Plant Metabolomics Reviews

Jute is one of the world's most important lignocellulosic fibre crops, yet its commercial value remains highly dependent on retting, a biologically mediated fibre extraction process still largely governed by empirical practices and variable environmental conditions. Recent advances in microbial ecology, enzymology, molecular biology, and bioprocess engineering have transformed retting from a traditional post-harvest operation into a controllable lignocellulosic bioconversion process. This review...

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The cereal-legume intercropping system achieves efficient utilization of nitrogen and phosphorus through interactions between roots and soil organisms, making it a key practice in sustainable agriculture. We systematically summarized the nitrogen and phosphorus mutual promotion mechanism mediated by root exudates and mycorrhizal networks in the cereal-legume intercropping system, and proposed future research directions. Cereal plants mobilize phosphorus in rhizosphere by secreting organic acids...

Abiotic stresses-drought, salinity, extreme temperature, flooding, and heavy-metal toxicity-constrain rice (Oryza sativa L.) yield worldwide, and the cellular programmes underlying them are unevenly distributed across cell types that bulk-tissue assays average together. This review examines, from a methodological standpoint, what single-cell and spatial omics technologies can and cannot establish about rice abiotic stress biology. We first define the modality space: single-cell omics measures...

Senotherapeutic agents targeting senescent cell (SnC) accumulation represent a promising frontier in aging research. These agents encompass senolytics that selectively eliminate accumulated SnCs and senomorphics that suppress the pathological persistence of the senescence-associated secretory phenotype (SASP). Concerns regarding off-target effects of synthetic senolytics have intensified interest in plant-derived alternatives that offer multitargeted mechanisms and favorable safety profiles....

Claviceps purpurea is a highly specialized biotrophic ascomycete that colonizes floral tissues of grasses, including economically important cereal crops, causing ergot disease and producing ergot alkaloids with significant agricultural, pharmaceutical, and biotechnological relevance. Despite extensive research on its biology and secondary metabolism, the molecular mechanisms underlying host recognition, floral specificity, establishment of biotrophy, and developmental differentiation remain...

Plant genomes exhibit extensive structural diversity generated by large-scale genomic alterations, collectively known as structural variations (SVs). Unlike single nucleotide polymorphisms (SNPs) and small insertions/deletions (indels), SVs can reshape genome architecture through changes in sequence content, gene dosage, regulatory landscapes, and chromosome organization. Recent advances in long-read sequencing (LRS), pan-genome construction, and multi-omics technologies have greatly expanded...

Combined drought-heat stress is not adequately described by adding the responses to drought and heat in isolation. Water limitation restricts evaporative cooling, whereas high temperature increases atmospheric demand and threatens photosynthesis, proteostasis, and reproduction. To assess what has been demonstrated rather than merely proposed, we combined a structured narrative review with a study-level evidence map spanning genomics, multi-omics, and emerging artificial intelligence (AI). The...

Soil microbiomes are essential for nutrient cycling, plant health, stress resilience, and sustainable agriculture. Recent advances in high-throughput sequencing, multi-omics technologies, systems biology, and artificial intelligence (AI) have transformed our understanding of plant-microbiome interactions and enabled the development of innovative microbiome engineering strategies. This review provides a comprehensive overview of the mechanisms governing plant-associated soil microbiome assembly,...

Background: Plant synthetic biology reprograms metabolic networks for the sustainable production of high-value compounds. Recent computational advances incorporate machine learning to accelerate the design-build-test-learn (DBTL) cycle, enabling more predictable and scalable engineering in photoautotrophic chassis. However, the translation of AI-generated designs into stable plant phenotypes remains constrained by incomplete plant-specific training datasets, tissue heterogeneity, and limited in...

Brassica crops, encompassing globally important vegetables and oilseeds, face severe threats from diverse biotic and abiotic stresses. Plant secondary metabolites constitute the chemical foundation of defence, and metabolomics has emerged as an effective systems biology tool for comprehensively dissecting stress-induced metabolic changes. Recent progress in applying metabolomics to elucidate defence mechanisms in Brassica crops is systematically synthesised here. Major stresses confronting...

Phytotoxic effects from allelopathy occur due to signaling pathways that induce alterations in hormonal balance within the plants, thereby hindering weed growth. Signaling crosstalk between various hormones and signaling pathways (Ca²⁺, MAPK, ROS) is involved in the molecular response mechanisms found through omics. Utilizing such mechanisms would help develop new environmentally friendly methods for sustainable weed management. Allelopathy serves as an essential component of plant-plant...

Non-volatile specialized metabolites function as chemical signals linking plant physiological state with environmental interactions. I propose that root-derived non-volatile metabolites are continuously transformed across the rhizosphere and plant tissues to generate dynamic signaling states that define plant resilience under stress and recovery. Together, these processes position plant metabolism as a mechanistic and predictive interface connecting cellular responses to ecological...

Powdery mildew (Podosphaera xanthii) is a major disease affecting gerbera (Gerbera hybrida, Asteraceae), and nitrogen availability is a key factor influencing disease development. Our objective was to determine how nitrate availability affects resistance to Podosphaera xanthii through changes in primary and secondary metabolism. Using greenhouse experiments and ¹H nuclear magnetic resonance-based metabolomics, we found that lower nitrate levels reduced infection, supporting the concept of...

Microbial volatile organic compounds (mVOCs) are low-molecular-weight metabolites released by bacteria and fungi in the rhizosphere and phyllosphere. mVOCs have emerged as important mediators of plant-microbes' communication and systemic defense priming. This review covers current knowledge of the biochemical diversity of the mVOCs, encompassing major classes of mVOCs, and their mechanisms of action in plant defense. We delineate the molecular signaling cascades activated by key mVOCs such as...

This scoping review systematically evaluated the effects of protein supplements on the gut microbiome, metabolites, integrity, and inflammation. Studies investigating plant- or animal-based protein supplements in adults were identified from five electronic databases. Data were thematically synthesized; study quality was appraised using the Mixed Methods Appraisal Tool. Fourteen studies were included: whey protein (n=9), pea protein (n=3), soy protein (n=2), and casein protein (n=1). Doses ranged...

The soil-borne necrotrophic fungus Sclerotium rolfsii is a globally important pathogen causing collar rot, southern blight, and damping-off in diverse crops, resulting in substantial losses in yield, particularly during warm and cloudy weather. Through processes like niche competition, antibiosis, induced systemic resistance, and enzymatic destruction of pathogen propagules, there is mounting evidence that the rhizosphere microbiome is crucial in influencing disease outcomes. This systemic...

Micro- and nanoplastics (MNPs) are emerging pollutants in agricultural ecosystems, accumulating in soils and adversely affecting plant growth and crop yields. Although their toxicity is increasingly reported, the role of stress mitigators in reducing MNPs-induced toxicity in soil-plant systems remains insufficiently summarized. This review evaluates current research on mitigation strategies, including nanoparticles, phytohormones, biochar, chemicals, nutrients, plant growth-promoting bacteria...

Climate change-induced stresses, including drought, heat, and salinity, are increasingly constraining wheat productivity globally and pose a significant threat to global food security. Although beneficial rhizosphere microorganisms are known to enhance wheat stress tolerance, the mechanisms underlying wheat-microbiome interactions under climate-stress conditions remain poorly understood. This review highlights that wheat actively recruits and reshapes stress-resilient microbial communities,...

Climate change intensifies abiotic stresses that limit crop productivity, requiring innovative strategies to enhance resilience without compromising sustainability. Nanoparticles (NPs) have emerged as potential modulators of plant stress responses by influencing molecular regulation, physiological adaptation, and stress resilience. However, current evidence remains fragmented because studies are dispersed across different NP types, crop species, abiotic stress conditions, and omics platforms,...