Quantifying chemodiversity considering biochemical and structural properties of compounds with the R package chemodiv

Neighbourhood effects on herbivory damage and chemical profiles in short-rotation coppice willows and their hybrids

Short rotation coppices (SRCs) represent an important source of biomass. Since they are grown in various mixtures, SRCs represent an excellent opportunity for assessing the effects of local plant neighbourhoods on their performance. We used a common garden experiment consisting of plots that varied in genotype diversity of SRC willows to test for the effects of chemical traits of individual plants and chemical variation in the plots where they grew on insect herbivory. We also explored whether the composition of willows planted in a plot affected their chemistry. To do this, we performed untargeted metabolomics and quantified various chemical traits related to the total set of metabolites we detected, flavonoids, and salicinoids in four willow genotypes. We measured the leaf herbivory that the plants suffered. The genotypes differed in most chemical traits, yet we found only limited effects of individual traits on herbivory damage. Instead, herbivory damage was positively correlated with structural variation in salicinoids in a plot. When analysing the effects of plot chemical variation on herbivory damage separately for each genotype, we found both positive and negative correlations between the two, suggesting both associational resistance and susceptibility. Finally, we also observed a significant effect of the interaction between genotype and plot composition on structural variation in plant chemistry. Overall, our results suggest that high chemical variation in mixed willow SRCs does not necessarily lower the herbivory damage, possibly due to spillover effects of insect herbivores among genotypes. Our results also show that different genotypes respond differently to plot composition in terms of herbivory damage and chemical composition, which may affect their suitability for growing in mixed stands.

Ontogeny and organ-specific steroidal glycoside diversity is associated with differential expression of steroidal glycoside pathway genes in two Solanum dulcamara leaf chemotypes

Solanaceous plants, such as Solanum dulcamara, produce steroidal glycosides (SGs). Leaf SG profiles vary among S. dulcamara individuals, leading to distinct phytochemical phenotypes ('chemotypes') and intraspecific phytochemical diversity ('chemodiversity'). However, if and how SG chemodiversity varies among organs and across ontogeny, and how this relates to SG metabolism gene expression is unknown. Among organs and across ontogeny, S. dulcamara plants with saturated (S) and unsaturated (U) SG leaf chemotypes were selected and clonally propagated. Roots, stems and leaves were harvested from vegetative and flowering plants. Extracts were analysed using untargeted LC-MS. Expression of candidate genes in SG metabolism (SdGAME9, SdGAME4, SdGAME25, SdS5αR2 and SdDPS) was analysed using RT-qPCRs. Our analyses showed that SG chemodiversity varies among organs and across ontogeny in S. dulcamara; SG richness (Dmg) was higher in flowering than vegetative plants. In vegetative plants, Dmg was higher for leaves than for roots. Lack of SdGAME25 expression in U-chemotype leaves, while readily expressed in roots and stems, suggests a pivotal role for SdGAME25 in differentiation of leaf chemotypes in vegetative and flowering plants. By acting as an ontogeny-dependent chemotypic switch, differential regulation of SdGAME25 enables adaptive allocation of SGs, thereby increasing SG chemodiversity in leaves. This indicates that differential expression and/or regulation of glycoalkaloid metabolism genes, rather than their presence or absence, explains observed chemotypic variation in SG chemodiversity among organs and across ontogeny.

Decoding the Structural Diversity: A New Horizon in Antimicrobial Prospecting and Mechanistic Investigation

The escalating crisis of antimicrobial resistance (AMR) underscores the urgent need for novel antimicrobials. One promising strategy is the exploration of structural diversity, as diverse structures can lead to diverse biological activities and mechanisms of action. This review delves into the role of structural diversity in antimicrobial discovery, highlighting its influence on factors such as target selectivity, binding affinity, pharmacokinetic properties, and the ability to overcome resistance mechanisms. We discuss various approaches for exploring structural diversity, including combinatorial chemistry, diversity-oriented synthesis, and natural product screening, and provide an overview of the common mechanisms of action of antimicrobials. We also describe techniques for investigating these mechanisms, such as genomics, proteomics, and structural biology. Despite significant progress, several challenges remain, including the synthesis of diverse compound libraries, the identification of active compounds, the elucidation of complex mechanisms of action, the emergence of AMR, and the translation of laboratory discoveries to clinical applications. However, emerging trends and technologies, such as artificial intelligence, high-throughput screening, next-generation sequencing, and open-source drug discovery, offer new avenues to overcome these challenges. Looking ahead, we envisage an exciting future for structural diversity-oriented antimicrobial discovery, with opportunities for expanding the chemical space, harnessing the power of nature, deepening our understanding of mechanisms of action, and moving toward personalized medicine and collaborative drug discovery. As we face the continued challenge of AMR, the exploration of structural diversity will be crucial in our search for new and effective antimicrobials.

Variation in Pesticide Toxicity in the Western Honey Bee (Apis mellifera) Associated with Consuming Phytochemically Different Monofloral Honeys

Insecticide toxicity to insect herbivores has long been known to vary across different host plants; this phenomenon has been widely documented in both foliage-feeders and sap-feeders. Species-specific phytochemical content of hostplant tissues is assumed to determine the pattern of induction of insect enzymes that detoxify insecticides, but specific phytochemicals have rarely been linked to host plant-associated variation in pesticide toxicity. Moreover, no studies to date have examined the effects of nectar source identity and phytochemical composition on the toxicity of insecticides to pollinators. In this study, we compared LD50 values for the insecticide bifenthrin, a frequent contaminant of nectar and pollen in agroecosystems, in the western honey bee, Apis mellifera, consuming three phytochemically different monofloral honeys: Nyssa ogeche (tupelo), Robinia pseudoacacia (black locust), and Fagopyrum esculentum (buckwheat). We found that bifenthrin toxicity (LD50) values for honey bees across different honey diets is linked to their species-specific phytochemical content. The profiles of phenolic acids and flavonoids of buckwheat and locust honeys are richer than is the profile of tupelo honey, with buckwheat honey containing the highest total content of phytochemicals and associated with the highest bifenthrin LD50 in honey bees. The vector fitting in the ordination analysis revealed positive correlations between LD50 values and two honey phytochemical richness estimates, Chao1 and Abundance-based Coverage Estimator (ACE). These findings suggest unequal effects among different phytochemicals, consistent with the interpretation that certain compounds, including ones that are rare, may have a more pronounced effect in mitigating pesticide toxicity.

Intraspecific chemical variation of Tanacetum vulgare affects plant growth and reproductive traits in field plant communities

The study investigated the impact of intraspecific plant chemodiversity on plant growth and reproductive traits at both the plant and plot levels. It also aimed to understand how chemodiversity at stand level affects ecosystem functioning and plant-plant interactions. We describe a biodiversity experiment in which we manipulated intraspecific plant chemodiversity at the plot level using six different chemotypes of common tansy (Tanacetum vulgare L., Asteraceae). We tested the effects of chemotype identity and plot-level chemotype richness on plant growth and reproductive traits and plot-level headspace emissions. The study found that plant chemotypes differed in growth and reproductive traits and that traits were affected by the chemotype richness of the plots. Although morphological differences among chemotypes became less pronounced over time, reproductive phenology patterns persisted. Plot-level trait means were also affected by the presence or absence of certain chemotypes in a plot, and the direction of the effect depended on the specific chemotype. However, chemotype richness did not lead to overyielding effects. Lastly, chemotype blends released from plant communities were neither richer nor more diverse with increasing plot-level chemotype richness, but became more dissimilar as they became more dissimilar in their leaf terpenoid profiles. We found that intraspecific plant chemodiversity is crucial in plant-plant interactions. We also found that the effects of chemodiversity on plant growth and reproductive traits were complex and varied depending on the chemotype richness of the plots. This long-term field experiment will allow further investigation into plant-insect interactions and insect community assembly in response to intraspecific chemodiversity.

Diel rhythm of volatile emissions from males and females of the olive fruit fly Bactrocera oleae using PTR-ToF and GC-MS

The olive fruit fly Bactrocera oleae, is the major key pest of olive groves worldwide. As an odor-driven species, its intraspecific communication has been thoroughly investigated, yielding a combination of spiroacetals, esters and hydrocarbons. However, its management with pheromone is still restricted to olean, the major pheromone component. Given the crucial role of circadian rhythm and pheromone blends in mediating flies reproductive behavior compared to single compounds, B. oleae headspace chemical profile was carefully examined, through the combination of Proton Transfer Reaction Time of Flight Mass Spectrometry (PTR-ToF) and Gas Chromatography coupled with Mass Spectrometry (GC-MS). This novel approach aimed at continuously investigating the temporal scale of volatilome profile of B. oleae individuals, as well as the determination of new candidate sex-borne compounds (particularly those emitted in traces or having low molecular weight), that may be relevant to the fly's chemical communication and were unreported due to limitations of frequently used analytical techniques. Our results describe the dynamics and diversity of B. oleae chemical profile, highlighting the emission of 90 compounds, with clear diel rhythm of release, of known pheromone components of B. oleae (e.g., olean, alpha-pinene and muscalure) and new candidates. In contrast to ammonia, acetaldehyde and muscalure, which were highly emitted during the afternoon by males and mixed groups, olean was mostly released by mature females and mixed groups, with a peak of emission during early-morning and afternoon. This emission of olean around dawn is reported for the first time, suggesting early-morning mating activity in B. oleae. Furthermore, esters, such as methyl tetradecanoate, which had been earlier identified as a pheromone for B. oleae, did not exhibit any discernible release patterns. These findings are the first to demonstrate the emission of chemicals, which are only produced when males and females are close to one another, with an emission peak during the afternoon (mating period), and that may have aphrodisiac properties for B. oleae males. These results emphasize the relevance of compounds with distinct diel rhythm and address their potential function as intraspecific messengers, according to their source and timing of release.

Spatially and temporally resolved metabolome of the human oral cavity

Saliva is a complex bodily fluid composed of secretions by major and minor salivary glands. Salivary glands and their secretions are known to be unevenly distributed in the human oral cavity. Moreover, saliva flow rate and composition vary across locations and time of the day. This remarkable heterogeneity of salivary secretions suggests that different subtypes of saliva fulfill different functions. By coupling a non-invasive and facile collection method with comprehensive metabolomic profiling, we investigated the spatial and temporal distributions of salivary components. We identified location-specific metabolite profiles, novel oscillating metabolites, and location-specific diurnal patterns. In summary, our study paves the way for a deeper and more comprehensive understanding of the complex dynamics and functionalities of the salivary metabolome and its integration in multi-omics studies related to oral and systemic (patho-)physiology.

Chemodiversity in flowers of Tanacetum vulgare has consequences on a florivorous beetle

The chemical composition of plant individuals can vary, leading to high intraspecific chemodiversity. Diversity of floral chemistry may impact the responses of flower-feeding insects. Tanacetum vulgare plants vary significantly in their leaf terpenoid composition, forming distinct chemotypes. We investigated the composition of terpenoids and nutrients of flower heads and pollen in plants belonging to three chemotypes - dominated either by β-thujone (BThu), artemisia ketone (Keto) or a mixture of (Z)-myroxide, santolina triene, and artemisyl acetate (Myrox) - using different analytical platforms. We tested the effects of these differences on preferences, weight gain and performance of adults of the shining flower beetle, Olibrus aeneus. The terpenoid composition and diversity of flower heads and pollen significantly differed among individuals belonging to the above chemotypes, while total concentrations of pollen terpenoids, sugars, amino acids, and lipids did not differ. Beetles preferred BThu over the Myrox chemotype in both olfactory and contact choice assays, while the Keto chemotype was marginally repellent according to olfactory assays. The beetles gained the least weight within 48 h and their initial mortality was highest when feeding exclusively on floral tissues of the Myrox chemotype. Short-term weight gain and long-term performance were highest when feeding on the BThu chemotype. In conclusion, the beetles showed chemotype-specific responses towards different T. vulgare chemotypes, which may be attributed to the terpenoid composition in flower heads and pollen rather than to differences in nutrient profiles. Both richness and overall diversity are important factors when determining chemodiversity of individual plants and their consequences on interacting insects.

Floral volatiles evoke partially similar responses in both florivores and pollinators and are correlated with non-volatile reward chemicals

BACKGROUND

Plants often use floral displays to attract mutualists and prevent antagonist attacks. Chemical displays detectable from a distance include attractive or repellent floral volatile organic compounds (FVOCs). Locally, visitors perceive contact chemicals including nutrients but also deterrent or toxic constituents of pollen and nectar. The FVOC and pollen chemical composition can vary intra- and interspecifically. For certain pollinator and florivore species, responses to these compounds are studied in specific plant systems, yet we lack a synthesis of general patterns comparing these two groups and insights into potential correlations between FVOC and pollen chemodiversity.

SCOPE

We reviewed how FVOCs and non-volatile floral chemical displays, i.e. pollen nutrients and toxins, vary in composition and affect the detection by and behaviour of insect visitors. Moreover, we used meta-analyses to evaluate the detection of and responses to FVOCs by pollinators vs. florivores within the same plant genera. We also tested whether the chemodiversity of FVOCs, pollen nutrients and toxins is correlated, hence mutually informative.

KEY RESULTS

According to available data, florivores could detect more FVOCs than pollinators. Frequently tested FVOCs were often reported as pollinator-attractive and florivore-repellent. Among FVOCs tested on both visitor groups, there was a higher number of attractive than repellent compounds. FVOC and pollen toxin richness were negatively correlated, indicating trade-offs, whereas a marginal positive correlation between the amount of pollen protein and toxin richness was observed.

CONCLUSIONS

Plants face critical trade-offs, because floral chemicals mediate similar information to both mutualists and antagonists, particularly through attractive FVOCs, with fewer repellent FVOCs. Furthermore, florivores might detect more FVOCs, whose richness is correlated with the chemical richness of rewards. Chemodiversity of FVOCs is potentially informative of reward traits. To gain a better understanding of the ecological processes shaping floral chemical displays, more research is needed on floral antagonists of diverse plant species and on the role of floral chemodiversity in visitor responses.

Impact of in vitro phytohormone treatments on the metabolome of the leafy liverwort Radula complanata (L.) Dumort

INTRODUCTION

Liverworts are a group of non-vascular plants that possess unique metabolism not found in other plants. Many liverwort metabolites have interesting structural and biochemical characteristics, however the fluctuations of these metabolites in response to stressors is largely unknown.

OBJECTIVES

To investigate the metabolic stress-response of the leafy liverwort Radula complanata.

METHODS

Five phytohormones were applied exogenously to in vitro cultured R. complanata and an untargeted metabolomic analysis was conducted. Compound classification and identification was performed with CANOPUS and SIRIUS while statistical analyses including PCA, ANOVA, and variable selection using BORUTA were conducted to identify metabolic shifts.

RESULTS

It was found that R. complanata was predominantly composed of carboxylic acids and derivatives, followed by benzene and substituted derivatives, fatty acyls, organooxygen compounds, prenol lipids, and flavonoids. The PCA revealed that samples grouped based on the type of hormone applied, and the variable selection using BORUTA (Random Forest) revealed 71 identified and/or classified features that fluctuated with phytohormone application. The stress-response treatments largely reduced the production of the selected primary metabolites while the growth treatments resulted in increased production of these compounds. 4-(3-Methyl-2-butenyl)-5-phenethylbenzene-1,3-diol was identified as a biomarker for the growth treatments while GDP-hexose was identified as a biomarker for the stress-response treatments.

CONCLUSION

Exogenous phytohormone application caused clear metabolic shifts in Radula complanata that deviate from the responses of vascular plants. Further identification of the selected metabolite features can reveal metabolic biomarkers unique to liverworts and provide more insight into liverwort stress responses.

Intraspecific chemodiversity provides plant individual- and neighbourhood-mediated associational resistance towards aphids

Some plant species express an extraordinarily high intraspecific diversity in phytochemicals (= chemodiversity). As discussed for biodiversity, higher chemodiversity may provide better protection against environmental stress, including herbivory. However, little is known about whether the resistance of a plant individual towards herbivores is mostly governed by its own chemodiversity or by associational resistance provided by conspecific neighbours. To investigate the role of chemodiversity in plant-aphid interactions, we used the Asteraceae Tanacetum vulgare, whose individuals differ pronouncedly in the composition of leaf terpenoids, forming distinct chemotypes. Plants were set up in a field consisting of plots containing five individuals of either the same or different chemotypes. Presence of winged aphids, indicating attraction, and abundance of winged and unwinged aphids, indicating fitness, were counted weekly on each plant. During the peak abundance of aphids, leaf samples were taken from all plants for re-analyses of the terpenoid composition and quantification of terpenoid chemodiversity, calculated on an individual plant (Shannon index, Hs_ind, also considered as α-chemodiversity) and plot level (Hs_plot, = β-chemodiversity). Aphid attraction was neither influenced by chemotype nor plot-type. The real-time odour environment may be very complex in this setting, impeding clear preferences. In contrast, the abundance was affected by both chemotype and plot-type. On average, more Uroleucon tanaceti aphids were found on plants of two of the chemotypes growing in homogenous compared to heterogenous plots, supporting the associational resistance hypothesis. For Macrosiphoniella tanacetaria aphids, the probability of presence differed between plot-types on one chemotype. Terpenoid chemodiversity expressed as a gradient revealed negative Hs_plot effects on U. tanaceti, but a positive correlation of Hs_ind with M. tanacetaria abundance. Aphids of M. fuscoviride were not affected by any level of chemodiversity. In conclusion, this study shows that not only the chemotype and chemodiversity of individual plants but also that of conspecific neighbours can influence certain plant-herbivore interactions. These effects are highly specific with regard to the plant chemotype and differ between aphid species and their morphs (winged vs. unwinged). Furthermore, our results highlight the importance of analysing chemodiversity at different levels.