Root exudates and rhizosphere microbiomes jointly determine temporal shifts in plant-soil feedbacks

Plants influence numerous soil biotic factors that can alter the performance of later growing plants-defined as plant-soil feedback (PSF). Here, we investigate whether PSF effects are linked with the temporal changes in root exudate diversity and the rhizosphere microbiome of two common grassland species (Holcus lanatus and Jacobaea vulgaris). Both plant species were grown separately establishing conspecific and heterospecific soils. In the feedback phase, we determined plant biomass, measured root exudate composition, and characterised rhizosphere microbial communities weekly (eight time points). Over time, we found a strong negative conspecific PSF on J. vulgaris in its early growth phase which changed into a neutral PSF, whereas H. lanatus exhibited a more persistent negative PSF. Root exudate diversity increased considerably over time for both plant species. Rhizosphere microbial communities were distinct in conspecific and heterospecific soils and showed strong temporal patterns. Bacterial communities converged over time. Using path models, PSF effects could be linked to the temporal dynamics of root exudate diversity, whereby shifts in rhizosphere microbial diversity contributed to temporal variation in PSF to a lesser extent. Our results highlight the importance of root exudates and rhizosphere microbial communities in driving temporal changes in the strength of PSF effects.

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.

Seasonal variation of secondary metabolites in nine different bryophytes

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

Current Challenges in Plant Eco-Metabolomics

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

The Impact of Competition and Allelopathy on the Trade-Off between Plant Defense and Growth in Two Contrasting Tree Species

In contrast to plant-animal interactions, the conceptual framework regarding the impact of secondary metabolites in mediating plant-plant interference is currently less well defined. Here, we address hypotheses about the role of chemically-mediated plant-plant interference (i.e., allelopathy) as a driver of Mediterranean forest dynamics. Growth and defense abilities of a pioneer (Pinus halepensis) and a late-successional (Quercus pubescens) Mediterranean forest species were evaluated under three different plant interference conditions: (i) allelopathy simulated by application of aqueous needle extracts of Pinus, (ii) resource competition created by the physical presence of a neighboring species (Pinus or Quercus), and (iii) a combination of both allelopathy and competition. After 24 months of experimentation in simulated field conditions, Quercus was more affected by plant interference treatments than was Pinus, and a hierarchical response to biotic interference (allelopathy < competition < allelopathy + competition) was observed in terms of relative impact on growth and plant defense. Both species modulated their respective metabolic profiles according to plant interference treatment and thus their inherent chemical defense status, resulting in a physiological trade-off between plant growth and production of defense metabolites. For Quercus, an increase in secondary metabolite production and a decrease in plant growth were observed in all treatments. In contrast, this trade-off in Pinus was only observed in competition and allelopathy + competition treatments. Although Pinus and Quercus expressed differential responses when subjected to a single interference condition, either allelopathy or competition, species responses were similar or positively correlated when strong interference conditions (allelopathy + competition) were imposed.

Drought enhances folivory by shifting foliar metabolomes in Quercus ilex trees

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

Strong relationship between elemental stoichiometry and metabolome in plants

Shifts in the elemental stoichiometry of organisms in response to their ontogeny and to changing environmental conditions should be related to metabolomic changes because elements operate mostly as parts of molecular compounds. Here we show this relationship in leaves of Erica multiflora throughout their seasonal development and in response to moderate experimental field conditions of drought and warming. The N/P ratio in leaves decreased in the metabolically active growing seasons, coinciding with an increase in the content of primary metabolites. These results support the growth-rate hypothesis that states that rapidly growing organisms present low N/P ratios because of the increase in allocation of P to RNA. The foliar N/K and P/K ratios were lower in summer and in the drought treatment, in accordance with the role of K in osmotic protection, and coincided with the increase of compounds related to the avoidance of water stress. These results provide strong evidence of the relationship between the changes in foliar C/N/P/K stoichiometry and the changes in the leaf's metabolome during plant growth and environmental stress. Thus these results represent a step in understanding the relationships between stoichiometry and an organism's lifestyle.