Hybridization of Neotyphodium endophytes enhances competitive ability of the host grass

Hybridization and introgression are prevalent in Southern European Erysimum (Brassicaceae) species

BACKGROUND AND AIMS

Hybridization is a common and important force in plant evolution. One of its outcomes is introgression - the transfer of small genomic regions from one taxon to another by hybridization and repeated backcrossing. This process is believed to be common in glacial refugia, where range expansions and contractions can lead to cycles of sympatry and isolation, creating conditions for extensive hybridization and introgression. Polyploidization is another genome-wide process with a major influence on plant evolution. Both hybridization and polyploidization can have complex effects on plant evolution. However, these effects are often difficult to understand in recently evolved species complexes.

METHODS

We combined flow cytometry, analyses of transcriptomic sequences and pollen tube growth assays to investigate the consequences of polyploidization, hybridization and introgression on the recent evolution of several Erysimum (Brassicaceae) species from the South of the Iberian Peninsula, a well-known glacial refugium. This species complex differentiated in the last 2 million years, and its evolution has been hypothesized to be determined mainly by polyploidization, interspecific hybridization and introgression.

KEY RESULTS

Our results support a scenario of widespread hybridization involving both extant and 'ghost' taxa. Several taxa studied here, most notably those with purple corollas, are polyploids, probably of allopolyploid origin. Moreover, hybridization in this group might be an ongoing phenomenon, as pre-zygotic barriers appeared weak in many cases.

CONCLUSIONS

The evolution of Erysimum spp. has been determined by hybridization to a large extent. Species with purple (polyploids) and yellow flowers (mostly diploid) exhibit a strong signature of introgression in their genomes, indicating that hybridization occurred regardless of colour and across ploidy levels. Although the adaptive value of such genomic exchanges remains unclear, our results demonstrate the significance of hybridization for plant diversification, which should be taken into account when studying plant evolution.

Bioprospecting Trichoderma: A Systematic Roadmap to Screen Genomes and Natural Products for Biocontrol Applications

Natural products derived from microbes are crucial innovations that would help in reaching sustainability development goals worldwide while achieving bioeconomic growth. Trichoderma species are well-studied model fungal organisms used for their biocontrol properties with great potential to alleviate the use of agrochemicals in agriculture. However, identifying and characterizing effective natural products in novel species or strains as biological control products remains a meticulous process with many known challenges to be navigated. Integration of recent advancements in various "omics" technologies, next generation biodesign, machine learning, and artificial intelligence approaches could greatly advance bioprospecting goals. Herein, we propose a roadmap for assessing the potential impact of already known or newly discovered Trichoderma species for biocontrol applications. By screening publicly available Trichoderma genome sequences, we first highlight the prevalence of putative biosynthetic gene clusters and antimicrobial peptides among genomes as an initial step toward predicting which organisms could increase the diversity of natural products. Next, we discuss high-throughput methods for screening organisms to discover and characterize natural products and how these findings impact both fundamental and applied research fields.

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.

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.

The Inhibitory Effect of Endophyte-Infected Tall Fescue on White Clover Can Be Alleviated by Glomus mosseae Instead of Rhizobia

In artificial ecosystems, mixed planting of gramineous and leguminous plants can have obvious advantages and is very common. Due to their improved growth performances and stress tolerance, endophyte-infected grasses are considered to be ideal plant species for grasslands. However, endophytic fungi can inhibit the growth of neighboring nonhost leguminous plants. In this study, we chose endophyte-infected and endophyte-free tall fescue (Lolium arundinaceum Darbyshire ex. Schreb.) and clover (Trifolium repens) as the experimental materials to explore whether arbuscular mycorrhizal fungi and rhizobium can alleviate the inhibitory effect of endophyte infection on clover. The results showed that endophytic fungi significantly reduced clover biomass. Arbuscular mycorrhizal fungi inoculation significantly increased the biomass of clover in both endophyte-infected tall fescue/clover and endophyte-free tall fescue/clover systems but the beneficial contribution of arbuscular mycorrhizal fungi was more obvious in the endophyte-infected tall fescue/clover system. Rhizobia inoculation could alleviate the detrimental effect of tall fescue on the growth of clover but did not alleviate the detrimental effect of endophyte infection on the growth of clover.

Contrasting effects of Rhizophagus irregularis versus bacterial and fungal seed endophytes on Trifolium repens plant-soil feedback

Interactions between plants and soil affect plant-plant interactions and community composition by modifying soils conditions in plant-soil feedback, where associated microbes have the most crucial role. Both arbuscular mycorrhizal fungi (AMF) and microbial seed endophytes have been demonstrated to influence, directly or indirectly, biotic or abiotic soil properties, thus affecting subsequent plant growth, and community structure. However, little is known about how plant endophyte communities, individually or in interaction with AMF, affect plant-soil feedback processes. Here, we investigated, through a manipulative experiment, the behavior of endophyte-free and endophyte-associated Trifolium repens plants grown in soils previously conditioned by conspecific endophyte-free and endophyte-associated plants, inoculated or not by Rhizophagus intraradices. Furthermore, we identified microbial endophytes directly from the inner tissues of seeds by high-throughput sequencing, to compare seed fungal and bacterial endophyte composition. Results demonstrated that the outcome of simultaneous occurrence of seed endophytes and AMF on plant behavior depended on matching the endophytic status, i.e., either the presence or absence of seed microbial endophytes, of the conditioning and response phase. Seed fungal endophytes generated strong conspecific negative feedback, while seed bacterial endophytes proved to shift the feedback from negative to positive. Moreover, the simultaneous occurrence of both seed endophytes with AMF could either generate or expand negative plant-soil feedback effects. Our results show that seed and root symbionts can play a significant role on setting conspecific plant-soil feedback.

Epichloë Fungal Endophytes-From a Biological Curiosity in Wild Grasses to an Essential Component of Resilient High Performing Ryegrass and Fescue Pastures

The relationship between Epichloë endophytes found in a wide range of temperate grasses spans the continuum from antagonistic to mutualistic. The diversity of asexual mutualistic types can be characterised by the types of alkaloids they produce in planta. Some of these are responsible for detrimental health and welfare issues of ruminants when consumed, while others protect the host plant from insect pests and pathogens. In many temperate regions they are an essential component of high producing resilient tall fescue and ryegrass swards. This obligate mutualism between fungus and host is a seed-borne technology that has resulted in several commercial products being used with high uptake rates by end-user farmers, particularly in New Zealand and to a lesser extent Australia and USA. However, this has not happened by chance. It has been reliant on multi-disciplinary research teams undertaking excellent science to understand the taxonomic relationships of these endophytes, their life cycle, symbiosis regulation at both the cellular and molecular level, and the impact of secondary metabolites, including an understanding of their mammalian toxicity and bioactivity against insects and pathogens. Additionally, agronomic trials and seed biology studies of these microbes have all contributed to the delivery of robust and efficacious products. The supply chain from science, through seed companies and retailers to the end-user farmer needs to be well resourced providing convincing information on the efficacy and ensuring effective quality control to result in a strong uptake of these Epichloë endophyte technologies in pastoral agriculture.

Fungal evolution: cellular, genomic and metabolic complexity

The question of how phenotypic and genomic complexity are inter-related and how they are shaped through evolution is a central question in biology that historically has been approached from the perspective of animals and plants. In recent years, however, fungi have emerged as a promising alternative system to address such questions. Key to their ecological success, fungi present a broad and diverse range of phenotypic traits. Fungal cells can adopt many different shapes, often within a single species, providing them with great adaptive potential. Fungal cellular organizations span from unicellular forms to complex, macroscopic multicellularity, with multiple transitions to higher or lower levels of cellular complexity occurring throughout the evolutionary history of fungi. Similarly, fungal genomes are very diverse in their architecture. Deep changes in genome organization can occur very quickly, and these phenomena are known to mediate rapid adaptations to environmental changes. Finally, the biochemical complexity of fungi is huge, particularly with regard to their secondary metabolites, chemical products that mediate many aspects of fungal biology, including ecological interactions. Herein, we explore how the interplay of these cellular, genomic and metabolic traits mediates the emergence of complex phenotypes, and how this complexity is shaped throughout the evolutionary history of Fungi.

Environmental factors affect the distribution of two Epichloë fungal endophyte species inhabiting a common host grove bluegrass (Poa alsodes)

AIM

The endophyte Epichloë alsodes, with known insecticidal properties, is found in a majority of Poa alsodes populations across a latitudinal gradient from North Carolina to New York. A second endophyte, E. schardlii var. pennsylvanica, with known insect-deterring effects, is limited to a few populations in Pennsylvania. We explored whether such disparate differences in distributions could be explained by selection from biotic and abiotic environmental factors.

LOCATION

Along the Appalachian Mountains from North Carolina to New York, USA.

TAXON

Fungi.

METHODS

Studied correlations of infection frequencies with abiotic and biotic environmental factors. Checked endophyte vertical transmission rates and effects on overwintering survival. With artificial inoculations for two host populations with two isolates per endophyte species, tested endophyte-host compatibility. Studied effects of isolates on host performances in greenhouse experiment with four water-nutrients treatments.

RESULTS

Correlation analysis revealed positive associations of E. alsodes frequency with July Max temperatures, July precipitation, and soil nitrogen and phosphorous and negative associations with insect damage and soil magnesium and potassium. Plants infected with E. alsodes had increased overwintering survival compared to plants infected with E. schardlii or uninfected (E-) plants. Artificial inoculations indicated that E. alsodes had better compatibility with a variety of host genotypes than did E. schardlii. The experiment with reciprocally inoculated plants grown under different treatments revealed a complexity of interactions among hosts, endophyte species, isolate within species, host plant origin, and environmental factors. Neither of the endophyte species increased plant biomass, but some of the isolates within each species had other effects on plant growth such as increased root:shoot ratio, number of tillers, and changes in plant height that might affect host fitness.

MAIN CONCLUSION

In the absence of clear and consistent effects of the endophytes on host growth, the differences in endophyte-mediated protection against herbivores may be the key factor determining distribution differences of the two endophyte species.

Various Phyllosphere and Soil Bacterial Communities of Natural Grasses and the Impact Factors in a Copper Tailings Dam

Copper mining caused severe damage to the ecological environment of mining areas. The combination of microbe and plant remediation has an application potential in improving the absorption and transformation efficiency of heavy metals. The phyllosphere is the largest biointerface on the planet, and bacteria are the dominant microbial inhabitants of the phyllosphere, believed to be critical to plant growth and health. This study investigated the phyllospheric and soil bacteria communities using high-throughput sequencing, and endophyte infection statuses of four natural grasses by toluidine blue heparin assay. Results showed variation in phyllospheric bacterial community structure. Gammaproteobacteria were the most abundant bacterial population. Bacilli were found in the phyllosphere of Bothriochloa ischaemum and Imperata cylindrica, while Clostridia were only found in Calamagrostis epigejos. Alphaproteobacteria were the dominant bacteria in soil. In addition, bacterial communities were influenced by endophytic infection statuses. Oxalobacteraceae was associated with soil carbon and sulfur. Enterobacteriaceae had negative correlation with the ratio of soil carbon and nitrogen, and had positive correlation with Cd content. These results offer useful insights into phyllospheric bacterial community variance in four different natural grasses in a copper tailings dam.

Variation in the Prevalence and Transmission of Heritable Symbionts Across Host Populations in Heterogeneous Environments

Heritable microbes are abundant in nature and influential to their hosts and the communities in which they reside. However, drivers of variability in the prevalence of heritable symbionts and their rates of transmission are poorly resolved, particularly across host populations experiencing variable biotic and abiotic environments. To fill these gaps, we surveyed 25 populations of two native grasses (Elymus virginicus and Elymus canadensis) across the southern Great Plains (USA). Both grass species host heritable endophytic fungi (genus Epichloё) and can hybridize where their ranges overlap. From a subset of hosts, we characterized endophyte genotype using genetic loci that link to bioactive alkaloid production. First, we found mean vertical transmission rates and population-level prevalence were positively correlated, specifically for E. virginicus. However, both endophyte prevalence and transmission varied substantially across populations and did not strongly correlate with abiotic variables, with one exception: endophyte prevalence decreased as drought stress decreased for E. virginicus hosts. Second, we evaluated the potential influence of biotic factors and found that, after accounting for climate, endophyte genotype explained significant variation in symbiont inheritance. We also contrasted populations where host species co-occurred in sympatry vs. allopatry. Sympatry could potentially increase interspecific hybridization, but this variable did not associate with patterns of symbiont prevalence or transmission success. Our results reveal substantial variability in symbiont prevalence and transmission across host populations and identify symbiont genotype, and to a lesser extent, the abiotic environment as sources of this variation.

Species boundaries in the human pathogen Paracoccidioides

The use of molecular taxonomy for identifying recently diverged species has transformed the study of speciation in fungi. The pathogenic fungus Paracoccidioides spp has been hypothesized to be composed of five phylogenetic species, four of which compose the brasiliensis species complex. Nuclear gene genealogies support this divergence scenario, but mitochondrial loci do not; while all species from the brasiliensis complex are differentiated at nuclear coding loci, they are not at mitochondrial loci. We addressed the source of this incongruity using 11 previously published gene fragments, 10 newly-sequenced nuclear non-coding loci, and 10 microsatellites. We hypothesized and further demonstrated that the mito-nuclear incongruence in the brasiliensis species complex results from interspecific hybridization and mitochondrial introgression, a common phenomenon in eukaryotes. Additional population genetic analyses revealed possible nuclear introgression but much less than that seen in the mitochondrion. Our results are consistent with a divergence scenario of secondary contact and subsequent mitochondrial introgression despite the continued persistence of species boundaries. We also suggest that yeast morphology slightly-but significantly-differs across all five Paracoccidioides species and propose to elevate four of these phylogenetic species to formally described taxonomic species.

Interspecific and intraspecific hybrid Epichloë species symbiotic with the North American native grass Poa alsodes

The endophyte presence and diversity in natural populations of Poa alsodes were evaluated along a latitudinal transect from the southern distribution range in North Carolina to New York. Two distinct Epichloë hybrid taxa were identified from 23 populations. Each taxon could easily be distinguished by polymerase chain reaction (PCR) genotyping with primers designed to mating type genes and alkaloid biosynthesis genes that encode key pathway steps for ergot alkaloids, indole-diterpenes, lolines, and peramine. The most commonly found Epichloë taxon, Poa alsodes Taxonomic Group-1 (PalTG-1), was detected in 22 populations at high infection frequencies (72-100%), with the exception of one population at high elevation (26% infection). The second taxon, PalTG-2, was observed only in five populations in Pennsylvania constituting 12% of infected samples. Phylogenetic analyses placed PalTG-1 as an interspecific hybrid of E. amarillans and E. typhina subsp. poae ancestors, and it is considered a new hybrid species, which the authors name Epichloë alsodes. PalTG-2 is an intraspecific hybrid of two E. typhina subsp. poae ancestors, similar to E. schardlii from the host Cinna arundinacea, which the authors propose as a new variety, Epichloë schardlii var. pennsylvanica. Epichloë alsodes isolates were all mating type MTA MTB and tested positive for dmaW, easC, perA, and some LOL genes, but only the alkaloid N-acetylnorloline was detected in E. alsodes-infected plant material. Epichloë schardlii var. pennsylvanica isolates were all mating type MTB MTB and tested positive for perA, but peramine was not produced. Both E. alsodes and E. schardlii var. pennsylvanica appeared to have complete perA genes, but point mutations were identified in E. alsodes that would render the encoded perA gene nonfunctional.

Does hybridization of endophytic symbionts in a native grass increase fitness in resource-limited environments?

Hybridization is common among plants, animals and microbes. However, the ecological consequences of hybridization for microbes are far less understood than for plants and animals. For symbiotic Epichloë fungi, hybridization is widespread and may augment the well-known benefits of the endophytes to their grass hosts, especially in stressful environments. We tested the hybrid fitness hypothesis (HFH) that hybrid endophytes enhance fitness in stressful environments relative to non-hybrid endophytes. In a long-term field experiment, we monitored growth and reproduction of hybrid-infected (H+), non-hybrid infected (NH+), naturally endophyte free (E-) plants and those plants from which the endophyte had been experimentally removed (H- and NH-) in resource-rich and resource-poor environments. Infection by both endophyte species enhanced growth and reproduction. H+ plants outperformed NH+ plants in terms of growth by the end of the experiment, supporting HFH. However, H+ plants only outperformed NH+ plants in the resource-rich treatment, contrary to HFH. Plant genotypes associated with each endophyte species had strong effects on growth and reproduction. Our results provide some support the HFH hypothesis but not based upon adaptation to stressful environments. Our results reinforce the notion of a complex interplay between endophyte and plant genotype and environmental factors that determine fitness of the symbiotum.

The Mechanisms and Consequences of Interspecific Competition Among Plants

During the past 100 years, studies spanning thousands of taxa across almost all biomes have demonstrated that competition has powerful negative effects on the performance of individuals and can affect the composition of plant communities, the evolution of traits, and the functioning of whole ecosystems. In this review, we highlight new and important developments that have the potential to greatly improve our understanding of how plants compete and the consequences of competition from individuals to communities in the following major areas of research: (a) mechanisms of competition, (b) competitive effect and response, (c) direct and indirect effects of competition, (d) population-level effects of competition, (e) biogeographical differences in competition, and (f) conditionality of competition. Ecologists have discovered much about competition, but the mechanisms of competition and how competition affects the organization of communities in nature still require both theoretical and empirical exploration.

Effects of Hybrid and Non-hybrid Epichloë Endophytes and Their Associated Host Genotypes on the Response of a Native Grass to Varying Environments

Asexual Epichloë endophytes are prevalent in cool season grasses, and many are of hybrid origin. Hybridization of asexual endophytes is thought to provide a rapid influx of genetic variation that may be adaptive to endophyte-host grass symbiota in stressful environments. For Arizona fescue (Festuca arizonica), hybrid symbiota are commonly found in resource-poor environments, whereas non-hybrid symbiota are more common in resource-rich environments. There have been very few experimental tests where infection, hybrid and non-hybrid status, and plant genotype have been controlled to tease apart their effects on host phenotype and fitness in different environments. We conducted a greenhouse experiment where hybrid (H) and non-hybrid (NH) endophytes were inoculated into plant genotypes that were originally uninfected (E-) or once infected with either the H or NH endophytes. Nine endophyte and plant genotypic group combinations were grown under low and high water and nutrient treatments. Inoculation with the resident H endophyte enhanced growth and altered allocation to roots and shoots, but these effects were greatest in resource-rich environments, contrary to expectations. We found no evidence of co-adaptation between endophyte species and their associated host genotypes. However, naturally E- plants performed better when inoculated with the hybrid endophyte, suggesting these plants were derived from H infected lineages. Our results show complex interactions between endophyte species of hybrid and non-hybrid origin with their host plant genotypes and environmental factors.

The Role of Hybridization in the Evolution and Emergence of New Fungal Plant Pathogens

Hybridization in fungi has recently been recognized as a major force in the generation of new fungal plant pathogens. These include the grass pathogen Zymoseptoria pseudotritici and the powdery mildew pathogen Blumeria graminis triticale of triticale. Hybridization also plays an important role in the transfer of genetic material between species. This process is termed introgressive hybridization and involves extensive backcrossing between hybrid and the parental species. Introgressive hybridization has contributed substantially to the successful spread of plant pathogens such as Ophiostoma ulmi and O. novo-ulmi, the causal agents of Dutch elm disease, and other tree pathogens such as the rust pathogen Melampsora. Hybridization occurs more readily between species that have previously not coexisted, so-called allopatric species. Reproductive barriers between allopatric species are likely to be more permissive allowing interspecific mating to occur. The bringing together of allopatric species of plant pathogens by global agricultural trade consequently increases the potential for hybridization between pathogen species. In light of global environmental changes, agricultural development, and the facilitated long-distance spread of fungal plant pathogens, hybridization should be considered an important mechanism whereby new pathogens may emerge. Recent studies have gained insight into the genetics and biology of fungal hybrids. Here I summarize current knowledge about hybrid speciation and introgressive hybridization. I propose that future studies will benefit greatly from the availability of large genome data sets and that genome data provide a powerful resource in combination with experimental approaches for analyses of hybrid species.

Fungal endophyte Phomopsis liquidambari affects nitrogen transformation processes and related microorganisms in the rice rhizosphere

The endophytic fungus Phomopsis liquidambari performs an important ecosystem service by assisting its host with acquiring soil nitrogen (N), but little is known regarding how this fungus influences soil N nutrient properties and microbial communities. In this study, we investigated the impact of P. liquidambari on N dynamics, the abundance and composition of N cycling genes in rhizosphere soil treated with three levels of N (urea). Ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and diazotrophs were assayed using quantitative real-time polymerase chain reaction and denaturing gradient gel electrophoresis at four rice growing stages (S0: before planting, S1: tillering stage, S2: grain filling stage, and S3: ripening stage). A significant increase in the available nitrate and ammonium contents was found in the rhizosphere soil of endophyte-infected rice under low N conditions. Moreover, P. liquidambari significantly increased the potential nitrification rates, affected the abundance and community structure of AOA, AOB, and diazotrophs under low N conditions in the S1 and S2 stages. The root exudates were determined due to their important role in rhizosphere interactions. P. liquidambari colonization altered the exudation of organic compounds by rice roots and P. liquidambari increased the concentration of soluble saccharides, total free amino acids and organic acids in root exudates. Plant-soil feedback mechanisms may be mediated by the rice-endophyte interaction, especially in nutrient-limited soil.

Effects of the Epichloë fungal endophyte symbiosis with Schedonorus pratensis on host grass invasiveness

Initial studies of grass-endophyte mutualisms using Schedonorus arundinaceus cultivar Kentucky-31 infected with the vertically transmitted endophyte Epichloë coenophiala found strong, positive endophyte effects on host-grass invasion success. However, more recent work using different cultivars of S. arundinaceus has cast doubt on the ubiquity of this effect, at least as it pertains to S. arundinaceus-E. coenophiala. We investigated the generality of previous work on vertically transmitted Epichloë-associated grass invasiveness by studying a pair of very closely related species: S. pratensis and E. uncinata. Seven cultivars of S. pratensis and two cultivars of S. arundinaceus that were developed with high- or low-endophyte infection rate were broadcast seeded into 2 × 2-m plots in a tilled, old-field grassland community in a completely randomized block design. Schedonorus abundance, endophyte infection rate, and co-occurring vegetation were sampled 3, 4, 5, and 6 years after establishment, and the aboveground invertebrate community was sampled in S. pratensis plots 3 and 4 years after establishment. Endophyte infection did not enable the host grass to achieve high abundance in the plant community. Contrary to expectations, high-endophyte S. pratensis increased plant richness relative to low-endophyte cultivars. However, as expected, high-endophyte S. pratensis marginally decreased invertebrate taxon richness. Endophyte effects on vegetation and invertebrate community composition were inconsistent among cultivars and were weaker than temporal effects. The effect of the grass-Epichloë symbiosis on diversity is not generalizable, but rather specific to species, cultivar, infection, and potentially site. Examining grass-endophyte systems using multiple cultivars and species replicated among sites will be important to determine the range of conditions in which endophyte associations benefit host grass performance and have subsequent effects on co-occurring biotic communities.

Vegetative hyphal fusion and subsequent nuclear behavior in Epichloë grass endophytes

Epichloë species (including the former genus Neotyphodium) are fungal symbionts of many agronomically important forage grasses, and provide their grass hosts with protection from a wide range of biotic and abiotic stresses. Epichloë species include many interspecific hybrids with allodiploid-like genomes, which may provide the potential for combined traits or recombination to generate new traits. Though circumstantial evidence suggests that such interspecific hybrids might have arisen from nuclear fusion events following vegetative hyphal fusion between different Epichloë strains, this hypothesis has not been addressed empirically. Here, we investigated vegetative hyphal fusion and subsequent nuclear behavior in Epichloë species. A majority of Epichloë strains, especially those having a sexual stage, underwent self vegetative hyphal fusion. Vegetative fusion also occurred between two hyphae from different Epichloë strains. Though Epichloë spp. are uninucleate fungi, hyphal fusion resulted in two nuclei stably sharing the same cytoplasm, which might ultimately lead to nuclear fusion. In addition, protoplast fusion experiments gave rise to uninucleate putative hybrids, which apparently had two markers, one from each parent within the same nucleus. These results are consistent with the notion that interspecific hybrids arise from vegetative hyphal fusion. However, we also discuss additional factors, such as post-hybridization selection, that may be important to explain the recognized prevalence of hybrids in Epichloë species.

Improvement of nitrogen accumulation and metabolism in rice (Oryza sativa L.) by the endophyte Phomopsis liquidambari

The fungal endophyte Phomopsis liquidambari can enhance nitrogen (N) uptake and metabolism of rice plants under hydroponic conditions. To investigate the effects of P. liquidambari on N accumulation and metabolism in rice (Oryza sativa L.) under field conditions during the entire growing season (S1, the seedling stage; S2, the tillering stage; S3, the heading stage; S4, the ripening stage), we utilized pot experiments to examine metabolic and physiological levels in both shoot and root tissues of rice, with endophyte (E+) and without endophyte (E-), in response to three different N levels. We found that under low-N treatment, P. liquidambari symbiosis increased the rice yield and N use efficiency by 12% and by 11.59%, respectively; that the total N contents in E+ rice plants at the four growth stages were separately increased by 29.05%, 14.65%, 21.06% and 18.38%, respectively; and that the activities of nitrate reductase and glutamine synthetase in E+ rice roots and shoots were significantly increased by fungal infection during the S1 to S3 stages. Moreover, P. liquidambari significantly increased the free NH4(+), NO3(-), amino acid and soluble protein contents in infected rice tissues under low-N treatment during the S1 to S3 stages. The obtained results offer novel data concerning the systemic changes induced by P. liquidambari in rice during the entire growth period and confirm the hypothesis that the rice-P. liquidambari interaction improved the N accumulation and metabolism of rice plants, consequently increasing rice N utilization in nutrient-limited soil.

Communities of endophytic sebacinales associated with roots of herbaceous plants in agricultural and grassland ecosystems are dominated by Serendipita herbamans sp. nov

Endophytic fungi are known to be commonly associated with herbaceous plants, however, there are few studies focusing on their occurrence and distribution in plant roots from ecosystems with different land uses. To explore the phylogenetic diversity and community structure of Sebacinales endophytes from agricultural and grassland habitats under different land uses, we analysed the roots of herbaceous plants using strain isolation, polymerase chain reaction (PCR), transmission electron microscopy (TEM) and co-cultivation experiments. A new sebacinoid strain named Serendipita herbamans belonging to Sebacinales group B was isolated from the roots of Bistorta vivipara, which is characterized by colourless monilioid cells (chlamydospores) that become yellow with age. This species was very common and widely distributed in association with a broad spectrum of herbaceous plant families in diverse habitats, independent of land use type. Ultrastructurally, the presence of S. herbamans was detected in the cortical cells of Plantago media, Potentilla anserina and Triticum aestivum. In addition, 13 few frequent molecular operational taxonomic units (MOTUs) or species were found across agricultural and grassland habitats, which did not exhibit a distinctive phylogenetic structure. Laboratory-based assays indicate that S. herbamans has the ability to colonize fine roots and stimulate plant growth. Although endophytic Sebacinales are widely distributed across agricultural and grassland habitats, TEM and nested PCR analyses reinforce the observation that these microorganisms are present in low quantity in plant roots, with no evidence of host specificity.

Effects of natural hybrid and non-hybrid Epichloë endophytes on the response of Hordelymus europaeus to drought stress

Interspecific hybrid endophytes of the genus Epichloë (Ascomycota, Clavicipitaceae) are prevalent in wild grass populations, possibly because of their larger gene variation, resulting in increased fitness benefits for host plants; however, the reasons are not yet known. We tested hypotheses regarding niche expansion mediated by hybrid endophytes, population-dependent interactions and local co-adaptation in the woodland grass Hordelymus europaeus, which naturally hosts both hybrid and non-hybrid endophyte taxa. Seedlings derived from seeds of four grass populations made endophyte free were re-inoculated with hybrid or non-hybrid endophyte strains, or left endophyte free. Plants were grown in the glasshouse with or without drought treatment. Endophyte infection increased plant biomass and tiller production by 10-15% in both treatments. Endophyte types had similar effects on growth, but opposite effects on reproduction: non-hybrid endophytes increased seed production, whereas hybrid endophytes reduced or prevented it completely. The results are consistent with the observation that non-hybrid endophytes in H. europaeus prevail at dry sites, but cannot explain the prevalence of hybrid endophytes. Thus, our results do not support the hypothesis of niche expansion of hybrid-infected plants. Moreover, plants inoculated with native relative to foreign endophytes yielded higher infections, but both showed similar growth and survival, suggesting weak co-adaptation.

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.

Currencies of mutualisms: sources of alkaloid genes in vertically transmitted epichloae

The epichloae (Epichloë and Neotyphodium species), a monophyletic group of fungi in the family Clavicipitaceae, are systemic symbionts of cool-season grasses (Poaceae subfamily Poöideae). Most epichloae are vertically transmitted in seeds (endophytes), and most produce alkaloids that attack nervous systems of potential herbivores. These protective metabolites include ergot alkaloids and indole-diterpenes (tremorgens), which are active in vertebrate systems, and lolines and peramine, which are more specific against invertebrates. Several Epichloë species have been described which are sexual and capable of horizontal transmission, and most are vertically transmissible also. Asexual epichloae are mainly or exclusively vertically transmitted, and many are interspecific hybrids with genomic contributions from two or three ancestral Epichloë species. Here we employ genome-scale analyses to investigate the origins of biosynthesis gene clusters for ergot alkaloids (EAS), indole-diterpenes (IDT), and lolines (LOL) in 12 hybrid species. In each hybrid, the alkaloid-gene and housekeeping-gene relationships were congruent. Interestingly, hybrids frequently had alkaloid clusters that were rare in their sexual ancestors. Also, in those hybrids that had multiple EAS, IDT or LOL clusters, one cluster lacked some genes, usually for late pathway steps. Possible implications of these findings for the alkaloid profiles and endophyte ecology are discussed.

Models of experimental competitive intensities predict home and away differences in invasive impact and the effects of an endophytic mutualist

Understanding the role of competition in the organization of communities is limited in part by the difficulty of extrapolating the outcomes of small-scale experiments to how such outcomes might affect the distribution and abundance of species. We modeled the community-level outcomes of competition, using experimentally derived competitive effects and responses between an exotic invasive plant, Centaurea stoebe, and species from both its native and nonnative ranges and using changes in these effects and responses elicited by experimentally establishing symbioses between C. stoebe and fungal endophytes. Using relative interaction intensities (RIIs) and holding other life-history factors constant, individual-based and spatially explicit models predicted competitive exclusion of all but one North American species but none of the European species, regardless of the endophyte status of C. stoebe. Concomitantly, C. stoebe was eliminated from the models with European natives but was codominant in models with North American natives. Endophyte symbiosis predicted increased dominance of C. stoebe in North American communities but not in European communities. However, when experimental variation was included, some of the model outcomes changed slightly. Our results are consistent with the idea that the effects of competitive intensity and mutualisms measured at small scales have the potential to play important roles in determining the larger-scale outcomes of invasion and that the stabilizing indirect effects of competition may promote species coexistence.