Arachidonic acid: an evolutionarily conserved signaling molecule modulates plant stress signaling networks

Exploring lipid remodeling and antioxidant responses in Chlorella pyrenoidosa exposed to streptomycin sulfate stress

Microalgae, particularly Chlorella pyrenoidosa, are valuable for bioactive compounds and biofuel production, but antibiotic use in large-scale cultivation can impact growth and biochemical productivity. This study examines the physiological and molecular responses of C. pyrenoidosa to streptomycin sulfate (STRS) stress. STRS exposure significantly reduced cell density (15.31 × 106 to 11.20 × 106 cells/mL, p < 0.001) and photosynthetic efficiency (Fv/fm from 0.45 to 0.15). Multi-omics analysis revealed a dual adaptive strategy: (1) activation of antioxidant defenses, including upregulated superoxide dismutase (SOD, 19-fold) and ascorbate peroxidase (APX, 32-fold); (2) lipid remodeling, with increased α-linolenic acid (ALA) content (17.43 % to 21.25 %, p < 0.001) due to β-oxidation downregulation. These findings enhance understanding of microalgal stress adaptation and highlight potential applications in biofuel and food/feed industries. Future studies should optimize genetic and cultivation strategies to enhance these adaptive traits while ensuring ecological sustainability.

Understanding salinity tolerance mechanisms in finger millet through metabolomics

Finger millet (Eleusine coracana Gaertn L.) is an underutilized but nutritionally rich climate resilient food crop that is generally cultivated on marginal lands. Soil salinization is a major abiotic stress that leads to a reduction in growth and yield by affecting various physiological and metabolic processes in plants. The existence of genotypic variation for salt tolerance in finger millet indicates the possibility of crop improvement via plant breeding. The overall objective of the study was to identify metabolic changes associated with improved salt tolerance in finger millet. Understanding tolerance mechanisms plays a pivotal role in the development of elite cultivars. Based on the consensus of several phenotypic data at the germination and seedling stages, we further evaluated two accessions (IE 518 and IE 405) with morphophysiological parameters and metabolomics to dissect the salinity tolerance mechanisms in finger millet. Significant phenotypic separation of IE 518 and IE 405 for salt tolerance was reflected through differences in several physiological processes such as maximum quantum yield of photosystem II (FV/FM), net photosynthesis rate (Pn), shoot Na+ ion accumulation, and oxidative stresses (electrolyte leakage and malondialdehyde content). However, both accessions showed retention of K+ ions, which underscores the role of ion homeostasis in finger millet. Pathway enrichment analysis with the uniquely salt regulated metabolites identified key metabolic pathways such as stress signaling, biotin metabolism, energy metabolism, amino acid biosynthesis, and sugar metabolism in IE 518. An enhanced accumulation of reducing sugars (mannose and melibiose) and amino acids (L-Proline and GABA) in IE 518 under salinity suggests maintaining osmotic balance as a key tolerance mechanism in finger millet.

Recent advances in the chemistry and biology of plant oxylipin hormones

Jasmonates, including jasmonic acid (JA) and its derivatives, are lipid-based signaling molecules critical for plant growth, development, and defense. Among these, jasmonoyl-L-isoleucine (JA-Ile) has been identified as a bioactive plant hormone that mediates various physiological responses. JA-Ile functions in planta as a 'molecular glue' in protein-protein associations to induce the defense-related gene expression for plant-pathogen and plant-insect communications, and it affects many aspects of plant development and stress responses. This review explores the historical journey of jasmonate research, emphasizing the discovery of JA-Ile, its biosynthesis, function as a molecular glue, and the ligand-receptor co-evolutional aspect. The elucidation of the SCFCOI1-JAZ receptor complex and the crystallization of this co-receptor system marked significant advancements in understanding the chemical background of jasmonate biology. This review focuses on the advances in the chemistry and biology of jasmonate bioscience in the past two decades.

The key metabolic pathway of roots and leaves responses in Arachis hypogaea under Al toxicity stress

BACKGROUND

Aluminum (Al) toxicity inhibits plant growth and alters gene expression and metabolite profiles. However, the molecular mechanisms underlying the effects of Al toxicity on peanut plants remain unclear. Transcriptome and metabolome analyses were conducted to investigate the responses of peanut leaves and roots to Al toxicity.

RESULTS

Al toxicity significantly inhibited peanut growth, disrupted antioxidant enzyme systems in roots and leaves, and impaired nutrient absorption. Under Al toxicity stress, the content of indole-3-acetic acid-aspartate (IAA-Asp) decreased by 23.94% in leaves but increased by 12.91% in roots. Methyl jasmonate (MeJA) levels in leaves increased dramatically by 2642.86%. Methyl salicylate (MeSA) content in leaves and roots increased significantly by 140.00% and 472.22%, respectively. Conversely, isopentenyl adenosine (IPA) content decreased by 78.95% in leaves and 20.66% in roots. Transcriptome analysis identified 5831 differentially expressed genes (DEGs) in leaves and 6405 DEGs in roots, whereas metabolomics analysis revealed 210 differentially accumulated metabolites (DAMs) in leaves and 240 DAMs in roots. Under Al toxicity stress, both leaves and roots were significantly enriched in the "linoleic acid metabolism" pathway. Genes such as lipoxygenase LOX1-5 and LOX2S were differentially expressed, and metabolites, including linoleic acid and its oxidized derivatives, were differentially accumulated, mitigating oxidative stress.

CONCLUSIONS

This study elaborates on the potential complex physiological and molecular mechanisms of peanuts under aluminum toxicity stress, and highlights the importance of linoleic acid metabolism in coping with aluminum toxicity. These findings enhance our understanding of the impact of aluminum toxicity on peanut development and the response of key metabolic pathways, providing potential molecular targets for genetic engineering to improve crop resistance to aluminum stress.

Whole transcriptomic analysis reveals the lncRNA-miRNA-mRNA regulatory mechanism underlying the heat-hardening formation in Mytilus coruscus

Heat-hardening is a critical adaptation mechanism that enables the mussel Mytilus coruscus to endure high-temperature events caused by low tides and adverse weather condition. However, the molecular regulatory mechanism underlying heat-hardening remains unclear. Herein, we analyzed the whole transcriptome of heat-hardening M. coruscus to explore formation mechanism of heat-hardening. M. coruscus were treated with 27 °C for 5 days, 3 h per day, to promote heat-hardening formation, and sampled at 6, 8, 10, 12, 14, and 16 days. We identified 203 differentially expressed lncRNAs (DE-lncRNAs), 11 differentially expressed miRNAs (DE-miRNAs) and 207 differentially expressed mRNAs (DE-mRNAs). GO and KEGG enrichment analysis revealed that the DE-mRNAs were mainly enriched in arachidonic acid metabolism pathway, apoptosis pathway, NOD-like receptor signaling pathway and the platelet-activated pathway, WGCNA results suggested that arachidonic acid metabolism and cytochrome P450 were significantly correlated with heat-hardening during formation. PLA2 was identified as an essential gene in heat-hardening, with high node degrees, enriched in the arachidonic acid metabolism pathway and regulated by a lncRNA (MSTRG.113849.1) and a miRNA (novel_miR_425). MSTRG.113849.1-novel_miR_425-PLA2 relationship pairs were identified for heat-hardening in M. coruscus. Our finding suggests that miRNAs and lncRNAs play pivotal roles in heat-hardening by targeting PLA2, providing a mechanism for M. coruscus to adapt to heat stress, which also offers a mechanism to adapt to stressors arising from a rapidly changing oceanic environment.

Rhizobacteria protective hydrogel to promote plant growth and adaption to acidic soil

Endophytic plant growth promoting rhizobacteria (PGPRs) could replace chemical fertilizers in sustainable agriculture. Unfortunately, they are susceptible to harsh environmental conditions. Here, we proposed a polymeric hydrogel (PMH) consisting of carboxymethyl chitosan, sodium alginate, and calcium chloride for loading and protecting endophytic PGPR. This hydrogel can load endophytic PGPRs to not only boost its growth-promoting efficiency, but also help them adapt more effectively to environments. Using endophytic PGPR Ensifer C5 as model bacteria and Brasscia napus as host, we demonstrate that the PMH facilitate the colonization of endophytic PGPRs in the apical and lateral root primordia regions. Further analysis indicates that the PMH modulate suberin deposition of the endodermal cell layers and regulate the accumulation of auxin at the root tip. Meanwhile, PMH enhances the antioxidant capacity and disease resistance properties of plants by increasing the content of arachidonic acid metabolism intermediates in the plant. Importantly, the combination of PMH and endophytic PGPRs increases the yields of B. napus by approximately 30% in the field. Furthermore, PMH attenuates the loss of endophytic PGPR activity in the acidic environments. Overall, this microbial encapsulation strategy is a promising way to protect fragile endophytic microorganisms, providing attractive avenues in sustainable agriculture.

Partial root-zone drying irrigation enhances synthesis of glutathione in barley roots to improve low temperature tolerance

Partial root-zone drying irrigation (PRD) has been widely employed to regulate crop root development and responses to environmental fluctuations. However, its role in reprogramming rhizospheric microorganisms and inducing plant stress tolerance remains largely unexplored. This study aimed to investigate the effects of PRD on the response of barley (Hordeum vulgare) plants to low temperatures under various irrigation regimes. Under low temperature, barley plants subjected to PRD exhibited a significantly enhanced net photosynthetic rate, stomatal conductance, and maximum quantum efficiency of photosystem II compared to fully irrigated plants. Additionally, these plants showed a reduction in relative conductance. These results suggest that PRD could be a viable strategy for enhancing crop stress tolerance through irrigation management. Metabolomic analysis revealed that PRD influenced the accumulation of glutathione and 9-octadecenamide in roots under low temperature, which was corroborated by transcriptome profiling data. Furthermore, the study highlighted the close association between this regulatory process and rhizosphere core microorganisms, such as Sphingobium and Mortierella, enriched in barley roots under PRD. This study revealed the mechanism underlying plant stress tolerance induction by PRD and the roles of rhizosphere microorganisms in this process. Also, the current study suggests that PRD is a promising strategy for enhancing crop stress tolerance through effective irrigation management.

Non-targeted metabolomics reveals fatty acid and associated pathways driving resistance to whitefly and tomato leafminer in wild tomato accessions

Wild tomato species exhibit natural insect resistance, yet the specific secondary metabolites and underlying mechanisms governing the resistance remain unclear. Moreover, defense expression dynamically adapts to insect herbivory, causing significant metabolic changes and species-specific secondary metabolite accumulation. The present study aims to identify the resistance-related metabolites in wild tomato accessions that influence the defense mechanism against whitefly (Bemisia tabaci Asia II 7) and leafminer (Phthorimaea absoluta). In this study, LC-HRMS-based non-targeted metabolomics of resistant wild (Solanum cheesmaniae and Solanum galapagense) and susceptible cultivated (Solanum lycopersicum) accessions following 6- and 12-h post-infestation (hpi) by B. tabaci Asia II 7 and P. absoluta revealed distinct sets of resistance-related constitutive (RRC) and induced (RRI) metabolites. The key resistance-related metabolites were those involved in the fatty acid and associated biosynthesis pathways (e.g., triacontane, di-heptanoic acid, dodecanoic acid, undecanoic acid, N-hexadecanoic acid, pentacosane, monogalactosyldiacylglycerols, sphinganine, and 12-hydroxyjasmonic acid), which are recognized for their direct or indirect role in mediating plant defense against insects. Additionally, the differential accumulation of metabolites was evident through partial least squares-discriminant analysis (PLS-DA), highlighting differences in metabolite profiles between resistant and susceptible accessions at 6 and 12 hpi of B. tabaci and P. absoluta. Volcano plot analysis revealed a higher number of significantly upregulated metabolites in wild accessions following herbivory. Moreover, wild tomato accessions responded uniquely to B. tabaci and P. absoluta, highlighting species-specific metabolic responses of tomato accessions to the two feeding guilds. This study uncovered biochemical mechanisms governing resistance in wild tomato accessions, elucidated the influence of dual herbivory on the plant metabolome, and offered well-characterized parent materials and candidate metabolites for breeding insect-resistant varieties.

Comparative Metabolite Profiling Between Cordyceps sinensis and Other Cordyceps by Untargeted UHPLC-MS/MS

Cordyceps sinensis is a second-class, nationally protected, medicinal fungi and serves as a functional nutrient in China. C. sinensis is extremely scarce due to its peculiar growing environment and the extensive gathering practices carried out by humans. A large number of counterfeit products for this fungi have also emerged in the market. At present, there is a lack of research on the differential metabolites of C. sinensis and its counterfeit products. The current study used an LC-MS non-targeted metabolomics method to compare the differences in metabolites between C. sinensis and other Cordyceps. The results indicated that there were significant differences in the metabolites between C. sinensis and the others. The 18 superclasses were found to have differences, involving lipids, organic acids, nucleosides, carbohydrates, amino acids, vitamins, and their derivatives. Compared with the other four groups of Cordyceps, 8 metabolites with significant differences were screened. In addition, the types and abundance of different metabolites of nucleosides of C. sinensis were superior compared to other Cordyceps (e.g., 5-Methyldioxycytidine, didanosine, cytidine, etc.). Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the metabolism of arginine and proline, and glycerophosphate metabolism were the two significant differences in the metabolic pathways between C. sinensis and other Cordyceps. The research results provide a reference for identifying the authenticity of C. sinensis using non-targeted metabolic methods.

Integrated analysis of physiological and metabolic data uncovers essential dynamic mechanisms involved in the maturation of cigar tobacco leaves

The quality of cigar tobacco leaves is profoundly affected by the timing of their harvest, with both early and late collections resulting in inferior characteristics. While the relationship between maturity and physiological metabolic processes is acknowledged, a comprehensive understanding of the physiological behavior of cigar leaves harvested at different stages remains elusive. This research investigated the physiological and metabolomic profiles of the cigar tobacco variety CX-014, grown in Danjiangkou City, Hubei Province, with leaves sampled at 35 (T1), 42 (T2), 49 (T3), and 56 (T4) days post-inflorescence removal. Leaf color transitioned from green to yellow, accompanied by the appearance of white mature spots. Notable increases in photosynthetic pigments and gas exchange parameters occurred between T1 and T2, followed by decline at T3 and T4. The optimal sugar-to-nicotine and potassium-to-chlorine ratios, critical determinants of smoking quality and tobacco combustibility, were observed at T3, indicating a superior chemical balance in leaves harvested at this stage. Metabolomic analysis revealed 2153 distinct metabolites, with the most significant changes occurring between T2 and T3, highlighting critical physiological transformations during this interval. Pathway enrichment analysis via KEGG pinpointed notable shifts in amino acid synthesis pathways, particularly those involving tryptophan, alanine, and aspartate. Tryptophan metabolism and zeatin biosynthesis were substantially altered, with compounds like indolepyruvic acid, N-formylpurine nucleotide, isopentenyladenine nucleotide, and dihydrozeatin showing marked reductions at T3. This study also explored how the timing of lower leaf harvest influences the physiological processes of middle leaves, finding that a plethora of metabolites associated with the breakdown of arachidonic acid-a primitive metazoan signaler implicated in plant stress and defense networks-were abundant in T3 leaves when lower leaves were harvested 43-38 days prior. Overall, these findings elucidates the complex physiological dynamics of cigar leaves during maturation, highlighting critical metabolites involved in essential metabolic pathways.

Beneficial Soil Fungus Kills Predatory Nematodes with Dehydropeptides Translocating into the Animal Gut

Mortierella alpina is a mold fungus that has gained attention for its positive correlation with soil health, plant growth, and applications as a crop biocontrol agent to suppress the threats of nematode pests. To date, the mechanisms underlying the protective traits of M. alpina against these plant parasites have remained elusive. Here we report that abundantly produced peptidic biosurfactants, malpinin A-D, exhibit robust inhibitory activity against nematodes. Nematode assays with malpinin congeners and chemically synthesized analogues revealed that the dehydro amino acid is critical for activity, whereas the N-terminal amino acid residues modulate the lipophilicity. Complementary imaging by fluorescence microscopy and Raman microspectroscopy, using externally fluorescence-labeled, semisynthetic malpinin or a biosynthetically alkyne-tagged probe generated by precursor-directed biosynthesis, visualized the translocation and enrichment of malpinin in the gut of the model nematode Caenorhabditis elegans. Our findings provide valuable insight into the use of M. alpina as a biocontrol agent, emphasizing the ecologically significant role of malpinins as a protective trait. In addition to solving a long-standing riddle, these findings have translational value for applications in agriculture.

Oxylipin Receptors and Their Role in Inter-Partner Signalling in a Model Cnidarian-Dinoflagellate Symbiosis

Oxylipin signalling is central in biology, mediating processes such as cellular homeostasis, inflammation and molecular signalling. It may also facilitate inter-partner communication in the cnidarian-dinoflagellate symbiosis, though this aspect remains understudied. In this study, four oxylipin receptors were characterised using immunohistochemistry and immunoblotting in the sea anemone Exaiptasia diaphana ('Aiptasia'): Prostaglandin E2 receptor 2 (EP2) and 4 (EP4), Transient Receptor Potential cation channel A1 (TRPA1) and Glutamate Receptor Ionotropic, Kainate 2 (GRIK2). Receptor abundance and localisation were compared between aposymbiotic anemones and symbiotic anemones hosting either native Breviolum minutum or non-native Durusdinium trenchii. All receptors were localised to the putative symbiosome of freshly isolated symbionts, suggesting a role in host-symbiont crosstalk. EP2, EP4 and TRPA1 abundance decreased in the gastrodermis of anemones hosting B. minutum, indicating potential downregulation of pathways mediated by these receptors. In contrast, GRIK2 abundance increased in anemones hosting D. trenchii in both the epidermis and gastrodermis; GRIK2 acts as a chemosensor of potential pathogens in other systems and could play a similar role here given D. trenchii's reputation as a sub-optimal partner for Aiptasia. This study contributes to the understanding of oxylipin signalling in the cnidarian-dinoflagellate symbiosis and supports further exploration of host-symbiont molecular signalling.

The potential of Burkholderia gladioli KRS027 in plant growth promotion and biocontrol against Verticillium dahliae revealed by dual transcriptome of pathogen and host

Verticillium dahliae is a destructive, soil-borne pathogen that causes significant losses on numerous important dicots. Recently, beneficial microbes inhabiting the rhizosphere have been exploited and used to control plant diseases. In the present study, Burkholderia gladioli KRS027 demonstrated excellent inhibitory effects against Verticillium wilt in cotton seedlings. Plant growth and development was promoted by affecting the biosynthesis and signaling pathways of brassinosteroids (BRs), gibberellins (GAs), and auxins, consequently promoting stem elongation, shoot apical meristem, and root apical tissue division in cotton. Furthermore, based on the host transcriptional response to V. dahliae infection, it was found that KRS027 modulates the plants to maintain cell homeostasis and respond to other pathogen stress. Moreover, KRS027 induced disruption of V. dahliae cellular structures, as evidenced by scanning electron microscopy (SEM) and transmission electron microscopy (TEM) analyses. Based on the comparative transcriptomic analysis between KRS027 treated and control group of V. dahliae, KRS027 induced substantial alterations in the transcriptome, particularly affecting genes encoding secreted proteins, small cysteine-rich proteins (SCRPs), and protein kinases. In addition, KRS027 suppressed the growth of different clonal lineages of V. dahliae strains through metabolites, and volatile organic compounds (VOCs) released by KRS027 inhibited melanin biosynthesis and microsclerotia development. These findings provide valuable insights into an alternative biocontrol strategy for Verticillium wilt, demonstrating that the antagonistic bacterium KRS027 holds promise as a biocontrol agent for promoting plant growth and managing disease occurrence.

Comparative Metabolome and Transcriptome Analysis Reveals the Defense Mechanism of Chinese Cabbage (Brassica rapa L. ssp. pekinensis) against Plasmodiophora brassicae Infection

Chinese cabbage (Brassica rapa L. ssp. pekinensis) ranks among the most cultivated and consumed vegetables in China. A major threat to its production is Plasmodiophora brassicae, which causes large root tumors, obstructing nutrient and water absorption and resulting in plant withering. This study used a widely targeted metabolome technique to identify resistance-related metabolites in resistant (DH40R) and susceptible (DH199S) Chinese cabbage varieties after inoculation with P. brassicae. This study analyzed disease-related metabolites during different periods, identifying 257 metabolites linked to resistance, enriched in the phenylpropanoid biosynthesis pathway, and 248 metabolites linked to susceptibility, enriched in the arachidonic acid metabolism pathway. Key metabolites and genes in the phenylpropanoid pathway were upregulated at 5 days post-inoculation (DPI), suggesting their role in disease resistance. In the arachidonic acid pathway, linoleic acid and gamma-linolenic acid were upregulated at 5 and 22 DPI in resistant plants, while arachidonic acid was upregulated at 22 DPI in susceptible plants, leading to the conclusion that arachidonic acid may be a response substance in susceptible plants after inoculation. Many genes enriched in these pathways were differentially expressed in DH40R and DH199S. The research provided insights into the defense mechanisms of Chinese cabbage against P. brassicae through combined metabolome and transcriptome analysis.

Oxidative stress and metabolic process responses of Chlorella pyrenoidosa to nanoplastic exposure: Insights from integrated analysis of transcriptomics and metabolomics

Oxidative stress is a universal interpretation for the toxicity mechanism of nanoplastics to microalgae. However, there is a lack of deeper insight into the regulation mechanism in microalgae response to oxidative stress, thus affecting the prevention and control for nanoplastics hazard. The integrated analysis of transcriptomics and metabolomics was employed to investigate the mechanism for the oxidative stress response of Chlorella pyrenoidosa to nanoplastics and subsequently lock the according core pathways and driver genes induced. Results indicated that the linoleic acid metabolism, glycine (Gly)-serine (Ser)-threonine (Thr) metabolism, and arginine and proline metabolism pathways of C. pyrenoidosa were collectively involved in oxidative stress. The analysis of linoleic acid metabolism suggested that nanoplastics prompted algal cells to secrete more allelochemicals, thereby leading to destroy the immune system of cells. Gly-Ser-Thr metabolism and arginine and proline metabolism pathways were core pathways involved in algal regulation of cell membrane function and antioxidant system. Key genes, such as LOX2.3, SHM1, TRPA1, and proC1, are drivers of regulating the oxidative stress of algae cells. This investigation lays the foundation for future applications of gene editing technology to limit the hazards of nanoplastics on aquatic organism.

Metabolome-driven microbiome assembly determining the health of ginger crop (Zingiber officinale L. Roscoe) against rhizome rot

BACKGROUND

Plant-associated microorganisms can be found in various plant niches and collectively comprise the plant microbiome. The plant microbiome assemblages have been extensively studied, primarily in model species. However, a deep understanding of the microbiome assembly associated with plant health is still needed. Ginger rhizome rot has been variously attributed to multiple individual causal agents. Due to its global relevance, we used ginger and rhizome rot as a model to elucidate the metabolome-driven microbiome assembly associated with plant health.

RESULTS

Our study thoroughly examined the biodiversity of soilborne and endophytic microbiota in healthy and diseased ginger plants, highlighting the impact of bacterial and fungal microbes on plant health and the specific metabolites contributing to a healthy microbial community. Metabarcoding allowed for an in-depth analysis of the associated microbial community. Dominant genera represented each microbial taxon at the niche level. According to linear discriminant analysis effect size, bacterial species belonging to Sphingomonas, Quadrisphaera, Methylobacterium-Methylorubrum, Bacillus, as well as the fungal genera Pseudaleuria, Lophotrichus, Pseudogymnoascus, Gymnoascus, Mortierella, and Eleutherascus were associated with plant health. Bacterial dysbiosis related to rhizome rot was due to the relative enrichment of Pectobacterium, Alcaligenes, Klebsiella, and Enterobacter. Similarly, an imbalance in the fungal community was caused by the enrichment of Gibellulopsis, Pyxidiophorales, and Plectosphaerella. Untargeted metabolomics analysis revealed several metabolites that drive microbiome assembly closely related to plant health in diverse microbial niches. At the same time, 6-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)oxane-2,3,4,5-tetrol was present at the level of the entire healthy ginger plant. Lipids and lipid-like molecules were the most significant proportion of highly abundant metabolites associated with ginger plant health versus rhizome rot disease.

CONCLUSIONS

Our research significantly improves our understanding of metabolome-driven microbiome structure to address crop protection impacts. The microbiome assembly rather than a particular microbe's occurrence drove ginger plant health. Most microbial species and metabolites have yet to be previously identified in ginger plants. The indigenous microbial communities and metabolites described can support future strategies to induce plant disease resistance. They provide a foundation for further exploring pathogens, biocontrol agents, and plant growth promoters associated with economically important crops. Video Abstract.

UV-B Stress-Triggered Amino Acid Reprogramming and ABA-Mediated Hormonal Crosstalk in Rhododendron chrysanthum Pall

Increased UV-B radiation due to ozone depletion adversely affects plants. This study focused on the metabolite dynamics of Rhododendron chrysanthum Pall. (R. chrysanthum) and the role of ABA in mitigating UV-B stress. Chlorophyll fluorescence metrics indicated that both JA and ABA increased UV-B resistance; however, the effect of JA was not as strong as that of ABA. Metabolomic analysis using UPLC-MS/MS (ultra-performance liquid chromatography and tandem mass spectrometry) revealed significant fluctuations in metabolites under UV-B and ABA application. UV-B decreased amino acids and increased phenolics, suggesting antioxidant defense activation. ABA treatment upregulated lipids and phenolic acids, highlighting its protective role. Multivariate analysis showed distinct metabolic clusters and pathways responding to UV-B and ABA, which impacted amino acid metabolism and hormone signal transduction. Exogenous ABA negatively regulated the JA signaling pathway in UV-B-exposed R. chrysanthum, as shown by KEGG enrichment. This study deepens understanding of plant stress-tolerance mechanisms and has implications for enhancing plant stress tolerance through metabolic and hormonal interventions.

Comparative Transcriptomics of Soybean Genotypes with Partial Resistance Toward Phytophthora sojae, Conrad, and M92-220 to Moderately Susceptible Fast Neutron Mutant Soybeans and Sloan

The breeding of disease-resistant soybeans cultivars to manage Phytophthora root and stem rot caused by the pathogen Phytophthora sojae involves combining quantitative disease resistance (QDR) and Rps gene-mediated resistance. To identify and confirm potential mechanisms of QDR toward P. sojae, we conducted a time course study comparing changes in gene expression among Conrad and M92-220 with high QDR to susceptible genotypes, Sloan, and three mutants derived from fast neutron irradiation of M92-220. Differentially expressed genes from Conrad and M92-220 indicated several shared defense-related pathways at the transcriptomic level but also defense pathways unique to each cultivar, such as stilbenoid, diarylheptanoid, and gingerol biosynthesis and monobactam biosynthesis. Gene Ontology pathway analysis showed that the susceptible fast neutron mutants lacked enrichment of three terpenoid-related pathways and two cell wall-related pathways at either one or both time points, in contrast to M92-220. The susceptible mutants also lacked enrichment of potentially important Kyoto Encyclopedia of Genes and Genomes pathways at either one or both time points, including sesquiterpenoid and triterpenoid biosynthesis; thiamine metabolism; arachidonic acid; stilbenoid, diarylheptanoid, and gingerol biosynthesis; and monobactam biosynthesis. Additionally, 31 genes that were differentially expressed in M92-220 following P. sojae infection were not expressed in the mutants. These 31 genes have annotations related to unknown proteins; valine, leucine, and isoleucine biosynthesis; and protein and lipid metabolic processes. The results of this study confirm previously proposed mechanisms of QDR, provide evidence for potential novel QDR pathways in M92-220, and further our understanding of the complex network associated with QDR mechanisms in soybean toward P. sojae.

Exploring the Metatranscriptome of Bacterial Communities of Two Moss Species Thriving in Different Environments-Terrestrial and Aquatic

Mosses host diverse bacterial communities essential for their fitness, nutrient acquisition, stress tolerance, and pathogen defense. Understanding the microbiome's taxonomic composition is the first step, but unraveling their functional capabilities is crucial for grasping their ecological significance. Metagenomics characterizes microbial communities by composition, while metatranscriptomics explores gene expression, providing insights into microbiome functionality beyond the structure. Here, we present for the first time a metatranscriptomic study of two moss species, Hypnum cupressiforme (Hedw.) and Platyhypnidium riparioides (Hedw.) Dixon., renowned as key biomonitors of atmospheric and water pollution. Our investigation extends beyond taxonomic profiling and offers a profound exploration of moss bacterial communities. Pseudomonadota and Actinobacteria are the dominant bacterial phyla in both moss species, but their proportions differ. In H. cupressiforme, Actinobacteria make up 62.45% and Pseudomonadota 32.48%, while in P. riparioides, Actinobacteria account for only 25.67% and Pseudomonadota 69.08%. This phylum-level contrast is reflected in genus-level differences. Our study also shows the expression of most genes related to nitrogen cycling across both microbiomes. Additionally, functional annotation highlights disparities in pathway prevalence, including carbon dioxide fixation, photosynthesis, and fatty acid biosynthesis, among others. These findings hint at potential metabolic distinctions between microbial communities associated with different moss species, influenced by their specific genotypes and habitats. The integration of metatranscriptomic data holds promise for enhancing our understanding of bryophyte-microbe partnerships, opening avenues for novel applications in conservation, bioremediation, and sustainable agriculture.

Deciphering Aphanomyces euteiches-pea-biocontrol bacterium interactions through untargeted metabolomics

Aphanomyces euteiches causes root rot in pea, leading to significant yield losses. However, the metabolites involved in this pathosystem have not been thoroughly studied. This study aimed to fill this gap and explore mechanisms of bacterial suppression of A. euteiches via untargeted metabolomics using pea grown in a controlled environment. Chemical isotope labeling (CIL), followed by liquid chromatography-mass spectrometry (LC-MS), was used for metabolite separation and detection. Univariate and multivariate analyses showed clear separation of metabolites from pathogen-treated pea roots and roots from other treatments. A three-tier approach positively or putatively identified 5249 peak pairs or metabolites. Of these, 403 were positively identified in tier 1; 940 were putatively identified with high confidence in tier 2. There were substantial changes in amino acid pool, and fatty acid and phenylpropanoid pathway products. More metabolites, including salicylic and jasmonic acids, were upregulated than downregulated in A. euteiches-infected roots. 1-aminocyclopropane-1-carboxylic acid and 12-oxophytodienoic acid were upregulated in A. euteiches + bacterium-treated roots compared to A. euteiches-infected roots. A great number of metabolites were up- or down-regulated in response to A. euteiches infection compared with the control and A. euteiches + bacterium-treated plants. The results of this study could facilitate improved disease management.

Plant Biostimulant as an Environmentally Friendly Alternative to Modern Agriculture

Ensuring the safety of crop production presents a significant challenge to humanity. Pesticides and fertilizers are commonly used to eliminate external interference and provide nutrients, enabling crops to sustain growth and defense. However, the addition of chemical substances does not meet the environmental standards required for agricultural production. Recently, natural sources such as biostimulants have been found to help plants with growth and defense. The development of biostimulants provides new solutions for agricultural product safety and has become a widely utilized tool in agricultural. The review summarizes the classification of biostimulants, including humic-based biostimulant, protein-based biostimulant, oligosaccharide-based biostimulant, metabolites-based biostimulants, inorganic substance, and microbial inoculant. This review attempts to summarize suitable alternative technology that can address the problems and analyze the current state of biostimulants, summarizes the research mechanisms, and anticipates future technological developments and market trends, which provides comprehensive information for researchers to develop biostimulants.

Multiomics Reveals Mechanisms of Alternaria oxytropis Inhibiting Pathogenic Fungi in Oxytropis ochrocephala

Endophytic fungi can benefit the host plant and increase the plant resistance. Now, there is no in-depth study of how Alternaria oxytropis (A. oxytropis) is enhancing the ability of inhibiting pathogenic fungi in Oxytropis ochrocephala (O. ochrocephala). In this study, the fungal community and metabolites associated with endophyte-infected (EI) and endophyte-free (EF) O. ochrocephala were compared by multiomics. The fungal community indicated that there was more A. oxytropis, less phylum Ascomycota, and less genera Leptosphaeria, Colletotrichum, and Comoclathris in the EI group. As metabolic biomarkers, the levels of swainsonine and apigenin-7-O-glucoside-4-O-rutinoside were significantly increased in the EI group. Through in vitro validation experiments, swainsonine and apigenin-7-O-glucoside-4-O-rutinoside can dramatically suppress the growth of pathogenic fungi Leptosphaeria sclerotioides and Colletotrichum americae-borealis by increasing the level of oxidative stress. This work suggested that O. ochrocephala containing A. oxytropis could increase the resistance to fungal diseases by markedly enhancing the content of metabolites inhibiting pathogenic fungi.

Toxicity assessment of perfluorooctanesulfonic acid (PFOS) on a spontaneous plant, velvetleaf (Abutilon theophrasti), via metabolomics

Spontaneous plants often play important ecological roles in terrestrial environments, but impacts of contaminants on spontaneous plants are seldom investigated. Per- and polyfluoroalkyl substances (PFAS), such as perfluorooctanesulfonic acid (PFOS) are ubiquitous in rural and urban soils. In this study, we assessed the effects of PFOS on a spontaneous plant, velvetleaf (Abutilon theophrasti), using endpoints such as plant growth, stress defense, PFOS uptake, and elemental and metabolite profile. We observed stunted growth in plants grown in PFOS-contaminated soils, with PFOS accumulating in their shoots by up to 3000 times more than the control plants. The other endpoints (decreased chlorophyll a synthesis, elevated oxidative stress, reduced shoot Mg concentration, and reduced biomass production) also explained the stunted growth of velvetleaf exposed to elevated PFOS concentrations. We found that 56 metabolites involved in 13 metabolic pathways were dysregulated. The synthesis of important antioxidants such as ascorbic acid, hydroxycinnamic acids (coumaric, caffeic, ferulic, and sinapic acids), and tocopherols decreased, resulting in loss of plant's defense to stress. PFOS also reduced the levels of growth-related and stress-coping metabolites including squalene, serotonin, noradrenalin, putrescine, and indole-3-propionic acid, which further corroborated the restricted growth of velvetleaf exposed to elevated PFOS. These findings provide insights on phytotoxicity of PFOS to velvetleaf, a resilient terrestrial spontaneous plant.

Non-Targeted Metabolomic Analysis of Arabidopsis thaliana (L.) Heynh: Metabolic Adaptive Responses to Stress Caused by N Starvation

As sessile organisms, plants develop the ability to respond and survive in changing environments. Such adaptive responses maximize phenotypic and metabolic fitness, allowing plants to adjust their growth and development. In this study, we analyzed the metabolic plasticity of Arabidopsis thaliana in response to nitrate deprivation by untargeted metabolomic analysis and using wild-type (WT) genotypes and the loss-of-function nia1/nia2 double mutant. Secondary metabolites were identified using seedlings grown on a hydroponic system supplemented with optimal or limiting concentrations of N (4 or 0.2 mM, respectively) and harvested at 15 and 30 days of age. Then, spectral libraries generated from shoots and roots in both ionization modes (ESI +/-) were compared. Totals of 3407 and 4521 spectral signals (m/z_rt) were obtained in the ESI+ and ESI- modes, respectively. Of these, approximately 50 and 65% were identified as differentially synthetized/accumulated. This led to the presumptive identification of 735 KEGG codes (metabolites) belonging to 79 metabolic pathways. The metabolic responses in the shoots and roots of WT genotypes at 4 mM of N favor the synthesis/accumulation of metabolites strongly related to growth. In contrast, for the nia1/nia2 double mutant (similar as the WT genotype at 0.2 mM N), metabolites identified as differentially synthetized/accumulated help cope with stress, regulating oxidative stress and preventing programmed cell death, meaning that metabolic responses under N starvation compromise growth to prioritize a defensive response.

Overlapping Local and Systemic Defense Induced by an Oomycete Fatty Acid MAMP and Brown Seaweed Extract in Tomato

Eicosapolyenoic fatty acids are integral components of oomycete pathogens that can act as microbe-associated molecular patterns to induce disease resistance in plants. Defense-inducing eicosapolyenoic fatty acids include arachidonic acid (AA) and eicosapentaenoic acid and are strong elicitors in solanaceous plants, with bioactivity in other plant families. Similarly, extracts of a brown seaweed, Ascophyllum nodosum, used in sustainable agriculture as a biostimulant of plant growth, may also induce disease resistance. A. nodosum, similar to other macroalgae, is rich in eicosapolyenoic fatty acids, which comprise as much as 25% of total fatty acid composition. We investigated the response of roots and leaves from AA or a commercial A. nodosum extract (ANE) on root-treated tomatoes via RNA sequencing, phytohormone profiling, and disease assays. AA and ANE significantly altered transcriptional profiles relative to control plants, inducing numerous defense-related genes with both substantial overlap and differences in gene expression patterns. Root treatment with AA and, to a lesser extent, ANE also altered both salicylic acid and jasmonic acid levels while inducing local and systemic resistance to oomycete and bacterial pathogen challenge. Thus, our study highlights overlap in both local and systemic defense induced by AA and ANE, with potential for inducing broad-spectrum resistance against pathogens. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Genome-Wide Tissue-Specific Genes Identification for Novel Tissue-Specific Promoters Discovery in Soybean

Promoters play a crucial role in controlling the spatial and temporal expression of genes at transcriptional levels in the process of higher plant growth and development. The spatial, efficient, and correct regulation of exogenous genes expression, as desired, is the key point in plant genetic engineering research. Constitutive promoters widely used in plant genetic transformation are limited because, sometimes, they may cause potential negative effects. This issue can be solved, to a certain extent, by using tissue-specific promoters. Compared with constitutive promoters, a few tissue-specific promoters have been isolated and applied. In this study, based on the transcriptome data, a total of 288 tissue-specific genes were collected, expressed in seven tissues, including the leaves, stems, flowers, pods, seeds, roots, and nodules of soybean (Glycine max). KEGG pathway enrichment analysis was carried out, and 52 metabolites were annotated. A total of 12 tissue-specific genes were selected via the transcription expression level and validated through real-time quantitative PCR, of which 10 genes showed tissue-specific expression. The 3-kb 5' upstream regions of ten genes were obtained as putative promoters. Further analysis showed that all the 10 promoters contained many tissue-specific cis-elements. These results demonstrate that high-throughput transcriptional data can be used as effective tools, providing a guide for high-throughput novel tissue-specific promoter discovery.

12-Oxophytodienoate Reductase Overexpression Compromises Tolerance to Botrytis cinerea in Hexaploid and Tetraploid Wheat

12-Oxophytodienoate reductase is the enzyme involved in the biosynthesis of phytohormone jasmonates, which are considered to be the major regulators of plant tolerance to biotic challenges, especially necrotrophic pathogens. However, we observe compromised tolerance to the necrotrophic fungal pathogen Botrytis cinerea in transgenic hexaploid bread wheat and tetraploid emmer wheat plants overexpressing 12-OXOPHYTODIENOATE REDUCTASE-3 gene from Arabidopsis thaliana, while in Arabidopsis plants themselves, endogenously produced and exogenously applied jasmonates exert a strong protective effect against B. cinerea. Exogenous application of methyl jasmonate on hexaploid and tetraploid wheat leaves suppresses tolerance to B. cinerea and induces the formation of chlorotic damages. Exogenous treatment with methyl jasmonate in concentrations of 100 µM and higher causes leaf yellowing even in the absence of the pathogen, in agreement with findings on the role of jasmonates in the regulation of leaf senescence. Thereby, the present study demonstrates the negative role of the jasmonate system in hexaploid and tetraploid wheat tolerance to B. cinerea and reveals previously unknown jasmonate-mediated responses.

Pseudophosphorylation of Arabidopsis jasmonate biosynthesis enzyme lipoxygenase 2 via mutation of Ser600 inhibits enzyme activity

Jasmonates are oxylipin phytohormones critical for plant resistance against necrotrophic pathogens and chewing herbivores. An early step in their biosynthesis is catalyzed by non-heme iron lipoxygenases (LOX; EC 1.13.11.12). In Arabidopsis thaliana, phosphorylation of Ser⁶⁰⁰ of AtLOX2 was previously reported, but whether phosphorylation regulates AtLOX2 activity is unclear. Here, we characterize the kinetic properties of recombinant WT AtLOX2 (AtLOX2^WT). AtLOX2^WT displays positive cooperativity with α-linolenic acid (α-LeA, jasmonate precursor), linoleic acid (LA), and arachidonic acid (AA) as substrates. Enzyme velocity with endogenous substrates α-LeA and LA increased with pH. For α-LeA, this increase was accompanied by a decrease in substrate affinity at alkaline pH; thus, the catalytic efficiency for α-LeA was not affected over the pH range tested. Analysis of Ser⁶⁰⁰ phosphovariants demonstrated that pseudophosphorylation inhibits enzyme activity. AtLOX2 activity was not detected in phosphomimics Atlox2^S600D and Atlox2^S600M when α-LeA or AA were used as substrates. In contrast, phosphonull mutant Atlox2^S600A exhibited strong activity with all three substrates, α-LeA, LA, and AA. Structural comparison between the AtLOX2 AlphaFold model and a complex between 8R-LOX and a 20C polyunsaturated fatty acid suggests a close proximity between AtLOX2 Ser⁶⁰⁰ and the carboxylic acid head group of the polyunsaturated fatty acid. This analysis indicates that Ser⁶⁰⁰ is located at a critical position within the AtLOX2 structure and highlights how Ser⁶⁰⁰ phosphorylation could affect AtLOX2 catalytic activity. Overall, we propose that AtLOX2 Ser⁶⁰⁰ phosphorylation represents a key mechanism for the regulation of AtLOX2 activity and, thus, the jasmonate biosynthesis pathway and plant resistance.

Changes in Metabolic Profile of Rice Leaves Induced by Humic Acids

The use of humic substances in agriculture as a biostimulant emerged as one of the promising methods to promote sustainable production. Different molecular, biochemical, and physiological processes are triggered, resulting in nutrient efficiency use and protection against abiotic stress. Understanding plant changes promoted by humic substances is essential for innovative and tailored biostimulation technologies. Cell metabolites are the final target of the response chain, and the metabolomic approach can be helpful in unveiling pathways related to plant response. This study aimed to evaluate a global metabolic alteration of rice leaves induced by humic acids (HA) applied in a hydroponics system. Using ¹H NMR and GC-TOF/MS analysis, we observed a significant decrease in all main metabolites classes in leaves treated with HA, including lipids, organic acids, amino acids, and carbohydrates. Metabolites in higher concentrations in HA-treated plants are candidates as markers of HA bioactivity, including amino acids, intermediates of tricarboxylic acid cycle, and lipids, and aromatic compounds related to plant-stress response.

Combined physiological and metabolomic analysis reveals the effects of different biostimulants on maize production and reproduction

Plant biostimulants (PBs) are a potential strategy to improve crop growth and grain quality. In the present study, 100 mg/L trehalose, chitosan, humic acid and gamma-aminobutyric acid treatments were applied to analyze the effects of maize production and reproductive characteristics. The contents of nitrogen, phosphorus and potassium and grain quality were significantly affected by the PBs, but not yield. The seed germination rate of all PB treatments was significantly reduced, but the drought resistance of progeny seedlings was significantly improved, with humic acid having the strongest effect. Liquid chromatography mass spectrometry analysis indicated that the disruption of the tricarboxylic acid cycle, probably due to the blockage of intermediate anabolism, reduced the supply of energy and nutrients in the early stages of germination, thus inhibiting seed germination, while the increased resistance of the offspring seedlings may be due to the up-regulation of the synthesis of unsaturated fatty acids and alkaloids by humic acid treatment. This study revealed the similarity and heterogeneity of the effects of different PBs on nutrient accumulation, yield characteristics and grain quality of maize, providing guidance for the application of PBs in intensive and sustainable agricultural production.

Therapeutic Potential of Plant Oxylipins

For immobile plants, the main means of protection against adverse environmental factors is the biosynthesis of various secondary (specialized) metabolites. The extreme diversity and high biological activity of these metabolites determine the researchers' interest in plants as a source of therapeutic agents. Oxylipins, oxygenated derivatives of fatty acids, are particularly promising in this regard. Plant oxylipins, which are characterized by a diversity of chemical structures, can exert protective and therapeutic properties in animal cells. While the therapeutic potential of some classes of plant oxylipins, such as jasmonates and acetylenic oxylipins, has been analyzed thoroughly, other oxylipins are barely studied in this regard. Here, we present a comprehensive overview of the therapeutic potential of all major classes of plant oxylipins, including derivatives of acetylenic fatty acids, jasmonates, six- and nine-carbon aldehydes, oxy-, epoxy-, and hydroxy-derivatives of fatty acids, as well as spontaneously formed phytoprostanes and phytofurans. The presented analysis will provide an impetus for further research investigating the beneficial properties of these secondary metabolites and bringing them closer to practical applications.

A very-long-chain fatty acid synthesis gene, SD38, influences plant height by activating ethylene biosynthesis in rice

As an important trait in crop breeding, plant height is associated with lodging resistance and yield. With the identification and cloning of several semi-dwarfing genes, increasing numbers of semi-dwarf cultivars have emerged, which has led to a 'green revolution' in rice (Oryza sativa) production. In this study, we identified a rice semi-dwarf mutant, semi-dwarf 38 (sd38), which showed significantly reduced cell length. SD38 encodes a fatty acid elongase, β-ketoacyl-CoA synthase, which is involved in the synthesis of very-long-chain fatty acids (VLCFAs). Expression analysis showed that SD38 was localized on the membrane of the endoplasmic reticulum, and was expressed in all analyzed tissues with differential abundance. The mutation of SD38 affected lipid metabolism in the sd38 mutant. A functional complementarity test in Saccharomyces cerevisiae indicated that SD38 was capable of complementing the deficiency of ELO3p activity in BY4741-elo3 knockout yeast cells by participating in the synthesis of C24:0 VLCFA. Significant changes were observed in the expression of genes involved in ethylene synthesis, which resulted in reduced content of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) in the sd38 mutant. Exogenously supplied VLCFA (C24:0) increased the expression levels of OsACS3, OsACS4, and OsACO7 and the plant height of sd38 mutant seedlings, similar to the effect of exogenous application of ACC and ethephon. These results reveal a relationship among VLCFAs, ethylene biosynthesis, and plant height and improve our understanding of plant height development in crops.

Combining Metabolic Analysis With Biological Endpoints Provides a View Into the Drought Resistance Mechanism of Carex breviculmis

Metabolomics is an effective tool to test the response of plants to environmental stress; however, the relationships between metabolites and biological endpoints remained obscure in response to drought stress. Carex breviculmis is widely used in forage production, turf management, and landscape application and it is particularly resistant to drought stress. We investigated the metabolomic responses of C. breviculmis to drought stress by imposing a 22-day natural soil water loss. The results showed that water-deficit restrained plant growth, reducing plant height, leaf fresh weight, and total weight, however, increasing soluble protein content and malondialdehyde content. In total, 129 differential metabolites in the leaves were detected between drought and control using the Ultrahigh Performance Liquid Chromatography-Mass Spectrometer (UPLC-MS) method. Drought enhanced most of the primary and secondary metabolites in the differential metabolites. Almost all the sugars, amino acids, organic acids, phytohormones, nucleotides, phenylpropanoids and polyketides in the differential metabolites were negatively correlated with plant height and leaf fresh weight, while they were positively correlated with soluble protein content and malondialdehyde content. Metabolic pathway analysis showed that drought stress significantly affected aminoacyl-tRNA biosynthesis, TCA cycling, starch and sucrose metabolism. Our study is the first statement on metabolomic responses to drought stress in the drought-enduring plant C. breviculmis. According to the result, the coordination between diverse metabolic pathways in C. breviculmis enables the plant to adapt to a drought environment. This study will provide a systematic framework for explaining the metabolic plasticity and drought tolerance mechanisms of C. breviculmis under drought stress.

Transcriptomics unveiled metabolic perturbations in Desmodesmus quadricauda by sulfacetamide: Key functional genes involved in the tolerance and biodegradation process

Antibiotic contamination in the environment has significant adverse effects on benthic microorganisms, which causes dysfunction of normal ecological processes. However, in-depth molecular mechanisms underlying the potential ecological impacts of these emerging pollutants are poorly understood. In this study, metabolic perturbations in a freshwater microalga, Desmodesmus quadricauda by sulfacetamide (SFM) were investigated using transcriptomics. The results found 28 genes in the tricarboxylic acid cycle and oxidative phosphorolysis pathways were significantly downregulated by 3.97 to 6.07, and 2.47 to 5.99 folds by 0.1 and 1 mg L^-1 SFM, respectively. These results indicated that SFM disrupted the microalgal cellular activities through inhibition of energy metabolism. Whilst, the upregulated genes have been most enriched in porphyrin and chlorophyll metabolism (hemE, hemL, hemY, chlD, chlP, PAO, and CAO), and arachidonic acid metabolism (GGT1_5 and gpx). Expression of these genes was significantly upregulated by up to 3.36 times for tolerance against SFM. Moreover, the genes encoding decarboxylase, oxidoreductases, α-amylase, hydrolases, O-acetyltransferase, and lyase were upregulated by >2 folds, which can induce di/hydroxylation, decarboxylation, bond cleavage and deamination. These findings provide insights into the molecular mechanisms of the ecotoxicological effects of antibiotics on microalgae, and supply useful information for their environmental risk assessment and management.

Plant Host Traits Mediated by Foliar Fungal Symbionts and Secondary Metabolites

Fungal symbionts living inside plant leaves ("endophytes") can vary from beneficial to parasitic, but the mechanisms by which the fungi affect the plant host phenotype remain poorly understood. Chemical interactions are likely the proximal mechanism of interaction between foliar endophytes and the plant, as individual fungal strains are often exploited for their diverse secondary metabolite production. Here, we go beyond single strains to examine commonalities in how 16 fungal endophytes shift plant phenotypic traits such as growth and physiology, and how those relate to plant metabolomics profiles. We inoculated individual fungi on switchgrass, Panicum virgatum L. This created a limited range of plant growth and physiology (2-370% of fungus-free controls on average), but effects of most fungi overlapped, indicating functional similarities in unstressed conditions. Overall plant metabolomics profiles included almost 2000 metabolites, which were broadly correlated with plant traits across all the fungal treatments. Terpenoid-rich samples were associated with larger, more physiologically active plants and phenolic-rich samples were associated with smaller, less active plants. Only 47 metabolites were enriched in plants inoculated with fungi relative to fungus-free controls, and of these, Lasso regression identified 12 metabolites that explained from 14 to 43% of plant trait variation. Fungal long-chain fatty acids and sterol precursors were positively associated with plant photosynthesis, conductance, and shoot biomass, but negatively associated with survival. The phytohormone gibberellin, in contrast, was negatively associated with plant physiology and biomass. These results can inform ongoing efforts to develop metabolites as crop management tools, either by direct application or via breeding, by identifying how associations with more beneficial components of the microbiome may be affected.

Lipid profiling differentiates the effect of ambient microenriched copper on a coral as an advanced tool for biomonitoring

Copper can be beneficial or harmful to coral at environmentally relevant levels, making environmental monitoring a challenging. Membrane lipids make the cell a dynamic environment according to the circumstances; thus, the lipid profile should be indicative of an environmental/physiological state. To gain more insight into the copper effect on coral health and be a basis of biomonitoring, glycerophosphocholine profiling of coral exposed to microenriched copper levels was conducted in this study. The copper microenrichments resulted in a diacritical effect of decreasing carbonic anhydrase activity, following a supplementation effect, on coral lipid metabolism. Microdifferences in copper levels are critical to determine the coral metabolic state and were therefore included in this study. In addition, an excellent quantitative model correlating the coral lipid variation with the exposed copper levels or the induced physiological effect was obtained to demonstrate its performance for biomonitoring.

Colonization with non-mycorrhizal culturable endophytic fungi enhances orchid growth and indole acetic acid production

BACKGROUND

Symbiotic associations of endophytic fungi have been proved by possessing an ability to produce hormones and metabolites for their host plant. Members of the Orchidaceae are obligate mycorrhizal species but a non-mycorrhizal association needs more investigation for their ability to promote plant growth and produce plant growth hormones. In the present study, endophytic fungi were isolated from the roots of Dendrobium longicornu Lindl., to investigate the root colonizing activity and role in plant growth and development.

RESULTS

Among 23 fungal isolates were identified both by morphological and molecular technique as Penicillium sp., Fusarium sp., Coniochaeta sp., Alternaria sp., and Cladosporium sp. The dominate species were Coniochaeta sp. and Cladosporium sp. The dominant species as per the isolation was Coniochaeta sp. These fungal strains were screened for growth-promoting activity of Cymbidium aloifolium (plantlet) consider as cross genus interaction and Dendrobium longicornu (protocorms) as a host plant in in-vitro condition. Importantly, Cladosporium sp., and Coniochaeta sp. showed successful colonization and peloton formation with roots of C. aloifolium. Moreover, it also enhanced acclimatization of plantlets. Fungal elicitors from nine fungal isolates enhanced the growth of the in vitro grown protocorms of D. longicornu. Key bioactive compounds detected in the fungal colonized plant extract were 2H-pyran-2-one, Cyclopropanecarboxylic acid, Oleic Acid and d-Mannitol, which may have a potential role in plant-microbe interaction. All fungal endophytes were able to synthesize the indole acetic acid (IAA) in presence of tryptophan. Moreover, fungal extract DLCCR7 treated with DL-tryptophan yielded a greater IAA concentration of 43 μg per ml than the other extracts. The iaaM gene involved in IAA synthesis pathway was amplified using iaaM gene primers successfully from Alternaria sp., Cladosporium sp., and Coniochaeta sp.

CONCLUSIONS

Hence, this study confirms the production of IAA by endophytes and demonstrated their host as well as cross-genus plant growth-promoting potential by producing metabolites required for the growth of the plant.

Lipid profiling of coral symbiosomes in response to copper-induced carbon limitation: A metabolic effect of algal symbionts on the host immune status

Copper micropollutants are known to constrain coral's assimilation of carbonate, affecting the carbon available to algal symbionts and thus inducing a light stress. However, little is known regarding the physiological relevance of lipid metabolism in coral symbiotic algae in a carbon-limited state. Membrane lipids exhibit multiple physicochemical properties that are collectively responsible for the dynamic structure of cells depending on the physiological demands of the circumstances. To gain insight into lipid metabolism's importance in this regard, glycerophosphocholine (GPC) profiling of symbiosomes in coral (Seriatopora caliendrum) exposed to environmentally relevant copper levels (2.2-7.5 μg/L) for 4 days was performed in this study. Notably, reducing the number of 22:6-processing GPCs and increasing that of lyso-GPCs likely addressed the demands of metabolizing excess light energy, such as affecting the membrane dynamics to promote mitochondrial uncoupling. The decrease in 22:6-processing GPCs additionally protected cellular membranes from elevated oxidative stress, reducing their susceptibility to peroxidation and offsetting oxidized lipid-induced effects on membrane dynamics. The change in plasmanylcholines specifically localized within the symbiosome membrane also met the membrane requirements for responding to oxidative stress conditions. Moreover, increasing the 20:4-possessing plasmanylcholines and lysoplasmanylcholines and reducing the 22:6-possessing plasmanylcholines likely resulted in an imbalance of the immune reaction, influencing the coral-algae symbiosis given the role of such plasmanylcholines in cell signaling. In summary, carbon limitations induced by copper enrichment lead to a shift in the membrane lipid profile of coral symbiosomes, accommodating themselves to light stress conditions while compromising the symbiosis's stability.

ORA47 is a transcriptional regulator of a general stress response hub

Transcriptional regulators of the general stress response (GSR) reprogram the expression of selected genes to transduce informational signals into cellular events, ultimately manifested in a plant's ability to cope with environmental challenges. Identification of the core GSR regulatory proteins will uncover the principal modules and their mode of action in the establishment of adaptive responses. To define the GSR regulatory components, we employed a yeast-one-hybrid assay to identify the protein(s) binding to the previously established functional GSR motif, termed the rapid stress response element (RSRE). This led to the isolation of octadecanoid-responsive AP2/ERF-domain transcription factor 47 (ORA47), a methyl jasmonate inducible protein. Subsequently, ORA47 transcriptional activity was confirmed using the RSRE-driven luciferase (LUC) activity assay performed in the ORA47 loss- and gain-of-function lines introgressed into the 4xRSRE::Luc background. In addition, the prime contribution of CALMODULIN-BINDING TRANSCRIPTIONAL ACTIVATOR3 (CAMTA3) protein in the induction of RSRE was reaffirmed by genetic studies. Moreover, exogenous application of methyl jasmonate led to enhanced levels of ORA47 and CAMTA3 transcripts, as well as the induction of RSRE::LUC activity. Metabolic analyses illustrated the reciprocal functional inputs of ORA47 and CAMTA3 in increasing JA levels. Lastly, transient assays identified JASMONATE ZIM-domain1 (JAZ1) as a repressor of RSRE::LUC activity. Collectively, the present study provides fresh insight into the initial features of the mechanism that transduces informational signals into adaptive responses. This mechanism involves the functional interplay between the JA biosynthesis/signaling cascade and the transcriptional reprogramming that potentiates GSR. Furthermore, these findings offer a window into the role of intraorganellar communication in the establishment of adaptive responses.

Effects of arbuscular mycorrhizal fungi on frond antimony enrichment, morphology, and proteomics in Pteris cretica var. nervosa during antimony phytoremediation

Pteris cretica var. nervosa is a dominant fern species found in antimony (Sb) mining areas, capable of forming symbiosis with arbuscular mycorrhizal fungi (AMF), especially with those members of the Glomus genus. Despite this fern's relevance and the potential contribution of mycorrhizal symbiosis to phytoremediation, the AMF's impact on P. var. nervosa phytoremediation of Sb remains unknown. Here, we exposed P. var. nervosa to different concentrations of Sb for 6 months. Our results showed that Sb reduced shoot biomass, enlarged the root/shoot ratio, and disrupted the fronds' intracellular structure. AMF inoculation, however, was able to moderate these phenotypic changes and increased the accumulation level of Sb in plants. From a proteomics analysis of this plant's fronds, a total of 283 proteins were identified. Notably, those proteins with catalytic function, carbon fixing and ATP metabolic function were highly enriched. K-means clustering demonstrated protein-changing patterns involved in multiple metabolic pathways during exposure to Sb. Further, these patterns can be moderated by AMF inoculation. Pearson correlations were used to assess the plant biomarkers-soil Sb relationships; This revealed a strong correlation between ribosome alteration and the root/shoot ratio when inoculated with AMF, and a positive correlation between photosynthesis proteins and chlorophyll (SPAD value). Our results indicate AMF could moderate the fronds impairment by maintaining the sufficient protein levels for ribosomal functioning, photosynthesis activity and to counter ROS production. We demonstrate the effective use of AMF associated with P. cretica var. nervosa for Sb phytoremediation and the potential of applying proteomics to better understand the mechanism behind this symbiotic plant physiological response.

Plant immunity inducers: from discovery to agricultural application

While conventional chemical fungicides directly eliminate pathogens, plant immunity inducers activate or prime plant immunity. In recent years, considerable progress has been made in understanding the mechanisms of immune regulation in plants. The development and application of plant immunity inducers based on the principles of plant immunity represent a new field in plant protection research. In this review, we describe the mechanisms of plant immunity inducers in terms of plant immune system activation, summarize the various classes of reported plant immunity inducers (proteins, oligosaccharides, chemicals, and lipids), and review methods for the identification or synthesis of plant immunity inducers. The current situation, new strategies, and future prospects in the development and application of plant immunity inducers are also discussed.

Transcriptomic Complexity in Strawberry Fruit Development and Maturation Revealed by Nanopore Sequencing

The use of alternative transcription start or termination sites (aTSS or aTTS) as well as alternative splicing (AS) produce diverse transcript isoforms, playing indispensable roles in the plant development and environmental adaptations. Despite the advances in the finding of the genome-wide alternatively spliced genes in strawberry, it remains unexplored how AS responds to the developmental cues and what relevance do these outcomes have to the gene function. In this study, we have systematically investigated the transcriptome complexity using long-read Oxford Nanopore Technologies along the four successive developmental stages. The full-length cDNA sequencing results unraveled thousands of previously unexplored transcript isoforms raised from aTSS, aTTS, and AS. The relative contributions of these three processes to the complexity of strawberry fruit transcripts were compared. The aTSS and aTTS were more abundant than the AS. Differentially expressed transcripts unraveled the key transitional role of the white fruit stage. Isoform switches of transcripts from 757 genes were observed. They were associated with protein-coding potential change and domain gain or loss as the main consequences. Those genes with switched isoforms take part in the key processes of maturation in the late stages. A case study using yeast two hybrid analysis supported the functional divergence of the two isoforms of the B-box protein 22. Our results provided a new comprehensive overview of the dynamic transcriptomic landscape during strawberry fruit development and maturation.

Conformational Change of Tetratricopeptide Repeats Region Triggers Activation of Phytochrome-Associated Protein Phosphatase 5

Phytochrome activity is not only controlled by light but also by post-translational modifications, e. g. phosphorylation. One of the phosphatases responsible for plant phytochrome dephosphorylation and thereby increased activity is the phytochrome-associated protein phosphatase 5 (PAPP5). We show that PAPP5 recognizes phospho-site mimicking mutants of phytochrome B, when being activated by arachidonic acid (AA). Addition of AA to PAPP5 decreases the α-helical content as tracked by CD-spectroscopy. These changes correspond to conformational changes of the regulatory tetratricopeptide repeats (TPR) region as shown by mapping data from hydrogen deuterium exchange mass spectrometry onto a 3.0 Å crystal structure of PAPP5. Surprisingly, parts of the linker between the TPR and PP2A domains and of the so-called C-terminal inhibitory motif exhibit reduced deuterium uptake upon AA-binding. Molecular dynamics analyses of PAPP5 complexed to a phyB phosphopeptide show that this C-terminal motif remains associated with the TPR region in the substrate bound state, suggesting that this motif merely serves for restricting the orientations of the TPR region relative to the catalytic PP2A domain. Given the high similarity to mammalian PP5 these data from a plant ortholog show that the activation mode of these PPP-type protein phosphatases is highly conserved.

Metabolic responses of date palm (Phoenix dactylifera L.) leaves to drought differ in summer and winter climate

Drought negatively impacts growth and productivity of plants, particularly in arid and semi-arid regions. Although drought events can take place in summer and winter, differences in the impact of drought on physiological processes between seasons are largely unknown. The aim of this study was to elucidate metabolic strategies of date palms in response to drought in summer and winter season. To identify such differences, we exposed date palm seedlings to a drought-recovery regime, both in simulated summer and winter climate. Leaf hydration, carbon discrimination (${\Delta}$13C), and primary and secondary metabolite composition and contents were analyzed. Depending on season, drought differently affected physiological and biochemical traits of the leaves. In summer, drought induced significantly decreased leaf hydration, concentrations of ascorbate, most sugars, primary and secondary organic acids, as well as phenolic compounds, while thiol, amino acid, raffinose and individual fatty acid contents were increased compared with well-watered plants. In winter, drought had no effect on leaf hydration, ascorbate and fatty acids contents, but resulted in increased foliar thiol and amino acid levels as observed in summer. Compared with winter, foliar traits of plants exposed to drought in summer only partly recovered after re-watering. Memory effects on water relations, and primary and secondary metabolites seem to prepare foliar traits of date palms for repeated drought events in summer. Apparently, a well-orchestrated metabolic network, including the anti-oxidative system, compatible solutes accumulation and osmotic adjustment, and maintenance of cell-membrane stability strongly reduces the susceptibility of date palms to drought. These mechanisms of drought compensation may be more frequently required in summer.

Molecular imaging of plant-microbe interactions on the Brachypodium seed surface

Plant growth-promoting rhizobacteria (PGPR) play a crucial role in biological control and pathogenic defense on and within plant tissues, however the mechanisms by which plants associate with PGPR to elicit such beneficial effects need further study. Here, we present time-of-flight secondary ion mass spectrometry (ToF-SIMS) imaging of Brachypodium distachyon (Brachypodium) seeds with and without exposure to two model PGPR, i.e., Gram-negative Pseudomonas fluorescens SBW25 (P.) and Gram-positive Arthrobacter chlorophenolicus A6 (A.). Delayed image extraction was used to image PGPR-treated seed sections to reveal morphological changes. ToF-SIMS spectral comparison, principal component analysis (PCA), and two-dimensional (2D) imaging show that the selected PGPR have different effects on the host seed surface, resulting in changes in chemical composition and morphology. Metabolite products and biomarkers, such as flavonoids, phenolic compounds, fatty acids, and indole-3-acetic acid (IAA), were identified on the PGPR-treated seed surfaces. These compounds have different distributions on the Brachypodium seed surface for the two PGPR, indicating that the different bacteria elicit distinct responses from the host. Our results illustrate that ToF-SIMS is an effective tool to study plant-microbe interactions and to provide insightful information with submicrometer lateral resolution of the chemical distributions associated with morphological features, potentially offering a new way to study the mechanisms underlying beneficial roles of PGPR.

Dietary Polyunsaturated Fatty Acids (PUFAs): Uses and Potential Health Benefits

PURPOSE OF REVIEW

Polyunsaturated fatty acids (PUFAs) are obtained from various sources, which can be incorporated in the routine diet to maintain the health. They provide protection from several diseases like osteoarthritis, cancer, and autoimmune disorders. Major focus is given to the PUFAs omega-3 (ω-3) and omega-6 (ω-6) fatty acids which are available in both terrestrial and in the marine environment. The main concern of this article is to review the key scientific reports in context with the human health consequences and advantages of the food sources of ω-3 and ω-6 fatty acids.

RECENT FINDINGS

ω-3 and ω-6 fatty acids are consumed by the population globally in the form of foods that are rich in fatty acids. Their nutritional effects have the capability to improve the physical functioning and metabolic rate of the body. These PUFAs contribute in various cellular activities like cell signaling, structural integrity and fluidity of cell membrane, the regulation of blood pressure, glucose level, the nervous system, inflammatory reactions, and hematic clotting. Animal and cell-based models represent that ω-3 and ω-6 PUFAs can regulate the skeletal muscle metabolism. The main concern of this article is to review the key scientific reports in context with the human health consequences and advantages of the food sources of ω-3 and ω-6 fatty acids.

Mono-Locus and Pyramided Resistant Grapevine Cultivars Reveal Early Putative Biomarkers Upon Artificial Inoculation With Plasmopara viticola

One of the most economically important grapevine diseases is Downy mildew (DM) caused by the oomycete Plasmopara viticola. A strategy to reduce the use of fungicides to compensate for the high susceptibility of V. vinifera is the selection of grapevine varieties showing pathogen-specific resistance. We applied a metabolomics approach to evaluate the metabolic modulation in mono-locus resistant genotypes carrying one locus associated with P. viticola resistance (Rpv) (BC4- Rpv1, Bianca- Rpv3-1, F12P160- Rpv12, Solaris- Rpv10), as well as in pyramided resistant genotypes carrying more than one Rpv (F12P60- Rpv3-1; Rpv12 and F12P127- Rpv3-1, Rpv3-3; Rpv10) taking as a reference the susceptible genotype Pinot Noir. In order to understand if different sources of resistance are associated with different degrees of resistance and, implicitly, with different responses to the pathogen, we considered the most important classes of plant metabolite primary compounds, lipids, phenols and volatile organic compounds at 0, 12, 48, and 96 h post-artificial inoculation (hpi). We identified 264 modulated compounds; among these, 22 metabolites were found accumulated in significant quantities in the resistant cultivars compared to Pinot Noir. In mono-locus genotypes, the highest modulation of the metabolites was noticed at 48 and 96 hpi, except for Solaris, that showed a behavior similar to the pyramided genotypes in which the changes started to occur as early as 12 hpi. Bianca, Solaris and F12P60 showed the highest number of interesting compounds accumulated after the artificial infection and with a putative effect against the pathogen. In contrast, Pinot Noir showed a less effective defense response in containing DM growth.

EPIP-Evoked Modifications of Redox, Lipid, and Pectin Homeostasis in the Abscission Zone of Lupine Flowers

Yellow lupine is a great model for abscission-related research given that excessive flower abortion reduces its yield. It has been previously shown that the EPIP peptide, a fragment of LlIDL (INFLORESCENCE DEFICIENT IN ABSCISSION) amino-acid sequence, is a sufficient molecule to induce flower abortion, however, the question remains: What are the exact changes evoked by this peptide locally in abscission zone (AZ) cells? Therefore, we used EPIP peptide to monitor specific modifications accompanied by early steps of flower abscission directly in the AZ. EPIP stimulates the downstream elements of the pathway-HAESA and MITOGEN-ACTIVATED PROTEIN KINASE6 and induces cellular symptoms indicating AZ activation. The EPIP treatment disrupts redox homeostasis, involving the accumulation of H2O2 and upregulation of the enzymatic antioxidant system including superoxide dismutase, catalase, and ascorbate peroxidase. A weakening of the cell wall structure in response to EPIP is reflected by pectin demethylation, while a changing pattern of fatty acids and acyl lipids composition suggests a modification of lipid metabolism. Notably, the formation of a signaling molecule-phosphatidic acid is induced locally in EPIP-treated AZ. Collectively, all these changes indicate the switching of several metabolic and signaling pathways directly in the AZ in response to EPIP, which inevitably leads to flower abscission.

Brachypodium Phenylalanine Ammonia Lyase (PAL) Promotes Antiviral Defenses against Panicum mosaic virus and Its Satellites

Brachypodium distachyon has recently emerged as a premier model plant for monocot biology, akin to Arabidopsis thaliana We previously reported genome-wide transcriptomic and alternative splicing changes occurring in Brachypodium during compatible infections with Panicum mosaic virus (PMV) and its satellite virus (SPMV). Here, we dissected the role of Brachypodium phenylalanine ammonia lyase 1 (PAL1), a key enzyme for phenylpropanoid and salicylic acid (SA) biosynthesis and the induction of plant defenses. Targeted metabolomics profiling of PMV-infected and PMV- plus SPMV-infected (PMV/SPMV) Brachypodium plants revealed enhanced levels of multiple defense-related hormones and metabolites such as cinnamic acid, SA, and fatty acids and lignin precursors during disease progression. The virus-induced accumulation of SA and lignin was significantly suppressed upon knockdown of B. distachyon PAL1 (BdPAL1) using RNA interference (RNAi). The compromised SA accumulation in PMV/SPMV-infected BdPAL1 RNAi plants correlated with weaker induction of multiple SA-related defense gene markers (pathogenesis related 1 [PR-1], PR-3, PR-5, and WRKY75) and enhanced susceptibility to PMV/SPMV compared to that of wild-type (WT) plants. Furthermore, exogenous application of SA alleviated the PMV/SPMV necrotic disease phenotypes and delayed plant death caused by single and mixed infections. Together, our results support an antiviral role for BdPAL1 during compatible host-virus interaction, perhaps as a last resort attempt to rescue the infected plant.IMPORTANCE Although the role of plant defense mechanisms against viruses are relatively well studied in dicots and in incompatible plant-microbe interactions, studies of their roles in compatible interactions and in grasses are lagging behind. In this study, we leveraged the emerging grass model Brachypodium and genetic resources to dissect Panicum mosaic virus (PMV)- and its satellite virus (SPMV)-compatible grass-virus interactions. We found a significant role for PAL1 in the production of salicylic acid (SA) in response to PMV/SPMV infections and that SA is an essential component of the defense response preventing the plant from succumbing to viral infection. Our results suggest a convergent role for the SA defense pathway in both compatible and incompatible plant-virus interactions and underscore the utility of Brachypodium for grass-virus biology.