Root metabolic plasticity underlies functional diversity in mycorrhiza-enhanced stress tolerance in tomato

Transcriptional Profiling to Assess the Effects of Biological Stimulant Atlanticell Micomix on Tomato Seedlings Under Salt Stress

Recent environmental changes in the Mediterranean region, attributable to anthropogenic climate change, present a substantial challenge to the adaptive evaluation of crops and the development of novel improvement strategies. In this study, we established a hydroponic tomato cultivation protocol under in vitro conditions to analyze the transcriptomic profile of seedlings exposed to salinity stress. The study also examined the impact of Atlanticell Micomix, a biological stimulant derived from a mixture of mycorrhizal microorganisms and rhizobacteria, on plant growth and development under standard conditions and in response to moderate salinity. Our transcriptomic analysis indicated a differential effect of biostimulant inoculation compared to the effect induced by salinity stress, involving genes such as GOX3 or DIR1, which are associated with the plant's defense response to adverse conditions. In addition, the presence of a cross-regulatory module between jasmonic acid and auxin, involving potential orthologs of IAA29 and JAZ, was proposed. The application of the biostimulant demonstrated a potential priming effect on the tomato seedlings, which might be useful in reversing the transcriptomic effects caused by salt stress. A comprehensive analysis of the pathways differentially affected by the treatments facilitates further investigation into the mechanisms underlying these effects.

Evaluating the stability of nursery-established arbuscular mycorrhizal fungal associations in apple rootstocks

Arbuscular mycorrhizal fungi (AMF) are promoted as commercial bioinoculants for sustainable agriculture. Little is known, however, about the survival of AMF inoculants in soil and their impacts on native or pre-established AMF communities in root tissue. The current study was designed to assess the stability of pre-existing/nursery-derived AMF in apple rootstocks after being planted into soil containing a known community of AMF with a limited number of species. Root-associated endophytic communities (bacteria and fungi) are known to differ depending on apple rootstock genotype. Thus, an additional aim of this study was to explore the effect of apple rootstock genotype on AMF community structure. A greenhouse experiment was conducted in which a variety of apple rootstock genotypes (G.890, G.935, M.26, and M.7) were inoculated with a commercially available, multi-species AMF consortium. Nursery-derived AMF communities were sequenced, and changes to AMF community structure following cultivation in pasteurized soil (inoculated and non-inoculated) were assessed using a Glomeromycota-specific phylogenetic tree, which included 91 different AMF species from 24 genera. Results show that inoculant colonization potential was limited and that apple rootstocks serve as a significant source of inoculum from the nursery where they are produced. Rootstocks established relationships with introduced AMF in a genotype-specific manner. Regardless of colonization success, however, the inoculant caused alterations to the resident AMF communities of both Geneva and Malling rootstocks, particularly low abundance taxa. In addition, phylogeny-based analysis revealed a unique, well-supported clade of unknown taxonomy, highlighting the importance of using phylogenetic-based classification for accurate characterization of AMF communities.IMPORTANCEUnderstanding the impacts of introduced AMF on residential AMF communities is essential to improving plant productivity in nursery and orchard systems. In general, there is a dearth of data on the interactions of commercial AMF inoculants with pre-established AMF communities living in symbiosis with the host plant. The interplay between apple rootstock genotype and the endophytic root microbiome is also an area where more research is needed. This study demonstrates the potential for nursery-established AMF associations to be maintained when transplanted into the field. In addition to providing insight into rootstock/AMF associations, our study calls attention to the current issues attendant with relying on web-based databases for determining AMF identity. The use of phylogenetic tools represents one possible solution and may be of value to industry practitioners in terms of improving product composition and consistency.

Response of Alternaria and Fusarium Species to Low Precipitation in a Drought-Tolerant Plant in Morocco

The plant mycobiome plays a crucial role in the host life cycle, influencing both healthy and diseased states, and is essential for plant tolerance to drought. In this study, we used ITS metabarcoding to investigate the fungal community of the drought-resistant plant Malva sylvestris L. in Morocco along a gradient of precipitation, encompassing subhumid and semi-arid environments. We sampled three biotopes: rhizosphere, bulk soil, and root endosphere. Our findings revealed an absence of beta-diversity differences between bulk soil and rhizosphere, indicating that the plant does not selectively influence its rhizosphere mycobiome. Additionally, ASVs belonging to the genus Alternaria represented up to 30% of reads in the plant's roots and correlated with drought (p = 0.006), indicating a potential role for this fungal genus in mitigating drought, possibly as part of the dark septate endophyte group. Root staining and microscopic observation revealed extensive colonization by fungal hyphae and microsclerotia-like structures. Furthermore, ASVs identified as Fusarium equiseti were also correlated with low precipitation and recognized as a hub taxon in the roots. However, it remains uncertain whether this species is pathogenic or beneficial to the plant. These insights contribute to our understanding of the plant mycobiome's role in drought tolerance and highlight the importance of specific fungal taxa in supporting plant health under varying environmental conditions. Future research should focus on characterizing these taxa's functional roles and their interactions with the host plant to further elucidate their contributions to drought resistance.

Plant Immunity Modulation in Arbuscular Mycorrhizal Symbiosis and Its Impact on Pathogens and Pests

Arbuscular mycorrhizal (AM) symbiosis is the oldest and most widespread mutualistic association on Earth and involves plants and soil fungi belonging to Glomeromycotina. A complex molecular, cellular, and genetic developmental program enables partner recognition, fungal accommodation in plant tissues, and activation of symbiotic functions such as transfer of phosphorus in exchange for carbohydrates and lipids. AM fungi, as ancient obligate biotrophs, have evolved strategies to circumvent plant defense responses to guarantee an intimate and long-lasting mutualism. They are among those root-associated microorganisms able to boost plants' ability to cope with biotic stresses leading to mycorrhiza-induced resistance (MIR), which can be effective across diverse hosts and against different attackers. Here, we examine the molecular mechanisms underlying the modulation of plant immunity during colonization by AM fungi and at the onset and display of MIR against belowground and aboveground pests and pathogens. Understanding the MIR efficiency spectrum and its regulation is of great importance to optimizing the biotechnological application of these beneficial microbes for sustainable crop protection.

The Effects of Rhizophagus irregularis Inoculation on Transcriptome of Medicago lupulina Leaves at Early Vegetative and Flowering Stages of Plant Development

The study is aimed at revealing the effects of Rhizophagus irregularis inoculation on the transcriptome of Medicago lupulina leaves at the early (second leaf formation) and later (flowering) stages of plant development. A pot experiment was conducted under conditions of low phosphorus (P) level in the substrate. M. lupulina plants were characterized by high mycorrhizal growth response and mycorrhization parameters. Library sequencing was performed on the Illumina HiseqXTen platform. Significant changes in the expression of 4863 (padj < 0.01) genes from 34049 functionally annotated genes were shown by Massive Analysis of cDNA Ends (MACE-Seq). GO enrichment analysis using the Kolmogorov-Smirnov test was performed, and 244 functional GO groups were identified, including genes contributing to the development of effective AM symbiosis. The Mercator online tool was used to assign functional classes of differentially expressed genes (DEGs). The early stage was characterized by the presence of six functional classes that included only upregulated GO groups, such as genes of carbohydrate metabolism, cellular respiration, nutrient uptake, photosynthesis, protein biosynthesis, and solute transport. At the later stage (flowering), the number of stimulated GO groups was reduced to photosynthesis and protein biosynthesis. All DEGs of the GO:0016036 group were downregulated because AM plants had higher resistance to phosphate starvation. For the first time, the upregulation of genes encoding thioredoxin in AM plant leaves was shown. It was supposed to reduce ROS level and thus, consequently, enhance the mechanisms of antioxidant protection in M. lupulina plants under conditions of low phosphorus level. Taken together, the obtained results indicate genes that are the most important for the effective symbiosis with M. lupulina and might be engaged in other plant species.

Arbuscular mycorrhizal fungi influence the intraspecific competitive ability of plants under field and glasshouse conditions

MAIN CONCLUSION

Nicotiana attenuata's capacity to interact with arbuscular mycorrhizal fungi influences its intraspecific competitive ability under field and glasshouse conditions, but not its overall community productivity. Arbuscular mycorrhizal (AM) fungi can alter the nutrient status and growth of plants, and they can also affect plant-plant, plant-herbivore, and plant-pathogen interactions. These AM effects are rarely studied in populations under natural conditions due to the limitation of non-mycorrhizal controls. Here we used a genetic approach, establishing field and glasshouse communities of AM-harboring Nicotiana attenuata empty vector (EV) plants and isogenic plants silenced in calcium- and calmodulin-dependent protein kinase expression (irCCaMK), and unable to establish AM symbioses. Performance and growth were quantified in communities of the same (monocultures) or different genotypes (mixed cultures) and both field and glasshouse experiments returned similar responses. In mixed cultures, AM-harboring EV plants attained greater stalk lengths, shoot and root biomasses, clearly out-competing the AM fungal-deficient irCCaMK plants, while in monocultures, both genotypes grew similarly. Competitive ability was also reflected in reproductive traits: EV plants in mixed cultures outperformed irCCaMK plants. When grown in monocultures, the two genotypes did not differ in reproductive performance, though total leaf N and P contents were significantly lower independent of the community type. Plant productivity in terms of growth and seed production at the community level did not differ, while leaf nutrient content of phosphorus and nitrogen depended on the community type. We infer that AM symbioses drastically increase N. attenuata's competitive ability in mixed communities resulting in increased fitness for the individuals harboring AM without a net gain for the community.

Phyto-microbiome to mitigate abiotic stress in crop plants

Plant-associated microbes include taxonomically diverse communities of bacteria, archaebacteria, fungi, and viruses, which establish integral ecological relationships with the host plant and constitute the phyto-microbiome. The phyto-microbiome not only contributes in normal growth and development of plants but also plays a vital role in the maintenance of plant homeostasis during abiotic stress conditions. Owing to its immense metabolic potential, the phyto-microbiome provides the host plant with the capability to mitigate the abiotic stress through various mechanisms like production of antioxidants, plant growth hormones, bioactive compounds, detoxification of harmful chemicals and toxins, sequestration of reactive oxygen species and other free radicals. A deeper understanding of the structure and functions of the phyto-microbiome and the complex mechanisms of phyto-microbiome mediated abiotic stress mitigation would enable its utilization for abiotic stress alleviation of crop plants and development of stress-resistant crops. This review aims at exploring the potential of phyto-microbiome to alleviate drought, heat, salinity and heavy metal stress in crop plants and finding sustainable solutions to enhance the agricultural productivity. The mechanistic insights into the role of phytomicrobiome in imparting abiotic stress tolerance to plants have been summarized, that would be helpful in the development of novel bioinoculants. The high-throughput modern approaches involving candidate gene identification and target gene modification such as genomics, metagenomics, transcriptomics, metabolomics, and phyto-microbiome based genetic engineering have been discussed in wake of the ever-increasing demand of climate resilient crop plants.

Distinct impact of arbuscular mycorrhizal isolates on tomato plant tolerance to drought combined with chronic and acute heat stress

Arbuscular mycorrhizal (AM) fungi could mitigate individual drought and heat stress in host plants. However, there are still major gaps in our understanding of AM symbiosis response to the combined stresses. Here, we compared seven AM fungi, Rhizophagus irregularis, Funneliformis mosseae, Funneliformis geosporum, Funneliformis verruculosum, Funneliformis coronatum, Septoglomus deserticola, Septoglomus constrictum, distributed to many world regions in terms of their impacts on tomato endurance to combined drought and chronic heat as well as combined drought and heat shock. A multidisciplinary approach including morphometric, ecophysiological, biochemical, targeted metabolic (by ultrahigh-performance LC-MS), and molecular analyses was applied. The variation among AM fungi isolates in the enhancement in leaf water potential, stomatal conductance, photosynthetic activity, and maximal PSII photochemical efficiency, proline accumulation, antioxidant enzymes (POD, SOD, CAT), and lowered ROS markers (H2O2, MDA) in host plants under combined stresses were observed. S. constrictum inoculation could better enhanced the host plant physiology and biochemical parameters, while F. geosporum colonization less positively influenced the host plants than other treatments under both combined stresses. F. mosseae- and S. constrictum-associated plants showed the common AM-induced modifications and AM species-specific alterations in phytohormones (ABA, SA, JA, IAA), aquaporin (SlSIP1-2; SlTIP2-3; SlNIP2-1; SlPIP2-1) and abiotic stress-responsive genes (SlAREB1, SlLEA, SlHSP70, SlHSP90) in host plants under combined stresses. Altogether, mycorrhizal mitigation of the negative impacts of drought + prolonged heat and drought + acute heat, with the variation among different AM fungi isolates, depending on the specific combined stress and stress duration.

AM fungal-bacterial relationships: what can they tell us about ecosystem sustainability and soil functioning?

Considering our growing population and our continuous degradation of soil environments, understanding the fundamental ecology of soil biota and plant microbiomes will be imperative to sustaining soil systems. Arbuscular mycorrhizal (AM) fungi extend their hyphae beyond plant root zones, creating microhabitats with bacterial symbionts for nutrient acquisition through a tripartite symbiotic relationship along with plants. Nonetheless, it is unclear what drives these AM fungal-bacterial relationships and how AM fungal functional traits contribute to these relationships. By delving into the literature, we look at the drivers and complexity behind AM fungal-bacterial relationships, describe the shift needed in AM fungal research towards the inclusion of interdisciplinary tools, and discuss the utilization of bacterial datasets to provide contextual evidence behind these complex relationships, bringing insights and new hypotheses to AM fungal functional traits. From this synthesis, we gather that interdependent microbial relationships are at the foundation of understanding microbiome functionality and deciphering microbial functional traits. We suggest using pattern-based inference tools along with machine learning to elucidate AM fungal-bacterial relationship trends, along with the utilization of synthetic communities, functional gene analyses, and metabolomics to understand how AM fungal and bacterial communities facilitate communication for the survival of host plant communities. These suggestions could result in improving microbial inocula and products, as well as a better understanding of complex relationships in terrestrial ecosystems that contribute to plant-soil feedbacks.

Effects of AMF inoculation on the eco-physiological characteristics of Imperata cylindrica under differing soil nitrogen conditions

Arbuscular mycorrhizal fungi (AMF) play a key role in terrestrial ecosystems, while the ecological restoration application of AMF in mining areas has been progressively gaining attention. This study simulated a low nitrogen (N) environment in copper tailings mining soil to explore inoculative effects of four AMF species on the eco-physiological characteristics of Imperata cylindrica, and provided plant-microbial symbiote with excellent resistance to copper tailings. Results show that N, soil type, AMF species, and associated interactions significantly affected ammonium (NH4  +), nitrate nitrogen (NO3  -), and total nitrogen (TN) content and photosynthetic characteristics of I. cylindrica. Additionally, interactions between soil type and AMF species significantly affected the biomass, plant height, and tiller number of I. cylindrica. Rhizophagus irregularis and Glomus claroideun significantly increased TN and NH4  + content in the belowground components I. cylindrica in non-mineralized sand. Moreover, the inoculation of these two fungi species significantly increased belowground NH4  + content in mineralized sand. The net photosynthetic rate positively correlated to aboveground total carbon (TC) and TN content under the high N and non-mineralized sand treatment. Moreover, Glomus claroideun and Glomus etunicatum inoculation significantly increased both net photosynthetic and water utilization rates, while F. mosseae inoculation significantly increased the transpiration rate under the low N treatment. Additionally, aboveground total sulfur (TS) content positively correlated to the intercellular carbon dioxide (CO₂) concentration, stomatal conductance, and the transpiration rate under the low N sand treatment. Furthermore, G. claroideun, G. etunicatum, and F. mosseae inoculation significantly increased aboveground NH4  + and belowground TC content of I. cylindrica, while G. etunicatum significantly increased belowground NH4  + content. Average membership function values of all physiological and ecological I. cylindrica indexes infected with AMF species were higher compared to the control group, while corresponding values of I. cylindrica inoculated with G. claroideun were highest overall. Finally, comprehensive evaluation coefficients were highest under both the low N and high N mineralized sand treatments. This study provides information on microbial resources and plant-microbe symbionts in a copper tailings area, while aiming to improve current nutrient-poor soil conditions and ecological restoration efficiency in copper tailings areas.

Metabolomics reveals arbuscular mycorrhizal fungi-mediated tolerance of walnut to soil drought

BACKGROUND

Arbuscular mycorrhizal fungi (AMF) have a positive effect on drought tolerance of plants after establishing reciprocal resymbiosis with roots, while the underlying mechanism is not deciphered. Metabolomics can explain the mechanism of plant response to environmental stress by analyzing the changes of all small molecular weight metabolites. The purpose of this study was to use Ultra High Performance Liquid Chromatography Q Exactive Mass Spectrometer to analyze changes in root metabolites of walnut (Juglans regia) after inoculation with an arbuscular mycorrhizal fungus Diversispora spurca under well-watered (WW) and drought stress (DS).

RESULTS

Sixty days of soil drought significantly inhibited root mycorrhizal colonization rate, shoot and root biomass production, and leaf water potential in walnut, while AMF inoculation significantly increased biomass production and leaf water potential, accompanied by a higher increase magnitude under DS versus under WW. A total of 3278 metabolites were identified. Under WW, AMF inoculation up-regulated 172 metabolites and down-regulated 61 metabolites, along with no changes in 1104 metabolites. However, under DS, AMF inoculation up-regulated 49 metabolites and down-regulated 116 metabolites, coupled with no changes in 1172 metabolites. Among them, juglone (a quinone found in walnuts) as the first ranked differential metabolite was up-regulated by AMF under WW but not under DS; 2,3,5-trihydroxy-5-7-dimethoxyflavanone as the first ranked differential metabolite was increased by AMF under DS but not under WW. The KEGG annotation showed a large number of metabolic pathways triggered by AMF, accompanied by different metabolic pathways under WW and DS. Among them, oxidative phosphorylation and phenylalanine metabolism and biosynthesis were triggered by AMF in response to WW and DS, where N-acetyl-L-phenylalanine was induced by AMF to increase under DS, while decreasing under WW.

CONCLUSION

This study provides new insights into the metabolic mechanisms of mycorrhiza-enhanced drought tolerance in walnuts.

Phosphorus availability drives mycorrhiza induced resistance in tomato

Arbuscular mycorrhizal (AM) symbiosis can provide multiple benefits to the host plant, including improved nutrition and protection against biotic stress. Mycorrhiza induced resistance (MIR) against pathogens and insect herbivores has been reported in different plant systems, but nutrient availability may influence the outcome of the interaction. Phosphorus (P) is a key nutrient for plants and insects, but also a regulatory factor for AM establishment and functioning. However, little is known about how AM symbiosis and P interact to regulate plant resistance to pests. Here, using the tomato-Funneliformis mosseae mycorrhizal system, we analyzed the effect of moderate differences in P fertilization on plant and pest performance, and on MIR against biotic stressors including the fungal pathogen Botrytis cinerea and the insect herbivore Spodoperta exigua. P fertilization impacted plant nutritional value, plant defenses, disease development and caterpillar survival, but these effects were modulated by the mycorrhizal status of the plant. Enhanced resistance of F. mosseae-inoculated plants against B. cinerea and S. exigua depended on P availability, as no protection was observed under the most P-limiting conditions. MIR was not directly explained by changes in the plant nutritional status nor to basal differences in defense-related phytohormones. Analysis of early plant defense responses to the damage associated molecules oligogalacturonides showed primed transcriptional activation of plant defenses occurring at intermediate P levels, but not under severe P limitation. The results show that P influences mycorrhizal priming of plant defenses and the resulting induced-resistance is dependent on P availability, and suggest that mycorrhiza fine-tunes the plant growth vs defense prioritization depending on P availability. Our results highlight how MIR is context dependent, thus unravel molecular mechanism based on plant defence in will contribute to improve the efficacy of mycorrhizal inoculants in crop protection.

Transcriptome analysis reveals the mechanisms for mycorrhiza-enhanced salt tolerance in rice

More than half of the global population relies on rice as a staple food, but salinization of soil presents a great threat to rice cultivation. Although previous studies have addressed the possible benefits of arbuscular mycorrhizal (AM) symbiosis for rice under salinity stress, the underlying molecular mechanisms are still unclear. In this study, we found that mycorrhizal rice had better shoot and reproductive growth and a significantly higher K⁺/Na⁺ ratio in the shoot. The reactive oxygen species (ROS) scavenging capacity in rice shoots was also improved by AM symbiosis. To elucidate the molecular mechanisms required for AM-improved salt tolerance, transcriptome analysis revealing the differentially expressed genes (DEGs) based on the response to AM symbiosis, salinity or specific tissue was performed. Thirteen percent of DEGs showed tissue-preferred responses to both AM symbiosis and salt stress and might be the key genes contributing to AM-enhanced salt tolerance. Gene Ontology (GO) enrichment analysis identified GO terms specifically appearing in this category, including cell wall, oxidoreductase activity, reproduction and ester-related terms. Interestingly, GO terms related to phosphate (Pi) homeostasis were also found, suggesting the possible role of the Pi-related signaling pathway involved in AM-enhanced salt tolerance. Intriguingly, under nonsaline conditions, AM symbiosis influenced the expression of these genes in a similar way as salinity, especially in the shoots. Overall, our results indicate that AM symbiosis may possibly use a multipronged approach to influence gene expression in a way similar to salinity, and this modification could help plants be prepared for salt stress.

Environmental interference of plant-microbe interactions

Environmental stresses can compromise the interactions of plants with beneficial microbes. In the present review, experimental results showing that stresses negatively affect the abundance and/or functionality of plant beneficial microbes are summarized. It is proposed that the environmental interference of these plant-microbe interactions is explained by the stress-mediated induction of plant signalling pathways associated with defence hormones and reactive oxygen species. These plant responses are recognized to regulate beneficial microbes within plants. The direct negative effect of stresses on microbes may also contribute to the environmental regulation of these plant mutualisms. It is also posited that, in stress situations, beneficial microbes harbour mechanisms that contribute to maintain the mutualistic associations. Beneficial microbes produce effector proteins and increase the antioxidant levels in plants that counteract the detrimental effects of plant stress responses on them. In addition, they deliver specific stress-protective mechanisms that assist to their plant hosts to mitigate the negative effects of stresses. Our study contributes to understanding how environmental stresses affect plant-microbe interactions and highlights why beneficial microbes can still deliver benefits to plants in stressful environments.

Molecular and Physiological Mechanisms to Mitigate Abiotic Stress Conditions in Plants

Agriculture production faces many abiotic stresses, mainly drought, salinity, low and high temperature. These abiotic stresses inhibit plants' genetic potential, which is the cause of huge reduction in crop productivity, decrease potent yields for important crop plants by more than 50% and imbalance agriculture's sustainability. They lead to changes in the physio-morphological, molecular, and biochemical nature of the plants and change plants' regular metabolism, which makes them a leading cause of losses in crop productivity. These changes in plant systems also help to mitigate abiotic stress conditions. To initiate the signal during stress conditions, sensor molecules of the plant perceive the stress signal from the outside and commence a signaling cascade to send a message and stimulate nuclear transcription factors to provoke specific gene expression. To mitigate the abiotic stress, plants contain several methods of avoidance, adaption, and acclimation. In addition to these, to manage stress conditions, plants possess several tolerance mechanisms which involve ion transporters, osmoprotectants, proteins, and other factors associated with transcriptional control, and signaling cascades are stimulated to offset abiotic stress-associated biochemical and molecular changes. Plant growth and survival depends on the ability to respond to the stress stimulus, produce the signal, and start suitable biochemical and physiological changes. Various important factors, such as the biochemical, physiological, and molecular mechanisms of plants, including the use of microbiomes and nanotechnology to combat abiotic stresses, are highlighted in this article.

Arbuscular mycorrhizal fungi: Effects on secondary metabolite accumulation of traditional Chinese medicines

Traditional Chinese medicine (TCM) has played a pivotal role in maintaining the health of people, and the intrinsic quality of TCM is directly related to the clinical efficacy. The medicinal ingredients of TCM are derived from the secondary metabolites of plant metabolism and are also the result of the coordination of various physiological activities in plants. Arbuscular mycorrhizal fungi (AMF) are among the most ubiquitous plant mutualists that enhance the growth and yield of plants by facilitating the uptake of nutrients and water. Symbiosis of AMF with higher plants promotes growth and helps in the accumulation of secondary metabolites. However, there is still no systematic analysis and summation of their roles in the application of TCM, biosynthesis and accumulation of active substances of herbs, as well as the mechanisms. AMF directly or indirectly affect the accumulation of secondary metabolites of TCM, which is the focus of this review. First, in this review, the effects of AMF symbiosis on the content of different secondary metabolites in TCM, such as phenolic acids, flavonoids, alkaloids and terpenoids, are summarized. Moreover, the mechanism of AMF regulating the synthesis of secondary metabolites was also considered, in combination with the establishment of mycorrhizal symbionts, response mechanisms of plant hormones, nutritional elements and expression of key enzyme their activities. Finally, combined with the current application prospects for AMF in TCM, future in-depth research is planned, thus providing a reference for improving the quality of TCM. In this manuscript, we review the research status of AMF in promoting the accumulation of secondary metabolites in TCM to provide new ideas and methods for improving the quality of TCM.

Epigenetic marks for mitigating abiotic stresses in plants

Abiotic stressors are one of the major factors affecting agricultural output. Plants have evolved adaptive systems to respond appropriately to various environmental cues. These responses can be accomplished by modulating or fine-tuning genetic and epigenetic regulatory mechanisms. Understanding the response of plants' molecular features to abiotic stress is a priority in the current period of continued environmental changes. Epigenetic modifications are necessary that control gene expression by changing chromatin status and recruiting various transcription regulators. The present study summarized the current knowledge on epigenetic modifications concerning plant responses to various environmental stressors. The functional relevance of epigenetic marks in regulating stress tolerance has been revealed, and epigenetic changes impact the effector genes. This study looks at the epigenetic mechanisms that govern plant abiotic stress responses, especially DNA methylation, histone methylation/acetylation, chromatin remodeling, and various metabolites. Plant breeders will benefit from a thorough understanding of these processes to create alternative crop improvement approaches. Genome editing with clustered regularly interspaced short palindromic repeat/CRISPR-associated proteins (CRISPR/Cas) provides genetic tools to make agricultural genetic engineering more sustainable and publicly acceptable.

The Costs and Benefits of Plant-Arbuscular Mycorrhizal Fungal Interactions

The symbiotic interaction between plants and arbuscular mycorrhizal (AM) fungi is often perceived as beneficial for both partners, though a large ecological literature highlights the context dependency of this interaction. Changes in abiotic variables, such as nutrient availability, can drive the interaction along the mutualism-parasitism continuum with variable outcomes for plant growth and fitness. However, AM fungi can benefit plants in more ways than improved phosphorus nutrition and plant growth. For example, AM fungi can promote abiotic and biotic stress tolerance even when considered parasitic from a nutrient provision perspective. Other than being obligate biotrophs, very little is known about the benefits AM fungi gain from plants. In this review, we utilize both molecular biology and ecological approaches to expand our understanding of the plant-AM fungal interaction across disciplines.

The Interactions between Arbuscular Mycorrhizal Fungi and Trichoderma longibrachiatum Enhance Maize Growth and Modulate Root Metabolome under Increasing Soil Salinity

Trichoderma longibrachiatum sp. are free-living filamentous fungi which are common in agro-ecosystems. However, few studies thus far have examined the interaction between Trichoderma longibrachiatum and arbuscular mycorrhizal (AM) fungi in saline soil and their potential for improving plant stress tolerance. Here, single, dual-inoculated (T. longibrachiatum MF, AM fungal community or Glomus sp.), and non-inoculated maize (Zea may L.) were subjected to different salinity levels (0, 75, 150, and 225 mM NaCl) to test the synergistic effects of dual inoculants on maize plants in different salt stress conditions. Plant performance and metabolic profiles were compared to find the molecular mechanisms underlying plant protection against salt stress. The first experiment revealed that dual inoculation of an AM fungal community and T. longibrachiatum MF improved the biomass and K⁺/Na⁺ ratio in maize under non-saline conditions, and generally enhanced AM fungal growth in root and soil under all but the 225 mM NaCl conditions. However, MF inoculant did not influence the structure of AM fungal communities in maize roots. In the second experiment, dual inoculation of Glomus sp. and T. longibrachiatum MF increased maize plant biomass, K⁺/Na⁺ ratio, and AM fungal growth in root and soil significantly at both 0 and 75 mM NaCl conditions. We identified metabolic compounds differentially accumulated in dual-inoculated maize that may underline their enhanced maize plant tolerance to increasing soil salinity. Our data suggested that the combination of Glomus sp. and T.longibrachiatum leads to interactions, which may play a potential role in alleviating the stress and improve crop productivity in salt-affected soils.

Role of Promising Secondary Metabolites to Confer Resistance Against Environmental Stresses in Crop Plants: Current Scenario and Future Perspectives

Plants often face incompatible growing environments like drought, salinity, cold, frost, and elevated temperatures that affect plant growth and development leading to low yield and, in worse circumstances, plant death. The arsenal of versatile compounds for plant consumption and structure is called metabolites, which allows them to develop strategies to stop enemies, fight pathogens, replace their competitors and go beyond environmental restraints. These elements are formed under particular abiotic stresses like flooding, heat, drought, cold, etc., and biotic stress such as a pathogenic attack, thus associated with survival strategy of plants. Stress responses of plants are vigorous and include multifaceted crosstalk between different levels of regulation, including regulation of metabolism and expression of genes for morphological and physiological adaptation. To date, many of these compounds and their biosynthetic pathways have been found in the plant kingdom. Metabolites like amino acids, phenolics, hormones, polyamines, compatible solutes, antioxidants, pathogen related proteins (PR proteins), etc. are crucial for growth, stress tolerance, and plant defense. This review focuses on promising metabolites involved in stress tolerance under severe conditions and events signaling the mediation of stress-induced metabolic changes are presented.

Use of Piriformospora indica to Promote Growth of Strawberry Daughter Plants

As an endophytic fungus, the growth-promoting effects of Piriformospora indica have been widely confirmed in many of its host plants. In this study, we investigated the influences of P. indica colonization on the growth of the daughter plants of two strawberry cultivars, ‘Benihoppe’ and ‘Sweet Charlie.’ The results showed that the fungus colonization significantly promoted the growth of the daughter plants of both of the two strawberry varieties. Its colonization greatly improved almost all of the growth parameters of the ‘Benihoppe’ daughter plants, including the above-ground fresh weight, above-ground dry weight, root fresh weight, root dry weight, plant height, petiole length, leaf area, number of roots and chlorophyll content. However, the fungus colonization showed significant improving effects on only the above-ground fresh weight, root fresh weight and root dry weight of ‘Sweet Charlie.’ Surprisingly, the average root length of ‘Benihoppe’ and ‘Sweet Charlie’ was suppressed by about 14.3% and 24.6%, respectively, by P. indica. Moreover, after P. indica colonization, the leaf nitrate reductase activity and root activity upregulated by 30.12% and 12.74%, and 21.85% and 21.16%, respectively, for the ‘Benihoppe’ and ‘Sweet Charlie’ daughter plants. Our study indicated that P. indica could promote the growth of strawberry daughter plants by improving rooting, strengthening photosynthetic pigments production and nutrient absorption and accelerating biomass accumulation. The fungus shows great potential to be used in the strawberry industry, especially in the breeding of daughter plants.

Root metabolome of plant-arbuscular mycorrhizal symbiosis mirrors the mutualistic or parasitic mycorrhizal phenotype

The symbiosis of arbuscular mycorrhizal fungi (AMF) with plants, the most ancient and widespread association, exhibits phenotypes that range from mutualism to parasitism. However, we still lack an understanding of the cellular-level mechanisms that differentiate and regulate these phenotypes. We assessed the modulation in growth parameters and root metabolome of two sorghum accessions inoculated with two AMF species (Rhizophagus irregularis, Gigaspora gigantea), alone and in a mixture under phosphorus (P) limiting conditions. Rhizophagus irregularis exhibited a mutualistic phenotype with increased P uptake and plant growth. This positive outcome was associated with a facilitatory metabolic response including higher abundance of organic acids and specialized metabolites critical to maintaining a functional symbiosis. However, G. gigantea exhibited a parasitic phenotype that led to plant growth depression and resulted in inhibitory plant metabolic responses including the higher abundance of p-hydroxyphenylacetaldoxime with antifungal properties. These findings suggest that the differential outcome of plant-AMF symbiosis could be regulated by or reflected in changes in the root metabolome that arises from the interaction of the plant species with the specific AMF species. A mutualistic symbiotic association prevailed when the host plants were exposed to a mixture of AMF. Our results provide a metabolome-level landscape of plant-AMF symbiosis and highlight the importance of the identity of both AMF and crop genotypes in facilitating a mutualistic AMF symbiosis.

Structure and diversity of fungal communities in long-term copper-contaminated agricultural soil

Copper (Cu) contamination threatens the stability of soil ecosystems. As important moderators of biochemical processes and soil remediation, the fungal community in contaminated soils has attracted much research interest. In this study, soil fungal diversity and community composition under long-term Cu contamination were investigated based on high-throughput sequencing. The co-occurrence networks were also constructed to display the co-occurrence patterns of the soil fungal community. The results showed that the richness and Chao1 index both significantly increased at 50 mg kg^-1 Cu and then significantly decreased at 1600 and 3200 mg kg^-1 Cu. Soil fungal diversity was significantly and positively correlated with plant dry weight. Specific tolerant taxa under different Cu contamination gradients were illustrated by linear discriminant analysis effect size (LEfSe). Soil Cu concentration and shoot dry weight were the strongest driving factors influencing fungal composition. The relative abundance of arbuscular mycorrhizal fungi increased first and then declined along with elevating Cu concentrations via FUNGuild analysis. The interactions among fungi were enhanced under light and moderate Cu contamination but weakened under heavy Cu contamination by random matrix theory (RMT)-based molecular ecological network analysis. Penicillium, identified as a keystone taxon in Cu-contaminated soils, had the function of removing heavy metals and detoxification, which might be vital to trigger the resistance of the fungal community to Cu contamination. The results may facilitate the identification of Cu pollution indicators and the development of in situ bioremediation technology for contaminated cultivated fields.

Effect of Inoculation with Arbuscular Mycorrhizal Fungi and Fungicide Application on the Secondary Metabolism of Solanum tuberosum Leaves

In potato (Solanum tuberosum) crops, the use of fungicides to control some diseases is widespread; however, it has been reported that this practice can modify the potato polyphenolic content, and new strategies oriented to the potato defense system are necessary. One alternative is the use of arbuscular mycorrhizal fungi (AMF) to improve the defense mechanisms of plants. In this study, phenolic profiles and antioxidant activities in leaves of three potato genotypes (CB2011-509, CB2011-104, and VR808) were evaluated in crops inoculated with three AMF strains (Claroideoglomus claroideum, Claroideoglomus lamellosum, and Fumneliformis mosseae) and with AMF in combination with the use of two commercial fungicides (MONCUT [M] and ReflectXtra [R]). Eight phenolic compounds were detected, mainly hydroxycinnamic acids (HCAD) and flavonols, in samples where the highest concentrations of HCAD were obtained, 5-caffeoylquinic acid was the most abundant phenolic. The antioxidant activity was higher using the cupric reducing antioxidant capacity (CUPRAC) and ferric reducing antioxidant power (FRAP) methods. The association of AMF with plants had benefits on the secondary metabolism; however, the response differed according to genotype. The different combinations of potato genotypes, AMF strain, and fungicide modified the content of phenolic compounds in leaves in different ways; the treatment using C. lamellosum and ReflectXtra was the ideal combination for the genotypes analyzed here, with the higher antioxidant response, which supports the further technological evaluation of efficient AMF strains and fungicides in potato crops.

Abiotic Stress and Belowground Microbiome: The Potential of Omics Approaches

Nowadays, the worldwide agriculture is experiencing a transition process toward more sustainable production, which requires the reduction of chemical inputs and the preservation of microbiomes’ richness and biodiversity. Plants are no longer considered as standalone entities, and the future of agriculture should be grounded on the study of plant-associated microorganisms and all their potentiality. Moreover, due to the climate change scenario and the resulting rising incidence of abiotic stresses, an innovative and environmentally friendly technique in agroecosystem management is required to support plants in facing hostile environments. Plant-associated microorganisms have shown a great attitude as a promising tool to improve agriculture sustainability and to deal with harsh environments. Several studies were carried out in recent years looking for some beneficial plant-associated microbes and, on the basis of them, it is evident that Actinomycetes and arbuscular mycorrhizal fungi (AMF) have shown a considerable number of positive effects on plants’ fitness and health. Given the potential of these microorganisms and the effects of climate change, this review will be focused on their ability to support the plant during the interaction with abiotic stresses and on multi-omics techniques which can support researchers in unearthing the hidden world of plant–microbiome interactions. These associated microorganisms can increase plants’ endurance of abiotic stresses through several mechanisms, such as growth-promoting traits or priming-mediated stress tolerance. Using a multi-omics approach, it will be possible to deepen these mechanisms and the dynamic of belowground microbiomes, gaining fundamental information to exploit them as staunch allies and innovative weapons against crop abiotic enemies threatening crops in the ongoing global climate change context.

Elucidating the Mechanisms Underlying Enhanced Drought Tolerance in Plants Mediated by Arbuscular Mycorrhizal Fungi

Plants are often subjected to various environmental stresses during their life cycle, among which drought stress is perhaps the most significant abiotic stress limiting plant growth and development. Arbuscular mycorrhizal (AM) fungi, a group of beneficial soil fungi, can enhance the adaptability and tolerance of their host plants to drought stress after infecting plant roots and establishing a symbiotic association with their host plant. Therefore, AM fungi represent an eco-friendly strategy in sustainable agricultural systems. There is still a need, however, to better understand the complex mechanisms underlying AM fungi-mediated enhancement of plant drought tolerance to ensure their effective use. AM fungi establish well-developed, extraradical hyphae on root surfaces, and function in water absorption and the uptake and transfer of nutrients into host cells. Thus, they participate in the physiology of host plants through the function of specific genes encoded in their genome. AM fungi also modulate morphological adaptations and various physiological processes in host plants, that help to mitigate drought-induced injury and enhance drought tolerance. Several AM-specific host genes have been identified and reported to be responsible for conferring enhanced drought tolerance. This review provides an overview of the effect of drought stress on the diversity and activity of AM fungi, the symbiotic relationship that exists between AM fungi and host plants under drought stress conditions, elucidates the morphological, physiological, and molecular mechanisms underlying AM fungi-mediated enhanced drought tolerance in plants, and provides an outlook for future research.

Changes in Bacterial Diversity and Composition in Response to Co-inoculation of Arbuscular Mycorrhizae and Zinc-Solubilizing Bacteria in Turmeric Rhizosphere

In the present study, the impact of co-inoculation of arbuscular mycorrhizal fungi (AM Rhizophagus sp., NCBI-MN710507) and Zinc solubilizing bacteria (ZSB2- Bacillus megaterium, NCBI-KY687496) on plant growth, soil dehydrogenase activity, soil respiration and the changes in bacterial diversity in rhizosphere of turmeric (Curcuma longa) were examined. Our results showed that higher plant height and dry biomass were observed in treatments co-inoculated with AM and ZSB2. Likewise, dehydrogenase activity and soil respiration were more significant in the co-inoculation treatment, indicating abundance of introduced as well as inherent microflora. Bacterial community analysis using 16S rRNA revealed changes in the structure and diversity of various taxa due to co-inoculation of AM and ZSB2. Alpha diversity indexes (Shannon and Chao1) and beta diversity indexes obtained through unweighted unifrac approach also showed variation among the treated samples. Chloroflexi was the dominant phylum followed by Proteobacteria, Actinobacteria and Acidobacteria which accounted for 80% of all treated samples. The composition of bacterial communities at genus level revealed that co-inoculation caused distinct bacterial profiles. The Linear discriminant analysis effect size revealed the dominance of ecologically significant genera such as Bradyrhizobium, Candidatus, Pedomicrbium, Thermoporothrix, Acinetobacter and Nitrospira in treatments co-inoculated with AM and ZSB2. On the whole, co-inoculated treatments revealed enhanced microbial activities and caused significant positive shifts in the bacterial diversity and abundance compared to treatments with sole application of ZSB2 or AM.

Effects of Arbuscular Mycorrhizal Fungi on Rice Growth Under Different Flooding and Shading Regimes

Arbuscular mycorrhizal fungi (AMF) are present in paddy fields, where they suffer from periodic soil flooding and sometimes shading stress, but their interaction with rice plants in these environments is not yet fully explained. Based on two greenhouse experiments, we examined rice-growth response to AMF under different flooding and/or shading regimes to survey the regulatory effects of flooding on the mycorrhizal responses of rice plants under different light conditions. AMF had positive or neutral effects on the growth and yields of both tested rice varieties under non-flooding conditions but suppressed them under all flooding and/or shading regimes, emphasizing the high importance of flooding and shading conditions in determining the mycorrhizal effects. Further analyses indicated that flooding and shading both reduced the AMF colonization and extraradical hyphal density (EHD), implying a possible reduction of carbon investment from rice to AMF. The expression profiles of mycorrhizal P pathway marker genes (GintPT and OsPT11) suggested the P delivery from AMF to rice roots under all flooding and shading conditions. Nevertheless, flooding and shading both decreased the mycorrhizal P benefit of rice plants, as indicated by the significant decrease of mycorrhizal P responses (MPRs), contributing to the negative mycorrhizal effects on rice production. The expression profiles of rice defense marker genes OsPR1 and OsPBZ1 suggested that regardless of mycorrhizal growth responses (MGRs), AMF colonization triggered the basal defense response, especially under shading conditions, implying the multifaceted functions of AMF symbiosis and their effects on rice performance. In conclusion, this study found that flooding and shading both modulated the outcome of AMF symbiosis for rice plants, partially by influencing the mycorrhizal P benefit. This finding has important implications for AMF application in rice production.

Evaluation of commercial composts and potting mixes and their ability to support arbuscular mycorrhizal fungi with maize (Zea mays) as host plant

The use of composts and potting mixes in food production systems is a promising way to counteract the effects of soil degradation and allows crop growth in soilless culture systems. Arbuscular mycorrhizal fungi (AMF) are a well-studied group of beneficial plant symbionts that have been shown to provide important ecosystem services. This study analysed the properties of nine commercial Australian potting mixes and composts and investigated whether they support colonization of maize plants with AMF in a plant growth bioassay. Physicochemical analyses showed highly variable properties between the substrates, with some extreme values that limited plant growth. DNA-based analysis revealed the presence of various plant pathogens, which was linked to inhibited plant growth in one substrate. Some substrates did not meet national quality standards, due to the concentrations of plant nutrients, heavy metals, or substrate maturity. Plant growth was mostly limited due to nitrogen immobilization, which required weekly fertilizer applications. Solid state ¹³C nuclear magnetic resonance spectroscopy gave insight into the decomposition state of the substrates. Plant roots in most substrates were well colonized with AMF (>60% root length), regardless of most substrate properties. Root colonization was negatively affected in only one substrate, likely due to ammonium toxicity. Results of this study show that not all commercial substrates adhered to national quality standards. Potting mixes and composts can support high mycorrhizal root colonization when plant growth is otherwise not limited.

Metabolomics analysis reveals the responses of tea plants to excessive calcium

BACKGROUND

The proper growth and development of tea plants requires moderately acidic soils and relatively low calcium levels, and excessive calcium at high pH can damage tea plant roots. To reveal the effects of calcium on the responses of tea plant to three pH levels (3.5, 5.0 and 6.5), a repeated test of two factors was designed.

RESULTS

Root growth and elemental analysis indicated that excessive calcium improved the growth of tea roots at low pH conditions, whereas it did not harm the growth of tea roots under normal and high pH conditions, especially at pH 6.5. Excessive calcium antagonized the absorption and utilization of magnesium by tea plants. Gas chromatography-mass spectrometry results showed that the addition of Ca²⁺ resulted in the primary metabolism in roots being more active at a low pH level. By contrast, it had obvious adverse effects on the accumulation of root metabolites with high calcium treatment at normal or high pH. Differential metabolites identified using ultra-performance liquid chromatography quadrupole time of flight mass spectrometry indicated that flavonoids demonstrated the largest number of changes, and their biosynthesis was partially enriched with excessive calcium at low and high pH conditions, whereas it was down-regulated under normal pH conditions. Kaempferol 3-(2'-rhamnosyl-6'-acetylgalactoside) 7-rhamnoside, quercetin 3-(6'-sinapoylsophorotrioside) and delphinidin 3-(3'-p-coumaroylglucoside) showed the greatest increase. The results of gene expression related to root growth and calcium regulation were consistent with root growth and root metabolism.

CONCLUSION

The overall results demonstrated that high Ca concentrations further aggravate the detrimental effects of high pH to tea roots. However, it is interesting that excessive calcium reduced the harm of a low pH on tea root growth to some extent. © 2021 Society of Chemical Industry.

Mycorrhizal symbiosis primes the accumulation of antiherbivore compounds and enhances herbivore mortality in tomato

Plant association with arbuscular mycorrhizal fungi (AMF) can increase their ability to overcome multiple stresses, but their impact on plant interactions with herbivorous insects is controversial. Here we show higher mortality of the leaf-chewer Spodoptera exigua when fed on tomato plants colonized by the AMF Funneliformis mosseae, evidencing mycorrhiza-induced resistance. In search of the underlying mechanisms, an untargeted metabolomic analysis through ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS) was performed. The results showed that mycorrhizal symbiosis had a very limited impact on the leaf metabolome in the absence of stress, but significantly modulated the response to herbivory in the damaged area. A cluster of over accumulated metabolites was identified in those leaflets damaged by S. exigua feeding in mycorrhizal plants, while unwounded distal leaflets responded similar to those from non-mycorrhizal plants. These primed-compounds were mostly related to alkaloids, fatty acid derivatives and phenylpropanoid-polyamine conjugates. The deleterious effect on larval survival of some of these compounds, including the alkaloid physostigmine, the fatty acid derivatives 4-oxododecanedioic acid and azelaic acid, was confirmed. Thus, our results evidence the impact of AMF on metabolic reprograming upon herbivory that leads to a primed accumulation of defensive compounds.

Mycorrhiza-Induced Resistance against Foliar Pathogens Is Uncoupled of Nutritional Effects under Different Light Intensities

The use of microbial inoculants, particularly arbuscular mycorrhizal fungi, has great potential for sustainable crop management, which aims to reduce the use of chemical fertilizers and pesticides. However, one of the major challenges of their use in agriculture is the variability of the inoculation effects in the field, partly because of the varying environmental conditions. Light intensity and quality affect plant growth and defense, but little is known about their impacts on the benefits of mycorrhizal symbioses. We tested the effects of five different light intensities on plant nutrition and resistance to the necrotrophic foliar pathogen Botrytis cinerea in mycorrhizal and non-mycorrhizal lettuce plants. Our results evidence that mycorrhiza establishment is strongly influenced by light intensity, both regarding the extension of root colonization and the abundance of fungal vesicles within the roots. Light intensity also had significant effects on plant growth, nutrient content, and resistance to the pathogen. The effect of the mycorrhizal symbiosis on plant growth and nutrient content depended on the light intensity, and mycorrhiza efficiently reduced disease incidence and severity under all light intensities. Thus, mycorrhiza-induced resistance can be uncoupled from mycorrhizal effects on plant nutrition. Therefore, mycorrhizal symbioses can be beneficial by providing biotic stress protection even in the absence of nutritional or growth benefits.

Metabolic Alterations in Pisum sativum Roots during Plant Growth and Arbuscular Mycorrhiza Development

Intensive exchange of nutrients is a crucial part of the complex interaction between a host plant and fungi within arbuscular mycorrhizal (AM) symbiosis. For the first time, the present study demonstrates how inoculation with AMF Rhizophagus irregularis affects the pea (Pisum sativum L.) root metabolism at key stages of plant development. These correspond to days 21 (vegetation), 42 (flowering initiation), and 56 (fruiting-green pod). Metabolome profiling was carried out by means of a state-of-the-art GC-MS technique. The content shifts revealed include lipophilic compounds, sugars, carboxylates, and amino acids. The metabolic alterations were principally dependent on the stage of plant development but were also affected by the development of AM fungi, a fact which highlights interaction between symbiotic partners. The comparison of the present data with the results of leaf metabolome profiling earlier obtained did not reveal common signatures of metabolic response to mycorrhization in leaves and roots. We supposed that the feedback for the development and symbiotic interaction on the part of the supraorganismic system (root + AM fungi) was the cause of the difference between the metabolic profile shift in leaf and root cells that our examination revealed. New investigations are required to expand our knowledge of metabolome plasticity of the whole organism and/or system of organisms, and such results might be put to use for the intensification of sustainable agriculture.

Unravelling the role of arbuscular mycorrhizal fungi in mitigating the oxidative burst of plants under drought stress

With continued climate changes, soil drought stress has become the main limiting factor for crop growth in arid and semi-arid regions. A typical characteristic of drought stress is the burst of reactive oxygen species (ROS), causing oxidative damage. Plant-associated microbes, such as arbuscular mycorrhizal fungi (AMF), can regulate physiological and molecular responses to tolerate drought stress, and they have a strong ability to cope with drought-induced oxidative damage via enhanced antioxidant defence systems. AMF produce a limited oxidative burst in the arbuscule-containing root cortical cells. Similar to plants, AMF modulate a fungal network in enzymatic (e.g. GmarCuZnSOD and GintSOD1) and non-enzymatic (e.g. GintMT1, GinPDX1 and GintGRX1) antioxidant defence systems to scavenge ROS. Plants also respond to mycorrhization to enhance stress tolerance via metabolites and the induction of genes. The present review provides an overview of the network of plant - arbuscular mycorrhizal fungus dialogue in mitigating oxidative stress. Future studies should involve identifying genes and transcription factors from both AMF and host plants in response to drought stress, and utilize transcriptomics, proteomics and metabolomics to clarify a clear dialogue mechanism between plants and AMF in mitigating oxidative burst.

Metabolomics and transcriptomics to decipher molecular mechanisms underlying ectomycorrhizal root colonization of an oak tree

Mycorrhizas are known to have a positive impact on plant growth and ability to resist major biotic and abiotic stresses. However, the metabolic alterations underlying mycorrhizal symbiosis are still understudied. By using metabolomics and transcriptomics approaches, cork oak roots colonized by the ectomycorrhizal fungus Pisolithus tinctorius were compared with non-colonized roots. Results show that compounds putatively corresponding to carbohydrates, organic acids, tannins, long-chain fatty acids and monoacylglycerols, were depleted in ectomycorrhizal cork oak colonized roots. Conversely, non-proteogenic amino acids, such as gamma-aminobutyric acid (GABA), and several putative defense-related compounds, including oxylipin-family compounds, terpenoids and B6 vitamers were induced in mycorrhizal roots. Transcriptomic analysis suggests the involvement of GABA in ectomycorrhizal symbiosis through increased synthesis and inhibition of degradation in mycorrhizal roots. Results from this global metabolomics analysis suggest decreases in root metabolites which are common components of exudates, and in compounds related to root external protective layers which could facilitate plant-fungal contact and enhance symbiosis. Root metabolic pathways involved in defense against stress were induced in ectomycorrhizal roots that could be involved in a plant mechanism to avoid uncontrolled growth of the fungal symbiont in the root apoplast. Several of the identified symbiosis-specific metabolites, such as GABA, may help to understand how ectomycorrhizal fungi such as P. tinctorius benefit their host plants.

Comprehensive Assessment of Ameliorative Effects of AMF in Alleviating Abiotic Stress in Tomato Plants

Population growth and food necessity envisaged the dire need for supplementation to a larger community balance in food production. With the advent of the green revolution, agriculture witnessed the insurrection of horticultural fruit crops and field crops in enormous modes. Nevertheless, chemical fertilizer usage foresees soil pollution and fertility loss. Utilization of biocontrol agents and plant growth promotion by microbial colonization enrooted significant restoration benefits. Constant reliability for healthy foods has been emancipated across the globe stressing high nutritive contents among indigenous field crops like tomato (Solanum lycopersicum). However, stress tolerance mechanisms and efficient abatement require deeper insights. The applicability of arbuscular mycorrhizal fungi (AMF) poses as an ultimate strategy to minimize the deleterious consequences of abiotic stress such as salt, drought, temperature and heavy metal stress sustainably. The rational modality employing the application of AMF is one of significant efforts to lessen cell damages under abiotic stress. The novelty of the compilation can be redressed to cohesive literature for combating stress. The literature review will provide agricultural scientists worldwide in providing a rational approach that can have possible implications in not only tomato but also other vegetable crops.

Endophytic Bacteria from the Sahara Desert Protect Tomato Plants Against Botrytis cinerea Under Different Experimental Conditions

Bacteria endophytes are living microorganisms that live inside plant tissues without visible harmful symptoms, providing a mutualistic interaction. In this study, different bacterial endophytic strains were isolated from different plants primed to live in an arid area, namely, the Sahara Desert. Up to 27 of these strains were selected based on their ability to inhibit Botrytis cinerea growth in dual-culture assay and by bacterial volatiles. The results presented in this study show the capacity of most of the bacterial strains to protect Solanum lycopersicum against the pathogenic fungus B. cinerea, under different experimental conditions. Five of these strains induced susceptibility in tomato plants and no callose accumulation upon fungal infection, pointing to callose deposition as a protective mechanism mediated by endophytic bacteria. Moreover, there was a significant correlation between the bacterial strains inducing callose and the level of protection against B. cinerea. On the other hand, hormone production by bacteria does not explain the relationship between protection and the differences between the phenotypic results obtained in vitro and those obtained in plant experiments. Induced resistance is highly specific in the inducer-plant-stress interaction.

Untapping the potential of plant mycobiomes for applications in agriculture

Plant-fungal interactions are widespread in nature, and their multiple benefits for plant growth and health have been amply demonstrated. Endophytic and epiphytic fungi can significantly increase plant resilience, improving plant nutrition, stress tolerance and defence. Although some of these interactions have been known for decades, the relevance of the plant mycobiome within the plant microbiome has been largely underestimated. Our limited knowledge of fungal biology and their interactions with plants in the broader phytobiome context has hampered the development of optimal biotechnological applications in agrosystems and natural ecosystems. Exciting recent technical and knowledge advances in the context of molecular and systems biology open a plethora of opportunities for developing this field of research.

Arbuscular Mycorrhizal Fungi Improve Tolerance of the Medicinal Plant Eclipta prostrata (L.) and Induce Major Changes in Polyphenol Profiles Under Salt Stresses

Eclipta prostrata (L.) is an important and well-known medicinal plant due to its valuable bioactive compounds. Microorganisms, including arbuscular mycorrhizal fungi (AMF), and salinity could directly impact plant metabolome, thus influencing their secondary metabolites and the efficacy of herbal medicine. In this study, the role of different single AMF species (Funneliformis mosseae, Septoglomus deserticola, Acaulospora lacunosa) and a mixture of six AMF species in plant growth and physio-biochemical characteristics of E. prostrata under non-saline conditions was investigated. Next, the most suitable AM treatment was chosen to examine the impact of AMF on physio-biochemical features and polyphenol profiles of E. prostrata under saline conditions (100 and 200 mM NaCl). The findings indicated that AMF mixture application resulted in more effective promotion on the aboveground part of non-saline plants than single AMF species. AM mixture application improved growth and salt tolerance of E. prostrata through increasing the activity of catalase, peroxidase (at 4 weeks), proline, and total phenolic content (at 8 weeks). Such benefits were not observed under high salinity, except for a higher total phenolic concentration in mycorrhizal plants at 8 weeks. Through high-performance liquid chromatography, 14 individual phenolic compounds were analyzed, with wedelolactone and/or 4,5-dicaffeoylquinic acid abundant in all treatments. Salinity and mycorrhizal inoculation sharply altered the polyphenol profiles of E. prostrata. Moderate salinity boosted phenolic compound production in non-AM plants at 4 weeks, while at 8 weeks, the decline in the content of phenolic compounds occurred in uncolonized plants subjected to both saline conditions. Mycorrhization augmented polyphenol concentration and yield under non-saline and saline conditions, depending on the growth stages and salt stress severity. Plant age influenced polyphenol profiles with usually a higher content of phenolic compounds in older plants and changed the production of individual polyphenols of both non-AM and AM plants under non-stress and salt stress conditions. A better understanding of factors (involving mycorrhiza and salinity) affecting the phenolic compounds of E. prostrata facilitates the optimization of individual polyphenol production in this medicinal plant.

Metabolomics Analysis Reveals Drought Responses of Trifoliate Orange by Arbuscular Mycorrhizal Fungi With a Focus on Terpenoid Profile

Soil water deficit seriously affects crop production, and soil arbuscular mycorrhizal fungi (AMF) enhance drought tolerance in crops by unclear mechanisms. Our study aimed to analyze changes in non-targeted metabolomics in roots of trifoliate orange (Poncirus trifoliata) seedlings under well-watered and soil drought after inoculation with Rhizophagus intraradices, with a focus on terpenoid profile. Root mycorrhizal fungal colonization varied from 70% under soil drought to 85% under soil well-watered, and shoot and root biomass was increased by AMF inoculation, independent of soil water regimes. A total of 643 secondary metabolites in roots were examined, and 210 and 105 differential metabolites were regulated by mycorrhizal fungi under normal water and drought stress, along with 88 and 17 metabolites being up-and down-regulated under drought conditions, respectively. KEGG annotation analysis of differential metabolites showed 38 and 36 metabolic pathways by mycorrhizal inoculation under normal water and drought stress conditions, respectively. Among them, 33 metabolic pathways for mycorrhization under drought stress included purine metabolism, pyrimidine metabolism, alanine, aspartate and glutamate metabolism, etc. We also identified 10 terpenoid substances, namely albiflorin, artemisinin (-)-camphor, capsanthin, β-caryophyllene, limonin, phytol, roseoside, sweroside, and α-terpineol. AMF colonization triggered the decline of almost all differential terpenoids, except for β-caryophyllene, which was up-regulated by mycorrhizas under drought, suggesting potential increase in volatile organic compounds to initiate plant defense responses. This study provided an overview of AMF-induced metabolites and metabolic pathways in plants under drought, focusing on the terpenoid profile.

Genetic Analysis of Root-to-Shoot Signaling and Rootstock-Mediated Tolerance to Water Deficit in Tomato

Developing drought-tolerant crops is an important strategy to mitigate climate change impacts. Modulating root system function provides opportunities to improve crop yield under biotic and abiotic stresses. With this aim, a commercial hybrid tomato variety was grafted on a genotyped population of 123 recombinant inbred lines (RILs) derived from Solanum pimpinellifolium, and compared with self- and non-grafted controls, under contrasting watering treatments (100% vs. 70% of crop evapotranspiration). Drought tolerance was genetically analyzed for vegetative and flowering traits, and root xylem sap phytohormone and nutrient composition. Under water deficit, around 25% of RILs conferred larger total shoot dry weight than controls. Reproductive and vegetative traits under water deficit were highly and positively correlated to the shoot water content. This association was genetically supported by linkage of quantitative trait loci (QTL) controlling these traits within four genomic regions. From a total of 83 significant QTLs, most were irrigation-regime specific. The gene contents of 8 out of 12 genomic regions containing 46 QTLs were found significantly enriched at certain GO terms and some candidate genes from diverse gene families were identified. Thus, grafting commercial varieties onto selected rootstocks derived from S. pimpinellifolium provides a viable strategy to enhance drought tolerance in tomato.

Metabolomic adjustments in the orchid mycorrhizal fungus Tulasnella calospora during symbiosis with Serapias vomeracea

All orchids rely on mycorrhizal fungi for organic carbon, at least during early development. In fact, orchid seed germination leads to the formation of a protocorm, a heterotrophic postembryonic structure colonized by intracellular fungal coils, thought to be the site of nutrient transfer. The molecular mechanisms underlying mycorrhizal interactions and metabolic changes induced by this symbiosis in both partners remain mostly unknown. We studied plant-fungus interactions in the mycorrhizal association between the Mediterranean orchid Serapias vomeracea and the basidiomycete Tulasnella calospora using nontargeted metabolomics. Plant and fungal metabolomes obtained from symbiotic structures were compared with those obtained under asymbiotic conditions. Symbiosis induced substantial metabolomic alterations in both partners. In particular, structural and signaling lipid compounds increased markedly in the external fungal mycelium growing near the symbiotic protocorms, whereas chito-oligosaccharides were identified uniquely in symbiotic protocorms. This work represents the first description of metabolic changes occurring in orchid mycorrhiza. These results - combined with previous transcriptomic data - provide novel insights on the mechanisms underlying the orchid mycorrhizal association and open intriguing questions on the role of fungal lipids in this symbiosis.

Induction and Priming of Plant Defense by Root-Associated Insect-Pathogenic Fungi

Plants evolved in close contact with a myriad of microorganisms, some of which formed associations with their roots, benefitting from carbohydrates and other plant resources. In exchange, they evolved to influence important plant functions, e.g. defense against insect herbivores and other antagonists. Here, we test whether a fungus, Metarhizium brunneum, which is mostly known as an insect pathogen, can also associate with plant roots and contribute to above-ground plant defense. Cauliflower (Brassica oleracea var. botrytis) seeds were sown together with M. brunneum-inoculated rice grains, and the resulting plants subjected to leaf herbivory by the specialist Plutella xylostella. Activity of myrosinases, the enzymes activating glucosinolates, was measured before and after herbivory; larval consumption and plant weight at the end of experiments. Metarhizium brunneum clearly established in the plant roots, and after herbivory myrosinase activity was substantially higher in M. brunneum-treated plants than in controls; before herbivory, M. brunneum-treated and control plants did not differ. Leaf consumption was slightly lower in the M. brunneum-treated plants whereas total biomass and allocation to above- or below-ground parts was not affected by the Metarhizium treatment. Thus, M. brunneum associates with roots and primes the plant for a stronger or faster increase in myrosinase activity upon herbivory. Consistent with this, myrosinase function has been suggested to be rate-limiting for induction of the glucosinolate-myrosinase defense system. Our results show that M. brunneum, in addition to being an insect pathogen, can associate with plant roots and prime plant defense.

The soil biotic community protects Rhododendron spp. across multiple clades from the oomycete Phytophthora cinnamomi at a cost to plant growth

The effects of whole soil biotic communities on plants is a result of positive and negative interactions from a complex suite of mutualists and pathogens. However, few experiments have evaluated the composite effects of whole soil biotic communities on plant growth and disease resistance. We conducted a factorial greenhouse experiment with 14 Rhododendron species grown with and without live conspecific soil biota and with and without the disease, Phytophthora cinnamomi. We tested the prediction that the presence of whole soil biotic communities influences survival in the presence of disease. We also explored functional trait correlations with disease susceptibility across the phylogeny. The presence of live soil biota led to higher survival in the presence of disease compared with sterilized soils, and the direction of this effect was consistent for seven species across four clades. The presence of live soil biota also significantly reduced plant growth rate and decreased shoot biomass, relative to plants grown in sterilized soil, indicating that live soil biota might influence plant allocation strategies. We found that Rhododendron species with higher Root Shoot Ratios were less susceptible to Phytophthora, suggesting that water relations influence disease susceptibility. Our findings that disease resistance and susceptibility occur independently across multiple clades and that whole soil biotic communities consistently enhance disease resistance across clades, suggest that soil biota may play an important role in disease resistance and can moderate disease-induced mortality.

Systemic induction of phosphatidylinositol-based signaling in leaves of arbuscular mycorrhizal rice plants

Most land plants form beneficial associations with arbuscular mycorrhizal (AM) fungi which improves mineral nutrition, mainly phosphorus, in the host plant in exchange for photosynthetically fixed carbon. Most of our knowledge on the AM symbiosis derives from dicotyledonous species. We show that inoculation with the AM fungus Funneliformis mosseae stimulates growth and increases Pi content in leaves of rice plants (O. sativa, cv Loto, ssp japonica). Although rice is a host for AM fungi, the systemic transcriptional responses to AM inoculation, and molecular mechanisms underlying AM symbiosis in rice remain largely elusive. Transcriptomic analysis identified genes systemically regulated in leaves of mycorrhizal rice plants, including genes with functions associated with the biosynthesis of phospholipids and non-phosphorus lipids (up-regulated and down-regulated, respectively). A coordinated regulation of genes involved in the biosynthesis of phospholipids and inositol polyphosphates, and genes involved in hormone biosynthesis and signaling (jasmonic acid, ethylene) occurs in leaves of mycorrhizal rice. Members of gene families playing a role in phosphate starvation responses and remobilization of Pi were down-regulated in leaves of mycorrhizal rice. These results demonstrated that the AM symbiosis is accompanied by systemic transcriptional responses, which are potentially important to maintain a stable symbiotic relationship in rice plants.

Root-to-shoot signalling in mycorrhizal tomato plants upon Botrytis cinerea infection

Arbuscular mycorrhizal symbiosis is restricted in roots, but it also improves shoot responses against leaf challenges, a phenomenon known as Mycorrhiza-Induced Resistance (MIR). This study focuses on mycorrhizal root signals that may orchestrate shoot defence responses. Metabolomic analysis of non-mycorrhizal and mycorrhizal plants upon Botrytis cinerea infection showed that roots rearrange their metabolome mostly in response to the symbiosis, whereas in shoots a stronger impact of the infection is observed. Specific clusters of compounds in shoots and roots display a priming profile suggesting an implication in the enhanced resistance observed in mycorrhizal plants. Among the primed pathways in roots, lignans showed the highest number of hits followed by oxocarboxylic acids, compounds of the amino acid metabolism, and phytohormones. The lignan yatein was present at higher concentrations in roots, root efflux and leaves of mycorrhizal plants This lignan displayed in vitro antimicrobial activity against B. cinerea and it was also functional protecting tomato plants. Besides, several JA defence-related genes were upregulated in mycorrhizal roots regardless of the pathogen infection, whereas PIN-II was primed in roots of mycorrhizal infected plants. These observations suggest that the enhanced resistance in shoots during MIR may be coordinated by lignans and oxylipins with the participation of roots.

The Salt Sensitivity Induced by Disruption of Cell Wall-Associated Kinase 1 (SlWAK1) Tomato Gene Is Linked to Altered Osmotic and Metabolic Homeostasis

Tomato cell wall-associated kinase 1 (SlWAK1) has only been studied in biotic stress response and hence its function in abiotic stress remains unknown. In a screening under salinity of an insertional mutant collection of tomato (Solanum lycopersicum L.), a mutant exhibiting lower degree of leaf chlorosis than wild type (WT) together with reduced leaf Na+ accumulation was selected. Genetic analysis of the mutation revealed that a single T-DNA insertion in the SlWAK1 gene was responsible of the mutant phenotype. Slwak1 null mutant reduced its shoot growth compared with WT, despite its improved Na+ homeostasis. SlWAK1 disruption affected osmotic homeostasis, as leaf water content was lower in mutant than in WT under salt stress. In addition, Slwak1 altered the source-sink balance under salinity, by increasing sucrose content in roots. Finally, a significant fruit yield reduction was found in Slwak1 vs. WT under long-term salt stress, mainly due to lower fruit weight. Our results show that disruption of SlWAK1 induces a higher sucrose transport from source leaf to sink root, negatively affecting fruit, the main sink at adult stage.

Unraveling Arbuscular Mycorrhiza-Induced Changes in Plant Primary and Secondary Metabolome

Arbuscular mycorrhizal fungi (AMF) is among the most ubiquitous plant mutualists that enhance plant growth and yield by facilitating the uptake of phosphorus and water. The countless interactions that occur in the rhizosphere between plants and its AMF symbionts are mediated through the plant and fungal metabolites that ensure partner recognition, colonization, and establishment of the symbiotic association. The colonization and establishment of AMF reprogram the metabolic pathways of plants, resulting in changes in the primary and secondary metabolites, which is the focus of this review. During initial colonization, plant-AMF interaction is facilitated through the regulation of signaling and carotenoid pathways. After the establishment, the AMF symbiotic association influences the primary metabolism of the plant, thus facilitating the sharing of photosynthates with the AMF. The carbon supply to AMF leads to the transport of a significant amount of sugars to the roots, and also alters the tricarboxylic acid cycle. Apart from the nutrient exchange, the AMF imparts abiotic stress tolerance in host plants by increasing the abundance of several primary metabolites. Although AMF initially suppresses the defense response of the host, it later primes the host for better defense against biotic and abiotic stresses by reprogramming the biosynthesis of secondary metabolites. Additionally, the influence of AMF on signaling pathways translates to enhanced phytochemical content through the upregulation of the phenylpropanoid pathway, which improves the quality of the plant products. These phytometabolome changes induced by plant-AMF interaction depends on the identity of both plant and AMF species, which could contribute to the differential outcome of this symbiotic association. A better understanding of the phytochemical landscape shaped by plant-AMF interactions would enable us to harness this symbiotic association to enhance plant performance, particularly under non-optimal growing conditions.

Exogenous strigolactones impact metabolic profiles and phosphate starvation signalling in roots

Strigolactones (SLs) are important ex-planta signalling molecules in the rhizosphere, promoting the association with beneficial microorganisms, but also affecting plant interactions with harmful organisms. They are also plant hormones in-planta, acting as modulators of plant responses under nutrient-deficient conditions, mainly phosphate (Pi) starvation. In the present work, we investigate the potential role of SLs as regulators of early Pi starvation signalling in plants. A short-term pulse of the synthetic SL analogue 2'-epi-GR24 promoted SL accumulation and the expression of Pi starvation markers in tomato and wheat under Pi deprivation. 2'-epi-GR24 application also increased SL production and the expression of Pi starvation markers under normal Pi conditions, being its effect dependent on the endogenous SL levels. Remarkably, 2'-epi-GR24 also impacted the root metabolic profile under these conditions, promoting the levels of metabolites associated to plant responses to Pi limitation, thus partially mimicking the pattern observed under Pi deprivation. The results suggest an endogenous role for SLs as Pi starvation signals. In agreement with this idea, SL-deficient plants were less sensitive to this stress. Based on the results, we propose that SLs may act as early modulators of plant responses to P starvation.

Arbuscular Mycorrhizal Symbiosis Primes Tolerance to Cucumber Mosaic Virus in Tomato

Tomato plants can establish symbiotic interactions with arbuscular mycorrhizal fungi (AMF) able to promote plant nutrition and prime systemic plant defenses against pathogens attack; the mechanism involved is known as mycorrhiza-induced resistance (MIR). However, studies on the effect of AMF on viral infection, still limited and not conclusive, indicate that AMF colonization may have a detrimental effect on plant defenses against viruses, so that the term "mycorrhiza-induced susceptibility" (MIS) has been proposed for these cases. To expand the case studies to a not yet tested viral family, that is, Bromoviridae, we investigated the effect of the colonization by the AMF Funneliformis mosseae on cucumber mosaic virus (CMV) infection in tomato by phenotypic, physiological, biochemical, and transcriptional analyses. Our results showed that the establishment of a functional AM symbiosis is able to limit symptoms development. Physiological and transcriptomic data highlighted that AMF mitigates the drastic downregulation of photosynthesis-related genes and the reduction of photosynthetic CO2 assimilation rate caused by CMV infection. In parallel, an increase of salicylic acid level and a modulation of reactive oxygen species (ROS)-related genes, toward a limitation of ROS accumulation, was specifically observed in CMV-infected mycorrhizal plants. Overall, our data indicate that the AM symbiosis influences the development of CMV infection in tomato plants and exerts a priming effect able to enhance tolerance to viral infection.