Comparative transcriptomics and metabolomics reveal specialized metabolite drought stress responses in switchgrass (Panicum virgatum)

Dehydration priming remodels protein abundance and phosphorylation level regulating tolerance to subsequent dehydration or salt stress in creeping bentgrass

Dehydration priming (DP) induces stress memory which plays a positive role in plant adaptability, but it is not well understood how DP differentially regulates subsequent dehydration (cis priming) or salt (trans priming) tolerance at the post-translational level. Purpose of this study was to identify proteins, phosphorylation levels and sites, and relevant metabolic pathways for DP-induced dehydration or salt tolerance in Agrostis stolonifera. DP-induced differentially regulated proteins (DRPs) were mostly located in the cytoplasm, chloroplast, and cell membrane, and differentially regulated phosphoproteins (DRPPs) were mostly nuclear proteins and cytoplasmic proteins. DP regulated common phosphorylation sites ([SP] and [RxxS]) under dehydration and salt conditions and also individually affected 8 or 11 phosphorylation sites under dehydration or salt stress. DP-regulated DRPPs were mainly rich in glycolysis and glutathione metabolism pathways, RNA splicing, and dynamin family proteins under dehydration stress, whereas DP-regulated salt tolerance was mainly related to chlorophyll metabolism, photosynthesis, MAPK signaling cascade, and ABC transporter I family at the phosphorylation level. In addition, the DP also significantly up-regulated phosphorylation of histones (ATXR3 and SETD1A) in response to subsequent dehydration and salt stress as well as abundances of antioxidant enzymes, dynamin family protein, and KCS6 under dehydration stress or abundances of PETE, HMGA, XTH, and ABCI6 under salt stress, respectively. Transcriptomics analysis further indicated that DP-regulated dehydration or salt tolerance was also related to transcriptional regulation in the early stage. Current results provided better understanding of the role of stress memory in plant adaptability to repeated or crossed stress via post-translational modifications (PTMs). SIGNIFICANCE: Recurrent moderate drought may buffer drought legacies in many plant species. When plants were exposed to repeated drought stress, their adaptability to subsequent stress could be enhanced, which is known as "stress memory". Dehydration priming has been found to be an important approach to induce stress memory. Current results provided better understanding of the role of stress memory in plant adaptability to repeated or crossed stress via post-translational modifications.

Integrated transcriptomic and metabolomic analyses reveal that MsSPHK1 - A sphingosine kinase gene negatively regulates drought tolerance in alfalfa (Medicago sativa L.)

Alfalfa is a valuable forage crop but voluntarily affected by drought. Understanding the mechanisms of drought resistance in alfalfa is crucial for improving resilient cultivars. In our study, we used four distinct alfalfa accessions two drought-tolerance (DT) and two drought-sensitive (DS) and identified transcriptional modules and candidate genes associated with the drought tolerance in the DS from transcriptomic analyses. Our metabolic profiling of 520 metabolites revealed significant variations between the DS and DT groups, particularly in the levels of flavonoids and nucleotides and their derivatives. The integrated analysis of transcriptome and metabolome analysis revealed that the glycine, serine, and threonine metabolism and the sphingolipid metabolism are associated with the drought resistance. When drought stress occurs, MsSRR (MsG 0180002649.01) and MsSPHK1 (MsG 0280006618.01) are significantly up-regulated, L-serine and dihydrosphingosine (DHS) significantly down-regulated in DS. By silencing the MsSPHK1 gene we found the drought resistance was significantly improved. This was evidenced by a significant increase in the activity of antioxidant enzymes such as SOD, POD, and CAT, compared to the control group. Additionally, the photosynthetic rate, stomatal conductance, and efficiency of photosystem II measured by Fv/Fm, phi2 and qL, were significantly higher in the silenced plants than in the control group. In conclusion, our results suggest that the increased level of dihydrosphingosine improves alfalfa resistance to drought stress. Moreover, the negative regulatory role of MsSPHK1 in drought tolerance provides a promising target for genetic manipulation to enhance the resilience of alfalfa to drought stress.

Integrating Physiology, Transcriptome, and Metabolome Analyses Reveals the Drought Response in Two Quinoa Cultivars with Contrasting Drought Tolerance

Quinoa (Chenopodium quinoa Willd.) is an annual broadleaf plant belonging to the Amaranthaceae family. It is a nutritious food crop and is considered to be drought-tolerant, but drought is still one of the most important abiotic stress factors limiting its yield. Quinoa responses to drought are related to drought intensity and genotype. This study used two different drought-responsive quinoa cultivars, LL1 (drought-tolerant) and ZK1 (drought-sensitive), to reveal the important mechanisms of drought response in quinoa by combining physiological, transcriptomic, and metabolomic analyses. The physiological analysis indicated that Chla/Chlb might be important for drought tolerance in quinoa. A total of 1756 and 764 differentially expressed genes (DEGs) were identified in LL1 and ZK1, respectively. GO (Gene Ontology) enrichment analysis identified 52 common GO terms, but response to abscisic acid (GO:0009737) and response to osmotic stress (GO:0006970) were only enriched in LL1. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis revealed that glycerophospholipid metabolism (ko00564) and cysteine and methionine metabolism (ko00270) ranked at the top of the list in both cultivars. A total of 1844 metabolites were identified by metabolomic analysis. "Lipids and lipid-like" molecules had the highest proportions. The DEMs in LL1 and ZK1 were mainly categorized 6 and 4 Human Metabolome Database (HMDB) superclasses, respectively. KEGG analysis revealed that the 'α-linolenic acid metabolism' was enriched in both LL1 and ZK1. Joint KEGG analysis also revealed that the 'α-linolenic acid metabolism' pathway was enriched by both the DEGs and DEMs of LL1. There were 17 DEGs and 8 DEMs enriched in this pathway, and methyl jasmonate (MeJA) may play an important role in the drought response of quinoa. This study will provide information for the identification of drought resistance in quinoa, research on the molecular mechanism of drought resistance, and genetic breeding for drought resistance in quinoa.

Comparative Metabolome and Transcriptome Analysis Revealed the Accumulative Mechanism of Rubusoside in Chinese Sweet Tea

Terpenoids are important secondary metabolites in Rubus. Rubusoside is a relatively specific diterpenoid bioactive component in the leaves of Chinese Sweet Tea (Rubus suavissimus). However, the terpenoid anabolic pathway of Rubus and the molecular mechanism underlying the specific accumulation of rubusoside in R. suavissimus remain unclear. Here, metabolomics and transcriptomics analyses were performed on differences in terpenoid metabolism levels between R. suavissimus (sweet leaves) and Rubus chingii (bitter leaves). Steviol glycosides and goshonosides primarily accumulated in R. suavissimus and R. chingii, respectively. Three pairs of highly homologous glycosyltransferase genes (UGT85A57, UGT75L20, and UGT75T4) associated with rubusoside biosynthesis in the two Rubus species were identified. The three pairs of UGT proteins in both species could glycosylate steviol. Thus, the transcriptional regulation of UGTs in R. suavissimus appears to play a pivotal role in rubusoside accumulation. Our findings provide insights into the differences in terpenoid metabolism between R. suavissimus and R. chingii and reveal the molecular mechanism of rubusoside accumulation in R. suavissimus.

CYP76BK1 orthologs catalyze furan and lactone ring formation in clerodane diterpenoids across the mint family

The Lamiaceae (mint family) is the largest known source of furanoclerodanes, a subset of clerodane diterpenoids with broad bioactivities including insect antifeedant properties. The Ajugoideae subfamily, in particular, accumulates significant numbers of structurally related furanoclerodanes. The biosynthetic capacity for formation of these diterpenoids is retained across most Lamiaceae subfamilies, including the early-diverging Callicarpoideae which forms a sister clade to the rest of Lamiaceae. VacCYP76BK1, a cytochrome P450 monooxygenase from Vitex agnus-castus, was previously found to catalyze the formation of the proposed precursor to furan and lactone-containing labdane diterpenoids. Through transcriptome-guided pathway exploration, we identified orthologs of VacCYP76BK1 in Ajuga reptans and Callicarpa americana. Functional characterization demonstrated that both could catalyze the oxidative cyclization of clerodane backbones to yield a furan ring. Subsequent investigation revealed a total of 10 CYP76BK1 orthologs across six Lamiaceae subfamilies. Through analysis of available chromosome-scale genomes, we identified four CYP76BK1 members as syntelogs within a conserved syntenic block across divergent subfamilies. This suggests an evolutionary lineage that predates the speciation of the Lamiaceae. Functional characterization of the CYP76BK1 orthologs affirmed conservation of function, as all catalyzed furan ring formation. Additionally, some orthologs yielded two novel lactone ring moieties. The presence of the CYP76BK1 orthologs across Lamiaceae subfamilies closely overlaps with the distribution of reported furanoclerodanes. Together, the activities and distribution of the CYP76BK1 orthologs identified here support their central role in furanoclerodane biosynthesis within the Lamiaceae family. Our findings lay the groundwork for biotechnological applications to harness the economic potential of this promising class of compounds.

Impact of nitrogen rates on biosynthesis pathways: A comparative study of diterpene synthases in clerodane diterpenoids and enzymes in benzylisoquinoline alkaloids

Tinospora sagittata is rich in secondary metabolites used in traditional medicine. However, environmental factors impact key enzymes in metabolite synthesis, highlighting the need for improved growth conditions. This study employs transcriptomics and metabolomics to assess nitrogen's impact on enzymes in secondary metabolites biosynthesis pathways. The gene expressions of berberine bridge enzymes (BBEs) like TsBBE2 had peak expression in low nitrogen treatments (A0 and A1) but were absent in higher nitrogen treatments (A2 and A3). Similar trends were observed for other enzymes such as (S)-scoulerine 9-O-methyltransferase (TsCMT3), Tetrahydroberberine oxidase (TsSTOX), and Columbamine O-methyltransferase (TsCoCOMT2-4) in response to nitrogen levels. In examining gene families related to diterpene synthases (diTPS), 1-deoxyxylulose 5-phosphate synthase (TsDXR1) expression increased with higher nitrogen fertilizer, while TsDXR2 peaked at maximal nitrogen levels. Geranylgeranyl diphosphate synthase (TsGGPP3 and TsGGPP5) decreased with nitrogen levels. (-)-kolavenyl diphosphate synthase (KPS) genes had higher expression in treatments, while ent-kaurene synthase (KSL) genes, especially TsKSL1 and TsKSL2, showed higher expression in control conditions with lower nitrogen fertilizer. Metabolite analysis confirmed more upregulated compounds in A3 compared to A0. These findings have practical implications for agriculture and pharmaceuticals, highlighting the link between nitrogen fertilization and specialized metabolism in medicinal plants.

Multi-omics integration analysis reveals the molecular mechanisms of drought adaptation in homologous tetraploid alfalfa(Medicago sativa 'Xinjiang-Daye')

Drought stress is a predominant abiotic factor leading to decreased alfalfa yield. Genomic ploidy differences contribute to varying adaptation mechanisms of different alfalfa cultivars to drought conditions. This study employed a multi-omics approach to characterize the molecular basis of drought tolerance in a tetraploid variant of alfalfa (Medicago sativa, Xinjiang-Daye). Under drought treatment, a total of 4446 genes, 859 proteins, and 524 metabolites showed significant differences in abundance. Integrative analysis of the multi-omics data revealed that regulatory modules involved in flavonoid biosynthesis, plant hormone signalling transduction, linoleic acid metabolism, and amino acid biosynthesis play crucial roles in alfalfa adaptation to drought stress. The severity of drought led to the substantial accumulation of flavonoids, plant hormones, free fatty acids, amino acids, and their derivatives in the leaves. Genes such as PAL, 4CL, CHI, CHS, PP2C, ARF_3, and AHP_4 play pivotal regulatory roles in flavonoid biosynthesis and hormone signalling pathways. Differential expression of the LOX gene emerged as a key factor in the elevated levels of free fatty acids. Upregulation of P5CS_1 and GOT1/2 contributed significantly to the accumulation of Pro and Phe contents. ERF19 emerged as a principal positive regulator governing the synthesis of the aforementioned compounds. Furthermore, observations suggest that Xinjiang-Daye alfalfa may exhibit widespread post-transcriptional regulatory mechanisms in adapting to drought stress. The study findings unveil the critical mechanisms by which Xinjiang-Daye alfalfa adapts to drought stress, offering novel insights for the improvement of alfalfa germplasm resources.

CYP76BK1 orthologs catalyze furan and lactone ring formation in clerodane diterpenoids across the mint family

The Lamiaceae (mint family) is the largest known source of furanoclerodanes, a subset of clerodane diterpenoids with broad bioactivities including insect antifeedant properties. The Ajugoideae subfamily, in particular, accumulates significant numbers of structurally related furanoclerodanes. The biosynthetic capacity for formation of these diterpenoids is retained across most Lamiaceae subfamilies, including the early-diverging Callicarpoideae which forms a sister clade to the rest of Lamiaceae. VacCYP76BK1, a cytochrome P450 monooxygenase from Vitex agnus-castus, was previously found to catalyze the formation of the proposed precursor to furan and lactone-containing labdane diterpenoids. Through transcriptome-guided pathway exploration, we identified orthologs of VacCYP76BK1 in Ajuga reptans and Callicarpa americana. Functional characterization demonstrated that both could catalyze the oxidative cyclization of clerodane backbones to yield a furan ring. Subsequent investigation revealed a total of ten CYP76BK1 orthologs across six Lamiaceae subfamilies. Through analysis of available chromosome-scale genomes, we identified four CYP76BK1 members as syntelogs within a conserved syntenic block across divergent subfamilies. This suggests an evolutionary lineage that predates the speciation of the Lamiaceae. Functional characterization of the CYP76BK1 orthologs affirmed conservation of function, as all catalyzed furan ring formation. Additionally, some orthologs yielded two novel lactone ring moieties. The presence of the CYP76BK1 orthologs across Lamiaceae subfamilies closely overlaps with the distribution of reported furanoclerodanes. Together, the activities and distribution of the CYP76BK1 orthologs identified here support their central role in furanoclerodane biosynthesis within the Lamiaceae family. Our findings lay the groundwork for biotechnological applications to harness the economic potential of this promising class of compounds.

Hordedane diterpenoid phytoalexins restrict Fusarium graminearum infection but enhance Bipolaris sorokiniana colonization of barley roots

Plant immunity is a multilayered process that includes recognition of patterns or effectors from pathogens to elicit defense responses. These include the induction of a cocktail of defense metabolites that typically restrict pathogen virulence. Here, we investigate the interaction between barley roots and the fungal pathogens Bipolaris sorokiniana (Bs) and Fusarium graminearum (Fg) at the metabolite level. We identify hordedanes, a previously undescribed set of labdane-related diterpenoids with antimicrobial properties, as critical players in these interactions. Infection of barley roots by Bs and Fg elicits hordedane synthesis from a 600-kb gene cluster. Heterologous reconstruction of the biosynthesis pathway in yeast and Nicotiana benthamiana produced several hordedanes, including one of the most functionally decorated products 19-β-hydroxy-hordetrienoic acid (19-OH-HTA). Barley mutants in the diterpene synthase genes of this cluster are unable to produce hordedanes but, unexpectedly, show reduced Bs colonization. By contrast, colonization by Fusarium graminearum, another fungal pathogen of barley and wheat, is 4-fold higher in the mutants completely lacking hordedanes. Accordingly, 19-OH-HTA enhances both germination and growth of Bs, whereas it inhibits other pathogenic fungi, including Fg. Analysis of microscopy and transcriptomics data suggest that hordedanes delay the necrotrophic phase of Bs. Taken together, these results show that adapted pathogens such as Bs can subvert plant metabolic defenses to facilitate root colonization.

Disentangling plant- and environment-mediated drivers of active rhizosphere bacterial community dynamics during short-term drought

Mitigating the effects of climate stress on crops is important for global food security. The microbiome associated with plant roots, the rhizobiome, can harbor beneficial microbes that alleviate stress, but the factors influencing their recruitment are unclear. We conducted a greenhouse experiment using field soil with a legacy of growing switchgrass and common bean to investigate the impact of short-term drought severity on the recruitment of active bacterial rhizobiome members. We applied 16S rRNA and 16S rRNA gene sequencing for both crops and metabolite profiling for switchgrass. We included planted and unplanted conditions to distinguish environment- versus plant-mediated rhizobiome drivers. Differences in community structure were observed between crops and between drought and watered and planted and unplanted treatments within crops. Despite crop-specific communities, drought rhizobiome dynamics were similar across the two crops. The presence of a plant more strongly explained the rhizobiome variation in bean (17%) than in switchgrass (3%), with a small effect of plant mediation during drought observed only for the bean rhizobiome. The switchgrass rhizobiome was stable despite changes in rhizosphere metabolite profiles between planted and unplanted treatments. We conclude that rhizobiome responses to short-term drought are crop-specific, with possible decoupling of plant exudation from rhizobiome responses.

Multifaceted insights into the environmental adaptability of Arnebia guttata under drought stress

Introduction

Global warming has led to increased environmental stresses on plants, notably drought. This affects plant distribution and species adaptability, with some medicinal plants showing enhanced drought tolerance and increased medicinal components. In this pioneering study, we delve into the intricate tapestry of Arnebia guttata, a medicinal plant renowned for its resilience in arid environments. By fusing a rich historical narrative with cutting-edge analytical methodologies, this research endeavors to demystify the plant's intricate response to drought stress, illuminating its profound implications for medicinal valorization.

Methods

The methodology includes a comprehensive textual research and resource investigation of A. guttata, regionalization studies, field sample distribution analysis, transcriptome and metabolome profiling, rhizosphere soil microbiome analysis, and drought stress experiments. Advanced computational tools like ArcGIS, MaxEnt, and various bioinformatics software were utilized for data analysis and modeling.

Results

The study identified significant genetic variations among A. guttata samples from different regions, correlating with environmental factors, particularly precipitation during the warmest quarter (BIO18). Metabolomic analysis revealed marked differences in metabolite profiles, including shikonin content, which is crucial for the plant's medicinal properties. Soil microbial community analysis showed variations that could impact plant metabolism and stress response. Drought stress experiments demonstrated A. guttata's resilience and its ability to modulate metabolic pathways to enhance drought tolerance.

Discussion

The findings underscore the complex interplay between genetic makeup, environmental factors, and microbial communities in shaping A. guttata's adaptability and medicinal value. The study provides insights into how drought stress influences the synthesis of active compounds and suggests that moderate stress could enhance the plant's medicinal properties. Predictive modeling indicates future suitable growth areas for A. guttata, aiding in resource management and conservation efforts. The research contributes to the sustainable development of medicinal resources and offers strategies for improving the cultivation of A. guttata.

Joint transcriptomic and metabolomic analysis provides new insights into drought resistance in watermelon (Citrullus lanatus)

Introduction

Watermelon is an annual vine of the family Cucurbitaceae. Watermelon plants produce a fruit that people love and have important nutritional and economic value. With global warming and deterioration of the ecological environment, abiotic stresses, including drought, have become important factors that impact the yield and quality of watermelon plants. Previous research on watermelon drought resistance has included analyzing homologous genes based on known drought-responsive genes and pathways in other species.

Methods

However, identifying key pathways and genes involved in watermelon drought resistance through high-throughput omics methods is particularly important. In this study, RNA-seq and metabolomic analysis were performed on watermelon plants at five time points (0 h, 1 h, 6 h, 12 h and 24 h) before and after drought stress.

Results

Transcriptomic analysis revealed 7829 differentially expressed genes (DEGs) at the five time points. The DEGs were grouped into five clusters using the k-means clustering algorithm. The functional category for each cluster was annotated based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database; different clusters were associated with different time points after stress. A total of 949 metabolites were divided into 10 categories, with lipids and lipid-like molecules accounting for the most metabolites. Differential expression analysis revealed 22 differentially regulated metabolites (DRMs) among the five time points. Through joint analysis of RNA-seq and metabolome data, the 6-h period was identified as the critical period for watermelon drought resistance, and the starch and sucrose metabolism, plant hormone signal transduction and photosynthesis pathways were identified as important regulatory pathways involved in watermelon drought resistance. In addition, 15 candidate genes associated with watermelon drought resistance were identified through joint RNA-seq and metabolome analysis combined with weighted correlation network analysis (WGCNA). Four of these genes encode transcription factors, including bHLH (Cla97C03G068160), MYB (Cla97C01G002440), HSP (Cla97C02G033390) and GRF (Cla97C02G042620), one key gene in the ABA pathway, SnRK2-4 (Cla97C10G186750), and the GP-2 gene (Cla97C05G105810), which is involved in the starch and sucrose metabolism pathway.

Discussion

In summary, our study provides a theoretical basis for elucidating the molecular mechanisms underlying drought resistance in watermelon plants and provides new genetic resources for the study of drought resistance in this crop.

Transcriptomic analysis of ncRNAs and mRNAs interactions during drought stress in switchgrass

Switchgrass (Panicum virgatum L.) plays a pivotal role as a bioenergy feedstock in the production of cellulosic ethanol and contributes significantly to enhancing ecological grasslands and soil quality. The utilization of non-coding RNAs (ncRNAs) has gained momentum in deciphering the intricate genetic responses to abiotic stress in various plant species. Nevertheless, the current research landscape lacks a comprehensive exploration of the responses of diverse ncRNAs, including long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs), to drought stress in switchgrass. In this study, we employed whole transcriptome sequencing to comprehensively characterize the expression profiles of both mRNA and ncRNAs during episodes of drought stress in switchgrass. Our analysis identified a total of 12,511 mRNAs, 59 miRNAs, 38 circRNAs, and 368 lncRNAs that exhibited significant differential expression between normal and drought-treated switchgrass leaves. Notably, the majority of up-regulated mRNAs displayed pronounced enrichment within the starch and sucrose metabolism pathway, as validated through KEGG analysis. Co-expression analysis illuminated that differentially expressed (DE) lncRNAs conceivably regulated 1308 protein-coding genes in trans and 7110 protein-coding genes in cis. Furthermore, both cis- and trans-target mRNAs of DE lncRNAs exhibited enrichment in four common KEGG pathways. The intricate interplay between lncRNAs and circRNAs with miRNAs via miRNA response elements was explored within the competitive endogenous RNA (ceRNA) network framework. As a result, we constructed elaborate regulatory networks, including lncRNA-novel_miRNA480-mRNA, lncRNA-novel_miRNA304-mRNA, lncRNA/circRNA-novel_miRNA122-PvSS4, and lncRNA/circRNA-novel_miRNA14-PvSS4, and subsequently validated the functionality of the target gene, starch synthase 4 (PvSS4). Furthermore, through the overexpression of PvSS4, we ascertained its capacity to enhance drought tolerance in yeast. However, it is noteworthy that PvSS4 did not exhibit any discernible impact under salt stress conditions. These findings, as presented herein, not only contribute substantively to our understanding of ceRNA networks but also offer a basis for further investigations into their potential functions in response to drought stress in switchgrass.

Integrative physiological, transcriptomic and metabolomic analysis reveals how the roots of two ornamental Hydrangea macrophylla cultivars cope with lead (Pb) toxicity

Lead (Pb) soil contamination has caused serious ecological and environmental issues. Hydrangea macrophylla is a potential Pb-contaminated soil remediation plant, however, their Pb stress defense mechanism is largely unknown. Here, the physiology, transcriptomic and metabolome of two H. macrophylla cultivars (ML, Pb-sensitive cultivar; JC, Pb-resistant cultivar) under Pb stress were investigated. The results demonstrated that JC performed superiorly, with activities of the antioxidant enzymes superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) were 1.25, 2.84, and 1.67 times higher than those of ML after Pb treatment, respectively, and the amount of soluble sugar in JC increased by 231.34 % compared with that in ML. The electrical conductivity (EC) value of the root exudates of JC was 43.71 % lower than that of ML under Pb stress. The non-targeted metabolomics analysis revealed 193 metabolites grouped into nine categories. Pb stress-induced differential expression of the 37 metabolites, among which the major metabolites up-regulated in ML were organic acids, while in JC, these were carbohydrates, fatty acids, organic acids and lipids. The transcriptomic analysis revealed that Pb exposure induced 1075 and 1314 differentially expressed genes (DEGs) in JC and ML, respectively. According to the functional annotation results, hub genes were primarily enriched in carbohydrate metabolism, root growth, and plant resistance to external stresses. A conjoint analysis of the two omics indicated that the cutin, suberine and wax biosynthesis pathway in JC played an essential role in Pb detoxification. These findings clarify the resistance mechanism of H. macrophylla to Pb stress and open up a new avenue for breeding H. macrophylla Pb-resistant cultivars.

Transcriptomic Insights into Abies koreana Drought Tolerance Conferred by Aureobasidium pullulans AK10

The conservation of the endangered Korean fir, Abies koreana, is of critical ecological importance. In our previous study, a yeast-like fungus identified as Aureobasidium pullulans AK10, was isolated and shown to enhance drought tolerance in A. koreana seedlings. In this study, the effectiveness of Au. pullulans AK10 treatment in enhancing drought tolerance in A. koreana was confirmed. Furthermore, using transcriptome analysis, we compared A. koreana seedlings treated with Au. pullulans AK10 to untreated controls under drought conditions to elucidate the molecular responses involved in increased drought tolerance. Our findings revealed a predominance of downregulated genes in the treated seedlings, suggesting a strategic reallocation of resources to enhance stress defense. Further exploration of enriched Kyoto Encyclopedia of Genes and Genomes pathways and protein-protein interaction networks revealed significant alterations in functional systems known to fortify drought tolerance, including the terpenoid backbone biosynthesis, calcium signaling pathway, pyruvate metabolism, brassinosteroid biosynthesis, and, crucially, flavonoid biosynthesis, renowned for enhancing plant drought resistance. These findings deepen our comprehension of how AK10 biostimulation enhances the resilience of A. koreana to drought stress, marking a substantial advancement in the effort to conserve this endangered tree species through environmentally sustainable treatment.

Integrated transcriptomics and metabolomics reveal specific phenolic and flavonoid accumulation in licorice (Glycyrrhiza uralensis Fisch.) induced by arbuscular mycorrhiza symbiosis under drought stress

Arbuscular mycorrhizal (AM) symbiosis can strengthen plant defense against abiotic stress, such as drought, through multiple mechanisms; however, the specialized chemical defenses induced by AM symbiosis are largely unknown. In a pot experiment, licorice (Glycyrrhiza uralensis Fisch.) inoculated with and without arbuscular mycorrhizal fungus Rhizophagus irregularis Schenck & Smith were grown under well-watered or water deficit conditions. Transcriptomic and metabolomic analyses were combined to investigate licorice root specialized metabolism induced by AM symbiosis under drought stress. Results showed that mycorrhizal plants had few dead leaves, less biomass reduction, and less differentially expressed genes and metabolite features in response to drought compared with nonmycorrhizal plants. Transcriptomic and metabolomic data revealed that mycorrhizal roots generally accumulated lignin regardless of the water regime; however, the expression of genes involved in lignin biosynthesis was significantly downregulated by drought stress in mycorrhizal plants. By contrast, AM inoculation significantly decreased specialized metabolites accumulation, including phenolics and flavonoids under well-watered conditions, whereas these decreases turned to be nonsignificant under drought stress. Moreover, these specific phenolics and flavonoids showed significant drought-induced accumulation pattern in mycorrhizal roots. These results highlight that accumulation of specific root phenolics and flavonoids may support the drought tolerance of mycorrhizal plants.

Endophytic Beauveria bassiana of Tomato Resisted the Damage from Whitefly Bemisia tabaci by Mediating the Accumulation of Plant-Specialized Metabolites

Beauveria bassiana acts as an endophytic fungus that controls herbivorous pests by stimulating plant defenses and inducing systemic resistance. Through multiomics analysis, 325 differential metabolites and 1739 differential expressed genes were observed in tomatoes treated with B. bassiana by root irrigation; meanwhile, 152 differential metabolites and 1002 differential genes were observed in tomatoes treated by local leaf spraying. Among the upregulated metabolites were α-solanine, 5-O-caffeoylshikimic acid, clerodendrin A, and peucedanin, which demonstrated anti-insect activity. These differential metabolites were primarily associated with alkaloid biosynthesis, flavonoid biosynthesis, and tryptophan metabolism pathways. Furthermore, the gene silencing of UDP-glucose:sterol glucosyltransferase, a gene involved in α-solanine synthesis, indicated that B. bassiana could inhibit the reproduction of whiteflies by regulating α-solanine. This study highlighted the ability of B. bassiana to modulate plant secondary metabolites and emphasized the significance of understanding and harnessing multitrophic interactions of endophytic B. bassiana for sustainable agriculture.

Anti-fungal bioactive terpenoids in the bioenergy crop switchgrass (Panicum virgatum) may contribute to ecotype-specific microbiome composition

Plant derived bioactive small molecules have attracted attention of scientists across fundamental and applied scientific disciplines. We seek to understand the influence of these phytochemicals on rhizosphere and root-associated fungi. We hypothesize that - consistent with accumulating evidence that switchgrass genotype impacts microbiome assembly - differential terpenoid accumulation contributes to switchgrass ecotype-specific microbiome composition. An initial in vitro Petri plate-based disc diffusion screen of 18 switchgrass root derived fungal isolates revealed differential responses to upland- and lowland-isolated metabolites. To identify specific fungal growth-modulating metabolites, we tested fractions from root extracts on three ecologically important fungal isolates - Linnemania elongata, Trichoderma sp. and Fusarium sp. Saponins and diterpenoids were identified as the most prominent antifungal metabolites. Finally, analysis of liquid chromatography-purified terpenoids revealed fungal inhibition structure - activity relationships (SAR). Saponin antifungal activity was primarily determined by the number of sugar moieties - saponins glycosylated at a single core position were inhibitory whereas saponins glycosylated at two core positions were inactive. Saponin core hydroxylation and acetylation were also associated with reduced activity. Diterpenoid activity required the presence of an intact furan ring for strong fungal growth inhibition. These results inform future breeding and biotechnology strategies for crop protection with reduced pesticide application.

Integration of transcriptomic and metabolomic analysis unveils the response mechanism of sugar metabolism in Cyclocarya paliurus seedlings subjected to PEG-induced drought stress

Cyclocarya paliurus (Batal.) Iljinskaja is a multiple function tree species used for functional food and valued timber production. Carbohydrates, especially water-soluble carbohydrates, play an important role in osmotic protection, signal transduction and carbon storage. Under the circumstance of global climate change the abiotic stress would restrict the development of C. paliurus plantation, whereas there is few knowledge on the regulatory mechanisms of sugar metabolism under drought stress in C. paliurus. To investigate the drought response of C. paliurus at molecular level, we conducted an integrated analysis of transcriptomic and metabolomic of C. paliurus at three PEG-induced drought stress levels (0%: control; 15%: moderate drought; 25%: severe drought) in short term. Both moderate and severe drought treatments activated the chemical defense with lowering relative water content, and enhancing the contents of soluble protein, proline and malondialdehyde in the leaves. Meanwhile, alterations in the expression of differentially expressed genes and carbohydrate metabolism profiles were observed among the treatments. Weighted gene co-expression network analysis (WGCNA) showed 3 key modules, 8 structural genes (such as genes encoding beta-fructofuranosidase (INV), sucrose synthase (SUS), raffinose synthase (RS)) and 14 regulatory transcription factors were closely linked to sugar metabolism. Our results provided the foundation to understand the response mechanism of sugar metabolism in C. paliurus under drought stress, and would drive progress in breeding of drought-tolerant varieties and plantation development of the species.

A 13-LOX participates in the biosynthesis of JAs and is related to the accumulation of baicalein and wogonin in Scutellaria baicalensis

Although baicalein and wogonin contents in Scutellaria baicalensis, a traditional Chinese herb, are known to be regulated by jasmonic acid, the exact mechanism by which jasmonic acid regulates the accumulation of baicalein and wogonin remains unclear. In this study, we discovered SbLOX3, a gene encoding 13-lipoxygenase from the roots of S. baicalensis, which plays an important role in the biosynthesis of jasmonic acid. The contents of methyl jasmonate, baicalin, wogonin, and three metabolic intermediates of methyl jasmonate, 13-HPOT, OPDA, and OPC-8, were downregulated in the hair roots of the SbLOX3 RNAi lines. We confirmed that SbLOX3 was induced by drought stress simulated by PEG and Fusarium oxysporum, which subsequently led to changes in the content of MeJA, baicalin, and wogonin. Taken together, our results indicate that a 13-LOX is involved in the biosynthesis of jasmonic acid, and regulates the accumulation of baicalein and wogonin in S. baicalensis roots.

Metabolomic Analysis of the Response of Haloxylon ammodendron and Haloxylon persicum to Drought

Haloxylon ammodendron and Haloxylon persicum, as typical desert plants in arid areas, show strong drought tolerance and environmental adaptability and are therefore ideal model plants for studying the molecular mechanisms of drought tolerance. A metabolomic analysis of H. ammodendron and H. persicum in their natural environment is lacking, and their metabolic response to drought therefore remains unclear. To elucidate the response of H. ammodendron and H. persicum to drought at the metabolic level, a non-targeted metabolomics analysis was carried out herein. Under a dry environment, H. ammodendron exhibited 296 and 252 differentially expressed metabolites (DEMs) in the positive and negative ion modes, respectively, whereas 452 and 354 DEMs were identified in the positive and negative ion modes in H. persicum, respectively. The results indicated that H. ammodendron responds to drought by increasing the content of organic nitrogen compounds and lignans, neolignans, and related compounds, and reducing the content of alkaloids and derivatives. By contrast, H. persicum adapts to the dry environment by increasing the content of organic acids and their derivatives and reducing the content of lignans, neolignans, and related compounds. In addition, H. ammodendron and H. persicum improved their osmoregulation ability, reactive oxygen species detoxification ability, and cell membrane stability by regulating the key metabolic pathways and anabolism of associated metabolites. This is the first metabolomics report on the response of H. ammodendron and H. persicum to drought in their natural environment, providing a foundation for the further study of their regulatory mechanisms under drought stress.

Omics Analysis Unveils the Pathway Involved in the Anthocyanin Biosynthesis in Tomato Seedling and Fruits

The purple tomato variety 'Indigo Rose' (InR) is favored due to its bright appearance, abundant anthocyanins and outstanding antioxidant capacity. SlHY5 is associated with anthocyanin biosynthesis in 'Indigo Rose' plants. However, residual anthocyanins still present in Slhy5 seedlings and fruit peel indicated there was an anthocyanin induction pathway that is independent of HY5 in plants. The molecular mechanism of anthocyanins formation in 'Indigo Rose' and Slhy5 mutants is unclear. In this study, we performed omics analysis to clarify the regulatory network underlying anthocyanin biosynthesis in seedling and fruit peel of 'Indigo Rose' and Slhy5 mutant. Results showed that the total amount of anthocyanins in both seedling and fruit of InR was significantly higher than those in the Slhy5 mutant, and most genes associated with anthocyanin biosynthesis exhibited higher expression levels in InR, suggesting that SlHY5 play pivotal roles in flavonoid biosynthesis both in tomato seedlings and fruit. Yeast two-hybrid (Y2H) results revealed that SlBBX24 physically interacts with SlAN2-like and SlAN2, while SlWRKY44 could interact with SlAN11 protein. Unexpectedly, both SlPIF1 and SlPIF3 were found to interact with SlBBX24, SlAN1 and SlJAF13 by yeast two-hybrid assay. Suppression of SlBBX24 by virus-induced gene silencing (VIGS) retarded the purple coloration of the fruit peel, indicating an important role of SlBBX24 in the regulation of anthocyanin accumulation. These results deepen the understanding of purple color formation in tomato seedlings and fruits in an HY5-dependent or independent manner via excavating the genes involved in anthocyanin biosynthesis based on omics analysis.

Divergent Metabolic Changes in Rhizomes of Lowland and Upland Switchgrass (Panicum virgatum) from Early Season through Dormancy Onset

High-biomass-yielding southerly adapted switchgrasses (Panicum virgatum L.) frequently suffer from unpredictable winter hardiness at more northerly sites arising from damage to rhizomes that prevent effective spring regrowth. Previously, changes occurring over the growing season in rhizomes sampled from a cold-adapted tetraploid upland cultivar, Summer, demonstrated a role for abscisic acid (ABA), starch accumulation, and transcriptional reprogramming as drivers of dormancy onset and potential keys to rhizome health during winter dormancy. Here, rhizome metabolism of a high-yielding southerly adapted tetraploid switchgrass cultivar, Kanlow-which is a significant source of genetics for yield improvement-was studied over a growing season at a northern site. Metabolite levels and transcript abundances were combined to develop physiological profiles accompanying greening through the onset of dormancy in Kanlow rhizomes. Next, comparisons of the data to rhizome metabolism occurring in the adapted upland cultivar Summer were performed. These data revealed both similarities as well as numerous differences in rhizome metabolism that were indicative of physiological adaptations unique to each cultivar. Similarities included elevated ABA levels and accumulation of starch in rhizomes during dormancy onset. Notable differences were observed in the accumulation of specific metabolites, the expression of genes encoding transcription factors, and several enzymes linked to primary metabolism.

Transcriptome Analysis of Roots from Wheat (Triticum aestivum L.) Varieties in Response to Drought Stress

Under climate change, drought is one of the most limiting factors that influences wheat (Triticum aestivum L.) production. Exploring stress-related genes is vital for wheat breeding. To identify genes related to the drought tolerance response, two common wheat cultivars, Zhengmai 366 (ZM366) and Chuanmai 42 (CM42), were selected based on their obvious difference in root length under 15% PEG-6000 treatment. The root length of the ZM366 cultivar was significantly longer than that of CM42. Stress-related genes were identified by RNA-seq in samples treated with 15% PEG-6000 for 7 days. In total, 11,083 differentially expressed genes (DEGs) and numerous single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) were identified. GO enrichment analysis revealed that the upregulated genes were mainly related to the response to water, acidic chemicals, oxygen-containing compounds, inorganic substances, and abiotic stimuli. Among the DEGs, the expression levels of 16 genes in ZM366 were higher than those in CM42 after the 15% PEG-6000 treatment based on RT-qPCR. Furthermore, EMS-induced mutants in Kronos (T. turgidum L.) of 4 representative DEGs possessed longer roots than the WT after the 15% PEG-6000 treatment. Altogether, the drought stress genes identified in this study represent useful gene resources for wheat breeding.