Plant Signaling and Metabolic Pathways Enabling Arbuscular Mycorrhizal Symbiosis

Trichoderma afroharzianum T22 Induces Rhizobia and Flavonoid-Driven Symbiosis to Promote Tolerance to Alkaline Stress in Garden Pea

Soil alkalinity is a limiting factor for crops, yet the role of beneficial fungi in mitigating this abiotic stress in garden pea is understudied. In this study, Trichoderma afroharzianum T22 colonised the roots of garden pea cultivars exposed to soil alkalinity in a host-specific manner. In alkaline-exposed Sugar Snap, T22 improved growth parameters, consistent with increased tissue mineral content, particularly Fe and Mn, as well as enhanced rhizosphere siderophore levels. The split-root assay demonstrated that the beneficial effects of T22 on alkaline stress mitigation are the result of a whole-plant association rather than localised root-specific effects. RNA-seq analysis showed 575 and 818 differentially expressed genes upregulated and downregulated in the roots inoculated with T22 under alkaline conditions. The upregulated genes were mostly involved in the flavonoid biosynthetic pathway (monooxygenase activity, ammonia-lyase activity, 4-coumarate-CoA ligase), along with genes related to mineral transport and redox homoeostasis. Further, a flavonoid precursor restored plant health even in the absence of T22, confirming the role of microbial symbiosis in mitigating alkaline stress. Interestingly, T22 restored the abundance of rhizobia, particularly Rhizobium leguminosarum and Rhizobium indicum, along with the induction of NifA, NifD, and NifH in nodules, suggesting a connection between T22 and rhizobia under soil alkalinity. Further, the elevated rhizosphere siderophore, root flavonoid, expression of PsCoA (4-coumarate-CoA ligase) as well as the relative abundance of TaAOX1 and R. leguminosarum diminished when T22 was substituted with exogenous Fe. This suggests that exogenous Fe eliminates the need for microbiome-driven mineral mobilisation, while T22-mediated alkaline stress mitigation depends on flavonoid-driven symbiosis and R. leguminosarum abundance. It was further supported by the positive interaction of T22 on R. leguminosarum growth in alkaline media. Thus, the beneficial effect of T22 on rhizobia likely stems from their interactions, not solely from the improved mineral status, particularly Fe, in plants. This study provides the first mechanistic insights into T22 interactions with host and rhizobia, advancing microbiome strategies to alleviate soil alkalinity in peas and other legumes.

Omics approaches to investigate pre-symbiotic responses of the mycorrhizal fungus Tulasnella sp. SV6 to the orchid host Serapias vomeracea

Like other plant-microbe symbioses, the establishment of orchid mycorrhiza (ORM) is likely to require specific communication and metabolic adjustments between the two partners. However, while modulation of plant and fungal metabolism has been investigated in fully established mycorrhizal tissues, the molecular changes occurring during the pre-symbiotic stages of the interaction remain largely unexplored in ORM. In this study, we investigated the pre-symbiotic responses of the ORM fungus Tulasnella sp. SV6 to plantlets of the orchid host Serapias vomeracea in a dual in vitro cultivation system. The fungal mycelium was harvested prior to physical contact with the orchid roots and the fungal transcriptome and metabolome were analyzed using RNA-seq and untargeted metabolomics approaches. The results revealed distinct transcriptomic and metabolomic remodelling of the ORM fungus in the presence of orchid plantlets, as compared to the free-living condition. The ORM fungus responds to the presence of the host plant with a significant up-regulation of genes associated with protein synthesis, amino acid and lipid biosynthesis, indicating increased metabolic activity. Metabolomic analysis supported the RNA-seq data, showing increased levels of amino acids and phospholipids, suggesting a remodelling of cell structure and signalling during the pre-symbiotic interaction. In addition, we identified an increase of transcripts of a small secreted protein that may play a role in early symbiotic signalling. Taken together, our results suggest that Tulasnella sp. SV6 may perceive information from orchid roots, leading to a readjustment of its transcriptomic and metabolomic profiles.

TaLAC129 is a negative regulator of arbuscular mycorrhizal symbiosis but enhanced the growth and yield of bread wheat

Arbuscular mycorrhizal (AM) symbiosis enhances nutrient acquisition and stress resilience in plants, yet the genetic mechanisms regulating this interaction in wheat remain poorly understood. This study explores the variation in AM colonization rates across a diverse set of wheat varieties and aims to identify key genes that regulate the wheat-AM symbiosis. Understanding these molecular mechanisms is crucial for improving nutrient uptake efficiency and stress resistance in wheat breeding programs. Here, we conducted a genome-wide association study (GWAS) of 291 wheat varieties and integrated transcriptomic data to identify TaLAC129, a laccase (LAC)-encoding gene, as a critical negative regulator of AM colonization in wheat roots. Overexpression of TaLAC129 significantly increased root LAC activity and lignin content, concurrently suppressing AM colonization. While this suppression reduced nitrogen (N), phosphorus (P), and potassium (K) uptake in stems, leaves, and glumes, it markedly enhanced nutrient utilization efficiency (NUE) in grains. Furthermore, TaLAC129 overexpression improved agronomic traits, including grains per panicle, 1000-grain weight, and overall yield. Our findings reveal the dual role of TaLAC129 in balancing AM symbiosis and nutrient allocation, offering a novel genetic target for breeding wheat varieties with improved yield and nutrient efficiency. This study provides critical insights into the molecular coordination between symbiotic trade-offs and agricultural productivity in cereal crops.

Does the flavonoid quercetin influence the generalist-selective nature of mycorrhizal interactions in invasive and non-invasive native woody plants?

It has been suggested that invasive plant species are more generalist than non-invasive species in their interactions with arbuscular mycorrhizal fungi (AMF), allowing them to associate with novel AMF communities. There is emerging evidence suggesting that the flavonoid quercetin may play a role in regulating these interactions as a signaling compound. In this study, we experimentally grew three invasive alien and three non-invasive native woody species with AMF communities collected from within (though foreign to invasives) and outside their current distribution ranges. After 96 days, we: (a) assessed mycorrhizal colonization rates; (b) evaluated the impact of these interactions on plant performance (growth and phosphorus nutrition); and (c) tested whether these responses were influenced by the addition of quercetin to the plant growth medium. Our findings reveal that the invasive species exhibited mycorrhizal colonization when grown with both novel AMF communities and benefited from them in terms of phosphorus (P) nutrition. In contrast, two of the three non- invasive native species showed mycorrhizal colonization and enhanced P nutrition only with AMF from their current distribution range, but not with novel AMF from outside their range, suggesting selective behavior in their mycorrhizal interactions. The addition of quercetin did not have a strong effect on mycorrhizal colonization in either invasive or non-invasive native species. However, quercetin promoted moderate increases in P nutrition in the two non-invasive native species when grown with the novel AMF communities. Overall, the results suggest that invasive species are more generalist in their AM symbiosis than two of the three non-invasive species, and that the addition of quercetin had a limited, moderate influence on their AM interactions.

Symbiotic synergy: How Arbuscular Mycorrhizal Fungi enhance nutrient uptake, stress tolerance, and soil health through molecular mechanisms and hormonal regulation

Arbuscular Mycorrhizal (AM) symbiosis is integral to sustainable agriculture and enhances plant resilience to abiotic and biotic stressors. Through their symbiotic association with plant roots, AM improves nutrient and water uptake, activates antioxidant defenses, and facilitates hormonal regulation, contributing to improved plant health and productivity. Plants release strigolactones, which trigger AM spore germination and hyphal branching, a process regulated by genes, such as D27, CCD7, CCD8, and MAX1. AM recognition by plants is mediated by receptor-like kinases (RLKs) and LysM domains, leading to the formation of arbuscules that optimize nutrient exchange. Hormonal regulation plays a pivotal role in this symbiosis; cytokinins enhance AM colonization, auxins support arbuscule formation, and brassinosteroids regulate root growth. Other hormones, such as salicylic acid, gibberellins, ethylene, jasmonic acid, and abscisic acid, also influence AM colonization and stress responses, further bolstering plant resilience. In addition to plant health, AM enhances soil health by improving microbial diversity, soil structure, nutrient cycling, and carbon sequestration. This symbiosis supports soil pH regulation and pathogen suppression, offering a sustainable alternative to chemical fertilizers and improving soil fertility. To maximize AM 's potential of AM in agriculture, future research should focus on refining inoculation strategies, enhancing compatibility with different crops, and assessing the long-term ecological and economic benefits. Optimizing AM applications is critical for improving agricultural resilience, food security, and sustainable farming practices.

Powdery mildew induces chloroplast storage lipid formation at the expense of host thylakoids to promote spore production

Powdery mildews are obligate biotrophic fungi that manipulate plant metabolism to supply lipids to the fungus, particularly during fungal asexual reproduction when lipid demand is high. We found levels of leaf storage lipids (triacylglycerols, TAGs) are 3.5-fold higher in whole Arabidopsis (Arabidopsis thaliana) leaves with a 15-fold increase in storage lipids at the infection site during fungal asexual reproduction. Lipid bodies, not observable in uninfected mature leaves, were found in and external to chloroplasts in mesophyll cells underlying the fungal feeding structure. Concomitantly, thylakoid disassembly occurred and thylakoid membrane lipid levels decreased. Genetic analyses showed that canonical endoplasmic reticulum TAG biosynthesis does not support powdery mildew spore production. Instead, Arabidopsis chloroplast-localized DIACYLGLYCEROL ACYLTRANSFERASE 3 (DGAT3) promoted fungal asexual reproduction. Consistent with the reported AtDGAT3 preference for 18:3 and 18:2 acyl substrates, which are dominant in thylakoid membrane lipids, dgat3 mutants exhibited a dramatic reduction in powdery mildew-induced chloroplast TAGs, attributable to decreases in TAG species largely comprised of 18:3 and 18:2 acyl substrates. This pathway for TAG biosynthesis in the chloroplast at the expense of thylakoids provides insights into obligate biotrophy and plant lipid metabolism, plasticity, and function. By understanding how photosynthetically active leaves can be converted into TAG producers, more sustainable and environmentally friendly plant oil production may be developed.

Ethylene promotes SMAX1 accumulation to inhibit arbuscular mycorrhiza symbiosis

Most land plants engage in arbuscular mycorrhiza (AM) symbiosis with Glomeromycotina fungi for better access to mineral nutrients. The plant hormone ethylene suppresses AM development, but a molecular explanation for this phenomenon is lacking. Here we show that ethylene inhibits the expression of many genes required for AM formation in Lotus japonicus. These genes include strigolactone biosynthesis genes, which are needed for fungal activation, and Common Symbiosis genes, which are required for fungal entry into the root. Application of strigolactone analogs and ectopic expression of the Common Symbiosis gene Calcium Calmodulin-dependent Kinase (CCaMK) counteracts the effect of ethylene. Therefore, ethylene likely inhibits AM development by suppressing expression of these genes rather than by inducing defense responses. These same genes are regulated by SUPPRESSOR OF MAX2 1 (SMAX1), a transcriptional repressor that is proteolyzed during karrikin signaling. SMAX1 is required for suppression of AM by ethylene, and SMAX1 abundance in nuclei increases after ethylene application. We conclude that ethylene suppresses AM by promoting accumulation of SMAX1. SMAX1 emerges as a signaling hub that integrates karrikin and ethylene signaling, thereby orchestrating development of a major plant symbiosis with a plant's physiological state.

Enhancing consistency in arbuscular mycorrhizal trait-based research to improve predictions of function

Arbuscular mycorrhizal (AM) fungi (phylum Glomeromycota) are obligate symbionts with plants influencing plant health, soil a(biotic) processes, and ecosystem functioning. Despite advancements in molecular techniques, understanding the role of AM fungal communities on a(biotic) processes based on AM fungal taxonomy remains challenging. This review advocates for a standardized trait-based framework to elucidate the life-history traits of AM fungi, focusing on their roles in three dimensions: host plants, soil, and AM fungal ecology. We define morphological, physiological, and genetic key traits, explore their functional roles and propose methodologies for their consistent measurement, enabling cross-study comparisons towards improved predictability of ecological function. We aim for this review to lay the groundwork for establishing a baseline of AM fungal trait responses under varying environmental conditions. Furthermore, we emphasize the need to include underrepresented taxa in research and utilize advances in machine learning and microphotography for data standardization.

Enhancing Sorghum Growth: Influence of Arbuscular Mycorrhizal Fungi and Sorgoleone

The low availability of phosphorus (P) in soil is one of the main constraints on crop production. Plants have developed several strategies to increase P use efficiency, including modifications in root morphology, the exudation of different compounds, and associations with microorganisms such as arbuscular mycorrhizal fungi (AMF). This study aimed to investigate the effect of sorgoleone compound on AMF colonization and its subsequent impact on P uptake, rhizosphere microbiota, and sorghum growth. The experiment was conducted in a greenhouse using the sorghum genotype P9401, known for low sorgoleone production. Three doses of purified sorgoleone (20 μM, 40 μM, and 80 μM) were added to low-P soil and plants were harvested after 45 days. Treatments included inoculation with the arbuscular mycorrhizal fungi Rhizophagus clarus and a negative control without inoculum. The addition of 40 and 80 μM of sorgoleone did not significantly increase mycorrhization. However, treatment with 20 μM sorgoleone combined with R. clarus inoculation significantly increased total sorghum biomass by 1.6-fold (p ≤ 0.05) compared to the non-inoculated treatment. AMF inoculation influenced only AMF colonization and the fungal microbiota, without affecting the bacterial community, whereas sorgoleone showed no effect on either. The activities of acid and alkaline phosphatases in the rhizospheric soil did not differ significantly among the treatments. Furthermore, the sorghum genes CYP71AM1, associated with sorgoleone biosynthesis, and Sb02g009880, Sb06g002560, Sb06g002540, and Sb03g029970 (related to phosphate transport induced by mycorrhiza) were significantly upregulated (p ≤ 0.05) in fine roots under these conditions. The 20 μM concentration of sorgoleone can enhance AMF colonization in sorghum and promote plant growth under low-P conditions, without significantly altering the microbiota.

The SlDLK2 receptor, involved in the control of arbuscular mycorrhizal symbiosis, regulates hormonal balance in roots

Arbuscular mycorrhiza (AM) represents a symbiotic mutualistic association between most land plants and Glomeromycota fungi. AM fungi develops specialized intraradical and highly branched structures, called arbuscules, where bidirectional exchange of nutrients between plant and fungi partners occurs, improving plant growth and fitness. Transcriptional reprogramming and hormonal regulation are necessary for the formation of the arbuscules. SlDLK2, a member of the third clade from the DWARF14 family of α, β-hydrolases closely related to the strigolactone receptor D14, is a negative regulator of arbuscule branching in tomato, but the underlying mechanisms are unknown. We explored the possible role of SlDLK2 on the regulation of hormonal balance. RNA-seq analysis was performed on roots from composite tomato plants overexpressing SlDLK2 and in control plants transformed with the empty vector. Analysis of transcriptomic data predicted that significantly repressed genes were enriched for genes related to hormone biosynthesis pathways, with a special relevance of carotenoid/apocarotenoid biosynthesis genes. Stable transgenic SlDLK2 overexpressing (OE) tomato lines were obtained, and hormone contents were analyzed in their roots and leaves. Interesting significant hormonal changes were found in roots of SlDLK2 OE lines with respect to the control lines, with a strong decrease on jasmonic acid and ABA. In addition, SlDLK2 OE roots showed a slight reduction in auxin contents and in one of the major strigolactones in tomato, solanacol. Overall, our results suggest that the negative regulation of AM symbiosis by SlDLK2 is associated with the repression of genes involved in the biosynthesis of AM-promoting hormones.

Rice rhizobiome engineering for climate change mitigation

The year 2023 was the warmest year since 1850. Greenhouse gases, including CO2 and methane, played a significant role in increasing global warming. Among these gases, methane has a 25-fold greater impact on global warming than CO2. Methane is emitted during rice cultivation by a group of rice rhizosphere microbes, termed methanogens, in low oxygen (hypoxic) conditions. To reduce methane emissions, it is crucial to decrease the methane production capacity of methanogens through water and fertilizer management, breeding of new rice cultivars, regulating root exudation, and manipulating rhizosphere microbiota. In this opinion article we review the recent developments in hypoxia ecology and methane emission mitigation and propose potential solutions based on the manipulation of microbiota and methanogens for the mitigation of methane emissions.

Unraveling plant-microbe symbioses using single-cell and spatial transcriptomics

Plant-microbe symbioses require intense interaction and genetic coordination to successfully establish in specific cell types of the host and symbiont. Traditional RNA-seq methodologies lack the cellular resolution to fully capture these complexities, but single-cell and spatial transcriptomics (ST) are now allowing scientists to probe symbiotic interactions at an unprecedented level of detail. Here, we discuss the advantages that novel spatial and single-cell transcriptomic technologies provide in studying plant-microbe endosymbioses and highlight key recent studies. Finally, we consider the remaining limitations of applying these approaches to symbiosis research, which are mainly related to the simultaneous capture of both plant and microbial transcripts within the same cells.

Different roles of the phytohormone gibberellin in the wide-spread arbuscular mycorrhiza and in orchid mycorrhiza

Gibberellin (GA) is a classical plant hormone that regulates many physiological processes, such as plant growth, development, and environmental responses. GA inhibits arbuscular mycorrhizal (AM) symbiosis, the most ancient and widespread type of mycorrhizal symbiosis. Knowledge about mycorrhizal symbioses at the molecular level has been obtained mainly in model plants such as legumes and rice. In contrast, molecular mechanisms in non-model plants are still unclear. Recent studies have revealed the novel roles of GA in mycorrhizal symbioses: its positive effect in Paris-type AM symbiosis in Eustoma grandiflorum and its negative effect on both seed germination and mycorrhizal symbiosis in orchids. This review focuses on the recent data on GA function in AM and orchid mycorrhizal symbioses.

Arbuscular mycorrhizal fungi and exogenous Ca2+ application synergistically enhance salt and alkali resistance in perennial ryegrass through diverse adaptive strategies

The challenge of soil salinization and alkalization, with its significant impact on crop productivity, has raised growing concerns with global population growth and enhanced environmental degradation. Although arbuscular mycorrhizal fungi (AMF) and calcium ions (Ca2+) are known to enhance plant resistance to stress, their combined effects on perennial ryegrass' tolerance to salt and alkali stress and the underlying mechanisms remain poorly understood. This study aimed to elucidate the roles of Arbuscular mycorrhizal (AM) fungus Rhizophagus irregularis and exogenous Ca2+ application in molecular and physiological responses to salt-alkali stress. AM symbiosis and exogenous Ca2+ application enhanced antioxidant enzyme activity and non-enzymatic components, promoting reactive oxygen species (ROS) scavenging and reducing lipid peroxidation while alleviating oxidative damage induced by salt-alkali stress. Furthermore, they enhanced osmotic balance by increasing soluble sugar content (Proportion of contribution of the osmotic adjustment were 34∼38 % in shoots and 30∼37 % in roots) under salt stress and organic acid content (Proportion of contribution of the osmotic adjustment were 32∼36 % in shoots and 37∼42 % in roots) under alkali stress. Changes in organic solute and inorganic cation-anion contents contributed to ion balance, while hormonal regulation played a role in these protective mechanisms. Moreover, the protective mechanisms involved activation of Ca2+-mediated signaling pathways, regulation of salt-alkali stress-related genes (including LpNHX1 and LpSOS1), increased ATPase activity, elevated ATP levels, enhanced Na+ extrusion, improved K+ absorption capacity, and a reduced Na+/K+ ratio, all contributing to the protection of photosynthetic pigments and the enhancement of photosynthetic efficiency. Ultimately, the combined application of exogenous Ca2+ and AMF synergistically alleviated the inhibitory effects of salt-alkali stress on perennial ryegrass growth. This finding suggested that exogenous Ca2+ may participate in the colonization of perennial ryegrass plants by R. irregularis, while AM symbiosis may activate Ca2+ pathways. Consequently, the combined treatment of AM and Ca2+ is beneficial for enhancing plant regulatory mechanisms and increasing crop yield under salt-alkali stress.

Evolution of small molecule-mediated regulation of arbuscular mycorrhiza symbiosis

The arbuscular mycorrhizal (AM) symbiosis formed by most extant land plants with symbiotic fungi evolved 450 Ma. AM promotes plant growth by improving mineral nutrient and water uptake, while the symbiotic fungi obtain carbon in return. A number of plant genes regulating the steps leading to an efficient symbiosis have been identified; however, our understanding of the metabolic processes involved in the symbiosis and how they were wired to symbiosis regulation during plant evolution remains limited. Among them, the exchange of chemical signals, the activation of dedicated biosynthesis pathways and the production of secondary metabolites regulating late stages of the AM symbiosis begin to be well described across several land plant clades. Here, we review our current understanding of these processes and propose future directions to fully grasp the phylogenetic distribution and role played by small molecules during this ancient plant symbiosis. This article is part of the theme issue 'The evolution of plant metabolism'.

Mycorrhizal and non-mycorrhizal perennial ryegrass roots exhibit differential regulation of lipid and Ca2+ signaling pathways in response to low and high temperature stresses

Lipids and Ca2+ are involved as intermediate messengers in temperature-sensing signaling pathways. Arbuscular mycorrhizal (AM) symbiosis is a mutualistic symbiosis between fungi and terrestrial plants that helps host plants cope with adverse environmental conditions. Nonetheless, the regulatory mechanisms of lipid- and Ca2+-mediated signaling pathways in mycorrhizal plants under cold and heat stress have not been determined. The present work focused on investigating the lipid- and Ca2+-mediated signaling pathways in arbuscular mycorrhizal (AM) and non-mycorrhizal (NM) roots under temperature stress and determining the role of Ca2+ levels in AM symbiosis and temperature stress tolerance in perennial ryegrass (Lolium perenne L.) Compared with NM plants, AM symbiosis increased phosphatidic acid (PA) and Ca2+ signaling in the roots of perennial ryegrass, increasing the expression of genes associated with low temperature (LT) stress, including LpICE1, LpCBF3, LpCOR27, LpCOR47, LpIRI, and LpAFP, and high temperature (HT) stress, including LpHSFC1b, LpHSFC2b, LpsHSP17.8, LpHSP22, LpHSP70, and LpHSP90, under LT and HT conditions. These effects result in modulated antioxidant enzyme activities, reduced lipid peroxidation, and suppressed growth inhibition caused by LT and HT stresses. Furthermore, exogenous Ca2+ application enhanced AM symbiosis, leading to the upregulation of Ca2+ signaling pathway genes in roots and ultimately promoting the growth of perennial ryegrass under LT and HT stresses. These findings shed light on lipid and Ca2+ signal transduction in AM-associated plants under LT and HT stresses, emphasizing that Ca2+ enhances cold and heat tolerance in mycorrhizal plants.

Unravelling the genetic basis and regulation networks related to fibre quality improvement using chromosome segment substitution lines in cotton

The elucidation of genetic architecture and molecular regulatory networks underlying complex traits remains a significant challenge in life science, largely due to the substantial background effects that arise from epistasis and gene-environment interactions. The chromosome segment substitution line (CSSL) is an ideal material for genetic and molecular dissection of complex traits due to its near-isogenic properties; yet a comprehensive analysis, from the basic identification of substitution segments to advanced regulatory network, is still insufficient. Here, we developed two cotton CSSL populations on the Gossypium hirsutum background, representing wide adaptation and high lint yield, with introgression from G. barbadense, representing superior fibre quality. We sequenced 99 CSSLs that demonstrated significant differences from G. hirsutum in fibre, and characterized 836 dynamic fibre transcriptomes in three crucial developmental stages. We developed a workflow for precise resolution of chromosomal substitution segments; the genome sequencing revealed substitutions collectively representing 87.25% of the G. barbadense genome. Together, the genomic and transcriptomic survey identified 18 novel fibre-quality-related quantitative trait loci with high genetic contributions and the comprehensive landscape of fibre development regulation. Furthermore, analysis determined unique cis-expression patterns in CSSLs to be the driving force for fibre quality alteration; building upon this, the co-expression regulatory network revealed biological relationships among the noted pathways and accurately described the molecular interactions of GhHOX3, GhRDL1 and GhEXPA1 during fibre elongation, along with reliable predictions for their interactions with GhTBA8A5. Our study will enhance more strategic employment of CSSL in crop molecular biology and breeding programmes.

Peanut-Colonized Piriformospora indica Enhanced Drought Tolerance by Modulating the Enzymes and Expression of Drought-Related Genes

Peanut (Arachis hypogaea L.) is an important cash and oil seed crop, mostly distributed in arid and semi-arid areas. In recent years, due to the influence of atmospheric circulation anomalies and other factors, drought has become frequent and increasingly serious in China. This has posed serious challenges to peanut production. The objective of this study was to investigate the potential of the endophytic fungus Piriformospora indica to form a symbiotic relationship with peanut plants and to evaluate the drought tolerance of P. indica-colonized peanut plants subjected to a simulated drought stress treatment using 20% polyethylene glycol 6000 (PEG6000). The endophytic fungus P. indica affected the physiological characteristics of the host plant by colonizing the plant roots, thereby conferring greater resistance to drought stress. This fungus strongly colonized the roots of peanuts and was found to enhance root activity after 24 h of P. indica colonization under PEG6000. Catalase (CAT) and peroxidase (POD) activities were increased at 24 h in peanut leaves colonized with P. indica. Expression of drought-related genes, such as AhNCED1, AhP5CS, and DREB2A was upregulated at 24 h of P. indica colonization. In addition, after PEG6000 treatment, proline, soluble protein, and abscisic acid (ABA) concentrations in plants were increased, while the accumulation of malondialdehyde (MDA), and hydrogen peroxide (H2O2) was decreased in P. indica colonized peanut. In conclusion, P. indica mediated peanut plant protection against the detrimental effects of drought resulted from enhanced antioxidant enzyme activities, and the upregulated expression of drought-related genes for lower membrane damage.

Gene expression signatures of mutualism and pathogenesis in flax roots

Introduction

Fusarium wilt, a devastating soil-borne fungal disease in flax (Linum usitatissimum), is caused by Fusarium oxysporum f. sp. lini, a hemibiotrophic plant pathogen that penetrates plant roots. There are several reports of the molecular response of L. usitatissimum to F. oxysporum f. sp. lini; however, comparisons of the effects of mutualistic and pathogenic fungi on plants are more limited.

Methods

In this study, we have integrated phenotyping and RNA-Seq approaches to examine the response of flax to F. oxysporum f.sp. lini and to a mutualistic arbuscular mycorrhizal fungus (AMF) Rhizoglomus irregulare. R. irregulare is a common soil fungus and also widely used as a commercial inoculant to improve plant growth. We measured flax growth parameters after plant inoculation with each or both fungi, in comparison with non-inoculated control. We performed transcriptome analysis of root tissues collected at 9 and 14 days post-inoculation.

Results

We identified several differentially expressed genes (DEGs) in response to pathogenic and mutualistic fungi. These included genes related to ethylene and salicylic acid biosynthesis, carbohydrate binding, oxidoreductases, and sugar transmembrane transporters. Genes related to calcium signaling, nutrient transport, lipid metabolism, cell wall, and polysaccharide-modifying were up-regulated by R. irregulare; however, the same genes were down-regulated by F. oxysporum f. sp. lini when treated independently. In the combined treatment, genes related to cell wall modifications, hormone regulation and nutrient uptake were up-regulated. These results suggest that inoculation with R. irregulare reduced gene expression related to F. oxysporum f. sp. lini infection, leading to a reduced response to the pathogen. In response to AMF, flax prioritized mutualism-related gene expression over defense, reversing the growth inhibition caused by F. oxysporum f. sp.lini in the combined treatment.

Discussion

This research provides insights into the protective effects of AMF, revealing the pre-symbiotic gene expression profile of flax in response to mutualism in comparison with pathogenicity. Potential target genes for crop improvement were identified, especially defense related genes.

New insights into decoding the lifestyle of endophytic Fusarium lateritium Fl617 via comparing genomes

Fungal-plant interactions have persisted for 460 million years, and almost all terrestrial plants on Earth have endophytic fungi. However, the mechanism of symbiosis between endophytic fungi and host plants has been inconclusive. In this dissertation, we used a strain of endophytic Fusarium lateritium (Fl617), which was found in the previous stage to promote disease resistance in tomato, and selected the pathogenic Fusarium oxysporum Fo4287 and endophytic Fusarium oxysporum Fo47, which are in the same host and the closest relatives of Fl617, to carry out a comparative genomics analysis of the three systems and to provide a new perspective for the elucidation of the special lifestyle of the fungal endophytes. We found that endophytic F. lateritium has a smaller genome, fewer clusters and genes associated with pathogenicity, and fewer plant cell wall degrading enzymes (PCWDEs). There were also relatively fewer secondary metabolisms and typical Fusarium spp. toxins, and a lack of the key Fusarium spp. pathogenicity factor, secreted in xylem (SIX), but the endophytic fungi may be more sophisticated in their regulation of the colonization process. It is hypothesized that the endophytic fungi may have maintained their symbiosis with plants due to the relatively homogeneous microenvironment in plants for a long period of time, considering only plant interactions and discarding the relevant pathogenicity factors, and that their endophytic evolutionary tendency may tend to be genome streamlining and to enhance the fineness of the regulation of plant interactions, thus maintaining their symbiotic status with plants.

Domestication of rice may have changed its arbuscular mycorrhizal properties by modifying phosphorus nutrition-related traits and decreasing symbiotic compatibility

Modern cultivated rice (Oryza sativa) typically experiences limited growth benefits from arbuscular mycorrhizal (AM) symbiosis. This could be due to the long-term domestication of rice under favorable phosphorus conditions. However, there is limited understanding of whether and how the rice domestication has modified AM properties. This study compared AM properties between a collection of wild (Oryza rufipogon) and domesticated rice genotypes and investigated the mechanisms underlying their differences by analyzing physiological, genomic, transcriptomic, and metabolomic traits critical for AM symbiosis. The results revealed significantly lower mycorrhizal growth responses and colonization intensity in domesticated rice compared to wild rice, and this change of AM properties may be associated with the domestication modifications of plant phosphorus utilization efficiency at physiological and genomic levels. Domestication also resulted in a decrease in the activity of the mycorrhizal phosphorus acquisition pathway, which may be attributed to reduced mycorrhizal compatibility of rice roots by enhancing defense responses like root lignification and reducing carbon supply to AM fungi. In conclusion, rice domestication may have changed its AM properties by modifying P nutrition-related traits and reducing symbiotic compatibility. This study offers new insights for improving AM properties in future rice breeding programs to enhance sustainable agricultural production.

The receptor-like kinase ARK controls symbiotic balance across land plants

The mutualistic arbuscular mycorrhizal (AM) symbiosis arose in land plants more than 450 million years ago and is still widely found in all major land plant lineages. Despite its broad taxonomic distribution, little is known about the molecular components underpinning symbiosis outside of flowering plants. The ARBUSCULAR RECEPTOR-LIKE KINASE (ARK) is required for sustaining AM symbiosis in distantly related angiosperms. Here, we demonstrate that ARK has an equivalent role in symbiosis maintenance in the bryophyte Marchantia paleacea and is part of a broad AM genetic program conserved among land plants. In addition, our comparative transcriptome analysis identified evolutionarily conserved expression patterns for several genes in the core symbiotic program required for presymbiotic signaling, intracellular colonization, and nutrient exchange. This study provides insights into the molecular pathways that consistently associate with AM symbiosis across land plants and identifies an ancestral role for ARK in governing symbiotic balance.

Mucoromycotina 'fine root endophytes': a new molecular model for plant-fungal mutualisms?

The most studied plant-fungal symbioses to date are the interactions between plants and arbuscular mycorrhizal (AM) fungi of the Glomeromycotina clade. Advancements in phylogenetics and microbial community profiling have distinguished a group of symbiosis-forming fungi that resemble AM fungi as belonging instead to the Mucoromycotina. These enigmatic fungi are now known as Mucoromycotina 'fine root endophytes' and could provide a means to understand the origins of plant-fungal symbioses. Most of our knowledge of the mechanisms of fungal symbiosis comes from investigations using AM fungi. Here, we argue that inclusion of Mucoromycotina fine root endophytes in future studies will expand our understanding of the mechanisms, evolution, and ecology of plant-fungal symbioses.

Walking on a tightrope: cell wall-associated kinases act as sensors and regulators of immunity and symbiosis

This article is a Commentary on Zhang et al. (2024), 242: 2180–2194.

Computer vision models enable mixed linear modeling to predict arbuscular mycorrhizal fungal colonization using fungal morphology

The presence of Arbuscular Mycorrhizal Fungi (AMF) in vascular land plant roots is one of the most ancient of symbioses supporting nitrogen and phosphorus exchange for photosynthetically derived carbon. Here we provide a multi-scale modeling approach to predict AMF colonization of a worldwide crop from a Recombinant Inbred Line (RIL) population derived from Sorghum bicolor and S. propinquum. The high-throughput phenotyping methods of fungal structures here rely on a Mask Region-based Convolutional Neural Network (Mask R-CNN) in computer vision for pixel-wise fungal structure segmentations and mixed linear models to explore the relations of AMF colonization, root niche, and fungal structure allocation. Models proposed capture over 95% of the variation in AMF colonization as a function of root niche and relative abundance of fungal structures in each plant. Arbuscule allocation is a significant predictor of AMF colonization among sibling plants. Arbuscules and extraradical hyphae implicated in nutrient exchange predict highest AMF colonization in the top root section. Our work demonstrates that deep learning can be used by the community for the high-throughput phenotyping of AMF in plant roots. Mixed linear modeling provides a framework for testing hypotheses about AMF colonization phenotypes as a function of root niche and fungal structure allocations.

Genome-Wide Identification and Characterization of the PHT1 Gene Family and Its Response to Mycorrhizal Symbiosis in Salvia miltiorrhiza under Phosphate Stress

Phosphorus (P) is a vital nutrient element that is essential for plant growth and development, and arbuscular mycorrhizal fungi (AMF) can significantly enhance P absorption. The phosphate transporter protein 1 (PHT1) family mediates the uptake of P in plants. However, the PHT1 gene has not yet been characterized in Salvia miltiorrhiza. In this study, to gain insight into the functional divergence of PHT1 genes, nine SmPHT1 genes were identified in the S. miltiorrhiza genome database via bioinformatics tools. Phylogenetic analysis revealed that the PHT1 proteins of S. miltiorrhiza, Arabidopsis thaliana, and Oryza sativa could be divided into three groups. PHT1 in the same clade has a similar gene structure and motif, suggesting that the features of each clade are relatively conserved. Further tissue expression analysis revealed that SmPHT1 was expressed mainly in the roots and stems. In addition, phenotypic changes, P content, and PHT1 gene expression were analyzed in S. miltiorrhiza plants inoculated with AMF under different P conditions (0 mM, 0.1 mM, and 10 mM). P stress and AMF significantly affected the growth and P accumulation of S. miltiorrhiza. SmPHT1;6 was strongly expressed in the roots colonized by AMF, implying that SmPHT1;6 was a specific AMF-inducible PHT1. Taken together, these results provide new insights into the functional divergence and genetic redundancy of the PHT1 genes in response to P stress and AMF symbiosis in S. miltiorrhiza.

A journey into the world of small RNAs in the arbuscular mycorrhizal symbiosis

Arbuscular mycorrhizal (AM) symbiosis is a mutualistic interaction between fungi and most land plants that is underpinned by a bidirectional exchange of nutrients. AM development is a tightly regulated process that encompasses molecular communication for reciprocal recognition, fungal accommodation in root tissues and activation of symbiotic function. As such, a complex network of transcriptional regulation and molecular signaling underlies the cellular and metabolic reprogramming of host cells upon AM fungal colonization. In addition to transcription factors, small RNAs (sRNAs) are emerging as important regulators embedded in the gene network that orchestrates AM development. In addition to controlling cell-autonomous processes, plant sRNAs also function as mobile signals capable of moving to different organs and even to different plants or organisms that interact with plants. AM fungi also produce sRNAs; however, their function in the AM symbiosis remains largely unknown. Here, we discuss the contribution of host sRNAs in the development of AM symbiosis by considering their role in the transcriptional reprogramming of AM fungal colonized cells. We also describe the characteristics of AM fungal-derived sRNAs and emerging evidence for the bidirectional transfer of functional sRNAs between the two partners to mutually modulate gene expression and control the symbiosis.

Spatial co-transcriptomics reveals discrete stages of the arbuscular mycorrhizal symbiosis

The symbiotic interaction of plants with arbuscular mycorrhizal (AM) fungi is ancient and widespread. Plants provide AM fungi with carbon in exchange for nutrients and water, making this interaction a prime target for crop improvement. However, plant-fungal interactions are restricted to a small subset of root cells, precluding the application of most conventional functional genomic techniques to study the molecular bases of these interactions. Here we used single-nucleus and spatial RNA sequencing to explore both Medicago truncatula and Rhizophagus irregularis transcriptomes in AM symbiosis at cellular and spatial resolution. Integrated, spatially registered single-cell maps revealed infected and uninfected plant root cell types. We observed that cortex cells exhibit distinct transcriptome profiles during different stages of colonization by AM fungi, indicating dynamic interplay between both organisms during establishment of the cellular interface enabling successful symbiosis. Our study provides insight into a symbiotic relationship of major agricultural and environmental importance and demonstrates a paradigm combining single-cell and spatial transcriptomics for the analysis of complex organismal interactions.

Single-cell transcriptomics is revolutionizing the improvement of plant biotechnology research: recent advances and future opportunities

Single-cell approaches are a promising way to obtain high-resolution transcriptomics data and have the potential to revolutionize the study of plant growth and development. Recent years have seen the advent of unprecedented technological advances in the field of plant biology to study the transcriptional information of individual cells by single-cell RNA sequencing (scRNA-seq). This review focuses on the modern advancements of single-cell transcriptomics in plants over the past few years. In addition, it also offers a new insight of how these emerging methods will expedite advance research in plant biotechnology in the near future. Lastly, the various technological hurdles and inherent limitations of single-cell technology that need to be conquered to develop such outstanding possible knowledge gain is critically analyzed and discussed.

Plant biotechnology research with single-cell transcriptome: recent advancements and prospects

KEY MESSAGE

Single-cell transcriptomic techniques have emerged as powerful tools in plant biology, offering high-resolution insights into gene expression at the individual cell level. This review highlights the rapid expansion of single-cell technologies in plants, their potential in understanding plant development, and their role in advancing plant biotechnology research. Single-cell techniques have emerged as powerful tools to enhance our understanding of biological systems, providing high-resolution transcriptomic analysis at the single-cell level. In plant biology, the adoption of single-cell transcriptomics has seen rapid expansion of available technologies and applications. This review article focuses on the latest advancements in the field of single-cell transcriptomic in plants and discusses the potential role of these approaches in plant development and expediting plant biotechnology research in the near future. Furthermore, inherent challenges and limitations of single-cell technology are critically examined to overcome them and enhance our knowledge and understanding.

Genome sequencing and functional analysis of a multipurpose medicinal herb Tinospora cordifolia (Giloy)

Tinospora cordifolia (Willd.) Hook.f. & Thomson, also known as Giloy, is among the most important medicinal plants that have numerous therapeutic applications in human health due to the production of a diverse array of secondary metabolites. To gain genomic insights into the medicinal properties of T. cordifolia, the genome sequencing was carried out using 10× Genomics linked read and Nanopore long-read technologies. The draft genome assembly of T. cordifolia was comprised of 1.01 Gbp, which is the genome sequenced from the plant family Menispermaceae. We also performed the genome size estimation for T. cordifolia, which was found to be 1.13 Gbp. The deep sequencing of transcriptome from the leaf tissue was also performed. The genome and transcriptome assemblies were used to construct the gene set, resulting in 17,245 coding gene sequences. Further, the phylogenetic position of T. cordifolia was also positioned as basal eudicot by constructing a genome-wide phylogenetic tree using multiple species. Further, a comprehensive comparative evolutionary analysis of gene families contraction/expansion and multiple signatures of adaptive evolution was performed. The genes involved in benzyl iso-quinoline alkaloid, terpenoid, lignin and flavonoid biosynthesis pathways were found with signatures of adaptive evolution. These evolutionary adaptations in genes provide genomic insights into the presence of diverse medicinal properties of this plant. The genes involved in the common symbiosis signalling pathway associated with endosymbiosis (Arbuscular Mycorrhiza) were found to be adaptively evolved. The genes involved in adventitious root formation, peroxisome biogenesis, biosynthesis of phytohormones, and tolerance against abiotic and biotic stresses were also found to be adaptively evolved in T. cordifolia.

Integration of rice apocarotenoid profile and expression pattern of Carotenoid Cleavage Dioxygenases reveals a positive effect of β-ionone on mycorrhization

Carotenoids are susceptible to degrading processes initiated by oxidative cleavage reactions mediated by Carotenoid Cleavage Dioxygenases that break their backbone, leading to products called apocarotenoids. These carotenoid-derived metabolites include the phytohormones abscisic acid and strigolactones, and different signaling molecules and growth regulators, which are utilized by plants to coordinate many aspects of their life. Several apocarotenoids have been recruited for the communication between plants and arbuscular mycorrhizal (AM) fungi and as regulators of the establishment of AM symbiosis. However, our knowledge on their biosynthetic pathways and the regulation of their pattern during AM symbiosis is still limited. In this study, we generated a qualitative and quantitative profile of apocarotenoids in roots and shoots of rice plants exposed to high/low phosphate concentrations, and upon AM symbiosis in a time course experiment covering different stages of growth and AM development. To get deeper insights in the biology of apocarotenoids during this plant-fungal symbiosis, we complemented the metabolic profiles by determining the expression pattern of CCD genes, taking advantage of chemometric tools. This analysis revealed the specific profiles of CCD genes and apocarotenoids across different stages of AM symbiosis and phosphate supply conditions, identifying novel reliable markers at both local and systemic levels and indicating a promoting role of β-ionone in AM symbiosis establishment.

Editorial for Special Issue "Bacterial Plant Communities: Diversity, Molecular Interactions, and Plant Growth Promotion-2nd Edition"

The study of bacterial communities associated with plants, particularly those of agronomic interest, has been investigated since the late 19th century, revealing the relationship between nodule formation in leguminous plants, nitrogen fixation, their contribution to the plant, and the imperative presence of rhizobia within these nodules [...].

The arbuscular mycorrhizal fungus Rhizophagus irregularis uses the copper exporting ATPase RiCRD1 as a major strategy for copper detoxification

Arbuscular mycorrhizal (AM) fungi establish a mutualistic symbiosis with most land plants. AM fungi regulate plant copper (Cu) acquisition both in Cu deficient and polluted soils. Here, we report characterization of RiCRD1, a Rhizophagus irregularis gene putatively encoding a Cu transporting ATPase. Based on its sequence analysis, RiCRD1 was identified as a plasma membrane Cu + efflux protein of the P1B1-ATPase subfamily. As revealed by heterologous complementation assays in yeast, RiCRD1 encodes a functional protein capable of conferring increased tolerance against Cu. In the extraradical mycelium, RiCRD1 expression was highly up-regulated in response to high concentrations of Cu in the medium. Comparison of the expression patterns of different players of metal tolerance in R. irregularis under high Cu levels suggests that this fungus could mainly use a metal efflux based-strategy to cope with Cu toxicity. RiCRD1 was also expressed in the intraradical fungal structures and, more specifically, in the arbuscules, which suggests a role for RiCRD1 in Cu release from the fungus to the symbiotic interface. Overall, our results show that RiCRD1 encodes a protein which could have a pivotal dual role in Cu homeostasis in R. irregularis, playing a role in Cu detoxification in the extraradical mycelium and in Cu transfer to the apoplast of the symbiotic interface in the arbuscules.

A Dual Transcriptomic Approach Reveals Contrasting Patterns of Differential Gene Expression During Drought in Arbuscular Mycorrhizal Fungus and Carrot

While arbuscular mycorrhizal (AM) fungi are known for providing host plants with improved drought tolerance, we know very little about the fungal response to drought in the context of the fungal-plant relationship. In this study, we evaluated the drought responses of the host and symbiont, using the fungus Rhizophagus irregularis with carrot (Daucus carota) as a plant model. Carrots inoculated with spores of R. irregularis DAOM 197198 were grown in a greenhouse. During taproot development, carrots were exposed to a 10-day water restriction. Compared with well-watered conditions, drought caused diminished photosynthetic activity and reduced plant growth in carrot with and without AM fungi. Droughted carrots had lower root colonization. For R. irregularis, 93% of 826 differentially expressed genes (DEGs) were upregulated during drought, including phosphate transporters, several predicted transport proteins of potassium, and the aquaporin RiAQPF2. In contrast, 78% of 2,486 DEGs in AM carrot were downregulated during drought, including the symbiosis-specific genes FatM, RAM2, and STR, which are implicated in lipid transfer from the host to the fungus and were upregulated exclusively in AM carrot during well-watered conditions. Overall, this study provides insight into the drought response of an AM fungus in relation to its host; the expression of genes related to symbiosis and nutrient exchange were downregulated in carrot but upregulated in the fungus. This study reveals that carrot and R. irregularis exhibit contrast in their regulation of gene expression during drought, with carrot reducing its apparent investment in symbiosis and the fungus increasing its apparent symbiotic efforts. [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.

Tree seedling functional traits mediate plant-soil feedback survival responses across a gradient of light availability

1. Though not often examined together, both plant-soil feedbacks (PSFs) and functional traits have important influences on plant community dynamics and could interact. For example, seedling functional traits could impact seedling survivorship responses to soils cultured by conspecific versus heterospecific adults. Furthermore, levels of functional traits could vary with soil culturing source. In addition, these relationships might shift with light availability, which can affect trait values, microbe abundance, and whether mycorrhizal colonization is mutualistic or parasitic to seedlings. 2. To determine the extent to which functional traits mediate PSFs via seedling survival, we conducted a field experiment. We planted seedlings of four temperate tree species across a gradient of light availability and into soil cores collected beneath conspecific (sterilized and live) and heterospecific adults. We monitored seedling survival twice per week over one growing season, and we randomly selected subsets of seedlings to measure mycorrhizal colonization and phenolics, lignin, and NSC levels at three weeks. 3. Though evidence for PSFs was limited, Acer saccharum seedlings exhibited positive PSFs (i.e., higher survival in conspecific than heterospecific soils). In addition, soil microbes had a negative effect on A. saccharum and Prunus serotina seedling survival, with reduced survival in live versus sterilized conspecific soil. In general, we found higher trait values (measured amounts of a given trait) in conspecific than heterospecific soils and higher light availability. Additionally, A. saccharum survival increased with higher levels of phenolics, which were higher in conspecific soils and high light. Quercus alba survival decreased with higher AMF colonization. 4. We demonstrate that functional trait values in seedlings as young as three weeks vary in response to soil source and light availability. Moreover, seedling survivorship was associated with trait values for two species, despite both drought and heavy rainfall during the growing season that may have obscured survivorship-trait relationships. These results suggest that seedling traits could have an important role in mediating the effects of local soil source and light levels on seedling survivorship and thus plant traits could have an important role in PSFs.

Aromatic amino acid biosynthesis impacts root hair development and symbiotic associations in Lotus japonicus

Legume roots can be symbiotically colonized by arbuscular mycorrhizal (AM) fungi and nitrogen-fixing bacteria. In Lotus japonicus, the latter occurs intracellularly by the cognate rhizobial partner Mesorhizobium loti or intercellularly with the Agrobacterium pusense strain IRBG74. Although these symbiotic programs show distinctive cellular and transcriptome signatures, some molecular components are shared. In this study, we demonstrate that 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase 1 (DAHPS1), the first enzyme in the biosynthetic pathway of aromatic amino acids (AAAs), plays a critical role in root hair development and for AM and rhizobial symbioses in Lotus. Two homozygous DAHPS1 mutants (dahps1-1 and dahps1-2) showed drastic alterations in root hair morphology, associated with alterations in cell wall dynamics and a progressive disruption of the actin cytoskeleton. The altered root hair structure was prevented by pharmacological and genetic complementation. dahps1-1 and dahps1-2 showed significant reductions in rhizobial infection (intracellular and intercellular) and nodule organogenesis and a delay in AM colonization. RNAseq analysis of dahps1-2 roots suggested that these phenotypes are associated with downregulation of several cell wall-related genes, and with an attenuated signaling response. Interestingly, the dahps1 mutants showed no detectable pleiotropic effects, suggesting a more selective recruitment of this gene in certain biological processes. This work provides robust evidence linking AAA metabolism to root hair development and successful symbiotic associations.

Trichoderma spp.-mediated mitigation of heat, drought, and their combination on the Arabidopsis thaliana holobiont: a metabolomics and metabarcoding approach

Introduction

The use of substances to increase productivity and resource use efficiency is now essential to face the challenge of feeding the rising global population with the less environmental impact on the ecosystems. Trichoderma-based products have been used as biopesticides, to inhibit pathogenic microorganisms, and as biostimulants for crop growth, nutrient uptake promotion, and resistance to abiotic stresses.

Methods

In this work, plant metabolomics combined with roots and rhizosphere bacterial metabarcoding were exploited to inspect the performance of Trichoderma spp. biostimulants on Arabidopsis thaliana under drought, heat and their combination and its impact on plant holobiont.

Results and discussion

An overall modulation of N-containing compounds, phenylpropanoids, terpenes and hormones could be pointed out by metabolomics. Moreover, metabarcoding outlined an impact on alpha and beta-diversity with an abundance of Proteobacteria, Pseudomonadales, Burkholderiales, Enterobacteriales and Azospirillales. A holobiont approach was applied as an integrated analytical strategy to resolve the coordinated and complex dynamic interactions between the plant and its rhizosphere bacteria using Arabidopsis thaliana as a model host 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.

Susceptibility and plant immune control-a case of mycorrhizal strategy for plant colonization, symbiosis, and plant immune suppression

Plants and microbes (mycorrhizal fungi to be precise) have evolved together over the past millions of years into an association that is mutualist. The plants supply the fungi with photosynthates and shelter, while the fungi reciprocate by enhancing nutrient and water uptake by the plants as well as, in some cases, control of soil-borne pathogens, but this fungi-plant association is not always beneficial. We argue that mycorrhizal fungi, despite contributing to plant nutrition, equally increase plant susceptibility to pathogens and herbivorous pests' infestation. Understanding of mycorrhizal fungi strategies for suppressing plant immunity, the phytohormones involved and the signaling pathways that aid them will enable the harnessing of tripartite (consisting of three biological systems)-plant-mycorrhizal fungi-microbe interactions for promoting sustainable production of crops.

Integrated miRNA-mRNA analysis reveals candidate miRNA family regulating arbuscular mycorrhizal symbiosis of Poncirus trifoliata

Over 70% land plants live in mutualistic symbiosis with arbuscular mycorrhizal (AM) fungi, and maintenance of symbiosis requires transcriptional and post-transcriptional regulation. The former has been widely studied, whereas the latter mediated by symbiotic microRNAs (miRNAs) remains obscure, especially in woody plants. Here, we performed high-throughput sequencing of the perennial woody citrus plant Poncirus trifoliata and identified 3750 differentially expressed genes (DEGs) and 42 miRNAs (DEmiRs) upon AM fungal colonization. By analyzing cis-regulatory elements in the promoters of the DEGs, we predicted 329 key AM transcription factors (TFs). A miRNA-mRNA regulatory network was then constructed by integrating these data. Several candidate miRNA families of P. trifoliata were identified whose members target known symbiotic genes, such as miR167h-AMT2;3 and miR156e-EXO70I, or key TFs, such as miR164d-NAC and miR477a-GRAS, thus are involved in AM symbiotic processes of fungal colonization, arbuscule development, nutrient exchange and phytohormone signaling. Finally, analysis of selected miRNA family revealed that a miR159b conserved in mycorrhizal plant species and a Poncirus-specific miR477a regulate AM symbiosis. The role of miR477a was likely to target GRAS family gene RAD1 in citrus plants. Our results not only revealed that miRNA-mRNA network analysis, especially miRNA-TF analysis, is effective in identifying miRNA family regulating AM symbiosis, but also shed light on miRNA-mediated post-transcriptional regulation of AM symbiosis in woody citrus plants.

ARBUSCULAR MYCORRHIZA-INDUCED KINASES AMK8 and AMK24 associate with the receptor-like kinase KINASE3 to regulate arbuscular mycorrhizal symbiosis in Lotus japonicus

Arbuscular mycorrhizal (AM) symbiosis is a widespread, ancient mutualistic association between plants and fungi, and facilitates nutrient uptake into plants. Cell surface receptor-like kinases (RLKs) and receptor-like cytoplasmic kinases (RLCKs) play pivotal roles in transmembrane signaling, while few RLCKs are known to function in AM symbiosis. Here, we show that 27 out of 40 AM-induced kinases (AMKs) are transcriptionally upregulated by key AM transcription factors in Lotus japonicus. Nine AMKs are only conserved in AM-host lineages, among which the SPARK-RLK-encoding gene KINASE3 (KIN3) and the RLCK paralogues AMK8 and AMK24 are required for AM symbiosis. KIN3 expression is directly regulated by the AP2 transcription factor CTTC MOTIF-BINDING TRANSCRIPTION FACTOR1 (CBX1), which regulates the reciprocal exchange of nutrients in AM symbiosis, via the AW-box motif in the KIN3 promoter. Loss of function mutations in KIN3, AMK8, or AMK24 result in reduced mycorrhizal colonization in L. japonicus. AMK8 and AMK24 physically interact with KIN3. KIN3 and AMK24 are active kinases and AMK24 directly phosphorylates KIN3 in vitro. Moreover, CRISPR-Cas9-mediated mutagenesis of OsRLCK171, the sole homolog of AMK8 and AMK24 in rice (Oryza sativa), leads to diminished mycorrhization with stunted arbuscules. Overall, our results reveal a crucial role of the CBX1-driven RLK/RLCK complex in the evolutionarily conserved signaling pathway enabling arbuscule formation.

A glycan receptor kinase facilitates intracellular accommodation of arbuscular mycorrhiza and symbiotic rhizobia in the legume Lotus japonicus

Receptors that distinguish the multitude of microbes surrounding plants in the environment enable dynamic responses to the biotic and abiotic conditions encountered. In this study, we identify and characterise a glycan receptor kinase, EPR3a, closely related to the exopolysaccharide receptor EPR3. Epr3a is up-regulated in roots colonised by arbuscular mycorrhizal (AM) fungi and is able to bind glucans with a branching pattern characteristic of surface-exposed fungal glucans. Expression studies with cellular resolution show localised activation of the Epr3a promoter in cortical root cells containing arbuscules. Fungal infection and intracellular arbuscule formation are reduced in epr3a mutants. In vitro, the EPR3a ectodomain binds cell wall glucans in affinity gel electrophoresis assays. In microscale thermophoresis (MST) assays, rhizobial exopolysaccharide binding is detected with affinities comparable to those observed for EPR3, and both EPR3a and EPR3 bind a well-defined β-1,3/β-1,6 decasaccharide derived from exopolysaccharides of endophytic and pathogenic fungi. Both EPR3a and EPR3 function in the intracellular accommodation of microbes. However, contrasting expression patterns and divergent ligand affinities result in distinct functions in AM colonisation and rhizobial infection in Lotus japonicus. The presence of Epr3a and Epr3 genes in both eudicot and monocot plant genomes suggest a conserved function of these receptor kinases in glycan perception.

A Fine-Tuning of the Plant Hormones, Polyamines and Osmolytes by Ectomycorrhizal Fungi Enhances Drought Tolerance in Pedunculate Oak

The drought sensitivity of the pedunculate oak (Quercus robur L.) poses a threat to its survival in light of climate change. Mycorrhizal fungi, which orchestrate biogeochemical cycles and particularly have an impact on the plant's defense mechanisms and metabolism of carbon, nitrogen, and phosphorus, are among the microbes that play a significant role in the mitigation of the effects of climate change on trees. The study's main objectives were to determine whether ectomycorrhizal (ECM) fungi alleviate the effects of drought stress in pedunculate oak and to investigate their priming properties. The effects of two levels of drought (mild and severe, corresponding to 60% and 30% of field capacity, respectively) on the biochemical response of pedunculate oak were examined in the presence and absence of ectomycorrhizal fungi. To examine whether the ectomycorrhizal fungi modulate the drought tolerance of pedunculate oak, levels of plant hormones and polyamines were quantified using UPLC-TQS and HPLC-FD techniques in addition to gas exchange measurements and the main osmolyte amounts (glycine betaine-GB and proline-PRO) which were determined spectrophotometrically. Droughts increased the accumulation of osmolytes, such as proline and glycine betaine, as well as higher polyamines (spermidine and spermine) levels and decreased putrescine levels in both, mycorrhized and non-mycorrhized oak seedlings. In addition to amplifying the response of oak to severe drought in terms of inducible proline and abscisic acid (ABA) levels, inoculation with ECM fungi significantly increased the constitutive levels of glycine betaine, spermine, and spermidine regardless of drought stress. This study found that compared to non-mycorrhized oak seedlings, unstressed ECM-inoculated oak seedlings had higher levels of salicylic (SA) and abscisic acid (ABA) but not jasmonic acid (JA), indicating a priming mechanism of ECM is conveyed via these plant hormones. According to a PCA analysis, the effect of drought was linked to the variability of parameters along the PC1 axe, such as osmolytes PRO, GB, polyamines, and plant hormones such as JA, JA-Ile, SAG, and SGE, whereas mycorrhization was more closely associated with the parameters gathered around the PC2 axe (SA, ODPA, ABA, and E). These findings highlight the beneficial function of the ectomycorrhizal fungi, in particular Scleroderma citrinum, in reducing the effects of drought stress in pedunculate oak.

Long-lasting impact of chitooligosaccharide application on strigolactone biosynthesis and fungal accommodation promotes arbuscular mycorrhiza in Medicago truncatula

The establishment of arbuscular mycorrhiza (AM) between plants and Glomeromycotina fungi is preceded by the exchange of chemical signals: fungal released Myc-factors, including chitooligosaccharides (CO) and lipo-chitooligosaccharides (LCO), activate plant symbiotic responses, while root-exuded strigolactones stimulate hyphal branching and boost CO release. Furthermore, fungal signaling reinforcement through CO application was shown to promote AM development in Medicago truncatula, but the cellular and molecular bases of this effect remained unclear. Here, we focused on long-term M. truncatula responses to CO treatment, demonstrating its impact on the transcriptome of both mycorrhizal and nonmycorrhizal roots over several weeks and providing an insight into the mechanistic bases of the CO-dependent promotion of AM colonization. CO treatment caused the long-lasting regulation of strigolactone biosynthesis and fungal accommodation-related genes. This was mirrored by an increase in root didehydro-orobanchol content, and the promotion of accommodation responses to AM fungi in root epidermal cells. Lastly, an advanced downregulation of AM symbiosis marker genes was observed at the latest time point in CO-treated plants, in line with an increased number of senescent arbuscules. Overall, CO treatment triggered molecular, metabolic, and cellular responses underpinning a protracted acceleration of AM development.

The RNAome landscape of tomato during arbuscular mycorrhizal symbiosis reveals an evolving RNA layer symbiotic regulatory network

Arbuscular mycorrhizal symbiosis (AMS) is an ancient plant-fungus relationship that is widely distributed in terrestrial plants. The formation of symbiotic structures and bidirectional nutrient exchange requires the regulation of numerous genes. However, the landscape of RNAome during plant AMS involving different types of regulatory RNA is poorly understood. In this study, a combinatorial strategy utilizing multiple sequencing approaches was used to decipher the landscape of RNAome in tomato, an emerging AMS model. The annotation of the tomato genome was improved by a multiple-platform sequencing strategy. A total of 3,174 protein-coding genes were upregulated during AMS, 42% of which were alternatively spliced. Comparative-transcriptome analysis revealed that genes from 24 orthogroups were consistently induced by AMS in eight phylogenetically distant angiosperms. Seven additional orthogroups were specifically induced by AMS in all surveyed dicot AMS host plants. However, these orthogroups were absent or not induced in monocots and/or non-AMS hosts, suggesting a continuously evolving AMS-responsive network in addition to a conserved core regulatory module. Additionally, we detected 587 lncRNAs, ten miRNAs, and 146 circRNAs that responded to AMS, which were incorporated to establish a tomato AMS-responsive, competing RNA-responsive endogenous RNA (ceRNA) network. Finally, a tomato symbiotic transcriptome database (TSTD, https://efg.nju.edu.cn/TSTD) was constructed to serve as a resource for deep deciphering of the AMS regulatory network. These results help elucidate the reconfiguration of the tomato RNAome during AMS and suggest a sophisticated and evolving RNA layer responsive network during AMS processes.

Plants Recruit Peptides and Micro RNAs to Regulate Nutrient Acquisition from Soil and Symbiosis

Plants engage in symbiotic relationships with soil microorganisms to overcome nutrient limitations in their environment. Among the best studied endosymbiotic interactions in plants are those with arbuscular mycorrhizal (AM) fungi and N-fixing bacteria called rhizobia. The mechanisms regulating plant nutrient homeostasis and acquisition involve small mobile molecules such as peptides and micro RNAs (miRNAs). A large number of CLE (CLAVATA3/EMBRYO SURROUNDING REGION-RELATED) and CEP (C-TERMINALLY ENCODED PEPTIDE) peptide hormones as well as certain miRNAs have been reported to differentially respond to the availability of essential nutrients such as nitrogen (N) and phosphorus (P). Interestingly, a partially overlapping pool of these molecules is involved in plant responses to root colonization by rhizobia and AM fungi, as well as mineral nutrition. The crosstalk between root endosymbiosis and nutrient availability has been subject of intense investigations, and new insights in locally or systemically mobile molecules in nutrient- as well as symbiosis-related signaling continue to arise. Focusing on the key roles of peptides and miRNAs, we review the mechanisms that shape plant responses to nutrient limitation and regulate the establishment of symbiotic associations with beneficial soil microorganisms.

The genome of the king protea, Protea cynaroides

The king protea (Protea cynaroides), an early-diverging eudicot, is the most iconic species from the Megadiverse Cape Floristic Region, and the national flower of South Africa. Perhaps best known for its iconic flower head, Protea is a key genus for the South African horticulture industry and cut-flower market. Ecologically, the genus and the family Proteaceae are important models for radiation and adaptation, particularly to soils with limited phosphorus bio-availability. Here, we present a high-quality chromosome-scale assembly of the P. cynaroides genome as the first representative of the fynbos biome. We reveal an ancestral whole-genome duplication event that occurred in the Proteaceae around the late Cretaceous that preceded the divergence of all crown groups within the family and its extant diversity in all Southern continents. The relatively stable genome structure of P. cynaroides is invaluable for comparative studies and for unveiling paleopolyploidy in other groups, such as the distantly related sister group Ranunculales. Comparative genomics in sequenced genomes of the Proteales shows loss of key arbuscular mycorrhizal symbiosis genes likely ancestral to the family, and possibly the order. The P. cynaroides genome empowers new research in plant diversification, horticulture and adaptation, particularly to nutrient-poor soils.

The global integrative network: integration of signaling and metabolic pathways

The crosstalk between signaling and metabolic pathways has been known to play key roles in human diseases and plant biological processes. The integration of signaling and metabolic pathways can provide an essential reference framework for crosstalk analysis. However, current databases use distinct structures to present signaling and metabolic pathways, which leads to the chaos in the integrated networks. Moreover, for the metabolic pathways, the metabolic enzymes and the reactions are disconnected by the current widely accepted layout of edges and nodes, which hinders the topological analysis of the integrated networks. Here, we propose a novel "meta-pathway" structure, which uses the uniformed structure to display the signaling and metabolic pathways, and resolves the difficulty in linking the metabolic enzymes to the reactions topologically. We compiled a comprehensive collection of global integrative networks (GINs) by merging the meta-pathways of 7077 species. We demonstrated the assembly of the signaling and metabolic pathways using the GINs of four species-human, mouse, Arabidopsis, and rice. Almost all of the nodes were assembled into one major network for each of the four species, which provided opportunities for robust crosstalk and topological analysis, and knowledge graph construction.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42994-022-00078-1.

The Perspective of Arbuscular Mycorrhizal Symbiosis in Rice Domestication and Breeding

In nature, symbiosis with arbuscular mycorrhizal (AM) fungi contributes to sustainable acquisition of phosphorus and other elements in over 80% of plant species; improving interactions with AM symbionts may mitigate some of the environmental problems associated with fertilizer application in grain crops such as rice. Recent developments of high-throughput genome sequencing projects of thousands of rice cultivars and the discovery of the molecular mechanisms underlying AM symbiosis suggest that interactions with AM fungi might have been an overlooked critical trait in rice domestication and breeding. In this review, we discuss genetic variation in the ability of rice to form AM symbioses and how this might have affected rice domestication. Finally, we discuss potential applications of AM symbiosis in rice breeding for more sustainable agriculture.