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Current Challenges in Plant Eco-Metabolomics

Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany
German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger-Str. 159, 07743 Jena, Germany
UFZ—Helmholtz-Centre for Environmental Research, Department Environmental Microbiology, Permoserstraße 15, 04318 Leipzig, Germany
Applied Bioinformatics Group, Center for Bioinformatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany
Leibniz Institute of Plant Biochemistry, Cell and Metabolic Biology, Weinberg 3, 06120 Halle (Saale), Germany
Institute of Analytical Chemistry, University of Leipzig, Linnéstr. 3, 04103 Leipzig, Germany
Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle (Saale), Germany
Molecular Interaction Ecology, Institute for Water and Wetland Research (IWWR), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
Department of Bioinformatics, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany
Weizmann Institute of Science, Faculty of Biochemistry, Department of Plant Sciences, 234 Herzl St., P.O. Box 26, Rehovot 7610001, Israel
Institute of Biology, University of Leipzig, Talstraße 33, 04109 Leipzig, Germany
Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
Institute of Informatics, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120 Halle (Saale), Germany
Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743 Jena, Germany
Group of Genetics, Breeding and Biochemistry of Brassica, Misión Biológica de Galicia (CSIC), Apartado 28, 36080 Pontevedra, Spain
Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
Research Group of Primate Kin Selection, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2018, 19(5), 1385;
Received: 28 February 2018 / Revised: 24 April 2018 / Accepted: 25 April 2018 / Published: 6 May 2018
(This article belongs to the Special Issue Metabolomics in the Plant Sciences 2017)
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. View Full-Text
Keywords: biochemistry; bioinformatics; ecology; ecometabolomics; metabolites biochemistry; bioinformatics; ecology; ecometabolomics; metabolites
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MDPI and ACS Style

Peters, K.; Worrich, A.; Weinhold, A.; Alka, O.; Balcke, G.; Birkemeyer, C.; Bruelheide, H.; Calf, O.W.; Dietz, S.; Dührkop, K.; Gaquerel, E.; Heinig, U.; Kücklich, M.; Macel, M.; Müller, C.; Poeschl, Y.; Pohnert, G.; Ristok, C.; Rodríguez, V.M.; Ruttkies, C.; Schuman, M.; Schweiger, R.; Shahaf, N.; Steinbeck, C.; Tortosa, M.; Treutler, H.; Ueberschaar, N.; Velasco, P.; Weiß, B.M.; Widdig, A.; Neumann, S.; Dam, N.M.v. Current Challenges in Plant Eco-Metabolomics. Int. J. Mol. Sci. 2018, 19, 1385.

AMA Style

Peters K, Worrich A, Weinhold A, Alka O, Balcke G, Birkemeyer C, Bruelheide H, Calf OW, Dietz S, Dührkop K, Gaquerel E, Heinig U, Kücklich M, Macel M, Müller C, Poeschl Y, Pohnert G, Ristok C, Rodríguez VM, Ruttkies C, Schuman M, Schweiger R, Shahaf N, Steinbeck C, Tortosa M, Treutler H, Ueberschaar N, Velasco P, Weiß BM, Widdig A, Neumann S, Dam NMv. Current Challenges in Plant Eco-Metabolomics. International Journal of Molecular Sciences. 2018; 19(5):1385.

Chicago/Turabian Style

Peters, Kristian, Anja Worrich, Alexander Weinhold, Oliver Alka, Gerd Balcke, Claudia Birkemeyer, Helge Bruelheide, Onno W. Calf, Sophie Dietz, Kai Dührkop, Emmanuel Gaquerel, Uwe Heinig, Marlen Kücklich, Mirka Macel, Caroline Müller, Yvonne Poeschl, Georg Pohnert, Christian Ristok, Victor Manuel Rodríguez, Christoph Ruttkies, Meredith Schuman, Rabea Schweiger, Nir Shahaf, Christoph Steinbeck, Maria Tortosa, Hendrik Treutler, Nico Ueberschaar, Pablo Velasco, Brigitte M. Weiß, Anja Widdig, Steffen Neumann, and Nicole M. van Dam. 2018. "Current Challenges in Plant Eco-Metabolomics" International Journal of Molecular Sciences 19, no. 5: 1385.

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