high yields of sugars from lignocellulose.

A pool-weighted perspective on the two-water-worlds hypothesis

The 'two-water-worlds' hypothesis is based on stable isotope differences in stream, soil and xylem waters in dual isotope space. It postulates no connectivity between bound and mobile soil waters, and preferential plant water uptake of bound soil water sources. We tested the pool-weighted impact of isotopically distinct water pools for hydrological cycling, the influence of species-specific water use and the degree of ecohydrological separation. We combined stable isotope analysis (δ¹⁸ O and δ² H) of ecosystem water pools of precipitation, groundwater, soil and xylem water of two distinct species (Quercus suber, Cistus ladanifer) with observations of soil water contents and sap flow. Shallow soil water was evaporatively enriched during dry-down periods, but enrichment faded strongly with depth and upon precipitation events. Despite clearly distinct water sources and water-use strategies, both species displayed a highly opportunistic pattern of root water uptake. Here we offer an alternative explanation, showing that the isotopic differences between soil and plant water vs groundwater can be fully explained by spatio-temporal dynamics. Pool weighting the contribution of evaporatively enriched soil water reveals only minor annual impacts of these sources to ecosystem water cycling (c. 11% of bulk soil water and c. 14% of transpired water).

Beyond isohydricity: The role of environmental variability in determining plant drought responses

Despite the appeal of the iso/anisohydric framework for classifying plant drought responses, recent studies have shown that such classifications can be strongly affected by a plant's environment. Here, we present measured in situ drought responses to demonstrate that apparent isohydricity can be conflated with environmental conditions that vary over space and time. In particular, we (a) use data from an oak species (Quercus douglasii) during the 2012-2015 extreme drought in California to demonstrate how temporal and spatial variability in the environment can influence plant water potential dynamics, masking the role of traits; (b) explain how these environmental variations might arise from climatic, topographic, and edaphic variability; (c) illustrate, through a "common garden" thought experiment, how existing trait-based or response-based isohydricity metrics can be confounded by these environmental variations, leading to Type-1 (false positive) and Type-2 (false negative) errors; and (d) advocate for the use of model-based approaches for formulating alternate classification schemes. Building on recent insights from greenhouse and vineyard studies, we offer additional evidence across multiple field sites to demonstrate the importance of spatial and temporal drivers of plants' apparent isohydricity. This evidence challenges the use of isohydricity indices, per se, to characterize plant water relations at the global scale.

Leaf biochemical adjustments in two Mediterranean resprouter species facing enhanced UV levels and reduced water availability before and after aerial biomass removal

Effects of supplemented UV radiation and diminished water supply on the leaf concentrations of phenols and antioxidants of two Mediterranean resprouter species, Arbutus unedo and Quercus suber, were assessed before and after entire aerial biomass removal. Potted seedlings of both species were grown outdoors for 8 months with enhanced UV-A + UV-B, enhanced UV-A or ambient UV, in combination with two watering conditions (field capacity or watering reduction). After this period, all aerial biomass was removed and new shoots (resprouts) developed for a further 8 months under the two treatments. In general, the investment in leaf phenols was substantially greater in A. unedo than in Q. suber, while Q. suber allocated more resources to non-phenolic antioxidants (ascorbate and glutathione). In response to enhanced UV-B radiation, Q. suber leaves rose their UV-screening capacity mainly via accumulation of kaempferols, accompanied by an increased concentration of rutins, being these effects exacerbated under low-watering conditions. Conversely, A. unedo leaves responded to UV-B radiation reinforcing the antioxidant machinery by increasing the overall amount of flavonols (especially quercetins) in seedlings, and of ascorbate and glutathione, along with catalase activity, in resprouts. Nevertheless, UV effects on the amount/activity of non-phenolic antioxidants of A. unedo resprouts were modulated by water supply. Indeed, the highest concentration of glutathione was found under the combination of enhanced UV-B radiation and reduced watering, suggesting an enlargement of the antioxidant response in A. unedo resprouts. Different biochemical responses to enhanced UV and drier conditions in seedlings and resprouts of these two species might modulate their competitive interactions in the near future.

Leaf litter microbial decomposition in salinized streams under intermittency

Human-induced salinization of freshwaters constitutes a growing global problem, whose consequences on streams functioning are largely unknown. Climate change projections predict enhanced evaporation, as well as an increase in extreme events and in variability of precipitation. This will result in more frequent, extended and severe drought periods that may aggravate water salinization of streams and rivers. In this study we conducted a microcosm experiment to assess the combined effects of three drought regimes - abrupt (AD), slow (SD) and very slow transition to dryness (VSD) - and three levels of salinization (0, 4, 6 g L^-1 NaCl) on microbial-mediated oak leaf decomposition over ten weeks. Salinization did not affect mass loss and associated microbial respiration of colonized oak leaves but significantly reduced the biomass and eliminated the sporulating capacity of fungi. Desiccation negatively affected leaf decomposition regardless of regime. Even though microbial respiration did not react to the different treatments, lower fungal biomass, diversity, and conidial production were observed under AD; for fungal biomass these effects were amplified at higher salt concentrations (particularly at 6 g L^-1). Our results indicate that effects of leaf litter desiccation depend on the rate of transition between wet and dry conditions and on the level of salt in the water. The two factors jointly affect decomposer survival and activity and, by extension, the dynamics of detrital food webs in streams.

Natural decay of archaeological oak wood versus artificial degradation processes - An FT-IR spectroscopy and X-ray diffraction study

Wood has been extensively used as a material for different applications over the years, therefore the understanding of different degradation processes in various environments is of great importance. In this study, the infrared spectroscopy, X-ray diffraction and chemometric methods were used to evaluate and compare the structure of archaeological and artificially degraded oak wood. The results clearly show that modifications in the structure of archaeological wood are related to the position of the material in the log (sapwood and heartwood), thus the extent of wood degradation. To identify the possible factors influencing these effects, the control wood samples were exposed to artificial white rot biodegradation with Coriolus (Trametes) versicolor and to alkali treatment (with NaOH solution). Due to the structural similarities between biodegraded wood and control or archaeological samples, this type of decay is likely to occur during natural ageing along with degradation produced by other environmental factors. Further, no real similarity was identified between the alkali treated wood and archaeological samples, indicating that such degradation does not affect wood under natural conditions.

Proteomics, Holm Oak (Quercus ilex L.) and Other Recalcitrant and Orphan Forest Tree Species: How do They See Each Other?

Proteomics has had a big impact on plant biology, considered as a valuable tool for several forest species, such as Quercus, Pines, Poplars, and Eucalyptus. This review assesses the potential and limitations of the proteomics approaches and is focused on Quercus ilex as a model species and other forest tree species. Proteomics has been used with Q. ilex since 2003 with the main aim of examining natural variability, developmental processes, and responses to biotic and abiotic stresses as in other species of the genus Quercus or Pinus. As with the progress in techniques in proteomics in other plant species, the research in Q. ilex moved from 2-DE based strategy to the latest gel-free shotgun workflows. Experimental design, protein extraction, mass spectrometric analysis, confidence levels of qualitative and quantitative proteomics data, and their interpretation are a true challenge with relation to forest tree species due to their extreme orphan and recalcitrant (non-orthodox) nature. Implementing a systems biology approach, it is time to validate proteomics data using complementary techniques and integrate it with the -omics and classical approaches. The full potential of the protein field in plant research is quite far from being entirely exploited. However, despite the methodological limitations present in proteomics, there is no doubt that this discipline has contributed to deeper knowledge of plant biology and, currently, is increasingly employed for translational purposes.

Impact of vegetation on the methane budget of a temperate forest

Upland forest soils are known to be the main biological sink for methane, but studies have shown that net methane uptake of a forest ecosystem can be reduced when methane emissions by vegetation are considered. We estimated the methane budget of a young oak plantation by considering tree stems but also the understorey vegetation. Automated chambers connected to a laser-based gas analyser, on tree stems, bare soil and soil covered with understorey vegetation, recorded CH₄ fluxes for 7 months at 3 h intervals. Tree stem emissions were low and equated to only 0.1% of the soil sink. Conversely, the presence of understorey vegetation increased soil methane uptake. This plant-driven enhancement of CH₄ uptake occurred when the soil was consuming methane. At the stand level, the methane budget shifted from -1.4 ± 0.4 kg C ha^-1 when we upscaled data obtained only on bare soil, to -2.9 ± 0.6 kg C ha^-1 when we considered soil area that was covered with understorey vegetation. These results indicate that aerenchymatous plant species, which are known to reduce the methane sink in wetlands, actually increase soil methane uptake two-fold in an upland forest by enhancing methane and oxygen transport and/or by promoting growth of methanotrophic populations.

Atmospheric pCO2 impacts leaf structural and physiological traits in Quercus petraea seedlings

Atmospheric p CO ₂ impacts Quercus petraea biomass production and cell wall composition of the leaves in favor of cellulose at the expense of lignin, and enhances foliar non-structural carbohydrate levels and sucrose contents in a pCO ₂ concentration-dependent manner. Sessile oak (Quercus petraea Liebl.) was grown for ca. half a year from seeds at ambient control (525 ppm), 750, 900, and 1000 ppm atmospheric pCO₂ under controlled conditions. Increasing pCO₂ enhanced biomass production, modified the cell wall composition of the leaves in favor of cellulose at the expense of lignin, and enhanced the foliar non-structural carbohydrate level, in particular the sucrose content; as well as total N content of leaves by increased levels of all major N fractions, i.e., soluble proteins, total amino acids, and structural N. The enhanced total amino acid level was largely due to 2-ketoglutarate and oxalo acetate-derived compounds. Increasing pCO₂ alleviated oxidative stress in the leaves as indicated by reduced H₂O₂ contents. High in vitro glutathione reductase activity at reduced H₂O₂ contents suggests enhanced ROS scavenging, but increased lipid peroxidation may also have contributed, as indicated by a negative correlation between malone dialdehyde and H₂O₂ contents. Almost all these effects were at least partially reversed, when pCO₂ exceeded 750 or 900 ppm. Apparently, the interaction of atmospheric pCO₂ with leaf structural and physiological traits of Q. petraea seedlings is characterized by a dynamic response depending on the pCO₂ level.

Seasonal changes of sucrose transporter expression and sugar partitioning in common European tree species

In temperate woody species, carbon transport from source to sink tissues is a striking physiological process, particularly considering seasonal changes. The functions of different tissues can also alternate across the seasons. In this regard, phloem loading and sugar distribution are important aspects of carbon partitioning, and sucrose uptake transporters (SUTs) play a key role in these processes. Therefore, the influence of seasons and different light-dark conditions on the expression of SUTs from 3-year-old Fagus sylvatica L., Quercus robur L. and Picea abies (L.) Karst. trees were analyzed. In addition, tissue-specific sugar and starch contents under these different environmental conditions were determined. Putative SUTs were identified in the gymnosperms (Picea abies, Ginkgo biloba L.), here for the first time, and also in the angiosperms (Q. robur, F. sylvatica). The identified SUT sequences of the different tree species cluster into three types, similar to other SUTs from herbaceous and tree species. Furthermore, the sequences from angiosperm and those from gymnosperm species form distinct clusters within the three types of SUTs. In F. sylvatica, Q. robur and P. abies, the expression levels of the different SUTs during seasons showed marked variations. Because of the high expression levels of type I SUTs in bark, wood and leaves during active growing phases in spring and summer, it can be assumed that they are involved in phloem loading, sucrose retrieval and possibly in further physiological processes. The expression patterns also indicate a flexible expression in all tissues depending on physiological requirements and environmental conditions. Compared with type I SUTs, the seasonal variations of type II SUT expression were less pronounced, whereas the seasonal variations of the type III SUT expression patterns were partly reverse. In addition to the seasonal regulation, the expressions of the different SUTs were also regulated by light in a diurnal manner.

Effect of soil water availability on intra-annual xylem and phloem formation and non-structural carbohydrate pools in stem of Quercus pubescens

Non-structural carbohydrates (NSCs, i.e., starch and soluble sugars) are frequently quantified in the context of tree response to stressful events (e.g., drought), because they serve as a carbon reservoir for growth and respiration, as well as providing a critical osmotic function to maintain turgor and vascular transport under different environmental conditions. We investigated the impact of soil water availability on intra-annual leaf phenology, radial growth dynamics and variation in NSC amounts in the stem of pubescent oak (Quercus pubescens Willd.). from a sub-Mediterranean region. For this purpose, trees growing at two nearby plots differing in bedrock and, consequently, soil characteristics (F-eutric cambisol on eocene flysch bedrock and L-rendzic leptosol on paleogenic limestone bedrock) were sampled. Non-structural carbohydrates were analysed in outer xylem and living phloem (separately for non-collapsed and collapsed parts). Results showed that xylem and phloem increments were 41.6% and 21.2%, respectively, wider in trees from F plot due to a higher rate of cell production. In contrast, the amount of NSCs and of soluble sugars significantly differed among the tissue parts and sampling dates but not between the two plots. Starch amounts were the highest in xylem, which could be explained by the abundance of xylem parenchyma cells. Two clear seasonal peaks of the starch amount were detected in all tissues, the first in September-November, in the period of leaf colouring and falling, and the second in March-April, i.e., at the onset of cambial cell production followed by bud development. The amounts of free sugars were highest in inner phloem + cambium, at the sites of active growth. Soil water availability substantially influenced secondary growth in the stem of Q. pubescens, whereas NSC amounts seemed to be less affected. The results show how the intricate relationships between soil properties, such as water availability, and tree performance should be considered when studying the impact of stressful events on the growth and functioning of trees.

Non-invasive imaging shows no evidence of embolism repair after drought in tree species of two genera

Drought stress can result in significant impairment of the plant hydraulic system via blockage of xylem conduits by gas emboli. Recovery after drought stress is an essential component of plant survival but is still a poorly understood process. In this study, we examined the capacity of woody species from two genera (Eucalyptus and Quercus) to refill embolized xylem vessels during a cycle of drought and recovery. Observations were made on intact plants of Eucalyptus calmudulensis, E. grandis, E. saligna and Quercus palustris using X-ray microtomography. We found no evidence of an effective xylem refilling mechanism in any of the plant species. Despite rehydration and recovery of plant water potential to near pre-drought levels, embolized vessels were not refilled up to 72 h after rewatering. In E. saligna, water droplets accumulated in previously air-filled vessels for a very small percentage of vessels. However, no instances of complete refilling that would restore embolized vessels to hydraulic function were observed. Our observations suggest that rapid refilling of embolized vessels after drought may not be a wide spread mechanism in woody plants and that embolism formed during drought represents long term cost to the plant hydraulic system.

Natural hybridisation among Quercus glabrescens, Q. rugosa and Q. obtusata (Fagaceae): Microsatellites and secondary metabolites markers

Natural hybridisation has significant ecological, genetic and evolutionary consequences altering morphological and chemical characters of individuals. Quercus glabrescens, Q. rugosa and Q. obtusata are white oak species well separated by their morphological characters when they occur in allopatry in Mexican temperate forests. However, in sympatry, individuals with atypical morphology have been observed, suggesting hybridisation events. In this study, we determined, with microsatellites and secondary metabolites, if interspecific gene flow occurs when these three oak species coexist in sympatry. In total, 180 individuals belonging to seven populations [three allopatric (one for each parental species) and four sympatric sites] were analysed. Allopatric populations represent well-defined genetic groups and the sympatric populations showed genetic evidence of hybridisation between Q. glabrescens × Q. rugosa and Q. glabrescens × Q. obtusata. The hybridisation percentage varied between sites and combination of involved species. We registered the presence of unique flavonoid compounds for Q. glabrescens (caffeic acid and flavonol 2), Q. rugosa (flavonol 5) and Q. obtusata (flavonol 1). Three compounds (quercetin rhamnoside, flavonol 3 and alkyl coumarate) were expressed in all taxa. Finally, the hybrid genotypes identified in this study (Q. glabrescens × Q. rugosa and Q. glabrescens × Q. obtusata) showed specific chemical profiles, resulting from a combination of those of their parental species. These results show that hybridisation events between these oak species alter chemical expression of secondary metabolites, creating a mosaic of resources and conditions that provide the substrate for different combinations of foliar-associated species such as herbivores, endophytic fungi or epiphyte plants.

How Quercus ilex L. saplings face combined salt and ozone stress: a transcriptome analysis

BACKGROUND

Similar to other urban trees, holm oaks (Quercus ilex L.) provide a physiological, ecological and social service in the urban environment, since they remove atmospheric pollution. However, the urban environment has several abiotic factors that negatively influence plant life, which are further exacerbated due to climate change, especially in the Mediterranean area. Among these abiotic factors, increased uptake of Na + and Cl - usually occurs in trees in the urban ecosystem; moreover, an excess of the tropospheric ozone concentration in Mediterranean cities further affects plant growth and survival. Here, we produced and annotated a de novo leaf transcriptome of Q. ilex as well as transcripts over- or under-expressed after a single episode of O3 (80 nl l-1, 5 h), a salt treatment (150 mM for 15 days) or a combination of these treatments, mimicking a situation that plants commonly face, especially in urban environments.

RESULTS

Salinity dramatically changed the profile of expressed transcripts, while the short O3 pulse had less effect on the transcript profile. However, the short O3 pulse had a very strong effect in inducing over- or under-expression of some genes in plants coping with soil salinity. Many differentially regulated genes were related to stress sensing and signalling, cell wall remodelling, ROS sensing and scavenging, photosynthesis and to sugar and lipid metabolism. Most differentially expressed transcripts revealed here are in accordance with a previous report on Q. ilex at the physiological and biochemical levels, even though the expression profiles were overall more striking than those found at the biochemical and physiological levels.

CONCLUSIONS

We produced for the first time a reference transcriptome for Q. ilex, and performed gene expression analysis for this species when subjected to salt, ozone and a combination of the two. The comparison of gene expression between the combined salt + ozone treatment and salt or ozone alone showed that even though many differentially expressed genes overlap all treatments, combined stress triggered a unique response in terms of gene expression modification. The obtained results represent a useful tool for studies aiming to investigate the effects of environmental stresses in urban-adapted tree species.

Seasonal changes of δD and δ18O in tree-ring cellulose of Quercus crispula suggest a change in post-photosynthetic processes during earlywood growth

Leaf photosynthetic and post-photosynthetic processes modulate the isotope ratios of tree-ring cellulose. Post-photosynthetic processes, such as the remobilization of stored starch in early spring, are important to understanding the mechanisms of xylem formation in tree stems; however, untangling the isotope ratio signals of photosynthetic and post-photosynthetic processes imprinted on tree rings is difficult. Portions of carbon-bound hydrogen and oxygen atoms are exchanged with medium water during post-photosynthetic processes. We investigated the δD and δ18O values of tree-ring cellulose using Quercus crispula Blume trees in two different habitats to evaluate seasonal changes in the exchange rate (f-value) of hydrogen or oxygen with medium water, and examined the associations of the post-photosynthetic processes. Theoretically, if the f-value is constant, δD and δ18O would be positively correlated due to meteorological factors, while variation in the f-value will create a discrepancy and weak correlation between δD and δ18O due to the exchange of carbon-bound hydrogen and oxygen with medium water. The values of δD decreased drastically from earlywood to latewood, while those of δ18O increased to a peak and then decreased toward the latewood. The estimated seasonal f-value was high at the beginning of earlywood and decreased toward the latewood. The post-photosynthetic processes associated with changes in the f-value were the remobilization of stored starch and triose cycling during cellulose synthesis because of the shortage of photo-assimilates in early spring. Although we did not evaluate relevant physiological parameters, the seasonal pattern of δD and δ18O in tree-ring cellulose of Q. crispula was clear, suggesting that the dual isotope (δD and δ18O) approach can be used to reveal the resource allocation mechanisms underlying seasonal xylem formation.

Resistance of native oak to recurrent drought conditions simulating predicted climatic changes in the Mediterranean region

The capacity of a Quercus pubescens forest to resist recurrent drought was assessed on an in situ experimental platform through the measurement of a large set of traits (ecophysiological and metabolic) studied under natural drought (ND) and amplified drought (AD) induced by partial rain exclusion. This study was performed during the third and fourth years of AD, which correspond to conditions of moderate AD in 2014 and harsher AD in 2015, respectively. Although water potential (Ψ) and net photosynthesis (Pn) were noticeably reduced under AD in 2015 compared to ND, trees showed similar growth and no oxidative stress. The absence of oxidative damage could be due to a strong accumulation of α-tocopherol, suggesting that this compound is a major component of the Q. pubescens antioxidant system. Other antioxidants were rather stable under AD in 2014, but slight changes started to be observed in 2015 (carotenoids and isoprene) due to harsher conditions. Our results indicate that Q. pubescens could be able to cope with AD, for at least 4 years, likely due to its antioxidant system. However, growth decrease was observed during the fifth year (2016) of AD, suggesting that this resistance could be threatened over longer periods of recurrent drought.

Soil Perturbation in Mediterranean Ecosystems Reflected by Differences in Free-Lipid Biomarker Assemblages

Environmental information provided by free lipids in soil samples collected from control and disturbed plots (Madrid, Spain) was assessed by comparing molecular assemblages of terpenoids and distribution patterns of alkanes and fatty acids (FAs) analyzed by gas chromatography-mass spectrometry (GC-MS). Wildfires in pine forests led to increased proportions of retene, dehydroabietin, and simonellite. Friedo-oleananes were characteristic in soils under angiosperms, and norambreinolide-type diterpenes were characteristic in soils encroached by Cistus bushes. Steroids were major compounds in pastured sites. Enhanced Shannon's lipid biodiversity index in disturbed soils compared with in control soils suggested patterns of recent lipids overlapping a preserved original lipid signature. The extent of the environmental impacts was illustrated as Euclidean distances between paired control and disturbed sites calculated using the compounds in alkyl homologous series as descriptors. As expected, reforestation, bush encroachment, wildfires, and cultivation were reflected by changes in the molecular record of lipids in soils.

ChIP-Seq reveals that QsMYB1 directly targets genes involved in lignin and suberin biosynthesis pathways in cork oak (Quercus suber)

BACKGROUND

Gene activity is largely controlled by transcriptional regulation through the action of transcription factors and other regulators. QsMYB1 is a member of the R2R3-MYB transcription factor family related to secondary growth, and in particular, with the cork development process. In order to identify the putative gene targets of QsMYB1 across the cork oak genome we developed a ChIP-Seq strategy.

RESULTS

Results provide direct evidence that QsMY1B targets genes encoding for enzymes involved in the lignin and suberin pathways as well as gene encoding for ABCG transporters and LTPs implicated in the transport of monomeric suberin units across the cellular membrane. These results highlight the role of QsMYB1 as a regulator of lignin and suberin biosynthesis, transport and assembly.

CONCLUSION

To our knowledge, this work constitutes the first ChIP-Seq experiment performed in cork oak, a non-model plant species with a long-life cycle, and these results will contribute to deepen the knowledge about the molecular mechanisms of cork formation and differentiation.

Root exudate metabolomes change under drought and show limited capacity for recovery

Root exudates comprise a large variety of compounds released by plants into the rhizosphere, including low-molecular-weight primary metabolites (particularly saccharides, amino acids and organic acids) and secondary metabolites (phenolics, flavonoids and terpenoids). Changes in exudate composition could have impacts on the plant itself, on other plants, on soil properties (e.g. amount of soil organic matter), and on soil organisms. The effects of drought on the composition of root exudates, however, have been rarely studied. We used an ecometabolomics approach to identify the compounds in the exudates of Quercus ilex (holm oak) under an experimental drought gradient and subsequent recovery. Increasing drought stress strongly affected the composition of the exudate metabolome. Plant exudates under drought consisted mainly of secondary metabolites (71% of total metabolites) associated with plant responses to drought stress, whereas the metabolite composition under recovery shifted towards a dominance of primary metabolites (81% of total metabolites). These results strongly suggested that roots exude the most abundant root metabolites. The exudates were changed irreversibly by the lack of water under extreme drought conditions, and the plants could not recover.