Ecological metabolomics: overview of current developments and future challenges

Qualitative and Untargeted Volatilome Fingerprinting of Aspergillus sp. and Bulbithecium sp. by HS-SPME-GCMS and Functional Interactions

Research on fungal volatile organic compounds (VOCs) has increased worldwide in the last 10 years, but marine fungal volatilomes remain underexplored. Similarly, the hormone-signaling pathways, agronomic significance, and biocontrol potential of VOCs in plant-associated fungi make the area of research extremely promising. In the current investigation, VOCs of the isolates-Aspergillus sp. GSBT S13 and GSBT S14 from marine sediments, and Bulbithecium sp. GSBT E3 from Eucalyptus foliage were extracted using Head Space solid phase microextraction, followed by gas chromatography-mass spectrometry, identification, statistical analyses, and prediction of functions by KEGG COMPOUND and STITCH 5.0 databases. The significance of this research is fingerprinting VOCs of the isolates from distinct origins, identification of compounds using three libraries (NIST02, NIST14, and W9N11), and using bioinformatic tools to perform functional analysis. The most important findings include the identification of previously unreported compounds in fungi-1-methoxy naphthalene, diethyl phthalate, pentadecane, pristane, and nonanal; the prediction of the involvement of small molecules in the degradation of aromatic compound pathways and activation, inhibition, binding, and catalysis of metabolites with predicted protein partners. This study has ample opportunity to validate the findings and understand the mechanism or mode of action, the interspecies interactions, and the role of the metabolites in geochemical cycles.

Dietary type (carnivore, herbivore and omnivore) and animal species modulate the nutritional metabolome of terrestrial species

Ecometabolomics could be implemented as a powerful tool in molecular ecology studies, but it is necessary to know the baseline of certain metabolites and understand how different traits could affect the metabolome of the animals. Therefore, the main objective of this study was to provide values for the nutritional metabolome profile of different diet groups and animal species, as well as to study the differences in the metabolomic profile due to the effect of diet type and species. To achieve this goal, blood samples were taken from healthy animals (n = 43) of different species: lion (Panthera leo), jaguar (Panthera onca), chimpanzee (Pan troglodytes), bison (Bison bison), gazelle (Gazella cuvieri) and fallow deer (Dama dama), and with different types of diet (carnivore, herbivore and omnivore). Each blood sample was analysed to determine nutritional metabolites. The main results this study provides are the nutritional metabolic profile of these animals based on the type of diet and the animal species. A significant effect of the dietary type was found on nutritional metabolite levels, with those metabolites related to protein metabolism (total protein and creatine) being higher in carnivores. There is also an effect of the species on nutritional metabolites, observing a metabolome differentiation between lion and jaguar. In the case of herbivores, bison showed higher levels of uric acid and cholesterol, and lower urea levels than gazelle and fallow deer. More molecular ecology studies are needed to further the knowledge of the metabolism of these animals.

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

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

Correlating Eucalyptus leaf metabolomics with preference of the bronze bug, Thaumastocoris peregrinus

Eucalyptus species are among the most planted trees in forestry production, an ever-increasing commercial activity worldwide. Forestry expansion demands a continuous search for preventive and sanitary measures against pests and diseases. Massive application of phytosanitary products is incompatible with the forestry sector, so forest health management must be based on other principles. In this context, studies on insect plant relationships mediated by plant metabolites may contribute information relevant to plant resistance and genotype selection. In this study, we analyzed the leaf metabolome of four Eucalyptus species commonly planted in southern South America, to correlate this chemical information with feeding preference of Thaumastocoris peregrinus (Hemiptera: Thaumastocoridae), an important pest of eucalypt plantations. Gas chromatography mass spectrometry analyses were performed on polar and non-polar leaf extracts from Eucalyptus globulus, Eucalyptus grandis, Eucalyptus robusta, and Eucalyptus tereticornis (Myrtaceae). Feeding preferences were assessed in two-choice laboratory bioassays resulting in a preference gradient of the four plant species. Moreover, a performance bioassay where we contrasted survival and development time between the most and least preferred plants, showed a clear correlation with preference both in survival and developmental time of the most susceptible nymph instar. We found that species with high or low feeding preferences differ significantly in several foliar metabolites, which may be acting as feeding stimulants or deterrents for T. peregrinus. These findings may provide useful criteria for choosing Eucalyptus genotypes when planting in bronze bug infested areas.

Assessing the promoting effect of compound microbial agents on flax dew retting: Based on the relationship between metabolites and core genera

In this study, 16S rRNA sequencing and GC-MS (gas chromatography-mass spectrometry) techniques were employed to examine the relationship between bacterial succession and metabolite alterations during the dew retting process of flax. The results indicated that the addition of compound microbial agents may affect the production and transformation of metabolites by re-establishing bacterial communities and promoting the degradation of pectic substances and the release of metabolites, and the best retting effect was achieved under the combined addition (BA). In addition, Chryseobacterium, Bacillus, and Pseudoonas were closely associated with the production of fatty acids and alcohols; the addition of compound microbial agents increased the content of critical metabolites while decreasing the environmental pollutant bis(2-ethylhexyl) phthalate. In summary, the addition of compound microbial agents can positively regulate the retting process of flax, shorten the retting cycle, improve the quality of flax fibre, and reduce the pollution of the environment.

Untargeted profiling of secondary metabolites and phytotoxins associated with stemphylium blight of lentil

Stemphylium botryosum alters lentil secondary metabolism and differentially affects resistant and susceptible genotypes. Untargeted metabolomics identifies metabolites and their potential biosynthetic pathways that play a crucial role in resistance to S. botryosum. The molecular and metabolic processes that mediate resistance to stemphylium blight caused by Stemphylium botryosum Wallr. in lentil are largely unknown. Identifying metabolites and pathways associated with Stemphylium infection may provide valuable insights and novel targets to breed for enhanced resistance. The metabolic changes following infection of four lentil genotypes by S. botryosum were investigated by comprehensive untargeted metabolic profiling employing reversed-phase or hydrophilic interaction liquid chromatography (HILIC) coupled to a Q-Exactive mass spectrometer. At the pre-flowering stage, plants were inoculated with S. botryosum isolate SB19 spore suspension and leaf samples were collected at 24, 96 and 144 h post-inoculation (hpi). Mock-inoculated plants were used as negative controls. After analyte separation, high-resolution mass spectrometry data was acquired in positive and negative ionization modes. Multivariate modeling revealed significant treatment, genotype and hpi effects on metabolic profile changes that reflect lentil response to Stemphylium infection. In addition, univariate analyses highlighted numerous differentially accumulated metabolites. By contrasting the metabolic profiles of SB19-inoculated and mock-inoculated plants and among lentil genotypes, 840 pathogenesis-related metabolites were detected including seven S. botryosum phytotoxins. These metabolites included amino acids, sugars, fatty acids and flavonoids in primary and secondary metabolism. Metabolic pathway analysis revealed 11 significant pathways including flavonoid and phenylpropanoid biosynthesis, which were affected upon S. botryosum infection. This research contributes to ongoing efforts toward a comprehensive understanding of the regulation and reprogramming of lentil metabolism under biotic stress, which will provide targets for potential applications in breeding for enhanced disease resistance.

Integrated omic techniques and their genomic features for invasive weeds

Many emerging invasive weeds display rapid adaptation against different stressful environments compared to their natives. Rapid adaptation and dispersal habits helped invasive populations have strong diversity within the population compared to their natives. Advances in molecular marker techniques may lead to an in-depth understanding of the genetic diversity of invasive weeds. The use of molecular techniques is rapidly growing, and their implications in invasive weed studies are considered powerful tools for genome purposes. Here, we review different approach used multi-omics by invasive weed studies to understand the functional structural and genomic changes in these species under different environmental fluctuations, particularly, to check the accessibility of advance-sequencing techniques used by researchers in genome sequence projects. In this review-based study, we also examine the importance and efficiency of different molecular techniques in identifying and characterizing different genes, associated markers, proteins, metabolites, and key metabolic pathways in invasive and native weeds. Use of these techniques could help weed scientists to further reduce the knowledge gaps in understanding invasive weeds traits. Although these techniques can provide robust insights about the molecular functioning, employing a single omics platform can rarely elucidate the gene-level regulation and the associated real-time expression of weedy traits due to the complex and overlapping nature of biological interactions. We conclude that different multi-omic techniques will provide long-term benefits in launching new genome projects to enhance the understanding of invasive weeds' invasion process.

Application of Metabolomics in Fungal Research

Metabolomics is an essential method to study the dynamic changes of metabolic networks and products using modern analytical techniques, as well as reveal the life phenomena and their inherent laws. Currently, more and more attention has been paid to the development of metabolic histochemistry in the fungus field. This paper reviews the application of metabolomics in fungal research from five aspects: identification, response to stress, metabolite discovery, metabolism engineering, and fungal interactions with plants.

Transcriptome and Metabolome Analyses Reveal Differences in Terpenoid and Flavonoid Biosynthesis in Cryptomeria fortunei Needles Across Different Seasons

Cryptomeria fortunei (Chinese cedar) has outstanding medicinal value due to its abundant flavonoid and terpenoid contents. The metabolite contents of C. fortunei needles differ across different seasons. However, the biosynthetic mechanism of these differentially synthesized metabolites (DSMs) is poorly understood. To improve our understanding of this process, we performed integrated non-targeted metabolomic liquid chromatography and gas chromatography mass spectrometry (LC-MS and GC-MS), and transcriptomic analyses of summer and winter needles. In winter, the C. fortunei needle ultrastructure was damaged, and the chlorophyll content and F _v/F _m were significantly (p < 0.05) reduced. Based on GC-MS and LC-MS, we obtained 106 and 413 DSMs, respectively; based on transcriptome analysis, we obtained a total of 41.17 Gb of clean data and assembled 33,063 unigenes, including 14,057 differentially expressed unigenes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that these DSMs/DEGs were significantly (p < 0.05) enriched in many biosynthesis pathways, such as terpenoids, photosynthates, and flavonoids. Integrated transcriptomic and metabonomic analyses showed that seasonal changes have the greatest impact on photosynthesis pathways, followed by terpenoid and flavonoid biosynthesis pathways. In summer Chinese cedar (SCC) needles, DXS, DXR, and ispH in the 2-methyl-pentaerythritol 4-phosphate (MEP) pathway and GGPS were highly expressed and promoted the accumulation of terpenoids, especially diterpenoids. In winter Chinese cedar (WCC) needles, 9 genes (HCT, CHS, CHI, F3H, F3'H, F3'5'H, FLS, DFR, and LAR) involved in flavonoid biosynthesis were highly expressed and promoted flavonoid accumulation. This study broadens our understanding of the metabolic and transcriptomic changes in C. fortunei needles caused by seasonal changes and provides a reference regarding the adaptive mechanisms of C. fortunei and the extraction of its metabolites.

Diversity of Herbicide-Resistance Mechanisms of Avena fatua L. to Acetyl-CoA Carboxylase-Inhibiting Herbicides in the Bajio, Mexico

Herbicide resistance is an evolutionary process that affects entire agricultural regions’ yield and productivity. The high number of farms and the diversity of weed management can generate hot selection spots throughout the regions. Resistant biotypes can present a diversity of mechanisms of resistance and resistance factors depending on selective conditions inside the farm; this situation is similar to predictions by the geographic mosaic theory of coevolution. In Mexico, the agricultural region of the Bajio has been affected by herbicide resistance for 25 years. To date, Avena fatua L. is one of the most abundant and problematic weed species. The objective of this study was to determine the mechanism of resistance of biotypes with failures in weed control in 70 wheat and barley crop fields in the Bajio, Mexico. The results showed that 70% of farms have biotypes with target site resistance (TSR). The most common mutations were Trp–1999–Cys, Asp–2078–Gly, Ile–2041–Asn, and some of such mutations confer cross-resistance to ACCase-inhibiting herbicides. Metabolomic fingerprinting showed four different metabolic expression patterns. The results confirmed that in the Bajio, there exist multiple selection sites for both resistance mechanisms, which proves that this area can be considered as a geographic mosaic of resistance.

Fish metabolome from sub-urban lakes of the Paris area (France) and potential influence of noxious metabolites produced by cyanobacteria

The recent democratization of high-throughput molecular phenotyping allows the rapid expansion of promising untargeted multi-dimensional approaches (e.g. epigenomics, transcriptomics, proteomics, and/or metabolomics). Indeed, these emerging omics tools, processed for ecologically relevant species, may present innovative perspectives for environmental assessments, that could provide early warning of eco(toxico)logical impairments. In a previous pilot study (Sotton et al., Chemosphere 2019), we explore by ¹H NMR the bio-indicative potential of metabolomics analyses on the liver of 2 sentinel fish species (Perca fluviatilis and Lepomis gibbosus) collected in 8 water bodies of the peri-urban Paris' area (France). In the present study, we further investigate on the same samples the high potential of high-throughput UHPLC-HRMS/MS analyses. We show that the LC-MS metabolome investigation allows a clear separation of individuals according to the species, but also according to their respective sampling lakes. Interestingly, similar variations of Perca and Lepomis metabolomes occur locally indicating that site-specific environmental constraints drive the metabolome variations which seem to be influenced by the production of noxious molecules by cyanobacterial blooms in certain lakes. Thus, the development of such reliable environmental metabolomics approaches appears to constitute an innovative bio-indicative tool for the assessment of ecological stress, such as toxigenic cyanobacterial blooms, and aim at being further follow up.

Microalgae show a range of responses to exometabolites of foreign species

Studies on microalgae interspecific interactions have so far focused either on nutrient competition or allelopathic effects due to excreted substances from Harmful Algal Bloom (HAB) species. Evidence from plants, bacteria and specific microalgae groups, point to a range of responses mediated by sensing or direct chemical impact of exometabolites from foreign species. Such processes remain under-investigated, especially in non-HAB microalgae, despite the importance of such knowledge in ecology and industrial applications. Here, we study the directional effect of exometabolites of 4 "foreign" species Heterosigma akashiwo, Phaeocystis sp., Tetraselmis sp. and Thalassiosira sp. to each of three "target" species across a total of 12 treatments. We disentangle these effects from nutrient competition by adding cell free medium of each "foreign" species into our treatment cultures. We measured the biomass response, to the foreign exometabolites, as cell number and photosynthetic biomass (Chla), whereas nutrient use was measured as residual phosphorus (PO₄) and intracellular phosphorus (P). Exometabolites from filtrate of foreign species were putatively annotated by untargeted metabolomics analysis and were discussed in association to observed responses of target species. Among others, these metabolites included L-histidinal, Tiliacorine and dimethylsulfoniopropionate (DMSP). Our findings show that species show a range of responses with the most common being biomass suppression, and less frequent biomass enhancement and intracellular P storage. Filtrate from the green microalgae Tetraselmis caused the most pronounced negative effects suggesting that non-HAB species can also cause negative chemical interference. A candidate metabolite inducing this response is L-histidinal which was measured in high abundance uniquely in Tetraselmis and its L-histidine form derived from bacteria was previously confirmed as a microalgal algicidal. H. akashiwo also induced biomass suppression on other microalgae and a candidate metabolite for this response is Tiliacorine, a plant-derived alkaloid with confirmed cytotoxic activity.

Time-series eco-metabolomics reveals extensive reshuffling in metabolome during transition from cold acclimation to de-acclimation in an alpine shrub

Recording environmentally induced variations in the metabolome in plants can be a promising approach for understanding the complex patterns of metabolic regulation and their eco-physiological consequences. Here, we studied metabolome-wide changes and eco-physiological adjustments occurring across the year at high elevation environments in the leaf tissue of Rhododendron anthopogon, an alpine evergreen shrub of the Himalaya. New leaves of R. anthopogon appear after the snow-melt and remain intact even when the plants get covered under snow (November-June). During this whole period, they may undergo several physiological and biochemical adjustments in response to fluctuating temperatures and light conditions. To understand these changes, we analyzed eco-physiological traits, that is, freezing resistance, dry matter content and % of nitrogen and the overall metabolome across 10 different time-points, from August until the snowfall in November 2017, and then from June to August 2018. As anticipated, the freezing resistance increased toward the onset of winters. The leaf tissues exhibited a complete reshuffling of the metabolome during the growth cycle and time-points segregated into four clusters directly correlating with distinct phases of acclimation: non-acclimation (August 22, 2017; August 14, 2018), early cold acclimation (September 12, September 29, October 11, 2017), late cold acclimation (October 23, November 4, 2017), and de-acclimation (June 15, June 28, July 14, 2018). Cold acclimation involved metabolic progression (101 metabolites) with an increase of up to 19.4-fold (gentiobiose), whereas de-acclimation showed regression (120 metabolites) with a decrease of up to 30-fold (sucrose). The changes in the metabolome during de-acclimation were maximum and were not just a reversal of cold acclimation. Our results provided insights into the direction and magnitude of physiological changes in Rhododendron anthopogon that occurred across the year.

Implications of mistletoe parasitism for the host metabolome: A new plant identity in the forest canopy

Mistletoe-host systems exemplify an intimate and chronic relationship where mistletoes represent protracted stress for hosts, causing long-lasting impact. Although host changes in morphological and reproductive traits due to parasitism are well known, shifts in their physiological system, altering metabolite concentrations, are less known due to the difficulty of quantification. Here, we use ecometabolomic techniques in the plant-plant interaction, comparing the complete metabolome of the leaves from mistletoe (Viscum album) and needles from their host (Pinus nigra), both parasitized and unparasitized, to elucidate host responses to plant parasitism. Our results show that mistletoe acquires metabolites basically from the primary metabolism of its host and synthesizes its own defence compounds. In response to mistletoe parasitism, pines modify a quarter of their metabolome over the year, making the pine canopy metabolome more homogeneous by reducing the seasonal shifts in top-down stratification. Overall, host pines increase antioxidant metabolites, suggesting oxidative stress, and also increase part of the metabolites required by mistletoe, which act as a permanent sink of host resources. In conclusion, by exerting biotic stress and thereby causing permanent systemic change, mistletoe parasitism generates a new host-plant metabolic identity available in forest canopy, which could have notable ecological consequences in the forest ecosystem.

Tree Species and Epiphyte Taxa Determine the "Metabolomic niche" of Canopy Suspended Soils in a Species-Rich Lowland Tropical Rainforest

Tropical forests are biodiversity hotspots, but it is not well understood how this diversity is structured and maintained. One hypothesis rests on the generation of a range of metabolic niches, with varied composition, supporting a high species diversity. Characterizing soil metabolomes can reveal fine-scale differences in composition and potentially help explain variation across these habitats. In particular, little is known about canopy soils, which are unique habitats that are likely to be sources of additional biodiversity and biogeochemical cycling in tropical forests. We studied the effects of diverse tree species and epiphytes on soil metabolomic profiles of forest floor and canopy suspended soils in a French Guianese rainforest. We found that the metabolomic profiles of canopy suspended soils were distinct from those of forest floor soils, differing between epiphyte-associated and non-epiphyte suspended soils, and the metabolomic profiles of suspended soils varied with host tree species, regardless of association with epiphyte. Thus, tree species is a key driver of rainforest suspended soil metabolomics. We found greater abundance of metabolites in suspended soils, particularly in groups associated with plants, such as phenolic compounds, and with metabolic pathways related to amino acids, nucleotides, and energy metabolism, due to the greater relative proportion of tree and epiphyte organic material derived from litter and root exudates, indicating a strong legacy of parent biological material. Our study provides evidence for the role of tree and epiphyte species in canopy soil metabolomic composition and in maintaining the high levels of soil metabolome diversity in this tropical rainforest. It is likely that a wide array of canopy microsite-level environmental conditions, which reflect interactions between trees and epiphytes, increase the microscale diversity in suspended soil metabolomes.

European oak chemical diversity - from ecotypes to herbivore resistance

Climate change is increasing insect pressure and forcing plants to adapt. Although chemotypic differentiation and phenotypic plasticity in spatially separated tree populations are known for decades, understanding their importance in herbivory resistance across forests remains challenging. We studied four oak forest stands in Germany using nontarget metabolomics, elemental analysis, and chemometrics and mapped the leaf metabolome of herbivore-resistant (T-) and herbivore-susceptible (S-) European oaks (Quercus robur) to Tortrix viridana, an oak pest that causes severe forest defoliation. Among the detected metabolites, we identified reliable metabolic biomarkers to distinguish S- and T-oak trees. Chemotypic differentiation resulted in metabolic shifts of primary and secondary leaf metabolism. Across forests, T-oaks allocate resources towards constitutive chemical defense enriched of polyphenolic compounds, e.g. the flavonoids kaempferol, kaempferol and quercetin glucosides, while S-oaks towards growth-promoting substances such as carbohydrates and amino-acid derivatives. This extensive work across natural forests shows that oaks' resistance and susceptibility to herbivory are linked to growth-defense trade-offs of leaf metabolism. The discovery of biomarkers and the developed predictive model pave the way to understand Quercus robur's susceptibility to herbivore attack and to support forest management, contributing to the preservation of oak forests in Europe.

Functional analysis of pristine estuarine marine sediments

Traditional environmental monitoring techniques are well suited to resolving acute exposure effects but lack resolution in determining subtle shifts in ecosystem functions resulting from chronic exposure(s). Surveillance with sensitive omics-based technologies could bridge this gap but, to date, most omics-based environmental studies have focused on previously degraded environments, identifying key metabolic differences resulting from anthropogenic perturbations. Here, we apply omics-based approaches to pristine environments to establish blueprints of microbial functionality within healthy estuarine sediment communities. We collected surface sediments (n = 50) from four pristine estuaries along the Western Cape York Peninsula of Far North Queensland, Australia. Sediment microbiomes were analyzed for 16S rRNA amplicon sequences, central carbon metabolism metabolites and associated secondary metabolites via targeted and untargeted metabolic profiling methods. Multivariate statistical analyses indicated heterogeneity among all the sampled estuaries, however, taxa-function relationships could be established that predicted community metabolism potential. Twenty-four correlated gene-metabolite pathways were identified and used to establish sediment microbial blueprints of essential carbon metabolism and amino acid biosynthesis that were positively correlated with community metabolic function outputs (2-oxisocapraote, tryptophan, histidine citrulline and succinic acid). In addition, an increase in the 125 KEGG genes related to metal homeostasis and metal resistance was observed, although, none of the detected metabolites related to these specific genes upon integration. However, there was a correlation between metal abundance and functional genes related to Fe and Zn metabolism. Our results establish a baseline microbial blueprint for the pristine sediment microbiome, one that drives important ecosystem services and to which future ecosurveillance monitoring can be compared.

Fungal Volatile Organic Compounds: More Than Just a Funky Smell?

Many volatile organic compounds (VOCs) associated with industry cause adverse health effects, but less is known about the physiological effects of biologically produced volatiles. This review focuses on the VOCs emitted by fungi, which often have characteristic moldy or "mushroomy" odors. One of the most common fungal VOCs, 1-octen-3-ol, is a semiochemical for many arthropod species and also serves as a developmental hormone for several fungal groups. Other fungal VOCs are flavor components of foods and spirits or are assayed in indirect methods for detecting the presence of mold in stored agricultural produce and water-damaged buildings. Fungal VOCs function as antibiotics as well as defense and plant-growth-promoting agents and have been implicated in a controversial medical condition known as sick building syndrome. In this review, we draw attention to the ubiquity, diversity, and toxicological significance of fungal VOCs as well as some of their ecological roles.

MolDiscovery: learning mass spectrometry fragmentation of small molecules

Identification of small molecules is a critical task in various areas of life science. Recent advances in mass spectrometry have enabled the collection of tandem mass spectra of small molecules from hundreds of thousands of environments. To identify which molecules are present in a sample, one can search mass spectra collected from the sample against millions of molecular structures in small molecule databases. The existing approaches are based on chemistry domain knowledge, and they fail to explain many of the peaks in mass spectra of small molecules. Here, we present molDiscovery, a mass spectral database search method that improves both efficiency and accuracy of small molecule identification by learning a probabilistic model to match small molecules with their mass spectra. A search of over 8 million spectra from the Global Natural Product Social molecular networking infrastructure shows that molDiscovery correctly identify six times more unique small molecules than previous methods.

Biotechnology for secure biocontainment designs in an emerging bioeconomy

Genetically modified organisms (GMOs) have emerged as an integral component of a sustainable bioeconomy, with an array of applications in agriculture, bioenergy, and biomedicine. However, the rapid development of GMOs and associated synthetic biology approaches raises a number of biosecurity concerns related to environmental escape of GMOs, detection thereof, and impact upon native ecosystems. A myriad of genetic safeguards have been deployed in diverse microbial hosts, ranging from classical auxotrophies to global genome recoding. However, to realize the full potential of microbes as biocatalytic platforms in the bioeconomy, a deeper understanding of the fundamental principles governing microbial responsiveness to biocontainment constraints, and interactivity of GMOs with the environment, is required. Herein, we review recent analytical biotechnological advances and strategies to assess biocontainment and microbial bioproductivity, as well as opportunities for predictive systems biodesigns towards securing a viable bioeconomy.

Metabolomics and transcriptomics to decipher molecular mechanisms underlying ectomycorrhizal root colonization of an oak tree

Mycorrhizas are known to have a positive impact on plant growth and ability to resist major biotic and abiotic stresses. However, the metabolic alterations underlying mycorrhizal symbiosis are still understudied. By using metabolomics and transcriptomics approaches, cork oak roots colonized by the ectomycorrhizal fungus Pisolithus tinctorius were compared with non-colonized roots. Results show that compounds putatively corresponding to carbohydrates, organic acids, tannins, long-chain fatty acids and monoacylglycerols, were depleted in ectomycorrhizal cork oak colonized roots. Conversely, non-proteogenic amino acids, such as gamma-aminobutyric acid (GABA), and several putative defense-related compounds, including oxylipin-family compounds, terpenoids and B6 vitamers were induced in mycorrhizal roots. Transcriptomic analysis suggests the involvement of GABA in ectomycorrhizal symbiosis through increased synthesis and inhibition of degradation in mycorrhizal roots. Results from this global metabolomics analysis suggest decreases in root metabolites which are common components of exudates, and in compounds related to root external protective layers which could facilitate plant-fungal contact and enhance symbiosis. Root metabolic pathways involved in defense against stress were induced in ectomycorrhizal roots that could be involved in a plant mechanism to avoid uncontrolled growth of the fungal symbiont in the root apoplast. Several of the identified symbiosis-specific metabolites, such as GABA, may help to understand how ectomycorrhizal fungi such as P. tinctorius benefit their host plants.

Resurrecting the metabolome: Rapid evolution magnifies the metabolomic plasticity to predation in a natural Daphnia population

Populations rely on already present plastic responses (ancestral plasticity) and evolution (including both evolution of mean trait values, constitutive evolution, and evolution of plasticity) to adapt to novel environmental conditions. Because of the lack of evidence from natural populations, controversy remains regarding the interplay between ancestral plasticity and rapid evolution in driving responses to new stressors. We addressed this topic at the level of the metabolome utilizing a resurrected natural population of the water flea Daphnia magna that underwent a human-caused increase followed by a reduction in predation pressure within ~16 years. Predation risk induced plastic changes in the metabolome which were mainly related to shifts in amino acid and sugar metabolism, suggesting predation risk affected protein and sugar utilization to increase energy supply. Both the constitutive and plastic components of the metabolic profiles showed rapid, probably adaptive evolution whereby ancestral plasticity and evolution contributed nearly equally to the total changes of the metabolomes. The subpopulation that experienced the strongest fish predation pressure and showed the strongest phenotypic response, also showed the strongest metabolomic response to fish kairomones, both in terms of the number of responsive metabolites and in the amplitude of the multivariate metabolomic reaction norm. More importantly, the metabolites with higher ancestral plasticity showed stronger evolution of plasticity when predation pressure increased, while this pattern reversed when predation pressure relaxed. Our results therefore highlight that the evolution in response to a novel pressure in a natural population magnified the metabolomic plasticity to this stressor.

Untargeted In Silico Compound Classification-A Novel Metabolomics Method to Assess the Chemodiversity in Bryophytes

In plant ecology, biochemical analyses of bryophytes and vascular plants are often conducted on dried herbarium specimen as species typically grow in distant and inaccessible locations. Here, we present an automated in silico compound classification framework to annotate metabolites using an untargeted data independent acquisition (DIA)–LC/MS–QToF-sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH) ecometabolomics analytical method. We perform a comparative investigation of the chemical diversity at the global level and the composition of metabolite families in ten different species of bryophytes using fresh samples collected on-site and dried specimen stored in a herbarium for half a year. Shannon and Pielou’s diversity indices, hierarchical clustering analysis (HCA), sparse partial least squares discriminant analysis (sPLS-DA), distance-based redundancy analysis (dbRDA), ANOVA with post-hoc Tukey honestly significant difference (HSD) test, and the Fisher’s exact test were used to determine differences in the richness and composition of metabolite families, with regard to herbarium conditions, ecological characteristics, and species. We functionally annotated metabolite families to biochemical processes related to the structural integrity of membranes and cell walls (proto-lignin, glycerophospholipids, carbohydrates), chemical defense (polyphenols, steroids), reactive oxygen species (ROS) protection (alkaloids, amino acids, flavonoids), nutrition (nitrogen- and phosphate-containing glycerophospholipids), and photosynthesis. Changes in the composition of metabolite families also explained variance related to ecological functioning like physiological adaptations of bryophytes to dry environments (proteins, peptides, flavonoids, terpenes), light availability (flavonoids, terpenes, carbohydrates), temperature (flavonoids), and biotic interactions (steroids, terpenes). The results from this study allow to construct chemical traits that can be attributed to biogeochemistry, habitat conditions, environmental changes and biotic interactions. Our classification framework accelerates the complex annotation process in metabolomics and can be used to simplify biochemical patterns. We show that compound classification is a powerful tool that allows to explore relationships in both molecular biology by “zooming in” and in ecology by “zooming out”. The insights revealed by our framework allow to construct new research hypotheses and to enable detailed follow-up studies.

Non-target metabolomics revealed the differences between Rh. tanguticum plants growing under canopy and open habitats

BACKGROUND

Rheum tanguticum (Rh. tanguticum) is an important traditional Chinese medicine plant, "Dahuang", which contains productive metabolites and occupies wide habitats on the Qinghai-Tibet plateau. Plants occupying wide habitats usually vary in phenotypes such as in morphology and metabolism, thereby developing into different ecotypes. Under canopy and open habitats are a pair of dissimilar habitats which possess Rh. tanguticum plants. However, few studies have focused on the effect of habitats on Rh. tanguticum growth, particularly combining morphological and metabolic changes. This study focused on Rh. tanguticum plants growing in under canopy and open habitats where morphology and metabolism changes were quantified using non-target metabolism methods.

RESULTS

The obtained results indicated that the two dissimilar habitats led to Rh. tanguticum developing into two distinct ecotypes where the morphology and metabolism were simultaneously changed. Under canopy habitats bred morphologically smaller Rh. tanguticum plants which had a higher level of metabolites (22 out of 31) which included five flavonoids, four isoflavonoids, and three anthracenes. On the other hand, the open habitats produced morphologically larger Rh. tanguticum plants having a higher level of metabolites (9 out of 31) including four flavonoids. 6 of the 31 metabolites were predicted to have effect targets, include 4 represent for under canopy habitats and 2 for open habitats. Totally, 208 targets were connected, among which 42 were communal targets for both under canopy and open habitats represent compounds, and 100 and 66 were unique targets for under canopy superior compounds and open habitats superior compounds, respectively. In addition, aloe-emodin, emodin, chrysophanol, physcion, sennoside A and sennoside B were all more accumulated in under canopy habitats, and among which aloe-emodin, emodin, chrysophanol and physcion were significantly higher in under canopy habitats.

CONCLUSIONS

This study determined that Rh. tanguticum growing in under canopy and in open habitats developed into two distinct ecotypes with morphological and metabolic differences. Results of network pharmacology study has indicated that "Dahuang" coming from different habitats, such as under canopy and open habitats, are different in effect targets and thus may have different medicinal use. According to target metabolomics, under canopy habitats may grow better "Dahuang".

Probing the Response of the Amphibious Plant Butomus umbellatus to Nutrient Enrichment and Shading by Integrating Eco-Physiological With Metabolomic Analyses

Amphibious plants, living in land-water ecotones, have to cope with challenging and continuously changing growth conditions in their habitats with respect to nutrient and light availability. They have thus evolved a variety of mechanisms to tolerate and adapt to these changes. Therefore, the study of these plants is a major area of ecophysiology and environmental ecological research. However, our understanding of their capacity for physiological adaptation and tolerance remains limited and requires systemic approaches for comprehensive analyses. To this end, in this study, we have conducted a mesocosm experiment to analyze the response of Butomus umbellatus, a common amphibious species in Denmark, to nutrient enrichment and shading. Our study follows a systematic integration of morphological (including plant height, leaf number, and biomass accumulation), ecophysiological (photosynthesis-irradiance responses, leaf pigment content, and C and N content in plant organs), and leaf metabolomic measurements using gas chromatography-mass spectrometry (39 mainly primary metabolites), based on bioinformatic methods. No studies of this type have been previously reported for this plant species. We observed that B. umbellatus responds to nutrient enrichment and light reduction through different mechanisms and were able to identify its nutrient enrichment acclimation threshold within the applied nutrient gradient. Up to that threshold, the morpho-physiological response to nutrient enrichment was profound, indicating fast-growing trends (higher growth rates and biomass accumulation), but only few parameters changed significantly from light to shade [specific leaf area (SLA); quantum yield (φ)]. Metabolomic analysis supported the morpho-physiological results regarding nutrient overloading, indicating also subtle changes due to shading not directly apparent in the other measurements. The combined profile analysis revealed leaf metabolite and morpho-physiological parameter associations. In this context, leaf lactate, currently of uncertain role in higher plants, emerged as a shading acclimation biomarker, along with SLA and φ. The study enhances both the ecophysiology methodological toolbox and our knowledge of the adaptive capacity of amphibious species. It demonstrates that the educated combination of physiological with metabolomic measurements using bioinformatic approaches is a promising approach for ecophysiology research, enabling the elucidation of discriminatory metabolic shifts to be used for early diagnosis and even prognosis of natural ecosystem responses to climate change.

Key metabolites associated with the onset of flowering of guar genotypes (Cyamopsis tetragonoloba (L.) Taub)

BACKGROUND

Guar (Cyamopsis tetragonoloba (L.) Taub.), a short-day plant, is an economically valuable legume crop. Seeds of guar serve as a source of galactomannan polysaccharide, known as guar gum, which is in demand in the gas and oil industries. The rapid and complete maturation of guar seeds depends on the flowering time of a particular genotype. It is known that flowering in guar is controlled by several gene systems. However, no information about the process and mechanisms that trigger flowering in guar on the molecular and biochemical levels was previously reported. The aim of the study was to investigate the metabolic landscape underlying transition to the flowering in guar using GC-MS-metabolomic analysis.

RESULTS

82 diverse guar genotypes (each in 8 replicates) from the VIR collection were grown under experimental conditions of high humidity and long photoperiod. In the stress environment some guar genotypes turned to flowering early (41 ± 1,8 days from the first true leaf appearance) while for others the serious delay of flowering (up to 95 ± 1,7 days) was observed. A total of 244 metabolites were detected by GC-MS analysis on the third true leaves stage of 82 guar genotypes. Among them some molecules were associated with the transition of the guar plants to flowering. Clear discrimination was observed in metabolomic profiles of two groups of «early flowering» and «delayed flowering» plants, with 65 metabolites having a significantly higher abundance in early flowering genotypes. Among them 7 key molecules were identified by S-plot, as potential biomarkers discriminating of «early flowering» and «delayed flowering» guar genotypes.

CONCLUSIONS

The metabolomic landscape accompanying transition to flowering in guar was firstly described. The results obtained can be used in subsequent genomic research for identifying metabolite-gene associations and revealing genes responsible for the onset of flowering and photoperiod sensitivity of guar. In addition, the detected key metabolites associated with flowering of guar can be employed as biomarkers allowing rapid screening of breeding material for the potentially early flowering genotypes.

Microbial Nitrogen Cycling in Antarctic Soils

The Antarctic continent is widely considered to be one of the most hostile biological habitats on Earth. Despite extreme environmental conditions, the ice-free areas of the continent, which constitute some 0.44% of the total continental land area, harbour substantial and diverse communities of macro-organisms and especially microorganisms, particularly in the more "hospitable" maritime regions. In the more extreme non-maritime regions, exemplified by the McMurdo Dry Valleys of South Victoria Land, nutrient cycling and ecosystem servicing processes in soils are largely driven by microbial communities. Nitrogen turnover is a cornerstone of ecosystem servicing. In Antarctic continental soils, specifically those lacking macrophytes, cold-active free-living diazotrophic microorganisms, particularly Cyanobacteria, are keystone taxa. The diazotrophs are complemented by heterotrophic bacterial and archaeal taxa which show the genetic capacity to perform elements of the entire N cycle, including nitrification processes such as the anammox reaction. Here, we review the current literature on nitrogen cycling genes, taxa, processes and rates from studies of Antarctic soils. In particular, we highlight the current gaps in our knowledge of the scale and contribution of these processes in south polar soils as critical data to underpin viable predictions of how such processes may alter under the impacts of future climate change.

Seasonal variations in leaf and branch trace elements and the influence of a 3-yr 100% rainfall exclusion on Pinus massoniana Lamb

Background

Trace elements are essential for the growth and survival of plants, and their concentrations and distributions in plants are effective reflections of ecological adaptation strategies. However, this aspect has seldom been addressed.

Method

Changes in the leaf and branch trace elements of Pinus massoniana Lamb, induced by seasonal dynamics and in response to a 3-yr 100% rainfall exclusion, were evaluated.

Results

The results showed that the concentrations of Fe, Cu, Zn, Cd, Ni and Cr in leaves of P. massoniana in the control group had high seasonal resolution. There were three groups according to their patterns over the growing season: (1) nutrient elements (Cu, Zn, Ni and Cd), which continuously decreased in concentration during the growing season, with the highest concentration in spring and the lowest in autumn; (2) accumulating element (Cr), which increased in concentration from spring to autumn; and (3) indifferent element (Fe), which increased in concentration from spring to summer and decreased in concentration from summer to autumn. The concentrations of trace elements in leaves and branches showed no significant differences with mild drought stress, except for Fe and Cr in leaves and Cr in branches, which significantly increased (p < 0.05) under the result of self-selection under mild drought stress. Therefore, the resultant seasonal and drought effects on trace element cycling in P. massoniana could provide theoretical support to respond to future climate change.

31P-NMR Metabolomics Revealed Species-Specific Use of Phosphorous in Trees of a French Guiana Rainforest

Productivity of tropical lowland moist forests is often limited by availability and functional allocation of phosphorus (P) that drives competition among tree species and becomes a key factor in determining forestall community diversity. We used non-target ³¹P-NMR metabolic profiling to study the foliar P-metabolism of trees of a French Guiana rainforest. The objective was to test the hypotheses that P-use is species-specific, and that species diversity relates to species P-use and concentrations of P-containing compounds, including inorganic phosphates, orthophosphate monoesters and diesters, phosphonates and organic polyphosphates. We found that tree species explained the 59% of variance in ³¹P-NMR metabolite profiling of leaves. A principal component analysis showed that tree species were separated along PC 1 and PC 2 of detected P-containing compounds, which represented a continuum going from high concentrations of metabolites related to non-active P and P-storage, low total P concentrations and high N:P ratios, to high concentrations of P-containing metabolites related to energy and anabolic metabolism, high total P concentrations and low N:P ratios. These results highlight the species-specific use of P and the existence of species-specific P-use niches that are driven by the distinct species-specific position in a continuum in the P-allocation from P-storage compounds to P-containing molecules related to energy and anabolic metabolism.

Ecometabolomics for a Better Understanding of Plant Responses and Acclimation to Abiotic Factors Linked to Global Change

The number of ecometabolomic studies, which use metabolomic analyses to disentangle organisms' metabolic responses and acclimation to a changing environment, has grown exponentially in recent years. Here, we review the results and conclusions of ecometabolomic studies on the impacts of four main drivers of global change (increasing frequencies of drought episodes, heat stress, increasing atmospheric carbon dioxide (CO2) concentrations and increasing nitrogen (N) loads) on plant metabolism. Ecometabolomic studies of drought effects confirmed findings of previous target studies, in which most changes in metabolism are characterized by increased concentrations of soluble sugars and carbohydrate derivatives and frequently also by elevated concentrations of free amino acids. Secondary metabolites, especially flavonoids and terpenes, also commonly exhibited increased concentrations when drought intensified. Under heat and increasing N loads, soluble amino acids derived from glutamate and glutamine were the most responsive metabolites. Foliar metabolic responses to elevated atmospheric CO2 concentrations were dominated by greater production of monosaccharides and associated synthesis of secondary metabolites, such as terpenes, rather than secondary metabolites synthesized along longer sugar pathways involving N-rich precursor molecules, such as those formed from cyclic amino acids and along the shikimate pathway. We suggest that breeding for crop genotypes tolerant to drought and heat stress should be based on their capacity to increase the concentrations of C-rich compounds more than the concentrations of smaller N-rich molecules, such as amino acids. This could facilitate rapid and efficient stress response by reducing protein catabolism without compromising enzymatic capacity or increasing the requirement for re-transcription and de novo biosynthesis of proteins.

The case for research integration, from genomics to remote sensing, to understand biodiversity change and functional dynamics in the world's lakes

Freshwater ecosystems are heavily impacted by multiple stressors, and a freshwater biodiversity crisis is underway. This realization has prompted calls to integrate global freshwater ecosystem data, including traditional taxonomic and newer types of data (e.g., eDNA, remote sensing), to more comprehensively assess change among systems, regions, and organism groups. We argue that data integration should be done, not only with the important purpose of filling gaps in spatial, temporal, and organismal representation, but also with a more ambitious goal: to study fundamental cross-scale biological phenomena. Such knowledge is critical for discerning and projecting ecosystem functional dynamics, a realm of study where generalizations may be more tractable than those relying on taxonomic specificity. Integration could take us beyond cataloging biodiversity losses, and toward predicting ecosystem change more broadly. Fundamental biology questions should be central to integrative, interdisciplinary research on causal ecological mechanisms, combining traditional measures and more novel methods at the leading edge of the biological sciences. We propose a conceptual framework supporting this vision, identifying key questions and uncertainties associated with realizing this research potential. Our framework includes five interdisciplinary "complementarities." First, research approaches may provide comparative complementarity when they offer separate realizations of the same focal phenomenon. Second, for translational complementarity, data from one research approach is used to translate that from another, facilitating new inferences. Thirdly, causal complementarity arises when combining approaches allows us to "fill in" cause-effect relationships. Fourth, contextual complementarity is realized when together research methodologies establish the wider ecological and spatiotemporal context within which focal biological responses occur. Finally, integration may allow us to cross inferential scales through scaling complementarity. Explicitly identifying the modes and purposes of integrating research approaches, and reaching across disciplines to establish appropriate collaboration will allow researchers to address major biological questions that are more than the sum of the parts.

Caterpillars on a phytochemical landscape: The case of alfalfa and the Melissa blue butterfly

Modern metabolomic approaches that generate more comprehensive phytochemical profiles than were previously available are providing new opportunities for understanding plant-animal interactions. Specifically, we can characterize the phytochemical landscape by asking how a larger number of individual compounds affect herbivores and how compounds covary among plants. Here we use the recent colonization of alfalfa (Medicago sativa) by the Melissa blue butterfly (Lycaeides melissa) to investigate the effects of indivdiual compounds and suites of covarying phytochemicals on caterpillar performance. We find that survival, development time, and adult weight are all associated with variation in nutrition and toxicity, including biomolecules associated with plant cell function as well as putative anti-herbivore action. The plant-insect interface is complex, with clusters of covarying compounds in many cases encompassing divergent effects on different aspects of caterpillar performance. Individual compounds with the strongest associations are largely specialized metabolites, including alkaloids, phenolic glycosides, and saponins. The saponins are represented in our data by more than 25 individual compounds with beneficial and detrimental effects on L. melissa caterpillars, which highlights the value of metabolomic data as opposed to approaches that rely on total concentrations within broad defensive classes.

Different "metabolomic niches" of the highly diverse tree species of the French Guiana rainforests

Tropical rainforests harbor a particularly high plant diversity. We hypothesize that potential causes underlying this high diversity should be linked to distinct overall functionality (defense and growth allocation, anti-stress mechanisms, reproduction) among the different sympatric taxa. In this study we tested the hypothesis of the existence of a metabolomic niche related to a species-specific differential use and allocation of metabolites. We tested this hypothesis by comparing leaf metabolomic profiles of 54 species in two rainforests of French Guiana. Species identity explained most of the variation in the metabolome, with a species-specific metabolomic profile across dry and wet seasons. In addition to this “homeostatic” species-specific metabolomic profile significantly linked to phylogenetic distances, also part of the variance (flexibility) of the metabolomic profile was explained by season within a single species. Our results support the hypothesis of the high diversity in tropical forest being related to a species-specific metabolomic niche and highlight ecometabolomics as a tool to identify this species functional diversity related and consistent with the ecological niche theory.

Metabolomic study of volatile compounds emitted by lavender grown under open-field conditions: a potential approach to investigate the yellow decline disease

INTRODUCTION

Fine lavender and lavandin are perfume and medicinal plants originate from the South of France and are widely cultivated for their essential oils. Recently, cultivated plants suffered from a severe decline in France, due to the propagation of the yellow decline disease. This disease is caused by the stolbur phytoplasma, a bacterium transmitted by a sap-sucking insect, the planthopper.

OBJECTIVES

In order to understand the complex relationships between host plant, pest, pathogen and environment responsible for the yellow decline of lavender, we use a metabolomic approach to highlight changes in chemical emissions from asymptomatic ("healthy") and symptomatic ("infected") plants.

METHODS

Volatile compounds produced by fine lavender and lavandin were collected in the field using a dynamic headspace extraction approach. Afterwards, compounds trapped on Tenax adsorbent were thermodesorbed and analysed using an automated thermal desorption-gas chromatography-mass spectrometry (ATD-GC-MS). Multivariate statistical analyses was performed using principal component analysis and partial least square discriminant analyses.

RESULTS

The untargeted screening of volatiles allowed the separation of asymptomatic and symptomatic plants according to their emissions. The approach was sufficiently accurate so as to separate the emissions according to the different stages of infection. Twelve compounds were found to be deregulated metabolites of yellow disease infection, common to fine lavender (variety 7713) and lavandin (variety abrial).

CONCLUSION

The metabolomic approach allowed for the effective identification of chemical variations between infected and healthy plants in a complex field environment.

1H-NMR Determination of Organic Compounds in Municipal Wastewaters and the Receiving Surface Waters in Eastern Cape Province of South Africa

Surface water is the recipient of pollutants from various sources, including improperly treated wastewater. Comprehensive knowledge of the composition of water is necessary to make it reusable in water-scarce environments. In this work, proton nuclear magnetic resonance (¹H-NMR) was combined with multivariate analysis to study the metabolites in four rivers and four wastewater treatment plants releasing treated effluents into the rivers. ¹H-NMR chemical shifts of the extracts in CDCl were acquired with Bruker 400. Chemical shifts of ¹H-NMR in chlorinated alkanes, amino compounds and fluorinated hydrocarbons were common to samples of wastewater and lower reaches or the rivers. ¹H-NMR chemical shifts of carbonyl compounds and alkyl phosphates were restricted to wastewater samples. Chemical shifts of phenolic compounds were associated with treated effluent samples. This study showed that the sources of these metabolites in the rivers were not only from improperly treated effluents but also from runoffs. Multivariate analyses showed that some of the freshwater samples were not of better quality than wastewater and treated effluents. Observations show the need for constant monitoring of rivers and effluent for the safety of the aquatic environment.

Orchids and their mycorrhizal fungi: an insufficiently explored relationship

Orchids are associated with diverse fungal taxa, including nonmycorrhizal endophytic fungi as well as mycorrhizal fungi. The orchid mycorrhizal (OM) symbiosis is an excellent model for investigating the biological interactions between plants and fungi due to their high dependency on these symbionts for growth and survival. To capture the complexity of OM interactions, significant genomic, numerous transcriptomic, and proteomic studies have been performed, unraveling partly the role of each partner. On the other hand, several papers studied the bioactive metabolites from each partner but rarely interpreted their significance in this symbiotic relationship. In this review, we focus from a biochemical viewpoint on the OM dynamics and its molecular interactions. The ecological functions of OM in plant development and stress resistance are described first, summarizing recent literature. Secondly, because only few studies have specifically looked on OM molecular interactions, the signaling pathways and compounds allowing the establishment/maintenance of mycorrhizal association involved in arbuscular mycorrhiza (AM) are discussed in parallel with OM. Based on mechanistic similarities between OM and AM, and recent findings on orchids' endophytes, a putative model representing the different molecular strategies that OM fungi might employ to establish this association is proposed. It is hypothesized here that (i) orchids would excrete plant molecule signals such as strigolactones and flavonoids but also other secondary metabolites; (ii) in response, OM fungi would secrete mycorrhizal factors (Myc factors) or similar compounds to activate the common symbiosis genes (CSGs); (iii) overcome the defense mechanism by evasion of the pathogen-associated molecular patterns (PAMPs)-triggered immunity and by secretion of effectors such as small inhibitor proteins; and (iv) finally, secrete phytohormones to help the colonization or disrupt the crosstalk of plant defense phytohormones. To challenge this putative model, targeted and untargeted metabolomics studies with special attention to each partner's contribution are finally encouraged and some technical approaches are proposed.

Assessment of the effects of metribuzin, glyphosate, and their mixtures on the metabolism of the model plant Lemna minor L. applying metabolomics

Chemical plant protection products (PPPs) is a major group of xenobiotics that are being released in the environment. Although the effects of individual active ingredients (a.i.) on organisms have been studied, information on those of mixtures, is fragmented. Aquatic environments are being polluted by PPPs, posing serious risks for the environment, human, and other organisms. Based on the potential of the model aquatic plant Lemna minor L. in the assessment of PPPs-caused stresses, we have undertaken the task of developing a metabolomics approach for the study of the effects of metribuzin and glyphosate, and their mixtures. Bioassays revealed that metribuzin exhibit higher toxicity than glyphosate and metabolomics highlighted corresponding changes in its metabolome. Treatments had a substantial impact on plants' amino acid pool, resulting in elevated levels of the majority of the identified amino acids. Results indicate that the increased proteolytic activity is a common effect of the a.i. and their mixtures. Additionally, the activation of salicylate-signaling pathways was recorded as a response to the toxicity caused by mixtures. Among the identified metabolites that were discovered as biomarkers were γ-aminobutyric acid (GABA), salicylate, caffeate, α,α-trehalose, and squalene, which play multiple roles in plants' metabolism such as, signaling, antioxidant, and structure protection. No reports exist on the combined effects of PPPs on Lemna and results confirm the applicability of Lemna metabolomics in the study of the combined effects of herbicides and its potential in the monitoring of the environmental health of aquatic environments based on fluctuations of the plant's metabolism.

Metabolomic profiles associated with exposure to per- and polyfluoroalkyl substances (PFASs) in aquatic environments

Per- and polyfluoroalkyl substances (PFASs) are frequently detected in aquatic environments. Longer chained perfluoroalkyl acids (PFAAs), in particular, have been found to bioaccumulate in a broad range of aquatic biota. PFAAs have a physiochemical similarity to naturally occurring fatty acids and could potentially disrupt metabolic processes, however, there has been limited study in this area, especially in aquatic species. In this study, the associations between PFAAs and metabolite profiles were investigated in crustaceans. Eastern School Prawn (Metapenaeus macleayi) were obtained from three different locations (n = 15 per location) with similar environmental conditions but different levels of PFAA contamination. The concentrations of PFAAs, fatty acids and amino acids were analysed and differences in PFAA and metabolite profiles were evaluated. Different PFAA profiles were mirrored by significant differences in the composition of both fatty acid and amino acid profiles, indicating a potential association between PFAA concentration and the composition of metabolites in prawns. These results highlight a need for further research investigating the impacts of PFAA exposure, with the current study providing a foundation for further investigation of the relationship between PFAA bioaccumulation and organism metabolism.

Chemical Diversity and Classification of Secondary Metabolites in Nine Bryophyte Species

The central aim in ecometabolomics and chemical ecology is to pinpoint chemical features that explain molecular functioning. The greatest challenge is the identification of compounds due to the lack of constitutive reference spectra, the large number of completely unknown compounds, and bioinformatic methods to analyze the big data. In this study we present an interdisciplinary methodological framework that extends ultra-performance liquid chromatography coupled to electrospray ionization quadrupole time-of-flight mass spectrometry (UPLC/ESI-QTOF-MS) with data-dependent acquisition (DDA-MS) and the automated in silico classification of fragment peaks into compound classes. We synthesize findings from a prior study that explored the influence of seasonal variations on the chemodiversity of secondary metabolites in nine bryophyte species. Here we reuse and extend the representative dataset with DDA-MS data. Hierarchical clustering, heatmaps, dbRDA, and ANOVA with post-hoc Tukey HSD were used to determine relationships of the study factors species, seasons, and ecological characteristics. The tested bryophytes showed species-specific metabolic responses to seasonal variations (50% vs. 5% of explained variation). Marchantia polymorpha, Plagiomnium undulatum, and Polytrichum strictum were biochemically most diverse and unique. Flavonoids and sesquiterpenoids were upregulated in all bryophytes in the growing seasons. We identified ecological functioning of compound classes indicating light protection (flavonoids), biotic and pathogen interactions (sesquiterpenoids, flavonoids), low temperature and desiccation tolerance (glycosides, sesquiterpenoids, anthocyanins, lactones), and moss growth supporting anatomic structures (few methoxyphenols and cinnamic acids as part of proto-lignin constituents). The reusable bioinformatic framework of this study can differentiate species based on automated compound classification. Our study allows detailed insights into the ecological roles of biochemical constituents of bryophytes with regard to seasonal variations. We demonstrate that compound classification can be improved with adding constitutive reference spectra to existing spectral libraries. We also show that generalization on compound classes improves our understanding of molecular ecological functioning and can be used to generate new research hypotheses.

Natural Products Diversity in Plant-Insect Interaction between Tithonia diversifolia (Asteraceae) and Chlosyne lacinia (Nymphalidae)

The chemical ecology of plant-insect interactions has been driving our understanding of ecosystem evolution into a more comprehensive context. Chlosyne lacinia (Lepidoptera: Nymphalidae) is an olygophagous insect herbivore, which mainly uses host plants of Heliantheae tribe (Asteraceae). Herein, plant-insect interaction between Tithonia diversifolia (Heliantheae) and Chlosyne lacinia was investigated by means of untargeted LC-MS/MS based metabolomics and molecular networking, which aims to explore its inherent chemical diversity. C. lacinia larvae that were fed with T. diversifolia leaves developed until fifth instar and completed metamorphosis to the adult phase. Sesquiterpene lactones (STL), flavonoids, and lipid derivatives were putatively annotated in T. diversifolia (leaves and non-consumed abaxial surface) and C. lacinia (feces, larvae, pupae, butterflies, and eggs) samples. We found that several furanoheliangolide-type STL that were detected in T. diversifolia were ingested and excreted in their intact form by C. lacinia larvae. Hence, C. lacinia caterpillars may have, over the years, developed tolerance mechanisms for STL throughout effective barriers in their digestive canal. Flavonoid aglycones were mainly found in T. diversifolia samples, while their glycosides were mostly detected in C. lacinia feces, which indicated that the main mechanism for excreting the consumed flavonoids was through their glycosylation. Moreover, lysophospholipids were predominately found in C. lacinia samples, which suggested that they were essential metabolites during pupal and adult stages. These findings provide insights into the natural products diversity of this plant-insect interaction and contribute to uncovering its ecological roles.

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.

Specificity of the metabolic signatures of fish from cyanobacteria rich lakes

With the increasing impact of the global warming, occurrences of cyanobacterial blooms in aquatic ecosystems are becoming a main worldwide ecological concern. Due to their capacity to produce potential toxic metabolites, interactions between the cyanobacteria, their cyanotoxins and the surrounding freshwater organisms have been investigated during the last past years. Non-targeted metabolomic analyses have the powerful capacity to study simultaneously a high number of metabolites and thus to investigate in depth the molecular signatures between various organisms encountering different environmental scenario, and potentially facing cyanobacterial blooms. In this way, the liver metabolomes of two fish species (Perca fluviatilis and Lepomis gibbosus) colonizing various peri-urban lakes of the Île-de-France region displaying high biomass of cyanobacteria, or not, were investigated. The fish metabolome hydrophilic fraction was analyzed by ¹H NMR analysis coupled with Batman peak treatment for the quantification and the annotation attempt of the metabolites. The results suggest that similar metabolome profiles occur in both fish species, for individuals collected from cyanobacterial blooming lakes compared to organism from non-cyanobacterial dominant environments. Overall, such environmental metabolomic pilot study provides new research perspectives in ecology and ecotoxicology fields, and may notably provide new information concerning the cyanobacteria/fish ecotoxicological interactions.

Ecometabolomic Analysis of Wild Populations of Pilocarpus pennatifolius (Rutaceae) Using Unimodal Analyses

Studies examining the diversity of plant specialized metabolites suggest that biotic and abiotic pressures greatly influence the qualitative and quantitative diversity found in a species. Large geographic distributions expose a species to a great variety of environmental pressures, thus providing an enormous opportunity for expression of environmental plasticity. Pilocarpus, a neotropical genus of Rutaceae, is rich in alkaloids, terpenoids, and coumarins, and is the only commercial source of the alkaloid pilocarpine for the treatment of glaucoma. Overharvesting of species in this genus for pilocarpine, has threatened natural populations of the species. The aim of this research was to understand how adaptation to environmental variation shapes the metabolome in multiple populations of the widespread species Pilocarpus pennatifolius. LCMS data from alkaloid and phenolic extracts of leaf tissue were analyzed with environmental predictors using unimodal unconstrained and constrained ordination methods for an untargeted metabolomics analysis. PLS-DA was used to further confirm the chemoecotypes of each site. The most important variables contributing to the alkaloid variation between the sites: mean temperature of wettest quarter, as well as the soil content of phosphorus, magnesium, and base saturation (V%). The most important contributing to the phenolic variation between the sites: mean temperature of the wettest quarter, temperature seasonality, calcium and soil electrical conductivity. This research will have broad implications in a variety of areas including biocontrol for pests, environmental and ecological plant physiology, and strategies for species conservation maximizing phytochemical diversity.

Atmo-ecometabolomics: a novel atmospheric particle chemical characterization methodology for ecological research

Aerosol particles play important roles in processes controlling the composition of the atmosphere and function of ecosystems. A better understanding of the composition of aerosol particles is beginning to be recognized as critical for ecological research to further comprehend the link between aerosols and ecosystems. While chemical characterization of aerosols has been practiced in the atmospheric science community, detailed methodology tailored to the needs of ecological research does not exist yet. In this study, we describe an efficient methodology (atmo-ecometabolomics), in step-by-step details, from the sampling to the data analyses, to characterize the chemical composition of aerosol particles, namely atmo-metabolome. This method employs mass spectrometry platforms such as liquid and gas chromatography mass spectrometries (MS) and Fourier transform ion cyclotron resonance MS (FT-ICR-MS). For methodology evaluation, we analyzed aerosol particles collected during two different seasons (spring and summer) in a low-biological-activity ecosystem. Additionally, to further validate our methodology, we analyzed aerosol particles collected in a more biologically active ecosystem during the pollination peaks of three different representative tree species. Our statistical results showed that our sampling and extraction methods are suitable for characterizing the atmo-ecometabolomes in these two distinct ecosystems with any of the analytical platforms. Datasets obtained from each mass spectrometry instrument showed overall significant differences of the atmo-ecometabolomes between spring and summer as well as between the three pollination peak periods. Furthermore, we have identified several metabolites that can be attributed to pollen and other plant-related aerosol particles. We additionally provide a basic guide of the potential use ecometabolomic techniques on different mass spectrometry platforms to accurately analyze the atmo-ecometabolomes for ecological studies. Our method represents an advanced novel approach for future studies in the impact of aerosol particle chemical compositions on ecosystem structure and function and biogeochemistry.

Chemistry of the Secondary Metabolites of Termites

Isolation, structure determination, synthesis, and biochemistry of the low-molecular-weight compounds of the secretion of exocrine glands of termites are described, with an emphasis on pheromones and defensive compounds.