Metabolomics by UHPLC-HRMS reveals the impact of heat stress on pathogen-elicited immunity in maize

Metabolomics-guided utilization of beneficial microbes for climate-resilient crops

In the rhizosphere, plants and microbes communicate chemically, especially under environmental stress. Over millions of years, plants and their microbiome have coevolved, sharing various chemicals, including signaling molecules. This mutual exchange impacts bacterial communication and influences plant metabolism. Inter-kingdom signal crosstalk affects bacterial colonization and plant fitness. Beneficial microbes and their metabolomes offer eco-friendly ways to enhance plant resilience and agriculture. Plant metabolites are pivotal in this dynamic interaction between host plants and their interacting beneficial microbes. Understanding these associations is key to engineering a robust microbiome for stress mitigation and improved plant growth. This review explores mechanisms behind plant-microbe interactions, the role of beneficial microbes and metabolomics, and the practical applications for addressing climate change's impact on agriculture. Integrating beneficial microbes' activities and metabolomics' application to study metabolome-driven interaction between host plants and their corresponding beneficial microbes holds promise for enhancing crop resilience and productivity.

Comparative analysis of defensive secondary metabolites in wild teosinte and cultivated maize under flooding and herbivory stress

Climate change is driving an alarming increase in the frequency and intensity of abiotic and biotic stress factors, negatively impacting plant development and agricultural productivity. To survive, plants respond by inducing changes in below and aboveground metabolism with concomitant alterations in defensive secondary metabolites. While plant responses to the isolated stresses of flooding and insect herbivory have been extensively studied, much less is known about their response in combination. Wild relatives of cultivated plants with robust stress tolerance traits provide an excellent system for comparing how diverse plant species respond to combinatorial stress, and provide insight into potential germplasms for stress-tolerant hybrids. In this study, we compared the below and aboveground changes in the secondary metabolites of maize (Zea mays) and a flood-tolerant wild relative Nicaraguan teosinte (Zea nicaraguensis) in response to flooding, insect herbivory, and their combination. Root tissue was analyzed for changes in belowground metabolism. Leaf total phenolic content and headspace volatile organic compound emission were analyzed for changes in aboveground secondary metabolism. Results revealed significant differences in the root metabolome profiles of teosinte and maize. Notably, the accumulation of the flavonoids apigenin, naringenin, and luteolin during flooding and herbivory differentiated teosinte from maize. Aboveground, terpenes, including trans-α-bergamotene and (E)-4,8-dimethylnona-1,3,7-triene, shaped compositional differences in their volatile profiles between flooding, herbivory, and their combination. Taken together, these results suggest teosinte may be more tolerant than maize due to dynamic metabolic changes during flooding and herbivory that help relieve stress and influence plant-insect interactions.

The impact of climate change on maize chemical defenses

Climate change is increasingly affecting agriculture, both at the levels of crops themselves, and by altering the distribution and damage caused by insect or microbial pests. As global food security depends on the reliable production of major crops such as maize (Zea mays), it is vital that appropriate steps are taken to mitigate these negative impacts. To do this a clear understanding of what the impacts are and how they occur is needed. This review focuses on the impact of climate change on the production and effectiveness of maize chemical defenses, including volatile organic compounds, terpenoid phytoalexins, benzoxazinoids, phenolics, and flavonoids. Drought, flooding, heat stress, and elevated concentrations of atmospheric carbon dioxide, all impact the production of maize chemical defenses, in a compound and tissue-specific manner. Furthermore, changes in stomatal conductance and altered soil conditions caused by climate change can impact environmental dispersal and effectiveness certain chemicals. This can alter both defensive barrier formation and multitrophic interactions. The production of defense chemicals is controlled by stress signaling networks. The use of similar networks to co-ordinate the response to abiotic and biotic stress can lead to complex integration of these networks in response to the combinatorial stresses that are likely to occur in a changing climate. The impact of multiple stressors on maize chemical defenses can therefore be different from the sum of the responses to individual stressors and challenging to predict. Much work remains to effectively leverage these protective chemicals in climate-resilient maize.

A comprehensive dynamic immune acetylproteomics profiling induced by Puccinia polysora in maize

Lysine-ε-acetylation (Kac) is a reversible post-translational modification that plays important roles during plant-pathogen interactions. Some pathogens can deliver secreted effectors encoding acetyltransferases or deacetylases into host cell to directly modify acetylation of host proteins. However, the function of these acetylated host proteins in plant-pathogen defense remains to be determined. Employing high-resolution tandem mass spectrometry, we analyzed protein abundance and lysine acetylation changes in maize infected with Puccinia polysora (P. polysora) at 0 h, 12 h, 24 h, 48 h and 72 h. A total of 7412 Kac sites from 4697 proteins were identified, and 1732 Kac sites from 1006 proteins were quantified. Analyzed the features of lysine acetylation, we found that Kac is ubiquitous in cellular compartments and preferentially targets lysine residues in the -F/W/Y-X-X-K (ac)-N/S/T/P/Y/G- motif of the protein, this Kac motif contained proteins enriched in basic metabolism and defense-associated pathways during fungal infection. Further analysis of acetylproteomics data indicated that maize regulates cellular processes in response to P. polysora infection by altering Kac levels of histones and non-histones. In addition, acetylation of pathogen defense-related proteins presented converse patterns in signaling transduction, defense response, cell wall fortification, ROS scavenging, redox reaction and proteostasis. Our results provide informative resources for studying protein acetylation in plant-pathogen interactions, not only greatly extending the understanding on the roles of acetylation in vivo, but also providing a comprehensive dynamic pattern of Kac modifications in the process of plant immune response.

Liguleless narrow and narrow odd dwarf act in overlapping pathways to regulate maize development and metabolism

Narrow odd dwarf (nod) and Liguleless narrow (Lgn) are pleiotropic maize mutants that both encode plasma membrane proteins, cause similar developmental patterning defects, and constitutively induce stress signaling pathways. To investigate how these mutants coordinate maize development and physiology, we screened for protein interactors of NOD by affinity purification. LGN was identified by this screen as a strong candidate interactor, and we confirmed the NOD-LGN molecular interaction through orthogonal experiments. We further demonstrated that LGN, a receptor-like kinase, can phosphorylate NOD in vitro, hinting that they could act in intersecting signal transduction pathways. To test this hypothesis, we generated Lgn-R;nod mutants in two backgrounds (B73 and A619), and found that these mutations enhance each other, causing more severe developmental defects than either single mutation on its own, with phenotypes including very narrow leaves, increased tillering, and failure of the main shoot. Transcriptomic and metabolomic analyses of the single and double mutants in the two genetic backgrounds revealed widespread induction of pathogen defense genes and a shift in resource allocation away from primary metabolism in favor of specialized metabolism. These effects were similar in each single mutant and heightened in the double mutant, leading us to conclude that NOD and LGN act cumulatively in overlapping signaling pathways to coordinate growth-defense tradeoffs in maize.

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

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.

RNAi-induced knockdown of white gene in the southern green stink bug (Nezara viridula L.)

The southern green stink bug (SGSB) Nezara viridula L. is one of the most common stink bug species in the United States and can cause significant yield loss in a variety of crops. A suitable marker for the assessment of gene-editing tools in SGSB has yet to be characterized. The white gene, first documented in Drosophila, has been a useful target to assess the efficiency of introduced mutations in many species as it controls pigmentation processes and mutants display readily identifiable phenotypes. In this study we used the RNAi technique to investigate functions and phenotypes associated with the white ortholog in the SGSB and to validate white as a marker for genetic transformation in this species. This study revealed that white may be a suitable marker for germline transformation in the SGSB as white transcript knockdown was not lethal, did not impair embryo development and provided a distinguishable phenotype. Our results demonstrated that the white ortholog in SGSB is involved in the pathway for ommochrome synthesis and suggested additional functions of this gene such as in the integument composition, management of hemolymph compounds and riboflavin mobilization.

Negative Effects of Rhizobacteria Association on Plant Recruitment of Generalist Predators

Plant-associated microbes can influence above- and belowground interactions between plants and other organisms and thus have significant potential for use in the management of agricultural ecosystems. However, fully realizing this potential will require improved understanding of the specific ways in which microbes influence plant ecology, which are both more complex and less well studied than the direct effects of microbes on host-plant physiology. Microbial effects on mutualistic and antagonistic interactions between plants and insects are of particular interest in this regard. This study examines the effects of two strains of Pseudomonas rhizobacteria on the direct and indirect (predator-mediated) resistance of tomato plants to a generalist herbivore (Spodoptera littoralis) and associated changes in levels of defense compounds. We observed no significant effects of rhizobacteria inoculation on caterpillar weight, suggesting that rhizobacteria did not influence direct resistance. However, the generalist predator Podisus maculiventris avoided plants inoculated with one of our rhizobacteria strains, Pseudomonas simiae. Consistent with these results, we found that inoculation with P. simiae influenced plant volatile emissions, but not levels of defense-related compounds. These findings show that rhizobacteria can negatively affect the attraction of generalist predators, while highlighting the complexity and context dependence of microbial effects on plant–insect interactions.

Unravelling Plant Responses to Stress-The Importance of Targeted and Untargeted Metabolomics

Climate change and an increasing population, present a massive global challenge with respect to environmentally sustainable nutritious food production. Crop yield enhancements, through breeding, are decreasing, whilst agricultural intensification is constrained by emerging, re-emerging, and endemic pests and pathogens, accounting for ~30% of global crop losses, as well as mounting abiotic stress pressures, due to climate change. Metabolomics approaches have previously contributed to our knowledge within the fields of molecular plant pathology and plant-insect interactions. However, these remain incredibly challenging targets, due to the vast diversity in metabolite volatility and polarity, heterogeneous mixtures of pathogen and plant cells, as well as rapid rates of metabolite turn-over. Unravelling the systematic biochemical responses of plants to various individual and combined stresses, involves monitoring signaling compounds, secondary messengers, phytohormones, and defensive and protective chemicals. This demands both targeted and untargeted metabolomics approaches, as well as a range of enzymatic assays, protein assays, and proteomic and transcriptomic technologies. In this review, we focus upon the technical and biological challenges of measuring the metabolome associated with plant stress. We illustrate the challenges, with relevant examples from bacterial and fungal molecular pathologies, plant-insect interactions, and abiotic and combined stress in the environment. We also discuss future prospects from both the perspective of key innovative metabolomic technologies and their deployment in breeding for stress resistance.

The utility of metabolomics as a tool to inform maize biology

With the rise of high-throughput omics tools and the importance of maize and its products as food and bioethanol, maize metabolism has been extensively explored. Modern maize is still rich in genetic and phenotypic variation, yielding a wide range of structurally and functionally diverse metabolites. The maize metabolome is also incredibly dynamic in terms of topology and subcellular compartmentalization. In this review, we examine a broad range of studies that cover recent developments in maize metabolism. Particular attention is given to current methodologies and to the use of metabolomics as a tool to define biosynthetic pathways and address biological questions. We also touch upon the use of metabolomics to understand maize natural variation and evolution, with a special focus on research that has used metabolite-based genome-wide association studies (mGWASs).