Metabolomics: an emerging frontier of systems biology in marine macrophytes

Metabolomics is a rapidly emerging discipline within functional genomics which is increasingly being applied to understand biochemical phenotypes across a range of biological systems. Metabolomics measures all (or a subset) metabolites in a cell at a specific time point, reflecting a snapshot of all the regulatory events responding to the external environmental conditions. Although metabolomics and systems biology approaches have been applied to the study of terrestrial plants, few marine macrophytes have been examined using these novel technologies. Marine macrophytes (including seaweeds and seagrasses) are marine ecosystem engineers delivering a range of ecologically and economically valuable biological services; however they are under threat from a wide range of anthropogenic stressors, climate variation, invasive species and pathogens. Investigating metabolomic regulation in these organisms is crucial to understand their acclimation, adaptation and defence responses to environmental challenges. This review describes the current analytical tools available to study metabolomics in marine macrophytes, along with their limitations for both targeted and non-targeted workflows. To illustrate recent advances in systems biology studies in marine macrophytes, we describe how metabolites are used in chemical defence to deter a broad range of invasive species and pathogens, as well as metabolomic reprogramming leading to acclimation or adaptive strategies to environmental and anthropogenic stresses. Where possible, the mechanistic processes associated with primary and secondary plant metabolism governing cellular homeostasis under extreme environments are discussed. Further, we provide a comprehensive overview of an in silico plant metabolome database that can be utilized to advance our knowledge from a system biology approach to marine macrophytes. Finally, functional integration of metabolomics with the allied “omics” disciplines of transcriptomics and proteomics, as well as the emerging discipline of “fluxomics” are discussed in the context of developing biological system networks, the identification of unknown gene/protein functions and the analysis of metabolic pathways in marine plants exposed to stress.