Advances in Plant Metabolomics and Its Applications in Stress and Single-Cell Biology

Abstract

In the past two decades, the post-genomic era envisaged high-throughput technologies, resulting in more species with available genome sequences. In-depth multi-omics approaches have evolved to integrate cellular processes at various levels into a systems biology knowledge base. Metabolomics plays a crucial role in molecular networking to bridge the gaps between genotypes and phenotypes. However, the greater complexity of metabolites with diverse chemical and physical properties has limited the advances in plant metabolomics. For several years, applications of liquid/gas chromatography (LC/GC)-mass spectrometry (MS) and nuclear magnetic resonance (NMR) have been constantly developed. Recently, ion mobility spectrometry (IMS)-MS has shown utility in resolving isomeric and isobaric metabolites. Both MS and NMR combined metabolomics significantly increased the identification and quantification of metabolites in an untargeted and targeted manner. Thus, hyphenated metabolomics tools will narrow the gap between the number of metabolite features and the identified metabolites. Metabolites change in response to environmental conditions, including biotic and abiotic stress factors. The spatial distribution of metabolites across different organs, tissues, cells and cellular compartments is a trending research area in metabolomics. Herein, we review recent technological advancements in metabolomics and their applications in understanding plant stress biology and different levels of spatial organization. In addition, we discuss the opportunities and challenges in multiple stress interactions, multi-omics, and single-cell metabolomics.

Keywords: abiotic and biotic stresses; metabolomics technologies; multi-omics; single-cell metabolomics; spatial metabolomics.

Figure 1

Historic views of metabolomics development and research. Publication numbers were obtained from PubMed search using plant metabolomics as keywords. (a) Increased interest in metabolomics research and applications over the past two centuries (MSI, mass spectrometry imaging); (b) Publications in plant metabolomics on an annual basis and the technologies employed (insert as a pie chart) in the past two decades. Please note that 2022 is for the first five months only.

Figure 2

Untargeted and targeted approaches for metabolomic analysis in plants.

Figure 3

Metabolic pathways and connections depicting primary metabolites and their derived specialized metabolites in response to abiotic and biotic stresses.

Figure 4

Publications generated on single-cell metabolomics in the past 20 years. Publication numbers were obtained from PubMed search using single-cell metabolomics as keywords. Please note that 2022 is for the first five months only.

Figure 5

Single-cell metabolomics workflow from different cell types (e.g., epidermal cells, guard cells, root hairs, floral organ cells, root tip stem cells, root nodule cells, hairy root culture cells, in vitro callus cultures, parenchyma and sclerenchyma cells, mesophyll and bundle sheath cells, and inner endodermal cells), and organelles including apoplast, chloroplast, and mitochondria. They were isolated from plant tissues using methods including laser microdissection, laser-ablation, laser capture microdissection-liquid vortex capture, micromanipulation, mechanical isolation, protoplasting, pressure probe, and cell sorting. NMR: Nuclear magnetic resonance; HPLC: High performance liquid chromatography; LMD LC-MS: Laser Microdissection liquid-chromatography mass spectrometry; LAAPPI: Laser ablation atmospheric pressure photoionization; GC: Gas chromatography; LAESI: Laser ablation electrospray ionization; picoPPESI: picolitre pressure-probe electrospray-ionization; fLAESI: Optical fiber-based laser ablation electrospray ionization; 21TFTICR-MS: 21 tesla (T) Fourier transform ion cyclotron resonance MS; LSC-MS: Live single-cell MS; UPLC: Ultra performance liquid chromatography; NanoESI: Nano electrospray ionization; MALDI: Matrix-assisted laser desorption and ionization.