Phytohormone production by the arbuscular mycorrhizal fungus Rhizophagus irregularis

First Peek into the Transcriptomic Response in Heat-Stressed Tomato Inoculated with Septoglomus constrictum

In this study, we report the interaction between an arbuscular mycorrhizal fungus, Septoglomus constrictum, and tomato plants under heat stress. For the first time, this interaction was studied by Illumina RNA-seq, followed by a comprehensive bioinformatic analysis that investigated root and leaf tissue samples. The genome-wide transcriptional profiling displayed fewer transcriptomic changes in the root under heat-stress conditions caused by S. constrictum. The top 50 DEGs suggested significant changes in the expression of genes encoding heat-shock proteins, transporter proteins, and genes of phytohormone metabolism involving jasmonic acid signalling. S. constrictum induced the upregulation of genes associated with pathways such as 'drought-responsive' and the 'development of root hair' in the root, as well as 'glycolipid desaturation', 'intracellular auxin transport', and 'ethylene biosynthesis' in the leaf. The pathways 'biotin biosynthesis' and 'threonine degradation' were found in both investigated tissue types. Expression analysis of transcription factors showed 2 and 11 upregulated transcription factors in heat-stressed root and leaf tissues, respectively. However, we did not find shared transcription factors. Heat-stressed arbuscular mycorrhizal plants suffered less oxidative stress when exposed to high temperatures. Colorimetric tests demonstrated less accumulation of H2O2 and MDA in heat-stressed mycorrhizal plants. This phenomenon was accompanied by the higher expression of six stress genes that encode peroxidases, glutathione S-transferase and ubiquitin carboxyl-terminal hydrolase in roots and leaves. Our findings provide a new perspective on elucidating the functional metabolic processes of tomato plants under mycorrhizal-heat stressed conditions.

Testing the trade-balance model: resource stoichiometry does not sufficiently explain AM effects

Variations in arbuscular mycorrhizae (AM) effects on plant growth (MGR) are commonly assumed to result from cost : benefit balances, with C as the cost and, most frequently, P as the benefit. The trade-balance model (TBM) adopts these assumptions and hypothesizes that mycorrhizal benefit depends on C : N : P stoichiometry. Although widely accepted, the TBM has not been experimentally tested. We isolated the parameters included in the TBM and tested these assumptions using it as framework. Oryza sativa plants were supplied with different N : P ratios at low light level, establishing different C : P and C : N exchange rates, and C, N or P limitation. MGR and effects on nutrient uptake, %M, ERM, photosynthesis and shoot starch were measured. C distribution to AM fungi played no role in MGR, and N was essential for all AM effects, including on P nutrition. C distribution to AM and MGR varied with the limiting nutrient (N or P), and evidence of extensive interplay between N and P was observed. The TBM was not confirmed. The results agreed with the exchange of surplus resources and source-sink regulation of resource distribution among plants and AMF. Rather than depending on exchange rates, resource exchange may simply obey both symbiont needs, not requiring further regulation.

Arbuscular mycorrhizal fungi, phosphorus and organic residues in Peltophorum dubium (Spreng.) Taub. seedlings

Studies have underscored a growingdemand for innovative practices in the cultivation of seedlings from forest species, with a notable emphasis on the utilization of organic waste, inoculation with arbuscular mycorrhizal fungi (AMF), and phosphate fertilization. This study aimed to evaluate the impact of organic residues, inoculation with AMF, and phosphorus on the growth and quality of Peltophorum dubium (Spreng.) Taub. seedlings. Two independent experiments were conducted. In Experiment I, treatments included inoculation with various AMF species: control (without inoculation), Clareoideoglomus etunicatum, Rhizophagus heterosporum, Rhizophagus clarum, and MIX (a combination of the three AMF species), all in conjunction with varying doses of phosphorus (0, 60, 120, 180, and 240 mg kg-1 soil). In Experiment II, treatments comprised a control group (without AMF) and inoculation with Glomus clarum, Gigaspora margarita, Gigaspora albida, Clareoideoglomus etunicatum, and MIX (a combination of the four AMF species), each associated with four substrates: S1) soil + coarse sand - SCS, S2) SCS + poultry manure, S3) SCS + cattle manure, and S4) SCS + sheep manure. Peltophorum dubium seedlings exhibited heightened growth with the inoculation of R. heterosporum, R. clarum, and MIX. Positive responses were observed in seedlings when exposed to organic residues, particularly sheep manure, resulting in increased biomass production and enhanced Dickson quality index. The AMF inoculation, specifically with R. heterosporum, R. clarum, and MIX, provided optimal growth conditions for P. dubium seedlings. Remarkably, the utilization of organic residues, notably substrates with chicken manure and cattle manure, exerted substantial positive effects on both growth and quality of P. dubium seedlings.

Transcriptome and Hormonal Analysis of Agaricus bisporus Basidiome Response to Hypomyces perniciosus Infection

Agaricus bisporus (Lange) Imbach is the most widely cultivated mushroom in the world. A. bisporus wet bubble disease is one of the most severe diseases of white button mushrooms and is caused by the fungal pathogen Hypomyces perniciosus. The pathogen causes a drastic reduction in mushroom yield because of malformation and deterioration of the basidiomes. However, the mechanism of the button mushroom's malformation development after infection with H. perniciosus remains obscure. Therefore, to reveal the mechanism of A. bisporus malformation caused by H. perniciosus, the interaction between the pathogen and host was investigated in this study using histopathological, physiological, and transcriptomic analyses. Results showed that irrespective of the growth stages of A. bisporus basidiomes infected with H. perniciosus, the host's malformed basidiomes and enlarged mycelia and basidia indicated that the earlier the infection with H. perniciosus, the more the malformation of the basidiomes. Analyzing physiological and transcriptomic results in tandem, we concluded that H. perniciosus causes malformation development of A. bisporus mainly by affecting the metabolism level of phytohormones (N6-isopentenyladenosine, cis-zeatin, and N6-[delta 2-isopentenyl]-adenine) of the host's fruiting bodies rather than using toxins. Our findings revealed the mechanism of the button mushroom's malformation development after infection with H. perniciosus, providing a reference for developing realistic approaches to control mushroom diseases. Our results further clarified the interaction between A. bisporus and H. perniciosus and identified the candidate genes for A. bisporus wet bubble disease resistance breeding. Additionally, our work provides a valuable theoretical basis and technical support for studying the interaction between other pathogenic fungi and their fungal hosts.

The Complex Interplay between Arbuscular Mycorrhizal Fungi and Strigolactone: Mechanisms, Sinergies, Applications and Future Directions

Plants, the cornerstone of life on Earth, are constantly struggling with a number of challenges arising from both biotic and abiotic stressors. To overcome these adverse factors, plants have evolved complex defense mechanisms involving both a number of cell signaling pathways and a complex network of interactions with microorganisms. Among these interactions, the relationship between symbiotic arbuscular mycorrhizal fungi (AMF) and strigolactones (SLs) stands as an important interplay that has a significant impact on increased resistance to environmental stresses and improved nutrient uptake and the subsequent enhanced plant growth. AMF establishes mutualistic partnerships with plants by colonizing root systems, and offers a range of benefits, such as increased nutrient absorption, improved water uptake and increased resistance to both biotic and abiotic stresses. SLs play a fundamental role in shaping root architecture, promoting the growth of lateral roots and regulating plant defense responses. AMF can promote the production and release of SLs by plants, which in turn promote symbiotic interactions due to their role as signaling molecules with the ability to attract beneficial microbes. The complete knowledge of this synergy has the potential to develop applications to optimize agricultural practices, improve nutrient use efficiency and ultimately increase crop yields. This review explores the roles played by AMF and SLs in plant development and stress tolerance, highlighting their individual contributions and the synergistic nature of their interaction.

Are Histidine Kinases of Arbuscular Mycorrhizal Fungi Involved in the Response to Ethylene and Cytokinins?

Signals are exchanged at all stages of the arbuscular mycorrhizal (AM) symbiosis between fungi and their host plants. Root-exuded strigolactones are well-known early symbiotic cues, but the role of other phytohormones as interkingdom signals has seldom been investigated. Here we focus on ethylene and cytokinins, for which candidate receptors have been identified in the genome of the AM fungus Rhizophagus irregularis. Ethylene is known from the literature to affect asymbiotic development of AM fungi, and in the present study, we found that three cytokinin forms could stimulate spore germination in R. irregularis. Heterologous complementation of a Saccharomyces cerevisiae mutant strain with the candidate ethylene receptor RiHHK6 suggested that this protein can sense and transduce an ethylene signal. Accordingly, its N-terminal domain expressed in Pichia pastoris displayed saturable binding to radiolabeled ethylene. Thus, RiHHK6 displays the expected characteristics of an ethylene receptor. In contrast, the candidate cytokinin receptor RiHHK7 did not complement the S. cerevisiae mutant strain or Medicago truncatula cytokinin receptor mutants and seemed unable to bind cytokinins, suggesting that another receptor is involved in the perception of these phytohormones. Taken together, our results support the hypothesis that AM fungi respond to a range of phytohormones and that these compounds bear multiple functions in the rhizosphere beyond their known roles as internal plant developmental regulators. Our analysis of two phytohormone receptor candidates also sheds new light on the possible perception mechanisms in AM fungi. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Lessons from arbuscular mycorrhizal fungal genomes

Arbuscular mycorrhizal fungi (AMF) have accompanied the majority of land plants since their evolution in the Devonian period with a symbiotic alliance centered on nutrient exchanges. The exploration of AMF genomes is providing clues to explain major questions about their biology, evolution, and ecology. The dynamics of nuclei across the fungal life cycle, the abundance of transposable elements, and the epigenome landscape are emerging as sources of intraspecific variability, which can be especially important in organisms with no or rare sexual reproduction such as AMF. These features have been hypothesized to support AMF adaptability to a wide host range and to environmental changes. New insights on plant-fungus communication and on the iconic function of phosphate transport were also recently obtained that overall contribute to a better understanding of this ancient and fascinating symbiosis.

Functional analysis of auxin derived from a symbiotic mycobiont

The biosynthesis of auxin or indole-3-acetic acid by microorganisms has a major impact on plant-microbe interactions. Several beneficial microbiota are known to produce auxin, which largely influences root development and growth in the host plants. Akin to findings in rhizobacteria, recent studies have confirmed the production of auxin by plant growth-promoting fungi too. Here, we show that Penicillium citrinum isolate B9 produces auxin as deduced by liquid chromatography tandem-mass spectrometry analysis. Such fungal auxin is secreted and contributes directly to enhanced root and shoot development and overall plant growth in Arabidopsis thaliana. Furthermore, auxin production by P. citrinum likely involves more than one tryptophan-dependent pathway. Using auxin biosynthesis inhibitor L-Kynurenine, we show that the indole-3-pyruvate pathway might be one of the key biosynthetic routes involved in such auxin production. Confocal microscopy of the DR5rev:GFP Arabidopsis reporter line helped demonstrate that P. citrunum B9-derived auxin is biologically active and is able to significantly enhance auxin signaling in roots during such improved root growth and plant development. Furthermore, the phenotypic growth defects arising from impaired auxin signaling in Arabidopsis taa1 mutant or upon L-Kynurenine treatment of wild-type Arabidopsis seedlings could be significantly alleviated by fungus B9-derived auxin, thus suggesting its positive role in plant growth promotion. Collectively, our results provide clear evidence that the production of auxin is one of the main mechanisms involved in induction of the beneficial plant growth by P. citrinum.

Transition to ripening in tomato requires hormone-controlled genetic reprogramming initiated in gel tissue

Ripening is the last stage of the developmental program in fleshy fruits. During this phase, fruits become edible and acquire their unique sensory qualities and post-harvest potential. Although our knowledge of the mechanisms that regulate fruit ripening has improved considerably over the past decades, the processes that trigger the transition to ripening remain poorly deciphered. While transcriptomic profiling of tomato (Solanum lycopersicum L.) fruit ripening to date has mainly focused on the changes occurring in pericarp tissues between the Mature Green and Breaker stages, our study addresses the changes between the Early Mature Green and Late Mature Green stages in the gel and pericarp separately. The data showed that the shift from an inability to initiate ripening to the capacity to undergo full ripening requires extensive transcriptomic reprogramming that takes place first in the locular tissues before extending to the pericarp. Genome-wide transcriptomic profiling revealed the wide diversity of transcription factor (TF) families engaged in the global reprogramming of gene expression and identified those specifically regulated at the Mature Green stage in the gel but not in the pericarp, thereby providing potential targets toward deciphering the initial factors and events that trigger the transition to ripening. The study also uncovered an extensive reformed homeostasis for most plant hormones, highlighting the multihormonal control of ripening initiation. Our data unveil the antagonistic roles of ethylene and auxin during the onset of ripening and show that auxin treatment delays fruit ripening via impairing the expression of genes required for System-2 autocatalytic ethylene production that is essential for climacteric ripening. This study unveils the detailed features of the transcriptomic reprogramming associated with the transition to ripening of tomato fruit and shows that the first changes occur in the locular gel before extending to pericarp and that a reformed auxin homeostasis is essential for the ripening to proceed.

Mycorrhizae influence plant vegetative and floral traits and intraspecific trait variation

PREMISE

Arbuscular mycorrhizal fungi (AMF) can strongly influence host plant vegetative growth, but less is known about AMF effects on other plant traits, the relative impacts of AMF on vegetative growth versus floral traits, or AMF-induced intraspecific variation in traits.

METHODS

In an experimental greenhouse study, we inoculated seven species of wildflowers with six species of AMF in a factorial design. We assessed how the AMF-forb combinations influenced plant survival, vegetative biomass, and floral traits and whether AMF effects on floral traits were similar in magnitude and direction to effects on vegetative biomass. For one forb species, we investigated intraspecific plant trait variation within and across AMF treatments.

RESULTS

AMF species varied from negative to positive in their effects on host plants. AMF often had inconsistent effects on vegetative biomass versus floral traits, and therefore, quantifying one or the other may provide a misleading representation of potential AMF effects. AMF treatments generated key variation in plant traits, especially floral traits, with potential consequences for plant-pollinator interactions. Given increased intraspecific trait variation in Linum lewisii plants across AMF species compared to uninoculated individuals or single AMF treatments, local AMF diversity and their host plant associations may scale up to influence community-wide patterns of trait variation and species interactions.

CONCLUSIONS

These results have implications for predicting how aboveground communities are affected by belowground communities. Including AMF effects on not just host plant biomass but also functional traits and trait variation will deepen our understanding of community structure and function, including pollination.

Arbuscular mycorrhizal colonization leads to a change of hormone profile in micropropagated plantlet Satureja khuzistanica Jam

Phytohormones are supposed to contribute to the establishment of mutualistic Arbuscular mycorrhiza (AM) symbioses. However, their role in the acclimation of micropropagated plantlet inoculated with AM is still unknown. To address this question, we performed a hormone profiling during the acclimation of Satureja khuzistanica plantlets inoculated with Rhizoglomus fasciculatum. The levels of indoleacetic acid (IAA), methyl indole acetic acid, cis-zeatin, cis zeatin ribose, jasmonate, jasmonoyl isoleucine, salicylic acid, abscisic acid (ABA) were analyzed. Further, the relative gene expression of AOS (Allene oxide synthase) as a key enzyme of jasmonate biosynthesis, in either inoculated or non-inoculated micropropagated plantlets was evaluated during acclimation period. The concentrations of IAA and cis-zeatin increased in the plantlets inoculated by AM whereas the concentration of ABA decreased upon 60 days acclimation in the whole shoot of plantlets of S. khuzistanica. The relative expression of AOS gene resulted in an increase of isoleucine jasmonate, the bioactive form of jasmonate. Based on our results, IAA and cis-zeatin probably contribute to maintaining growth, and AM reduces transition stress by modifying ABA and jasmonate concentrations.

Volatile organic compounds shape belowground plant-fungi interactions

Volatile organic compounds (VOCs), a bouquet of chemical compounds released by all life forms, play essential roles in trophic interactions. VOCs can facilitate a large number of interactions with different organisms belowground. VOCs-regulated plant-plant or plant-insect interaction both below and aboveground has been reported extensively. Nevertheless, there is little information about the role of VOCs derived from soilborne pathogenic fungi and beneficial fungi, particularly mycorrhizae, in influencing plant performance. In this review, we show how plant VOCs regulate plant-soilborne pathogenic fungi and beneficial fungi (mycorrhizae) interactions. How fungal VOCs mediate plant-soilborne pathogenic and beneficial fungi interactions are presented and the most common methods to collect and analyze belowground volatiles are evaluated. Furthermore, we suggest a promising method for future research on belowground VOCs.

Transcriptome analysis reveals the regulatory mode by which NAA promotes the growth of Armillaria gallica

A symbiotic relationship is observed between Armillaria and the Chinese herbal medicine Gastrodia elata (G. elata). Armillaria is a nutrient source for the growth of G. elata, and its nutrient metabolism efficiency affects the growth and development of G. elata. Auxin has been reported to stimulate Armillaria species, but the molecular mechanism remains unknown. We found that naphthalene acetic acid (NAA) can also promote the growth of A. gallica. Moreover, we identified a total of 2071 differentially expressed genes (DEGs) by analyzing the transcriptome sequencing data of A. gallica at 5 and 10 hour of NAA treatment. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that these unigenes were significantly enriched in the metabolism pathways of arginine, proline, propanoate, phenylalanine and tryptophan. The expression levels of the general amino acid permease (Gap), ammonium transporter (AMT), glutamate dehydrogenase (GDH), glutamine synthetase (GS), Zn(II) 2Cys6 and C2H2 transcription factor genes were upregulated. Our transcriptome analysis showed that the amino acid and nitrogen metabolism pathways in Armillaria were rapidly induced within hours after NAA treatment. These results provide valuable insights into the molecular mechanisms by which NAA promotes the growth of Armillaria species.

Arbuscular mycorrhizal fungi inoculation and phosphorus application improve growth, physiological traits, and grain yield of rice under alternate wetting and drying irrigation

Climate change and agricultural malpractices are exacerbating drought in many parts of the world causing a substantial agricultural production loss. The improvement of drought tolerance in rice is crucial for maintaining productivity and ensuring global food security. Alternate wetting and drying (AWD) irrigation along with plant-microbe interaction through arbuscular mycorrhizal fungi (AMF) is a potential approach for enhancing rice production through AMF-induced up-regulation of tolerance and resilience against drought stress. Therefore, the ameliorative role of AMF inoculation and phosphorus (P) application on growth, physiological traits, and grain yield of rice was evaluated under water stress imposed through AWD irrigation. A factorial experiment consisting of four fertilizer treatments where the P percentage varied along with the recommended dose of nitrogen (N) with or without AMF inoculation (P₁₀₀ as the control, P₁₀₀ + AMF, P₇₅ + AMF, and P₅₀ + AMF), three soil water potential levels (0, -15, and -30 kPa), and two cultivation methods (wet direct seeding and transplanting) was conducted in a polyhouse. The subscript values of 100, 75, and 50 under P represent 100%, 75%, and 50% of the recommended field application dose. Data were collected on selected growth parameters, physiological traits, levels of mycorrhizal colonization, yield and its components, and water productivity of rice. The results revealed that P₁₀₀ + AMF inoculated plants had 11%, 14%, 74%, and 54% higher leaf greenness, leaf relative water content, net photosynthetic rate, and grain yield, respectively, for wet direct-seeded plants at reduced soil water potential (-30 kPa) compared with non-inoculated plants (P₁₀₀). Free proline accumulation gradually enhanced with decreasing soil water potential, and it was maximized by 77% at -30 kPa compared with 0 kPa for P₅₀ + AMF (for transplanted plants). Free proline accumulation was also higher with decreasing soil water potential in AMF-inoculated plants than non-inoculated plants regardless of cultivation methods. Leaf osmotic potential was reduced by -0.5 to -1.2 MPa at -30 kPa compared with 0 kPa under different fertilizer doses. However, AMF inoculation (P₁₀₀ + AMF and P₇₅ + AMF) improved leaf osmotic potential of plants under severe water stress (-30 kPa) maintained through AWD irrigation resulting in better osmotic adjustment than non-inoculated plants. AMF inoculation improved the response of most of the evaluated physiological traits of rice and enhanced grain yield with higher P availability (even with a 25% reduction in its recommended dose) in the rhizosphere under drought stress. Thus, it can be concluded that AMF inoculation coupled with judicious P management is a promising approach for improving physiological and biochemical traits, grain yield, and water productivity of rice under AWD irrigation regardless of cultivation methods.

Current advances and research prospects for agricultural and industrial uses of microbial strains available in world collections

Microorganisms are an important component of the ecosystem and have an enormous impact on human lives. Moreover, microorganisms are considered to have desirable effects on other co-existing species in a variety of habitats, such as agriculture and industries. In this way, they also have enormous environmental applications. Hence, collections of microorganisms with specific traits are a crucial step in developing new technologies to harness the microbial potential. Microbial culture collections (MCCs) are a repository for the preservation of a large variety of microbial species distributed throughout the world. In this context, culture collections (CCs) and microbial biological resource centres (mBRCs) are vital for the safeguarding and circulation of biological resources, as well as for the progress of the life sciences. Ex situ conservation of microorganisms tagged with specific traits in the collections is the crucial step in developing new technologies to harness their potential. Type strains are mainly used in taxonomic study, whereas reference strains are used for agricultural, biotechnological, pharmaceutical research and commercial work. Despite the tremendous potential in microbiological research, little effort has been made in the true sense to harness the potential of conserved microorganisms. This review highlights (1) the importance of available global microbial collections for man and (2) the use of these resources in different research and applications in agriculture, biotechnology, and industry. In addition, an extensive literature survey was carried out on preserved microorganisms from different collection centres using the Web of Science (WoS) and SCOPUS. This review also emphasizes knowledge gaps and future perspectives. Finally, this study provides a critical analysis of the current and future roles of microorganisms available in culture collections for different sustainable agricultural and industrial applications. This work highlights target-specific potential microbial strains that have multiple important metabolic and genetic traits for future research and use.

How do arbuscular mycorrhizas affect reproductive functional fitness of host plants?

Arbuscular mycorrhizal (AM) symbiosis in soil may be directly or indirectly involved in the reproductive process of sexually reproducing plants (seed plants), and affect their reproductive fitness. However, it is not clear how underground AM symbiosis affects plant reproductive function. Here, we reviewed the studies on the effects of AM symbiosis on plant reproductive fitness including both male function (pollen) and female function (seed). AM symbiosis regulates the development and function of plant sexual organs by affecting the nutrient using strategy and participating in the formation of hormone networks and secondary compounds in host plants. The nutrient supply (especially phosphorus supply) of AM symbiosis may be the main factor affecting plant's reproductive function. Moreover, the changes in hormone levels and secondary metabolite content induced by AM symbiosis can also affect host plants reproductive fitness. These effects can occur in pollen formation and transport, pollen tube growth and seed production, and seedling performance. Finally, we discuss other possible effects of AM symbiosis on the male and female functional fitness, and suggest several additional factors that may be involved in the influence of AM symbiosis on the reproductive fitness of host plants. We believe that it is necessary to accurately identify and verify the mechanisms driving the changes of reproductive fitness of host plant in symbiotic networks in the future. A more thorough understanding of the mechanism of AM symbiosis on reproductive function will help to improve our understanding of AM fungus ecological roles and may provide references for improving the productivity of natural and agricultural ecosystems.

Mycorrhizal symbiosis reprograms ion fluxes and fatty acid metabolism in wild jujube during salt stress

Chinese jujube (Ziziphus jujuba) is an important fruit tree in China, and soil salinity is the main constraint affecting jujube production. It is unclear how arbuscular mycorrhizal (AM) symbiosis supports jujube adaptation to salt stress. Herein, we performed comparative physiological, ion flux, fatty acid (FA) metabolomic, and transcriptomic analyses to examine the mechanism of AM jujube responding to salt stress. AM seedlings showed better performance during salt stress. AM symbiosis altered phytohormonal levels: indole-3-acetic acid and abscisic acid contents were significantly increased in AM roots and reduced by salt stress. Mycorrhizal colonization enhanced root H+ efflux and K+ influx, while inducing expression of plasma membrane-type ATPase 7 (ZjAHA7) and high-affinity K+ transporter 2 (ZjHAK2) in roots. High K+/Na+ homeostasis was maintained throughout salt exposure. FA content was elevated in AM leaves as well as roots, especially for palmitic acid, oleic acid, trans oleic acid, and linoleic acid, and similar effects were also observed in AM poplar (Populus. alba × Populus. glandulosa cv. 84K) and Medicago truncatula, indicating AM symbiosis elevating FA levels could be a conserved physiological effect. Gene co-expression network analyses uncovered a core gene set including 267 genes in roots associated with AM symbiosis and conserved transcriptional responses, for example, FA metabolism, phytohormone signal transduction, SNARE interaction in vesicular transport, and biotin metabolism. In contrast to widely up-regulated genes related to FA metabolism in AM roots, limited genes were affected in leaves. We propose a model of AM symbiosis-linked reprogramming of FA metabolism and provide a comprehensive insight into AM symbiosis with a woody species adaptation to salt stress.

Synergism between Streptomyces viridosporus HH1 and Rhizophagus irregularis Effectively Induces Defense Responses to Fusarium Wilt of Pea and Improves Plant Growth and Yield

Fusarium wilt is a detrimental disease of pea crop, resulting in severe damage and a reduction in its yield. Developing synergistically enhanced bioagents for disease management and growth promotion is pivotal for food safety, security, and sustainability. In this study, biocontrol potential of treating pea plants with Streptomycesviridosporus HH1 and/or their colonization with Rhizophagusirregularis against infection with Fusarium wilt was investigated. Impacts on the expression profiles of defense-related genes, biochemical, and ultrastructural levels, as well as the growth and yield of pea plants in response to these treatments, were also investigated. Data obtained indicated the antifungal activity of S. viridosporus HH1 against F. oxysporum f.sp. pisi in vitro. Furthermore, the GC-MS analysis revealed production of different bioactive compounds by S. viridosporus HH1, including 2,3-butanediol, thioglycolic acid, and phthalic acid. The results from the greenhouse experiment exhibited a synergistic biocontrol activity, resulting in a 77% reduction in disease severity in pea plants treated with S. viridosporus HH1 and colonized with R. irregularis. In this regard, this dual treatment overexpressed the responsive factor JERF3 (5.6-fold) and the defense-related genes β-1,3-glucanase (8.2-fold) and the pathogenesis-related protein 1 (14.5-fold), enhanced the total phenolic content (99.5%), induced the antioxidant activity of peroxidase (64.3%) and polyphenol oxidase (31.6%) enzymes in pea plants, reduced the antioxidant stress, and improved their hypersensitivity at the ultrastructural level in response to the Fusarium wilt pathogen. Moreover, a synergistic growth-promoting effect was also recorded in pea plants in response to this dual treatment. In this regard, due to this dual treatment, elevated levels of photosynthetic pigments and improved growth parameters were observed in pea leaves, leading to an increment in the yield (113%). In addition, application of S. viridosporus enhanced the colonization levels with R. irregularis in pea roots. Based on the obtained data, we can conclude that treating pea plants with S. viridosporus HH1 and colonization with R. irregularis have synergistic biocontrol activity and growth-promoting effects on pea plants against Fusarium wilt. Despite its eco-safety and effectiveness, a field evaluation of this treatment before a use recommendation is quite necessary.

Evolutionary footprint of plant immunity

There are pieces of evidence from genomic footprints and fossil records indicating that plants have co-evolved with microbes after terrestrialization for more than 407 million years. Therefore, to truly comprehend plant evolution, we need to understand the co-evolutionary process and history between plants and microbes. Recent developments in genomes and transcriptomes of a vast number of plant species as well as microbes have greatly expanded our knowledge of the evolution of the plant immune system. In this review, we summarize recent advances in the co-evolution between plants and microbes with emphasis on the plant side and point out future research needed for understanding plant-microbial co-evolution. Knowledge of the evolution and variation of the plant immune system will better equip us on designing crops with boosted performance in agricultural fields.

Phytohormone Profile of Medicago in Response to Mycorrhizal Fungi, Aphids, and Gibberellic Acid

Although gibberellic acid (GA) is widely used in agriculture, it is unclear whether exogenous GA makes aphid-infested, mycorrhizal plants more susceptible to herbivory. This study investigates the role of GA in modulating defenses in barrel medic plants (Medicago truncatula) that are infested with pea aphids (Acyrthosiphon pisum) and colonized by the beneficial symbiont Rhizophagus intraradices. Mock- and R. intraradices-inoculated potted plants were grown in a topsoil: sand mix for 42 days and were treated with GA or solvent. Subsequently, plants were exposed to herbivory or no aphid herbivory for 36 h and 7 days. Afterwards, plant growth parameters, aphid fitness, and foliar phytohormone concentrations were measured. The results revealed that GA regulates plant defenses during arbuscular mycorrhizal (AM) fungus–plant–aphid interactions as aphids that fed for 7 days on mycorrhizal, GA-untreated plants weighed more than those that fed on mycorrhizal, GA-treated plants. No major differences were detected in phytohormone levels at 36 h. Overall, mycorrhizal plants showed more shoot biomass compared to non-mycorrhizal controls. The arbuscule density and fungal biomass of R. intraradices were not altered by exogenous GA and aphid herbivory based on molecular markers. This study indicates that exogenous GA may help reduce aphid fitness when feeding on mycorrhizal plants.

Ascophyllum nodosum Extract and Mycorrhizal Colonization Synergistically Trigger Immune Responses in Pea Plants against Rhizoctonia Root Rot, and Enhance Plant Growth and Productivity

Rhizoctonia root rot is one of the most destructive diseases affecting pea crops, resulting in up to 75% loss. In this study, the biocontrol activity of seaweed (Ascophyllum nodosum) extract at 1, 2, and 3% and/or mycorrhization of pea roots was investigated against Rhizoctonia root rot under greenhouse conditions. In addition, their effects on the transcriptional, physiological, ultrastructural, and growth status of pea plants were also studied. The results showed that the mycorrhizal colonization of pea roots and the application of the seaweed extract at 3% synergistically overexpressed the responsive factor (JERF3) recording 18.2-fold, and the defense-related genes peroxidase (23.2-fold) and chitinase II (31.8-fold). In addition, this treatment improved the activity of the antioxidant enzymes POD and PPO, increased the phenolic content in pea roots, and triggered multiple hypersensitivity reactions at the ultrastructural level of the cell, leading to a 73.1% reduction in disease severity. Moreover, a synergistic growth-promoting effect on pea plants was also observed. The photosynthetic pigments in pea leaves were enhanced in response to this dual treatment, which significantly improved their yield (24 g/plant). The inducing effect of mycorrhizal colonization on plant resistance and growth has been extensively studied. However, developing improved and synergistically acting biological agents for plant disease control and growth promotion as alternatives to the chemical fungicides is crucial for safety and food security. Based on these results, it can be concluded that the mycorrhizal colonization of pea roots and soaking their seeds in the A. nodosum extract at 3% have a promising and improved biocontrol activity against R. solani, and a growth-promoting effect on pea plants. However, field applications should be evaluated prior to any use recommendations.

Genome-Scale Modeling Specifies the Metabolic Capabilities of Rhizophagus irregularis

Rhizophagus irregularis is one of the most extensively studied arbuscular mycorrhizal fungi (AMF) that forms symbioses with and improves the performance of many crops. Lack of transformation protocol for R. irregularis renders it challenging to investigate molecular mechanisms that shape the physiology and interactions of this AMF with plants. Here, we used all published genomics, transcriptomics, and metabolomics resources to gain insights into the metabolic functionalities of R. irregularis by reconstructing its high-quality genome-scale metabolic network that considers enzyme constraints. Extensive validation tests with the enzyme-constrained metabolic model demonstrated that it can be used to (i) accurately predict increased growth of R. irregularis on myristate with minimal medium; (ii) integrate enzyme abundances and carbon source concentrations that yield growth predictions with high and significant Spearman correlation (ρS = 0.74) to measured hyphal dry weight; and (iii) simulate growth rate increases with tighter association of this AMF with the host plant across three fungal structures. Based on the validated model and system-level analyses that integrate data from transcriptomics studies, we predicted that differences in flux distributions between intraradical mycelium and arbuscles are linked to changes in amino acid and cofactor biosynthesis. Therefore, our results demonstrated that the enzyme-constrained metabolic model can be employed to pinpoint mechanisms driving developmental and physiological responses of R. irregularis to different environmental cues. In conclusion, this model can serve as a template for other AMF and paves the way to identify metabolic engineering strategies to modulate fungal metabolic traits that directly affect plant performance.

IMPORTANCE Mounting evidence points to the benefits of the symbiotic interactions between the arbuscular mycorrhiza fungus Rhizophagus irregularis and crops; however, the molecular mechanisms underlying the physiological responses of this fungus to different host plants and environments remain largely unknown. We present a manually curated, enzyme-constrained, genome-scale metabolic model of R. irregularis that can accurately predict experimentally observed phenotypes. We show that this high-quality model provides an entry point into better understanding the metabolic and physiological responses of this fungus to changing environments due to the availability of different nutrients. The model can be used to design metabolic engineering strategies to tailor R. irregularis metabolism toward improving the performance of host plants.

The Endophytic Fungus Cyanodermella asteris Influences Growth of the Nonnatural Host Plant Arabidopsis thaliana

Cyanodermella asteris is a fungal endophyte from Aster tataricus, a perennial plant from the northern part of Asia. Here, we demonstrated an interaction of C. asteris with Arabidopsis thaliana, Chinese cabbage, rapeseed, tomato, maize, or sunflower resulting in different phenotypes such as shorter main roots, massive lateral root growth, higher leaf and root biomass, and increased anthocyanin levels. In a variety of cocultivation assays, it was shown that these altered phenotypes are caused by fungal CO₂, volatile organic compounds, and soluble compounds, notably astins. Astins A, C, and G induced plant growth when they were individually included in the medium. In return, A. thaliana stimulates the fungal astin C production during cocultivation. Taken together, our results indicate a bilateral interaction between the fungus and the plant. A stress response in plants is induced by fungal metabolites while plant stress hormones induced astin C production of the fungus. Interestingly, our results not only show unidirectional influence of the fungus on the plant but also vice versa. The plant is able to influence growth and secondary metabolite production in the endophyte, even when both organisms do not live in close contact, suggesting the involvement of volatile compounds.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Hormonomic Changes Driving the Negative Impact of Broomrape on Plant Host Interactions with Arbuscular Mycorrhizal Fungi

Belowground interactions of plants with other organisms in the rhizosphere rely on extensive small-molecule communication. Chemical signals released from host plant roots ensure the development of beneficial arbuscular mycorrhizal (AM) fungi which in turn modulate host plant growth and stress tolerance. However, parasitic plants have adopted the capacity to sense the same signaling molecules and to trigger their own seed germination in the immediate vicinity of host roots. The contribution of AM fungi and parasitic plants to the regulation of phytohormone levels in host plant roots and root exudates remains largely obscure. Here, we studied the hormonome in the model system comprising tobacco as a host plant, Phelipanche spp. as a holoparasitic plant, and the AM fungus Rhizophagus irregularis. Co-cultivation of tobacco with broomrape and AM fungi alone or in combination led to characteristic changes in the levels of endogenous and exuded abscisic acid, indole-3-acetic acid, cytokinins, salicylic acid, and orobanchol-type strigolactones. The hormonal content in exudates of broomrape-infested mycorrhizal roots resembled that in exudates of infested non-mycorrhizal roots and differed from that observed in exudates of non-infested mycorrhizal roots. Moreover, we observed a significant reduction in AM colonization of infested tobacco plants, pointing to a dominant role of the holoparasite within the tripartite system.

A roadmap of plant membrane transporters in arbuscular mycorrhizal and legume-rhizobium symbioses

Most land plants live in close contact with beneficial soil microbes: the majority of land plant species establish symbiosis with arbuscular mycorrhizal fungi, while most legumes, the third largest plant family, can form a symbiosis with nitrogen-fixing rhizobia. These microbes contribute to plant nutrition via endosymbiotic processes that require modulating the expression and function of plant transporter systems. The efficient contribution of these symbionts involves precisely controlled integration of transport, which is enabled by the adaptability and plasticity of their transporters. Advances in our understanding of these systems, driven by functional genomics research, are rapidly filling the gap in knowledge about plant membrane transport involved in these plant-microbe interactions. In this review, we synthesize recent findings associated with different stages of these symbioses, from the pre-symbiotic stage to nutrient exchange, and describe the role of host transport systems in both mycorrhizal and legume-rhizobia symbioses.

Effects of Laccaria bicolor on Gene Expression of Populus trichocarpa Root under Poplar Canker Stress

Poplars can be harmed by poplar canker. Inoculation with mycorrhizal fungi can improve the resistance of poplars to canker, but the molecular mechanism is still unclear. In this study, an aseptic inoculation system of L. bicolor-P. trichocarpa-B. dothidea was constructed, and transcriptome analysis was performed to investigate regulation by L. bicolor of the expression of genes in the roots of P. trichocarpa during the onset of B. dothidea infection, and a total of 3022 differentially expressed genes (DEGs) were identified. Weighted correlation network analysis (WGCNA) was performed on these DEGs, and 661 genes' expressions were considered to be affected by inoculation with L. bicolor and B. dothidea. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that these 661 DEGs were involved in multiple pathways such as signal transduction, reactive oxygen metabolism, and plant-pathogen interaction. Inoculation with L. bicolor changed the gene expression pattern of the roots, evidencing its involvement in the disease resistance response of P. trichocarpa. This research reveals the mechanism of L. bicolor in inducing resistance to canker of P. trichocarpa at the molecular level and provides a theoretical basis for the practical application of mycorrhizal fungi to improve plant disease resistance.

Dialog between Kingdoms: Enemies, Allies and Peptide Phytohormones

Various plant hormones can integrate developmental and environmental responses, acting in a complex network, which allows plants to adjust their developmental processes to changing environments. In particular, plant peptide hormones regulate various aspects of plant growth and development as well as the response to environmental stress and the interaction of plants with their pathogens and symbionts. Various plant-interacting organisms, e.g., bacterial and fungal pathogens, plant-parasitic nematodes, as well as symbiotic and plant-beneficial bacteria and fungi, are able to manipulate phytohormonal level and/or signaling in the host plant in order to overcome plant immunity and to create the habitat and food source inside the plant body. The most striking example of such phytohormonal mimicry is the ability of certain plant pathogens and symbionts to produce peptide phytohormones of different classes. To date, in the genomes of plant-interacting bacteria, fungi, and nematodes, the genes encoding effectors which mimic seven classes of peptide phytohormones have been found. For some of these effectors, the interaction with plant receptors for peptide hormones and the effect on plant development and defense have been demonstrated. In this review, we focus on the currently described classes of peptide phytohormones found among the representatives of other kingdoms, as well as mechanisms of their action and possible evolutional origin.

Plant Growth Promoting Rhizobacteria, Arbuscular Mycorrhizal Fungi and Their Synergistic Interactions to Counteract the Negative Effects of Saline Soil on Agriculture: Key Macromolecules and Mechanisms

Soil saltiness is a noteworthy issue as it results in loss of profitability and development of agrarian harvests and decline in soil health. Microorganisms associated with plants contribute to their growth promotion and salinity tolerance by employing a multitude of macromolecules and pathways. Plant growth promoting rhizobacteria (PGPR) have an immediate impact on improving profitability based on higher crop yield. Some PGPR produce 1-aminocyclopropane-1-carboxylic (ACC) deaminase (EC 4.1.99.4), which controls ethylene production by diverting ACC into α-ketobutyrate and ammonia. ACC deaminase enhances germination rate and growth parameters of root and shoot in different harvests with and without salt stress. Arbuscular mycorrhizal fungi (AMF) show a symbiotic relationship with plants, which helps in efficient uptake of mineral nutrients and water by the plants and also provide protection to the plants against pathogens and various abiotic stresses. The dual inoculation of PGPR and AMF enhances nutrient uptake and productivity of several crops compared to a single inoculation in both normal and stressed environments. Positively interacting PGPR + AMF combination is an efficient and cost-effective recipe for improving plant tolerance against salinity stress, which can be an extremely useful approach for sustainable agriculture.

Contribution of Arbuscular Mycorrhizal Fungi, Phosphate-Solubilizing Bacteria, and Silicon to P Uptake by Plant

Phosphorus (P) availability is usually low in soils around the globe. Most soils have a deficiency of available P; if they are not fertilized, they will not be able to satisfy the P requirement of plants. P fertilization is generally recommended to manage soil P deficiency; however, the low efficacy of P fertilizers in acidic and in calcareous soils restricts P availability. Moreover, the overuse of P fertilizers is a cause of significant environmental concerns. However, the use of arbuscular mycorrhizal fungi (AMF), phosphate-solubilizing bacteria (PSB), and the addition of silicon (Si) are effective and economical ways to improve the availability and efficacy of P. In this review the contributions of Si, PSB, and AMF in improving the P availability is discussed. Based on what is known about them, the combined strategy of using Si along with AMF and PSB may be highly useful in improving the P availability and as a result, its uptake by plants compared to using either of them alone. A better understanding how the two microorganism groups and Si interact is crucial to preserving soil fertility and improving the economic and environmental sustainability of crop production in P deficient soils. This review summarizes and discusses the current knowledge concerning the interactions among AMF, PSB, and Si in enhancing P availability and its uptake by plants in sustainable agriculture.

Irving T, Chakraborty S, Ané JM. Perception of lipo-chitooligosaccharides by the bioenergy crop Populus

Populus sp. is a developing feedstock for second-generation biofuel production. To ensure its success as a sustainable biofuel source, it is essential to capitalize on the ability of Populus sp. to associate with beneficial plant-associated microbes (e.g., mycorrhizal fungi) and engineer Populus sp. to associate with non-native symbionts (e.g., rhizobia). Here, we review recent research into the molecular mechanisms that control ectomycorrhizal associations in Populus sp. with particular emphasis on the discovery that ectomycorrhizal fungi produce lipochitooligosaccharides capable of activating the common symbiosis pathway. We also present new evidence that lipo-chitooligosaccharides produced by both ectomycorrhizal fungi and various species of rhizobia that do not associate with Populus sp. can induce nuclear calcium spiking in the roots of Populus sp. Thus, we argue Populus sp. already possesses the molecular machinery necessary for perceiving rhizobia, and the next step in engineering symbiosis with rhizobia should be focused on inducing bacterial accommodation and nodule organogenesis. The gene Nodule INception is central to these processes, and several putative orthologs are present in Populus sp. Manipulating the promoters of these genes to match that of plants in the nitrogen-fixing clade may be sufficient to introduce nodulation in Populus sp.

Indole-3-Acetic Acid Is Synthesized by the Endophyte Cyanodermella asteris via a Tryptophan-Dependent and -Independent Way and Mediates the Interaction with a Non-Host Plant

The plant hormone indole-3-acetic acid (IAA) is one of the main signals playing a role in the communication between host and endophytes. Endophytes can synthesize IAA de novo to influence the IAA homeostasis in plants. Although much is known about IAA biosynthesis in microorganisms, there is still less known about the pathway by which IAA is synthesized in fungal endophytes. The aim of this study is to examine a possible IAA biosynthesis pathway in Cyanodermella asteris. In vitro cultures of C. asteris were incubated with the IAA precursors tryptophan (Trp) and indole, as well as possible intermediates, and they were additionally treated with IAA biosynthesis inhibitors (2-mercaptobenzimidazole and yucasin DF) to elucidate possible IAA biosynthesis pathways. It was shown that (a) C. asteris synthesized IAA without adding precursors; (b) indole-3-acetonitrile (IAN), indole-3-acetamide (IAM), and indole-3-acetaldehyde (IAD) increased IAA biosynthesis; and (c) C. asteris synthesized IAA also by a Trp-independent pathway. Together with the genome information of C. asteris, the possible IAA biosynthesis pathways found can improve the understanding of IAA biosynthesis in fungal endophytes. The uptake of fungal IAA into Arabidopsis thaliana is necessary for the induction of lateral roots and other fungus-related growth phenotypes, since the application of the influx inhibitor 2-naphthoxyacetic acid (NOA) but not the efflux inhibitor N-1-naphtylphthalamic acid (NPA) were altering these parameters. In addition, the root phenotype of the mutation in an influx carrier, aux1, was partially rescued by C. asteris.

Cytokinin and Ethylene Cell Signaling Pathways from Prokaryotes to Eukaryotes

Cytokinins (CKs) and ethylene (ET) are among the most ancient organic chemicals on Earth. A wide range of organisms including plants, algae, fungi, amoebae, and bacteria use these substances as signaling molecules to regulate cellular processes. Because of their ancestral origin and ubiquitous occurrence, CKs and ET are also considered to be ideal molecules for inter-kingdom communication. Their signal transduction pathways were first historically deciphered in plants and are related to the two-component systems, using histidine kinases as primary sensors. Paradoxically, although CKs and ET serve as signaling molecules in different kingdoms, it has been supposed for a long time that the canonical CK and ET signaling pathways are restricted to terrestrial plants. These considerations have now been called into question following the identification over recent years of genes encoding CK and ET receptor homologs in many other lineages within the tree of life. These advances shed new light on the dissemination and evolution of these hormones as both intra- and inter-specific communication molecules in prokaryotic and eukaryotic organisms.