Current Challenges in Plant Eco-Metabolomics

Affiliation
Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany,
Peters, Kristian;
GND
1142023273
Affiliation
German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany,
Worrich, Anja;
GND
1026825288
ORCID
0000-0003-1418-7788
Affiliation
German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany,
Weinhold, Alexander;
Affiliation
Applied Bioinformatics Group, Center for Bioinformatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany,
Alka, Oliver;
Affiliation
Leibniz Institute of Plant Biochemistry, Cell and Metabolic Biology, Weinberg 3, 06120 Halle (Saale), Germany,
Balcke, Gerd;
ORCID
0000-0002-8538-8838
Affiliation
Institute of Analytical Chemistry, University of Leipzig, Linnéstr. 3, 04103 Leipzig, Germany,
Birkemeyer, Claudia;
Affiliation
German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany,
Bruelheide, Helge;
ORCID
0000-0001-5280-2265
Affiliation
Molecular Interaction Ecology, Institute for Water and Wetland Research (IWWR), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands,
Calf, Onno W.;
Affiliation
Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany,
Dietz, Sophie;
GND
1168810922
Affiliation
Department of Bioinformatics, Friedrich Schiller University Jena
Dührkop, Kai;
ORCID
0000-0003-0796-6417
Affiliation
Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany,
Gaquerel, Emmanuel;
Affiliation
Weizmann Institute of Science, Faculty of Biochemistry, Department of Plant Sciences, 234 Herzl St., P.O. Box 26, Rehovot 7610001, Israel,
Heinig, Uwe;
Affiliation
Institute of Biology, University of Leipzig, Talstraße 33, 04109 Leipzig, Germany,
Kücklich, Marlen;
ORCID
0000-0003-4122-6797
Affiliation
Molecular Interaction Ecology, Institute for Water and Wetland Research (IWWR), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands,
Macel, Mirka;
Affiliation
Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany,
Müller, Caroline;
Affiliation
German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany,
Poeschl, Yvonne;
GND
1131364872
Affiliation
Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena
Pohnert, Georg;
ORCID
0000-0002-1446-977X
Affiliation
German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany,
Ristok, Christian;
ORCID
0000-0002-2861-4093
Affiliation
Group of Genetics, Breeding and Biochemistry of Brassica, Misión Biológica de Galicia (CSIC), Apartado 28, 36080 Pontevedra, Spain,
Rodríguez, Victor Manuel;
Affiliation
Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany,
Ruttkies, Christoph;
ORCID
0000-0003-3159-3534
Affiliation
Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany,
Schuman, Meredith;
Affiliation
Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany,
Schweiger, Rabea;
Affiliation
Weizmann Institute of Science, Faculty of Biochemistry, Department of Plant Sciences, 234 Herzl St., P.O. Box 26, Rehovot 7610001, Israel,
Shahaf, Nir;
GND
128763922
ORCID
0000-0001-6966-0814
Affiliation
Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena
Steinbeck, Christoph;
Affiliation
Group of Genetics, Breeding and Biochemistry of Brassica, Misión Biológica de Galicia (CSIC), Apartado 28, 36080 Pontevedra, Spain,
Tortosa, Maria;
ORCID
0000-0001-8032-9890
Affiliation
Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany,
Treutler, Hendrik;
GND
1047788152
Affiliation
Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena
Ueberschaar, Nico;
Affiliation
Group of Genetics, Breeding and Biochemistry of Brassica, Misión Biológica de Galicia (CSIC), Apartado 28, 36080 Pontevedra, Spain,
Velasco, Pablo;
Affiliation
Institute of Biology, University of Leipzig, Talstraße 33, 04109 Leipzig, Germany,
Weiß, Brigitte M.;
ORCID
0000-0003-1772-8770
Affiliation
German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany,
Widdig, Anja;
ORCID
0000-0002-7899-7192
Affiliation
Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany,
Neumann, Steffen;
GND
1214830226
Affiliation
German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany,
Dam, Nicole M. van

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.

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