Current Challenges in Plant Eco-Metabolomics.

Kristian Peters,Georg Pohnert,Sophie Dietz,Emmanuel Gaquerel,Hendrik Treutler,Anja Widdig,Pablo Velasco,Christoph Ruttkies,Anja Worrich,Rabea Schweiger,Steffen Neumann,Marlen Kücklich,Alexander Weinhold,Claudia Birkemeyer,Nico Ueberschaar,Christoph Steinbeck,Christian Ristok,Yvonne Poeschl,Oliver Alka,Uwe Heinig,Helge Bruelheide,Nir Shahaf,Caroline Müller,Kai Dührkop,María Tortosa ,B Weiß ,Gerd Ulrich Balcke ,Meredith C Schuman ,Onno W Calf ,Víctor M Rodríguez ,Mirka Máčel ,Nicole M Van Dam

doi:10.3390/ijms19051385

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.

Highlights

Technological advances in chromatography coupled with mass spectrometry permit snapshots of most low molecular weight polar and semi-polar metabolites in organisms at once, without targeting specific biochemical compounds [1]
There are several metabolomics acquisition techniques, but liquid chromatography coupled with mass spectrometry (LC/MS), gas chromatography coupled with MS (GC/MS) and nuclear magnetic resonance spectroscopy (NMR) are the most commonly used methods
We focus on XCMS and OpenMS even though we found many studies that used other tools and algorithms that are available to process and align raw metabolite data (Tables 1 and 3; [132,157])

Summary

Introduction

Technological advances in chromatography coupled with mass spectrometry permit snapshots of most low molecular weight (typically 50–1000 Da) polar and semi-polar metabolites in organisms at once, without targeting specific biochemical compounds [1]. This technology is called “metabolomics” and is used widely in biochemistry and biotechnology for various types of organisms, including plants, soil microbiota and mammals [2,3,4]. This universality and the coverage of a wide range of bioactive compounds initiated a new research field called “Eco-Metabolomics”—the application of metabolomics to ecology and, understanding

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Methods

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Conclusion