Organ-specific metabolic responses to drought in Pinus pinaster Ait

Comparative Stem Transcriptome Analysis Reveals Pathways Associated with Drought Tolerance in Maritime Pine Grafts

The maritime pine (Pinus pinaster Ait.) is a highly valuable Mediterranean conifer. However, recurrent drought events threaten its propagation and conservation. P. pinaster populations exhibit remarkable differences in drought tolerance. To explore these differences, we analyzed stem transcriptional profiles of grafts combining genotypes with contrasting drought responses under well-watered and water-stress regimes. Our analysis underscored that P. pinaster drought tolerance is mainly associated with constitutively expressed genes, which vary based on genotype provenance. However, we identified key genes encoding proteins involved in water stress response, abscisic acid signaling, and growth control including a PHD chromatin regulator, a histone deubiquitinase, the ABI5-binding protein 3, and transcription factors from Myb-related, DOF NAC and LHY families. Additionally, we identified that drought-tolerant rootstock could enhance the drought tolerance of sensitive scions by regulating the accumulation of transcripts involved in carbon mobilization, osmolyte biosynthesis, flavonoid and terpenoid metabolism, and reactive oxygen species scavenging. These included genes encoding galactinol synthase, CBL-interacting serine/threonine protein kinase 5, BEL1-like homeodomain protein, dihydroflavonol 4-reductase, and 1-deoxy-D-xylulose-5-phosphate. Our results revealed several hub genes that could help us to understand the molecular and physiological response to drought of conifers. Based on all the above, grafting with selected drought-tolerant rootstocks is a promising method for propagating elite recalcitrant conifer species, such as P. pinaster.

Under Stress: Searching for Genes Involved in the Response of Abies pinsapo Boiss to Climate Change

Currently, Mediterranean forests are experiencing the deleterious effects of global warming, which mainly include increased temperatures and decreased precipitation in the region. Relict Abies pinsapo fir forests, endemic in the southern Iberian Peninsula, are especially sensitive to these recent environmental disturbances, and identifying the genes involved in the response of this endangered tree species to climate-driven stresses is of paramount importance for mitigating their effects. Genomic resources for A. pinsapo allow for the analysis of candidate genes reacting to warming and aridity in their natural habitats. Several members of the complex gene families encoding late embryogenesis abundant proteins (LEAs) and heat shock proteins (HSPs) have been found to exhibit differential expression patterns between wet and dry seasons when samples from distinct geographical locations and dissimilar exposures to the effects of climate change were analyzed. The observed changes were more perceptible in the roots of trees, particularly in declining forests distributed at lower altitudes in the more vulnerable mountains. These findings align with previous studies and lay the groundwork for further research on the molecular level. Molecular and genomic approaches offer valuable insights for mitigating climate stress and safeguarding this endangered conifer.

Comparative Analysis of the Wood Metabolites of Three Poplar Clones Using UPLC-Triple-TOF-MS

Poplar, a woody tree species, is widely used for industrial production and as a protective forest belt. Different clones of poplar exhibit clear variation in terms of morphological and physiological features, however, the impact of the genetic variation on the composition and abundance of wood metabolite have not been fully determined. In this study, ultra-high pressure liquid chromatography-triple time of flight-mass spectrometer (UPLC-Triple-TOF-MS) was used to explore the metabolite changes in poplar wood from three clones, including Populus deltoides CL. '55/65', P. deltoides CL. 'Danhong', and P. nigra CL. 'N179'. A total of 699 metabolites were identified. Clustering analysis and principal component analysis display that the metabolic differences of wood have allowed distinguishing different species of poplar. Meanwhile, eight significantly different metabolites were screened between P. deltoides and P. nigra, which may be considered as valuable markers for chemotaxonomy. In addition, the highly discriminant 352 metabolites were obtained among the three clones, and those may be closely related to the distinction in unique properties (e.g., growth, rigidity and tolerance) of the poplar wood cultivars. This study provides a foundation for further studies on wood metabolomics in poplar, and offers chemotaxonomic markers that will stimulate the early screening of potentially superior trees.

How Central Carbon Metabolites of Mexican Mint (Plectranthus amboinicus) Plants Are Impacted under Different Watering Regimes

Plants are sessile, and their ability to reprogram their metabolism to adapt to fluctuations in soil water level is crucial but not clearly understood. A study was performed to determine alterations in intermediate metabolites involved in central carbon metabolism (CCM) following exposure of Mexican mint (Plectranthus amboinicus) to varying watering regimes. The water treatments were regular watering (RW), drought (DR), flooding (FL), and resumption of regular watering after flooding (DHFL) or after drought (RH). Leaf cluster formation and leaf greening were swift following the resumption of regular watering. A total of 68 key metabolites from the CCM routes were found to be significantly (p < 0.01) impacted by water stress. Calvin cycle metabolites in FL plants, glycolytic metabolites in DR plants, total tricarboxylic acid (TCA) cycle metabolites in DR and DHFL plants, and nucleotide biosynthetic molecules in FL and RH plants were significantly (p < 0.05) increased. Pentose phosphate pathway (PPP) metabolites were equally high in all the plants except DR plants. Total Calvin cycle metabolites had a significantly (p < 0.001) strong positive association with TCA cycle (r = 0.81) and PPP (r = 0.75) metabolites. Total PPP metabolites had a moderately positive association with total TCA cycle metabolites (r = 0.68; p < 0.01) and a negative correlation with total glycolytic metabolites (r = -0.70; p < 0.005). In conclusion, the metabolic alterations of Mexican mint plants under different watering regimes were revealed. Future studies will use transcriptomic and proteomic approaches to identify genes and proteins that regulate the CCM route.

Leaf transcriptome analysis of Medicago ruthenica revealed its response and adaptive strategy to drought and drought recovery

BACKGROUND

Drought is one of the main causes of losses in forage crop yield and animal production. Medicago ruthenica (L.) cv. Zhilixing is a high-yielding alfalfa cultivar also known for its high tolerance to drought. We analyzed the transcriptome profile of this cultivar throughout drought stress and recovery and we were able to describe its phased response through the expression profiles of overlapping gene networks and drought-specific genes.

RESULTS

The ABA and auxin signal transduction pathways are overlapping pathways in response to drought and drought recovery in forage crops. Medicago ruthenica (L.) cv. Zhilixing adopts different strategies at different degrees of drought stress. On the 9th day of drought, transcriptional regulations related to osmoregulation are enhanced mainly through increased activities of carbohydrate and amino acid metabolism, while photosynthetic activities were reduced to slow down growth. With drought prolonging, on the 12th day of drought, the synthesis of proline and other stored organic substances was suppressed in general. After recovery, Medicago ruthenica synthesizes flavonoids through the flavonoid biosynthesis pathway to remove accumulated ROS and repair the oxidative damage from water stress. In addition, the regulation of circadian rhythm seems to accelerate the drought recovery process.

CONCLUSIONS

Medicago ruthenica adapts to drought by regulating the osmoregulatory system and photosynthesis, which appears to involve the ABA and auxin signaling pathways as key regulators. Furthermore, the synthesis of flavonoids and the regulation of the circadian rhythm can accelerate the recovery process. These results enriched our knowledge of molecular responses to drought and drought recovery in Medicago ruthenica and provide useful information for the development of new legume forage grass varieties with improved adaptability to drought stress.

Aerial and underground organs display specific metabolic strategies to cope with water stress under rising atmospheric CO2 in Fagus sylvatica L

Beech is known to be a moderately drought-sensitive tree species, and future increases in atmospheric concentrations of CO₂ ([CO₂ ]) could influence its ecological interactions, also with changes at the metabolic level. The metabolome of leaves and roots of drought-stressed beech seedlings grown under two different [CO₂ ] (400 (aCO₂ ) and 800 (eCO₂ ) ppm) was analyzed together with gas exchange parameters and water status. Water stress estimated from predawn leaf water potential (Ψ_pd ) was similar under both [CO₂ ], although eCO₂ had a positive impact on net photosynthesis and intrinsic water use efficiency. The aerial and underground organs showed different metabolomes. Leaves mainly stored C metabolites, while those of N and P accumulated differentially in roots. Drought triggered the proline and N-rich amino acids biosynthesis in roots through the activation of arginine and proline pathways. Besides the TCA cycle, polyols and soluble sugar biosynthesis were activated in roots, with no clear pattern seen in the leaves, prioritizing the root functioning as metabolites sink. eCO₂ slightly altered this metabolic acclimation to drought, reflecting mitigation of its effect. The leaves showed only minor changes, investing C surplus in secondary metabolites and malic acid. The TCA cycle metabolites and osmotically active substances increased in roots, but many other metabolites decreased as if the water stress was dampened. Above- and belowground plant metabolomes were differentially affected by two drivers of climate change, water scarcity and high [CO₂ ], showing different chemical responsiveness that could modulate the tree adaptation to future climatic scenarios.

Drought affects the fate of non-structural carbohydrates in hinoki cypress

Tree species that close stomata early in response to drought are likely to suffer from an imbalance between limited carbohydrate supply due to reduced photosynthesis and metabolic demand. Our objective was to clarify the dynamic responses of non-structural carbohydrates to drought in a water-saving species, the hinoki cypress (Chamaecyparis obtusa Sieb. et Zucc.). To this end, we pulse-labeled young trees with 13CO2 10 days after the beginning of the drought treatment. Trees were harvested 7 days later, early during drought progression, and 86 days later when they had suffered from a long and severe drought. The labeled carbon (C) was traced in phloem extract, in the organic matter and starch of all the organs, and in the soluble sugars (sucrose, glucose and fructose) of the most metabolically active organs (foliage, green branches and fine roots). No drought-related changes in labeled C partitioning between belowground and aboveground organs were observed. The C allocation between non-structural carbohydrates was altered early during drought progression: starch concentration was lower by half in the photosynthetic organs, while the concentration of almost all soluble sugars tended to increase. The preferential allocation of labeled C to glucose and fructose reflected an increased demand for soluble sugars for osmotic adjustment. After 3 months of a lethal drought, the concentrations of soluble sugars and starch were admittedly lower in drought-stressed trees than in the controls, but the pool of non-structural carbohydrates was far from completely depleted. However, the allocation to storage had been impaired by drought; photosynthesis and the sugar translocation rate had also been reduced by drought. Failure to maintain cell turgor through osmoregulation and to refill embolized xylem due to the depletion in soluble sugars in the roots could have resulted in tree mortality in hinoki cypress, though the total pool of carbohydrate was not completely depleted.

Transcriptomic and Metabolomic Analyses Reveal Key Metabolites, Pathways and Candidate Genes in Sophora davidii (Franch.) Skeels Seedlings Under Drought Stress

Soil aridification and desertification are particularly prominent in China's karst areas, severely limiting crop yields and vegetation restoration. Therefore, it is very important to identify naturally drought-tolerant plant species. Sophora davidii (Franch.) Skeels is resistant to drought and soil infertility, is deeply rooted and is an excellent plant material for soil and water conservation. We studied the transcriptomic and metabolomic changes in S. davidii in response to drought stress (CK, control; LD, mild drought stress; MD, moderate drought stress; and SD, severe drought stress). Sophora davidii grew normally under LD and MD stress but was inhibited under SD stress; the malondialdehyde (MDA), hydrogen peroxide (H₂O₂), soluble sugar, proline, chlorophyll a, chlorophyll b and carotenoid contents and ascorbate peroxidase (APX) activity significantly increased, while the superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) activities and soluble protein content significantly decreased. In the LD/CK, MD/CK and SD/CK comparison groups, there were 318, 734 and 1779 DEGs, respectively, and 100, 168 and 281 differentially accumulated metabolites, respectively. Combined analysis of the transcriptomic and metabolomic data revealed the metabolic regulation of S. davidii in response to drought stress. First, key candidate genes such as PRR7, PRR5, GI, ELF3, PsbQ, PsaK, INV, AMY, E2.4.1.13, E3.2.1.2, NCED, PP2C, PYL, ABF, WRKY33, P5CS, PRODH, AOC3, HPD, GPX, GST, CAT and SOD1 may govern the drought resistance of S. davidii. Second, three metabolites (oxidised glutathione, abscisic acid and phenylalanine) were found to be related to drought tolerance. Third, several key candidate genes and metabolites involved in 10 metabolic pathways were identified, indicating that these metabolic pathways play an important role in the response to drought in S. davidii and possibly other plant species.

Plant Flavonoids in Mediterranean Species: A Focus on Flavonols as Protective Metabolites under Climate Stress

Flavonoids are specialized metabolites largely widespread in plants where they play numerous roles including defense and signaling under stress conditions. These compounds encompass several chemical subgroups such as flavonols which are one the most represented classes. The most studied flavonols are kaempferol, quercetin and myricetin to which research attributes antioxidative properties and a potential role in UV-defense through UV-screening mechanisms making them critical for plant adaptation to climate change. Despite the great interest in flavonol functions in the last decades, some functional aspects remain under debate. This review summarizes the importance of flavonoids in plant defense against climate stressors and as signal molecules with a focus on flavonols in Mediterranean plant species. The review emphasizes the relationship between flavonol location (at the organ, tissue and cellular scales) and their function as defense metabolites against climate-related stresses. It also provides evidence that biosynthesis of flavonols, or flavonoids as a whole, could be a crucial process allowing plants to adapt to climate change, especially in the Mediterranean area which is considered as one of the most sensitive regions to climate change over the globe.

Genetic basis of growth, spring phenology, and susceptibility to biotic stressors in maritime pine

Forest ecosystems are increasingly challenged by extreme events, for example, drought, storms, pest attacks, and fungal pathogen outbreaks, causing severe ecological and economic losses. Understanding the genetic basis of adaptive traits in tree species is of key importance to preserve forest ecosystems, as genetic variation in a trait (i.e., heritability) determines its potential for human-mediated or evolutionary change. Maritime pine (Pinus pinaster Aiton), a conifer widely distributed in southwestern Europe and northwestern Africa, grows under contrasted environmental conditions promoting local adaptation. Genetic variation at adaptive phenotypes, including height, spring phenology, and susceptibility to two fungal pathogens (Diplodia sapinea and Armillaria ostoyae) and an insect pest (Thaumetopoea pityocampa), was assessed in a range-wide clonal common garden of maritime pine. Broad-sense heritability was significant for height (0.219), spring phenology (0.165-0.310), and pathogen susceptibility (necrosis length caused by D. sapinea, 0.152; and by A. ostoyae, 0.021, measured on inoculated, excised branches under controlled conditions), but not for pine processionary moth incidence in the common garden. The correlations of trait variation among populations revealed contrasting trends for pathogen susceptibility to D. sapinea and A. ostoyae with respect to height. Taller trees showed longer necrosis length caused by D. sapinea while shorter trees were more affected by A. ostoyae. Moreover, maritime pine populations from areas with high summer temperatures and frequent droughts were less susceptible to D. sapinea but more susceptible to A. ostoyae. Finally, an association study using 4227 genome-wide SNPs revealed several loci significantly associated with each trait (range of 3-26), including a possibly disease-induced translation initiation factor, eIF-5, associated with needle discoloration caused by D. sapinea. This study provides important insights to develop genetic conservation and breeding strategies integrating species responses to biotic stressors.

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.

Metabolomics and Molecular Approaches Reveal Drought Stress Tolerance in Plants

Metabolic regulation is the key mechanism implicated in plants maintaining cell osmotic potential under drought stress. Understanding drought stress tolerance in plants will have a significant impact on food security in the face of increasingly harsh climatic conditions. Plant primary and secondary metabolites and metabolic genes are key factors in drought tolerance through their involvement in diverse metabolic pathways. Physio-biochemical and molecular strategies involved in plant tolerance mechanisms could be exploited to increase plant survival under drought stress. This review summarizes the most updated findings on primary and secondary metabolites involved in drought stress. We also examine the application of useful metabolic genes and their molecular responses to drought tolerance in plants and discuss possible strategies to help plants to counteract unfavorable drought periods.

Rootstock effects on scion gene expression in maritime pine

Pines are the dominant conifers in Mediterranean forests. As long-lived sessile organisms that seasonally have to cope with drought periods, they have developed a variety of adaptive responses. However, during last decades, highly intense and long-lasting drought events could have contributed to decay and mortality of the most susceptible trees. Among conifer species, Pinus pinaster Ait. shows remarkable ability to adapt to different environments. Previous molecular analysis of a full-sib family designed to study drought response led us to find active transcriptional activity of stress-responding genes even without water deprivation in tolerant genotypes. To improve our knowledge about communication between above- and below-ground organs of maritime pine, we have analyzed four graft-type constructions using two siblings as rootstocks and their progenitors, Gal 1056 and Oria 6, as scions. Transcriptomic profiles of needles from both scions were modified by the rootstock they were grafted on. However, the most significant differential gene expression was observed in drought-sensitive Gal 1056, while in drought-tolerant Oria 6, differential gene expression was very much lower. Furthermore, both scions grafted onto drought-tolerant rootstocks showed activation of genes involved in tolerance to abiotic stress, and is most remarkable in Oria 6 grafts where higher accumulation of transcripts involved in phytohormone action, transcriptional regulation, photosynthesis and signaling has been found. Additionally, processes, such as those related to secondary metabolism, were mainly associated with the scion genotype. This study provides pioneering information about rootstock effects on scion gene expression in conifers.

Insights into the plant responses to drought and decoding the potential of root associated microbiome for inducing drought tolerance

Global increase in water scarcity is a serious problem for sustaining crop productivity. The lack of water causes the degeneration of the photosynthetic apparatus, an imbalance in key metabolic pathways, an increase in free radical generation as well as weakens the root architecture of plants. Drought is one of the major stresses that directly interferes with the osmotic status of plant cells. Abscisic acid (ABA) is known to be a key player in the modulation of drought responses in plants and involvement of both ABA-dependent and ABA-independent pathways have been observed during drought. Concomitantly, other phytohormones such as auxins, ethylene, gibberellins, cytokinins, jasmonic acid also confer drought tolerance and a crosstalk between different phytohormones and transcription factors at the molecular level exists. A number of drought-responsive genes and transcription factors have been utilized for producing transgenic plants for improved drought tolerance. Despite relentless efforts, biotechnological advances have failed to design completely stress tolerant plants until now. The root microbiome is the hidden treasure that possesses immense potential to revolutionize the strategies for inducing drought resistance in plants. Root microbiota consist of plant growth-promoting rhizobacteria, endophytes and mycorrhizas that form a consortium with the roots. Rhizospheric microbes are proliferous producers of phytohormones, mainly auxins, cytokinin, and ethylene as well as enzymes like the 1-aminocyclopropane-1-carboxylate deaminase (ACC deaminase) and metabolites like exopolysaccharides that help to induce systemic tolerance against drought. This review, therefore focuses on the major mechanisms of plant-microbe interactions under drought-stressed conditions and emphasizes the importance of drought-tolerant microbes for sustaining and improving the productivity of crop plants under stress.

Stem metabolism under drought stress - a paradox of increasing respiratory substrates and decreasing respiratory rates

Metabolic changes underpinning drought-induced variations in stem respiration (R_s ) are unknown. We measured R_s rates and metabolite and gene expression profiles in Ulmus minor Mill. and Quercus ilex L. seedlings subjected to increasing levels of drought stress to better understand how carbon, nitrogen and energy metabolism interact during drought. In both species, only plants showing extreme stress symptoms - i.e. negligible rates of leaf stomatal conductance and photosynthesis, and high stem dehydration (30-50% of maximum water storage) and contraction (50-150 μm week^-1 ) - exhibited lower R_s rates than well-watered plants. Abundance of low-molecular weight sugars (e.g. glucose and fructose) and sugar alcohols (e.g. mannitol) increased with drought, at more moderate stress and to a higher extent in Q. ilex than U. minor. Abundance of amino acids increased at more severe stress, more abruptly, and to a higher extent in U. minor, coinciding with leaf senescence, which did not occur in Q. ilex. Organic acids changed less in response to drought: threonate and glycerate increased, and citrate decreased although slightly in both species. Transcripts of genes coding for enzymes of the Krebs cycle decreased in Q. ilex and increased in U. minor in conditions of extreme drought stress. The maintenance of R_s under severe growth and photosynthetic restrictions reveals the importance of stem mitochondrial activity in drought acclimation. The eventual decline in R_s diverts carbon substrates from entering the Krebs cycle that may help to cope with osmotic and oxidative stress during severe drought and to recover hydraulic functionality afterwards.

Specific leaf metabolic changes that underlie adjustment of osmotic potential in response to drought by four Quercus species

Osmotic adjustment is almost ubiquitous as a mechanism of response to drought in many forest species. Recognized as an important mechanism of increasing turgor under water stress, the metabolic basis for osmotic adjustment has been described in only a few species. We set an experiment with four species of the genus Quercus ranked according to drought tolerance and leaf habit from evergreen to broad-leaved deciduous. A cycle of watering deprivation was imposed on seedlings, resulting in well-watered (WW) and water-stressed (WS) treatments, and their water relations were assessed from pressure-volume curves. Leaf predawn water potential (Ψpd) significantly decreased in WS seedlings, which was followed by a drop in leaf osmotic potential at full turgor (Ψπ100). The lowest values of Ψπ100 followed the ranking of decreasing drought tolerance: Quercus ilex L. < Quercus faginea Lam. < Quercus pyrenaica Willd. < Quercus petraea Matt. Liebl. The leaf osmotic potential at the turgor loss point (ΨTLP) followed the same pattern as Ψπ100 across species and treatments. The pool of carbohydrates, some organic acids and cyclitols were the main osmolytes explaining osmotic potential across species, likewise to the osmotic adjustment assessed from the decrease in leaf Ψπ100 between WW and WS seedlings. Amino acids were very responsive to WS, particularly γ-aminobutyric acid in Q. pyrenaica, but made a relatively minor contribution to osmotic potential compared with other groups of compounds. In contrast, the cyclitol proto-quercitol made a prominent contribution to the changes in osmotic potential regardless of watering treatment or species. However, different metabolites, such as quinic acid, played a more important role in osmotic adjustment in Q. ilex, distinguishing it from the other species studied. In conclusion, while osmotic adjustment was present in all four Quercus species, the molecular processes underpinning this response differed according to their phylogenetic history and specific ecology.

Transcriptome Analysis of Needle and Root of Pinus Massoniana in Response to Continuous Drought Stress

Pinus massoniana Lamb. is an important coniferous tree species in ecological environment construction and sustainable forestry development. The function of gene gradual change and coexpression modules of needle and root parts of P. massoniana under continuous drought stress is unclear. The physiological and transcriptional expression profiles of P. massoniana seedlings from 1a half-sibling progeny during drought stress were measured and analyzed. As a result, under continuous drought conditions, needle peroxidase (POD) activity and proline content continued to increase. The malondialdehyde (MDA) content in roots continuously increased, and the root activity continuously decreased. The needles of P. massoniana seedlings may respond to drought mainly through regulating abscisic acid (ABA) and jasmonic acid (JA) hormone-related pathways. Roots may provide plant growth through fatty acid β-oxidative decomposition, and peroxisomes may contribute to the production of ROS, resulting in the upregulation of the antioxidant defense system. P. massoniana roots and needles may implement the same antioxidant mechanism through the glutathione metabolic pathway. This study provides basic data for identifying the drought response mechanisms of the needles and roots of P. massoniana.

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.

Wood profiling by non-targeted high-resolution mass spectrometry: Part 1, Metabolite profiling in Cedrela wood for the determination of the geographical origin

The determination of the geographical origin of wood can be highly relevant for several reasons: On the one hand, it can help to prevent illegal logging and timber trade, on the other hand, it is of special interest for archaeological artefacts made of wood, as well as for a variety of biological questions. For this reason, different extraction methods were first tested for the analysis of polar and non-polar metabolites using liquid chromatography coupled electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC-ESI-QTOF-MS). A two-phase extraction with chloroform, methanol and water proved to be particularly successful. Subsequently, cedrela (Cedrela odorata) samples from South America were measured to distinguish geographic origin. Using multivariate data analysis, numerous origin-dependent differences could be extracted. The identification of the marker substances indicated that several metabolic pathways were affected by the geographical influences, some of them probably indicating pest infections.

Full-Length Transcriptome Analysis of Four Different Tissues of Cephalotaxus oliveri

Cephalotaxus oliveri is a tertiary relict conifer endemic to China, regarded as a national second-level protected plant in China. This species has experienced severe changes in temperature and precipitation in the past millions of years, adapting well to harsh environments. In view of global climate change and its endangered conditions, it is crucial to study how it responds to changes in temperature and precipitation for its conservation work. In this study, single-molecule real-time (SMRT) sequencing and Illumina RNA sequencing were combined to generate the complete transcriptome of C. oliveri. Using the RNA-seq data to correct the SMRT sequencing data, the four tissues obtained 63,831 (root), 58,108 (stem), 33,013 (leaf) and 62,436 (male cone) full-length unigenes, with a N50 length of 2523, 3480, 3181, and 3267 bp, respectively. Additionally, 35,887, 11,306, 36,422, and 25,439 SSRs were detected for the male cone, leaf, root, and stem, respectively. The number of long non-coding RNAs predicted from the root was the largest (11,113), and the other tissues were 3408 (stem), 3193 (leaf), and 3107 (male cone), respectively. Functional annotation and enrichment analysis of tissue-specific expressed genes revealed the special roles in response to environmental stress and adaptability in the different four tissues. We also characterized the gene families and pathways related to abiotic factors. This work provides a comprehensive transcriptome resource for C. oliveri, and this resource will facilitate further studies on the functional genomics and adaptive evolution of C. oliveri.

UPLC-QTof-MSE Metabolomics Reveals Changes in Leaf Primary and Secondary Metabolism of Hop (Humulus lupulus L.) Plants under Drought Stress

The hop (Humulus lupulus L.) is an important specialty crop used in beer production. Untargeted UPLC-QTof-MS^E metabolomics was used to determine metabolite changes in the leaves of hop plants under varying degrees of drought stress. Principal component analysis revealed that drought treatments produced qualitatively distinct changes in the overall chemical composition of three out of four genotypes tested (i.e., Cascade, Sultana, and a wild var. neomexicanus accession but not Aurora), although differences among treatments were smaller than differences among genotypes. A total of 14 compounds consistently increased or decreased in response to drought stress, and this effect was generally progressive as the severity of drought increased. A total of 10 of these marker compounds were tentatively identified as follows: five glycerolipids, glutaric acid, pheophorbide A, abscisic acid, roseoside, and dihydromyricetin. Some of the observed metabolite changes likely occur across all plants under drought conditions, while others may be specific to hops or to the type of drought treatments performed.

Molecular study of drought response in the Mediterranean conifer Pinus pinaster Ait.: Differential transcriptomic profiling reveals constitutive water deficit-independent drought tolerance mechanisms

Adaptation of long-living forest trees to respond to environmental changes is essential to secure their performance under adverse conditions. Water deficit is one of the most significant stress factors determining tree growth and survival. Maritime pine (Pinus pinaster Ait.), the main source of softwood in southwestern Europe, is subjected to recurrent drought periods which, according to climate change predictions for the years to come, will progressively increase in the Mediterranean region. The mechanisms regulating pine adaptive responses to environment are still largely unknown. The aim of this work was to go a step further in understanding the molecular mechanisms underlying maritime pine response to water stress and drought tolerance at the whole plant level. A global transcriptomic profiling of roots, stems, and needles was conducted to analyze the performance of siblings showing contrasted responses to water deficit from an ad hoc designed full-sib family. Although P. pinaster is considered a recalcitrant species for vegetative propagation in adult phase, the analysis was conducted using vegetatively propagated trees exposed to two treatments: well-watered and moderate water stress. The comparative analyses led us to identify organ-specific genes, constitutively expressed as well as differentially expressed when comparing control versus water stress conditions, in drought-sensitive and drought-tolerant genotypes. Different response strategies can point out, with tolerant individuals being pre-adapted for coping with drought by constitutively expressing stress-related genes that are detected only in latter stages on sensitive individuals subjected to drought.

Rising [CO2] effect on leaf drought-induced metabolome in Pinus pinaster Aiton: Ontogenetic- and genotypic-specific response exhibit different metabolic strategies

Rising atmospheric CO₂ concentrations ([CO₂]) together with water deficit can influence ecological interactions of trees through an array of chemically driven changes in plant leaves. In four drought stressed Pinus pinaster genotypes, grown under two levels of atmospheric [CO₂] (ambient (aCO₂) and enriched (eCO₂)) the metabolome of adult and juvenile needles was analyzed to know if the metabolic responses to this environmental situation could be genotype-dependent and vary according to the stage of needle ontogeny. Drought had the highest incidence, followed by needle ontogeny, being lower the eCO₂ effect. The eCO₂ reduced, eliminated or countered the 50 (adult needles) - 44% (juvenile) of the drought-induced changes, suggesting that CO₂-enriched plants could perceived less oxidative stress under drought, and proving that together, these two abiotic factors triggered a metabolic response different from that under single factors. Genotype drought tolerance and ontogenetic stage determined the level of metabolite accumulation and the plasticity to eCO₂ under drought, which was mainly reflected in antioxidant levels and tree chemical defense. At re-watering, previously water stressed plants showed both, reduced C and N metabolism, and a "drought memory effect", favoring antioxidants and osmolyte storage. This effect showed variations regarding genotype drought-tolerance, needle ontogeny and [CO₂], with remarkable contribution of terpenoids. Chemical defense and drought tolerance were somehow linked, increasing chemical defense during recovery in the most drought-sensitive individuals. The better adaptation of trees to drought under eCO₂, as well as their ability to recover better from water stress, are essential for the survival of forest trees.

Effect of Monochamus galloprovincialis feeding on Pinus pinaster and Pinus pinea, oleoresin and insect volatiles

In Portugal, the pine black sawyer Monochamus galloprovincialis is the principal vector of the pinewood nematode, Bursaphelenchus xylophilus, the causal agent of pine wilt disease (PWD), a lethal phyopathogen with major ecological and economic consequences to European forestry. The aim of this study was to determine the influence of M. galloprovincialis feeding on the volatiles emitted by pine trees. This study focused on the pine species which are most relevant to Portugal, that is, Pinus pinaster (maritime pine) and Pinus pinea (stone or umbrella pine), assessing to what extent pine chemotypes might influence feeding by the insect vector. Preliminary evaluation of each maritime pine essential oil allowed recognizing the existence of two main chemotypes (C1 and C2) and absence of chemical variability in P. pinea. Emission of volatiles from pine trees was evaluated before and during 24 h of feeding by a mixed-sex pair of newly emerged, unfed M. galloprovincialis. Volatiles were also collected from the oleoresin released from the feeding wounds as well as from the insects after feeding. Pine volatiles were collected by solid phase microextraction (SPME) and insect volatiles extracted with pentane, and all analysed by gas chromatography-mass spectrometry (GC-MS) and by GC for component identification and quantification, respectively. Of the seventeen emitted volatiles detected in SPME analyses of P. pinaster, β-pinene, α-pinene, β-caryophyllene, and germacrene D showed the highest average fold increases as a result of M. galloprovincialis feeding. When grouped by P. pinaster chemotype, C1 and C2 groups of trees showed different patterns of responses. β-Caryophyllene and germacrene D showed the highest fold increase in C1 trees, whereas β-pinene and α-pinene clearly dominated in C2 trees. Likewise, the oleoresin volatiles from C1 trees were dominated by δ-3-carene and/or β-pinene, whereas α-pinene and β-pinene were the main volatile components from oleoresin of C2 trees. Nine components were detected in P. pinea volatiles, of which limonene showed the highest fold increase as a result of insect feeding. The volatiles collected from the insects after they had fed on P. pinaster included α-pinene, β-pinene, and abietic acid, and by the straight-chain n-alkanes n-C27, n-C29, and n-C25, together with the methyl-branched hydrocarbons 3-meC29, 2-meC28, and 3-meC27. A better understanding of the responses of different P. pinaster chemotypes to feeding by M. galloprovincialis may be helpful in the development of new lures to improve pine sawyer trapping in integrated pest management for control of PWD.

Ascorbic Acid-The Little-Known Antioxidant in Woody Plants

Reactive oxygen species (ROS) are constantly produced by metabolically active plant cells. The concentration of ROS may determine their role, e.g., they may participate in signal transduction or cause oxidative damage to various cellular components. To ensure cellular homeostasis and minimize the negative effects of excess ROS, plant cells have evolved a complex antioxidant system, which includes ascorbic acid (AsA). AsA is a multifunctional metabolite with strong reducing properties that allows the neutralization of ROS and the reduction of molecules oxidized by ROS in cooperation with glutathione in the Foyer-Halliwell-Asada cycle. Antioxidant enzymes involved in AsA oxidation and reduction switches evolved uniquely in plants. Most experiments concerning the role of AsA have been performed on herbaceous plants. In addition to extending our understanding of this role in additional taxa, fundamental knowledge of the complex life cycle stages of woody plants, including their development and response to environmental factors, will enhance their breeding and amend their protection. Thus, the role of AsA in woody plants compared to that in nonwoody plants is the focus of this paper. The role of AsA in woody plants has been studied for nearly 20 years. Studies have demonstrated that AsA is important for the growth and development of woody plants. Substantial changes in AsA levels, as well as reduction and oxidation switches, have been reported in various physiological processes and transitions described mainly in leaves, fruits, buds, and seeds. Evidently, AsA exhibits a dual role in the photoprotection of the photosynthetic apparatus in woody plants, which are the most important scavengers of ozone. AsA is associated with proper seed production and, thus, woody plant reproduction. Similarly, an important function of AsA is described under drought, salinity, temperature, light stress, and biotic stress. This report emphasizes the involvement of AsA in the ecological advantages, such as nutrition recycling due to leaf senescence, of trees and shrubs compared to nonwoody plants.

Experimental Design and Sample Preparation in Forest Tree Metabolomics

Appropriate experimental design and sample preparation are key steps in metabolomics experiments, highly influencing the biological interpretation of the results. The sample preparation workflow for plant metabolomics studies includes several steps before metabolite extraction and analysis. These include the optimization of laboratory procedures, which should be optimized for different plants and tissues. This is particularly the case for trees, whose tissues are complex matrices to work with due to the presence of several interferents, such as oleoresins, cellulose. A good experimental design, tree tissue harvest conditions, and sample preparation are crucial to ensure consistency and reproducibility of the metadata among datasets. In this review, we discuss the main challenges when setting up a forest tree metabolomics experiment for mass spectrometry (MS)-based analysis covering all technical aspects from the biological question formulation and experimental design to sample processing and metabolite extraction and data acquisition. We also highlight the importance of forest tree metadata standardization in metabolomics studies.

Differential metabolic responses of shrubs and grasses to water additions in arid karst region, southwestern China

Increasing precipitation has been predicted to occur in the karst areas in southwestern regions of China. However, it is little known how various plants respond to increasing precipitation in this region. Here we determined the impacts of water addition on leaf metabolites of grasses (Cymbopogon distans and Arundinella sitosa) and shrubs (Carissa spinarum and Bauhinia brachycarpa) in this area. Four levels of water additions (CK, T1, T2 and T3 indicating 0%, +20%, +40% and +60% relative to the current monthly precipitation, respectively) were designed. Sphingolipids substantially increased in the leaves of all four species with increasing water supply which suggests that these plants adopted biochemical strategy to tolerate the wet stress. However, both shrubs showed decreases in valine and threonine (amino acids), threonate, succinate and ascorbic acid (organic acids), galactose and rhamnose (sugars) and epicatchin and oleamides (secondary metabolites) with increasing water supply. Both grasses increased in the total metabolites at T1, but the total metabolites in A. sitosa significantly decreased at T2 and T3 while remains unchanged in C. distans. Tri-carboxylic acid cycle and amino acid metabolism in shrubs and shikimate pathway in grasses were strongly affected with water supply. Overall, shrubs and grasses respond differentially to variation in water addition in terms of metabolomics, which is helpful in understanding how plants respond to climate change.

Metabolic response to elevated CO2 levels in Pinus pinaster Aiton needles in an ontogenetic and genotypic-dependent way

Global climate changes involve elevated atmospheric [CO₂], fostering the carbon allocation to tree sink tissues, partitioning it into metabolic pathways. We use metabolomics analysis in adult and juvenile needles of four Pinus pinaster genotypes exposed to two levels of growth [CO₂]: ambient (400 μmol mol^-1) and enriched (800 μmol mol^-1), to know if the metabolic responses are genotype-dependent and vary according to the stage of needle ontogeny. The eCO₂-induced changes in the needle metabolomes are more significant in secondary metabolism pathways and especially meaningful in juvenile needles. The heteroblasty has important consequences in the expression of the metabolome, and on the plasticity to CO₂, determining the level of specific metabolite accumulation, showing an interdependence between adult and juvenile needles. The P. pinaster needle metabolomes also show clear quantitative differences linked to genotype, as well as regarding the metabolic response to eCO₂, showing both, common and genotype-specific biochemical responses. Thus, the changes in flavonol levels are mainly genotype-independent, while those in terpenoid and free fatty acids are mainly genotype-dependent, ratifying the importance of genotype to determine the metabolic response to eCO₂. To understand the adaptation mechanisms that tree species can develop to cope with eCO₂ it is necessary to know the genetically distinct responses within a species to recognize the CO₂-induced changes from the divergent approaches, what can facilitate knowing also the possible interrelation of the physiological and metabolic responses. That could explain the controversial effects of eCO₂ on the carbon-based metabolite in conifers, at the inter- and intra-specific level.