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

Divergent rainforest tree microbiomes between phases of the monsoon cycle, host plants and tissues

The Australian Monsoon Tropics (AMT) contain some of the most biodiverse forests on the continent. Little is known about the dynamics of rainforest plant microbiomes in general, and there have been no community-level studies on Australian rainforest endophytes, their seasonality, tissue and host specificity. We tested whether community composition of tropical tree endophytes (fungi and bacteria) differs: (i) at different points during a monsoon cycle, (ii) between leaf and stem tissues, (iii) between forest microclimates (gully/ridge), and between (iv) host plant species, and (v) host plant clade, using amplicon sequencing of the bacterial 16S and fungal ITS2 gene regions. Results indicated that the composition of rainforest plant microbiomes differs between wet and dry seasons, which may be explained by physiological shifts in host plants due to annual climate fluctuations from mesic to xeric. Endophyte microbiomes differed between leaves and stems. Distinct fungal communities were associated with host species and clades, with some trees enriched in a number of fungal taxa compared to host plants in other clades. Diversity of bacterial endophytes in plant stems increased in the dry season. We conclude that the microbiomes of tropical plants are responsive to monsoonal climate variation, are highly compartmentalised between plant tissues, and may be partly shaped by the relatedness of their host plants.

Epichloë Endophytes Shape the Foliar Endophytic Fungal Microbiome and Alter the Auxin and Salicylic Acid Phytohormone Levels in Two Meadow Fescue Cultivars

Plants harbor a large diversity of endophytic microbes. Meadow fescue (Festuca pratensis) is a cool-season grass known for its symbiotic relationship with the systemic and vertically-via seeds-transmitted fungal endophyte Epichloë uncinata, yet its effects on plant hormones and the microbial community is largely unexplored. Here, we sequenced the endophytic bacterial and fungal communities in the leaves and roots, analyzing phytohormone concentrations and plant performance parameters in Epichloë-symbiotic (E+) and Epichloë-free (E-) individuals of two meadow fescue cultivars. The endophytic microbial community differed between leaf and root tissues independent of Epichloë symbiosis, while the fungal community was different in the leaves of Epichloë-symbiotic and Epichloë-free plants in both cultivars. At the same time, Epichloë symbiosis decreased salicylic acid and increased auxin concentrations in leaves. Epichloë-symbiotic plants showed higher biomass and higher seed mass at the end of the season. Our results demonstrate that Epichloë symbiosis alters the leaf fungal microbiota, which coincides with changes in phytohormone concentrations, indicating that Epichloë endophytes affect both plant immune responses and other fungal endophytes. Whether the effect of Epichloë endophytes on other fungal endophytes is connected to changes in phytohormone concentrations remains to be elucidated.

Epichloë Increases Root Fungal Endophyte Richness and Alters Root Fungal Endophyte Composition in a Changing World

Plants harbor a variety of fungal symbionts both above- and belowground, yet little is known about how these fungi interact within hosts, especially in a world where resource availability is changing due to human activities. Systemic vertically transmitted endophytes such as Epichloë spp. may have particularly strong effects on the diversity and composition of later-colonizing symbionts such as root fungal endophytes, especially in primary successional systems. We made use of a long-term field experiment in Great Lakes sand dunes to test whether Epichloë colonization of the dune-building grass, Ammophila breviligulata, could alter fungal root endophyte species richness or community composition in host plants. We also tested whether nitrogen addition intensified the effects of Epichlöe on the root endophyte community. We found that Epichloë increased richness of root endophytes in Ammophila by 17% overall, but only shifted community composition of root endophytes under nitrogen-enriched conditions. These results indicate that Epichlöe acts as a key species within Ammophila, changing richness and composition of the root mycobiome and integrating above- and belowground mycobiome interactions. Further, effects of Epichloë on root endophyte communities were enhanced by N addition, indicating that this fungal species may become even more important in future environments.

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

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

Antimicrobial activity and metabolite profiling of endophytic fungi in Digitaria bicornis (Lam) Roem. and Schult. and Paspalidium flavidum (Retz.) A. Camus

Endophytic fungal occurrences were studied in aerial regions of Digitaria bicornis and Paspalidium flavidum by three isolation methods: potato dextrose agar (PDA), malt extract agar (MEA), and moist blotters. Seventy species of 29 genera of endophytic fungi in D. bicornis and 71 species of 30 genera in P. flavidum were documented. Endophytic fungal communities were grouped into 40 and 43 anamorphic ascomycetes (21 and 23 genera) and 20 teleomorphic ascomycetes (6 and 7 genera) in D. bicornis and P. flavidum, respectively. PDA supported the expression of larger number of fungal communities than MEA and MB; and P. flavidum hosted more number of endophytic fungi than D. bicornis. Seasons played an important role in supporting the assemblage of fungal endophytes. Endophytic fungal species richness and assemblages in plant regions were determined for alpha, beta, and gamma diversities. The ethyl acetate followed by methanolic extracts of certain fungal species showed good antagonistic and antibacterial activities. Among fungal endophytes, Curvularia protuberata and Penicillium citrinum exhibited high antagonistic and antibacterial activities. The high-resolution orbitrap liquid chromatography-mass spectrometry of ethyl acetate crude extracts of C. protuberata and P. citrinum revealed the presence of antifungal and antimicrobial, besides a host of compounds in the extracts. The present study indicated that grass endophytes are the sources of compounds with antimicrobial and other pharmacological activities.

Habitat-scale heterogeneity maintains fungal endophyte diversity in two native prairie legumes

The assembly of fungal endophyte communities within plants depends on the complex interactions of fungal taxa, their host plants, and the abiotic environment. Prairie plant communities provide a unique avenue to explore the interplay of biotic and abiotic factors affecting endophyte communities, since the historical distribution of prairies spans a broad range of temperature and precipitation, while the distances between small fragments of contemporary prairie communities may challenge the dispersal capabilities of these otherwise ubiquitous fungi. We sampled foliar fungal endophytes from two native prairie legumes, purple and white prairie clovers (Dalea purpurea and D. candida), in 17 remnant prairie sites across Minnesota in order to evaluate the relative contributions of abiotic factors, host species, and dispersal limitation to the diversity and structure of these communities. We found that similarity of communities was significantly associated with their location along a temperature and precipitation gradient, and we showed a distance-decay relationship that suggests dispersal limitations only over very large spatial scales. Although the effect of host species was small relative to these other factors, the two Dalea species maintained distinct communities within sites where they co-occur. Our results illustrate the capacity of many of these endophyte taxa to disperse over large distances and across heterogeneous biotic and abiotic environments and suggest that the interplay of biotic and abiotic factors maintains high diversity observed in endophyte communities.

Festulolium and fungal endophyte associations: host status for Meloidogyne incognita and nematotoxic plant extracts

Festulolium hybrids are forage grasses used worldwide in temperate climates. They are associated with the fungal endophyte Epichloë uncinata, which aids in nutrient uptake, drought tolerance, and production of metabolites that protect against parasites and herbivores. Epichloë uncinata produces loline alkaloids, which can deter insect pests. Festulolium has not been widely studied for susceptibility to plant-parasitic nematodes, so Festulolium lines, with and without fungal endophytes, were tested in the greenhouse for host status to the root-knot nematode Meloidogyne incognita. All were poor hosts, regardless of line or endophyte status. Pepper seedlings planted into soil following removal of the Festulolium plants were infected by nematodes, likely because of surviving nematodes from the original inoculation combined with some reproduction on Festulolium. Lolines were found in shoots and roots of all endophyte-associated lines, and some types of lolines in roots increased after nematode infection. Methanolic extracts from roots and shoots of a tested Festulolium line did not inhibit egg hatch, but killed nearly a third of second-stage juveniles whether an endophyte was present or not. Further studies would indicate whether these Festulolium lines aid in suppressing field populations of M. incognita.

Festulolium hybrids are forage grasses used worldwide in temperate climates. They are associated with the fungal endophyte Epichloë uncinata, which aids in nutrient uptake, drought tolerance, and production of metabolites that protect against parasites and herbivores. Epichloë uncinata produces loline alkaloids, which can deter insect pests. Festulolium has not been widely studied for susceptibility to plant-parasitic nematodes, so Festulolium lines, with and without fungal endophytes, were tested in the greenhouse for host status to the root-knot nematode Meloidogyne incognita. All were poor hosts, regardless of line or endophyte status. Pepper seedlings planted into soil following removal of the Festulolium plants were infected by nematodes, likely because of surviving nematodes from the original inoculation combined with some reproduction on Festulolium. Lolines were found in shoots and roots of all endophyte-associated lines, and some types of lolines in roots increased after nematode infection. Methanolic extracts from roots and shoots of a tested Festulolium line did not inhibit egg hatch, but killed nearly a third of second-stage juveniles whether an endophyte was present or not. Further studies would indicate whether these Festulolium lines aid in suppressing field populations of M. incognita.

Agricultural and Other Biotechnological Applications Resulting from Trophic Plant-Endophyte Interactions

Endophytic microbiota plays a role not only in supplying plants with the basic nutrients indispensable for their growth, but also helps them in the mechanisms of adaptation to various environmental stresses (i.e., salinity, drought), which is important in the aspect of crop yields. From the agricultural and biotechnological points of view, the knowledge of endophytes and their roles in increasing crop yields, plant resistance to diseases, and helping to survive environmental stress is extremely desirable. This paper reviews some of the beneficial plant–microbe interactions that might be potentially used in both agriculture (plant growth stimulation effect, adaptation of host organisms in salinity and drought conditions, and support of defense mechanisms in plants), and in biotechnology (bioactive metabolites, application of endophytes for bioremediation and biotransformation processes, and production of biofertilizers and biopreparations). Importantly, relatively recent reports on endophytes from the last 10 years are summarized in this paper.

Testing for loss of Epichloë and non-epichloid symbionts under altered rainfall regimes

PREMISE

Microbial symbionts can buffer plant hosts from environmental change. Therefore, understanding how global change factors alter the associations between hosts and their microbial symbionts may improve predictions of future changes in host population dynamics and microbial diversity. Here, we investigated how one global change factor, precipitation, affected the maintenance or loss of symbiotic fungal endophytes in a C₃ grass host. Specifically, we examined the distinct responses of Epichloë (vertically transmitted and systemic) and non-epichloid endophytes (typically horizontally transmitted and localized) by considering (1) how precipitation altered associations with Epichloë and non-epichloid endophytic taxa across host ontogeny, and (2) interactive effects of water availability and Epichloë on early seedling life history stages.

METHODS

We manipulated the presence of Epichloë amarillans in American beachgrass (Ammophila breviligulata) in a multiyear field experiment that imposed three precipitation regimes (ambient or ±30% rainfall). In laboratory assays, we investigated the interactive effects of water availability and Epichloë on seed viability and germination.

RESULTS

Reduced precipitation decreased the incidence of Epichloë in leaves in the final sampling period, but had no effect on associations with non-epichloid taxa. Epichloë reduced the incidence of non-epichloid endophytes, including systemic p-endophytes, in seeds. Laboratory assays suggested that association with Epichloë is likely maintained, in part, due to increased seed viability and germination regardless of water availability.

CONCLUSIONS

Our study empirically demonstrates several pathways for plant symbionts to be lost or maintained across host ontogeny and suggests that reductions in precipitation can drive the loss of a plant's microbial symbionts.

Heritable Epichloë symbiosis shapes fungal but not bacterial communities of plant leaves

Keystone microbial species have driven eco-evolutionary processes since the origin of life. However, due to our inability to detect the majority of microbiota, members of diverse microbial communities of fungi, bacteria and viruses have largely been ignored as keystone species in past literature. Here we tested whether heritable Epichloë species of pooidae grasses modulate microbiota of their shared host plant.

Fungal Endophyte Communities of Three Agricultural Important Grass Species Differ in Their Response Towards Management Regimes

Despite the importance of endophytic fungi for plant health, it remains unclear how these fungi are influenced by grassland management practices. Here, we investigated the effect of fertilizer application and mowing frequency on fungal endophyte communities and their life strategies in aerial tissues of three agriculturally important grass species (Dactylis glomerata L., Festuca rubra L. and Lolium perenne L.) over two consecutive years. Our results showed that the management practices influenced fungal communities in the plant holobiont, but observed effects differed between grass species and sampling year. Phylogenetic diversity of fungal endophytes in D. glomerata was significantly affected by mowing frequency in 2010, whereas fertilizer application and the interaction of fertilization with mowing frequency had a significant impact on community composition of L. perenne in 2010 and 2011, respectively. Taken together, our research provides a basis for future studies on responses of fungal endophytes towards management practices. To the best of our knowledge, this is the first study simultaneously assessing fungal endophyte communities in aerial parts of three agriculturally important grass species over two consecutive years.