Physiological and transcriptomic response of Medicago truncatula to colonization by high- or low-benefit arbuscular mycorrhizal fungi

Leaf transcriptomic responses to arbuscular mycorrhizal symbioses exerting growth depressions in tomato

Arbuscular mycorrhizal (AM) fungi play important roles in sustainable agriculture, given that they provide multiple benefits for numerous crops. Conversely, negative plant growth effects induced by AM fungi are also occasionally observed. However, little information is available regarding the responses of symbiosis. In this study, compared with an absence of AM fungus inoculation, tomato seedlings inoculated with Funneliformis mosseae or Rhizophagus intraradices were characterized by reduced shoot and root growth. The two AM fungi decreased the carbon contents and the carbon-nitrogen ratios in shoots. To gain further insights into the underlying mechanisms, transcriptomic analyses were performed in the study. A total of 190 and 870 differentially expressed genes (DEGs) were identified in the F. mosseae vs. control and R. intraradices vs. control comparisons, respectively. KEGG enrichment analysis of the former 190 DEGs revealed significant enrichment of the "Protein processing in endoplasmic reticulum," "Flavonoid biosynthesis," "Flavone and flavonol biosynthesis," and "Stilbenoid, diarylheptanoid, and gingerol biosynthesis" pathways, whereas "DNA replication," "Photosynthesis - antenna proteins," "Cutin, suberine, and wax biosynthesis," "Protein processing in endoplasmic reticulum," and "Glycerophospholipid metabolism" were identified as pathways significantly enriched with the latter 870 DEGs. GO functional analysis revealed that among both groups of DEGs, large numbers of genes were assigned the "Response to stimulus" term. Moreover, many of the enriched terms were associated with stimulus and stress response processes, including response to salt stress, heat, and reactive oxygen species. Therefore, the findings indicated that AM fungi may trigger defense-related responses in hosts, even though the symbioses performed growth depressions. These findings will contribute to advancing our current understanding of AM fungi.

Fungal Endophytes: An Insight into Diversity, Stress Tolerance, Biocontrol and Plant Growth-Promoting Potentials

Food and human health are closely related to each other. A healthy diet contributes to excellent health. However, chemical-based agricultural products delivered the poisons in our tray, which cause fatal illnesses like cancer. Overuse of chemical-based fertilizer, herbicides, insecticides, pesticides, etc. is responsible for decreasing soil health status and the development of resistant variants of phytopathogens. Endophytes may overcome such issues effectively without showing any harmful effects. Endophytes are microorganisms that invade intercellular or intracellular parts of host plants without causing any apparent symptoms of infection. Endophytes are broad groups of microorganisms; they may be algae, fungi, bacteria, or ascomycetes. Among them, endophytic fungi are a major group of endophytes that reside inside the host plant body. Types and biodiversity of fungal endophytes make them a potent biological agent for sustainable agricultural management because of their vast geographical distribution. Historically fungal endophytes are broadly categorized into two groups as clavicipitaceous and non-clavicipitaceous based on phylogeny and life history traits. Based on various criteria such as in planta biodiversity, colonization, transmission and fitness to the host, non-clavicipitaceous fungi classified into three distinct classes. They promote plant growth and development by overcoming biotic and abiotic stress and by accelerating systematic inducing resistance (SIR) in plants. They harbor a variety of bioactive compounds like., alkaloids, terpenoids, phenolic acid, steroids, tannins, and saponins that act as antifungal, antibacterial, anticancer, antioxidant, and insecticidal agents. These bioactive compounds have a great potential role in sustainable agricultural management. This review highlights the potential role of fungal endophytes in the field of sustainable agricultural practices to overcome biotic and abiotic stress along with plant growth-promoting activities rather than the use of chemicals in agro-ecosystems.

Rhizobacteria and Arbuscular Mycorrhizal Fungi (AMF) Community in Growth Management and Mitigating Stress in Millets: A Plant-Soil Microbe Symbiotic Relationship

Millets, commonly referred to as the "future crop," provide a practical solution for addressing hunger and reducing the impact of climate change. The nutritional and physiological well-being of soil is crucial for the survival and resilience of plants while countering environmental stressors, both abiotic and biotic, that arise from the current climate change scenario. The health and production of millet are directly influenced by the soil microbial community. Millets have several plant growth-promoting rhizobacteria such as Pseudomonas, Azotobacter, Bacillus, Rhizobium, and fungi like Penicillium sp., that increase nutrient uptake, growth, and productivity and protect against abiotic and biotic stressors. Rhizobacteria enhance plant productivity by many mechanisms, including the release of plant hormones and secondary metabolic compounds, the conversion of nutrients into soluble forms, the ability to fix nitrogen, and the provision of resistance to both biotic and abiotic stresses. The microbial populations in the rhizosphere have a significant impact on the growth and production of millet such as enhancing soil fertility and plant nourishment. Additionally, arbuscular mycorrhizal fungi invade the roots of millets. The taxon Glomus is the most prevalent in association with millet plant soil, followed by Acaulospora, Funneliformis, and Rhizophagus. The symbiotic relationship between arbuscular mycorrhizal fungi and millet plants improves plant growth and nutrient absorption under diverse soil and environmental circumstances, including challenging abiotic factors like drought and salinity.

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.

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.

Colonization by orchid mycorrhizal fungi primes induced systemic resistance against necrotrophic pathogen

Orchids and arbuscular mycorrhiza (AM) plants evolved independently and have different structures and fungal partners, but they both facilitate nutrient uptake. Orchid mycorrhiza (OM) supports orchid seed germination, but unlike AM, its role in disease resistance of mature plants is largely unknown. Here, we examined whether OM induces systemic disease resistance against a necrotrophic pathogen in a similar fashion to AM. We investigated the priming effect of mycorrhizal fungi inoculation on resistance of a terrestrial orchid, Bletilla striata, to soft rot caused by Dickeya fangzhongdai. We found that root colonization by a compatible OM fungus primed B. striata seedlings and induced systemic resistance against the infection. Transcriptome analysis showed that priming was mediated by the downregulation of jasmonate and ethylene pathways and that these pathways are upregulated once infection occurs. Comparison with the reported transcriptome of AM fungus-colonized rice leaves revealed similar mechanisms in B. striata and in rice. These findings highlight a novel aspect of commonality between OM and AM plants in terms of induced systemic resistance.

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.

Influence of arbuscular mycorrhizal fungi density on growth and metabolism of Handroanthus serratifolius (Vahl) S.O. Grose seedlings

Studies on the relationship between Handroanthus serratifolius and arbuscular mycorrhizal fungi (AMF) are limited in the literature. The influence of AMF spore density on plant development is fundamental information to determining the degree of benefits in this relationship. Therefore, the objective of this study was to investigate the effects of different AMF spore densities on thirty-day-old H. serratifolius seedlings, focusing on growth and biochemical parameters using a completely randomized experimental design with three different spore densities and control. The spore densities were classified as low, medium, and high, with 1.54, 3.08, and 12.35 spores g-1 , respectively. Plant growth analysis, mycorrhizal colonization, nitrogen compound concentration, and carbohydrate analysis were performed. The medium spore density treatment showed the greatest increases in biomass, height, leaf area, and root volume. Furthermore, greater absorption of phosphorus and better dynamics in nitrogen metabolism were observed in mycorrhizal plants compared to the control since the ammonium and nitrate compounds were rapidly incorporated into protein and chlorophyll compounds. The carbohydrate analysis revealed the influence of source-sink dynamics on sugar concentration in different plant parts. These findings support the importance of determining the appropriate spore density for assessing the symbiotic relationship between forest species and AMF.

The Root-Colonizing Endophyte Piriformospora indica Supports Nitrogen-Starved Arabidopsis thaliana Seedlings with Nitrogen Metabolites

The root-colonizing endophytic fungus Piriformospora indica promotes the root and shoot growth of its host plants. We show that the growth promotion of Arabidopsis thaliana leaves is abolished when the seedlings are grown on media with nitrogen (N) limitation. The fungus neither stimulated the total N content nor did it promote 15NO3- uptake from agar plates to the leaves of the host under N-sufficient or N-limiting conditions. However, when the roots were co-cultivated with 15N-labelled P. indica, more labels were detected in the leaves of N-starved host plants but not in plants supplied with sufficient N. Amino acid and primary metabolite profiles, as well as the expression analyses of N metabolite transporter genes suggest that the fungus alleviates the adaptation of its host from the N limitation condition. P. indica alters the expression of transporter genes, which participate in the relocation of NO3-, NH4+ and N metabolites from the roots to the leaves under N limitation. We propose that P. indica participates in the plant's metabolomic adaptation against N limitation by delivering reduced N metabolites to the host, thus alleviating metabolic N starvation responses and reprogramming the expression of N metabolism-related genes.

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

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

A snapshot of the transcriptome of Medicago truncatula (Fabales: Fabaceae) shoots and roots in response to an arbuscular mycorrhizal fungus and the pea aphid (Acyrthosiphon pisum) (Hemiptera: Aphididae)

Plants simultaneously interact with belowground symbionts such as arbuscular mycorrhizal (AM) fungi and aboveground antagonists such as aphids. Generally, plants gain access to valuable resources including nutrients and water through the AM symbiosis and are more resistant to pests. Nevertheless, aphids' performance improves on mycorrhizal plants, and it remains unclear whether a more nutritious food source and/or attenuated defenses are the contributing factors. This study examined the shoot and root transcriptome of barrel medic (Medicago truncatula Gaertn.) plants highly colonized by the AM fungus Rhizophagus irregularis (Blaszk., Wubet, Renker, and Buscot) C. Walker and A. Schüßler (Glomerales: Glomeraceae) and exposed to 7 days of mixed age pea aphid (Acyrthosiphon pisum (Harris)) herbivory. The RNA-seq samples chosen for this study showed that aphids were heavier when fed mycorrhizal plants compared to nonmycorrhizal plants. We hypothesized that (i) insect-related plant defense pathways will be downregulated in shoots of mycorrhizal plants with aphids compared to nonmycorrhizal plants with aphids; (ii) pathways involved in nutrient acquisition, carbohydrate-related and amino acid transport will be upregulated in shoots of mycorrhizal plants with aphids compared to nonmycorrhizal plants with aphids; and (iii) roots of mycorrhizal plants with aphids will exhibit mycorrhiza-induced resistance. The transcriptome data revealed that the gene repertoire related to defenses, nutrient transport, and carbohydrates differs between nonmycorrhizal and mycorrhizal plants with aphids, which could explain the weight gain in aphids. We also identified novel candidate genes that are differentially expressed in nonmycorrhizal plants with aphids, thus setting the stage for future functional studies.

SWEET transporters of Medicago lupulina in the arbuscular-mycorrhizal system in the presence of medium level of available phosphorus

Arbuscular mycorrhiza (AM) fungi receive photosynthetic products and sugars from plants in exchange for contributing to the uptake of minerals, especially phosphorus, from the soil. The identification of genes controlling AM symbiotic efficiency may have practical application in the creation of highly productive plant-microbe systems. The aim of our work was to evaluate the expression levels of SWEET sugar transporter genes, the only family in which sugar transporters specific to AM symbiosis can be detected. We have selected a unique "host plant-AM fungus" model system with high response to mycorrhization under medium phosphorus level. This includes a plant line which is highly responsive to inoculation by AM fungi, an ecologically obligate mycotrophic line MlS-1 from black medick (Medicago lupulina) and the AM fungus Rhizophagus irregularis strain RCAM00320, which has a high efficiency in a number of plant species. Using the selected model system, differences in the expression levels of 11 genes encoding SWEET transporters in the roots of the host plant were evaluated during the development of or in the absence of symbiosis of M. lupulina with R. irregularis at various stages of the host plant development in the presence of medium level of phosphorus available for plant nutrition in the substrate. At most stages of host plant development, mycorrhizal plants had higher expression levels of MlSWEET1b, MlSWEET3c, MlSWEET12 and MlSWEET13 compared to AM-less controls. Also, increased expression relative to control during mycorrhization was observed for MlSWEET11 at 2nd and 3rd leaf development stages, for MlSWEET15c at stemming (stooling) stage, for MlSWEET1a at 2nd leaf development, stemming and lateral branching stages. The MlSWEET1b gene can be confidently considered a good marker with specific expression for effective development of AM symbiosis between M. lupulina and R. irregularis in the presence of medium level of phosphorus available to plants in the substrate.

Carbohydrate and lipid balances in the positive plant phenotypic response to arbuscular mycorrhiza: increase in sink strength

The exchange of phosphorus (P) and carbon (C) between plants and arbuscular mycorrhizal fungi (AMF) is a major determinant of their mutualistic symbiosis. We explored the C dynamics in tomato (Solanum lycorpersicum) inoculated or not with Rhizophagus irregularis to study their growth response under different NaH₂ PO₄ concentrations (Null P, 0 mM; Low P, 0.065 mM; High P, 1.3 mM). The percentage of AMF colonization was similar in plants under Null and Low P, but severely reduced under High P. However, the AMF mass biomarker 16:1ω5 revealed higher fungal accumulation in inoculated roots under Low P, while more AMF spores were produced in the Null P. Under High P, AMF biomass and spores were strongly reduced. Plant growth response to mycorrhiza was negative under Null P, showing reduction in height, biovolume index, and source leaf (SL) area. Under Low P, inoculated plants showed a positive response (e.g., increased SL area), while inoculated plants under High P were similar to non-inoculated plants. AMF promoted the accumulation of soluble sugars in the SL under all fertilization levels, whereas the soluble sugar level decreased in roots under Low P in inoculated plants. Transcriptional upregulation of SlLIN6 and SlSUS1, genes related to carbohydrate metabolism, was observed in inoculated roots under Null P and Low P, respectively. We conclude that P-limiting conditions that increase AMF colonization stimulate plant growth due to an increase in the source and sink strength. Our results suggest that C partitioning and allocation to different catabolic pathways in the host are influenced by AMF performance.