Ecological metabolomics: overview of current developments and future challenges

We Are What We Eat: A Stoichiometric and Ecometabolomic Study of Caterpillars Feeding on Two Pine Subspecies of Pinus sylvestris

Many studies have addressed several plant-insect interaction topics at nutritional, molecular, physiological, and evolutionary levels. However, it is still unknown how flexible the metabolism and the nutritional content of specialist insect herbivores feeding on different closely related plants can be. We performed elemental, stoichiometric, and metabolomics analyses on leaves of two coexisting Pinus sylvestris subspecies and on their main insect herbivore; the caterpillar of the processionary moth (Thaumetopoea pityocampa). Caterpillars feeding on different pine subspecies had distinct overall metabolome structure, accounting for over 10% of the total variability. Although plants and insects have very divergent metabolomes, caterpillars showed certain resemblance to their plant-host metabolome. In addition, few plant-related secondary metabolites were found accumulated in caterpillar tissues which could potentially be used for self-defense. Caterpillars feeding on N and P richer needles had lower N and P tissue concentration and higher C:N and C:P ratios, suggesting that nutrient transfer is not necessarily linear through trophic levels and other plant-metabolic factors could be interfering. This exploratory study showed that little chemical differences between plant food sources can impact the overall metabolome of specialist insect herbivores. Significant nutritional shifts in herbivore tissues could lead to larger changes of the trophic web structure.

Metabotype variation in a field population of tansy plants influences aphid host selection

It is well known that plant volatiles influence herbivores in their selection of a host plant; however, less is known about how the nonvolatile metabolome affects herbivore host selection. Metabolic diversity between intraspecific plants can be characterized using non-targeted mass spectrometry that gives us a snapshot overview of all metabolic processes occurring within a plant at a particular time. Here, we show that non-targeted metabolomics can be used to reveal links between intraspecific chemical diversity and ecological processes in tansy (Tanacetum vulgare). First, we show that tansy plants can be categorized into five subgroups based up on their metabolic profiles, and that these "metabotypes" influenced natural aphid colonization in the field. Second, this grouping was not due to induced metabolomic changes within the plant due to aphid feeding but rather resulted from constitutive differences in chemical diversity between plants. These findings highlight the importance of intraspecific chemical diversity within one plant population and provide the first report of a non-targeted metabolomic field study in chemical ecology.

Root metabolic plasticity underlies functional diversity in mycorrhiza-enhanced stress tolerance in tomato

Arbuscular mycorrhizal (AM) symbioses can improve plant tolerance to multiple stresses. We compared three AM fungi (AMF) from different genera, one of them isolated from a dry and saline environment, in terms of their ability to increase tomato tolerance to moderate or severe drought or salt stress. Plant physiological parameters and metabolic profiles were compared in order to find the molecular mechanisms underlying plant protection against stress. Mycorrhizal growth response was determined, and ultrahigh-performance LC-MS was used to compare the metabolic profile of plants under the different treatments. All AMF increased plant tolerance to stress, and the positive effects of the symbiosis were correlated with the severity of the stress. The AMF isolated from the stressful environment was the most effective in improving plant tolerance to salt stress. Differentially accumulated compounds were identified and the antistress properties of some of them were confirmed. We demonstrate that AM symbioses increase plant metabolic plasticity to cope with stress. Some responses were common to all AMF tested, while others were specifically related to particular isolates. Important metabolism reprograming was evidenced upon salt stress, and we identified metabolic pathways and compounds differentially accumulated in mycorrhizas that may underlie their enhanced tolerance to stress.

Plastic and genetic responses of a common sedge to warming have contrasting effects on carbon cycle processes

Climate warming affects plant physiology through genetic adaptation and phenotypic plasticity, but little is known about how these mechanisms influence ecosystem processes. We used three elevation gradients and a reciprocal transplant experiment to show that temperature causes genetic change in the sedge Eriophorum vaginatum. We demonstrate that plants originating from warmer climate produce fewer secondary compounds, grow faster and accelerate carbon dioxide (CO₂) release to the atmosphere. However, warmer climate also caused plasticity in E. vaginatum, inhibiting nitrogen metabolism, photosynthesis and growth and slowing CO₂ release into the atmosphere. Genetic differentiation and plasticity in E. vaginatum thus had opposing effects on CO₂ fluxes, suggesting that warming over many generations may buffer, or reverse, the short‐term influence of this species over carbon cycle processes. Our findings demonstrate the capacity for plant evolution to impact ecosystem processes, and reveal a further mechanism through which plants will shape ecosystem responses to climate change.

Metabolomic profiling of matured coconut water during post-harvest storage revealed discrimination and distinct changes in metabolites

The metabolites of coconut water stored at room temperature were analyzed using UPLC-MS/MS and multivariate statistical analysis to identify the differential biomarkers and metabolic pathways during post-harvest storage. Principal component analysis (PCA), partial least squares-discriminate analysis (PLS-DA), and orthogonal projections to latent structures discriminant analysis (OPLS-DA) were employed to analyze the UPLC-MS/MS data set of 34 matured coconut water samples collected after 0, 1, 2, 3, 4, and 5 months of storage (MOS); moreover, the p-value and fold change were chosen to identify the differential biomarkers; furthermore, a KEGG pathway was applied to analyze the metabolic pathways. All samples were discriminated well in the OPLS-DA model and were divided into two clusters: groups A (0 MOS, and so on), B, C, and D were in one cluster, and groups E and F were in another. A total of 18 biomarkers were identified among all groups and 12 biomarkers between groups A and E, from which we concluded that the post-harvest storage life of matured coconut water shall not exceed 3 months and the pathways of the TCA cycle, protein hydrolysis from coconut meat, and interconversion among amino acids were mainly enriched during the post-harvest storage.

Seasonal variation of secondary metabolites in nine different bryophytes

Bryophytes occur in almost all land ecosystems and contribute to global biogeochemical cycles, ecosystem functioning, and influence vegetation dynamics. As growth and biochemistry of bryophytes are strongly dependent on the season, we analyzed metabolic variation across seasons with regard to ecological characteristics and phylogeny. Using bioinformatics methods, we present an integrative and reproducible approach to connect ecology with biochemistry. Nine different bryophyte species were collected in three composite samples in four seasons. Untargeted liquid chromatography coupled with mass spectrometry (LC/MS) was performed to obtain metabolite profiles. Redundancy analysis, Pearson's correlation, Shannon diversity, and hierarchical clustering were used to determine relationships among species, seasons, ecological characteristics, and hierarchical clustering. Metabolite profiles of Marchantia polymorpha and Fissidens taxifolius which are species with ruderal life strategy (R-selected) showed low seasonal variability, while the profiles of the pleurocarpous mosses and Grimmia pulvinata which have characteristics of a competitive strategy (C-selected) were more variable. Polytrichum strictum and Plagiomnium undulatum had intermediary life strategies. Our study revealed strong species-specific differences in metabolite profiles between the seasons. Life strategies, growth forms, and indicator values for light and soil were among the most important ecological predictors. We demonstrate that untargeted Eco-Metabolomics provide useful biochemical insight that improves our understanding of fundamental ecological strategies.

Computational workflow to study the seasonal variation of secondary metabolites in nine different bryophytes

In Eco-Metabolomics interactions are studied of non-model organisms in their natural environment and relations are made between biochemistry and ecological function. Current challenges when processing such metabolomics data involve complex experiment designs which are often carried out in large field campaigns involving multiple study factors, peak detection parameter settings, the high variation of metabolite profiles and the analysis of non-model species with scarcely characterised metabolomes. Here, we present a dataset generated from 108 samples of nine bryophyte species obtained in four seasons using an untargeted liquid chromatography coupled with mass spectrometry acquisition method (LC/MS). Using this dataset we address the current challenges when processing Eco-Metabolomics data. Here, we also present a reproducible and reusable computational workflow implemented in Galaxy focusing on standard formats, data import, technical validation, feature detection, diversity analysis and multivariate statistics. We expect that the representative dataset and the reusable processing pipeline will facilitate future studies in the research field of Eco-Metabolomics.

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.

NMR-based metabolomic profiling of Peganum harmala L. reveals dynamic variations between different growth stages

Xerophytes play an active role in preventing soil denudation and desertification in arid and semi-arid areas. Peganum harmala L. (Zygophyllaceae family), a seasonally growing, poisonous and drought-tolerant plant, is widely distributed in the Xinjiang Uygur Autonomous Region and used as a traditional herbal medicine as well as, in winter, a fodder source. Previous research has focused on the pharmacological activity of isolated compounds and stress responses to growth environments. However, the metabolic profile of P. harmala and variations in its metabolites, including medicinally active and stress resistance components, have not been illustrated during different growth stages. Here, we collected plant samples in May, August, October and December. We determined the metabolic composition of methanol extracts using NMR spectroscopy, and comparisons of four growth stages were accomplished by applying statistical analysis. The results showed that vasicine, choline and sucrose were significantly elevated in samples harvested in May. Significantly higher amounts of betaine, lysine, 4-hydroxyisoleucine and proline were found in samples collected in August than in samples collected in other months, and the concentrations of phosphorylcholine, glucose, acetic acid and vasicinone were highest in December. The relationships between differential biomarkers and plant physiological states affected by diverse growth environmental factors were discussed. Our result deepened the understanding of metabolic mechanisms in plant development and confirmed the advantage of using NMR-based metabolomic treatments in quality evaluation when P. harmala is used for different purposes.

Discovering variation of secondary metabolite diversity and its relationship with disease resistance in Cornus florida L

Understanding intraspecific relationships between genetic and functional diversity is a major goal in the field of evolutionary biology and is important for conserving biodiversity. Linking intraspecific molecular patterns of plants to ecological pressures and trait variation remains difficult due to environment-driven plasticity. Next-generation sequencing, untargeted liquid chromatography-mass spectrometry (LC-MS) profiling, and interdisciplinary approaches integrating population genomics, metabolomics, and community ecology permit novel strategies to tackle this problem. We analyzed six natural populations of the disease-threatened Cornus florida L. from distinct ecological regions using genotype-by-sequencing markers and LC-MS-based untargeted metabolite profiling. We tested the hypothesis that higher genetic diversity in C. florida yielded higher chemical diversity and less disease susceptibility (screening hypothesis), and we also determined whether genetically similar subpopulations were similar in chemical composition. Most importantly, we identified metabolites that were associated with candidate loci or were predictive biomarkers of healthy or diseased plants after controlling for environment. Subpopulation clustering patterns based on genetic or chemical distances were largely congruent. While differences in genetic diversity were small among subpopulations, we did observe notable similarities in patterns between subpopulation averages of rarefied-allelic and chemical richness. More specifically, we found that the most abundant compound of a correlated group of putative terpenoid glycosides and derivatives was correlated with tree health when considering chemodiversity. Random forest biomarker and genomewide association tests suggested that this putative iridoid glucoside and other closely associated chemical features were correlated to SNPs under selection.

Current Challenges in Plant Eco-Metabolomics

The relatively new research discipline of Eco-Metabolomics is the application of metabolomics techniques to ecology with the aim to characterise biochemical interactions of organisms across different spatial and temporal scales. Metabolomics is an untargeted biochemical approach to measure many thousands of metabolites in different species, including plants and animals. Changes in metabolite concentrations can provide mechanistic evidence for biochemical processes that are relevant at ecological scales. These include physiological, phenotypic and morphological responses of plants and communities to environmental changes and also interactions with other organisms. Traditionally, research in biochemistry and ecology comes from two different directions and is performed at distinct spatiotemporal scales. Biochemical studies most often focus on intrinsic processes in individuals at physiological and cellular scales. Generally, they take a bottom-up approach scaling up cellular processes from spatiotemporally fine to coarser scales. Ecological studies usually focus on extrinsic processes acting upon organisms at population and community scales and typically study top-down and bottom-up processes in combination. Eco-Metabolomics is a transdisciplinary research discipline that links biochemistry and ecology and connects the distinct spatiotemporal scales. In this review, we focus on approaches to study chemical and biochemical interactions of plants at various ecological levels, mainly plant⁻organismal interactions, and discuss related examples from other domains. We present recent developments and highlight advancements in Eco-Metabolomics over the last decade from various angles. We further address the five key challenges: (1) complex experimental designs and large variation of metabolite profiles; (2) feature extraction; (3) metabolite identification; (4) statistical analyses; and (5) bioinformatics software tools and workflows. The presented solutions to these challenges will advance connecting the distinct spatiotemporal scales and bridging biochemistry and ecology.

Rhizosphere Protists Change Metabolite Profiles in Zea mays

Plant growth and productivity depend on the interactions of the plant with the associated rhizosphere microbes. Rhizosphere protists play a significant role in this respect: considerable efforts have been made in the past to reveal the impact of protist-bacteria interactions on the remobilization of essential nutrients for plant uptake, or the grazing induced changes on plant-growth promoting bacteria and the root-architecture. However, the metabolic responses of plants to the presence of protists or to protist-bacteria interactions in the rhizosphere have not yet been analyzed. Here we studied in controlled laboratory experiments the impact of bacterivorous protists in the rhizosphere on maize plant growth parameters and the bacterial community composition. Beyond that we investigated the induction of plant biochemical responses by separately analyzing above- and below-ground metabolite profiles of maize plants incubated either with a soil bacterial inoculum or with a mixture of soil bacteria and bacterivorous protists. Significantly distinct leaf and root metabolite profiles were obtained from plants which grew in the presence of protists. These profiles showed decreased levels of a considerable number of metabolites typical for the plant stress reaction, such as polyols, a number of carbohydrates and metabolites connected to phenolic metabolism. We assume that this decrease in plant stress is connected to the grazing induced shifts in rhizosphere bacterial communities as shown by distinct T-RFLP community profiles. Protist grazing had a clear effect on the overall bacterial community composition, richness and evenness in our microcosms. Given the competition of plant resource allocation to either defense or growth, we propose that a reduction in plant stress levels caused directly or indirectly by protists may be an additional reason for corresponding positive effects on plant growth.

Moving beyond the van Krevelen Diagram: A New Stoichiometric Approach for Compound Classification in Organisms

van Krevelen diagrams (O/C vs H/C ratios of elemental formulas) have been widely used in studies to obtain an estimation of the main compound categories present in environmental samples. However, the limits defining a specific compound category based solely on O/C and H/C ratios of elemental formulas have never been accurately listed or proposed to classify metabolites in biological samples. Furthermore, while O/C vs H/C ratios of elemental formulas can provide an overview of the compound categories, such classification is inefficient because of the large overlap among different compound categories along both axes. We propose a more accurate compound classification for biological samples analyzed by high-resolution mass spectrometry based on an assessment of the C/H/O/N/P stoichiometric ratios of over 130 000 elemental formulas of compounds classified in 6 main categories: lipids, peptides, amino sugars, carbohydrates, nucleotides, and phytochemical compounds (oxy-aromatic compounds). Our multidimensional stoichiometric compound classification (MSCC) constraints showed a highly accurate categorization of elemental formulas to the main compound categories in biological samples with over 98% of accuracy representing a substantial improvement over any classification based on the classic van Krevelen diagram. This method represents a signficant step forward in environmental research, especially ecological stoichiometry and eco-metabolomics studies, by providing a novel and robust tool to improve our understanding of the ecosystem structure and function through the chemical characterization of biological samples.

Metabolomic Profiles of Dinophysis acuminata and Dinophysis acuta Using Non-Targeted High-Resolution Mass Spectrometry: Effect of Nutritional Status and Prey

Photosynthetic species of the genus Dinophysis are obligate mixotrophs with temporary plastids (kleptoplastids) that are acquired from the ciliate Mesodinium rubrum, which feeds on cryptophytes of the Teleaulax-Plagioselmis-Geminigera clade. A metabolomic study of the three-species food chain Dinophysis-Mesodinium-Teleaulax was carried out using mass spectrometric analysis of extracts of batch-cultured cells of each level of that food chain. The main goal was to compare the metabolomic expression of Galician strains of Dinophysis acuminata and D. acuta that were subjected to different feeding regimes (well-fed and prey-limited) and feeding on two Mesodinium (Spanish and Danish) strains. Both Dinophysis species were able to grow while feeding on both Mesodinium strains, although differences in growth rates were observed. Toxin and metabolomic profiles of the two Dinophysis species were significantly different, and also varied between different feeding regimes and different prey organisms. Furthermore, significantly different metabolomes were expressed by a strain of D. acuminata that was feeding on different strains of the ciliate Mesodinium rubrum. Both species-specific metabolites and those common to D. acuminata and D. acuta were tentatively identified by screening of METLIN and Marine Natural Products Dictionary databases. This first metabolomic study applied to Dinophysis acuminata and D.acuta in culture establishes a basis for the chemical inventory of these species.

Fluvial biofilms exposed to desiccation and pharmaceutical pollution: New insights using metabolomics

In many arid and semi-arid systems, biological communities in river ecosystems are submitted to flow interruption and desiccation, as well as to the impact of urban wastewaters. In this work, we studied (using a LC-LTQ-Orbitrap) the metabolomic response of biofilm communities exposed to both hydrological and chemical stressors. Fluvial biofilms were exposed to a mixture of 9 pharmaceuticals at a total concentration of 5000ng/L (mimicking concentrations and compounds found in polluted aquatic environments) and/or to seven days of desiccation, under laboratory conditions. The biosynthesis of fatty acids was the main metabolic pathway disrupted in biofilms. Endogenous biofilm's metabolites (metabolome) altered due to these stressors were identified. The metabolites that significantly changed only due to one of the stressors could be proposed as potential specific biomarkers. A biomarker of pharmaceutical exposure was the lysophosphatidic acid, which decreased a 160%, while for desiccation stearidonic acid (increased 160%), 16-Oxohexadecanoic acid (increased 340%) and palmitoleic acid (decreased 290%) were the biomarkers proposed. Besides, other metabolites showed different responses depending on the treatment, such as palmitic acid, linolenic acid, behenic acid, lignoceric acid and azelaic acid. The Carbon:Phosphorus (C:P) molar ratio increased due to all stress factors, whereas the algal community composition changed mainly due to desiccation. A possible relationship between those changes observed in structural parameters and the metabolome of biofilms was explored. Overall, our findings support the use of metabolomics to unravel at molecular level the effects from chemical and physical stressors on complex microbial communities, such as biofilms, and pinpoint biomarkers of exposure.

Eco-Metabolomics and Metabolic Modeling: Making the Leap From Model Systems in the Lab to Native Populations in the Field

Experimental high-throughput analysis of molecular networks is a central approach to characterize the adaptation of plant metabolism to the environment. However, recent studies have demonstrated that it is hardly possible to predict in situ metabolic phenotypes from experiments under controlled conditions, such as growth chambers or greenhouses. This is particularly due to the high molecular variance of in situ samples induced by environmental fluctuations. An approach of functional metabolome interpretation of field samples would be desirable in order to be able to identify and trace back the impact of environmental changes on plant metabolism. To test the applicability of metabolomics studies for a characterization of plant populations in the field, we have identified and analyzed in situ samples of nearby grown natural populations of Arabidopsis thaliana in Austria. A. thaliana is the primary molecular biological model system in plant biology with one of the best functionally annotated genomes representing a reference system for all other plant genome projects. The genomes of these novel natural populations were sequenced and phylogenetically compared to a comprehensive genome database of A. thaliana ecotypes. Experimental results on primary and secondary metabolite profiling and genotypic variation were functionally integrated by a data mining strategy, which combines statistical output of metabolomics data with genome-derived biochemical pathway reconstruction and metabolic modeling. Correlations of biochemical model predictions and population-specific genetic variation indicated varying strategies of metabolic regulation on a population level which enabled the direct comparison, differentiation, and prediction of metabolic adaptation of the same species to different habitats. These differences were most pronounced at organic and amino acid metabolism as well as at the interface of primary and secondary metabolism and allowed for the direct classification of population-specific metabolic phenotypes within geographically contiguous sampling sites.

Salinity affects metabolomic profiles of different trophic levels in a food chain

Salinization is one of the most important abiotic stressors in an ecosystem. To examine how exposing a host plant to excess salt affects the consequent performance and metabolism of insects in a food chain, we determined the life history traits and the metabolite profiles in rice (Oryza sativa), the herbivore Sitobion avenae, and its predator Harmonia axyridis. When compared with performance under normal (non-stressed) conditions, exposing plants to 50mM NaCl significantly delayed the timing of development for S. avenae fed on rice and H. axyridis and also reduced the body mass of the latter. Our GC-MS-based analysis revealed clear differences in metabolite profiles between trophic levels or treatment conditions. Salinity apparently increased the levels of main components in rice, but decreased levels of major components in S. avenae and H. axyridis. In addition, 16 metabolites showed salinity-related contrasts in this trophic interaction for our rice-S. avenae-H. axyridis system. Salinity impeded the accumulation of metabolites, especially several sugars, amino acids, organic acids, and fatty acids in both insects, a response that was possibly associated with the negative impacts on their growth and reproduction under stress conditions.

Close and distant: Contrasting the metabolism of two closely related subspecies of Scots pine under the effects of folivory and summer drought

Metabolomes, as chemical phenotypes of organisms, are likely not only shaped by the environment but also by common ancestry. If this is the case, we expect that closely related species of pines will tend to reach similar metabolomic solutions to the same environmental stressors. We examined the metabolomes of two sympatric subspecies of Pinus sylvestris in Sierra Nevada (southern Iberian Peninsula), in summer and winter and exposed to folivory by the pine processionary moth. The overall metabolomes differed between the subspecies but both tended to respond more similarly to folivory. The metabolomes of the subspecies were more dissimilar in summer than in winter, and iberica trees had higher concentrations of metabolites directly related to drought stress. Our results are consistent with the notion that certain plant metabolic responses associated with folivory have been phylogenetically conserved. The larger divergence between subspecies metabolomes in summer is likely due to the warmer and drier conditions that the northern iberica subspecies experience in Sierra Nevada. Our results provide crucial insights into how iberica populations would respond to the predicted conditions of climate change under an increased defoliation in the Mediterranean Basin.

Impact of Soil Warming on the Plant Metabolome of Icelandic Grasslands

Climate change is stronger at high than at temperate and tropical latitudes. The natural geothermal conditions in southern Iceland provide an opportunity to study the impact of warming on plants, because of the geothermal bedrock channels that induce stable gradients of soil temperature. We studied two valleys, one where such gradients have been present for centuries (long-term treatment), and another where new gradients were created in 2008 after a shallow crustal earthquake (short-term treatment). We studied the impact of soil warming (0 to +15 °C) on the foliar metabolomes of two common plant species of high northern latitudes: Agrostis capillaris, a monocotyledon grass; and Ranunculus acris, a dicotyledonous herb, and evaluated the dependence of shifts in their metabolomes on the length of the warming treatment. The two species responded differently to warming, depending on the length of exposure. The grass metabolome clearly shifted at the site of long-term warming, but the herb metabolome did not. The main up-regulated compounds at the highest temperatures at the long-term site were saccharides and amino acids, both involved in heat-shock metabolic pathways. Moreover, some secondary metabolites, such as phenolic acids and terpenes, associated with a wide array of stresses, were also up-regulated. Most current climatic models predict an increase in annual average temperature between 2-8 °C over land masses in the Arctic towards the end of this century. The metabolomes of A. capillaris and R. acris shifted abruptly and nonlinearly to soil warming >5 °C above the control temperature for the coming decades. These results thus suggest that a slight warming increase may not imply substantial changes in plant function, but if the temperature rises more than 5 °C, warming may end up triggering metabolic pathways associated with heat stress in some plant species currently dominant in this region.

Global metabolome changes induced by cyanobacterial blooms in three representative fish species

Cyanobacterial blooms induce important ecological constraints for aquatic organisms and strongly impact the functioning of aquatic ecosystems. In the past decades, the effects of the cyanobacterial secondary metabolites, so called cyanotoxins, have been extensively studied in fish. However, many of these studies have used targeted approaches on specific molecules, which are thought to react to the presence of these specific cyanobacterial compounds. Since a few years, untargeted metabolomic approaches provide a unique opportunity to evaluate the global response of hundreds of metabolites at a glance. In this way, our study provides the first utilization of metabolomic analyses in order to identify the response of fish exposed to bloom-forming cyanobacteria. Three relevant fish species of peri-urban lakes of the European temperate regions were exposed for 96h either to a microcystin (MC)-producing or to a non-MC-producing strain of Microcystis aeruginosa and metabolome changes were characterized in the liver of fish. The results suggest that a short-term exposure to those cyanobacterial biomasses induces metabolome changes without any response specificity linked to the fish species considered. Candidate metabolites are involved in energy metabolism and antioxidative response, which could potentially traduce a stress response of fish submitted to cyanobacteria. These results are in agreement with the already known information and could additionally bring new insights about the molecular interactions between cyanobacteria and fish.

Metabolic pathways regulated by abscisic acid, salicylic acid and γ-aminobutyric acid in association with improved drought tolerance in creeping bentgrass (Agrostis stolonifera)

Abscisic acid (ABA), salicylic acid (SA) and γ-aminobutyric acid (GABA) are known to play roles in regulating plant stress responses. This study was conducted to determine metabolites and associated pathways regulated by ABA, SA and GABA that could contribute to drought tolerance in creeping bentgrass (Agrostis stolonifera). Plants were foliar sprayed with ABA (5 μM), GABA (0.5 mM) and SA (10 μM) or water (untreated control) prior to 25 days drought stress in controlled growth chambers. Application of ABA, GABA or SA had similar positive effects on alleviating drought damages, as manifested by the maintenance of lower electrolyte leakage and greater relative water content in leaves of treated plants relative to the untreated control. Metabolic profiling showed that ABA, GABA and SA induced differential metabolic changes under drought stress. ABA mainly promoted the accumulation of organic acids associated with tricarboxylic acid cycle (aconitic acid, succinic acid, lactic acid and malic acid). SA strongly stimulated the accumulation of amino acids (proline, serine, threonine and alanine) and carbohydrates (glucose, mannose, fructose and cellobiose). GABA enhanced the accumulation of amino acids (GABA, glycine, valine, proline, 5-oxoproline, serine, threonine, aspartic acid and glutamic acid) and organic acids (malic acid, lactic acid, gluconic acid, malonic acid and ribonic acid). The enhanced drought tolerance could be mainly due to the enhanced respiration metabolism by ABA, amino acids and carbohydrates involved in osmotic adjustment (OA) and energy metabolism by SA, and amino acid metabolism related to OA and stress-defense secondary metabolism by GABA.

Metabolomic data suggest regulation of black howler monkey (Alouatta pigra) diet composition at the molecular level

In addition to macronutrients, foods consist of a complex set of chemical compounds that can influence dietary selectivity and consumer physiology. Metabolomics allow us to describe this complexity by quantifying all small molecules, or metabolites, in a food item. In this study we use GC-MS based metabolomics to describe the metabolite profiles of foods consumed by one population of Mexican black howler monkeys (Alouatta pigra) over a 10-month period. Our data indicate that each food exhibited a distinct metabolite profile, and the average weekly intake of metabolites such as neochlorogenic acid and serotonin (5-hydroxytryptamine) was correlated with the consumption of certain plant parts. We speculate that these patterns result in temporal changes in howler monkey physiology such as food retention time. In contrast, variation in the weekly intake of metabolites such as oxalic acid was 70% less than variation in the concentration of the same metabolites across food items, suggesting that howler monkeys regulated the intake of these metabolites, possibly to avoid physiological consequences such as kidney stone formation. Finally, seasonal variation in the consumption of individual nutrient and non-nutrient metabolites were correlated with changes in the relative abundances of associated gut microbial taxa, implying indirect effects of food item metabolites on howler monkey nutritional ecology that likely drive foraging decisions. While additional research is needed to validate these findings, the patterns we report serve as important baseline data for understanding the effects of plant metabolites on the food choice in primates.

Metabolomics Reveals Cryptic Interactive Effects of Species Interactions and Environmental Stress on Nitrogen and Sulfur Metabolism in Seagrass

Eutrophication of estuaries and coastal seas is accelerating, increasing light stress on subtidal marine plants and changing their interactions with other species. To date, we have limited understanding of how such variations in environmental and biological stress modify the impact of interactions among foundational species and eventually affect ecosystem health. Here, we used metabolomics to assess the impact of light reductions on interactions between the seagrass Zostera marina, an important habitat-forming marine plant, and the abundant and commercially important blue mussel Mytilus edulis. Plant performance varied with light availability but was unaffected by the presence of mussels. Metabolomic analysis, on the other hand, revealed an interaction between light availability and presence of M. edulis on seagrass metabolism. Under high light, mussels stimulated seagrass nitrogen and energy metabolism. Conversely, in low light mussels impeded nitrogen and energy metabolism, and enhanced responses against sulfide toxicity, causing inhibited oxidative energy metabolism and tissue degradation. Metabolomic analysis thereby revealed cryptic changes to seagrass condition that could not be detected by traditional approaches. Our findings suggest that coastal eutrophication and associated reductions in light may shift seagrass-bivalve interactions from mutualistic to antagonistic, which is important for conservation management of seagrass meadows.

Metabolic adaptations in a range-expanding arthropod

Despite an increasing number of studies documenting life‐history evolution during range expansions or shifts, we lack a mechanistic understanding of the underlying physiological processes. In this explorative study, we used a metabolomics approach to study physiological changes associated with the recent range expansion of the two‐spotted spider mite (Tetranychus urticae). Mite populations were sampled along a latitudinal gradient from range core to edge and reared under benign common garden conditions for two generations. Using gas chromatography–mass spectrometry, we obtained metabolic population profiles, which showed a gradual differentiation along the latitudinal gradient, indicating (epi)genetic changes in the metabolome in association with range expansion. These changes seemed not related with shifts in the mites’ energetic metabolism, but rather with differential use of amino acids. Particularly, more dispersive northern populations showed lowered concentrations of several essential and nonessential amino acids, suggesting a potential downregulation of metabolic pathways associated with protein synthesis.

Are the metabolomic responses to folivory of closely related plant species linked to macroevolutionary and plant-folivore coevolutionary processes?

The debate whether the coevolution of plants and insects or macroevolutionary processes (phylogeny) is the main driver determining the arsenal of molecular defensive compounds of plants remains unresolved. Attacks by herbivorous insects affect not only the composition of defensive compounds in plants but also the entire metabolome. Metabolomes are the final products of genotypes and are constrained by macroevolutionary processes, so closely related species should have similar metabolomic compositions and may respond in similar ways to attacks by folivores. We analyzed the elemental compositions and metabolomes of needles from three closely related Pinus species with distant coevolutionary histories with the caterpillar of the processionary moth respond similarly to its attack. All pines had different metabolomes and metabolic responses to herbivorous attack. The metabolomic variation among the species and the responses to folivory reflected their macroevolutionary relationships, with P. pinaster having the most divergent metabolome. The concentrations of terpenes were in the attacked trees supporting the hypothesis that herbivores avoid plant individuals with higher concentrations. Our results suggest that macroevolutionary history plays important roles in the metabolomic responses of these pine species to folivory, but plant-insect coevolution probably constrains those responses. Combinations of different evolutionary factors and trade-offs are likely responsible for the different responses of each species to folivory, which is not necessarily exclusively linked to plant-insect coevolution.

Why stay in a bad relationship? The effect of local host phenology on a generalist butterfly feeding on a low-ranked host

BACKGROUND

In plant-feeding insects, the evolutionary retention of polyphagy remains puzzling. A better understanding of the relationship between these organisms and changes in the metabolome of their host plants is likely to suggest functional links between them, and may provide insights into how polyphagy is maintained.

RESULTS

We investigated the phenological change of Cynoglossum officinale, and how a generalist butterfly species, Vanessa cardui, responded to this change. We used untargeted metabolite profiling to map plant seasonal changes in both primary and secondary metabolites. We compared these data to differences in larval performance on vegetative plants early and late in the season. We also performed two oviposition preference experiments to test females' ability to choose between plant developmental stages (vegetative and reproductive) early and late in the season. We found clear seasonal changes in plant primary and secondary metabolites that correlated with larval performance. The seasonal change in plant metabolome reflected changes in both nutrition and toxicity and resulted in zero survival in the late period. However, large differences among families in larval ability to feed on C. officinale suggest that there is genetic variation for performance on this host. Moreover, females accepted all plants for oviposition, and were not able to discriminate between plant developmental stages, in spite of the observed overall differences in metabolite profile potentially associated with differences in suitability as larval food.

CONCLUSIONS

In V. cardui, migratory behavior, and thus larval feeding times, are not synchronized with plant phenology at the reproductive site. This lack of synchronization, coupled with the observed lack of discriminatory oviposition, obviously has potential fitness costs. However, this "opportunistic" behavior may as well function as a source of potential host plant evolution, promoting for example the acceptance of new plants.

Similar local, but different systemic, metabolomic responses of closely related pine subspecies to folivory by caterpillars of the processionary moth

Plants respond locally and systemically to herbivore attack. Most of the research conducted on plant-herbivore relationships at element and molecular levels have focused on the elemental composition or/and certain molecular compounds or specific families of defence metabolites showing that herbivores tend to select plant individuals or species with higher nutrient concentrations and avoid those with higher levels of defence compounds. We performed stoichiometric and metabolomics, both local and systemic, analyses in two subspecies of Pinus sylvestris under attack from caterpillars of the pine processionary moth, an important pest in the Mediterranean Basin. Both pine subspecies responded locally to folivory mainly by increasing relative concentrations of terpenes and some phenolics. Systemic responses differed between pine subspecies, and most of the metabolites presented intermediate concentrations between those of the affected parts and unattacked trees. Our results support the hypothesis that foliar nutrient concentrations are not a key factor for plant selection by adult female processionary moths for oviposition, since folivory was not associated with any of the elements analysed. Phenolic compounds generally did not increase in the attacked trees, questioning the suggestion of induction of phenolics following folivory attack and the anti-feeding properties of phenolics. Herbivory attack produced a general systemic shift in pines, in both primary and secondary metabolism, which was less intense and chemically different from the local responses. Local pine responses were similar between pine subspecies, while systemic responses were more distant.

Shifts in plant foliar and floral metabolomes in response to the suppression of the associated microbiota

BACKGROUND

The phyllospheric microbiota is assumed to play a key role in the metabolism of host plants. Its role in determining the epiphytic and internal plant metabolome, however, remains to be investigated. We analyzed the Liquid Chromatography-Mass Spectrometry (LC-MS) profiles of the epiphytic and internal metabolomes of the leaves and flowers of Sambucus nigra with and without external antibiotic treatment application.

RESULTS

The epiphytic metabolism showed a degree of complexity similar to that of the plant organs. The suppression of microbial communities by topical applications of antibiotics had a greater impact on the epiphytic metabolome than on the internal metabolomes of the plant organs, although even the latter changed significantly both in leaves and flowers. The application of antibiotics decreased the concentration of lactate in both epiphytic and organ metabolomes, and the concentrations of citraconic acid, acetyl-CoA, isoleucine, and several secondary compounds such as terpenes and phenols in the epiphytic extracts. The metabolite pyrogallol appeared in the floral epiphytic community only after the treatment. The concentrations of the amino acid precursors of the ketoglutarate-synthesis pathway tended to decrease in the leaves and to increase in the foliar epiphytic extracts.

CONCLUSIONS

These results suggest that anaerobic and/or facultative anaerobic bacteria were present in high numbers in the phyllosphere and in the apoplasts of S. nigra. The results also show that microbial communities play a significant role in the metabolomes of plant organs and could have more complex and frequent mutualistic, saprophytic, and/or parasitic relationships with internal plant metabolism than currently assumed.

Metabolomics in chemical ecology

Chemical ecology elucidates the nature and role of natural products as mediators of organismal interactions. The emerging techniques that can be summarized under the concept of metabolomics provide new opportunities to study such environmentally relevant signaling molecules. Especially comparative tools in metabolomics enable the identification of compounds that are regulated during interaction situations and that might play a role as e.g. pheromones, allelochemicals or in induced and activated defenses. This approach helps overcoming limitations of traditional bioassay-guided structure elucidation approaches. But the power of metabolomics is not limited to the comparison of metabolic profiles of interacting partners. Especially the link to other -omics techniques helps to unravel not only the compounds in question but the entire biosynthetic and genetic re-wiring, required for an ecological response. This review comprehensively highlights successful applications of metabolomics in chemical ecology and discusses existing limitations of these novel techniques. It focuses on recent developments in comparative metabolomics and discusses the use of metabolomics in the systems biology of organismal interactions. It also outlines the potential of large metabolomics initiatives for model organisms in the field of chemical ecology.

Development of an NMR microprobe procedure for high-throughput environmental metabolomics of Daphnia magna

Nuclear magnetic resonance (NMR) is the primary platform used in high-throughput environmental metabolomics studies because its non-selectivity is well suited for non-targeted approaches. However, standard NMR probes may limit the use of NMR-based metabolomics for tiny organisms because of the sample volumes required for routine metabolic profiling. Because of this, keystone ecological species, such as the water flea Daphnia magna, are not commonly studied because of the analytical challenges associated with NMR-based approaches. Here, the use of a 1.7-mm NMR microprobe in analyzing tissue extracts from D. magna is tested. Three different extraction procedures (D2O-based buffer, Bligh and Dyer, and acetonitrile : methanol : water) were compared in terms of the yields and breadth of polar metabolites. The D2O buffer extraction yielded the most metabolites and resulted in the best reproducibility. Varying amounts of D. magna dry mass were extracted to optimize metabolite isolation from D. magna tissues. A ratio of 1-1.5-mg dry mass to 40 µl of extraction solvent provided excellent signal-to-noise and spectral resolution using (1)H NMR. The metabolite profile of a single daphnid was also investigated (approximately 0.2 mg). However, the signal-to-noise of the (1)H NMR was considerably lower, and while feasible for select applications would likely not be appropriate for high-throughput NMR-based metabolomics. Two-dimensional NMR experiments on D. magna extracts were also performed using the 1.7-mm NMR probe to confirm (1)H NMR metabolite assignments. This study provides an NMR-based analytical framework for future metabolomics studies that use D. magna in ecological and ecotoxicity studies.

The vegetative buds of Salix myrsinifolia are responsive to elevated UV-B and temperature

The predicted rise in temperature and variable changes in ultraviolet-B radiation will have marked effects on plant growth and metabolism. Different vegetative parts of trees have been studied to detect the impacts of enhanced temperature and UV-B, but the effects on buds have rarely been considered. In the present study, Salix myrsinifolia clones were subjected to enhanced UV-B and temperature over two growing seasons starting from 2009, and measured springtime bud development and concentrations of phenolic compounds. In 2010 and 2011 the buds under increased temperature were up to 30% longer than those in control plots. On the other hand, UV-B combined with elevated temperature significantly decreased bud length by 4-5% in 2010. This effect was stronger in males than in females. The vegetative buds contained high constitutive amounts of chlorogenic acid derivatives, which may explain the weak increase in hyperin and chlorogenic acid that are usual UV-B sheltering compounds. The elevated temperature treatment significantly increased salicin content (about 18% in males and 22% in females), while triandrin concentration decreased by only 50% in females. Our results indicate that vegetative bud size is highly affected by seasonal temperature, while UV-B induced a weaker and transient effect.

Warming differentially influences the effects of drought on stoichiometry and metabolomics in shoots and roots

Plants in natural environments are increasingly being subjected to a combination of abiotic stresses, such as drought and warming, in many regions. The effects of each stress and the combination of stresses on the functioning of shoots and roots have been studied extensively, but little is known about the simultaneous metabolome responses of the different organs of the plant to different stresses acting at once. We studied the shift in metabolism and elemental composition of shoots and roots of two perennial grasses, Holcus lanatus and Alopecurus pratensis, in response to simultaneous drought and warming. These species responded differently to individual and simultaneous stresses. These responses were even opposite in roots and shoots. In plants exposed to simultaneous drought and warming, terpenes, catechin and indole acetic acid accumulated in shoots, whereas amino acids, quinic acid, nitrogenous bases, the osmoprotectants choline and glycine betaine, and elements involved in growth (nitrogen, phosphorus and potassium) accumulated in roots. Under drought, warming further increased the allocation of primary metabolic activity to roots and changed the composition of secondary metabolites in shoots. These results highlight the plasticity of plant metabolomes and stoichiometry, and the different complementary responses of shoots and roots to complex environmental conditions.

Extending the Concept of Diversity Partitioning to Characterize Phenotypic Complexity

Most components of an organism's phenotype can be viewed as the expression of multiple traits. Many of these traits operate as complexes, where multiple subsidiary parts function and evolve together. As trait complexity increases, so does the challenge of describing complexity in intuitive, biologically meaningful ways. Traditional multivariate analyses ignore the phenomenon of individual complexity and provide relatively abstract representations of variation among individuals. We suggest adopting well-known diversity indices from community ecology to describe phenotypic complexity as the diversity of distinct subsidiary components of a trait. Using a hierarchical framework, we illustrate how total trait diversity can be partitioned into within-individual complexity (α diversity) and between-individual components (β diversity). This approach complements traditional multivariate analyses. The key innovations are (i) addition of individual complexity within the same framework as between-individual variation and (ii) a group-wise partitioning approach that complements traditional level-wise partitioning of diversity. The complexity-as-diversity approach has potential application in many fields, including physiological ecology, ecological and community genomics, and transcriptomics. We demonstrate the utility of this complexity-as-diversity approach with examples from chemical and microbial ecology. The examples illustrate biologically significant differences in complexity and diversity that standard analyses would not reveal.

Entometabolomics: applications of modern analytical techniques to insect studies

Metabolomic analyses can reveal associations between an organism's metabolome and further aspects of its phenotypic state, an attractive prospect for many life-sciences researchers. The metabolomic approach has been employed in some, but not many, insect study systems, starting in 1990 with the evaluation of the metabolic effects of parasitism on moth larvae. Metabolomics has now been applied to a variety of aspects of insect biology, including behaviour, infection, temperature stress responses, CO 2 sedation, and bacteria-insect symbiosis. From a technical and reporting standpoint, these studies have adopted a range of approaches utilising established experimental methodologies. Here, we review current literature and evaluate the metabolomic approaches typically utilised by entomologists. We suggest that improvements can be made in several areas, including sampling procedures, the reduction in sampling and equipment variation, the use of sample extracts, statistical analyses, confirmation, and metabolite identification. Overall, it is clear that metabolomics can identify correlations between phenotypic states and underlying cellular metabolism that previous, more targeted, approaches are incapable of measuring. The unique combination of untargeted global analyses with high-resolution quantitative analyses results in a tool with great potential for future entomological investigations.

Non-targeted metabolomic profile of Fagus sylvatica L. leaves using liquid chromatography with mass spectrometry and gas chromatography with mass spectrometry

INTRODUCTION

Fagus sylvatica L. is one of the most widely distributed broad-leaved tree species in central and western Europe, important to the forest sector and an accurate biomarker of climate change.

OBJECTIVE

To profile the beech leaf metabolome for future studies in order to investigate deeper into the characterisation of its metabolic response.

METHODS

Leaf extracts were analysed using LC-MS by electrospray ionisation in negative mode from m/z 100-1700 and GC-MS by electron ionisation in scan mode from m/z 35-800.

RESULTS

The LC-MS profile resulted in 56 compounds, of which 43 were identified and/or structurally characterised, including hydroxycinnamic acid derivatives, flavan-3-ols and proanthocyanidins, and flavonols. From a second analysis based on GC-MS, a total of 111 compounds were identified, including carbohydrates, polyalcohols, amino acids, organic acids, fatty acids, phenolic compounds, terpenoids, sterols and other related compounds. Many of the compounds identified were primary metabolites involved in major plant metabolic pathways, however, some secondary metabolites were also detected. Some of them play roles as tolerance-response osmoregulators and osmoprotectors in abiotic stress, or as anti-oxidants that reduce the effect of reactive oxygen species and promote many protective functions in plants.

CONCLUSIONS

This study provides a broad and relevant insight into the metabolic status of F. sylvatica leaves, and serves as a base for future studies on physiological and molecular mechanisms involved in biotic or abiotic stress.

Plant metabolite profiles and the buffering capacities of ecosystems

In spite of some inherent challenges, metabolite profiling is becoming increasingly popular under field conditions. It has been used successfully to address topics like species interactions, connections between growth and chemical stoichiometry or the plant's stress response. Stress exerts a particularly clear impact on plant metabolomes and has become a central topic in many metabolite profiling experiments in the fields. In contrast to phytochambers, however, external stress is often at least partially absorbed by the environment when measuring under field conditions. Such stress-buffering capacities of (agro)-ecosystems are of crucial interest given the ever-increasing anthropogenic impact on ecosystems and this review promotes the idea of using plant metabolite profiles for respective measurements. More specifically I propose to use parameters of the response of key plant species to a given stress treatment as proxies for measuring and comparing stress-buffering capacities of ecosystems. Stress response parameters accessible by metabolite profiling comprise for example the intensity or duration of the impact of stress or the ability of the plant organism to recover from this impact after a given time. Analyses of ecosystem stress-buffering capacities may improve our understanding of how ecosystems cope with stress and may improve our abilities to predict ecosystem changes.

Opposite metabolic responses of shoots and roots to drought

Shoots and roots are autotrophic and heterotrophic organs of plants with different physiological functions. Do they have different metabolomes? Do their metabolisms respond differently to environmental changes such as drought? We used metabolomics and elemental analyses to answer these questions. First, we show that shoots and roots have different metabolomes and nutrient and elemental stoichiometries. Second, we show that the shoot metabolome is much more variable among species and seasons than is the root metabolome. Third, we show that the metabolic response of shoots to drought contrasts with that of roots; shoots decrease their growth metabolism (lower concentrations of sugars, amino acids, nucleosides, N, P, and K), and roots increase it in a mirrored response. Shoots are metabolically deactivated during drought to reduce the consumption of water and nutrients, whereas roots are metabolically activated to enhance the uptake of water and nutrients, together buffering the effects of drought, at least at the short term.

Recent Advances in the Application of Metabolomics to Studies of Biogenic Volatile Organic Compounds (BVOC) Produced by Plant

In many plants, biogenic volatile organic compounds (BVOCs) are produced as specialized metabolites that contribute to the characteristics of each plant. The varieties and composition of BVOCs are chemically diverse by plant species and the circumstances in which the plants grow, and also influenced by herbivory damage and pathogen infection. Plant-produced BVOCs are receptive to many organisms, from microorganisms to human, as both airborne attractants and repellants. In addition, it is known that some BVOCs act as signals to prime a plant for the defense response in plant-to-plant communications. The compositional profiles of BVOCs can, thus, have profound influences in the physiological and ecological aspects of living organisms. Apart from that, some of them are commercially valuable as aroma/flavor compounds for human. Metabolomic technologies have recently revealed new insights in biological systems through metabolic dynamics. Here, the recent advances in metabolomics technologies focusing on plant-produced BVOC analyses are overviewed. Their application markedly improves our knowledge of the role of BVOCs in chemosystematics, ecological influences, and aroma research, as well as being useful to prove the biosynthetic mechanisms of BVOCs.

Metabolomics and proteomics reveal impacts of chemically mediated competition on marine plankton

Competition is a major force structuring marine planktonic communities. The release of compounds that inhibit competitors, a process known as allelopathy, may play a role in the maintenance of large blooms of the red-tide dinoflagellate Karenia brevis, which produces potent neurotoxins that negatively impact coastal marine ecosystems. K. brevis is variably allelopathic to multiple competitors, typically causing sublethal suppression of growth. We used metabolomic and proteomic analyses to investigate the role of chemically mediated ecological interactions between K. brevis and two diatom competitors, Asterionellopsis glacialis and Thalassiosira pseudonana. The impact of K. brevis allelopathy on competitor physiology was reflected in the metabolomes and expressed proteomes of both diatoms, although the diatom that co-occurs with K. brevis blooms (A. glacialis) exhibited more robust metabolism in response to K. brevis. The observed partial resistance of A. glacialis to allelopathy may be a result of its frequent exposure to K. brevis blooms in the Gulf of Mexico. For the more sensitive diatom, T. pseudonana, which may not have had opportunity to evolve resistance to K. brevis, allelopathy disrupted energy metabolism and impeded cellular protection mechanisms including altered cell membrane components, inhibited osmoregulation, and increased oxidative stress. Allelopathic compounds appear to target multiple physiological pathways in sensitive competitors, demonstrating that chemical cues in the plankton have the potential to alter large-scale ecosystem processes including primary production and nutrient cycling.

High specificity in plant leaf metabolic responses to arbuscular mycorrhiza

The chemical composition of plants (phytometabolome) is dynamic and modified by environmental factors. Understanding its modulation allows to improve crop quality and decode mechanisms underlying plant-pest interactions. Many studies that investigate metabolic responses to the environment focus on single model species and/or few target metabolites. However, comparative studies using environmental metabolomics are needed to evaluate commonalities of chemical responses to certain challenges. We assessed the specificity of foliar metabolic responses of five plant species to the widespread, ancient symbiosis with a generalist arbuscular mycorrhizal fungus. Here we show that plant species share a large 'core metabolome' but nevertheless the phytometabolomes are modulated highly species/taxon-specifically. Such a low conservation of responses across species highlights the importance to consider plant metabolic prerequisites and the long time of specific plant-fungus coevolution. Thus, the transferability of findings regarding phytometabolome modulation by an identical AM symbiont is severely limited even between closely related species.

Drought enhances folivory by shifting foliar metabolomes in Quercus ilex trees

At the molecular level, folivory activity on plants has mainly been related to the foliar concentrations of nitrogen (N) and/or particular metabolites. We studied the responses of different nutrients and the whole metabolome of Quercus ilex to seasonal changes and to moderate field experimental conditions of drought, and how this drought may affect folivory activity, using stoichiometric and metabolomic techniques. Foliar potassium (K) concentrations increased in summer and consequently led to higher foliar K : phosphorus (P) and lower carbon (C) : K and N : K ratios. Foliar N : P ratios were not lowest in spring as expected by the growth rate hypothesis. Trees exposed to moderate drought presented higher concentrations of total sugars and phenolics and these trees also experienced more severe folivory attack. The foliar increases in K, sugars and antioxidant concentrations in summer, the driest Mediterranean season, indicated enhanced osmoprotection under natural drought conditions. Trees under moderate drought also presented higher concentrations of sugars and phenolics; a plant response to avoid water loss. These shifts in metabolism produced an indirect relationship between increased drought and folivory activity.

Climate and taxonomy underlie different elemental concentrations and stoichiometries of forest species: the optimum "biogeochemical niche"

We previously hypothesised the existence of a "biogeochemical niche" occupied by each plant species. Different species should have a specific elemental composition, stoichiometry and allocation as a consequence of their particular metabolism, physiology and structure (morphology) linked to their optimal functioning under the environmental (abiotic and biotic) conditions where they have evolved. We tested this hypothesis using data from the Catalan Forestry Inventory that covers different forest groups growing under a large climatic gradient. Mediterranean species that occupy hotter-drier environments have lower leaf N, P and K concentrations than non-Mediterranean forest species. Within a determined climatic biome, different species competing in the same space have different elemental compositions and allocations linked to their taxonomical differences and their phenotypic plasticity. Gymnosperms have a proportionally higher elemental allocation to leaves than to wood, higher C concentrations, and lower N, P and K concentrations mainly in the stem and branches than angiosperms. The differences among species are linked to asymmetrical use of different elements, suggesting that the biogeochemical niche is a final expression and consequence of long-term species adaptation to particular abiotic factors, ecological role (stress tolerant, ruderal, competitor), different soil occupation and use of resources to avoid interspecific competition, and finally of a certain degree of flexibility to adapt to current environmental shifts.

Metabolic responses of Quercus ilex seedlings to wounding analysed with nuclear magnetic resonance profiling

Plants defend themselves against herbivory at several levels. One of these is the synthesis of inducible chemical defences. Using NMR metabolomic techniques, we studied the metabolic changes of plant leaves after a wounding treatment simulating herbivore attack in the Mediterranean sclerophyllous tree Quercus ilex. First, an increase in glucose content was observed in wounded plants. There was also an increase in the content of C-rich secondary metabolites such as quinic acid and quercitol, both related to the shikimic acid pathway and linked to defence against biotic stress. There was also a shift in N-storing amino acids, from leucine and isoleucine to asparagine and choline. The observed higher content of asparagine is related to the higher content of choline through serine that was proved to be the precursor of choline. Choline is a general anti-herbivore and pathogen deterrent. The study shows the rapid metabolic response of Q. ilex in defending its leaves, based on a rapid increase in the production of quinic acid, quercitol and choline. The results also confirm the suitability of (1)H NMR-based metabolomic profiling studies to detect global metabolome shifts after wounding stress in tree leaves, and therefore its suitability in ecometabolomic studies.

Integrating phenotypic plasticity within an Ecological Genomics framework: recent insights from the genomics, evolution, ecology, and fitness of plasticity

E.B. Ford's 1964 book Ecological Genetics was a call for biologists to engage in multidisciplinary work in order to elucidate the link between genotype, phenotype, and fitness for ecologically relevant traits. In this review, we argue that the integration of an ecological genomics framework in studies of phenotypic plasticity is a promising approach to elucidate the causal links between genes and the environment, particularly during colonization of novel environments, environmental change, and speciation. This review highlights some of the questions and hypotheses generated from a mechanistic, evolutionary, and ecological perspective, in order to direct the continued and future use of genomic tools in the study of phenotypic plasticity.