Integrative multi-omics analyses of date palm (Phoenix dactylifera) roots and leaves reveal how the halophyte land plant copes with sea water.

Date palm (Phoenix dactylifera L.) is able to grow and complete its life cycle while being rooted in highly saline soils. Which of the many well-known salt-tolerance strategies are combined to fine-tune this remarkable resilience is unknown. The precise location, whether in the shoot or the root, where these strategies are employed remains uncertain, leaving us unaware of how the various known salt-tolerance mechanisms are integrated to fine-tune this remarkable resilience. To address this shortcoming, we exposed date palm to a salt stress dose equivalent to seawater for up to 4 weeks and applied integrative multi-omics analyses followed by targeted metabolomics, hormone, and ion analyses. Integration of proteomic into transcriptomic data allowed a view beyond simple correlation, revealing a remarkably high degree of convergence between gene expression and protein abundance. This sheds a clear light on the acclimatization mechanisms employed, which depend on reprogramming of protein biosynthesis. For growth in highly saline habitats, date palm effectively combines various salt-tolerance mechanisms found in both halophytes and glycophytes: "avoidance" by efficient sodium and chloride exclusion at the roots, and "acclimation" by osmotic adjustment, reactive oxygen species scavenging in leaves, and remodeling of the ribosome-associated proteome in salt-exposed root cells. Combined efficiently as in P. dactylifera L., these sets of mechanisms seem to explain the palm's excellent salt stress tolerance.

B-GATA factors are required to repress high-light stress responses in Marchantia polymorpha and Arabidopsis thaliana.

GATAs are evolutionarily conserved zinc-finger transcription factors from eukaryotes. In plants, GATAs can be subdivided into four classes, A-D, based on their DNA-binding domain, and into further subclasses based on additional protein motifs. B-GATAs with a so-called leucine-leucine-methionine (LLM)-domain can already be found in algae. In angiosperms, the B-GATA family is expanded and can be subdivided in to LLM- or HAN-domain B-GATAs. Both, the LLM- and the HAN-domain are conserved domains of unknown biochemical function. Interestingly, the B-GATA family in the liverwort Marchantia polymorpha and the moss Physcomitrium patens is restricted to one and four family members, respectively. And, in contrast to vascular plants, the bryophyte B-GATAs contain a HAN- as well as an LLM-domain. Here, we characterise mutants of the single B-GATA from Marchantia polymorpha. We reveal that this mutant has defects in thallus growth and in gemma formation. Transcriptomic studies uncover that the B-GATA mutant displays a constitutive high-light (HL) stress response, a phenotype that we then also confirm in mutants of Arabidopsis thaliana LLM-domain B-GATAs, suggesting that the B-GATAs have a protective role towards HL stress.

Isoprene-Emitting Tobacco Plants Are Less Affected by Moderate Water Deficit under Future Climate Change Scenario and Show Adjustments of Stress-Related Proteins in Actual Climate.

Isoprene-emitting plants are better protected against thermal and oxidative stresses, which is a desirable trait in a climate-changing (drier and warmer) world. Here we compared the ecophysiological performances of transgenic isoprene-emitting and wild-type non-emitting tobacco plants during water stress and after re-watering in actual environmental conditions (400 ppm of CO2 and 28 °C of average daily temperature) and in a future climate scenario (600 ppm of CO2 and 32 °C of average daily temperature). Furthermore, we intended to complement the present knowledge on the mechanisms involved in isoprene-induced resistance to water deficit stress by examining the proteome of transgenic isoprene-emitting and wild-type non-emitting tobacco plants during water stress and after re-watering in actual climate. Isoprene emitters maintained higher photosynthesis and electron transport rates under moderate stress in future climate conditions. However, physiological resistance to water stress in the isoprene-emitting plants was not as marked as expected in actual climate conditions, perhaps because the stress developed rapidly. In actual climate, isoprene emission capacity affected the tobacco proteomic profile, in particular by upregulating proteins associated with stress protection. Our results strengthen the hypothesis that isoprene biosynthesis is related to metabolic changes at the gene and protein levels involved in the activation of general stress defensive mechanisms of plants.

Differences of nitrogen metabolism in date palm (Phoenix dactylifera) seedlings subjected to water deprivation and salt exposure.

Drought and salt exposure are among the most prevalent and severe abiotic stressors causing serious agricultural yield losses, alone and in combination. Little is known about differences and similarities in the effects of these two stress factors on plant metabolic regulation, particularly on nitrogen metabolism. Here, we studied the effects of water deprivation and salt exposure on water relations and nitrogen metabolites in leaves and roots of date palm seedlings. Both, water deprivation and salt exposure had no significant effects on plant water content or stable carbon (C) and nitrogen (N) isotope signatures. Significant effects of water deprivation on total C and N concentrations were only observed in roots, i.e., decreased total C and increased total N concentrations. Whereas salt exposure initially decreased total C and increased total N concentrations significantly in roots, foliar total C concentration was increased upon prolonged exposure. Initially C/N ratios declined in roots of plants from both treatments and upon prolonged salt exposure also in the leaves. Neither treatment affected soluble protein and structural N concentrations in leaves or roots, but resulted in the accumulation of most amino acids, except for glutamate and tryptophan, which remained stable, and serine, which decreased, in roots. Accumulation of the most abundant amino acids, lysine and proline, was observed in roots under both treatments, but in leaves only upon salt exposure. This finding indicates a similar role of these amino acids as compatible solutes in the roots in response to salt und drought, but not in the leaves. Upon prolonged treatment, amino acid concentrations returned to levels found in unstressed plants in leaves of water deprived, but not salt exposed, plants. The present results show both water deprivation and salt exposure strongly impact N metabolism of date palm seedlings, but in a different manner in leaves and roots.

Interaction with the entomopathogenic fungus Beauveria bassiana influences tomato phenome and promotes resistance to Botrytis cinerea infection.

Plants are central to complex networks of multitrophic interactions. Increasing evidence suggests that beneficial microorganisms (BMs) may be used as plant biostimulants and pest biocontrol agents. We investigated whether tomato (Solanum lycopersicum) plants are thoroughly colonized by the endophytic and entomopathogenic fungus Beauveria bassiana, and how such colonization affects physiological parameters and the phenotype of plants grown under unstressed conditions or exposed to the pathogenic fungus Botrytis cinerea. As a positive control, a strain of the well-known biocontrol agent and growth inducer Trichoderma afroharzianum was used. As multitrophic interactions are often driven by (or have consequences on) volatile organic compounds (VOCs) released by plants constitutively or after induction by abiotic or biotic stresses, VOC emissions were also studied. Both B. bassiana and T. afroharzianum induced a significant but transient (one to two-day-long) reduction of stomatal conductance, which may indicate rapid activation of defensive (rejection) responses, but also limited photosynthesis. At later stages, our results demonstrated a successful and complete plant colonization by B. bassiana, which induced higher photosynthesis and lower respiration rates, improved growth of roots, stems, leaves, earlier flowering, higher number of fruits and yield in tomato plants. Beauveria bassiana also helped tomato plants fight B. cinerea, whose symptoms in leaves were almost entirely relieved with respect to control plants. Less VOCs were emitted when plants were colonized by B. bassiana or infected by B. cinerea, alone or in combination, suggesting no activation of VOC-dependent defensive mechanisms in response to both fungi.

Metabolic responses of date palm (Phoenix dactylifera L.) leaves to drought differ in summer and winter climate.

Drought negatively impacts growth and productivity of plants, particularly in arid and semi-arid regions. Although drought events can take place in summer and winter, differences in the impact of drought on physiological processes between seasons are largely unknown. The aim of this study was to elucidate metabolic strategies of date palms in response to drought in summer and winter season. To identify such differences, we exposed date palm seedlings to a drought-recovery regime, both in simulated summer and winter climate. Leaf hydration, carbon discrimination (${\Delta}$13C), and primary and secondary metabolite composition and contents were analyzed. Depending on season, drought differently affected physiological and biochemical traits of the leaves. In summer, drought induced significantly decreased leaf hydration, concentrations of ascorbate, most sugars, primary and secondary organic acids, as well as phenolic compounds, while thiol, amino acid, raffinose and individual fatty acid contents were increased compared with well-watered plants. In winter, drought had no effect on leaf hydration, ascorbate and fatty acids contents, but resulted in increased foliar thiol and amino acid levels as observed in summer. Compared with winter, foliar traits of plants exposed to drought in summer only partly recovered after re-watering. Memory effects on water relations, and primary and secondary metabolites seem to prepare foliar traits of date palms for repeated drought events in summer. Apparently, a well-orchestrated metabolic network, including the anti-oxidative system, compatible solutes accumulation and osmotic adjustment, and maintenance of cell-membrane stability strongly reduces the susceptibility of date palms to drought. These mechanisms of drought compensation may be more frequently required in summer.

Ragweed plants grown under elevated CO2 levels produce pollen which elicit stronger allergic lung inflammation.

BACKGROUND: Common ragweed has been spreading as a neophyte in Europe. Elevated CO2 levels, a hallmark of global climate change, have been shown to increase ragweed pollen production, but their effects on pollen allergenicity remain to be elucidated. METHODS: Ragweed was grown in climate-controlled chambers under normal (380 ppm, control) or elevated (700 ppm, based on RCP4.5 scenario) CO2 levels. Aqueous pollen extracts (RWE) from control- or CO2 -pollen were administered in vivo in a mouse model for allergic disease (daily for 3-11 days, n = 5) and employed in human in vitro systems of nasal epithelial cells (HNECs), monocyte-derived dendritic cells (DCs), and HNEC-DC co-cultures. Additionally, adjuvant factors and metabolites in control- and CO2 -RWE were investigated using ELISA and untargeted metabolomics. RESULTS: In vivo, CO2 -RWE induced stronger allergic lung inflammation compared to control-RWE, as indicated by lung inflammatory cell infiltrate and mediators, mucus hypersecretion, and serum total IgE. In vitro, HNECs stimulated with RWE increased indistinctively the production of pro-inflammatory cytokines (IL-8, IL-1ß, and IL-6). In contrast, supernatants from CO2 -RWE-stimulated HNECs, compared to control-RWE-stimulated HNECS, significantly increased TNF and decreased IL-10 production in DCs. Comparable results were obtained by stimulating DCs directly with RWEs. The metabolome analysis revealed differential expression of secondary plant metabolites in control- vs CO2 -RWE. Mixes of these metabolites elicited similar responses in DCs as compared to respective RWEs. CONCLUSION: Our results indicate that elevated ambient CO2 levels elicit a stronger RWE-induced allergic response in vivo and in vitro and that RWE increased allergenicity depends on the interplay of multiple metabolites.

Climate and development modulate the metabolome and antioxidative system of date palm leaves.

Date palms are remarkably tolerant to environmental stresses, but the mechanisms involved remain poorly characterized. Leaf metabolome profiling was therefore performed on mature (ML) and young (YL) leaves of 2-year-old date palm seedlings that had been grown in climate chambers that simulate summer and winter conditions in eastern Saudi Arabia. Cultivation under high temperature (summer climate) resulted in higher YL H2O2 leaf levels despite increases in dehydroascorbate reductase (DHAR) activities. The levels of raffinose and galactinol, tricarboxylic acid cycle intermediates, and total amino acids were higher under these conditions, particularly in YL. The accumulation of unsaturated fatty acids, 9,12-octadecadienoic acid and 9,12,15-octadecatrienoic acid, was lower in ML. In contrast, the amounts of saturated tetradecanoic acid and heptadecanoic acid were increased in YL under summer climate conditions. The accumulation of phenolic compounds was favored under summer conditions, while flavonoids accumulated under lower temperature (winter climate) conditions. YL displayed stronger hydration, lower H2O2 levels, and more negative δ 13C values, indicating effective reactive oxygen species scavenging. These findings, which demonstrate the substantial metabolic adjustments that facilitate tolerance to the high temperatures in YL and ML, suggest that YL may be more responsive to climate change.

How do cryptochromes and UVR8 interact in natural and simulated sunlight?

Cryptochromes (CRYs) and UV RESISTANCE LOCUS 8 (UVR8) photoreceptors perceive UV-A/blue (315-500 nm) and UV-B (280-315 nm) radiation in plants, respectively. While the roles of CRYs and UVR8 have been studied in separate controlled-environment experiments, little is known about the interaction between these photoreceptors. Here, Arabidopsis wild-type Ler, CRYs and UVR8 photoreceptor mutants (uvr8-2, cry1cry2 and cry1cry2uvr8-2), and a flavonoid biosynthesis-defective mutant (tt4) were grown in a sun simulator. Plants were exposed to filtered radiation for 17 d or for 6 h, to study the effects of blue, UV-A, and UV-B radiation. Both CRYs and UVR8 independently enabled growth and survival of plants under solar levels of UV, while their joint absence was lethal under UV-B. CRYs mediated gene expression under blue light. UVR8 mediated gene expression under UV-B radiation, and in the absence of CRYs, also under UV-A. This negative regulation of UVR8-mediated gene expression by CRYs was also observed for UV-B. The accumulation of flavonoids was also consistent with this interaction between CRYs and UVR8. In conclusion, we provide evidence for an antagonistic interaction between CRYs and UVR8 and a role of UVR8 in UV-A perception.

Reduced microbial potential for the degradation of phenolic compounds in the rhizosphere of apple plantlets grown in soils affected by replant disease.

BACKGROUND: Apple replant disease (ARD) is a syndrome that occurs in areas where apple plants or closely related species have been previously cultivated. Even though ARD is a well-known phenomenon, which has been observed in different regions worldwide and occurs independent of the soil type, its causes still remain unclear. RESULTS: As expected, the biomass of plants grown in replant soil was significantly lower compared to those grown in control (virgin) soil. A shotgun metagenome analysis showed a clear differentiation between the rhizosphere and bulk soil compartments independent from the soil used. However, significant differences associated with apple replant disease were only observed in the rhizosphere compartment, for which we detected changes in the abundance of major bacterial genera. Interestingly, reads assigned to Actinobacteria were significantly reduced in relative abundance in rhizosphere samples of the soil affected by replant disease. Even though reads assigned to pathogenic fungi were detected, their relative abundance was low and did not differ significantly between the two different soils. Differences in microbiome structure also resulted in shifts in functional pattern. We observed an increase in genes related to stress sensing in the rhizosphere of soils affected by replant disease, whereas genes linked to nutrient sensing and uptake dominated in control soils. Moreover, we observed a lower abundance of genes coding for enzymes which trigger the degradation of aromatic compounds in rhizosphere of soils affected by replant disease, which is probably connected with higher concentration of phenolic compounds, generally associated with disease progression. CONCLUSIONS: Our study shows, for the first time, how apple replanting affects soil functioning by altering the soil microbiome. Particularly, the decrease in the abundance of genes which code for enzymes catalyzing the degradation of aromatic compounds, observed in the rhizosphere of plants grown in soil affected by apple replant disease, is of interest. Apple rootstocks are known to synthetize many phenolic compounds, including defense related phytoalexins, which have been considered for long to be connected with the emergence of replant disease. The knowledge gained in this study might help to develop targeted strategies to overcome or at least reduce the effects of ARD symptoms.

Physiological responses of date palm (Phoenix dactylifera) seedlings to acute ozone exposure at high temperature.

Vegetation in the Arabian Peninsula is facing high and steadily rising tropospheric ozone pollution. However, little is known about the impacts of elevated ozone on date palms, one of the most important indigenous economic species. To elucidate the physiological responses of date palm to peak levels of acute ozone exposure, seedlings were fumigated with 200 ppb ozone for 8 h. Net CO2 assimilation rate, stomatal conduction, total carbon, its isotope signature and total sugar contents in leaves and roots were not significantly affected by the treatment and visible symptoms of foliar damage were not induced. Ozone exposure did not affect hydrogen peroxide and thiol contents but diminished the activities of glutathione reductase and dehydroascorbate reductase, stimulated the oxidation of ascorbate, and resulted in elevated total ascorbate contents. Total nitrogen, soluble protein and lignin contents remained unchanged upon ozone exposure, but the abundance of low molecular weight nitrogen (LMWN) compounds such as amino acids and nitrate as well as other anions were strongly diminished in leaves and roots. Other nitrogen pools did not benefit from the decline of LMWN, indicating reduced uptake and/or enhanced release of these compounds into the soil as a systemic response to aboveground ozone exposure. Several phenolic compounds, concurrent with fatty acids and stearyl alcohol, accumulated in leaves, but declined in roots, whereas total phenol contents significantly increased in the roots. Together these results indicate that local and systemic changes in both, primary and secondary metabolism contribute to the high tolerance of date palms to short-term acute ozone exposure.

Carbon allocation from source to sink leaf tissue in relation to flavonoid biosynthesis in variegated Pelargonium zonale under UV-B radiation and high PAR intensity.

We studied the specific effects of high photosynthetically active radiation (PAR, 400-700 nm) and ecologically relevant UV-B radiation (0.90 W m(-2)) on antioxidative and phenolic metabolism by exploiting the green-white leaf variegation of Pelargonium zonale plants. This is a suitable model system for examining "source-sink" interactions within the same leaf. High PAR intensity (1350 µmol m(-2) s(-1)) and UV-B radiation induced different responses in green and white leaf sectors. High PAR intensity had a greater influence on green tissue, triggering the accumulation of phenylpropanoids and flavonoids with strong antioxidative function. Induced phenolics, together with ascorbate, ascorbate peroxidase (APX, EC 1.11.1.11) and catalase (CAT, EC 1.11.1.6) provided efficient defense against potential oxidative pressure. UV-B-induced up-regulation of non-phenolic H2O2 scavengers in green leaf sectors was greater than high PAR-induced changes, indicating a UV-B role in antioxidative defense under light excess; on the contrary, minimal effects were observed in white tissue. However, UV-B radiation had greater influence on phenolics in white leaf sections compared to green ones, inducing accumulation of phenolic glycosides whose function was UV-B screening rather than antioxidative. By stimulation of starch and sucrose breakdown and carbon allocation in the form of soluble sugars from "source" (green) tissue to "sink" (white) tissue, UV-B radiation compensated the absence of photosynthetic activity and phenylpropanoid and flavonoid biosynthesis in white sectors.

Ultraviolet-B component of sunlight stimulates photosynthesis and flavonoid accumulation in variegated Plectranthus coleoides leaves depending on background light.

We used variegated Plectranthus coleoides as a model plant with the aim of clarifying whether the effects of realistic ultraviolet-B (UV-B) doses on phenolic metabolism in leaves are mediated by photosynthesis. Plants were exposed to UV-B radiation (0.90 W m(-2) ) combined with two photosynthetically active radiation (PAR) intensities [395 and 1350 µmol m(-2) s(-1) , low light (LL) and high light (HL)] for 9 d in sun simulators. Our study indicates that UV-B component of sunlight stimulates CO2 assimilation and stomatal conductance, depending on background light. UV-B-specific induction of apigenin and cyanidin glycosides was observed in both green and white tissues. However, all the other phenolic subclasses were up to four times more abundant in green leaf tissue. Caffeic and rosmarinic acids, catechin and epicatechin, which are endogenous peroxidase substrates, were depleted at HL in green tissue. This was correlated with increased peroxidase and ascorbate peroxidase activities and increased ascorbate content. The UV-B supplement to HL attenuated antioxidative metabolism and partly recovered the phenolic pool indicating stimulation of the phenylpropanoid pathway. In summary, we propose that ortho-dihydroxy phenolics are involved in antioxidative defence in chlorophyllous tissue upon light excess, while apigenin and cyanidin in white tissue have preferentially UV-screening function.

Contrasting carbon allocation responses of juvenile European beech (Fagus sylvatica) and Norway spruce (Picea abies) to competition and ozone.

Allocation of recent photoassimilates of juvenile beech and spruce in response to twice-ambient ozone (2 × O(3)) and plant competition (i.e. intra vs. inter-specific) was examined in a phytotron study. To this end, we employed continuous (13)CO(2)/(12)CO(2) labeling during late summer and pursued tracer kinetics in CO(2) released from stems. In beech, allocation of recent photoassimilates to stems was significantly lowered under 2 × O(3) and increased in spruce when grown in mixed culture. As total tree biomass was not yet affected by the treatments, C allocation reflected incipient tree responses providing the mechanistic basis for biomass partitioning as observed in longer experiments. Compartmental modeling characterized functional properties of substrate pools supplying respiratory C demand. Respiration of spruce appeared to be exclusively supplied by recent photoassimilates. In beech, older C, putatively located in stem parenchyma cells, was a major source of respiratory substrate, reflecting the fundamental anatomical disparity between angiosperm beech and gymnosperm spruce.

UV-B mediated metabolic rearrangements in poplar revealed by non-targeted metabolomics.

Plants have to cope with various abiotic stresses including UV-B radiation (280-315 nm). UV-B radiation is perceived by a photoreceptor, triggers morphological responses and primes plant defence mechanisms such as antioxidant levels, photoreapir or accumulation of UV-B screening pigments. As poplar is an important model system for trees, we elucidated the influence of UV-B on overall metabolite patterns in poplar leaves grown under high UV-B radiation. Combining non-targeted metabolomics with gas exchange analysis and confocal microscopy, we aimed understanding how UV-B radiation triggers metabolome-wide changes, affects isoprene emission, photosynthetic performance, epidermal light attenuation and finally how isoprene-free poplars adjust their metabolome under UV-B radiation. Exposure to UV-B radiation caused a comprehensive rearrangement of the leaf metabolome. Several hundreds of metabolites were up- and down-regulated over various pathways. Our analysis, revealed the up-regulation of flavonoids, anthocyanins and polyphenols and the down-regulation of phenolic precursors in the first 36 h of UV-B treatment. We also observed a down-regulation of steroids after 12 h. The accumulation of phenolic compounds leads to a reduced light transmission in UV-B-exposed plants. However, the accumulation of phenolic compounds was reduced in non-isoprene-emitting plants suggesting a metabolic- or signalling-based interaction between isoprenoid and phenolic pathways.

UV responses of Lolium perenne raised along a latitudinal gradient across Europe: a filtration study.

Lolium perenne (cv. AberDart) was grown at 14 locations along a latitudinal gradient across Europe (37-68°N) to study the impact of ultraviolet radiation (UV) and climate on aboveground growth and foliar UV-B absorbing compounds. At each location, plants were grown outdoors for 5 weeks in a replicated UV-B filtration experiment consisting of open, UV-B transparent (cellulose diacetate) and UV-B opaque (polyester) environments. Fourier transform-infrared spectroscopy was used to compare plant metabolite profiles in relation to treatment and location. UV radiation and climatic parameters were determined for each location from online sources and the data were assessed using a combination of anova and multiple regression analyses. Most of the variation in growth between the locations was attributable to the combination of climatic parameters, with minimum temperature identified as an important growth constraint. However, no single environmental parameter could consistently account for the variability in plant growth. Concentrations of foliar UV-B absorbing compounds showed a positive trend with solar UV across the latitudinal gradient; however, this relationship was not consistent in all treatments. The most striking experimental outcome from this study was the effect of presence or absence of filtration frames on UV-absorbing compounds. Overall, the study demonstrates the value of an European approach in studying the impacts of natural UV across a large latitudinal gradient. We have shown the feasibility of coordinated UV filtration at multiple sites but have also highlighted the need for open controls and careful interpretation of plant responses.

Drought effects on allocation of recent carbon: from beech leaves to soil CO2 efflux.

*Recent studies have highlighted a direct, fast transfer of recently assimilated C from the tree canopy to the soil. However, the effect of environmental changes on this flux remains largely unknown. *We investigated the effects of drought on the translocation of recently assimilated C, by pulse-labelling 1.5-yr-old beech tree mesocosms with (13)CO(2). (13)C signatures were then measured daily for 1 wk in leaves, twigs, coarse and fine root water-soluble and total organic matter, phloem organic matter, soil microbial biomass and soil CO(2) efflux. *Drought reduced C assimilation and doubled the residence time of recently assimilated C in leaf biomass. In phloem organic matter, the (13)C label peaked immediately after labelling then decayed exponentially in the control treatment, while under drought it peaked 4 d after labelling. In soil microbial biomass, the label peaked 1 d after labelling in the control treatment, whereas under drought no peak was measured. Two days after labelling, drought decreased the contribution of recently assimilated C to soil CO(2) efflux by 33%. *Our study showed that drought reduced the coupling between canopy photosynthesis and belowground processes. This will probably affect soil biogeochemical cycling, with potential consequences including slower soil nitrogen cycling and changes in C-sequestration potential under future climate conditions.