Proteomic insight into the mitigation of wheat root drought stress by arbuscular mycorrhizae

Expression patterns of candidate genes for the Lr46/Yr29 "slow rust" locus in common wheat (Triticum aestivum L.) and associated miRNAs inform of the gene conferring the Puccinia triticina resistance trait

Leaf rust caused by Puccinia triticina (Pt) is one of the most impactful diseases causing substantial losses in common wheat (Triticum aestivum L.) crops. In adult plants resistant to Pt, a horizontal adult plant resistance (APR) is observed: APR protects the plant against multiple pathogen races and is distinguished by durable persistence under production conditions. The Lr46/Yr29 locus was mapped to chromosome 1B of common wheat genome, but the identity of the underlying gene has not been demonstrated although several candidate genes have been proposed. This study aimed to analyze the expression of nine candidate genes located at the Lr46/Yr29 locus and their four complementary miRNAs (tae-miR5384-3p, tae-miR9780, tae-miR9775, and tae-miR164), in response to Pt infection. The plant materials tested included five reference cultivars in which the molecular marker csLV46G22 associated with the Lr46/Yr29-based Pt resistance was identified, as well as one susceptible control cultivar. Biotic stress was induced in adult plants by inoculation with fungal spores under controlled conditions. Plant material was sampled before and at 6, 12, 24, 48 hours post inoculation (hpi). Differences in expression of candidate genes at the Lr46/Yr29 locus were analyzed by qRT-PCR and showed that the expression of the genes varied at the analyzed time points. The highest expression of Lr46/Yr29 candidate genes (Lr46-Glu1, Lr46-Glu2, Lr46-Glu3, Lr46-RLK1, Lr46-RLK2, Lr46-RLK3, Lr46-RLK4, Lr46-Snex, and Lr46-WRKY) occurred at 12 and 24 hpi and such expression profiles were obtained only for one candidate gene among the nine genes analyzed (Lr46-Glu2), indicating that it may be a contributing factor in the resistance response to Pt infection.

Harnessing root-soil-microbiota interactions for drought-resilient cereals

Cereal plants form complex networks with their associated microbiome in the soil environment. A complex system including variations of numerous parameters of soil properties and host traits shapes the dynamics of cereal microbiota under drought. These multifaceted interactions can greatly affect carbon and nutrient cycling in soil and offer the potential to increase plant growth and fitness under drought conditions. Despite growing recognition of the importance of plant microbiota to agroecosystem functioning, harnessing the cereal root microbiota remains a significant challenge due to interacting and synergistic effects between root traits, soil properties, agricultural practices, and drought-related features. A better mechanistic understanding of root-soil-microbiota associations could lead to the development of novel strategies to improve cereal production under drought. In this review, we discuss the root-soil-microbiota interactions for improving the soil environment and host fitness under drought and suggest a roadmap for harnessing the benefits of these interactions for drought-resilient cereals. These methods include conservative trait-based approaches for the selection and breeding of plant genetic resources and manipulation of the soil environments.

Diversity of Expression Patterns of Lr34, Lr67, and Candidate Genes towards Lr46 with Analysis of Associated miRNAs in Common Wheat Hybrids in Response to Puccinia triticina Fungus

Leaf rust caused by Puccinia triticina (Pt) is one of the most dangerous diseases causing significant losses in common wheat crops. In adult plants resistant to rust, a horizontal adult plant resistance (APR) type is observed, which protects the plant against multiple pathogen races and is distinguished by greater persistence under production conditions. Crucial pleiotropic slow-rust genes such as Lr34, Lr46, Lr67, and Lr68, in combination with other genes of lesser influence, continue to increase durable resistance to rust diseases. Based on our previous results, we selected four candidate genes for Lr46 out of ten candidates and analysed them for expression before and after inoculation by P. triticina. As part of our study, we also investigated the expression patterns of miRNA molecules complementary to Lr34 and the candidate genes. The aim of the study was to analyse the expression profiles of candidate genes for the Lr46 gene and the Lr34 and Lr67 genes responsible for the differential leaf-rust resistance of hybrid forms of the F1 generation resulting from crosses between the Glenlea cultivar and cultivars from Polish breeding companies. In addition, the expression of five miRNAs (tae-miR9653b, tae-miR5384-3p, tae-miR9780, tae-miR9775 and tae-miR164), complementary to Lr34, and selected candidate genes were analysed using stem-loop RT-PCR and ddPCR. Biotic stress was induced in adult plants by inoculation with Pt fungal spores, under controlled conditions. Plant material was collected before and 6, 12, 24, and 48 h after inoculation (hpi). Differences in expression patterns of Lr34, Lr67, and candidate genes (for Lr46) were analysed by qRT-PCR and showed that gene expression changed at the analysed time points. Identification of molecular markers coupled to the Lr genes studied was also carried out to confirm the presence of these genes in wheat hybrids. qRT-PCR was used to examine the expression levels of the resistance genes. The highest expression of Lr46/Yr29 genes (Lr46-Glu2, Lr46-RLK1, Lr46-RLK2, and Lr46-RLK3) occurred at 12 and 24 hpi, and such expression profiles were obtained for only one candidate gene among the four genes analysed (Lr46-Glu2), indicating that it may be involved in resistance mechanisms of response to Pt infection.

Genome-wide association study in two-row spring barley landraces identifies QTL associated with plantlets root system architecture traits in well-watered and osmotic stress conditions

Water availability is undoubtedly one of the most important environmental factors affecting crop production. Drought causes a gradual deprivation of water in the soil from top to deep layers and can occur at diverse stages of plant development. Roots are the first organs that perceive water deficit in soil and their adaptive development contributes to drought adaptation. Domestication has contributed to a bottleneck in genetic diversity. Wild species or landraces represent a pool of genetic diversity that has not been exploited yet in breeding program. In this study, we used a collection of 230 two-row spring barley landraces to detect phenotypic variation in root system plasticity in response to drought and to identify new quantitative trait loci (QTL) involved in root system architecture under diverse growth conditions. For this purpose, young seedlings grown for 21 days in pouches under control and osmotic-stress conditions were phenotyped and genotyped using the barley 50k iSelect SNP array, and genome-wide association studies (GWAS) were conducted using three different GWAS methods (MLM GAPIT, FarmCPU, and BLINK) to detect genotype/phenotype associations. In total, 276 significant marker-trait associations (MTAs; p-value (FDR)< 0.05) were identified for root (14 and 12 traits under osmotic-stress and control conditions, respectively) and for three shoot traits under both conditions. In total, 52 QTL (multi-trait or identified by at least two different GWAS approaches) were investigated to identify genes representing promising candidates with a role in root development and adaptation to drought stress.

Beneficial Root-Associated Microbiome during Drought and Flooding Stress in Plants

Crop productivity is seriously threatened by the rise in the frequency and severity of drought and flood events around the world. Reduced drought and flooding stress in vulnerable species and ecosystems depends on our ability to comprehend how drought and flooding affect plant physiology and plant-associated microbes. Involvement of both abscisic acid ABA-dependent and ABA-independent pathways has been noted during drought. Hypoxic conditions impede hydraulic conductance, nutrient uptake and plant growth and development, as well as root aerobic respiration. The root microbiome, which works with the roots during drought and flood, is made up of plant growth-promoting rhizosphere, endophytes and mycorrhizas. A large number of phytohormones, primarily auxins, cytokinin and ethylene, as well as enzymes like 1-Aminocyclopropane-1-Carboxylate deaminase (ACC deaminase) and metabolites like exopolysaccharides are produced by rhizospheric microbes. These phytohormones, enzymes and metabolites have role in the induction of systemic drought tolerance in plants. Under hypoxia, anaerobic microbes with the potential to harm the plant due to their pathogenic behavior or soil denitrification ability are more likely to be present in the rhizosphere and roots. This review concentrates on the primary mechanisms of plant-microbe interactions under drought and flood stress as well as the importance of flood and drought-tolerant microbes in maintaining and increasing crop plant productivity under stress.

Role of foliar biostimulants (of plant origin) on grapevine adaptation to climate change

Heat waves and drought stress are typical aspects of current climate change, significantly affecting the grapevine physiology in many world growing areas. Biostimulants can play an important role in reducing the negative effects of climate change; that’s why this experiment was set up in order to test two new foliar biostimulants (protein hydrolysates of plant origin). The field experiment was carried out in 2017 and 2018 in Oltrepo pavese area (Lombardia region, northwest Italy, 270 m asl), on a six-year-old vineyard of V. vinifera L. cv. Merlot clone 181 grafted on Gravesac, Guyot trellis, 4,000 vines/ha and not irrigated. Two new protein hydrolysates of plant origin were sprayed twice, just after fruit set and 15 days later, by using 2.5 L/ha. Leaf proteomics and metabolomics were studied in 2017, while productive and qualitative data were recorded in both years at harvest (September 1st, 2017 and August 28th 2018). The most significant findings were: (a) the treatments slowed down the grape ripening, by stimulating vegetative activity and reducing sugar accumulation; (b) less heat and drought stress symptoms were observed in the canopies of treated vines, as compared to the control ones.

The pivotal role of cultivar affinity to arbuscular mycorrhizal fungi in determining mycorrhizal responsiveness to water deficit

Arbuscular mycorrhizal fungi (AMF) have gained remarkable importance, having been proved to alleviate drought stress-induced damage in wheat due to their ability to ameliorate plant water use efficiency and antioxidant enzyme activity. However, despite the current relevance of the topic, the molecular and physiological processes at the base of this symbiosis never consider the single cultivar affinity to mycorrhization as an influencing factor for the metabolic response in the AMF-colonized plant. In the present study, the mycorrhizal affinity of two durum wheat species (T. turgidum subsp. durum (Desf.)) varieties, Iride and Ramirez, were investigated. Successively, an untargeted metabolomics approach has been used to study the fungal contribution to mitigating water deficit in both varieties. Iride and Ramirez exhibited a high and low level of mycorrhizal symbiosis, respectively; resulting in a more remarkable alteration of metabolic pathways in the most colonised variety under water deficit conditions. However, the analysis highlighted the contribution of AMF to mitigating water deficiency in both varieties, resulting in the up- and down-regulation of many amino acids, alkaloids, phenylpropanoids, lipids, and hormones.

Comparative analysis of combined phosphorus and drought stress-responses in two winter wheat

Phosphorus stress and drought stress are common abiotic stresses for wheat. In this study, two winter wheat varieties "Xindong20" and "Xindong23" were cultured in a hydroponic system using Hoagland nutrient solution and treated with drought stress under conventional (CP: 1.0 mmol/L) and low (LP: 0.05 mmol/L) phosphorus levels. Under drought stress, the root growth was better under LP than under CP. Under LP, root phosphorus content was increased by 94.2% in Xindong20 and decreased by 48.9% in Xindong23 at 3 d after re-watering, compared with those at 0 d under drought stress. However, the potassium (K) content was the highest among the four elements studied and the phosphorus (P) and calcium (Ca) content were reduced in the root of the two varieties. Under CP, the zinc (Zn) content was higher than that under LP in Xindong23. The GeneChip analysis showed that a total of 4,577 and 202 differentially expressed genes (DEGs) were detected from the roots of Xindong20 and Xindong23, respectively. Among them, 89.9% of DEGs were involved in organelles and vesicles in Xindong20, and 69.8% were involved in root anatomical structure, respiratory chain, electron transport chain, ion transport, and enzyme activity in Xindong23. Overall, LP was superior to CP in mitigating drought stress on wheat, and the regulatory genes were also different in the two varieties. Xindong20 had higher drought tolerance for more up-regulated genes involved in the responses compared to Xindong23.

The arbuscular mycorrhizal fungus Rhizophagus clarus improves physiological tolerance to drought stress in soybean plants

Soybean (Glycine max L.) is an economically important crop, and is cultivated worldwide, although increasingly long periods of drought have reduced the productivity of this plant. Research has shown that inoculation with arbuscular mycorrhizal fungi (AMF) provides a potential alternative strategy for the mitigation of drought stress. In the present study, we measured the physiological and morphological performance of two soybean cultivars in symbiosis with Rhizophagus clarus that were subjected to drought stress (DS). The soybean cultivars Anta82 and Desafio were grown in pots inoculated with R. clarus. Drought stress was imposed at the V3 development stage and maintained for 7 days. A control group, with well-irrigated plants and no AMF, was established simultaneously in the greenhouse. The mycorrhizal colonization rate, and the physiological, morphological, and nutritional traits of the plants were recorded at days 3 and 7 after drought stress conditions were implemented. The Anta82 cultivar presented the highest percentage of AMF colonization, and N and K in the leaves, whereas the DS group of the Desafio cultivar had the highest water potential and water use efficiency, and the DS + AMF group had thermal dissipation that permitted higher values of Fv/Fm, A, and plant height. The results of the principal components analysis demonstrated that both cultivars inoculated with AMF performed similarly under DS to the well-watered plants. These findings indicate that AMF permitted the plant to reduce the impairment of growth and physiological traits caused by drought conditions.

Research Progress in the Field of Microbial Mitigation of Drought Stress in Plants

Plants defend themselves against ecological stresses including drought. Therefore, they adopt various strategies to cope with stress, such as seepage and drought tolerance mechanisms, which allow plant development under drought conditions. There is evidence that microbes play a role in plant drought tolerance. In this study, we presented a review of the literature describing the initiation of drought tolerance mediated by plant inoculation with fungi, bacteria, viruses, and several bacterial elements, as well as the plant transduction pathways identified via archetypal functional or morphological annotations and contemporary "omics" technologies. Overall, microbial associations play a potential role in mediating plant protection responses to drought, which is an important factor for agricultural manufacturing systems that are affected by fluctuating climate.

Potential of Trichoderma harzianum and Its Metabolites to Protect Wheat Seedlings against Fusarium culmorum and 2,4-D

Wheat is a critically important crop. The application of fungi, such as Trichoderma harzianum, to protect and improve crop yields could become an alternative solution to synthetic chemicals. However, the interaction between the fungus and wheat in the presence of stress factors at the molecular level has not been fully elucidated. In the present work, we exposed germinating seeds of wheat (Triticum aestivum) to the plant pathogen Fusarium culmorum and the popular herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) in the presence of T. harzianum or its extracellular metabolites. Then, the harvested roots and shoots were analyzed using spectrometry, 2D-PAGE, and MALDI-TOF/MS techniques. Although F. culmorum and 2,4-D were found to disturb seed germination and the chlorophyll content, T. harzianum partly alleviated these negative effects and reduced the synthesis of zearalenone by F. culmorum. Moreover, T. harzianum decreased the activity of oxidoreduction enzymes (CAT and SOD) and the contents of the oxylipins 9-Hode, 13-Hode, and 13-Hotre induced by stress factors. Under the influence of various growth conditions, changes were observed in over 40 proteins from the wheat roots. Higher volumes of proteins and enzymes performing oxidoreductive functions, such as catalase, ascorbate peroxidase, cytochrome C peroxidase, and Cu/Zn superoxide dismutase, were found in the Fusarium-inoculated and 2,4-D-treated wheat roots. Additionally, observation of the level of 12-oxo-phytodienoic acid reductase involved in the oxylipin signaling pathway in wheat showed an increase. Trichoderma and its metabolites present in the system leveled out the mentioned proteins to the control volumes. Among the 30 proteins examined in the shoots, the expression of the proteins involved in photosynthesis and oxidative stress response was found to be induced in the presence of the herbicide and the pathogen. In summary, these proteomic and metabolomic studies confirmed that the presence of T. harzianum results in the alleviation of oxidative stress in wheat induced by 2,4-D or F. culmorum.

Microbial Biostimulants as Response to Modern Agriculture Needs: Composition, Role and Application of These Innovative Products

An increasing need for a more sustainable agriculturally-productive system is required in order to preserve soil fertility and reduce soil biodiversity loss. Microbial biostimulants are innovative technologies able to ensure agricultural yield with high nutritional values, overcoming the negative effects derived from environmental changes. The aim of this review was to provide an overview on the research related to plant growth promoting microorganisms (PGPMs) used alone, in consortium, or in combination with organic matrices such as plant biostimulants (PBs). Moreover, the effectiveness and the role of microbial biostimulants as a biological tool to improve fruit quality and limit soil degradation is discussed. Finally, the increased use of these products requires the achievement of an accurate selection of beneficial microorganisms and consortia, and the ability to prepare for future agriculture challenges. Hence, the implementation of the microorganism positive list provided by EU (2019/1009), is desirable.

Insights into the plant responses to drought and decoding the potential of root associated microbiome for inducing drought tolerance

Global increase in water scarcity is a serious problem for sustaining crop productivity. The lack of water causes the degeneration of the photosynthetic apparatus, an imbalance in key metabolic pathways, an increase in free radical generation as well as weakens the root architecture of plants. Drought is one of the major stresses that directly interferes with the osmotic status of plant cells. Abscisic acid (ABA) is known to be a key player in the modulation of drought responses in plants and involvement of both ABA-dependent and ABA-independent pathways have been observed during drought. Concomitantly, other phytohormones such as auxins, ethylene, gibberellins, cytokinins, jasmonic acid also confer drought tolerance and a crosstalk between different phytohormones and transcription factors at the molecular level exists. A number of drought-responsive genes and transcription factors have been utilized for producing transgenic plants for improved drought tolerance. Despite relentless efforts, biotechnological advances have failed to design completely stress tolerant plants until now. The root microbiome is the hidden treasure that possesses immense potential to revolutionize the strategies for inducing drought resistance in plants. Root microbiota consist of plant growth-promoting rhizobacteria, endophytes and mycorrhizas that form a consortium with the roots. Rhizospheric microbes are proliferous producers of phytohormones, mainly auxins, cytokinin, and ethylene as well as enzymes like the 1-aminocyclopropane-1-carboxylate deaminase (ACC deaminase) and metabolites like exopolysaccharides that help to induce systemic tolerance against drought. This review, therefore focuses on the major mechanisms of plant-microbe interactions under drought-stressed conditions and emphasizes the importance of drought-tolerant microbes for sustaining and improving the productivity of crop plants under stress.

A Milk Foodomics Investigation into the Effect of Pseudomonas fluorescens Growth under Cold Chain Conditions

Pseudomonas fluorescens is a psychrotrophic species associated with milk spoilage because of its lipolytic and proteolytic activities. Consequently, monitoring P. fluorescens or its antecedent activity in milk is critical to preventing quality defects of the product and minimizing food waste. Therefore, in this study, untargeted metabolomics and peptidomics were used to identify the changes in milk related to P. fluorescens activity by simulating the low-temperature conditions usually found in milk during the cold chain. Both unsupervised and supervised multivariate statistical approaches showed a clear effect caused by the P. fluorescens inoculation on milk samples. Our results showed that the levels of phosphatidylglycerophosphates and glycerophospholipids were directly related to the level of contamination. In addition, our metabolomic approach allowed us to detect lipid and protein degradation products that were directly correlated with the degradative metabolism of P. fluorescens. Peptidomics corroborated the proteolytic propensity of P. fluorescens-contaminated milk, but with lower sensitivity. The results obtained from this study provide insights into the alterations related to P. fluorescens 39 contamination, both pre and post heat treatment. This approach could represent a potential tool to retrospectively understand the actual quality of milk under cold chain storage conditions, either before or after heat treatments.

Optimización en la aclimatación de plántulas micropropagadas de banano (Musa sp.) utilizando tres insumos orgánicos

El éxito de la micropropagación de plantas in vitro depende en parte de la fase de aclimatación, esta etapa presenta problemas de supervivencia y conlleva extensas semanas de adaptación. En este sentido, la utilización de microorganismos eficientes nativos son una alternativa biotecnológica para adaptar plantas in vitro. El presente trabajo tiene como objetivo evaluar el efecto de la aplicación de Trichoderma ghanense, micorrizas arbusculares y un biofertilizante líquido en plantas meristemáticas de banano variedad William en las fases de aclimatación y vivero. Para los ensayos en las fases de aclimatación y vivero se realizaron 20 tratamientos y se utilizó un diseño factorial 2(k) con una duración de seis semanas en ambas fases. Los resultados demuestran que en la fase de aclimatación el mejor tratamiento fue el B10 con incrementos del 29,6 % de altura y 19,9 % de diámetro respecto al control; mientras que, para el área foliar fue el B19 con 84,7 % de incremento en comparación al control. En fase de vivero el mejor tratamiento fue el B19 presentando incrementos del 14,5 % altura, 19,3 % diámetro del pseudotallo, 13,4 % área foliar, 91,8 % longitud radicular, 39,98 % peso húmedo y 90,5 % peso seco en comparación al control. Ambas fases alcanzaron porcentaje de micorrización mayores al 45 %. Los porcentajes de supervivencia fueron del 100 % en fase de aclimatación. Por lo expuesto, se concluye que los insumos orgánicos constituyen una alternativa para el manejo y adaptación de plantas producidas in vitro.

The application of exogenous PopW increases the tolerance of Solanum lycopersicum L. to drought stress through multiple mechanisms

Tomato is a major cultivated vegetable species of great economic importance throughout the world, but its fruit yield is severely impaired by drought stress. PopW, a harpin protein from Ralstonia solanacearum ZJ3721, plays vital roles in various plant defence responses and growth. In this study, we observed that the foliar application of PopW increased tomato drought tolerance. Our results showed that compared with water-treated plants, PopW-treated plants presented a significantly higher recovery rate and leaf relative water content under drought-stress conditions. PopW decreased the malondialdehyde content and relative electrical conductivity by 40.2% and 21%, respectively. Drought disrupts redox homeostasis through the excessive accumulation of reactive oxygen species (ROS). PopW-treated plants displayed an obvious reduction in ROS accumulation due to enhanced activities of the antioxidant enzyme catalase, superoxide dismutase and peroxidase. Moreover, PopW promoted early stomatal closure, thereby minimizing the water loss rate of plants under drought stress. Further investigation revealed that endogenous abscisic acid (ABA) levels and the transcript levels of drought-responsive genes involved in ABA signal transduction pathways increased in response to PopW. These results confirm that PopW increases drought tolerance through multiple mechanisms involving an enhanced water-retention capacity, balanced redox homeostasis, increased osmotic adjustment, reduced membrane damage and decreased stomatal aperture, suggesting that the application of exogenous PopW may be a potential method to enhance tomato drought tolerance.

Metabolomic, proteomic and physiological insights into the potential mode of action of thymol, a phytotoxic natural monoterpenoid phenol

Thymol is a natural phenolic monoterpene widely produced by different species belonging to the Labiateae family. Although the thymol phytotoxicity is well known, the knowledge of its potential toxic mechanism is still limited. In this regard, the model species Arabidopsis thaliana was treated for 16 days by sub-irrigation with 300 μM of thymol. The results confirmed the high phytotoxic potential of this phenolic compound, which caused a reduction in plant growth and development. Thymol induced a water status alteration accompanied by an increase in ABA content and stomatal closure. Furthermore, leaves appeared necrotic in the margins and their temperature rinsed. The increase in H₂O₂ content suggested an oxidative stress experienced by treated plants. Both metabolomic and proteomic analysis confirmed this hypothesis showing a strong increase in osmoprotectants content, such as galactinol and proline, and a significant up-accumulation of proteins involved in ROS detoxification. Furthermore, the down-accumulation of proteins and pigments involved in the photosynthetic machinery, the increase in light sensitivity and the lower PSII efficiency well indicated a reduction in photosynthetic activity. Overall, we can postulate that thymol-induced phytotoxicity could be related to a combined osmotic and oxidative stress that resulted in reduced plant development.

Seed Metabolism and Pathogen Resistance Enhancement in Pisum sativum During Colonization of Arbuscular Mycorrhizal Fungi: An Integrative Metabolomics-Proteomics Approach

Pulses are one of the most important categories of food plants, and Pea (Pisum sativum L.) as a member of pulses is considered a key crop for food and feed and sustainable agriculture. Integrative multi-omics and microsymbiont impact studies on the plant's immune system are important steps toward more productive and tolerant food plants and thus will help to find solutions against food poverty. Didymella pinodes is a main fungal pathogen of pea plants. Arbuscular mycorrhizal fungi (AMF) promote plant growth and alleviate various stresses. However, it remained unclear as to how the AMF effect on seed metabolism and how this influences resistance against the pathogen. This study assesses the AMF impacts on yield components and seed quality upon D. pinodes infection on two different P. sativum cultivars, susceptible versus tolerant, grown in pots through phenotypic and seed molecular analyses. We found that AMF symbiosis affects the majority of all tested yield components as well as a reduction of disease severity in both cultivars. Seeds of mycorrhizal pea plants showed strong responses of secondary metabolites with nutritional, medicinal, and pharmaceutical attributes, also involved in pathogen response. This is further supported by proteomic data, functionally determining those primary and secondary metabolic pathways, involved in pathogen response and induced upon AMF-colonization. The data also revealed cultivar specific effects of AMF symbiosis that increase understanding of genotype related differences. Additionally, a suite of proteins and secondary metabolites are presented, induced in seeds of P. sativum upon AMF-colonization and pathogen attack, and possibly involved in induced systemic resistance against D. pinodes, useful for modern breeding strategies implementing microsymbionts toward increased pathogen resistance.

Incorporating Phylogenetic Information in Microbiome Differential Abundance Studies Has No Effect on Detection Power and FDR Control

We consider the problem of incorporating evolutionary information (e.g., taxonomic or phylogenic trees) in the context of metagenomics differential analysis. Recent results published in the literature propose different ways to leverage the tree structure to increase the detection rate of differentially abundant taxa. Here, we propose instead to use a different hierarchical structure, in the form of a correlation-based tree, as it may capture the structure of the data better than the phylogeny. We first show that the correlation tree and the phylogeny are significantly different before turning to the impact of tree choice on detection rates. Using synthetic data, we show that the tree does have an impact: smoothing p-values according to the phylogeny leads to equal or inferior rates as smoothing according to the correlation tree. However, both trees are outperformed by the classical, non-hierarchical, Benjamini–Hochberg (BH) procedure in terms of detection rates. Other procedures may use the hierarchical structure with profit but do not control the False Discovery Rate (FDR) a priori and remain inferior to a classical Benjamini–Hochberg procedure with the same nominal FDR. On real datasets, no hierarchical procedure had significantly higher detection rate that BH. Intuition advocates that the use of hierarchical structures should increase the detection rate of differentially abundant taxa in microbiome studies. However, our results suggest that current hierarchical procedures are still inferior to standard methods and more effective procedures remain to be invented.

Protein Expression Profile and Transcriptome Characterization of Penicillium expansum Induced by Meyerozyma guilliermondii

Antagonistic yeasts can inhibit fungal growth. In our previous research, Meyerozyma guilliermondii, one of the antagonistic yeasts, exhibited antagonistic activity against Penicillium expansum. However, the mechanisms, especially the molecular mechanisms of inhibiting activity of M. guilliermondii, are not clear. In this study, the protein expression profile and transcriptome characterization of P. expansum induced by M. guilliermondii were investigated. In P. expansum induced by M. guilliermondii, 66 proteins were identified as differentially expressed, among them six proteins were upregulated and 60 proteins were downregulated, which were associated with oxidative phosphorylation, ATP synthesis, basal metabolism, and response regulation. Simultaneously, a transcriptomic approach based on RNA-Seq was applied to annotate the genome of P. expansum and then studied the changes of gene expression in P. expansum treated with M. guilliermondii. The results showed that differentially expressed genes such as HEAT, Phosphoesterase, Polyketide synthase, ATPase, and Ras-association were significantly downregulated, in contrast to Cytochromes P450, Phosphatidate cytidylyltransferase, and Glutathione S-transferase, which were significantly upregulated. Interestingly, the downregulated differentially expressed proteins and genes have a corresponding relationship; these results revealed that these proteins and genes were important in the growth of P. expansum treated with M. guilliermondii.

Physiological, Ecological, and Biochemical Implications in Tomato Plants of Two Plant Biostimulants: Arbuscular Mycorrhizal Fungi and Seaweed Extract

The worldwide use of plant biostimulants (PBs) represents an environmentally friendly tool to increase crop yield and productivity. PBs include different substances, compounds, and growth-promoting microorganism formulations, such as those derived from arbuscular mycorrhizal fungi (AMF) or seaweed extracts (SEs), which are used to regulate or enhance physiological processes in plants. This study analyzed the physiological, ecological, and biochemical implications of the addition of two PBs, AMF or SE (both alone and in combination), on tomato plants (Solanum lycopersicum L. cv. "Rio Fuego"). The physiological responses evaluated were related to plant growth and photosynthetic performance. The ecological benefits were assessed based on the success of AMF colonization, flowering, resistance capacity, nonphotochemical quenching (NPQ), and polyphenol content. Biochemical effects were evaluated via protein, lipid, carbohydrate, nitrogen, and phosphorous content. Each PB was found to benefit tomato plants in a different but complementary manner. AMF resulted in an energetically expensive (high ETR_MAX but low growth) but protective (high NPQ and polyphenol content) response. AMF + nutritive solution (NS) induced early floration but resulted in low protein, carbohydrate, and lipid content. Both AMF and AMF + NS favored foliar instead of root development. In contrast, SE and SE + NS favored protein content and root development and did not promote flowering. However, the combination of both PBs (AMF + SE) resulted in an additive effect, reflected in an increase in both foliar and root growth as well as protein and carbohydrate content. Moreover, a synergistic effect was also found, which was expressed in accelerated flowering and AMF colonization. We present evidence of benefits to plant performance (additive and synergistic) due to the interactive effects between microbial (AMF) and nonmicrobial (SEs) PBs and propose that the complementary modes of action of both PBs may be responsible for the observed positive effects due to the new and emerging properties of their components instead of exclusively being the result of known constituents. These results will be an important contribution to biostimulant research and to the development of a second generation of PBs in which combined and complementary mechanisms may be functionally designed.

Interaction of Tomato Genotypes and Arbuscular Mycorrhizal Fungi under Reduced Irrigation

Climate change is increasing drought events and decreasing water availability. Tomato is commonly transplanted to an open field after seedling production in a nursery, requiring large volumes of water. Arbuscular mycorrhizal (AM) fungi help plants cope with drought stress; however, their effects depend on plant genotype and environmental conditions. In this study, we assessed the interactions among different tomato seedling genotypes and two AM fungi, Funneliformis mosseae and Rhizophagus intraradices, under two water regimes, full and reduced. Our results showed that F. mosseae was more effective than R. intraradices in the mitigation of drought stress both in old and modern genotypes. However, seedlings inoculated with R. intraradices recorded the highest values of leaf area. ‘Pearson’ and ‘Everton’ genotypes inoculated with F. mosseae recorded the highest values of root, leaf, and total dry weights under reduced and full irrigation regimes, respectively. In addition, ‘Pearson’ and ‘H3402’ genotypes inoculated with F. mosseae under a reduced irrigation regime displayed high values of water use efficiency. Our results highlight the importance of using AM fungi to mitigate drought stress in nursery production of tomato seedlings. However, the development of ad hoc AM fungal formulations, which consider genotype x AM fungi interactions, is fundamental for achieving the best agronomic performances.

ABA signaling rather than ABA metabolism is involved in trehalose-induced drought tolerance in tomato plants

Trehalose increased drought tolerance of tomato plants, accompanied by reduced water loss and closed stomata, which was associated with the upregulated ABA signaling-related genes expression, but not in ABA accumulation. Drought is one of the principal abiotic stresses that negatively influence the growth of plant and yield. Trehalose has great agronomic potential to improve the stress tolerance of plants. However, little information is available on the role of ABA and its signaling components in trehalose-induced drought tolerance. The aim of this study is to elucidate the potential mechanism by which trehalose regulates ABA in response to drought stress. In this study, 6-week-old tomato (Solanum lycopersicum cv. Ailsa Craig) plants were treated with 0 or 15.0 mM trehalose solution. Results showed that trehalose treatment significantly enhanced drought tolerance of tomato plants, accompanied by encouraged stomatal closure and protected chloroplast ultrastructure. Compared with controls, trehalose-treated plants showed lower hydrogen peroxide content and higher antioxidant enzymes activities, which contributed to alleviate oxidative damage caused by drought. Moreover, trehalose treatment decreased ABA content, which was followed by the downregulation of ABA biosynthesis genes expression and the upregulation of ABA catabolism genes expression. In contrast, exogenous trehalose upregulated transcript levels of ABA signaling-related genes, including SlPYL1/3/4/5/6/7/9, SlSnRK2.3/4, SlAREB1/2, and SlDREB1. These results suggested that trehalose treatment enhanced drought tolerance of tomato plants, and it's ABA signaling rather than ABA metabolism that was involved in trehalose-induced drought tolerance in tomato plants. These findings provide evidence for the physiological role of trehalose and bring about a new understanding of the possible relationship between trehalose and ABA.

Microbes in Cahoots with Plants: MIST to Hit the Jackpot of Agricultural Productivity during Drought

Drought conditions marked by water deficit impede plant growth thus causing recurrent decline in agricultural productivity. Presently, research efforts are focussed towards harnessing the potential of microbes to enhance crop production during drought. Microbial communities, such as arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria (PGPR) buddy up with plants to boost crop productivity during drought via microbial induced systemic tolerance (MIST). The present review summarizes MIST mechanisms during drought comprised of modulation in phytohormonal profiles, sturdy antioxidant defence, osmotic grapnel, bacterial exopolysaccharides (EPS) or AMF glomalin production, volatile organic compounds (VOCs), expression of fungal aquaporins and stress responsive genes, which alters various physiological processes such as hydraulic conductance, transpiration rate, stomatal conductivity and photosynthesis in host plants. Molecular studies have revealed microbial induced differential expression of various genes such as ERD15 (Early Response to Dehydration 15), RAB18 (ABA-responsive gene) in Arabidopsis, COX1 (regulates energy and carbohydrate metabolism), PKDP (protein kinase), AP2-EREBP (stress responsive pathway), Hsp20, bZIP1 and COC1 (chaperones in ABA signalling) in Pseudomonas fluorescens treated rice, LbKT1, LbSKOR (encoding potassium channels) in Lycium, PtYUC3 and PtYUC8 (IAA biosynthesis) in AMF inoculated Poncirus, ADC, AIH, CPA, SPDS, SPMS and SAMDC (polyamine biosynthesis) in PGPR inoculated Arabidopsis, 14-3-3 genes (TFT1-TFT12 genes in ABA signalling pathways) in AMF treated Solanum, ACO, ACS (ethylene biosynthesis), jasmonate MYC2 gene in chick pea, PR1 (SA regulated gene), pdf1.2 (JA marker genes) and VSP1 (ethylene-response gene) in Pseudomonas treated Arabidopsis plants. Moreover, the key role of miRNAs in MIST has also been recorded in Pseudomonas putida RA treated chick pea plants.

Metabolomic responses triggered by arbuscular mycorrhiza enhance tolerance to water stress in wheat cultivars

Under global climate change forecasts, the pressure of environmental stressors (and in particular drought) on crop productivity is expected to rise and challenge further global food security. The application of beneficial microorganisms may represent an environment friendly tool to secure improved crop performance and yield stability. Accordingly, this current study aimed at elucidating the metabolomic responses triggered by mycorrhizal (Funneliformis mosseae) inoculation of durum (Triticum durum Desf.; cv. 'Mongibello') and bread wheat cultivars (Triticum aestivum L.; cv. 'Chinese Spring') under full irrigation and water deficit regimes. Metabolomics indicated a similar regulation of secondary metabolism in both bread and durum wheat cultivars following water limiting conditions. Nonetheless, a mycorrhizal fungi (AMF) x cultivar interaction could be observed, with the bread wheat cultivar being more affected by arbuscular colonization under water limiting conditions. Discriminant compounds could be mostly related to sugars and lipids, both being positively modulated by AMF colonization under water stress. Moreover, a regulation of metabolites related to oxidative stress and a tuning of crosstalk between phytohormones were also evidenced. Among the latter, the stimulation of the brassinosteroids biosynthetic pathway was particularly evident in inoculated wheat roots, supporting the hypothesis of their involvement in enhancing plant response to water stress and modulation of oxidative stress conditions. This study proposes new insights on the modulation of the tripartite interaction plant-AMF-environmental stress.

Metabolomics Provides Valuable Insight for the Study of Durum Wheat: A Review

Metabolomics is increasingly being applied in various fields offering a highly informative tool for high-throughput diagnostics. However, in plant sciences, metabolomics is underused, even though plant studies are relatively easy and cheap when compared to those on humans and animals. Despite their importance for human nutrition, cereals, and especially wheat, remain understudied from a metabolomics point of view. The metabolomics of durum wheat has been essentially neglected, although its genetic structure allows the inference of common mechanisms that can be extended to other wheat and cereal species. This review covers the present achievements in durum wheat metabolomics highlighting the connections with the metabolomics of other cereal species (especially bread wheat). We discuss the metabolomics data from various studies and their relationships to other "-omics" sciences, in terms of wheat genetics, abiotic and biotic stresses, beneficial microbes, and the characterization and use of durum wheat as feed, food, and food ingredient.

Protein Profiling of Arabidopsis Roots Treated With Humic Substances: Insights Into the Metabolic and Interactome Networks

Background and Aim: Humic substances (HSs) influence the chemical and physical properties of the soil, and are also known to affect plant physiology and nutrient uptake. This study aimed to elucidate plant metabolic pathways and physiological processes influenced by HS activity. Methods: Arabidopsis roots were treated with HS for 8 h. Quantitative mass spectrometry-based proteomics analysis of root proteins was performed using the iTRAQ (Isobaric Tag for Relative and Absolute Quantification) technique. Out of 902 protein families identified and quantified for HS treated vs. untreated roots, 92 proteins had different relative content. Bioinformatic tools such as STRING, KEGG, IIS and Cytoscape were used to interpret the biological function, pathway analysis and visualization of network amongst the identified proteins. Results: From this analysis it was possible to evaluate that all of the identified proteins were functionally classified into several categories, mainly redox homeostasis, response to inorganic substances, energy metabolism, protein synthesis, cell trafficking, and division. Conclusion: In the present study an overview of the metabolic pathways most modified by HS biological activity is provided. Activation of enzymes of the glycolytic pathway and up regulation of ribosomal protein indicated a stimulation in energy metabolism and protein synthesis. Regulation of the enzymes involved in redox homeostasis suggest a pivotal role of reactive oxygen species in the signaling and modulation of HS-induced responses.

Genome-Wide Association Studies Reveal Genomic Regions Associated With the Response of Wheat (Triticum aestivum L.) to Mycorrhizae Under Drought Stress Conditions

In the majority of wheat growing areas worldwide, the incidence of drought stress has increased significantly resulting in a negative impact on plant development and grain yield. Arbuscular mycorrhizal symbiosis is known to improve drought stress tolerance of wheat. However, quantitative trait loci (QTL) involved in the response to drought stress conditions in the presence of mycorrhizae are largely unknown. Therefore, a diverse set consisting of 94 bread wheat genotypes was phenotyped under drought stress and well watered conditions in the presence and absence of mycorrhizae. Grain yield and yield components, drought stress related traits as well as response to mycorrhizae were assessed. In parallel, wheat accessions were genotyped by using the 90k iSelect chip, resulting in a set of 15511 polymorphic and mapped SNP markers, which were used for genome-wide association studies (GWAS). In general, drought stress tolerance of wheat was significantly increased in the presence of mycorrhizae compared to drought stress tolerance in the absence of mycorrhizae. However, genotypes differed in their response to mycorrhizae under drought stress conditions. Several QTL regions on different chromosomes were detected associated with grain yield and yield components under drought stress conditions. Furthermore, two genome regions on chromosomes 3D and 7D were found to be significantly associated with the response to mycorrhizae under drought stress conditions. Overall, the results reveal that inoculation of wheat with mycorrhizal fungi significantly improves drought stress tolerance and that QTL regions associated with the response to mycorrhizae under drought stress conditions exist in wheat. Further research is necessary to validate detected QTL regions. However, this study may be the starting point for the identification of candidate genes associated with drought stress tolerance and response to mycorrhizae under drought stress conditions. Maybe in future, these initial results will help to contribute to use mycorrhizal fungi effectively in agriculture and combine new approaches i.e., use of genotypic variation in response to mycorrhizae under drought stress conditions with existing drought tolerance breeding programs to develop new drought stress tolerant genotypes.

Omics approaches revealed how arbuscular mycorrhizal symbiosis enhances yield and resistance to leaf pathogen in wheat

Besides improved mineral nutrition, plants colonised by arbuscular mycorrhizal (AM) fungi often display increased biomass and higher tolerance to biotic and abiotic stresses. Notwithstanding the global importance of wheat as an agricultural crop, its response to AM symbiosis has been poorly investigated. We focused on the role of an AM fungus on mineral nutrition of wheat, and on its potential protective effect against Xanthomonas translucens. To address these issues, phenotypical, molecular and metabolomic approaches were combined. Morphological observations highlighted that AM wheat plants displayed an increased biomass and grain yield, as well as a reduction in lesion area following pathogen infection. To elucidate the molecular mechanisms underlying the mycorrhizal phenotype, we investigated changes of transcripts and proteins in roots and leaves during the double (wheat-AM fungus) and tripartite (wheat-AM fungus-pathogen) interaction. Transcriptomic and proteomic profiling identified the main pathways involved in enhancing plant biomass, mineral nutrition and in promoting the bio-protective effect against the leaf pathogen. Mineral and amino acid contents in roots, leaves and seeds, and protein oxidation profiles in leaves, supported the omics data, providing new insight into the mechanisms exerted by AM symbiosis to confer stronger productivity and enhanced resistance to X. translucens in wheat.

Proteomic approach to understand the molecular physiology of symbiotic interaction between Piriformospora indica and Brassica napus

Many studies have been now focused on the promising approach of fungal endophytes to protect the plant from nutrient deficiency and environmental stresses along with better development and productivity. Quantitative and qualitative protein characteristics are regulated at genomic, transcriptomic, and posttranscriptional levels. Here, we used integrated in-depth proteome analyses to characterize the relationship between endophyte Piriformospora indica and Brassica napus plant highlighting its potential involvement in symbiosis and overall growth and development of the plant. An LC-MS/MS based label-free quantitative technique was used to evaluate the differential proteomics under P. indica treatment vs. control plants. In this study, 8,123 proteins were assessed, of which 46 showed significant abundance (34 downregulated and 12 upregulated) under high confidence conditions (p-value ≤ 0.05, fold change ≥2, confidence level 95%). Mapping of identified differentially expressed proteins with bioinformatics tools such as GO and KEGG pathway analysis showed significant enrichment of gene sets involves in metabolic processes, symbiotic signaling, stress/defense responses, energy production, nutrient acquisition, biosynthesis of essential metabolites. These proteins are responsible for root's architectural modification, cell remodeling, and cellular homeostasis during the symbiotic growth phase of plant's life. We tried to enhance our knowledge that how the biological pathways modulate during symbiosis?

Plant Abiotic Stress Proteomics: The Major Factors Determining Alterations in Cellular Proteome

HIGHLIGHTS: Major environmental and genetic factors determining stress-related protein abundance are discussed.Major aspects of protein biological function including protein isoforms and PTMs, cellular localization and protein interactions are discussed.Functional diversity of protein isoforms and PTMs is discussed. Abiotic stresses reveal profound impacts on plant proteomes including alterations in protein relative abundance, cellular localization, post-transcriptional and post-translational modifications (PTMs), protein interactions with other protein partners, and, finally, protein biological functions. The main aim of the present review is to discuss the major factors determining stress-related protein accumulation and their final biological functions. A dynamics of stress response including stress acclimation to altered ambient conditions and recovery after the stress treatment is discussed. The results of proteomic studies aimed at a comparison of stress response in plant genotypes differing in stress adaptability reveal constitutively enhanced levels of several stress-related proteins (protective proteins, chaperones, ROS scavenging- and detoxification-related enzymes) in the tolerant genotypes with respect to the susceptible ones. Tolerant genotypes can efficiently adjust energy metabolism to enhanced needs during stress acclimation. Stress tolerance vs. stress susceptibility are relative terms which can reflect different stress-coping strategies depending on the given stress treatment. The role of differential protein isoforms and PTMs with respect to their biological functions in different physiological constraints (cellular compartments and interacting partners) is discussed. The importance of protein functional studies following high-throughput proteome analyses is presented in a broader context of plant biology. In summary, the manuscript tries to provide an overview of the major factors which have to be considered when interpreting data from proteomic studies on stress-treated plants.