Fungal endophytes of grasses

An insight into endophytic antimicrobial compounds: an updated analysis

Resistance in micro-organisms against antimicrobial compounds is an emerging phenomenon in the modern era as compared to the traditional world which brings new challenges to discover novel antimicrobial compounds from different available sources, such as, medicinal plants, various micro-organisms, like, bacteria, fungi, algae, actinomycetes, and endophytes. Endophytes reside inside the plants without exerting any harmful impact on the host plant along with providing ample of benefits. In addition, they are capable of producing diverse antimicrobial compounds similar to their host, allowing them to serve as useful micro-organism for a range of therapeutic purposes. In recent years, a large number of studies on the antimicrobial properties of endophytic fungi have been carried out globally. These antimicrobials have been used to treat various bacterial, fungal, and viral infections in humans. In this review, the potential of fungal endophytes to produce diverse antimicrobial compounds along with their various benefits to their host have been focused on. In addition, classification systems of endophytic fungi as well as the need for antimicrobial production with genetic involvement and some of the vital novel antimicrobial compounds of endophytic origin can further be utilized in the pharmaceutical industries for various formulations along with the role of nanoparticles as antimicrobial agents have been highlighted.

Identification of Three Epichloë Endophytes from Hordeum bogdanii Wilensky in China

Cool season grasses often form reciprocal symbiotic relationships with endophytic fungal species in genus Epichloë. In this study, we characterized three fungal endophytes isolated from the grass Hordeum bogdanii native to northwest China. Based on morphological characteristics and phylogenetic analyses of tefA, tubB, and actG sequences, we identified them as Epichloë sp. HboTG-2 (H. bogdanii Taxonomic Group 2: E. bromicola × E. typhina). Alkaloid synthesis related genes analysis showed that Epichloë sp. HboTG-2 may have the ability only to produce peramine which is toxic to insects but not to animals. In the process of this study, we did not observe sexual structures or epiphyllous growth on leaves of infected plants.

Effects of endophytic fungi on the secondary metabolites of Hordeum bogdanii under alkaline stress

It is currently unclear whether the mechanism of endophytic fungi improving the alkali tolerance of Hordeum bogdanii affects secondary metabolites. Unveiling this knowledge is crucial for understanding the tolerance mechanism of H. bogdanii to alkaline stress. The aim of this study was to investigate how endophytic fungi affect secondary metabolites of H. bogdanii under alkaline stress at different concentrations. Endophyte-infected (E +) and endophyte-free (E−) individuals of H. bogdanii were used as materials in this study. The method of indoor vermiculite aseptic planting was adopted. After mixed alkali stress treatment, the roots, stems, and leaves of the plants were collected to measure the indicators related to secondary metabolites. The results showed that endophytic fungi improved the alkali resistance of H. bogdanii by improving the related indicators of secondary metabolites. endophytic fungi significantly increased the contents of phosphorus, polyphenols, and alkaloids, and the activities of polyphenol oxidase and acid phosphatase, and significantly reduced flavonoid content. The content of polyphenols and alkaloids in stems, polyphenol oxidase activity in stems and leaves, and acid phosphatase activity in leaves were significantly affected. The findings of this study may aid in amplifying the alkali resistance mechanism of endophytic fungi to H. bogdanii as well as provide insights into improving the alkali resistance of other plants.

Transcriptome analysis of Epichloë strains in tall fescue in response to drought stress

Epichloë coenophiala, a systemic fungal symbiont (endophyte) of tall fescue (Lolium arundinaceum), has been documented to confer to this grass better persistence than plants lacking the endophyte, especially under stress conditions such as drought. The response, if any, of the endophyte to imposition of stress on the host plant has not been characterized previously. Therefore, we investigated effects on gene expression by E. coenophiala and a related endophyte when plant-endophyte symbiota were subjected to acute water-deficit stress. Plants harboring different endophyte strains were grown in sand in the greenhouse, then half were deprived of water for 48 h and the other half were watered controls. RNA was isolated from different plant tissues, and mRNA sequencing (RNA-seq) was conducted to identify genes that were differentially expressed comparing stress treatment with control. We compared two different plants harboring the common toxic E. coenophiala strain (CTE) and two non-ergot-alkaloid-producing Epichloë strains in tall fescue pseudostems, and in a second experiment we compared responses of E. coenophiala CTE in plant pseudostem and crown tissues. The endophytes responded to the stress with increased expression of genes involved in oxidative stress response, oxygen radical detoxification, C-compound carbohydrate metabolism, heat shock, and cellular transport pathways. The magnitude of fungal gene responses during stress varied among plant-endophyte symbiota. Responses in pseudostems and crowns involved some common pathways as well as some tissue-specific pathways. The fungal response to water-deficit stress involved gene expression changes in similar pathways that have been documented for plant stress responses, indicating that Epichloë spp. and their host plants either coordinate stress responses or separately activate similar stress response mechanisms that work together for mutual protection.

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.

Virus invasions of the New Zealand flora

More than 200 plant viruses and many of their invertebrate vectors have invaded New Zealand (NZ) in the last two centuries. All of these invaders are associated with introduced agricultural, horticultural and/or weed species. At least 16 of the viruses have invaded the native flora, including some rare and critically endangered species. Patterns are emerging: aphid transmitted viruses which are able to infect species from a number of families are prominent. For example, cucumber mosaic virus infects native species from seven families. There are also examples of viruses with more restricted host ranges invading individual families, particularly the native grasses. The yellow dwarf viruses have escaped from cereals and pasture into native grasses. Some of the species are also native to Australia and the Pacific Islands and the review and its literature should be of interest to those working further afield. Prospects for controlling or mitigating the effects of the viruses in agricultural systems have limited application in the native flora but they are relevant to propagation and rescue strategies. Biosecurity measures are not only the first line of defence against threats to agriculture but also to the conservation estate. The protection of native floras from virus invasion is another justification for the control measures and legislative procedures already in place to protect agriculture. High throughput sequencing to detect all viruses at the border, and genetic engineering and RNAi technologies to mitigate the effects of invasions are promising developments for the protection of the native flora.

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.

Chitin Deacetylases Are Required for Epichloë festucae Endophytic Cell Wall Remodeling During Establishment of a Mutualistic Symbiotic Interaction with Lolium perenne

Epichloë festucae forms a mutualistic symbiotic association with Lolium perenne. This biotrophic fungus systemically colonizes the intercellular spaces of aerial tissues to form an endophytic hyphal network and also grows as an epiphyte. However, little is known about the cell wall-remodeling mechanisms required to avoid host defense and maintain intercalary growth within the host. Here, we use a suite of molecular probes to show that the E. festucae cell wall is remodeled by conversion of chitin to chitosan during infection of L. perenne seedlings, as the hyphae switch from free-living to endophytic growth. When hyphae transition from endophytic to epiphytic growth, the cell wall is remodeled from predominantly chitosan to chitin. This conversion from chitin to chitosan is catalyzed by chitin deacetylase. The genome of E. festucae encodes three putative chitin deacetylases, two of which (cdaA and cdaB) are expressed in planta. Deletion of either of these genes results in disruption of fungal intercalary growth in the intercellular spaces of plants infected with these mutants. These results establish that these two genes are required for maintenance of the mutualistic symbiotic interaction between E. festucae and L. perenne.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Fungal Endophytes: A Promising Frontier for Discovery of Novel Bioactive Compounds

For years, fungi have served as repositories of bioactive secondary metabolites that form the backbone of many existing drugs. With the global rise in infections associated with antimicrobial resistance, in addition to the growing burden of non-communicable disease, such as cancer, diabetes and cardiovascular ailments, the demand for new drugs that can provide an improved therapeutic outcome has become the utmost priority. The exploration of microbes from understudied and specialized niches is one of the promising ways of discovering promising lead molecules for drug discovery. In recent years, a special class of plant-associated fungi, namely, fungal endophytes, have emerged as an important source of bioactive compounds with unique chemistry and interesting biological activities. The present review focuses on endophytic fungi and their classification, rationale for selection and prioritization of host plants for fungal isolation and examples of strategies that have been adopted to induce the activation of cryptic biosynthetic gene clusters to enhance the biosynthetic potential of fungal endophytes.

A Critical Review on Communication Mechanism within Plant-Endophytic Fungi Interactions to Cope with Biotic and Abiotic Stresses

Endophytic fungi infect plant tissues by evading the immune response, potentially stimulating stress-tolerant plant growth. The plant selectively allows microbial colonization to carve endophyte structures through phenotypic genes and metabolic signals. Correspondingly, fungi develop various adaptations through symbiotic signal transduction to thrive in mycorrhiza. Over the past decade, the regulatory mechanism of plant-endophyte interaction has been uncovered. Currently, great progress has been made on plant endosphere, especially in endophytic fungi. Here, we systematically summarize the current understanding of endophytic fungi colonization, molecular recognition signal pathways, and immune evasion mechanisms to clarify the transboundary communication that allows endophytic fungi colonization and homeostatic phytobiome. In this work, we focus on immune signaling and recognition mechanisms, summarizing current research progress in plant-endophyte communication that converge to improve our understanding of endophytic fungi.

Non-Transgenic CRISPR-Mediated Knockout of Entire Ergot Alkaloid Gene Clusters in Slow-Growing Asexual Polyploid Fungi

The Epichloë species of fungi include seed-borne symbionts (endophytes) of cool-season grasses that enhance plant fitness, although some also produce alkaloids that are toxic to livestock. Selected or mutated toxin-free endophytes can be introduced into forage cultivars for improved livestock performance. Long-read genome sequencing revealed clusters of ergot alkaloid biosynthesis (EAS) genes in Epichloë coenophiala strain e19 from tall fescue (Lolium arundinaceum) and Epichloë hybrida Lp1 from perennial ryegrass (Lolium perenne). The two homeologous clusters in E. coenophiala-a triploid hybrid species-were 196 kb (EAS1) and 75 kb (EAS2), and the E. hybrida EAS cluster was 83 kb. As a CRISPR-based approach to target these clusters, the fungi were transformed with ribonucleoprotein (RNP) complexes of modified Cas9 nuclease (Cas9-2NLS) and pairs of single guide RNAs (sgRNAs), plus a transiently selected plasmid. In E. coenophiala, the procedure generated deletions of EAS1 and EAS2 separately, as well as both clusters simultaneously. The technique also gave deletions of the EAS cluster in E. hybrida and of individual alkaloid biosynthesis genes (dmaW and lolC) that had previously proved difficult to delete in E. coenophiala. Thus, this facile CRISPR RNP approach readily generates non-transgenic endophytes without toxin genes for use in research and forage cultivar improvement.

Endophytic Fungi Activated Similar Defense Strategies of Achnatherum sibiricum Host to Different Trophic Types of Pathogens

It is well documented that Epichloë endophytes can enhance the resistance of grasses to herbivory. However, reports on resistance to pathogenic fungi are limited, and their conclusions are variable. In this study, we chose pathogenic fungi with different trophic types, namely, the biotrophic pathogen Erysiphales species and the necrotrophic pathogen Curvularia lunata, to test the effects of Epichloë on the pathogen resistance of Achnatherum sibiricum. The results showed that, compared to Erysiphales species, C. lunata caused a higher degree of damage and lower photochemical efficiency (Fv/Fm) in endophyte−free (E−) leaves. Endophytes significantly alleviated the damage caused by these two pathogens. The leaf damaged area and Fv/Fm of endophyte−infected (E+) leaves were similar between the two pathogen treatments, indicating that the beneficial effects of endophytes were more significant when hosts were exposed to C. lunata than when they were exposed to Erysiphales species. We found that A. sibiricum initiated jasmonic acid (JA)−related pathways to resist C. lunata but salicylic acid (SA)–related pathways to resist Erysiphales species. Endophytic fungi had no effect on the content of SA but increased the content of JA and total phenolic compounds, which suggest that endophyte infection might enhance the resistance of A. sibiricum to these two different trophic types of pathogens through similar pathways.

Polycomb Repression without Bristles: Facultative Heterochromatin and Genome Stability in Fungi

Genome integrity is essential to maintain cellular function and viability. Consequently, genome instability is frequently associated with dysfunction in cells and associated with plant, animal, and human diseases. One consequence of relaxed genome maintenance that may be less appreciated is an increased potential for rapid adaptation to changing environments in all organisms. Here, we discuss evidence for the control and function of facultative heterochromatin, which is delineated by methylation of histone H3 lysine 27 (H3K27me) in many fungi. Aside from its relatively well understood role in transcriptional repression, accumulating evidence suggests that H3K27 methylation has an important role in controlling the balance between maintenance and generation of novelty in fungal genomes. We present a working model for a minimal repressive network mediated by H3K27 methylation in fungi and outline challenges for future research.

Horizontal gene transfer of Fhb7 from fungus underlies Fusarium head blight resistance in wheat

Fusarium head blight (FHB), a fungal disease caused by Fusarium species that produce food toxins, currently devastates wheat production worldwide, yet few resistance resources have been discovered in wheat germplasm. Here, we cloned the FHB resistance gene Fhb7 by assembling the genome of Thinopyrum elongatum, a species used in wheat distant hybridization breeding. Fhb7 encodes a glutathione S-transferase (GST) and confers broad resistance to Fusarium species by detoxifying trichothecenes through de-epoxidation. Fhb7 GST homologs are absent in plants, and our evidence supports that Th. elongatum has gained Fhb7 through horizontal gene transfer (HGT) from an endophytic Epichloë species. Fhb7 introgressions in wheat confers resistance to both FHB and crown rot in diverse wheat backgrounds without yield penalty, providing a solution for Fusarium resistance breeding.

Phosphatidic acid produced by phospholipase D is required for hyphal cell-cell fusion and fungal-plant symbiosis

Although lipid signaling has been shown to serve crucial roles in mammals and plants, little is known about this process in filamentous fungi. Here we analyze the contribution of phospholipase D (PLD) and its product phosphatidic acid (PA) in hyphal morphogenesis and growth of Epichloë festucae and Neurospora crassa, and in the establishment of a symbiotic interaction between E. festucae and Lolium perenne. Growth of E. festucae and N. crassa PLD deletion strains in axenic culture, and for E. festucae in association with L. perenne, were analyzed by light-, confocal- and electron microscopy. Changes in PA distribution were analyzed in E. festucae using a PA biosensor and the impact of these changes on the endocytic recycling and superoxide production investigated. We found that E. festucae PldB, and the N. crassa ortholog, PLA-7, are required for polarized growth and cell fusion and contribute to ascospore development, whereas PldA/PLA-8 are dispensable for these functions. Exogenous addition of PA rescues the cell-fusion phenotype in E. festucae. PldB is also crucial for E. festucae to establish a symbiotic association with L. perenne. This study identifies a new component of the cell-cell communication and cell fusion signaling network for hyphal morphogenesis and growth of filamentous fungi.

Fungal Endophyte Colonization Patterns Alter Over Time in the Novel Association Between Lolium perenne and Epichloë Endophyte AR37

Infection of the pasture grass Lolium perenne with the seed-transmitted fungal endophyte Epichloë festucae enhances its resilience to biotic and abiotic stress. Agricultural benefits of endophyte infection can be increased by generating novel symbiotic associations through inoculating L. perenne with selected Epichloë strains. Natural symbioses have coevolved over long periods. Thus, artificial symbioses will probably not have static properties, but symbionts will coadapt over time improving the fitness of the association. Here we report for the first time on temporal changes in a novel association of Epichloë strain AR37 and the L. perenne cultivar Grasslands Samson. Over nine generations, a seed maintenance program had increased the endophyte seed transmission rates to > 95% (from an initial 76%). We observed an approximately fivefold decline in endophyte biomass concentration in vegetative tissues over time (between generations 2 and 9). This indicates strong selection pressure toward reducing endophyte-related fitness costs by reducing endophyte biomass, without compromising the frequency of endophyte transmission to seed. We observed no obvious changes in tillering and only minor transcriptomic changes in infected plants over time. Functional analysis of 40 plant genes, showing continuously decreasing expression over time, suggests that adaptation of host metabolism and defense mechanisms are important for increasing the fitness of this association, and possibly fitness of such symbioses in general. Our results indicate that fitness of novel associations is likely to improve over time and that monitoring changes in novel associations can assist in identifying key features of endophyte-mediated enhancement of host fitness.

Characterization of the complete chloroplast genome of Festuca sinensis (Gramineae)

The complete chloroplast genome from Festuca sinensis, an important perennial bunchgrass of the Gramineae, is determined in this study. The whole chloroplast genome sequence of F. sinensis has been characterized by Illumina pair-end sequencing. The circular genome is 134,177 bp long, containing a large single-copy region (LSC) of 79,367 bp and a small single-copy region (SSC) of 12,510 bp, which are separated by a pair of 21,150 bp inverted repeat regions (IRs). It encodes a total of 150 genes, including 93 protein-coding genes (75 PCG species), 49 tRNA genes (30 tRNA species) and eight ribosomal RNA genes (4 rRNA species). The most of gene species occur as a single copy, while 30 gene species occur in double copies. The overall A + T content of is 61.6%, while the corresponding values of the LSC, SSC, and IR regions are 63.7, 67.4, and 56.0%, respectively. Phylogenetic analysis suggested that Festuca sinensis was relatively close to Festuca ovina compared with other species of Festuca genera in Gramineae among the species analyzed. This complete chloroplast genome will provide valuable insight into conservation and exploitation efforts for this species as well as useful resources for studying the Gramineae phylogeny.

Endophytes from wild cereals protect wheat plants from drought by alteration of physiological responses of the plants to water stress

Endophytes contribute to plant performance, especially under harsh conditions. We therefore hypothesized that wild plants have retained beneficial endophytes that are less abundant or not present in related crop plants. To test this hypothesis, we selected two endophytes that were found in Sharon goatgrass, an ancestor of wheat, and tested their effect on bread wheat. Both endophytes infected wheat and improved sustainability and performance under water-limited conditions. To determine how the endophytes modify plant development, we measured parameters of plant growth and physiological status and performed a comparative metabolomics analysis. Endophyte-treated wheat plants had reduced levels of stress damage markers and reduced accumulation of stress-adaptation metabolites. Metabolomics profiling revealed significant differences in the response to water stress of endophyte-treated plants compared with untreated plants. Our results demonstrate the potential of endophytes from wild plants for improvement of related crops and show that the beneficial effects of two endophytes are associated with alteration of physiological responses to water-limited conditions.

Transcriptomics of Epichloë-Grass Symbioses in Host Vegetative and Reproductive Stages

Epichloë species are fungal symbionts (endophytes) of cool-season grasses that transmit vertically via inflorescence primordia (IP), ovaries (OV), and ultimately, embryos. Epichloë coenophiala, an endophyte of tall fescue (Schedonorus arundinaceus), provides multiple protective benefits to the grass. We conducted transcriptome analysis of the tall fescue-E. coenophiala symbiosis, comparing IP, OV, vegetative pseudostems (PS), and the lemma and palea (LP) (bracts) of the young floret. Transcriptomes of host OV and PS exhibited almost no significant differences attributable to endophyte presence or absence. Comparison of endophyte gene expression in different plant parts revealed numerous differentially expressed genes (DEGs). The 150 endophyte DEGs significantly higher in PS over OV included genes for alkaloid biosynthesis and sugar or amino acid transport. The 277 endophyte DEGs significantly higher in OV over PS included genes for protein chaperones (including most heat-shock proteins), trehalose synthesis complex, a bax inhibitor-1 protein homolog, the CLC chloride ion channel, catalase, and superoxide dismutase. Similar trends were apparent in the Brachypodium sylvaticum-Epichloë sylvatica symbiosis. Gene expression profiles in tall fescue IP and LP indicated that the endophyte transcriptome shift began early in host floral development. We discuss possible roles of the endophyte DEGs in colonization of reproductive grass tissues.

Repeat elements organise 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae

Structural features of genomes, including the three-dimensional arrangement of DNA in the nucleus, are increasingly seen as key contributors to the regulation of gene expression. However, studies on how genome structure and nuclear organisation influence transcription have so far been limited to a handful of model species. This narrow focus limits our ability to draw general conclusions about the ways in which three-dimensional structures are encoded, and to integrate information from three-dimensional data to address a broader gamut of biological questions. Here, we generate a complete and gapless genome sequence for the filamentous fungus, Epichloë festucae. We use Hi-C data to examine the three-dimensional organisation of the genome, and RNA-seq data to investigate how Epichloë genome structure contributes to the suite of transcriptional changes needed to maintain symbiotic relationships with the grass host. Our results reveal a genome in which very repeat-rich blocks of DNA with discrete boundaries are interspersed by gene-rich sequences that are almost repeat-free. In contrast to other species reported to date, the three-dimensional structure of the genome is anchored by these repeat blocks, which act to isolate transcription in neighbouring gene-rich regions. Genes that are differentially expressed in planta are enriched near the boundaries of these repeat-rich blocks, suggesting that their three-dimensional orientation partly encodes and regulates the symbiotic relationship formed by this organism.

Knowing your neighbourhood-the effects of Epichloë endophytes on foliar fungal assemblages in perennial ryegrass in dependence of season and land-use intensity

Epichloë endophytes associated with cool-season grass species can protect their hosts from herbivory and can suppress mycorrhizal colonization of the hosts' roots. However, little is known about whether or not Epichloë endophyte infection can also change the foliar fungal assemblages of the host. We tested 52 grassland study sites along a land-use intensity gradient in three study regions over two seasons (spring vs. summer) to determine whether Epichloë infection of the host grass Lolium perenne changes the fungal community structure in leaves. Foliar fungal communities were assessed by Next Generation Sequencing of the ITS rRNA gene region. Fungal community structure was strongly affected by study region and season in our study, while land-use intensity and infection with Epichloë endophytes had no significant effects. We conclude that effects on non-systemic endophytes resulting from land use practices and Epichloë infection reported in other studies were masked by local and seasonal variability in this study's grassland sites.

Seed Transmission of Epichloë Endophytes in Lolium perenne Is Heavily Influenced by Host Genetics

Vertical transmission of symbiotic Epichloë endophytes from host grasses into progeny seed is the primary mechanism by which the next generation of plants is colonized. This process is often imperfect, resulting in endophyte-free seedlings which may have poor ecological fitness if the endophyte confers protective benefits to its host. In this study, we investigated the influence of host genetics and environment on the vertical transmission of Epichloë festucae var. lolii strain AR37 in the temperate forage grass Lolium perenne. The efficiency of AR37 transmission into the seed of over 500 plant genotypes from five genetically diverse breeding populations was determined. In Populations I-III, which had undergone previous selection for high seed infection by AR37, mean transmission was 88, 93, and 92%, respectively. However, in Populations IV and V, which had not undergone previous selection, mean transmission was 69 and 70%, respectively. The transmission values, together with single-nucleotide polymorphism data obtained using genotyping-by-sequencing for each host, was used to develop a genomic prediction model for AR37 seed transmission. The predictive ability of the model was estimated at r = 0.54. While host genotype contributed greatly to differences in AR37 seed transmission, undefined environmental variables also contributed significantly to seed transmission across different years and geographic locations. There was evidence for a small host genotype-by-environment effect; however this was less pronounced than genotype or environment alone. Analysis of endophyte infection levels in parent plants within Populations I and IV revealed a loss of endophyte infection over time in Population IV only. This population also had lower average tiller infection frequencies than Population I, suggesting that AR37 failed to colonize all the daughter tillers and therefore seeds. However, we also observed that infection of seed by AR37 may fail during or after initiation of floral development from plants where all tillers remained endophyte-infected over time. While the effects of environment and host genotype on fungal endophyte transmission have been evaluated previously, this is the first study that quantifies the relative impacts of host genetics and environment on endophyte vertical transmission.

Two closely related Rho GTPases, Cdc42 and RacA, of the en-dophytic fungus Epichloë festucae have contrasting roles for ROS production and symbiotic infection synchronized with the host plant

Epichloë festucae is an endophytic fungus which systemically colonizes temperate grasses to establish symbiotic associations. Maintaining symptomless infection is a key requirement for endophytes, a feature that distinguishes them from pathogenic fungi. While pathogenic fungi extend their hyphae by tip growth, hyphae of E. festucae systemically colonize the intercellular space of expanding host leaves via a unique mechanism of hyphal intercalary growth. This study reports that two homologous Rho GTPases, Cdc42 and RacA, have distinctive roles in the regulation of E. festucae growth in planta. Here we highlight the vital role of Cdc42 for intercalary hyphal growth, as well as involvement of RacA in regulation of hyphal network formation, and demonstrate the consequences of mutations in these genes on plant tissue infection. Functions of Cdc42 and RacA are mediated via interactions with BemA and NoxR respectively, which are expected components of the ROS producing NOX complex. Symbiotic defects found in the racA mutant were rescued by introduction of a Cdc42 with key amino acids substitutions crucial for RacA function, highlighting the significance of the specific interactions of these GTPases with BemA and NoxR for their functional differentiation in symbiotic infection.

Endophytic fungi alter sucking bug responses to cotton reproductive structures

All plants including cotton host a wide range of microorganisms as endophytes. There is a growing appreciation of the prevalence, ecological significance and management potential of facultative fungal endophytes in protecting plants from pests, pathogens and environmental stressors. Hemipteran sucking bugs have emerged as major pests across the U.S. cotton belt, reducing yields directly by feeding on developing reproductive structures and indirectly by vectoring plant pathogens. We used no-choice and simultaneous choice assays to examine the host selection behavior of western tarnished plant bugs (Lygus hesperus) and southern green stink bugs (Nezara viridula) in response to developing flower buds and fruits from cotton plants colonized by 1 of 2 candidate beneficial fungal endophytes, Phialemonium inflatum or Beauveria bassiana. Both insect species exhibited strong negative responses to flower buds (L. hesperus) and fruits (N. viridula) from plants that had been colonized by candidate endophytic fungi relative to control plants under both no-choice and choice conditions. Behavioral responses of both species indicated that the insects were deterred prior to contact with plant tissues from endophyte-colonized plants, suggesting a putative role for volatile compounds in mediating the negative response. Our results highlight the role of fungal endophytes as plant mutualists that can have positive effects on plant resistance to pests.

Analysis of simple sequence repeat (SSR) structure and sequence within Epichloë endophyte genomes reveals impacts on gene structure and insights into ancestral hybridization events

Epichloë grass endophytes comprise a group of filamentous fungi of both sexual and asexual species. Known for the beneficial characteristics they endow upon their grass hosts, the identification of these endophyte species has been of great interest agronomically and scientifically. The use of simple sequence repeat loci and the variation in repeat elements has been used to rapidly identify endophyte species and strains, however, little is known of how the structure of repeat elements changes between species and strains, and where these repeat elements are located in the fungal genome. We report on an in-depth analysis of the structure and genomic location of the simple sequence repeat locus B10, commonly used for Epichloë endophyte species identification. The B10 repeat was found to be located within an exon of a putative bZIP transcription factor, suggesting possible impacts on polypeptide sequence and thus protein function. Analysis of this repeat in the asexual endophyte hybrid Epichloë uncinata revealed that the structure of B10 alleles reflects the ancestral species that hybridized to give rise to this species. Understanding the structure and sequence of these simple sequence repeats provides a useful set of tools for readily distinguishing strains and for gaining insights into the ancestral species that have undergone hybridization events.

Transcriptome response of Lolium arundinaceum to its fungal endophyte Epichloë coenophiala

Tall fescue (Lolium arundinaceum) is one of the primary forage and turf grasses in temperate regions of the world. A number of favourable characteristics of tall fescue are enhanced by its seed-transmissible fungal symbiont (endophyte) Epichloë coenophiala. Our approach was to assemble the tall fescue transcriptome, then identify differentially expressed genes (DEGs) for endophyte-symbiotic (E+) vs endophyte-free (E-) clones in leaf blades, pseudostems, crowns and roots. RNA-seq reads were used to construct a tall fescue reference transcriptome and compare gene expression profiles. Over all tissues examined, 478 DEGs were identified between the E+ and E- clones for at least one tissue (more than two-fold; P < 0.0001, 238 E+ > E- and 240 E- > E+), although no genes were differentially expressed in all four tissues. Gene ontology (GO) terms, GO:0010200 (response to chitin), GO:0002679 (respiratory burst during defence response) and GO:0035556 (intracellular signal transduction) were significantly overrepresented among 25 E- > E+ DEGs in leaf blade, and a number of other DEGs were associated with defence and abiotic response. In particular, endophyte effects on various WRKY transcription factors may have implications for symbiotic stability, endophyte distribution in the plant, or defence against pathogens.

cAMP Signaling Regulates Synchronised Growth of Symbiotic Epichloë Fungi with the Host Grass Lolium perenne

The seed-transmitted fungal symbiont, Epichloë festucae, colonizes grasses by infecting host tissues as they form on the shoot apical meristem (SAM) of the seedling. How this fungus accommodates the complexities of plant development to successfully colonize the leaves and inflorescences is unclear. Since adenosine 3', 5'-cyclic monophosphate (cAMP)-dependent signaling is often essential for host colonization by fungal pathogens, we disrupted the cAMP cascade by insertional mutagenesis of the E. festucae adenylate cyclase gene (acyA). Consistent with deletions of this gene in other fungi, acyA mutants had a slow radial growth rate in culture, and hyphae were convoluted and hyper-branched suggesting that fungal apical dominance had been disrupted. Nitro blue tetrazolium (NBT) staining of hyphae showed that cAMP disruption mutants were impaired in their ability to synthesize superoxide, indicating that cAMP signaling regulates accumulation of reactive oxygen species (ROS). Despite significant defects in hyphal growth and ROS production, E. festucae ΔacyA mutants were infectious and capable of forming symbiotic associations with grasses. Plants infected with E. festucae ΔacyA were marginally less robust than the wild-type (WT), however hyphae were hyper-branched, and leaf tissues heavily colonized, indicating that the tight regulation of hyphal growth normally observed in maturing leaves requires functional cAMP signaling.

Genome-Wide Analysis of Codon Usage Bias in Epichloë festucae

Analysis of codon usage data has both practical and theoretical applications in understanding the basics of molecular biology. Differences in codon usage patterns among genes reflect variations in local base compositional biases and the intensity of natural selection. Recently, there have been several reports related to codon usage in fungi, but little is known about codon usage bias in Epichloë endophytes. The present study aimed to assess codon usage patterns and biases in 4870 sequences from Epichloë festucae, which may be helpful in revealing the constraint factors such as mutation or selection pressure and improving the bioreactor on the cloning, expression, and characterization of some special genes. The GC content with 56.41% is higher than the AT content (43.59%) in E. festucae. The results of neutrality and effective number of codons plot analyses showed that both mutational bias and natural selection play roles in shaping codon usage in this species. We found that gene length is strongly correlated with codon usage and may contribute to the codon usage patterns observed in genes. Nucleotide composition and gene expression levels also shape codon usage bias in E. festucae. E. festucae exhibits codon usage bias based on the relative synonymous codon usage (RSCU) values of 61 sense codons, with 25 codons showing an RSCU larger than 1. In addition, we identified 27 optimal codons that end in a G or C.

Analysis of Cryptic, Systemic Botrytis Infections in Symptomless Hosts

Botrytis species are generally considered to be aggressive, necrotrophic plant pathogens. By contrast to this general perception, however, Botrytis species could frequently be isolated from the interior of multiple tissues in apparently healthy hosts of many species. Infection frequencies reached 50% of samples or more, but were commonly less, and cryptic infections were rare or absent in some plant species. Prevalence varied substantially from year to year and from tissue to tissue, but some host species routinely had high prevalence. The same genotype was found to occur throughout a host, representing mycelial spread. Botrytis cinerea and Botrytis pseudocinerea are the species that most commonly occur as cryptic infections, but phylogenetically distant isolates of Botrytis were also detected, one of which does not correspond to previously described species. Sporulation and visible damage occurred only when infected tissues were stressed, or became mature or senescent. There was no evidence of cryptic infection having a deleterious effect on growth of the host, and prevalence was probably greater in plants grown in high light conditions. Isolates from cryptic infections were often capable of causing disease (to varying extents) when spore suspensions were inoculated onto their own host as well as on distinct host species, arguing against co-adaptation between cryptic isolates and their hosts. These data collectively suggest that several Botrytis species, including the most notorious pathogenic species, exist frequently in cryptic form to an extent that has thus far largely been neglected, and do not need to cause disease on healthy hosts in order to complete their life-cycles.

Phylogenomics and evolution of secondary metabolism in plant-associated fungi

Fungi produce a myriad of secondary metabolites, compounds that are not required for basic cellular processes, but are thought to be central to ecological functions. Genomic sequencing of fungi has revealed a greater diversity of secondary metabolism than previously realized, including novel taxonomic distributions of known compounds and uncharacterized gene clusters in well-studied organisms. Here we provide an overview of the major groups of metabolites, their ecological functions, the genetic systems that produce them, and the patterns and processes associated with evolutionary diversification of secondary metabolism in plant-associated filamentous ascomycetes.

Advancing the science of microbial symbiosis to support invasive species management: a case study on Phragmites in the Great Lakes

A growing body of literature supports microbial symbiosis as a foundational principle for the competitive success of invasive plant species. Further exploration of the relationships between invasive species and their associated microbiomes, as well as the interactions with the microbiomes of native species, can lead to key new insights into invasive success and potentially new and effective control approaches. In this manuscript, we review microbial relationships with plants, outline steps necessary to develop invasive species control strategies that are based on those relationships, and use the invasive plant species Phragmites australis (common reed) as an example of how development of microbial-based control strategies can be enhanced using a collective impact approach. The proposed science agenda, developed by the Collaborative for Microbial Symbiosis and Phragmites Management, contains a foundation of sequential steps and mutually-reinforcing tasks to guide the development of microbial-based control strategies for Phragmites and other invasive species. Just as the science of plant-microbial symbiosis can be transferred for use in other invasive species, so too can the model of collective impact be applied to other avenues of research and management.

Fungal effectors and plant susceptibility

Plants can be colonized by fungi that have adopted highly diverse lifestyles, ranging from symbiotic to necrotrophic. Colonization is governed in all systems by hundreds of secreted fungal effector molecules. These effectors suppress plant defense responses and modulate plant physiology to accommodate fungal invaders and provide them with nutrients. Fungal effectors either function in the interaction zone between the fungal hyphae and host or are transferred to plant cells. This review describes the effector repertoires of 84 plant-colonizing fungi. We focus on the mechanisms that allow these fungal effectors to promote virulence or compatibility, discuss common plant nodes that are targeted by effectors, and provide recent insights into effector evolution. In addition, we address the issue of effector uptake in plant cells and highlight open questions and future challenges.

Peramine and lolitrem B from endophyte-grass associations cascade up the food chain

Endophytic fungi in cool-season grass species produce herbivore-toxic alkaloids, which are assumed to harm higher trophic levels along food chains. Previous studies have shown fitness disadvantages for higher trophic levels that feed on aphids that were exclusively reared on perennial ryegrass (Lolium perenne) infected with the endophytic fungus Neotyphodium lolii. However, it is unknown whether the alkaloids produced by the fungus-grass association can be assimilated by plant sap-sucking insects like aphids. Using an ultra high performance liquid chromatography method combined with mass spectrometry, we provide the first evidence that the alkaloids peramine and lolitrem B are present in aphids (Rhopalosiphum padi) and in aphid predators when the aphids are reared on endophyte-infected grass. We conclude that alkaloids can enter the plant sap of the grass and are responsible for longer pupal stages of the ladybird Harmonia axyridis and for fitness disadvantages of aphids and their predators as shown in previous studies.

Current European Labyrinthula zosterae are not virulent and modulate seagrass (Zostera marina) defense gene expression

Pro- and eukaryotic microbes associated with multi-cellular organisms are receiving increasing attention as a driving factor in ecosystems. Endophytes in plants can change host performance by altering nutrient uptake, secondary metabolite production or defense mechanisms. Recent studies detected widespread prevalence of Labyrinthula zosterae in European Zostera marina meadows, a protist that allegedly caused a massive amphi-Atlantic seagrass die-off event in the 1930's, while showing only limited virulence today. As a limiting factor for pathogenicity, we investigated genotype × genotype interactions of host and pathogen from different regions (10-100 km-scale) through reciprocal infection. Although the endophyte rapidly infected Z. marina, we found little evidence that Z. marina was negatively impacted by L. zosterae. Instead Z. marina showed enhanced leaf growth and kept endophyte abundance low. Moreover, we found almost no interaction of protist × eelgrass-origin on different parameters of L. zosterae virulence/Z. marina performance, and also no increase in mortality after experimental infection. In a target gene approach, we identified a significant down-regulation in the expression of 6/11 genes from the defense cascade of Z. marina after real-time quantitative PCR, revealing strong immune modulation of the host's defense by a potential parasite for the first time in a marine plant. Nevertheless, one gene involved in phenol synthesis was strongly up-regulated, indicating that Z. marina plants were probably able to control the level of infection. There was no change in expression in a general stress indicator gene (HSP70). Mean L. zosterae abundances decreased below 10% after 16 days of experimental runtime. We conclude that under non-stress conditions L. zosterae infection in the study region is not associated with substantial virulence.

Histone H3K9 and H3K27 methylation regulates fungal alkaloid biosynthesis in a fungal endophyte-plant symbiosis

Epichloё festucae is a filamentous fungus that forms a mutually beneficial symbiotic association with Lolium perenne. This endophyte synthesizes bioprotective lolitrems (ltm) and ergot alkaloids (eas) in planta but the mechanisms regulating expression of the corresponding subtelomeric gene clusters are not known. We show here that the status of histone H3 lysine 9 and lysine 27 trimethylation (H3K9me3/H3K27me3) at these alkaloid gene loci are critical determinants of transcriptional activity. Using ChIP-qPCR we found that levels of H3K9me3 and H3K27me3 were reduced at these loci in plant infected tissue compared to axenic culture. Deletion of E. festucae genes encoding the H3K9- (ClrD) or H3K27- (EzhB) methyltransferases led to derepression of ltm and eas gene expression under non-symbiotic culture conditions and a further enhancement of expression in the double deletion mutant. These changes in gene expression were matched by corresponding reductions in H3K9me3 and H3K27me3 marks. Both methyltransferases are also important for the symbiotic interaction between E. festucae and L. perenne. Our results show that the state of H3K9 and H3K27 trimethylation of E. festucae chromatin is an important regulatory layer controlling symbiosis-specific expression of alkaloid bioprotective metabolites and the ability of this symbiont to form a mutualistic interaction with its host.

Do fungivores trigger the transfer of protective metabolites from host plants to arbuscular mycorrhizal hyphae?

A key objective in ecology is to understand how cooperative strategies evolve and are maintained in species networks. Here, we focus on the tri-trophic relationship between arbuscular mycorrhizal (AM) fungi, host plants, and fungivores to ask if host plants are able to protect their mutualistic mycorrhizal partners from being grazed. Specifically, we test whether secondary metabolites are transferred from hosts to fungal partners to increase their defense against fungivores. We grew Plantago lanceolata hosts with and without mycorrhizal inoculum, and in the presence or absence of fungivorous springtails. We then measured fungivore effects on host biomass and mycorrhizal abundance (using quantitative PCR) in roots and soil. We used high-performance liquid chromatography to measure host metabolites in roots, shoots, and hyphae, focusing on catalpol, aucubin, and verbascoside. Our most striking result was that the metabolite catalpol was consistently found in AM fungal hyphae in host plants exposed to fungivores. When fungivores were absent, catalpol was undetectable in hyphae. Our results highlight the potential for plant-mediated protection of the mycorrhizal hyphal network.

Root ethylene signalling is involved in Miscanthus sinensis growth promotion by the bacterial endophyte Herbaspirillum frisingense GSF30(T)

The bacterial endophyte Herbaspirillum frisingense GSF30(T) is a colonizer of several grasses grown in temperate climates, including the highly nitrogen-efficient perennial energy grass Miscanthus. Inoculation of Miscanthus sinensis seedlings with H. frisingense promoted root and shoot growth but had only a minor impact on nutrient concentrations. The bacterium affected the root architecture and increased fine-root structures. Although H. frisingense has the genetic requirements to fix nitrogen, only minor changes in nitrogen concentrations were observed. Herbaspirillum agglomerates were identified primarily in the root apoplast but also in the shoots. The short-term (3h) and long-term (3 weeks) transcriptomic responses of the plant to bacterial inoculation revealed that H. frisingense induced rapid changes in plant hormone signalling, most prominent in jasmonate signalling. Ethylene signalling pathways were also affected and persisted after 3 weeks in the root. Growth stimulation of the root by the ethylene precursor 1-aminocyclopropane 1-carboxylic acid was dose dependent and was affected by H. frisingense inoculation. Minor changes in the proteome were identified after 3 weeks. This study suggests that H. frisingense improves plant growth by modulating plant hormone signalling pathways and provides a framework to understand the beneficial effects of diazotrophic plant-growth-promoting bacteria, such as H. frisingense, on the biomass grass Miscanthus.

The epichloae: alkaloid diversity and roles in symbiosis with grasses

Epichloae (Epichloë and Neotyphodium species; Clavicipitaceae) are fungi that live in systemic symbioses with cool-season grasses, and many produce alkaloids that are deterrent or toxic to herbivores. The epichloae colonize much of the aerial plant tissues, and most benignly colonize host seeds to transmit vertically. Of their four chemical classes of alkaloids, the ergot alkaloids and indole-diterpenes are active against mammals and insects, whereas peramine and lolines specifically affect insects. Comparative genomic analysis of Clavicipitaceae reveals a distinctive feature of the epichloae, namely, large repeat blocks in their alkaloid biosynthesis gene loci. Such repeat blocks can facilitate gene losses, mutations, and duplications, thus enhancing diversity of alkaloid structures within each class. We suggest that alkaloid diversification is selected especially in the vertically transmissible epichloae.