Current Challenges in Plant Eco-Metabolomics

Abstract

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.

Semi‐polar root exudates in natural grassland communities

“…Techniques as the collection of exudates in hydroponic or rhizobox systems are not applicable in field experiments. An untargeted metabolomics approach, instead, allows the detection and, to some extent, identification of metabolites which otherwise would be neglected (van Dam & Bouwmeester, 2016;Peters et al, 2018). Another often limiting point is the frequent use of targeted metabolic profiling.…”

“…Although this approach allows studying the role of a particular metabolite in the rhizosphere network, it cannot reflect the complexity of the functional linkage of metabolites such as semi-polar compounds in a complete exudate profile. An untargeted metabolomics approach, instead, allows the detection and, to some extent, identification of metabolites which otherwise would be neglected (van Dam & Bouwmeester, 2016;Peters et al, 2018).…”

Ecology and Evolution of Intraspecific Chemodiversity of Plants

“…For example, within tree species such as Populus nigra L. (black poplar; Salicaceae) and other Populus spp., variation in phenolics and other metabolite classes is found (Boeckler et al 2013, Moritz et al 2017. Populations of herbaceous species such as Solanum dulcamara (L.) (bittersweet nightshade; Solanaceae) show pronounced differences in their glycoalkaloid profiles between individuals (Calf et al 2018). In Tanacetum vulgare L. (common tansy; Asteraceae) currently more than 30 chemotypes have been described, which are characterised by the dominant leaf and flower terpenoid(s) (Clancy et al 2016, Keskitalo et al 2001, Wolf et al 2011.…”

“…The net balance of costs and benefits may determine whether a particular chemical phenotype can survive or even increase in frequency in natural communities. However, the effects of individual specialised metabolites are rarely uniform; a compound deterring many generalist herbivores may be a stimulant for specialists (Calf et al 2018, Reifenrath and Müller 2008, Schoonhoven et al 2005. Similarly, floral volatiles attracting pollinators may also make the plant more apparent to herbivores, picking up the same floral scent Blüthgen 2010, Unsicker et al 2009).…”

PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud

“…Metabolomics is the study of small molecules in organisms which can reveal detailed insights into metabolic biochemistry, e.g. changes in concentrations of specific molecules, metabolic fluxes between cells or compartments, identification of molecules that are involved in the pathogenesis of a disease, the study of the biochemical phenotype of animals, plants and even soil microorganisms [1][2][3] The principal metabolomics technologies of mass spectrometry (MS) and nuclear magnetic resonance spectroscopy (NMR) typically generate large data sets that require computationally intensive analyses [4]. For example, biomedical investigations can involve large cohorts with many thousands of metabolite profiles and can produce terabytes of data [5].…”