Modulators or facilitators? Roles of lipids in plant root-microbe interactions

Metabolic profiling and antibacterial activity of tree wood extracts obtained under variable extraction conditions

INTRODUCTION

Tree bacterial diseases are a threat in forestry due to their increasing incidence and severity. Understanding tree defence mechanisms requires evaluating metabolic changes arising during infection. Metabolite extraction affects the chemical diversity of the samples and, therefore, the biological relevance of the data. Metabolite extraction has been standardized for several biological models. However, little information is available regarding how it influences wood extract's chemical diversity.

OBJECTIVES

This study aimed to develop a methodological approach to obtain extracts from different tree species with the highest reproducibility and chemical diversity possible, to ensure proper coverage of the trees' metabolome.

METHODS

A full factorial design was used to evaluate the effect of solvent type, extraction temperature and number of extraction cycles on the metabolic profile, chemical diversity and antibacterial activity of four tree species.

RESULTS

Solvent, temperature and their interaction significantly affected the extracts' chemical diversity, while the number of extraction cycles positively correlated with yield and antibacterial activity. Although 60% of the features were recovered in all the tested conditions, differences in the presence and abundance of specific chemical classes per tree were observed, including organooxygen compounds, prenol lipids, carboxylic acids, and flavonoids.

CONCLUSIONS

Each tree species has a unique metabolic profile, which means that no single protocol is universally effective. Extraction at 50 °C for three cycles using 80% methanol or chloroform/methanol/water showed the best results and is suggested for studying wood metabolome. These observations highlight the need to tailor extraction protocols to each tree species to ensure comprehensive metabolome coverage for metabolic profiling.

Salt stress affects the bacterial communities in rhizosphere soil of rice

Salt is a primary factor limiting the utilization of saline lands in coastal beach areas, with rhizosphere microorganisms playing a crucial role in enhancing crop stress resistance and exhibiting high sensitivity to environmental changes. Rice (Oryza sativa L.) is the preferred crop for reclaiming salinized soils. This study determined the microbial communities in rhizosphere soil of rice under different salt stress treatments by high-throughput sequencing. We found that salt stress changed the bacterial community diversity, structure and function in rhizosphere soil of rice. Salt stress significantly reduced the richness and diversity of bacterial communities in rhizosphere soil of rice. The bacterial community was characterized by higher abundance of the phyla Chloroflexi, Proteobacteria and Actinobacteria; the relative abundances of Firmicutes, Acidobacteriota and Myxococcota were decreased, while Bacteroidota and Cyanobacteria were increased under salt stress. The functions of bacterial communities in rhizosphere soil of rice mainly include chemoheterotrophy, aerobic_chemoheterotrophy, phototrophy etc., chemoheterotrophy and aerobic_chemoheterotrophy were significantly higher NS3 (adding 3‰ NaCl solution to the base soil) treatment than NS6 (adding 6‰ NaCl solution to the base soil) treatment. These findings provide a theoretical foundation for the development of specialized salt-tolerant microbial agents for rice cultivation and offer a viable strategy for improving the soil environment of saline coastal lands through the application of beneficial microorganisms.

Enterobacter ludwigii b3 in the rhizosphere of wild rice assists cultivated rice in mitigating drought stress by direct and indirect methods

Drought is the primary factor limiting rice production in ecosystems. Wild rice rhizosphere bacteria possess the potential to assist in the stress resistance of cultivated rice. This study examines the impact of wild rice rhizosphere bacteria on cultivated rice under drought conditions. From the rhizosphere soil of wild rice, 20 potential drought-resistant strains were isolated. Subsequent to the screening, the most effective strain b3, was identified as Enterobacter ludwigii. Pot experiments were conducted on the cultivated Changbai 9 rice. It was found that inoculation with the E. ludwigii b3 strain improved the drought resistance of the rice, promotion of rice growth (shoot height increased by 13.47 %), increased chlorophyll content (chlorophyll a, chlorophyll b and carotenoid increased by 168.74 %, 130.68 % and 87.89 %), improved antioxidant system (content of glutathione was increased by 60.35 %), and accumulation of osmotic regulation substances (soluble sugar and soluble protein increased by 70.36 % and 142.03 %). Furthermore, E. ludwigii b3 had a transformative effect on the rhizosphere bacterial community of cultivated rice, increasing its abundance and diversity while simultaneously recruiting beneficial rhizosphere bacteria, resulting in a more complex community. Additionally, E. ludwigii b3 acted directly and indirectly on cultivated rice through its metabolites (organic acids, amino acids, flavonoids and other substances), which helped alleviate drought stress. In conclusion, the E. ludwigii b3 shows promise as a drought-resistant strain and has the potential to improve the growth and productivity of cultivated rice in arid agricultural ecosystems. This study represents the first investigation of E. ludwigii in the rhizosphere of wild rice under drought conditions on cultivated rice.

The Reverse Ecology-Based Approach to Design a Bacterial Consortium as Soybean Bioinoculant

Bioinoculants traditionally rely on selecting efficient microbes from the soil with potential growth-enhancing traits for plants. However, such approaches often neglect microbe-microbe and microbe-plant interactions. In this study, we applied a reverse ecology framework to design and assess a bacterial consortium tailored for soybeans. Our analysis identified Paenibacillus polymyxa, Methylobacterium brachiatum, and Enterobacter sp. as key strains for their synergistic potential in promoting soybean growth. Computational analyses revealed that these selected strains exhibited low competitiveness and metabolic compatibility. Specifically, their complementary metabolic profiles suggested minimal competition for resources and potential for mutualistic interactions. In vitro experiments further supported these findings, demonstrating that the consortium maintained stable growth without inhibitory effects among strains. In addition, greenhouse validation experiments confirmed the efficacy of the microbial consortium in enhancing soybean growth such as root and shoot development and biomass production. Overall, this study underscores the potential of reverse ecology in optimizing microbial consortia design for bioinoculant applications.

Potential Regulatory Effects of Arbuscular Mycorrhizal Fungi on Lipid Metabolism of Maize in Response to Low-Temperature Stress

The specific mechanisms underlying membrane lipid remodeling and changes in gene expression induced by arbuscular mycorrhizal fungi (AMF) in low-temperature-stressed plants are still unclear. In this study, physiological, transcriptomic, and lipidomic analyses were used to elucidate the physiological mechanisms by which AMF can enhance the adaptation of maize plants to low-temperature stress. The results showed that the relative electrical conductivity and malondialdehyde content of maize leaves were decreased after the inoculation with AMF, indicating that AMF reduced the peroxidation of membrane lipids and maintained the fluidity of the cell membrane. Transcriptomic analysis showed the presence of 702 differentially expressed genes induced by AMF in maize plants exposed to low-temperature stress. Furthermore, lipidomic analysis revealed changes in 10 lipid classes in AMF-inoculated maize plants compared with their noninoculated counterparts under low-temperature stress conditions. Lipid remodeling is an important strategy that arbuscular mycorrhizal plants adopt to cope with low-temperature stress.

Soil and stone terraces offset the negative impacts of sloping cultivation on soil microbial diversity and functioning by protecting soil carbon

Cultivation of sloping land is a main cause for soil erosion. Conservation practices, such as soil and stone terraces, may reduce the impacts of erosion but their impacts on soil microbial diversity and functioning related to carbon (C) and nutrient metabolisms remain unclear. This study was conducted to evaluate the effects of slope gradients (5°, 8°, 15°, 25°) and conservation practices (cultivated, uncultivated, soil terrace, and stone terrace) on bacterial and fungal diversities, metagenomic and metabolomic functioning associated with basic soil properties. Our results showed that steep slopes at 25° significantly decreased soil pH, silt percentage, and bacterial and fungal abundances, but that soil and stone terraces increased soil organic C (SOC), silt and clay contents, and fungal abundance compared to sloping cultivated lands. In addition, soil and stone terraces increased both bacterial and fungal alpha diversities, and relative abundances of Crenarchaeota, Nitrospirota, and Latescibacterota, but reduced the proportions of Actinobacteriota and Patescibacteria, thus shifting microbial beta diversities, which were significantly associated with increased SOC and silt content. For metagenomics, soil and stone terraces greatly increased the relative abundance of functional genes related to Respiration, Virulence, disease and defense, Stress response, and nitrogen and potassium metabolisms, such as Denitrification and Potassium homeostasis. For soil metabolomics, a total of 22 soil metabolites was enriched by soil and stone terraces, such as Lipids and lipid-like molecules (Arachidonic acid, Gamma-Linolenic acid, and Pentadecanoic acid), and Organoheterocyclic compounds (Adenine, Laudanosine, Methylpyrazine, and Nicotinic acid). To sum up, soil and stone terraces could reduce some of the negative impacts of steep slope cultivation on soil microbial diversity as well as their metagenomic and metabolomic functioning related to C and nutrient metabolism useful for soil health improvement, potentially bolstering the impact of sustainable practices in erosion hotspots around the world.

Microbial colonisation rewires the composition and content of poplar root exudates, root and shoot metabolomes

BACKGROUND

Trees are associated with a broad range of microorganisms colonising the diverse tissues of their host. However, the early dynamics of the microbiota assembly microbiota from the root to shoot axis and how it is linked to root exudates and metabolite contents of tissues remain unclear. Here, we characterised how fungal and bacterial communities are altering root exudates as well as root and shoot metabolomes in parallel with their establishment in poplar cuttings (Populus tremula x tremuloides clone T89) over 30 days of growth. Sterile poplar cuttings were planted in natural or gamma irradiated soils. Bulk and rhizospheric soils, root and shoot tissues were collected from day 1 to day 30 to track the dynamic changes of fungal and bacterial communities in the different habitats by DNA metabarcoding. Root exudates and root and shoot metabolites were analysed in parallel by gas chromatography-mass spectrometry.

RESULTS

Our study reveals that microbial colonisation triggered rapid and substantial alterations in both the composition and quantity of root exudates, with over 70 metabolites exclusively identified in remarkably high abundances in the absence of microorganisms. Noteworthy among these were lipid-related metabolites and defence compounds. The microbial colonisation of both roots and shoots exhibited a similar dynamic response, initially involving saprophytic microorganisms and later transitioning to endophytes and symbionts. Key constituents of the shoot microbiota were also discernible at earlier time points in the rhizosphere and roots, indicating that the soil constituted a primary source for shoot microbiota. Furthermore, the microbial colonisation of belowground and aerial compartments induced a reconfiguration of plant metabolism. Specifically, microbial colonisation predominantly instigated alterations in primary metabolism in roots, while in shoots, it primarily influenced defence metabolism.

CONCLUSIONS

This study highlighted the profound impact of microbial interactions on metabolic pathways of plants, shedding light on the intricate interplay between plants and their associated microbial communities. Video Abstract.

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.

Transcriptome Regulation Mechanisms Difference between Female and Male Buchloe dactyloides in Response to Drought Stress and Rehydration

Drought, a pervasive global challenge, significantly hampers plant growth and crop yields, with drought stress being a primary inhibitor. Among resilient species, Buchloe dactyloides, a warm-season and dioecious turfgrass, stands out for its strong drought resistance and minimal maintenance requirements, making it a favored choice in ecological management and landscaping. However, there is limited research on the physiological and molecular differences in drought resistance between male and female B. dactyloides. To decipher the transcriptional regulation dynamics of these sexes in response to drought, RNA-sequencing analysis was conducted using the 'Texoka' cultivar as a model. A 14-day natural drought treatment, followed by a 7-day rewatering period, was applied. Notably, distinct physiological responses emerged between genders during and post-drought, accompanied by a more pronounced differential expression of genes (DEGs) in females compared to males. Further, KEGG and GO enrichment analysis revealed different DEGs enrichment pathways of B. dactyloides in response to drought stress. Analysis of the biosynthesis and signaling transduction pathways showed that drought stress significantly enhanced the biosynthesis and signaling pathway of ABA in both female and male B. dactyloides plants, contrasting with the suppression of IAA and JA pathways. Also, we discovered BdMPK8-like as a potential enhancer of drought tolerance in yeast, highlighting novel mechanisms. This study demonstrated the physiological and molecular mechanisms differences between male and female B. dactyloides in response to drought stress, providing a theoretical basis for the corresponding application of female and male B. dactyloides. Additionally, it enriches our understanding of drought resistance mechanisms in dioecious plants, opening avenues for future research and genetic improvement.

Phospholipid production and signaling by a plant defense inducer against Podosphaera xanthii is genotype-dependent

Biotrophic phytopathogenic fungi such as Podosphaera xanthii have evolved sophisticated mechanisms to adapt to various environments causing powdery mildews leading to substantial yield losses. Today, due to known adverse effects of pesticides, development of alternative control means is crucial and can be achieved by combining plant protection products with resistant genotypes. Using plant defense inducers, natural molecules that stimulate plant immune system mimicking pathogen attack is sustainable, but information about their mode of action in different hosts or host genotypes is extremely limited. Reynoutria sachalinensis extract, a known plant defense inducer, especially through the Salicylic acid pathway in Cucurbitaceae crops against P. xanthii, was employed to analyze the signaling cascade of defense activation. Here, we demonstrate that R. sachalinensis extract enhances phospholipid production and signaling in a Susceptible to P. xanthii courgette genotype, while limited response is observed in an Intermediate Resistance genotype due to genetic resistance. Functional enrichment and cluster analysis of the upregulated expressed genes revealed that inducer application promoted mainly lipid- and membrane-related pathways in the Susceptible genotype. On the contrary, the Intermediate Resistance genotype exhibited elevated broad spectrum defense pathways at control conditions, while inducer application did not promote any significant changes. This outcome was obvious and at the metabolite level. Main factor distinguishing the Intermediate Resistance form the Susceptible genotype was the epigenetic regulated increased expression of a G3P acyltransferase catalyzing phospholipid production. Our study provides evidence on phospholipid-based signaling after plant defense inducer treatment, and the selective role of plant's genetic background.

Chemical and physical characteristics of wheat root mucilage influenced by Serendipita indica symbiosis: a comparison among four cultivars

Although there is evidence to suggest that the endophytic fungus Serendipita indica plays a crucial role in enhancing plant tolerance against biotic/abiotic stressors, less is known about the impacts of this symbiosis association on root mucilage chemical composition and its physical functions. The mucilage of inoculated and non-inoculated seedlings of four wheat cultivars (i.e., Roshan, Ghods, Kavir and Pishtaz) were extracted using an aeroponic method. Total solute concentration (TCm), carbon content (Cmucilage), electrical conductivity (EC), pH, fatty acids, surface tension (σm), and viscosity (ηm) of mucilage were measured. Ghods and Kavir had the highest and lowest root colonization percents, respectively. Saturated fatty acids, including palmitic and stearic acids, were dominant over unsaturated fatty acids in wheat root mucilage. However, their compositions were significantly different among wheat cultivars. S. indica colonization, especially for Ghods, increased the TCm, Cmucilage, and palmitic acid. Moreover, root mucilage of S. indica-inoculated Ghods had lower σm and greater ηm. An increased amount of powerful surfactants like palmitic acid in the mucilage of S. indica inoculated treatments led to lower σm and greater ηm. Such studies provide further support for the idea that plant-released mucilage plays a major role in modifying the physical environment of the rhizosphere. This knowledge toward truly understanding the rhizosphere can be potentially used for improving the rhizosphere soil quality and increasing crop growth and yield.

Lipids and Lipid-Mediated Signaling in Plant-Pathogen Interactions

Plant lipids are essential cell constituents with many structural, storage, signaling, and defensive functions. During plant-pathogen interactions, lipids play parts in both the preexisting passive defense mechanisms and the pathogen-induced immune responses at the local and systemic levels. They interact with various components of the plant immune network and can modulate plant defense both positively and negatively. Under biotic stress, lipid signaling is mostly associated with oxygenated natural products derived from unsaturated fatty acids, known as oxylipins; among these, jasmonic acid has been of great interest as a specific mediator of plant defense against necrotrophic pathogens. Although numerous studies have documented the contribution of oxylipins and other lipid-derived species in plant immunity, their specific roles in plant-pathogen interactions and their involvement in the signaling network require further elucidation. This review presents the most relevant and recent studies on lipids and lipid-derived signaling molecules involved in plant-pathogen interactions, with the aim of providing a deeper insight into the mechanisms underpinning lipid-mediated regulation of the plant immune system.

A Look into Ocular Diseases: The Pivotal Role of Omics Sciences in Ophthalmology Research

Precision medicine is a new medical approach which considers both population characteristics and individual variability to provide customized healthcare. The transition from traditional reactive medicine to personalized medicine is based on a biomarker-driven process and a deep knowledge of biological mechanisms according to which the development of diseases occurs. In this context, the advancements in high-throughput omics technologies represent a unique opportunity to discover novel biomarkers and to provide an unbiased picture of the biological system. One of the medical fields in which omics science has started to be recently applied is that of ophthalmology. Ocular diseases are very common, and some of them could be highly disabling, thus leading to vision loss and blindness. The pathogenic mechanism of most ocular diseases may be dependent on various genetic and environmental factors, whose effect has not been yet completely understood. In this context, large-scale omics approaches are fundamental to have a comprehensive evaluation of the whole system and represent an essential tool for the development of novel therapies. This Review summarizes the recent advancements in omics science applied to ophthalmology in the last ten years, in particular by focusing on proteomics, metabolomics and lipidomics applications from an analytical perspective. The role of high-efficiency separation techniques coupled to (high-resolution) mass spectrometry ((HR)MS) is also discussed, as well as the impact of sampling, sample preparation and data analysis as integrating parts of the analytical workflow.

Sterols, pleiotropic players in plant-microbe interactions

Plant-microbe interactions (PMIs) are regulated through a wide range of mechanisms in which sterols from plants and microbes are involved in numerous ways, including recognition, transduction, communication, and/or exchanges between partners. Phytosterol equilibrium is regulated by PMIs through expression of genes involved in phytosterol biosynthesis, together with their accumulation. As such, PMI outcomes also include plasma membrane (PM) functionalization events, in which phytosterols have a central role, and activation of sterol-interacting proteins involved in cell signaling. In spite (or perhaps because) of such multifaceted abilities, an overall mechanism of sterol contribution is difficult to determine. However, promising approaches exploring sterol diversity, their contribution to PMI outcomes, and their localization would help us to decipher their crucial role in PMIs.

Maize functional requirements drive the selection of rhizobacteria under long-term fertilization practices

Rhizosphere microbiomes are pivotal for crop fitness, but the principles underlying microbial assembly during root-soil interactions across soils with different nutrient statuses remain elusive. We examined the microbiomes in the rhizosphere and bulk soils of maize plants grown under six long-term (≥ 29 yr) fertilization experiments in three soil types across middle temperate to subtropical zones. The assembly of rhizosphere microbial communities was primarily driven by deterministic processes. Plant selection interacted with soil types and fertilization regimes to shape the structure and function of rhizosphere microbiomes. Predictive functional profiling showed that, to adapt to nutrient-deficient conditions, maize recruited more rhizobacteria involved in nutrient availability from bulk soil, although these functions were performed by different species. Metagenomic analyses confirmed that the number of significantly enriched Kyoto Encyclopedia of Genes and Genomes Orthology functional categories in the rhizosphere microbial community was significantly higher without fertilization than with fertilization. Notably, some key genes involved in carbon, nitrogen, and phosphorus cycling and purine metabolism were dominantly enriched in the rhizosphere soil without fertilizer input. In conclusion, our results show that maize selects microbes at the root-soil interface based on microbial functional traits beneficial to its own performance, rather than selecting particular species.

Metabolite profiling and histochemical localization of alkaloids in Hippeastrum papilio (Ravena) van Scheepen

Hippeastrum papilio (Amaryllidaceae) is a promising new source of galanthamine - an alkaloid used for the cognitive treatment of Alzheimer's disease. The biosynthesis and accumulation of alkaloids are tissue - and organ-specific. In the present study, histochemical localization of alkaloids in H. papilio's plant organs with Dragendorff's reagent, revealed their presence in all studied samples. Alkaloids were observed in vascular bundles, vacuoles, and intracellular spaces, while in other plant tissues and structures depended on the plant organ. The leaf parenchyma and the vascular bundles were indicated as alkaloid-rich structures which together with the high proportion of alkaloids in the phloem sap (49.3% of the Total Ion Current - TIC, measured by GC-MS) indicates the green tissues as a possible site of galanthamine biosynthesis. The bulbs and roots showed higher alkaloid content compared to the leaf parts. The highest alkaloid content was found in the inner bulb part. GC-MS metabolite profiling of H. papilio's root, bulb, and leaves revealed about 82 metabolites (>0.01% of TIC) in the apolar, polar, and phenolic acid fractions, including organic acids, fatty acids, sterols, sugars, amino acids, free phenolic acids, and conjugated phenolic acids. The most of organic and fatty acids were in the peak part of the root, while the outermost leaf was enriched with sterols. The outer and middle parts of the bulb had the highest amount of saccharides, while the peak part of the middle leaf had most of the amino acids, free and conjugated phenolic acids.

Fulvic Acid Promotes Legume-Rhizobium Symbiosis by Stimulating Endogenous Flavonoids Synthesis and Secretion

Fulvic acid (FA) promotes symbiosis between legumes and rhizobia. To elucidate from the aspect of symbiosis, the effects of root irrigation of water-soluble humic materials (WSHM) or foliar spraying of its highly active component, FA, on soybean root exudates and on rhizosphere microorganisms were investigated. As a result, WSHM/FA treatments significantly altered root exudate metabolite composition, and isoflavonoids were identified as key contributors in both treatments compared to the control. Increased expression of genes related to the isoflavonoid biosynthesis were validated by RT-qPCR in both treatments, which notably elevated the synthesis of symbiotic signals genistein, daidzin, coumestrol, and biochanin A. Moreover, the WSHM/FA treatments induced a change in rhizosphere microbial community, coupled with an increase in the relative abundance of rhizobia. Our findings showed that WSHM/FA promotes symbiosis by stimulating the endogenous flavonoid synthesis and leads to rhizobia accumulation in the rhizosphere. This study provides new insights into mechanisms underlying the FA-mediated promotion of symbiosis.

Genotype-Dependent Response of Root Microbiota and Leaf Metabolism in Olive Seedlings Subjected to Drought Stress

Under stress or in optimum conditions, plants foster a specific guild of symbiotic microbes to strengthen pivotal functions including metabolic regulation. Despite that the role of the plant genotype in microbial selection is well documented, the potential of this genotype-specific microbial assembly in maintaining the host homeostasis remains insufficiently investigated. In this study, we aimed to assess the specificity of the foliar metabolic response of contrasting olive genotypes to microbial inoculation with wet-adapted consortia of plant-growth-promoting rhizobacteria (PGPR), to see if previously inoculated plants with indigenous or exogenous microbes would display any change in their leaf metabolome once being subjected to drought stress. Two Tunisian elite varieties, Chetoui (drought-sensitive) and Chemleli (drought-tolerant), were tested under controlled and stressed conditions. Leaf samples were analyzed by gas chromatography-mass spectrometry (GC-TOFMS) to identify untargeted metabolites. Root and soil samples were used to extract microbial genomic DNA destined for bacterial community profiling using 16S rRNA amplicon sequencing. Respectively, the score plot analysis, cluster analysis, heat map, Venn diagrams, and Krona charts were applied to metabolic and microbial data. Results demonstrated dynamic changes in the leaf metabolome of the Chetoui variety in both stress and inoculation conditions. Under the optimum state, the PGPR consortia induced noteworthy alterations in metabolic patterns of the sensitive variety, aligning with the phytochemistry observed in drought-tolerant cultivars. These variations involved fatty acids, tocopherols, phenols, methoxyphenols, stilbenoids, triterpenes, and sugars. On the other hand, the Chemleli variety displaying comparable metabolic profiles appeared unaffected by stress and inoculation probably owing to its tolerance capacity. The distribution of microbial species among treatments was distinctly uneven. The tested seedlings followed variety-specific strategies in selecting beneficial soil bacteria to alleviate stress. A highly abundant species of the wet-adapted inoculum was detected only under optimum conditions for both cultivars, which makes the moisture history of the plant genotype a selective driver shaping microbial community and thereby a useful tool to predict microbial activity in large ecosystems.

Melatonin alleviates cadmium toxicity by regulating root endophytic bacteria community structure and metabolite composition in apple

The level of cadmium (Cd) accumulation in orchard soils is increasing, and excess Cd will cause serious damage to plants. Melatonin is a potent natural antioxidant and has a potential role in alleviating Cd stress. This study aimed to investigate the effects of exogenous melatonin on a root endophyte bacteria community and metabolite composition under Cd stress. The results showed that melatonin significantly scavenged the reactive oxygen species and restored the photosynthetic system (manifested by the improved photosynthetic parameters, total chlorophyll content and the chlorophyll fluorescence parameters (Fv/Fm)), increased the activity of antioxidant enzymes (the activities of catalase, superoxide dismutase, peroxidase and ascorbate oxidase) and reduced the concentration of Cd in the roots and leaves of apple plants. High-throughput sequencing showed that melatonin increased the endophytic bacterial community richness significantly and changed the community structure under Cd stress. The abundance of some potentially beneficial endophytic bacteria (Ohtaekwangia, Streptomyces, Tabrizicola and Azovibrio) increased significantly, indicating that the plants may absorb potentially beneficial microorganisms to resist Cd stress. The metabolomics results showed that melatonin significantly changed the composition of root metabolites, and the relative abundance of some metabolites decreased, suggesting that melatonin may resist Cd stress by depleting root metabolites. In addition, co-occurrence network analysis indicated that some potentially beneficial endophytes may be influenced by specific metabolites. These results provide a theoretical basis for studying the effects of melatonin on the endophytic bacterial community and metabolic composition in apple plants.

Root chemistry and microbe interactions contribute to metal(loid) tolerance of an aromatic plant - Vetiver grass

Aromatic plants, such as vetiver grass (Chrysopogon zizanioides), possess strong abilities to resist environmental stresses. However, whether such abilities stem from the interaction between specific chemical characteristics and the associated microbes in roots and rhizosphere remains unclear. We conducted pot experiments to analyze stress-tolerant parameters, organic compounds, and bacterial communities in roots and rhizosphere of vetiver under typical metal(loid) stress [cadmium (Cd), arsenic (As), or Cd + As] over time. The results showed that the vetiver displayed limited toxic symptoms in terms of oxidative stress-antioxidant balance and chlorophyll content. The root low-molecular-weight organic acids (LMWOAs), fatty acids, and sterols were highly sensitive to growth stage (increased from the 4-month to the 8-month stage), and less sensitive to metal(loid) stress. The sugar contents in the rhizosphere soils also notably increased over time. Such endo and rhizosphere chemical changes strongly correlated with and enriched the functional bacteria including Streptomyces, which can resist stress and promote plant growth. The compound-bacteria interaction highly depended on growth stage. Vetiver demonstrated a progressive adaptation to stresses through metabolite modulation and cellular defense reinforcement. Our study evidenced that vetiver shapes the interaction between organic compounds and bacterial community in the root-soil interface and provides notable stress-resistant functions.

Comparative metabolomic study of fungal foliar endophytes and their long-lived host Astrocaryum sciophilum: a model for exploring the chemodiversity of host-microbe interactions

Introduction

In contrast to the dynamics observed in plant/pathogen interactions, endophytic fungi have the capacity to establish enduring associations within their hosts, leading to the development of a mutually beneficial relationship that relies on specialized chemical interactions. Research indicates that the presence of endophytic fungi has the ability to significantly modify the chemical makeup of the host organism. Our hypothesis proposes the existence of a reciprocal exchange of chemical signals between plants and fungi, facilitated by specialized chemical processes that could potentially manifest within the tissues of the host. This research aimed to precisely quantify the portion of the cumulative fungal endophytic community's metabolome detectable within host leaves, and tentatively evaluate its relevance to the host-endophyte interplay. The understory palm Astrocaryum sciophilum (Miq.) Pulle was used as a interesting host plant because of its notable resilience and prolonged life cycle, in a tropical ecosystem.

Method

Using advanced metabolome characterization, including UHPLC-HRMS/MS and molecular networking, the study explored enriched metabolomes of both host leaves and 15 endophytic fungi. The intention was to capture a metabolomic "snapshot" of both host and endophytic community, to achieve a thorough and detailed analysis.

Results and discussion

This approach yielded an extended MS-based molecular network, integrating diverse metadata for identifying host- and endophyte-derived metabolites. The exploration of such data (>24000 features in positive ionization mode) enabled effective metabolome comparison, yielding insights into cultivable endophyte chemodiversity and occurrence of common metabolites between the holobiont and its fungal communities. Surprisingly, a minor subset of features overlapped between host leaf and fungal samples despite significant plant metabolome enrichment. This indicated that fungal metabolic signatures produced in vitro remain sparingly detectable in the leaf. Several classes of primary metabolites were possibly shared. Specific fungal metabolites and/or compounds of their chemical classes were only occasionally discernible in the leaf, highlighting endophytes partial contribution to the overall holobiont metabolome. To our knowledge, the metabolomic study of a plant host and its microbiome has rarely been performed in such a comprehensive manner. The general analytical strategy proposed in this paper seems well-adapted for any study in the field of microbial- or microbiome-related MS and can be applied to most host-microbe interactions.

Foliar Spraying of Chlorpyrifos Triggers Plant Production of Linolenic Acid Recruiting Rhizosphere Bacterial Sphingomonas sp

Plants have developed an adaptive strategy for coping with biotic or abiotic stress by recruiting specific microorganisms from the soil pool. Recent studies have shown that the foliar spraying of pesticides causes oxidative stress in plants and leads to changes in the rhizosphere microbiota, but the mechanisms by which these microbiota change and rebuild remain unclear. Herein, we provide for the first-time concrete evidence that rice plants respond to the stress of application of the insecticide chlorpyrifos (CP) by enhancing the release of amino acids, lipids, and nucleotides in root exudates, leading to a shift in rhizosphere bacterial community composition and a strong enrichment of the genus Sphingomonas sp. In order to investigate the underlying mechanisms, we isolated a Sphingomonas representative isolate and demonstrated that it is both attracted by and able to consume linolenic acid, one of the root exudates overproduced after pesticide application. We further show that this strain selectively colonizes roots of treated plants and alleviates pesticide stress by degrading CP and releasing plant-beneficial metabolites. These results indicate a feedback loop between plants and their associated microbiota allowing to respond to pesticide-induced stress.

Exploring the potential role of hydrogen sulfide and jasmonic acid in plants during heavy metal stress

In plants, hydrogen sulfide (H2S) is mainly considered as a gaseous transmitter or signaling molecule that has long been recognized as an essential component of numerous plant cellular and physiological processes. Several subcellular compartments in plants use both enzymatic and non-enzymatic mechanisms to generate H2S. Under normal and stress full conditions exogenous administration of H2S supports a variety of plant developmental processes, including growth and germination, senescence, defense, maturation and antioxidant machinery in plants. Due to their gaseous nature, they are efficiently disseminated to various areas of the cell to balance antioxidant pools and supply sulphur to the cells. Numerous studies have also been reported regarding H2S ability to reduce heavy metal toxicity when combined with other signaling molecules like nitric oxide (NO), abscisic acid (ABA), calcium ion (Ca2+), hydrogen peroxide (H2O2), salicylic acid (SA), ethylene (ETH), jasmonic acid (JA), proline (Pro), and melatonin. The current study focuses on multiple pathways for JA and H2S production as well as their signaling functions in plant cells under varied circumstances, more specifically under heavy metal, which also covers role of H2S and Jasmonic acid during heavy metal stress and interaction of hydrogen sulfide with Jasmonic acid.

Rhizosphere interface microbiome reassembly by arbuscular mycorrhizal fungi weakens cadmium migration dynamics

The prevalence of cadmium (Cd)-polluted agricultural soils is increasing globally, and arbuscular mycorrhizal fungi (AMF) can reduce the absorption of heavy metals by plants and improve mineral nutrition. However, the immobilization of the rhizosphere on cadmium is often overlooked. In this study, Glomus mosseae and Medicago sativa were established as symbiotes, and Cd migration and environmental properties in the rhizosphere were analyzed. AMF reduced Cd migration, and Cd2+ changed to an organic-bound state. AMF symbiosis treatment and Cd exposure resulted in microbial community variation, exhibiting a distinct deterministic process (|βNTI| > 2), which ultimately resulted in a core microbiome function of heavy metal resistance and nutrient cycling. AMF increased available N and P, extracellular enzyme activity (LaC, LiP, and CAT), organic matter content (TOC, EOC, and GRSP), and Eh of the rhizosphere soil, significantly correlating with decreased Cd migration (p < 0.05). Furthermore, AMF significantly affected root metabolism by upregulating 739 metabolites, with flavonoids being the main factor causing microbiome variation. The structural equation model and variance partial analysis revealed that the superposition of the root metabolites, microbial, and soil exhibited the maximum explanation rate for Cd migration reduction (42.4%), and the microbial model had the highest single explanation rate (15.5%). Thus, the AMF in the rhizosphere microenvironment can regulate metabolite-soil-microbial interactions, reducing Cd migration. In summary, the study provides a new scientific explanation for how AMF improves plant Cd tolerance and offers a sustainable solution that could benefit both the environment and human health.

A 3-year application of different mycorrhiza-based plant biostimulants distinctively modulates photosynthetic performance, leaf metabolism, and fruit quality in grapes (Vitis vinifera L.)

The use of microbial biostimulants in agriculture is recognized as a sustainable approach to promoting crop productivity and quality due to improved nutrient uptake, enhanced stress tolerance, and improved ability to cope with non-optimal environments. The present paper aimed to comparatively investigate the effect of seven different commercial mycorrhizal-based treatments in terms of yield, phytochemical components, and technological traits of Malvasia di Candia Aromatica grape (Vitis vinifera L.) plants. Metabolomic analysis and photosynthetic performance were first investigated in leaves to point out biochemical differences related to plant growth. Higher photosynthetic efficiency and better PSII functioning were found in biostimulant-treated vines, reflecting an overall decrease in photoinhibition compared to untreated plants. Untargeted metabolomics followed by multivariate statistics highlighted a robust reprogramming of primary (lipids) and secondary (alkaloids and terpenoids) metabolites in treated plants. The analysis of berry yield and chemical components exhibited significant differences depending on the biostimulant product. Generally, berries obtained from treated plants displayed improved contents of polyphenols and sugars, while yield remained unchanged. These results elucidated the significant role of microbial biostimulants in determining the quality of grape berries and eliciting biochemical changes in vines.

Transcriptome Analyses Revealed the Wax and Phenylpropanoid Biosynthesis Pathways Related to Disease Resistance in Rootstock-Grafted Cucumber

Cucumbers (Cucumis sativus L.) are a global popular vegetable and are widely planted worldwide. However, cucumbers are susceptible to various infectious diseases such as Fusarium and Verticillium wilt, downy and powdery mildew, and bacterial soft rot, which results in substantial economic losses. Grafting is an effective approach widely used to control these diseases. The present study investigated the role of wax and the phenylpropanoid biosynthesis pathway in black-seed pumpkin rootstock-grafted cucumbers. Our results showed that grafted cucumbers had a significantly higher cuticular wax contents on the fruit surface than that of self-rooted cucumbers at all stages observed. A total of 1132 differently expressed genes (DEGs) were detected in grafted cucumbers compared with self-rooted cucumbers. Pathway enrichment analysis revealed that phenylpropanoid biosynthesis, phenylalanine metabolism, plant circadian rhythm, zeatin biosynthesis, and diterpenoid biosynthesis were significantly enriched. In this study, 1 and 13 genes involved in wax biosynthesis and the phenylpropanoid biosynthesis pathway, respectively, were up-regulated in grafted cucumbers. Our data indicated that the up-regulated genes in the wax and phenylpropanoid biosynthesis pathways may contribute to disease resistance in rootstock-grafted cucumbers, which provides promising targets for enhancing disease resistance in cucumbers by genetic manipulation.

Spatiotemporal control of root immune responses during microbial colonization

The entire evolutionary trajectory of plants towards large and complex multi-cellular organisms has been accompanied by incessant interactions with omnipresent unicellular microbes. This led to the evolution of highly complex microbial communities, whose members display the entire spectrum of pathogenic to mutualistic behaviors. Plant roots are dynamic, fractally growing organs and even small Arabidopsis roots harbor millions of individual microbes of diverse taxa. It is evident that microbes at different positions on a root surface could experience fundamentally different environments, which, moreover, rapidly change over time. Differences in spatial scales between microbes and roots compares to humans and the cities they inhabit. Such considerations make it evident that mechanisms of root-microbe interactions can only be understood if analyzed at relevant spatial and temporal scales. This review attempts to provide an overview of the rapid recent progress that has been made in mapping and manipulating plant damage and immune responses at cellular resolution, as well as in visualizing bacterial communities and their transcriptional activities. We further discuss the impact that such approaches will have for a more predictive understanding of root-microbe interactions.

Metabolomic profiles reveals the dose-dependent effects of rice grain yield and nutritional quality upon exposure zero-valent iron nanoparticles

Zero-valent iron nanoparticles (nZVI) were widely used material in environmental remediation, which has attracted increasing concern for their safety. Previous studies have shown that the addition of nZVI could inhibit rice seedling growth. However, the effect of nZVI on the soil-rice system during the entire life cycle was not reported. Furthermore, the effect of nZVI on the quality of rice grain has also not been studied. Therefore, we investigated the effects of rice grain yield and nutritional quality upon exposure nZVI. The results showed that the soil pH value, redox potential and Fe (II) content in the nZVI-treated group were decreased in a dose-dependent manner. Interestingly, 2500 mg/kg nZVI significantly decreased the relative abundance of several functional microbial communities (10.52-73.53 %) associated with carbon and nitrogen cycles in response to plants compared to the control. Meanwhile, the nZVI treatment clearly reduced grain yield (8.71-18.21 %). Furthermore, the content of protein (51.72-57.79 %) and several essential nutrients (Zn, Cu, Mn and Mo) in the nZVI-treated grains was also decreased in a dose-dependent manner. The results of grain metabolomics indicated that nZVI could interfere with the relative expression of lysine and glutathione by regulating the metabolic pathways of antioxidant and protein synthesis in rice.

A Metabolome Analysis and the Immunity of Phlomis purpurea against Phytophthora cinnamomi

Phlomis purpurea grows spontaneously in the southern Iberian Peninsula, namely in cork oak (Quercus suber) forests. In a previous transcriptome analysis, we reported on its immunity against Phytophthora cinnamomi. However, little is known about the involvement of secondary metabolites in the P. purpurea defense response. It is known, though, that root exudates are toxic to this pathogen. To understand the involvement of secondary metabolites in the defense of P. purpurea, a metabolome analysis was performed using the leaves and roots of plants challenged with the pathogen for over 72 h. The putatively identified compounds were constitutively produced. Alkaloids, fatty acids, flavonoids, glucosinolates, polyketides, prenol lipids, phenylpropanoids, sterols, and terpenoids were differentially produced in these leaves and roots along the experiment timescale. It must be emphasized that the constitutive production of taurine in leaves and its increase soon after challenging suggests its role in P. purpurea immunity against the stress imposed by the oomycete. The rapid increase in secondary metabolite production by this plant species accounts for a concerted action of multiple compounds and genes on the innate protection of Phlomis purpurea against Phytophthora cinnamomi. The combination of the metabolome with the transcriptome data previously disclosed confirms the mentioned innate immunity of this plant against a devastating pathogen. It suggests its potential as an antagonist in phytopathogens' biological control. Its application in green forestry/agriculture is therefore possible.

Perenniality, more than genotypes, shapes biological and chemical rhizosphere composition of perennial wheat lines

Perennial grains provide various ecosystem services compared to the annual counterparts thanks to their extensive root system and permanent soil cover. However, little is known about the evolution and diversification of perennial grains rhizosphere and its ecological functions over time. In this study, a suite of -OMICSs - metagenomics, enzymomics, metabolomics and lipidomics - was used to compare the rhizosphere environment of four perennial wheat lines at the first and fourth year of growth in comparison with an annual durum wheat cultivar and the parental species Thinopyrum intermedium. We hypothesized that wheat perenniality has a greater role in shaping the rhizobiome composition, biomass, diversity, and activity than plant genotypes because perenniality affects the quality and quantity of C input - mainly root exudates - hence modulating the plant-microbes crosstalk. In support of this hypothesis, the continuous supply of sugars in the rhizosphere along the years created a favorable environment for microbial growth which is reflected in a higher microbial biomass and enzymatic activity. Moreover, modification in the rhizosphere metabolome and lipidome over the years led to changes in the microbial community composition favoring the coexistence of more diverse microbial taxa, increasing plant tolerance to biotic and abiotic stresses. Despite the dominance of the perenniality effect, our data underlined that the OK72 line rhizobiome distinguished from the others by the increase in abundance of Pseudomonas spp., most of which are known as potential beneficial microorganisms, identifying this line as a suitable candidate for the study and selection of new perennial wheat lines.

Information theory and machine learning illuminate large-scale metabolomic responses of Brachypodium distachyon to environmental change

Plant responses to environmental change are mediated via changes in cellular metabolomes. However, <5% of signals obtained from liquid chromatography tandem mass spectrometry (LC-MS/MS) can be identified, limiting our understanding of how metabolomes change under biotic/abiotic stress. To address this challenge, we performed untargeted LC-MS/MS of leaves, roots, and other organs of Brachypodium distachyon (Poaceae) under 17 organ-condition combinations, including copper deficiency, heat stress, low phosphate, and arbuscular mycorrhizal symbiosis. We found that both leaf and root metabolomes were significantly affected by the growth medium. Leaf metabolomes were more diverse than root metabolomes, but the latter were more specialized and more responsive to environmental change. We found that 1 week of copper deficiency shielded the root, but not the leaf metabolome, from perturbation due to heat stress. Machine learning (ML)-based analysis annotated approximately 81% of the fragmented peaks versus approximately 6% using spectral matches alone. We performed one of the most extensive validations of ML-based peak annotations in plants using thousands of authentic standards, and analyzed approximately 37% of the annotated peaks based on these assessments. Analyzing responsiveness of each predicted metabolite class to environmental change revealed significant perturbations of glycerophospholipids, sphingolipids, and flavonoids. Co-accumulation analysis further identified condition-specific biomarkers. To make these results accessible, we developed a visualization platform on the Bio-Analytic Resource for Plant Biology website (https://bar.utoronto.ca/efp_brachypodium_metabolites/cgi-bin/efpWeb.cgi), where perturbed metabolite classes can be readily visualized. Overall, our study illustrates how emerging chemoinformatic methods can be applied to reveal novel insights into the dynamic plant metabolome and stress adaptation.

Microbiota-mediated nitrogen fixation and microhabitat homeostasis in aerial root-mucilage

BACKGROUND

Plants sustain intimate relationships with diverse microbes. It is well-recognized that these plant-associated microbiota shape individual performance and fitness of host plants, but much remains to be explored regarding how they exert their function and maintain their homeostasis.

RESULTS

Here, using pink lady (Heterotis rotundifolia) as a study plant, we investigated the phenomenon of microbiota-mediated nitrogen fixation and elucidated how this process is steadily maintained in the root mucilage microhabitat. Metabolite and microbiota profiling showed that the aerial root mucilage is enriched in carbohydrates and diazotrophic bacteria. Nitrogen isotope-labeling experiments, ¹⁵N natural abundance, and gene expression analysis indicated that the aerial root-mucilage microbiota could fix atmospheric nitrogen to support plant growth. While the aerial root mucilage is a hotspot of nutrients, we did not observe high abundance of other environmental and pathogenic microbes inside. We further identified a fungus isolate in mucilage that has shown broad-spectrum antimicrobial activities, but solely allows the growth of diazotrophic bacteria. This "friendly" fungus may be the key driver to maintain nitrogen fixation function in the mucilage microhabitat. Video Abstract CONCLUSION: The discovery of new biological function and mucilage-habitat friendly fungi provides insights into microbial homeostasis maintenance of microenvironmental function and rhizosphere ecology.

Chemical communication in plant-microbe beneficial interactions: a toolbox for precise management of beneficial microbes

Harnessing the power of beneficial microbes in the rhizosphere to improve crop performance is a key goal of sustainable agriculture. However, the precise management of rhizosphere microbes for crop growth and health remains challenging because we lack a comprehensive understanding of the plant-rhizomicrobiome relationship. In this review, we discuss the latest research progress on root colonisation by representative beneficial microbes (e.g. Bacillus spp. and Pseudomonas spp.). We also highlight the bidirectional chemical communication between microbes and plant roots for precise functional control of beneficial microbes in the rhizosphere, as well as advances in understanding how beneficial microbes overcome the immune system of plants. Finally, we propose future research objectives that will help us better understand the complex network of plant-microbe interactions.

Root exudate-derived compounds stimulate the phosphorus solubilizing ability of bacteria

Low phosphorus (P) availability in soils is a major challenge for sustainable food production, as most soil P is often unavailable for plant uptake and effective strategies to access this P are limited. Certain soil occurring bacteria and root exudate-derived compounds that release P are in combination promising tools to develop applications that increase phosphorus use efficiency in crops. Here, we studied the ability of root exudate compounds (galactinol, threonine, and 4-hydroxybutyric acid) induced under low P conditions to stimulate the ability of bacteria to solubilize P. Galactinol, threonine, and 4-hydroxybutyric acid were incubated with the P solubilizing bacterial strains Enterobacter cloacae, Pseudomonas pseudoalcaligenes, and Bacillus thuringiensis under either inorganic (calcium phosphate) or organic (phytin) forms of plant-unavailable P. Overall, we found that the addition of individual root exudate compounds did not support bacterial growth rates. However, root exudates supplemented to the different bacterial appeared to enhance P solubilizing activity and overall P availability. Threonine and 4-hydroxybutyric acid induced P solubilization in all three bacterial strains. Subsequent exogenous application of threonine to soils improved the root growth of corn, enhanced nitrogen and P concentrations in roots and increased available levels of potassium, calcium and magnesium in soils. Thus, it appears that threonine might promote the bacterial solubilization and plant-uptake of a variety of nutrients. Altogether, these findings expand on the function of exuded specialized compounds and propose alternative approaches to unlock existing phosphorus reservoirs of P in crop lands.

Environmental Response to Root Secondary Metabolite Accumulation in Paeonia lactiflora: Insights from Rhizosphere Metabolism and Root-Associated Microbial Communities

Paeonia lactiflora is a commercial crop with horticultural and medicinal value. Although interactions between plants and microbes are increasingly evident and considered to be drivers of ecosystem service, the regulatory relationship between microbial communities and the growth and root metabolites of P. lactiflora is less well known. Here, soil metabolomics indicated that carbohydrates and organic acids were enriched in the rhizosphere (RS) with higher diversity. Moreover, the variation of root-associated microbiotas between the bulk soil (BS) and the RS of P. lactiflora was investigated via 16S rRNA and internally transcribed spacer (ITS) amplicon sequencing. The RS displayed a low-diversity community dominated by copiotrophs, whereas the BS showed an oligotroph-dominated, high-diversity community. Hierarchical partitioning showed that cation exchange capacity (CEC) was the main factor affecting microbial community diversity. The null model and the dispersion niche continuum index (DNCI) suggested that stochastic processes (dispersal limitation) dominated the community assembly of both the RS and BS. The bacterial-fungal interkingdom networks illustrated that the RS possessed more complex and stable co-occurrence patterns. Meanwhile, positive link numbers and positive cohesion results revealed more cooperative relationships among microbes in the RS. Additionally, random forest model prediction and two partial least-squares path model (PLS-PM) analyses showed that the P. lactiflora root secondary metabolites were comprehensively impacted by soil water content (SWC), mean annual precipitation (MAP), pH (abiotic), and Alternaria (biotic). Collectively, this study provides a theoretical basis for screening the microbiome associated with the active components of P. lactiflora. IMPORTANCE Determining the taxonomic and functional components of the rhizosphere microbiome, as well as how they differ from those of the bulk soil microbiome, is critical for manipulating them to improve plant growth performance and increase agricultural yields. Soil metabolic profiles can help enhance the understanding of rhizosphere exudates. Here, we explored the regulatory relationship across environmental variables (root-associated microbial communities and soil metabolism) in the accumulation of secondary metabolites of P. lactiflora. Overall, this work improves our knowledge of how the rhizosphere affects soil and microbial communities. These observations improve the understanding of plant-microbiome interactions and introduce new horizons for synthetic community investigations as well as the creation of microbiome technologies for agricultural sustainability.

Metabolomic Analysis Reveals the Effect of Insecticide Chlorpyrifos on Rice Plant Metabolism

Pesticides as important agricultural inputs play a vital role in protecting crop plants from diseases and pests; however, the effect of pesticides on crop plant physiology and metabolism is still undefined. In this study, the effect of insecticide chlorpyrifos at three doses on rice plant physiology and metabolism was investigated. Our results revealed that chlorpyrifos cause oxidative stress in rice plants and even inhibit plant growth and the synthesis of protein and chlorophyll at high doses. The metabolomic results suggested that chlorpyrifos could affect the metabolic profiling of rice tissues and a total of 119 metabolites with significant changes were found, mainly including organic acids, amino acids, lipids, polyphenols, and flavonoids. Compared to the control, the content of glutamate family amino acids were significantly disturbed by chlorpyrifos, where defense-related proline and glutathione were significantly increased; however, glutamic acid, N-acetyl-glutamic acid and N-methyl-glutamic acid were significantly decreased. Many unsaturated fatty acids, such as linolenic acid and linoleic acid, and their derivatives lysophospholipids and phospholipids, were significantly accumulated in chlorpyrifos groups, which could act as osmolality substances to help rice cells relieve chlorpyrifos stress. Three organic acids, aminobenzoic acid, quinic acid, and phosphoenolpyruvic acid, involved in plant defenses, were significantly accumulated with the fold change ranging from 1.32 to 2.19. In addition, chlorpyrifos at middle- and high-doses caused the downregulation of most flavonoids. Our results not only revealed the effect of insecticide chlorpyrifos on rice metabolism, but also demonstrated the value of metabolomics in elucidating the mechanisms of plant responses to stresses.

Allylamines, Benzylamines, and Fungal Cell Permeability: A Review of Mechanistic Effects and Usefulness against Fungal Pathogens

Allylamines, naftifine and terbinafine, and the benzylamine, butenafine, are antifungal agents with activity on the fungal cell membrane. These synthetic compounds specifically inhibit squalene epoxidase, a key enzyme in fungal sterol biosynthesis. This results in a deficiency in ergosterol, a major fungal membrane sterol that regulates membrane fluidity, biogenesis, and functions, and whose damage results in increased membrane permeability and leakage of cellular components, ultimately leading to fungal cell death. With the fungal cell membrane being predominantly made up of lipids including sterols, these lipids have a vital role in the pathogenesis of fungal infections and the identification of improved therapies. This review will focus on the fungal cell membrane structure, activity of allylamines and benzylamines, and the mechanistic damage they cause to the membrane. Furthermore, pharmaceutical preparations and clinical uses of these drugs, mainly in dermatophyte infections, will be reviewed.

Plant Growth Promotion and Heat Stress Amelioration in Arabidopsis Inoculated with Paraburkholderia phytofirmans PsJN Rhizobacteria Quantified with the GrowScreen-Agar II Phenotyping Platform

High temperatures inhibit plant growth. A proposed strategy for improving plant productivity under elevated temperatures is the use of plant growth-promoting rhizobacteria (PGPR). While the effects of PGPR on plant shoots have been extensively explored, roots-particularly their spatial and temporal dynamics-have been hard to study, due to their below-ground nature. Here, we characterized the time- and tissue-specific morphological changes in bacterized plants using a novel non-invasive high-resolution plant phenotyping and imaging platform-GrowScreen-Agar II. The platform uses custom-made agar plates, which allow air exchange to occur with the agar medium and enable the shoot to grow outside the compartment. The platform provides light protection to the roots, the exposure of it to the shoots, and the non-invasive phenotyping of both organs. Arabidopsis thaliana, co-cultivated with Paraburkholderia phytofirmans PsJN at elevated and ambient temperatures, showed increased lengths, growth rates, and numbers of roots. However, the magnitude and direction of the growth promotion varied depending on root type, timing, and temperature. The root length and distribution per depth and according to time was also influenced by bacterization and the temperature. The shoot biomass increased at the later stages under ambient temperature in the bacterized plants. The study offers insights into the timing of the tissue-specific, PsJN-induced morphological changes and should facilitate future molecular and biochemical studies on plant-microbe-environment interactions.

Microbiome-metabolome analysis directed isolation of rhizobacteria capable of enhancing salt tolerance of Sea Rice 86

Soil salinization has been recognized as one of the main factors causing the decrease of cultivated land area and global plant productivity. Application of salt tolerant plants and improvement of plant salt tolerance are recognized as the major routes for saline soil restoration and utilization. Sea rice 86 (SR86) is known as a rice cultivar capable of growing in saline soil. Genome sequencing and transcriptome analysis of SR86 have been conducted to explore its salt tolerance mechanisms while the contribution of rhizobacteria is underexplored. In the present study, we examined the rhizosphere bacterial diversity and soil metabolome of SR86 seedlings under different salinity to understand their contribution to plant salt tolerance. We found that salt stress could significantly change rhizobacterial diversity and rhizosphere metabolites. Keystone taxa were identified via co-occurrence analysis and the correlation analysis between keystone taxa and rhizosphere metabolites indicated lipids and their derivatives might play an important role in plant salt tolerance. Further, four plant growth promoting rhizobacteria (PGPR), capable of promoting the salt tolerance of SR86, were isolated and characterized. These findings might provide novel insights into the mechanisms of plant salt tolerance mediated by plant-microbe interaction, and promote the isolation and application of PGPR in the restoration and utilization of saline soil.

Untargeted metabolite profiling to elucidate rhizosphere and leaf metabolome changes of wheat cultivars (Triticum aestivum L.) treated with the plant growth-promoting rhizobacteria Paenibacillus alvei (T22) and Bacillus subtilis

The rhizosphere is a highly complex and biochemically diverse environment that facilitates plant–microbe and microbe–microbe interactions, and this region is found between plant roots and the bulk soil. Several studies have reported plant root exudation and metabolite secretion by rhizosphere-inhabiting microbes, suggesting that these metabolites play a vital role in plant–microbe interactions. However, the biochemical constellation of the rhizosphere soil is yet to be fully elucidated and thus remains extremely elusive. In this regard, the effects of plant growth-promoting rhizobacteria (PGPR)–plant interactions on the rhizosphere chemistry and above ground tissues are not fully understood. The current study applies an untargeted metabolomics approach to profile the rhizosphere exo-metabolome of wheat cultivars generated from seed inoculated (bio-primed) with Paenibacillus (T22) and Bacillus subtilis strains and to elucidate the effects of PGPR treatment on the metabolism of above-ground tissues. Chemometrics and molecular networking tools were used to process, mine and interpret the acquired mass spectrometry (MS) data. Global metabolome profiling of the rhizosphere soil of PGPR-bio-primed plants revealed differential accumulation of compounds from several classes of metabolites including phenylpropanoids, organic acids, lipids, organoheterocyclic compounds, and benzenoids. Of these, some have been reported to function in plant–microbe interactions, chemotaxis, biocontrol, and plant growth promotion. Metabolic perturbations associated with the primary and secondary metabolism were observed from the profiled leaf tissue of PGPR-bio-primed plants, suggesting a distal metabolic reprograming induced by PGPR seed bio-priming. These observations gave insights into the hypothetical framework which suggests that PGPR seed bio-priming can induce metabolic changes in plants leading to induced systemic response for adaptation to biotic and abiotic stress. Thus, this study contributes knowledge to ongoing efforts to decipher the rhizosphere metabolome and mechanistic nature of biochemical plant–microbe interactions, which could lead to metabolome engineering strategies for improved plant growth, priming for defense and sustainable agriculture.

Next-generation enhanced-efficiency fertilizers for sustained food security

Nitrogen losses in agricultural systems can be reduced through enhanced-efficiency fertilizers (EEFs), which control the physicochemical release from fertilizers and biological nitrogen transformations in soils. The adoption of EEFs by farmers requires evidence of consistent performance across soils, crops and climates, paired with information on the economic advantages. Here we show that the benefits of EEFs due to avoided social costs of nitrogen pollution considerably outweigh their costs-and must be incorporated in fertilizer policies. We outline new approaches to the design of EEFs using enzyme inhibitors with modifiable chemical structures and engineered, biodegradable coatings that respond to plant rhizosphere signalling molecules.

Biostimulant Effects of Chaetomium globosum and Minimedusa polyspora Culture Filtrates on Cichorium intybus Plant: Growth Performance and Metabolomic Traits

In this study, we investigated the biostimulant effect of fungal culture filtrates obtained from Chaetomium globosum and Minimedusa polyspora on growth performance and metabolomic traits of chicory (Cichorium intybus) plants. For the first time, we showed that M. polyspora culture filtrate exerts a direct plant growth-promoting effect through an increase of biomass, both in shoots and roots, and of the leaf area. Conversely, no significant effect on morphological traits and biomass yield was observed in C. intybus plants treated with C. globosum culture filtrate. Based on ¹H-NMR metabolomics data, differential metabolites and their related metabolic pathways were highlighted. The treatment with C. globosum and M. polyspora culture filtrates stimulated a common response in C. intybus roots involving the synthesis of 3-OH-butyrate through the decrease in the synthesis of fatty acids and sterols, as a mechanism balancing the NADPH/NADP⁺ ratio. The fungal culture filtrates differently triggered the phenylpropanoid pathway in C. intybus plants: C. globosum culture filtrate increased phenylalanine and chicoric acid in the roots, whereas M. polyspora culture filtrate stimulated an increase of 4-OH-benzoate. Chicoric acid, whose biosynthetic pathway in the chicory plant is putative and still not well known, is a very promising natural compound playing an important role in plant defense. On the contrary, benzoic acids serve as precursors for a wide variety of essential compounds playing crucial roles in plant fitness and defense response activation. To the best of our knowledge, this is the first study that shows the biostimulant effect of C. globosum and M. polyspora culture filtrates on C. intybus growth and metabolome, increasing the knowledge on fungal bioresources for the development of biostimulants.

Metabolomics as an emerging tool to study plant-microbe interactions

In natural environments, interaction between plant roots and microorganisms are common. These interactions between microbial species and plants inhabited by them are being studied using various techniques. Metabolomics research based on mass spectrometric techniques is one of the crucial approaches that underpins system biology and relies on precision instrument analysis. In the last decade, this emerging field has received extensive attention. It provides a qualitative and quantitative approach for determining the mechanisms of symbiosis of bacteria and fungi with plants and also helps to elucidate the tolerance mechanisms of host plants against various abiotic stresses. However, this -omics application and its tools in plant-microbe interaction studies is still underutilized compared with genomic and transcriptomic methods. Therefore, it is crucial to bring this field forward to bear on the study of plant resistance and susceptibility. This review describes the current status of methods and progress in metabolomics applications for plant-microbe interaction studies discussing current challenges and future prospects.

The end of hunger: fertilizers, microbes and plant productivity

It is a grand challenge to ensure the food security for a predicted world population of exceeding 9.7 billion by 2050, especially in an era of global climate change, land degradation and biodiversity loss. Current agricultural productions are mainly relying on synthetic chemical fertilisers to boost plant productivity but have undesirable effects on the environment and soil biodiversity. A promising direction in sustainable agriculture is to harness naturally occurring processes of beneficial plant-associated microbiomes to ensure sustained crop production and global food security. Despite the significant progress made in the development of beneficial microbes as inoculants to enhance plant performance, challenges remain with the translation of knowledge of plant and soil microbiomes to successful microbial products in the agricultural sector. Here, we highlight how fertilizer technology should be renovated by harnessing microbiome-based innovations to promote plant productivity and contribute to the end of hunger.