Nomenclatural realignment of Neotyphodium species with genus Epicholë

Grass-Endophyte Interactions and Their Associated Alkaloids as a Potential Management Strategy for Plant Parasitic Nematodes

Claviceptaceous endophytic fungi in the genus Epichloë mostly form a symbiotic relationship with cool-season grasses. Epichloë spp. are capable of producing bioactive alkaloids such as peramines, lolines, ergot alkaloids, and indole-diterpenes, which protect the host plant from herbivory by animals, insects, and nematodes. The host also benefits from enhanced tolerance to abiotic stresses, such as salt, drought, waterlogging, cold, heavy metals, and low nitrogen stress. The bioactive alkaloids produced can have both direct and indirect effects towards plant parasitic nematodes. Direct interaction with nematodes' motile stages can cause paralysis (nematostatic effect) or death (nematicidal effect). Indirectly, the metabolites may induce host immunity which inhibits feeding and subsequent nematode development. This review highlights the different mechanisms through which this interaction and the metabolites produced have been explored in the suppression of plant parasitic nematodes and also how the specific interactions between different grass genotypes and endophyte strains result in variable suppression of different nematode species. An understanding of the different grass-endophyte interactions and their successes and failures in suppressing various nematode species is essential to enable the proper selection of grass-endophyte combinations to identify the alkaloids produced, concentrations required, and determine which nematodes are sensitive to which specific alkaloids.

Endophytes Alleviate Drought-Derived Oxidative Damage in Achnatherum inebrians Plants Through Increasing Antioxidants and Regulating Host Stress Responses

Endophytes generally increase antioxidant contents of plants subjected to environmental stresses. However, the mechanisms by which endophytes alter the accumulation of antioxidants in plant tissues are not entirely clear. We hypothesized that, in stress situations, endophytes would simultaneously reduce oxidative damage and increase antioxidant contents of plants and that the accumulation of antioxidants would be a consequence of the endophyte ability to regulate the expression of plant antioxidant genes. We investigated the effects of the fungal endophyte Epichloë gansuensis (C.J. Li & Nan) on oxidative damage, antioxidant contents, and expression of representative genes associated with antioxidant pathways in Achnatherum inebrians (Hance) Keng plants subjected to low (15%) and high (60%) soil moisture conditions. Gene expression levels were measured using RNA-seq. As expected, the endophyte reduced the oxidative damage by 17.55% and increased the antioxidant contents by 53.14% (on average) in plants subjected to low soil moisture. In line with the accumulation of antioxidants in plant tissues, the endophyte increased the expression of most plant genes associated with the biosynthesis of antioxidants (e.g., MIOX, crtB, gpx) while it reduced the expression of plant genes related to the metabolization of antioxidants (e.g., GST, PRODH, ALDH). Our findings suggest that endophyte ability of increasing antioxidant contents in plants may reduce the oxidative damage caused by stresses and that the fungal regulation of plant antioxidants would partly explain the accumulation of these compounds in plant tissues.

Microbial symbionts buffer hosts from the demographic costs of environmental stochasticity

Species' persistence in increasingly variable climates will depend on resilience against the fitness costs of environmental stochasticity. Most organisms host microbiota that shield against stressors. Here, we test the hypothesis that, by limiting exposure to temporally variable stressors, microbial symbionts reduce hosts' demographic variance. We parameterized stochastic population models using data from a 14-year symbiont-removal experiment including seven grass species that host Epichloë fungal endophytes. Results provide novel evidence that symbiotic benefits arise not only through improved mean fitness, but also through dampened inter-annual variance. Hosts with "fast" life-history traits benefited most from symbiont-mediated demographic buffering. Under current climate conditions, contributions of demographic buffering were modest compared to benefits to mean fitness. However, simulations of increased stochasticity amplified benefits of demographic buffering and made it the more important pathway of host-symbiont mutualism. Microbial-mediated variance buffering is likely an important, yet cryptic, mechanism of resilience in an increasingly variable world.

Anti-herbivory defences delivered by Epichloë fungal endophytes: a quantitative review of alkaloid concentration variation among hosts and plant parts

BACKGROUND AND AIMS

In the subfamily Poöideae (Poaceae), certain grass species possess anti-herbivore alkaloids synthesized by fungal endophytes that belong to the genus Epichloë (Clavicipitaceae). The protective role of these symbiotic endophytes can vary, depending on alkaloid concentrations within specific plant-endophyte associations and plant parts.

METHODS

We conducted a literature review to identify articles containing alkaloid concentration data for various plant parts in six important pasture species, Lolium arundinaceum, Lolium perenne, Lolium pratense, Lolium multiflorum|Lolium rigidum and Festuca rubra, associated with their common endophytes. We considered the alkaloids lolines (1-aminopyrrolizidines), peramine (pyrrolopyrazines), ergovaline (ergot alkaloids) and lolitrem B (indole-diterpenes). While all these alkaloids have shown bioactivity against insect herbivores, ergovaline and lolitrem B are harmful for mammals.

KEY RESULTS

Loline alkaloid levels were higher in the perennial grasses L. pratense and L. arundinaceum compared to the annual species L. multiflorum and L. rigidum, and higher in reproductive tissues than in vegetative structures. This is probably due to the greater biomass accumulation in perennial species that can result in higher endophyte mycelial biomass. Peramine concentrations were higher in L. perenne than in L. arundinaceum and not affected by plant part. This can be attributed to the high within-plant mobility of peramine. Ergovaline and lolitrem B, both hydrophobic compounds, were associated with plant parts where fungal mycelium is usually present, and their concentrations were higher in plant reproductive tissues. Only loline alkaloid data were sufficient for below-ground tissue analyses and concentrations were lower than in above-ground parts.

CONCLUSIONS

Our study provides a comprehensive synthesis of fungal alkaloid variation across host grasses and plant parts, essential for understanding the endophyte-conferred defence extent. The patterns can be understood by considering endophyte growth within the plant and alkaloid mobility. Our study identifies research gaps, including the limited documentation of alkaloid presence in roots and the need to investigate the influence of different environmental conditions.

Interactions between Epichloë endophyte and the plant microbiome impact nitrogen responses in host Achnatherum inebrians plants

The clavicipitaceous fungus Epichloë gansuensis forms symbiotic associations with drunken horse grass (Achnatherum inebrians), providing biotic and abiotic stress protection to its host. However, it is unclear how E. gansuensis affects the assembly of host plant-associated bacterial communities after ammonium nitrogen (NH4+-N) treatment. We examined the shoot- and root-associated bacterial microbiota and root metabolites of A. inebrians when infected (I) or uninfected (F) with E. gansuensis endophyte. The results showed more pronounced NH4+-N-induced microbial and metabolic changes in the endophyte-infected plants compared to the endophyte-free plants. E. gansuensis significantly altered bacterial community composition and β-diversity in shoots and roots and increased bacterial α-diversity under NH4+-N treatment. The relative abundance of 117 and 157 root metabolites significantly changed with E. gansuensis infection under water and NH4+-N treatment compared to endophyte-free plants. Root bacterial community composition was significantly related to the abundance of the top 30 metabolites [variable importance in the projection (VIP) > 2 and VIP > 3] contributing to differences between I and F plants, especially alkaloids. The correlation network between root microbiome and metabolites was complex. Microorganisms in the Proteobacteria and Firmicutes phyla were significantly associated with the R00693 metabolic reaction of cysteine and methionine metabolism. Co-metabolism network analysis revealed common metabolites between host plants and microorganisms.IMPORTANCEOur results suggest that the effect of endophyte infection is sensitive to nitrogen availability. Endophyte symbiosis altered the composition of shoot and root bacterial communities, increasing bacterial diversity. There was also a change in the class and relative abundance of metabolites. We found a complex co-occurrence network between root microorganisms and metabolites, with some metabolites shared between the host plant and its microbiome. The precise ecological function of the metabolites produced in response to endophyte infection remains unknown. However, some of these compounds may facilitate plant-microbe symbiosis by increasing the uptake of beneficial soil bacteria into plant tissues. Overall, these findings advance our understanding of the interactions between the microbiome, metabolome, and endophyte symbiosis in grasses. The results provide critical insight into the mechanisms by which the plant microbiome responds to nutrient stress in the presence of fungal endophytes.

Intergenerational consequences of an auxin-like herbicide on plant sensitivity to a graminicide mediated by a fungal endophyte

In agroecosystems, herbicides are the predominant anthropogenic selection pressure for agriculture weed species. While weeds are the primary target, herbicides can have adverse impacts on non-target plant beneficial microorganisms. We aimed to investigate the influence of a foliar endophytic fungus (Epichloë occultans) on the sensitivity of Lolium multiflorum to a graminicide herbicide (diclofop-methyl) during both plant ontogeny and progeny. Susceptible individuals to diclofop-methyl with and without endophyte were pre-exposed to the auxin 2,4-D herbicide. This herbicide is known to stimulate the metabolic detoxification mechanism (CYP-450) of diclofop-methyl. Regardless of the endophyte, 2,4-D pre-treatment increased mother plant survival to nearly 100 % under diclofop treatment but not in the progeny. Furthermore, maternal plant exposure to 2,4-D reduced endophyte transmission to the seeds and from seed-to-seedlings. Our findings suggest that, despite a reduction in diclofop-methyl sensitivity during the ontogeny of mother plants, 2,4-D-mediated induction of likely CYP-450 metabolism is not intergenerationally transmitted and shows detrimental effects on the symbiotic endophyte persistence.

Epichloë Endophyte Enhanced Insect Resistance of Host Grass Leymus Chinensis by Affecting Volatile Organic Compound Emissions

In plant-herbivore interactions, plant volatile organic compounds (VOCs) play an important role in anti-herbivore defense. Grasses and Epichloë endophytes often form defensive mutualistic symbioses. Most Epichloë species produce alkaloids to protect hosts from herbivores, but there is no strong evidence that endophytes can affect the insect resistance of their hosts by altering VOC emissions. In this study, a native dominant grass, sheepgrass (Leymus chinensis), and its herbivore, oriental migratory locust (Locusta migratoria), were used as experimental materials. We studied the effect of endophyte-associated VOC emissions on the insect resistance of L. chinensis. The results showed that endophyte infection enhanced insect resistance of the host, and locusts preferred the odor of endophyte-free (EF) leaves to that of endophyte-infected (EI) leaves. We determined the VOC profile of L. chinensis using gas chromatography-mass spectrometry (GC-MS), and found that endophyte infection decreased the pentadecane (an alkane) emission from uneaten plants, and increased the nonanal (an aldehyde) emission from eaten plants. The olfactory response experiment showed that locusts were attracted by high concentration of pentadecane, while repelled by high concentration of nonanal, indicating that Epichloë endophytes may increase locust resistance of L. chinensis by decreasing pentadecane while increasing nonanal emission. Our results suggest that endophytes can induce VOC-mediated defense in hosts in addition to producing alkaloids, contributing to a better understanding the endophyte-plant-herbivore interactions.

High-affinity iron uptake is required for optimal Epichloë festucae colonization of Lolium perenne and seed transmission

Epichloë festucae uses a siderophore-mediated system to acquire iron, which is important to maintain endophyte-grass symbioses. Here we investigate the roles of the alternative iron acquisition system, reductive iron assimilation (RIA), via disruption of the fetC gene, which encodes a multicopper ferroxidase, either alone (i.e., ΔfetC) or in combination with disruption of the gene sidA, which encodes a siderophore biosynthesis enzyme (i.e., ΔfetC/ΔsidA). The phenotypic characteristics of these mutants were compared to ΔsidA and wild-type (WT) strains during growth under axenic culture conditions (in culture) and in symbiosis with the host grass, perennial ryegrass (in planta). Under iron deficiency, the colony growth rate of ΔfetC was slightly slower than that of WT, while the growth of ΔsidA and ΔfetC/ΔsidA mutants was severely suppressed. Siderophore analyses indicated that ΔfetC mutants hyperaccumulate ferriepichloënin A (FEA) at low iron concentrations and ferricrocin and FEA at higher iron concentrations. When compared to WT, all mutant strains displayed hyperbranching hyphal structures and a reduced ratio of Epichloë DNA to total DNA in planta. Furthermore, host colonization and vertical transmission through infection of the host seed were significantly reduced in the ΔfetC/ΔsidA mutants, confirming that high-affinity iron uptake is a critical process for Epichloë transmission. Thus, RIA and siderophore iron uptake are complementary systems required for the maintenance of iron metabolism, fungal growth, and symbiosis between E. festucae and perennial ryegrass.

Characterization of the Biosynthetic Gene Cluster for the Ribosomally Synthesized Cyclic Peptide Epichloëcyclins in Epichloë festucae

The various grass-induced epichloëcyclins of the Epichloë spp. are ribosomally synthesized and post-translationally modified peptides (RiPPs), produced as small, secreted cyclopeptides from a single gene, gigA. Here, four clustered and coregulated genes (gigA, gigB, gigC, and kexB) with predicted roles in epichloëcyclin production in Epichloë festucae were evaluated through gene disruption. Subsequent chemical analysis indicates that GigB is a DUF3328 domain-containing protein associated with cyclization of epichloëcyclins; GigC is a methyltransferase enzyme responsible for N-methylation of desmethylepichloëcyclins; and KexB is a subtilisin-like enzyme, partly responsible for the propeptide cleavage of epichloëcyclin intermediates. Symbiotic effects on the host phenotype were not observed for gigA, gigC, or kexB mutants, although ΔgigB infection correlated with increased host tiller height and biomass, while only ΔkexB exhibited an effect on endophyte morphology. Disrupting epichloëcyclin biosynthesis showed negligible influence on the biosynthesis of E. festucae-associated alkaloids. Epichloëcyclins may perform other secondary metabolism functions in Epichloë and other fungi.

The fungus Clonostachys epichloë alters the influence of the Epichloë endophyte on seed germination and the biomass of Puccinellia distans grass

The fungal grass endophyte Epichloë typhina (Pers.) Tul. & C. Tul. (Ascomycota: Clavicipitaceae) grows intercellulary in aerial plant parts and reproduces asexually by invading host seeds. In this phase, it enhances seed production and germination, which accelerates its vertical spread. This relationship may be distorted by other seed-born fungi, whose spread is not so directly dependent on the success of the grass. Recently, the fungus Clonostachys epichloë Schroers has been observed on Puccinellia distans (Jacq.) Parl seeds originating from grass clumps infested with stromata, sexual structures of Epichloë typhina that are formed in spring on some host culms, preventing flower and seed development ('choke disease'). C. epichloë shows mycoparasitic activity toward Epichloë stromata by reducing the production of ascospores, which are responsible for horizontal transmission of the fungus. The aim of this study was to investigate the effect of seed-borne C. epichloë on seed germination, as well as the size and weight of P. distans seedlings and to examine whether C. epichloë alters the influence of Epichloë in the early developmental stages of P. distans. The results showed that if C. epichloë acts on seeds together with E. typhina endophytes, the seeds were negatively affected due to the elimination of the positive effect of the latter in terms of both seed germination rate and seedling length. At the same time, C. epichloë increased the proportion of E. typhina-untreated germinated seeds. Additionally, only the joint action of the two fungi, E. typhina and C. epichloë, effectively stimulated seedling dry mass; the presence of E. typhina alone was not sufficient to noticeably affect seedling size. Based on the increasing commonality of C. epichloë on Epichloë stromata, as well as its potential to be used in biocontrol of 'choke disease', we should take a closer look at this fungus, not only in terms of its mycoparasitic ability, but also in terms of its cumulative impact on the whole Epichloë-grass system.

Endophytic Fungi Regulate HbNHX1 Expression and Ion Balance in Hordeum bogdanii under Alkaline Stress

Plants cope with abiotic stress in several ways, including by collaborating with microorganisms. Epichloë, an endophytic fungus, has been shown to improve plant tolerance to extreme external environments. Hordeum bogdanii is a known salt-tolerant plant with the potential to improve alkaline lands. NHX1 plays a key role in the transport of ions in the cell and is overexpressed in plants with increased salt tolerance. However, the expression levels of HbNHX1 in Epichloë endophytic fungal symbionts in H. bogdanii have not been elucidated. We used Hordeum bogdanii (E+) with the endophytic fungi Epichloë bromicola and H. bogdanii (E-) without the endophytic fungi and compared the differences in the ion content and HbNHX1 expression between the shoots and roots of E+ and E- plants under alkaline stress. The absorption capacity of both K⁺ and Na⁺ of H. bogdanii with endophytic fungi was higher than that without endophytic fungi. In the absence of alkaline stress, endophytic fungi significantly reduced the Cl^- content in the host H. bogdanii. Alkaline stress reduced SO₄^2- content in H. bogdanii; however, compared with E-, endophytic fungi increased the content of SO₄^2- in E+ plants. With an increase in the alkaline concentration, the expression of HbNHX1 in the roots of H. bogdanii with endophytic fungus exhibited an upward trend, whereas the expression in the shoots exhibited a downward trend first and then an upward trend. Under 100 mmol·L^-1 mixed alkaline stress, the expression of HbNHX1 in E+ was significantly higher than that in E-, indicating that endophytic fungi could increase the Na⁺ region in vacuoles. The external environment affects the regulation of endophytic fungi in H. bogdanii and that endophytic fungi can play a key role in soil salinization. Therefore, the findings of this study will provide technical support and a theoretical basis for better utilization of endophytic fungi from H. bogdanii in saline land improvement.

Effect of Epichloë gansuensis Endophyte on Seed-Borne Microbes and Seed Metabolites in Achnatherum inebrians

The seed-borne microbiota and seed metabolites of the grass Achnatherum inebrians, either host to Epichloë gansuensis (endophyte infected [EI]) or endophyte free (EF), were investigated. This study determined the microbial communities both within the seed (endophytic) and on the seed surface (epiphytic) and of the protective glumes by using Illumina sequencing technology. Epichloë gansuensis decreased the richness of the seed-borne microbiota except for the epiphytic fungi of glumes and also decreased the diversity of seed-borne microbiota. In addition, metabolites of seeds and glumes were detected using liquid chromatography-mass spectrometry (LC-MS). Unlike with the seeds of EF plants, the presence of E. gansuensis resulted in significant changes in the content of 108 seed and 31 glume metabolites. A total of 319 significant correlations occurred between seed-borne microbiota and seed metabolites; these correlations comprised 163 (147 bacterial and 16 fungal) positive correlations and 156 (136 bacterial and 20 fungal) negative correlations. Meanwhile, there were 42 significant correlations between glume microbiota and metabolites; these correlations comprised 28 positive (10 bacterial and 18 fungal) and 14 negative (9 bacterial and 5 fungal) correlations. The presence of E. gansuensis endophyte altered the communities and diversities of seed-borne microbes and altered the composition and content of seed metabolites, and there were many close and complex relationships between microbes and metabolites. IMPORTANCE The present study was to investigate seed-borne microbiota and seed metabolites in Achnatherum inebrians using high-throughput sequencing and LC-MS technology. Epichloë gansuensis decreased the richness of the seed-borne microbiota except for the epiphytic fungi of glumes and also decreased the diversity of seed-borne microbiota. Compared with endophyte-free plants, the content of 108 seed and 31 glume metabolites of endophyte-infected plants was significantly changed. There were 319 significant correlations between seed-borne microbiota and seed metabolites and 42 significant correlations between glume microbiota and metabolites.

Effect of increasing concentration of ergot alkaloids in the diet of feedlot cattle: performance, welfare, and health parameters

This study was designed to evaluate the effects of feeding increasing dietary concentrations of ergot alkaloids from cereal grains (EA; 0, 0.75, 1.5, 3.0 mg/kg of dietary DM) to feedlot cattle over backgrounding (BG) and finishing (FS) phases on health, welfare, and growth performance. Two hundred and forty commercial steers (280 ± 32 kg BW) were stratified by weight and randomly allocated to 16 pens (15 steers/pen), 4 of which were equipped with the GrowSafe system (1 pen/treatment) to measure individual feed intake. Each pen was randomly assigned to a treatment (n = 4/treatment). Treatments included 1) control (CTRL), no added EA; 2) CTRL + 0.75 mg/kg EA (EA075); 3) CTRL + 1.5 mg/kg EA (EA150); and 4) CTRL + 3.0 mg/kg EA (EA300). Steers were fed barley-based BG diets containing 40% concentrate: 60% silage (DM basis) for 84 d. Steers were then transitioned over 28 d to an FS diet (90% concentrate: 10% silage DM basis) and fed for 119 d before slaughter. The diet fed to EA300 steers was replaced with the CTRL diet after 190 d on feed (DOF), due to EA-induced hyperthermia starting at 165 DOF. In the BG phase, average meal length (P = 0.01) and size (P = 0.02), daily feeding duration (P = 0.03), final body weight (BW; P = 0.03), and total BW gain (P = 0.02) linearly decreased with increasing EA levels, while gain to feed (G:F) responded quadratically (P = 0.04), with EA150 having the poorest value. Increasing concentrations of EA in the diet linearly increased rectal temperature (P < 0.01) throughout the trial. Over the full FS phase, a quadratic response was observed for ADG (P = 0.05), final BW (P = 0.05), total BW gain (P = 0.02), and carcass weight (P = 0.05) with steers fed EA150 having the lowest performance, as EA300 steers were transferred to CTRL diet after 190 DOF. Dressing percentage (P = 0.02) also responded quadratically, with the lowest values observed for EA300. Thus, EA reduced ADG during BG and FS phases, although more prominently in FS, likely due to increased ambient temperatures and high-energy diet in FS triggering hyperthermia. When EA300 steers were transferred to the CTRL diet, compensatory gain promoted higher hot carcass weight (HCW) when compared with steers fed EA150. In conclusion, feeding feedlot steers diets with > 0.75 mg/kg EA caused reductions in performance and welfare concerns, although this breakpoint may be affected by duration of feeding, environmental temperatures, and EA profiles in the feed.

Epichloë endophyte interacts with saline-alkali stress to alter root phosphorus-solubilizing fungal and bacterial communities in tall fescue

Epichloë endophytes, present in aboveground tissues, modify belowground microbial community. This study was conducted to investigate endophyte (Epichloë coenophialum) associated with tall fescue (Lolium arundinaceum) interacted with an altered saline-alkali stress (0, 200 and 400 mmol/l) to affect the belowground phosphorus solubilizing microorganisms including phosphorus solubilizing fungi (PSF) and bacteria (PSB). We found that a significant interaction between E. coenophialum and saline-alkali stress occurred in the diversity and composition of PSF in tall fescue roots. Under saline-alkali stress conditions (200 and 400 mmol/l), E. coenophialum significantly increased the PSF diversity and altered its composition in the roots, decreasing the relative abundance of dominant Cladosporium and increasing the relative abundance of Fusarium. However, there was no significant interaction between E. coenophialum and saline-alkali stress on the PSB diversity in tall fescue roots. E. coenophialum significantly reduced the diversity of PSB in the roots, and E. coenophialum effects did not depend on the saline-alkali stress treatment. Structural equation modeling (SEM) showed that E. coenophialum presence increased soil available phosphorus concentration under saline-alkali stress primarily by affecting PSF diversity instead of the diversity and composition of PSB.

Transcriptomic Analyses Reveals Molecular Regulation of Photosynthesis by Epichloë endophyte in Achnatherum inebrians under Blumeria graminis Infection

Photosynthesis is essential for the growth of all green plants, and the presence of an Epichloë endophyte enhances the photosynthesis of Achnatherum inebrians (drunken horse grass, DHG), including when it is under attack by fungal pathogens. However, few studies have examined the mechanism of the increased photosynthetic activity at the molecular level of A. inebrians when it is under pathogen stress. The present study investigated the effects of the presence of the Epichloë endophyte on the net photosynthetic rate, intercellular CO2 concentration, stomatal conductance, and transpiration rate of DHG plants under a Blumeria graminis infection condition, and we compared the transcriptomes using RNA sequencing. The results showed that the photosynthetic rate of Epichloë endophyte-infected (E+) plants was higher under the B. graminis infection condition, and also without this pathogen, when it was compared with Epichloë endophyte-free (E-) plants. The E+ plants uninfected with B. graminis had 15 up-regulated unigenes that are involved in photosynthesis which were compared to the E- plants that were uninfected with this pathogen. This suggests that the presence of an Epichloë endophyte up-regulates the genes that are involved in the process of photosynthesis.

Effect of Sodium Selenite on the Metabolite Profile of Epichloë sp. Mycelia from Festuca sinensis in Solid Culture

Selenium (Se) is an essential micronutrient with many beneficial effects for humans and other living organisms. Numerous microorganisms in culture systems enrich and convert inorganic selenium to organic selenium. In this study, Epichloë sp. from Festuca sinensis was exposed to increasing Na2SeO3 concentrations (0, 0.1, 0.2, 0.3, and 0.4 mmol/L) in Petri dishes with potato dextrose agar (PDA) for 8 weeks. Epichloë sp. mycelia were immediately collected after mycelial diameters were measured at 4, 5, 6, 7, and 8 weeks of cultivation, respectively. Gas chromatography-mass spectrometer (GC-MS) analysis was performed on different groups of Epichloë sp. mycelia. Different changes were observed as Epichloë sp. was exposed to different selenite conditions and cultivation time. The colony diameter of Epichloë sp. decreased in response to increased selenite concentrations, whereas the inhibitory effects diminished over time. Seventy-two of the 203 identified metabolites did not differ significantly across selenite treatments within the same time point, while 82 compounds did not differ significantly between multiple time points of the same Se concentration. However, the relative levels of 122 metabolites increased the most under selenite conditions. Specifically, between the 4th and 8th weeks, there were increases in 2-keto-isovaleric acid, uridine, and maltose in selenite treatments compared to controls. Selenium increased glutathione levels and exhibited antioxidant properties in weeks 4, 5, and 7. Additionally, we observed that different doses of selenite could promote the production of carbohydrates such as isomaltose, cellobiose, and sucrose; fatty acids such as palmitoleic acid, palmitic acid, and stearic acid; and amino acids such as lysine and tyrosine in Epichloë sp. mycelia. Therefore, Epichloë sp. exposed to selenite stress may benefit from increased levels of some metabolite compounds.

Toxicological Assessment of Pure Lolitrem B and Ryegrass Seed Infected with the AR37 Endophyte Using Mice

Fungal endophytes in perennial ryegrass are essential to New Zealand’s pastoral system due to anti-insect effects. However, endophytes also produce compounds which can be detrimental to animals. Furthermore, as these toxins have been detected in the milk and fat of animals grazing common-toxic (containing lolitrem B) or AR37 endophyte-infected herbage they could enter the human food chain. To assess the risk to human health mice were fed for 90 days with three dose rates of lolitrem B and of AR37. Parameters indicative of animal health were measured as well as chemical, hematological and histological analysis of samples collected on day 90. Since endophyte toxin residues have been detected in milk, they could be transferred from mother to offspring via breast milk. To evaluate possible effects on reproduction two complete generations of mice were fed lolitrem B or AR37. At the dose rates given no adverse effects were observed in either study. The 100-fold safety factor to allow the use of animal data in human health assessments was applied and by considering the concentrations of lolitrem B or AR37 metabolites which could be ingested by a consumer it is highly unlikely that they pose any risk to human health.

Genetic Diversity of Epichloë Endophytes Associated with Brachypodium and Calamagrostis Host Grass Genera including Two New Species

Fungi of genus Epichloë (Ascomycota, Clavicipitaceae) are common endophytic symbionts of Poaceae, including wild and agronomically important cool-season grass species (subfam. Poöideae). Here, we examined the genetic diversity of Epichloë from three European species of Brachypodium (B. sylvaticum, B. pinnatum and B. phoenicoides) and three species of Calamagrostis (C. arundinacea, C. purpurea and C. villosa), using DNA sequences of tubB and tefA genes. In addition, microsatellite markers were obtained from a larger set of isolates from B. sylvaticum sampled across Europe. Based on phylogenetic analyses the isolates from Brachypodium hosts were placed in three different subclades within the Epichloë typhina complex (ETC) but did not strictly group according to host grass species, suggesting that the host does not always select for particular endophyte genotypes. Analysis of microsatellite markers confirmed the presence of genetically distinct lineages of Epichloësylvatica on B. sylvaticum, which appeared to be tied to different modes of reproduction (sexual or asexual). Among isolates from Calamagrostis hosts, two subclades were detected which were placed outside ETC. These endophyte lineages are recognized as distinct species for which we propose the names E. calamagrostidis Leuchtm. & Schardl, sp. nov. and E. ftanensis Leuchtm. & A.D. Treindl, sp. nov. This study extends knowledge of the phylogeny and evolutionary diversification of Epichloë endophytes that are symbionts of wild Brachypodium and Calamagrostis host grasses.

A First Draft of the Core Fungal Microbiome of Schedonorus arundinaceus with and without Its Fungal Mutualist Epichloë coenophiala

Tall fescue (Schedonorus arundinaceus) is a cool-season grass which is commonly infected with the fungal endophyte Epichloë coenophiala. Although the relationship between tall fescue and E. coenophiala is well-studied, less is known about its broader fungal communities. We used next-generation sequencing of the ITS2 region to describe the complete foliar fungal microbiomes in a set of field-grown tall fescue plants over two years, and whether these fungal communities were affected by the presence of Epichloë. We used the Georgia 5 cultivar of tall fescue, grown in the field for six years prior to sampling. Plants were either uninfected with E. coenophiala, or they were infected with one of two E. coenophiala strains: The common toxic strain or the AR542 strain (sold commerically as MaxQ). We observed 3487 amplicon sequence variants (ASVs) across all plants and identified 43 ASVs which may make up a potential core microbiome. Fungal communities did not differ strongly between Epichloë treatments, but did show a great deal of variation between the two years. Plant fitness also changed over time but was not influenced by E. coenophiala infection.

Cuticular Wax Modification by Epichloë Endophyte in Achnatherum inebrians under Different Soil Moisture Availability

The cuticular wax serves as the outermost hydrophobic barrier of plants against nonstomatal water loss and various environmental stresses. An objective of this study was to investigate the contribution of the mutualistic fungal endophyte Epichloë gansuensis to leaf cuticular wax of Achnatherum inebrians under different soil moisture availability. Through a pot experiment and gas chromatography−mass spectrometry (GC−MS) analysis, our results indicated that the hydrocarbons were the dominant components of leaf cuticular wax, and the proportion of alcohols, aldehydes, amines, and ethers varied with the presence or absence of E. gansuensis and different soil moisture availability. Amines and ethers are unique in endophyte-free (EF) A. inebrians plants and endophyte-infected (EI) A. inebrians plants, respectively. By transcriptome analysis, we found a total of 13 differentially expressed genes (DEGs) related to cuticular biosynthesis, including FabG, desB, SSI2, fadD, BiP, KCS, KAR, FAR, and ABCB1. A model is proposed which provides insights for understanding cuticular wax biosynthesis in the association of A. inebrians plants with E. gansuensis. These results may help guide the functional analyses of candidate genes important for improving the protective layer of cuticular wax of endophyte-symbiotic plants.

Telomere-to-Telomere Genome Sequences across a Single Genus Reveal Highly Variable Chromosome Rearrangement Rates but Absolute Stasis of Chromosome Number

Genome rearrangements in filamentous fungi are prevalent but little is known about the modalities of their evolution, in part because few complete genomes are available within a single genus. To address this, we have generated and compared 15 complete telomere-to-telomere genomes across the phylogeny of a single genus of filamentous fungi, Epichloë. We find that the striking distinction between gene-rich and repeat-rich regions previously reported for isolated species is ubiquitous across the Epichloë genus. We built a species phylogeny from single-copy gene orthologs to provide a comparative framing to study chromosome composition and structural change through evolutionary time. All Epichloë genomes have exactly seven nuclear chromosomes, but despite this conserved ploidy, analyses reveal low synteny and substantial rearrangement of gene content across the genus. These rearrangements are highly lineage-dependent, with most occurring over short evolutionary distances, with long periods of structural stasis. Quantification of chromosomal rearrangements shows they are uncorrelated with numbers of substitutions and evolutionary distances, suggesting that different modes of evolution are acting to create nucleotide and chromosome-scale changes.

Interactive Effects of Epichloë Endophytes and Arbuscular Mycorrhizal Fungi on Saline-Alkali Stress Tolerance in Tall Fescue

Epichloë endophytes and arbuscular mycorrhizal fungi (AMFs) are two important symbiotic microorganisms of tall fescue (Lolium arundinaceum). Our research explores the combined effects of endophytes and AMF on saline-alkali stress. The finding revealed that a significant interaction between Epichloë endophytes and AMF, and saline-alkali stress occurred in the growth and physiological parameters of tall fescue. Endophyte infection significantly enhanced tall fescue resistance to saline-alkali stress by increasing shoot and root biomass and nutrient uptake (organic carbon, total nitrogen, and total phosphorus concentration), and accumulating K⁺ while decreasing Na⁺ concentration. Furthermore, the beneficial effect of endophytes was enhanced by the beneficial AMF, Claroideoglomus etunicatum (CE) but was reduced by the detrimental AMF, Funneliformis mosseae (FM). Our findings highlight the importance of interactions among multiple microorganisms for plant performance under saline-alkali stress.

The effect of Epichloë endophyte on phyllosphere microbes and leaf metabolites in Achnatherum inebrians

Upon exposure to the prevailing environment, leaves become increasingly colonized by fungi and bacteria located on the surface (epiphytic) or within (endophytic) the leaves. Many cool season grasses, including Achnatherum inebrians, host a seed-borne, intercellular, mutualistic Epichloë fungal endophyte, the growth of which is synchronized with the host grass. A study utilizing illumina sequencing was used to examine the epiphytic and endophytic microbial communities in Epichloë endophyte-infected and endophyte-free A. inebrians plants growing under hot dry field conditions. The presence of Epichloë endophyte increased the Shannon and decreased Simpson diversity of bacterial and fungal communities. Sphingomonas and Hymenobacter bacteria and Filobasidium and Mycosphaerella fungi were growing largely epiphytically, whereas Methylobacterium, Escherichia-Shigella, and the fungus Blumeria were mostly found within leaves with the location of colonization influenced by the Epichloë endophyte. In addition, leaf metabolites in Epichloë-infected and Epichloë-free leaves were examined using LC/MS. Epichloë was significantly correlated with 132 metabolites.

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Epichloë altered the composition and diversity of phyllosphere microbial communities

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414 detected metabolites were annotated, of which the 132 differential metabolites

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There were 229 significant correlations between metabolites and microbial phyla

Effect of Fungal Endophyte Epichloë bromicola Infection on Cd Tolerance in Wild Barley (Hordeum brevisubulatum)

Hydroponic Hordeum brevisubulatum (wild barley) was used as material in the greenhouse to study the effects of endophyte infection on plant growth, Cd absorption and transport, subcellular distribution, and Cd chemical forms under CdCl2 stress. Endophytic fungi respond positively to chlorophyll content and photosynthetic efficiency under Cd stress. The order of Cd absorption in different parts of the plant was: roots > stems > leaves. Endophyte infection increased the plant’s absorption and transport of Cd while causing a significant difference in the stem, which was associated with the distribution density of endophyte hyphae. The proportion of organelle Cd in endophyte-infected wild barley was significantly higher, which facilitated more Cd transport to aboveground. Cd stress showed a slight effect on the chemical forms of Cd in leaves. The proportion of phosphate, oxalate, and residual Cd increased in the stem. Cd existed in the form of inorganic salt, organic acid, pectin, and protein in roots. Endophyte infection reduced the Cd content of the more toxic chemical forms to protect the normal progress of plant physiological functions. Therefore, the isolation of cell walls and vacuoles is a key mechanism for plant Cd tolerance and detoxification. As endophyte infections have more ability to absorb Cd in plants, H. brevisubulatum−Epichloë bromicola symbionts can improve heavy metal contaminated soil and water.

Integrative interactomics applied to bovine fescue toxicosis

Bovine fescue toxicosis (FT) is caused by grazing ergot alkaloid-producing endophyte (Epichloë coenophiala)-infected tall fescue. Endophyte’s effects on the animal’s microbiota and metabolism were investigated recently, but its effects in planta or on the plant–animal interactions have not been considered. We examined multi-compartment microbiota–metabolome perturbations using multi-‘omics (16S and ITS2 sequencing, plus untargeted metabolomics) in Angus steers grazing non-toxic (Max-Q) or toxic (E+) tall fescue for 28 days and in E+ plants. E+ altered the plant/animal microbiota, decreasing most ruminal fungi, with mixed effects on rumen bacteria and fecal microbiota. Metabolic perturbations occurred in all matrices, with some plant-animal overlap (e.g., Vitamin B6 metabolism). Integrative interactomics revealed unique E+ network constituents. Only E+ had ruminal solids OTUs within the network and fecal fungal OTUs in E+ had unique taxa (e.g., Anaeromyces). Three E+-unique urinary metabolites that could be potential biomarkers of FT and targeted therapeutically were identified.

Bermudagrass Cultivars with Different Tolerance to Nematode Damage Are Characterized by Distinct Fungal but Similar Bacterial and Archaeal Microbiomes

Turfgrass landscapes have expanded rapidly in recent decades and are a major vegetation type in urbanizing ecosystems. While turfgrass areas provide numerous ecosystem services in urban environments, ecological side effects from intensive management are raising concerns regarding their sustainability. One potentially promising approach to ameliorate the ecological impact and decrease the use of agricultural chemicals is to take advantage of naturally evolved turfgrass-associated microbes by harnessing beneficial services provided by microbiomes. Unfortunately, especially compared to agricultural crops, the microbiomes of turfgrasses are not well understood. Here, we analyzed microbial communities inhabiting the leaf and root endospheres as well as soil in two bermudagrass cultivars, ‘Latitude 36’ and ‘TifTuf’, which exhibit distinct tolerance to nematode damage, with the goal of identifying potential differences in the microbiomes that might explain their distinct phenotype. We used 16S rRNA gene V4 and ITS2 amplicon sequencing to characterize the microbiomes in combination with microbial cultivation efforts to identify potentially beneficial endophytic fungi and bacteria. Our results show that Latitude 36 and TifTuf showed markedly different fungal microbiomes, each harboring unique taxa from Ascomycota and Glomeromycota, respectively. In contrast, less difference was observed from bacterial and archaeal microbiomes, which were dominated by Bacteroidetes and Thaumarchaeota, respectively. The TifTuf microbiomes exhibited lower microbial diversity compared to Latitude 36. Many sequences could not be classified to a higher taxonomic resolution, indicating a relatively high abundance of hitherto undescribed microorganisms. Our results provide new insights into the structure and composition of turfgrass microbiomes but also raise important questions regarding the functional attributes of key taxa.

Epichloë scottii sp. nov., a new endophyte isolated from Melica uniflora is the missing ancestor of Epichloë disjuncta

Here we describe a new, haploid and stroma forming species within the genus Epichloë, as Epichloë scottii sp. nov. The fungus was isolated from Melica uniflora growing in Bad Harzburg, Germany. Phylogenetic reconstruction using a combined dataset of the tubB and tefA genes strongly support that E. scottii is a distinct species and the so far unknown ancestor species of the hybrid E. disjuncta. A distribution analysis showed a high infection rate in close vicinity of the initial sampling site and only two more spots with low infection rates. Genetic variations in key genes required for alkaloid production suggested that E. scottii sp. nov. might not be capable of producing any of the major alkaloids including ergot alkaloid, loline, indole-diterpene and peramine. All isolates and individuals found in the distribution analysis were identified as mating-type B explaining the lack of mature stromata during this study. We further release a telomere-to-telomere de novo assembly of all seven chromosomes and the mitogenome of E. scottii sp. nov.

Endophytic fungi and drought tolerance: ecophysiological adjustment in shoot and root of an annual mesophytic host grass

Epichloid endophytic fungi, vertically transmitted symbionts of grasses, can increase plant tolerance to biotic and abiotic stress. Our aim was to identify ecophysiological mechanisms by which the endophyte Epichloë occultans confers drought tolerance to the annual grass Lolium multiflorum Lam. Endophyte-associated or endophyte-free plants were either well-watered or subjected to water deficit. We evaluated plant biomass, root length and nitrogen concentration, and we assessed intrinsic water use efficiency (iWUE) and its components net photosynthesis and stomatal conductance, by carbon and oxygen isotope analysis of shoot tissues. Endophyte-free plants produced more biomass than endophyte-associated ones at field capacity, while water deficit strongly reduced endophyte-free plants biomass. As a result, both types of plants produced similar biomass under water restriction. Based on oxygen isotope composition of plant cellulose, stomatal conductance decreased with water deficit in both endophyte-associated and endophyte-free plants. Meanwhile, carbon isotope composition indicated that iWUE increased with water deficit only in endophyte-associated plants. Thus, the isotope data indicated that net photosynthesis decreased more strongly in endophyte-free plants under water deficit. Additionally, endophyte presence reduced root length but increased its hydraulic conductivity. In conclusion, endophytic fungi confer drought tolerance to the host grass by adjusting shoot and root physiology.

Endophyte Infected Tall Fescue: Plant Symbiosis to Animal Toxicosis

Endophyte-infected fescue is a major cool season forage used for livestock production in the United States and through other areas of the world. A unique aspect of this forage resource is the symbiotic relationship with an endophytic fungus (Epichloë coenophiala) that has detrimental impact on herbivores due to toxic ergot alkaloids. Research over the past 50 years has unveiled details regarding this symbiotic relationship. This review focuses on the origin of tall fescue in the United States and the consequences of its wide-spread utilization as a livestock forage, along with the discovery and toxicodynamics of ergot alkaloids produced by E. coenophiala. The majority of past ergot alkaloid research has focused on observing phenotypic changes that occur in livestock affected by ergot alkaloids, but recent investigation of the metabolome, transcriptome, and proteome have shown that fescue toxicity-related illnesses are much more complex than previous research suggests.

A Metabolomic Study of Epichloë Endophytes for Screening Antifungal Metabolites

Epichloë endophytes, fungal endosymbionts of Pooidae grasses, are commonly utilized in forage and turf industries because they produce beneficial metabolites that enhance resistance against environmental stressors such as insect feeding and disease caused by phytopathogen infection. In pastoral agriculture, phytopathogenic diseases impact both pasture quality and animal production. Recently, bioactive endophyte strains have been reported to secrete compounds that significantly inhibit the growth of phytopathogenic fungi in vitro. A screen of previously described Epichloë-produced antifeedant and toxic alkaloids determined that the antifungal bioactivity observed is not due to the production of these known metabolites, and so there is a need for methods to identify new bioactive metabolites. The process described here is applicable more generally for the identification of antifungals in new endophytes. This study aims to characterize the fungicidal potential of novel, ‘animal friendly’ Epichloë endophyte strains NEA12 and NEA23 that exhibit strong antifungal activity using an in vitro assay. Bioassay-guided fractionation, followed by metabolite analysis, identified 61 metabolites that, either singly or in combination, are responsible for the observed bioactivity. Analysis of the perennial ryegrass-endophyte symbiota confirmed that NEA12 and NEA23 produce the prospective antifungal metabolites in symbiotic association and thus are candidates for compounds that promote disease resistance in planta. The “known unknown” suite of antifungal metabolites identified in this study are potential biomarkers for the selection of strains that enhance pasture and turf production through better disease control.

Chromosome-level genomes provide insights into genome evolution, organization and size in Epichloe fungi

Epichloe fungi are endophytes of cool season grasses, both wild species and commercial cultivars, where they may exhibit mutualistic or pathogenic lifestyles. The Epichloe-grass symbiosis is of great interest to agricultural research for the fungal bioprotective properties conferred to host grasses but also serves as an ideal system to study the evolution of fungal plant-pathogens in natural environments. Here, we assembled and annotated gapless chromosome-level genomes of two pathogenic Epichloe sibling species. Both genomes have a bipartite genome organization, with blocks of highly syntenic gene-rich regions separated by blocks of AT-rich DNA. The AT-rich regions show an extensive signature of RIP (repeat-induced point mutation) and the expansion of this compartment accounts for the large difference in genome size between the two species. This study reveals how the rapid evolution of repeat structure can drive divergence between closely related taxa and highlights the evolutionary role of dynamic compartments in fungal genomes.

Seed-borne fungal endophytes constrain reproductive success of host plants under ozone pollution

Tropospheric ozone is among the global change factors that pose a threat to plants and microorganisms. Symbiotic microorganisms can assist plants to cope with stress, but their role in the tolerance of plants to ozone is poorly understood. Here, we subjected endophyte-symbiotic and non-symbiotic plants of Lolium multiflorum, an annual species widely distributed in temperate grasslands, to high and low (i.e., charcoal-filtered air) ozone levels at vegetative and reproductive phases. Exposure to high ozone reduced leaf photochemical efficiency and greenness in both symbiotic and non-symbiotic plants. However, ozone-induced oxidative damage at biochemical level (i.e., lipid peroxidation) was mostly detected in symbiotic plants. Ozone exposure at the vegetative phase did not affect the reproductive investment in seeds, indicating full recovery from stress. Ozone exposure at the reproductive phase reduced biomass and seed production only in symbiotic plants indicating a symbiont-associated cost. At low ozone, endophyte-symbiotic plants showed a steeper slope in the relationship between seed number and seed weight (i.e., a number-weight trade-off) compared to non-symbiotic plants. However, when plants were treated at the reproductive phase, ozone increased the imbalance between seed number and seed weight in both endophyte-symbiotic and non-symbiotic plants. Plants with endophytes at the reproductive stage produced fewer seeds, which were not compensated by increased seed weight. Thus, fungal mycelium growing within ovaries or ozone-induced antioxidant systems may result in costs that finally depress the fitness of plants. Despite ozone pollution could destabilize plant-endophyte mutualisms and render them dysfunctional, other endophyte-mediated benefits (e.g., resistance to herbivory, tolerance to drought) could over-compensate these losses and explain the high incidence of the symbiosis in nature.

Interactive Effects of Epichloë Endophyte, Dormancy-Breaking Treatments and Geographic Origin on Seed Germination of Achnatherum inebrians

Background: the cool-season grass Achnatherum inebrians (drunken horse grass) is an important species in the northwest grasslands of China. This grass engages in a symbiotic relationship with Epichloë endophytes, which affect host plants by increasing growth, repelling herbivores, and increasing tolerance to stressful environments. Methods: in this work, we evaluated the interaction effects of the endophyte on various dormancy-breaking treatments on A. inebrians seeds from six different locations. We used both endophyte-infected plants and noninfected plants and applied four dormancy-breaking methods to test germination. Results: our results showed that the germination rate of endophytic Achnatherum inebrians seeds from the Xiahe site (with highest altitude) was significantly higher than that from other sites when water soaking was applied (p < 0.05). Endophytic seeds had a greater germination rate, and soluble sugar, indole acetic acid (IAA), and gibberellin (GA) contents, under any condition. There was a significant interaction among the method, endophyte status, and origin regarding germination (p < 0.001); particularly, the effects of warm water soaking and endophyte infection on the germination of seeds from the Xiahe site was significant (p < 0.05). Conclusions: the infection of Epichloë endophyte is able to increase the content of soluble sugar, IAA, and GA, and stimulate the seed germination of A. inebrians.

Antagonism to Plant Pathogens by Epichloë Fungal Endophytes-A Review

Epichloë is a genus of filamentous fungal endophytes that has co-evolved with cool-season grasses with which they form long-term, symbiotic associations. The most agriculturally important associations for pasture persistence for grazing livestock are those between asexual vertically transmitted Epichloë strains and the pasture species, perennial ryegrass, and tall fescue. The fungus confers additional traits to their host grasses including invertebrate pest deterrence and drought tolerance. Selected strains of these mutualistic endophytes have been developed into highly efficacious biocontrol products and are widely utilized within the Americas, Australia, and New Zealand for pasture persistence. Less publicized is the antagonism Epichloë endophytes display towards multiple species of saprophytic and pathogenic microbes. This opinion piece will review the current literature on antimicrobial properties exhibited by this genus of endophyte and discuss the reasons why this trait has historically remained a research curiosity rather than a trait of commercial significance.

Effects of Epichloë sinensis Endophyte and Host Ecotype on Physiology of Festuca sinensis under Different Soil Moisture Conditions

This study explored the effects of the Epichloë sinensis endophyte on growth, photosynthesis, ionic content (K+ and Ca2+), phytohormones (abscisic acid-ABA, cytokinin-CTK, indolE-3-acetic acid-IAA, and gibberellin-GA), and elements-C, N, P (in the shoot and root) in two ecotypes of Festuca sinensis (ecotypes 111 and 141) under different soil water conditions (35% and 65% relative saturation moisture content (RSMC)). The results showed that 35% RSMC inhibited the plants' growth, and compared with 65% RSMC, there was a significant (p < 0.05) decrease in the growth and photosynthesis indices, the contents of CTK and GA, Ca2+ concentration, and the contents of C, N, and P (in both the aboveground and underground parts) under 35% RSMC. E. sinensis had beneficial effects on host growth and stress tolerance. Under both 35% and 65% RSMC, the presence of E. sinensis significantly (p < 0.05) increased host plant height, tiller number, root length, root volume, shoot dry weight, chlorophyll content, and the rate of photosynthesis of both ecotypes. Furthermore, the shoot C, N, and P contents in plants infected with E. sinensis (E+) from the two ecotypes, under both conditions of RSMC, were significantly (p < 0.05) higher than those in corresponding plants that were not infected with E. sinensis (E-). Under 35% RSMC, the contents of ABA, K+, Ca2+, and root P contents in E+ plants were significantly (p < 0.05) higher than those in corresponding E- plants in both ecotypes. However, under 65% RSMC, root C, N, and P contents in E+ plants of ecotype 111 and 141 were significantly (p < 0.05) higher than those in corresponding E- plants. In addition, the host ecotype also had effects on host growth and stress tolerance; the growth and photosynthetic indices of ecotype 141 were significantly (p < 0.05) higher than those of ecotype 111 under 35% RSMC, which suggested that ecotype 141 is more competitive than ecotype 111 under water deficiency conditions. These findings suggest that the endophyte improved the host plant resistance to water deficiency by maintaining the growth of the plant, improving photosynthesis, accumulating K+ and Ca2+, promoting nutrient absorption, and adjusting the metabolism of plant hormones.

Transcriptome Analysis Revealed Plant Hormone Biosynthesis and Response Pathway Modification by Epichloëgansuensis in Achnatheruminebrians under Different Soil Moisture Availability

The present study was designed to explore the effects of the endophyte Epichloë gansuensis on gene expression related to plant hormone biosynthesis and response pathways and the content of salicylic acid (SA) and jasmonic acid (JA) hormones of Achnatherum inebrians, under different moisture conditions. Through a pot experiment and transcriptome analysis, we found a total of 51 differentially expressed genes (DEGs) related to hormone biosynthesis and response pathways, including 12 auxin related genes, 8 cytokinin (CTK) related genes, 3 gibberellin (GA) related genes, 7 abscisic acid (ABA) related genes, 7 ethylene (ET) related genes, 12 JA related genes and 4 SA related genes. Furthermore, key genes of JA and SA biosynthesis and response pathways, such as LOX2S, AOS, OPR, ACX, JMT, JAZ, PAL, NPR1, TGA and PR-1, showed different degrees of upregulation or downregulation. Under 60% soil moisture content, the JA content of endophyte-free (EF) A. inebrians was significantly (p < 0.05) higher than that of endophyte-infected (EI) A. inebrians. Under 30% and 60% soil moisture content, the SA content of EF A. inebrians was significantly (p < 0.05) higher than that of EI A. inebrians. SA content of EI A. inebrians under 30% and 60% soil moisture content was significantly (p < 0.05) higher than that under 15% soil moisture content. With both EI and EF plants, the SA and JA levels, respectively, are very similar at 15% soil moisture content. This study has revealed that E. gansuensis differentially activated plant hormone synthesis and signal transduction pathways of A. inebrians plants under different soil moisture availability.

Getting ready for the ozone battle: Vertically transmitted fungal endophytes have transgenerational positive effects in plants

Ground-level ozone is a global air pollutant with high toxicity and represents a threat to plants and microorganisms. Although beneficial microorganisms can improve host performance, their role in connecting environmentally induced maternal plant phenotypes to progeny (transgenerational effects [TGE]) is unknown. We evaluated fungal endophyte-mediated consequences of maternal plant exposure to ozone on performance of the progeny under contrasting scenarios of the same factor (high and low) at two stages: seedling and young plant. With no variation in biomass, maternal ozone-induced oxidative damage in the progeny that was lower in endophyte-symbiotic plants. This correlated with an endophyte-mediated higher concentration of proline, a defence compound associated with stress control. Interestingly, ozone-induced TGE was not associated with reductions in plant survival. On the contrary, there was an overall positive effect on seedling survival in the presence of endophytes. The positive effect of maternal ozone increasing young plant survival was irrespective of symbiosis and only expressed under high ozone condition. Our study shows that hereditary microorganisms can modulate the capacity of plants to transgenerationally adjust progeny phenotype to atmospheric change.

The Role of Fungal Microbiome Components on the Adaptation to Salinity of Festuca rubra subsp. pruinosa

Festuca rubra subsp. pruinosa is a perennial grass that inhabits sea cliffs, a habitat where salinity and low nutrient availability occur. These plants have a rich fungal microbiome, and particularly common are their associations with Epichloë festucae in aboveground tissues and with Fusarium oxysporum and Periconia macrospinosa in roots. In this study, we hypothesized that these fungi could affect the performance of F. rubra plants under salinity, being important complements for plant habitat adaptation. Two lines of F. rubra, each one consisting of Epichloë-infected and Epichloë-free clones, were inoculated with the root endophytes (F. oxysporum and P. macrospinosa) and subjected to a salinity treatment. Under salinity, plants symbiotic with Epichloë had lower Na+ content than non-symbiotic plants, but this effect was not translated into plant growth. P. macrospinosa promoted leaf and root growth in the presence and absence of salinity, and F. oxysporum promoted leaf and root growth in the presence and absence of salinity, plus a decrease in leaf Na+ content under salinity. The growth responses could be due to functions related to improved nutrient acquisition, while the reduction of Na+ content might be associated with salinity tolerance and plant survival in the long term. Each of these three components of the F. rubra core mycobiome contributed with different functions, which are beneficial and complementary for plant adaptation to its habitat in sea cliffs. Although our results do not support an obvious role of Epichloë itself in FRP salt tolerance, there is evidence that Epichloë can interact with root endophytes, affecting host plant performance.

Does Epichloë Endophyte Enhance Host Tolerance to Root Hemiparasite?

Epichloë endophytes have been shown to be mutualistic symbionts of cool-season grasses under most environmental conditions. Although pairwise interactions between hemiparasites and their hosts are heavily affected by host-associated symbiotic microorganisms, little attention has been paid to the effects of microbe-plant interactions, particularly endophytic symbiosis, in studies examining the effects of parasitic plants on host performance. In this study, we performed a greenhouse experiment to examine the effects of hereditary Epichloë endophyte symbiosis on the growth of two host grasses (Stipa purpurea and Elymus tangutorum) in the presence or absence of a facultative root hemiparasite (Pedicularis kansuensis Maxim). We observed parasitism of both hosts by P. kansuensis: when grown with a host plant, the hemiparasite decreased the performance of the host while improving its own biomass and survival rate of the hemiparasite. Parasitized endophyte-infected S. purpurea plants had higher biomass, tillers, root:shoot ratio, and photosynthetic parameters and a lower number of functional haustoria than the endophyte-free S. purpurea conspecifics. By contrast, parasitized endophyte-infected E. tangutorum had a lower biomass, root:shoot ratio, and photosynthetic parameters and a higher number of haustoria and functional haustoria than their endophyte-free counterparts. Our results reveal that the interactions between the endophytes and the host grasses are context dependent and that plant-plant interactions can strongly affect their mutualistic interactions. Endophytes originating from S. purpurea alleviate the host biomass reduction by P. kansuensis and growth depression in the hemiparasite. These findings shed new light on using grass-endophyte symbionts as biocontrol methods for the effective and sustainable management of this weedy hemiparasite.

Disruption of Traditional Grazing and Fire Regimes Shape the Fungal Endophyte Assemblages of the Tall-Grass Brachypodium rupestre

The plant microbiome is likely to play a key role in the resilience of communities to the global climate change. This research analyses the culturable fungal mycobiota of Brachypodium rupestre across a sharp gradient of disturbance caused by an intense, anthropogenic fire regime. This factor has dramatic consequences for the community composition and diversity of high-altitude grasslands in the Pyrenees. Plants were sampled at six sites, and the fungal assemblages of shoots, rhizomes, and roots were characterized by culture-dependent techniques. Compared to other co-occurring grasses, B. rupestre hosted a poorer mycobiome which consisted of many rare species and a few core species that differed between aerial and belowground tissues. Recurrent burnings did not affect the diversity of the endophyte assemblages, but the percentages of infection of two core species -Omnidemptus graminis and Lachnum sp. -increased significantly. The patterns observed might be explained by (1) the capacity to survive in belowground tissues during winter and rapidly spread to the shoots when the grass starts its spring growth (O. graminis), and (2) the location in belowground tissues and its resistance to stress (Lachnum sp.). Future work should address whether the enhanced taxa have a role in the expansive success of B. rupestre in these anthropized environments.

Effects of nutrient addition on endophyte-associated grass invasion in a long-term, old-field community experiment

Strictly vertically transmitted (hereditary) Epichloë spp. fungal endophytes are symbionts with cool-season pooid host grasses. Such endophytes may increase host invasiveness in the non-native, introduced ranges. However, because costs and benefits for the host can vary with the growing conditions, the endophyte may become locally or temporally extinct when costs outweigh benefits. Our long-term field experiment involved the introduction of seven Schedonorus pratensis (meadow fescue) cultivars hosting Epichloë uncinata endophyte, which represent host-grass populations differing in genetic backgrounds and Epichloë infection frequencies, to an unmanaged old field. In the first 6 years, the host grasses persisted but did not become invasive in the plant community, regardless of their endophyte infection frequency. Subsequently, we hypothesized that increasing nutrient availability would decrease endophyte costs and thus increase the host's success and abundance. We fertilized half of the plots for four additional years and re-examined S. pratensis invasiveness. We predicted that increased nutrient availability would increase S. pratensis abundance and E. uncinata frequency and concentration, as well as decrease plant community diversity, relative to unfertilized plots. Fertilization increased endophyte concentrations in three low-endophyte host populations. However, E. uncinata did not enable S. pratensis populations to achieve high abundance or to reduce plant community diversity in the old field, with or without fertilization. Thus, nutrient availabililty and host invasiveness appear to be decoupled in this study system.

Global Changes in Asexual Epichloë Transcriptomes during the Early Stages, from Seed to Seedling, of Symbiotum Establishment

Asexual Epichloë fungi are strictly seed-transmitted endophytic symbionts of cool-season grasses and spend their entire life cycle within the host plant. Endophyte infection can confer protective benefits to its host through the production of bioprotective compounds. Inversely, plants provide nourishment and shelter to the resident endophyte in return. Current understanding of the changes in global gene expression of asexual Epichloë endophytes during the early stages of host-endophyte symbiotum is limited. A time-course study using a deep RNA-sequencing approach was performed at six stages of germination, using seeds infected with one of three endophyte strains belonging to different representative taxa. Analysis of the most abundantly expressed endophyte genes identified that most were predicted to have a role in stress and defence responses. The number of differentially expressed genes observed at early time points was greater than those detected at later time points, suggesting an active transcriptional reprogramming of endophytes at the onset of seed germination. Gene ontology enrichment analysis revealed dynamic changes in global gene expression consistent with the developmental processes of symbiotic relationships. Expression of pathway genes for biosynthesis of key secondary metabolites was studied comprehensively and fuzzy clustering identified some unique expression patterns. Furthermore, comparisons of the transcriptomes from three endophyte strains in planta identified genes unique to each strain, including genes predicted to be associated with secondary metabolism. Findings from this study highlight the importance of better understanding the unique properties of individual endophyte strains and will serve as an excellent resource for future studies of host-endophyte interactions.

The Response of the Associations of Grass and Epichloë Endophytes to the Increased Content of Heavy Metals in the Soil

The rapid development of civilization increases the area of land exposed to the accumulation of toxic compounds, including heavy metals, both in water and soil. Endophytic fungi associated with many species of grasses are related to the resistance of plants to biotic and abiotic stresses, which include heavy metals. This paper reviews different aspects of symbiotic interactions between grass species and fungal endophytes from the genera Epichloë with special attention paid to the elevated concentration of heavy metals in growing substrates. The evidence shows the high resistance variation of plant endophyte symbiosis on the heavy metals in soil outcome. The fungal endophytes confer high heavy metal tolerance, which is the key feature in its practical application with their host plants, i.e., grasses in phytoremediation.

Comparison of Plant Metabolites in Root Exudates of Lolium perenne Infected with Different Strains of the Fungal Endophyte Epichloë festucae var. lolii

Lolium perenne infected with the fungal endophyte Epichloë festucae var. lolii have specific, endophyte strain-dependent, chemical phenotypes in their above-ground tissues. Differences in these chemical phenotypes have been largely associated with classes of fungal-derived alkaloids which protect the plant against many insect pests. However, the use of new methodologies, such as various omic techniques, has demonstrated that many other chemical changes occur in both primary and secondary metabolites. Few studies have investigated changes in plant metabolites exiting the plant in the form of root exudates. As root exudates play an essential role in the acquisition of nutrients, microbial associations, and defense in the below-ground environment, it is of interest to understand how plant root exudate chemistry is influenced by the presence of strains of a fungal endophyte. In this study, we tested the influence of four strains of E. festucae var. lolii (E+ (also known as Lp19), AR1, AR37, NEA2), and uninfected controls (E-), on L. perenne growth and the composition of root exudate metabolites. Root exudates present in the hydroponic water were assessed by untargeted metabolomics using Accurate-Mass Quadrupole Time-of-Flight (Q-TOF) liquid chromatography-mass spectrometry (LC-MS). The NEA2 endophyte strain resulted in the greatest plant biomass and the lowest endophyte concentration. We found 84 metabolites that were differentially expressed in at least one of the endophyte treatments compared to E- plants. Two compounds were strongly associated with one endophyte treatment, one in AR37 (m/z 135.0546 RT 1.17), and one in E+ (m/z 517.1987 RT 9.26). These results provide evidence for important changes in L. perenne physiology in the presence of different fungal endophyte strains. Further research should aim to connect changes in root exudate chemical composition with soil ecosystem processes.

The Impact of Alkaloid-Producing Epichloë Endophyte on Forage Ryegrass Breeding: A New Zealand Perspective

For 30 years, forage ryegrass breeding has known that the germplasm may contain a maternally inherited symbiotic Epichloë endophyte. These endophytes produce a suite of secondary alkaloid compounds, dependent upon strain. Many produce ergot and other alkaloids, which are associated with both insect deterrence and livestock health issues. The levels of alkaloids and other endophyte characteristics are influenced by strain, host germplasm, and environmental conditions. Some strains in the right host germplasm can confer an advantage over biotic and abiotic stressors, thus acting as a maternally inherited desirable ‘trait’. Through seed production, these mutualistic endophytes do not transmit into 100% of the crop seed and are less vigorous than the grass seed itself. This causes stability and longevity issues for seed production and storage should the ‘trait’ be desired in the germplasm. This makes understanding the precise nature of the relationship vitally important to the plant breeder. These Epichloë endophytes cannot be ‘bred’ in the conventional sense, as they are asexual. Instead, the breeder may modulate endophyte characteristics through selection of host germplasm, a sort of breeding by proxy. This article explores, from a forage seed company perspective, the issues that endophyte characteristics and breeding them by proxy have on ryegrass breeding, and outlines the methods used to assess the ‘trait’, and the application of these through the breeding, production, and deployment processes. Finally, this article investigates opportunities for enhancing the utilisation of alkaloid-producing endophytes within pastures, with a focus on balancing alkaloid levels to further enhance pest deterrence and improving livestock outcomes.

Synergism between calcium nitrate applications and fungal endophytes to increase sugar concentration in Festuca sinensis under cold stress

Epichloë endophytes have been shown to increase tolerance to biotic and abiotic stresses in many cool-season grasses. We investigated the impact of endophyte infection of Festuca sinensis, on root metabolic activity, photosynthetic pigments, leaf relative water content (RWC) and soluble carbohydrates in a field experiment carried out during chilling and irrigation with Ca(NO₃)₂. A highly significant (P < 0.001) correlation for Epichloë endophytes was observed for root metabolic activity. Ca(NO₃)₂ affected very significantly root metabolic activity and total chlorophyll (P < 0.001). Low temperature led to highly significant (P < 0.001) reductions in root metabolic activity, RWC, total chlorophyll, chlorophyll a/b ratio, and carotenoid contents. In addition, the fructose concentrations of shoots were greater on the 14th day than on the 28th day and before treatment, whilst the glucose concentration of roots was much higher on the 28th day than before and after 14 days treatment. Moreover, our results indicated that the addition of calcium nitrate contributed to higher levels of total chlorophylls, soluble sugars, sucrose, fructose or glucose in the shoots and roots in both E+ and E- plants during long periods of chilling. These results suggest that Epichloë endophyte infection and/or exogenous calcium nitrate can confer better tolerance to cold stress.

A Systematic Review on the Effects of Epichloë Fungal Endophytes on Drought Tolerance in Cool-Season Grasses

Symptomless fungal endophytes in the genus Epichloë are repeatedly mentioned to increase tolerance of cool-season grasses to a wide range of environmental stress factors, mainly drought. However, the generality of this idea is challenged because (i) most studies have been conducted on two economically important forage grasses {tall fescue [Festuca arundinacea (Schreb.) Dumort] and perennial ryegrass (Lolium perenne L.)}, (ii) endophyte-mediated mechanisms and effects on plant responses to drought have shown to be highly variable across species, and that (iii) symbiosis incidence in plant populations occurring in extremely arid environments is usually low. We question this idea by reviewing the existing information about Epichloë fungal endophyte effects on drought tolerance in cool-season grasses. We combined standard review, vote counting, and calculation of effect sizes to synthesize the literature, identify information gaps, and guide future research. The total number of studies was higher for domesticated than for wild species, a ratio that was balanced when papers with data quality for effect size calculus were considered. After the drought, endophyte-infected plants accumulated more aboveground and belowground biomass than non-infected counterparts, while no effect on tillering was observed. However, these effects remained significant for wild (even on tillering) but not for domesticated species. Interestingly, despite the continuous effort in determining physiological mechanisms behind the endophyte effects, no studies evaluated plant fecundity as a measure of ecological fitness nor vital rates (such as survival) as to escalate individual-level variables to population. Together with the high variability in results, our work shows that generalizing a positive effect of fungal endophytes in plant tolerance to drought may be misleading. Future studies combining field surveys with manipulative experiments would allow us to unravel the role of fungal endophytes in plant adaptation by considering the evolutionary history of species and populations to the different ecological contexts.