Advances and perspectives in the metabolomics of stomatal movement and the disease triangle

Microbiota dynamics and source tracing during the growing, aging, and decomposing processes of Eucommia ulmoides leaves

Eucommia ulmoides, an important tree, faces serious threat to its growth from environmental stress, particularly climate change. Using plant microbes to enhance host adaptation to respond climate change challenges has been recognized as a viable and sustainable strategy. However, it is still unclear how the perennial tree microbiota varies across phenological stages and the links between respective changes in aboveground and belowground niches. Here, we sequenced 27 root and 27 leaf samples of E. ulmoides using 16S rRNA and ITS amplicon sequencing techniques. These samples were obtained from the three main phenological stages of leaves, including leaf growing, aging and decomposing stages. Results showed that the diversity, composition, and function of the leaf microbiota of E. ulmoides showed more obvious changes at three phenological time points compared to roots. Regarding alpha diversity, the root microbiota showed no difference across three sampling stages, while the leaf microbiota varied with sampling stages. Regarding beta diversity, the root microbiota clustered from different sampling stages, while the leaf microbiota exhibited distinct separation. Regarding composition and function, the dominant taxa and main functions of the root microbiota were the same in three sampling stages, while the leaf microbiota in the decomposing stage was obviously different from the remaining two stages. Additionally, taxa overlap and source-sink relationship existed between E. ulmoides microbiota. Specifically, the degree of overlap among root microbiota was higher than that of leaf microbiota in three sampling stages. The bidirectional source-sink relationship that existed between the root and leaf niches varied with sampling stage. During the leaf growing and aging stages, the proportion of microbial members migrating from roots to leaves was higher than the proportion of members migrating from leaves to roots. During the leaf decomposing stage, the migration characteristics of the fungal community between the root and leaf niches maintained the same as in the remaining two stages, but the proportion of bacterial members migrating from leaves to roots was significantly higher than that of members migrating from roots to leaves. Our findings provide crucial foundational information for utilizing E. ulmoides microbiota to benefit their host under climate change challenges.

Profiling of bioactive secondary metabolites from Aspergillus niger against a guava wilt pathogen, Fusarium oxysporum f. sp. psidii

Guava wilt is a devastating soil-borne disease that causes significant losses in guava orchards. Management of the disease is very challenging once established in the field. Therefore, there is a need to explore for an effective, economical, and sustainable management strategies. Aspergillus niger, a bio-control fungus, has been demonstrated effectiveness against various soil-borne pathogens including guava wilt pathogens. It produces a diverse hydrolysing enzymes and secondary metabolites. However, no extensive study has been undertaken to profile the secondary metabolites of A. niger. In this investigation, we assessed eleven A. niger strains (AN-1 to AN-11) against four guava wilt pathogens (Fusarium oxysporum f. sp. psidii, F. falciforme, F. chlamydosporum, and F. verticillioides) using a dual culture assay. All strains demonstrated effective by restricting the mycelial growth of pathogens, among them AN-11 displayed maximum inhibition of 86.33%, followed by the AN-3 (84.27%). The UPLC-QToF-ESIMS analysis was undertaken to explore the secondary metabolites of AN-11 responsible for inhibiting F. oxysporum f. sp. psidii. The crude extracts were obtained from F. oxysporum f. sp. psidii, AN-11 and their interaction using ethyl acetate as a solvent. After evaporating, the crude fractions were analysed using UPLC-QToF-ESIMS with an Acquity UPLC and a SCIEX SelexION Triple QuadTM 5500 System. From the ethyl acetate extract of F. oxysporum f. sp. psidii, approximately 14 metabolites involved in pathogenicity were identified. Similarly, analysis of AN-11 crude extract revealed 25 metabolites, and notably, 41 metabolites were identified during the interaction between AN-11 and F. oxysporum f. sp. psidii, including kotanin, isokotanin A, aurofusarin, kojic acid, pyranonigrin, aurasperone F, hexylitaconic acid, asperazine, bicoumanigrin, chloramphenicol, cephalosporin C, fusarin C, zearalonone, fonsecin B, malformin A, and others. Among these, 21 metabolites were produced only during the interaction and have antimicrobial properties. This study highlights the significant potential of the AN-11 strain in generating a diverse array of non-volatile secondary metabolites with antimicrobial properties. These metabolites could be further extracted and investigated for their efficacy against other soil borne pathogens and potentially developed into formulations for controlling plant diseases.

Differential responses of the phyllosphere abundant and rare microbes of Eucommia ulmoides to phytohormones

Phyllosphere microbiota play a crucial role in plant productivity and adaptation, and the abundant and rare microbial taxa often possess distinct characteristics and ecological functions. However, it is unclear whether the different subcommunities of phyllosphere microbiota respond variably to the factors that influence their formation, which limits the understanding of community assembly. The effects of two phytohormones, namely, indole-3-acetic acid (IAA) and N6-(delta 2-isopentenyl)-adenine (IP), on the phyllosphere microbial subcommunities of Eucommia ulmoides were investigated using potted experiments. The results demonstrated that the phytohormones induced significant variations in the composition, diversity, and function of the abundant microbial subcommunity in the phyllosphere of E. ulmoides, however, their effects on the rare subcommunity were negligible, and their effects on the moderate subcommunity were between those of the abundant and rare taxa. The phytohormones also induced significant alterations in the phenotypic and physiological properties of E. ulmoides, which indirectly affected the phyllosphere microbial community. Leaf thickness and average leaf area were the main phenotypic variables that affected the composition of the phyllosphere microbial community. The total alkaloid content and activity of superoxide dismutase (SOD) were the main physiological variables that affected the composition of the phyllosphere microbial community. The phenotypic and physiological indices of E. ulmoides explained the variations in the phyllosphere microbial subcommunities in descending order: abundant > moderate > rare taxa. These variables explained a significant proportion of the variations in the abundant taxa, and an insignificant proportion of the variations in the rare taxa. This study improves our understanding of the assembly of the phyllosphere microbiota, which provides important theoretical knowledge for future sustainable agriculture and forestry management based on the precise regulation of phyllosphere microbiota.

Fighting for Survival at the Stomatal Gate

Stomata serve as the battleground between plants and plant pathogens. Plants can perceive pathogens, inducing closure of the stomatal pore, while pathogens can overcome this immune response with their phytotoxins and elicitors. In this review, we summarize new discoveries in stomata-pathogen interactions. Recent studies have shown that stomatal movement continues to occur in a close-open-close-open pattern during bacterium infection, bringing a new understanding of stomatal immunity. Furthermore, the canonical pattern-triggered immunity pathway and ion channel activities seem to be common to plant-pathogen interactions outside of the well-studied Arabidopsis-Pseudomonas pathosystem. These developments can be useful to aid in the goal of crop improvement. New technologies to study intact leaves and advances in available omics data sets provide new methods for understanding the fight at the stomatal gate. Future studies should aim to further investigate the defense-growth trade-off in relation to stomatal immunity, as little is known at this time.

Creation of a Plant Metabolite Spectral Library for Untargeted and Targeted Metabolomics

Large-scale high throughput metabolomic technologies are indispensable components of systems biology in terms of discovering and defining the metabolite parts of the system. However, the lack of a plant metabolite spectral library limits the metabolite identification of plant metabolomic studies. Here, we have created a plant metabolite spectral library using 544 authentic standards, which increased the efficiency of identification for untargeted metabolomic studies. The process of creating the spectral library was described, and the mzVault library was deposited in the public repository for free download. Furthermore, based on the spectral library, we describe a process of creating a pseudo-targeted method, which was applied to a proof-of-concept study of Arabidopsis leaf extracts. As authentic standards become available, more metabolite spectra can be easily incorporated into the spectral library to improve the mzVault package.

Lipid transfer proteins involved in plant-pathogen interactions and their molecular mechanisms

Nonspecific lipid transfer proteins (LTPs) are small, cysteine-rich proteins that play numerous functional roles in plant growth and development, including cutin wax formation, pollen tube adhesion, cell expansion, seed development, germination, and adaptation to changing environmental conditions. LTPs contain eight conserved cysteine residues and a hydrophobic cavity that provides a wide variety of lipid-binding specificities. As members of the pathogenesis-related protein 14 family (PR14), many LTPs inhibit fungal or bacterial growth, and act as positive regulators in plant disease resistance. Over the past decade, these essential immunity-related roles of LTPs in plant immune processes have been documented in a growing body of literature. In this review, we summarize the roles of LTPs in plant-pathogen interactions, emphasizing the underlying molecular mechanisms in plant immune responses and specific LTP functions.

Impacts of global change on the phyllosphere microbiome

Plants form complex interaction networks with diverse microbiomes in the environment, and the intricate interplay between plants and their associated microbiomes can greatly influence ecosystem processes and functions. The phyllosphere, the aerial part of the plant, provides a unique habitat for diverse microbes, and in return the phyllosphere microbiome greatly affects plant performance. As an open system, the phyllosphere is subjected to environmental perturbations, including global change, which will impact the crosstalk between plants and their microbiomes. In this review, we aim to provide a synthesis of current knowledge of the complex interactions between plants and the phyllosphere microbiome under global changes and to identify future priority areas of research on this topic.

Protein glycosylation changes during systemic acquired resistance in Arabidopsis thaliana

N-glycosylation, an important post-translational modification of proteins in all eukaryotes, has been clearly shown to be involved in numerous diseases in mammalian systems. In contrast, little is known regarding the role of protein N-glycosylation in plant defensive responses to pathogen infection. We identified, for the first time, glycoproteins related to systemic acquired resistance (SAR) in an Arabidopsis thaliana model, using a glycoproteomics platform based on high-resolution mass spectrometry. 407 glycosylation sites corresponding to 378 glycopeptides and 273 unique glycoproteins were identified. 65 significantly changed glycoproteins with 80 N-glycosylation sites were detected in systemic leaves of SAR-induced plants, including numerous GDSL-like lipases, thioglucoside glucohydrolases, kinases, and glycosidases. Functional enrichment analysis revealed that significantly changed glycoproteins were involved mainly in N-glycan biosynthesis and degradation, phenylpropanoid biosynthesis, cutin and wax biosynthesis, and plant-pathogen interactions. Comparative analysis of glycoproteomics and proteomics data indicated that glycoproteomics analysis is an efficient method for screening proteins associated with SAR. The present findings clarify glycosylation status and sites of A. thaliana proteins, and will facilitate further research on roles of glycoproteins in SAR induction.

Phyllosphere Microorganisms: Sources, Drivers, and Their Interactions with Plant Hosts

The leaves of plants are colonized by various microorganisms. In comparison to the rhizosphere, less is known about the characteristics and ecological functions of phyllosphere microorganisms. Phyllosphere microorganisms mainly originate from soil, air, and seeds. The composition of phyllosphere microorganisms is mainly affected by ecological and abiotic factors. Phyllosphere microorganisms execute multiple ecological functions by influencing leaf functions and longevity, seed mass, fruit development, and homeostasis of host growth. A plant can respond to phyllosphere microorganisms by secondary metabolite secretion and its immune system. Meanwhile, phyllosphere microorganisms play an important role in ecological stability and environmental safety assessment. However, as a result of the instability of the phyllosphere environment and the poor cultivability of phyllosphere microorganisms in the current research, there are still many limitations, such as the lack of insight into the mechanisms of plant-microorganism interactions, the roles of phyllosphere microorganisms in plant growth processes, the responses of phyllosphere microorganisms to plant metabolites, etc. This review summarizes the latest progress made in the research of the phyllosphere in recent years. This is beneficial for deepening our understanding of phyllosphere microorganisms and promoting the research of plant-atmosphere interactions, plant pathogens, and plant biological control.

Comparison of chemical constituents of Bupleurum marginatum var. stenophyllum and Bupleurum chinense DC. using UHPLC-Q-TOF-MS based on a metabonomics approach

The overall chemical composition of Bupleurum marginatum var. stenophyllum and Bupleurum chinense DC. was compared in this study. Metabolites were identified using ultra-high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry. Multivariate statistical analysis techniques such as principal component analysis were used to conduct metabonomics analysis and study the correlation between different components. Principal component analysis results showed a clear distinction among medicinal materials of different origins and divided them into different categories, consistent with the results of hierarchical cluster analysis. Both partial least squares discriminant analysis (PLS-DA) and orthogonal partial least squares discriminant analysis (OPLS-DA) showed that the two materials could be distinguished clearly. Using PLS-DA and OPLS-DA combined with the S-plot and a variable importance in the projection (VIP) score >1, 24 differential metabolites were screened and identified; all of the metabolites were triterpenoid saponins. In addition, SPSS 25.0 and Metabo Analyst 4.0 were used to analyze significant differences in the relative contents of different compounds in the two materials. This study has successfully provided not only a new direction for research based on the chemical substances identified and the quality evaluation of Bupleuri Radix but also a better theoretical basis for the expansion of medicinal sources and their clinical application.

Protein Phosphorylation Changes During Systemic Acquired Resistance in Arabidopsis thaliana

Systemic acquired resistance (SAR) in plants is a defense response that provides resistance against a wide range of pathogens at the whole-plant level following primary infection. Although the molecular mechanisms of SAR have been extensively studied in recent years, the role of phosphorylation that occurs in systemic leaves of SAR-induced plants is poorly understood. We used a data-independent acquisition (DIA) phosphoproteomics platform based on high-resolution mass spectrometry in an Arabidopsis thaliana model to identify phosphoproteins related to SAR establishment. A total of 8011 phosphorylation sites from 3234 proteins were identified in systemic leaves of Pseudomonas syringae pv. maculicola ES4326 (Psm ES4326) and mock locally inoculated plants. A total of 859 significantly changed phosphoproteins from 1119 significantly changed phosphopeptides were detected in systemic leaves of Psm ES4326 locally inoculated plants, including numerous transcription factors and kinases. A variety of defense response-related proteins were found to be differentially phosphorylated in systemic leaves of Psm ES4326 locally inoculated leaves, suggesting that these proteins may be functionally involved in SAR through phosphorylation or dephosphorylation. Significantly changed phosphoproteins were enriched mainly in categories related to response to abscisic acid, regulation of stomatal movement, plant-pathogen interaction, MAPK signaling pathway, purine metabolism, photosynthesis-antenna proteins, and flavonoid biosynthesis. A total of 28 proteins were regulated at both protein and phosphorylation levels during SAR. RT-qPCR analysis revealed that changes in phosphorylation levels of proteins during SAR did not result from changes in transcript abundance. This study provides comprehensive details of key phosphoproteins associated with SAR, which will facilitate further research on the molecular mechanisms of SAR.