Diversity, taxonomic composition, and functional aspects of fungal communities in living, senesced, and fallen leaves at five sites across North America

Leaf Health Status Regulates Endophytic Microbial Community Structure, Network Complexity, and Assembly Processes in the Leaves of the Rare and Endangered Plant Species Abies fanjingshanensis

The rare and endangered plant species Abies fanjingshanensis, which has a limited habitat, a limited distribution area, and a small population, is under severe threat, particularly due to poor leaf health. The plant endophytic microbiome is an integral part of the host, and increasing evidence indicates that the interplay between plants and endophytic microbes is a key determinant for sustaining plant fitness. However, little attention has been given to the differences in the endophytic microbial community structure, network complexity, and assembly processes in leaves with different leaf health statuses. Here, we investigated the endophytic bacterial and fungal communities in healthy leaves (HLs) and non-healthy leaves (NLs) of A. fanjingshanensis using 16S rRNA gene and internal transcribed spacer sequencing and evaluated how leaf health status affects the co-occurrence patterns and assembly processes of leaf endophytic microbial communities based on the co-occurrence networks, the niche breadth index, a neutral community model, and C-score metrics. HLs had significantly greater endophytic bacterial and fungal abundance and diversity than NLs, and there were significant differences in the endophytic microbial communities between HLs and NLs. Leaf-health-sensitive endophytic microbes were taxonomically diverse and were mainly grouped into four ecological clusters according to leaf health status. Poor leaf health reduced the complexity of the endophytic bacterial and fungal community networks, as reflected by a decrease in network nodes and edges and an increase in degrees of betweenness and assortativity. The stochastic processes of endophytic bacterial and fungal community assembly were weakened, and the deterministic processes became more important with declining leaf health. These results have important implications for understanding the ecological patterns and interactions of endophytic microbial communities in response to changing leaf health status and provide opportunities for further studies on exploiting plant endophytic microbes to conserve this endangered Abies species.

Fungal Endophytes: Discovering What Lies within Some of Canada's Oldest and Most Resilient Grapevines

Plant diseases and pests reduce crop yields, accounting for global crop losses of 30% to 50%. In conventional agricultural production systems, these losses are typically controlled by applying chemical pesticides. However, public pressure is mounting to curtail agrochemical use. In this context, employing beneficial endophytic microorganisms is an increasingly attractive alternative to the use of conventional chemical pesticides in agriculture. A multitude of fungal endophytes are naturally present in plants, producing enzymes, small peptides, and secondary metabolites due to their bioactivity, which can protect hosts from pathogens, pests, and abiotic stresses. The use of beneficial endophytic microorganisms in agriculture is an increasingly attractive alternative to conventional pesticides. The aim of this study was to characterize fungal endophytes isolated from apparently healthy, feral wine grapes in eastern Canada that have grown without agrochemical inputs for decades. Host plants ranged from unknown seedlings to long-lost cultivars not widely propagated since the 1800s. HPLC-MS was used to identify unique endophyte-derived chemical compounds in the host plants, while dual-culture competition assays showed a range in endophytes' ability to suppress the mycelial growth of Botrytis, which is typically controlled in viticulture with pesticides. Twelve of the most promising fungal endophytes isolated were identified using multilocus sequencing and morphology, while DNA barcoding was employed to identify some of their host vines. These fungal endophyte isolates, which consisted of both known and putative novel strains, belonged to seven genera in six families and five orders of Ascomycota. Exploring the fungal endophytes in these specimens may yield clues to the vines' survival and lead to the discovery of novel biocontrol agents.

Endophyte genomes support greater metabolic gene cluster diversity compared with non-endophytes in Trichoderma

Trichoderma is a cosmopolitan genus with diverse lifestyles and nutritional modes, including mycotrophy, saprophytism, and endophytism. Previous research has reported greater metabolic gene repertoires in endophytic fungal species compared to closely-related non-endophytes. However, the extent of this ecological trend and its underlying mechanisms are unclear. Some endophytic fungi may also be mycotrophs and have one or more mycoparasitism mechanisms. Mycotrophic endophytes are prominent in certain genera like Trichoderma, therefore, the mechanisms that enable these fungi to colonize both living plants and fungi may be the result of expanded metabolic gene repertoires. Our objective was to determine what, if any, genomic features are overrepresented in endophytic fungi genomes in order to undercover the genomic underpinning of the fungal endophytic lifestyle. Here we compared metabolic gene cluster and mycoparasitism gene diversity across a dataset of thirty-eight Trichoderma genomes representing the full breadth of environmental Trichoderma's diverse lifestyles and nutritional modes. We generated four new Trichoderma endophyticum genomes to improve the sampling of endophytic isolates from this genus. As predicted, endophytic Trichoderma genomes contained, on average, more total biosynthetic and degradative gene clusters than non-endophytic isolates, suggesting that the ability to create/modify a diversity of metabolites potential is beneficial or necessary to the endophytic fungi. Still, once the phylogenetic signal was taken in consideration, no particular class of metabolic gene cluster was independently associated with the Trichoderma endophytic lifestyle. Several mycoparasitism genes, but no chitinase genes, were associated with endophytic Trichoderma genomes. Most genomic differences between Trichoderma lifestyles and nutritional modes are difficult to disentangle from phylogenetic divergences among species, suggesting that Trichoderma genomes maybe particularly well-equipped for lifestyle plasticity. We also consider the role of endophytism in diversifying secondary metabolism after identifying the horizontal transfer of the ergot alkaloid gene cluster to Trichoderma.

Persephacin Is a Broad-Spectrum Antifungal Aureobasidin Metabolite That Overcomes Intrinsic Resistance in Aspergillus fumigatus

Fungi pose a persistent threat to humankind with worrying indications that emerging and re-emerging pathogens (e.g., Candida auris, Coccidioides spp., drug-resistant Aspergilli, and more) exhibit resistance to the limited number of approved antifungals. To address this problem, our team is exploring endophytic fungi as a resource for the discovery of new antifungal natural products. The rationale behind this decision is based on evidence that endophytes engage with plants in mutualistic relationships wherein some fungi actively participate by producing chemical defense measures that suppress pathogenic microorganisms. To improve the odds of bioactive metabolite discovery, we developed a new hands-free laser-cutting system capable of generating >50 plant samples per minute that, in turn, enabled our team to prepare and screen large numbers of endophytic fungi. One of the fungal isolates obtained in this way was identified as an Elsinoë sp. that produced a unique aureobasidin analogue, persephacin (1). Some distinctive features of 1 are the absence of both phenylalanine residues combined with the incorporation of a novel amino acid residue, persephanine (9). Compound 1 exhibits potent antifungal effects against a large number of pathogenic yeast (including several clinical C. auris strains), as well as phylogenetically diverse filamentous fungi (e.g., Aspergillus fumigatus). In an ex vivo eye infection model, compound 1 outperformed standard-of-care treatments demonstrating the ability to suppress fluconazole-resistant Candida albicans and A. fumigatus at a concentration (0.1% solution) well below the clinically recommended levels used for fluconazole and natamycin (2% and 5% solutions, respectively). In 3D tissue models for acute dermal and ocular safety, 1 was found to be nontoxic and nonirritating at concentrations required to elicit antifungal activity. Natural product 1 appears to be a promising candidate for further investigation as a broad-spectrum antifungal capable of controlling a range of pathogens that negatively impact human, animal, and plant health.

Cryptic functional diversity within a grass mycobiome

Eukaryotic hosts harbor tremendously diverse microbiomes that affect host fitness and response to environmental challenges. Fungal endophytes are prominent members of plant microbiomes, but we lack information on the diversity in functional traits affecting their interactions with their host and environment. We used two culturing approaches to isolate fungal endophytes associated with the widespread, dominant prairie grass Andropogon gerardii and characterized their taxonomic diversity using rDNA barcode sequencing. A randomly chosen subset of fungi representing the diversity of each leaf was then evaluated for their use of different carbon compound resources and growth on those resources. Applying community phylogenetic analyses, we discovered that these fungal endophyte communities are comprised of phylogenetically distinct assemblages of slow- and fast-growing fungi that differ in their use and growth on differing carbon substrates. Our results demonstrate previously undescribed and cryptic functional diversity in carbon resource use and growth in fungal endophyte communities of A. gerardii.

Uniting the Role of Endophytic Fungi against Plant Pathogens and Their Interaction

Endophytic fungi are used as the most common microbial biological control agents (MBCAs) against phytopathogens and are ubiquitous in all plant parts. Most of the fungal species have roles against a variety of plant pathogens. Fungal endophytes provide different services to be used as pathogen control agents, using an important aspect in the form of enhanced plant growth and induced systemic resistance, produce a variety of antifungal secondary metabolites (lipopeptides, antibiotics and enzymes) through colonization, and compete with other pathogenic microorganisms for growth factors (space and nutrients). The purpose of this review is to highlight the biological control potential of fungal species with antifungal properties against different fungal plant pathogens. We focused on the introduction, biology, isolation, identification of endophytic fungi, and their antifungal activity against fungal plant pathogens. The endosymbionts have developed specific genes that exhibited endophytic behavior and demonstrated defensive responses against pathogens such as antibiosis, parasitism, lytic enzyme and competition, siderophore production, and indirect responses by induced systemic resistance (ISR) in the host plant. Finally, different microscopic detection techniques to study microbial interactions (endophytic and pathogenic fungal interactions) in host plants are briefly discussed.

Facilitating Reforestation Through the Plant Microbiome: Perspectives from the Phyllosphere

Tree planting and natural regeneration contribute to the ongoing effort to restore Earth's forests. Our review addresses how the plant microbiome can enhance the survival of planted and naturally regenerating seedlings and serve in long-term forest carbon capture and the conservation of biodiversity. We focus on fungal leaf endophytes, ubiquitous defensive symbionts that protect against pathogens. We first show that fungal and oomycetous pathogen richness varies greatly for tree species native to the United States (n = 0-876 known pathogens per US tree species), with nearly half of tree species either without pathogens in these major groups or with unknown pathogens. Endophytes are insurance against the poorly known and changing threat of tree pathogens. Next, we review studies of plant phyllosphere feedback, but knowledge gaps prevent us from evaluating whether adding conspecific leaf litter to planted seedlings promotes defensive symbiosis, analogous to adding soil to promote positive feedback. Finally, we discuss research priorities for integrating the plant microbiome into efforts to expand Earth's forests.

Traits along the leaf economics spectrum are associated with communities of foliar endophytic symbionts

Leaf traits of plants worldwide are classified according to the Leaf Economics Spectrum (LES), which links leaf functional traits to evolutionary life history strategies. As a continuum ranging from thicker, tough leaves that are low in nitrogen (N) to thinner, softer, leaves that are high in N, the LES brings together physical, chemical, and ecological traits. Fungal endophytes are common foliar symbionts that occur in healthy, living leaves, especially in tropical forests. Their community composition often differs among co-occurring host species in ways that cannot be explained by environmental conditions or host phylogenetic relationships. Here, we tested the over-arching hypothesis that LES traits act as habitat filters that shape communities of endophytes both in terms of composition, and in terms of selecting for endophytes with particular suites of functional traits. We used culture-based and culture-free surveys to characterize foliar endophytes in mature leaves of 30 phylogenetically diverse plant species with divergent LES traits in lowland Panama, and then measured functional traits of dominant endophyte taxa in vitro. Endophytes were less abundant and less diverse in thick, tough, leaves compared to thin, softer, leaves in the same forest, even in closely related plants. Endophyte communities differed according to leaf traits, including leaf punch strength and carbon and nitrogen content. The most common endophyte taxa in leaves at different ends of the LES differ in their cellulase, protease, chitinase, and antipathogen activity. Our results extend the LES framework for the first time to diverse and ecologically important endophytes, opening new hypotheses regarding the degree to which foliar symbionts respond to, and extend, the functional traits of leaves they inhabit.

Organic Connection of Holobiont Components and the Essential Roles of Core Microbes in the Holobiont Formation of Feral Brassica napus

Brassica napus (Rapeseed) is an econfomically important oil-producing crop. The microbial interactions in the plant holobiont are fundamental to the understanding of plant growth and health. To investigate the microbial dynamics in the holobiont of feral B. napus, a total of 215 holobiont samples, comprised of bulk soil, primary root, lateral root, dead leaf, caulosphere, basal leaf, apical leaf, carposphere, and anthosphere, were collected from five different grassland sites in South Korea. The soil properties differed in different sampling sites, but prokaryotic communities were segregated according to plant holobiont components. The structures of the site-specific SparCC networks were similar across the regions. Recurrent patterns were found in the plant holobionts in the recurrent network. Ralstonia sp., Massilia sp., and Rhizobium clusters were observed consistently and were identified as core taxa in the phyllosphere, dead leaf microbiome, and rhizosphere, respectively. Arthropod-related microbes, such as Wolbachia sp., Gilliamella sp., and Corynebacteriales amplicon sequence variants, were found in the anthosphere. PICRUSt2 analysis revealed that microbes also possessed specific functions related to holobiont components, such as functions related to degradation pathways in the dead leaf microbiome. Structural equation modeling analysis showed the organic connections among holobiont components and the essential roles of the core microbes in the holobiont formations in natural ecosystem. Microbes coexisting in a specific plant showed relatively stable community structures, even though the regions and soil characteristics were different. Microbes in each plant component were organically connected to form their own plant holobiont. In addition, plant-related microbes, especially core microbes in each holobiont, showed recurrent interaction patterns that are essential to an understanding of the survival and coexistence of plant microbes in natural ecosystems.

Comparative transcriptomics of fungal endophytes in co-culture with their moss host Dicranum scoparium reveals fungal trophic lability and moss unchanged to slightly increased growth rates

Mosses harbor fungi whose interactions within their hosts remain largely unexplored. Trophic ranges of fungal endophytes from the moss Dicranum scoparium were hypothesized to encompass saprotrophism. This moss is an ideal host to study fungal trophic lability because of its natural senescence gradient, and because it can be grown axenically. Dicranum scoparium was co-cultured with each of eight endophytic fungi isolated from naturally occurring D. scoparium. Moss growth rates, and gene expression levels (RNA sequencing) of fungi and D. scoparium, were compared between axenic and co-culture treatments. Functional lability of two fungal endophytes was tested by comparing their RNA expression levels when colonizing living vs dead gametophytes. Growth rates of D. scoparium were unchanged, or increased, when in co-culture. One fungal isolate (Hyaloscyphaceae sp.) that promoted moss growth was associated with differential expression of auxin-related genes. When grown with living vs dead gametophytes, Coniochaeta sp. switched from having upregulated carbohydrate transporter activity to upregulated oxidation-based degradation, suggesting an endophytism to saprotrophism transition. However, no such transition was detected for Hyaloscyphaceae sp. Individually, fungal endophytes did not negatively impact growth rates of D. scoparium. Our results support the long-standing hypothesis that some fungal endophytes can switch to saprotrophism.

Alternaria alternata as endophyte and pathogen

Alternaria alternata is a common species of fungus frequently isolated from plants as both an endophyte and a pathogen. Although the current definition of A. alternata rests on a foundation of morphological, genetic and genomic analyses, doubts persist regarding the scope of A. alternata within the genus due to the varied symbiotic interactions and wide host range observed in these fungi. These doubts may be due in large part to the history of unstable taxonomy in Alternaria, based on limited morphological characters for species delimitation and host specificity associated with toxins encoded by genes carried on conditionally dispensable chromosomes. This review explores the history of Alternaria taxonomy, focusing in particular on the use of nutritional mode and host associations in species delimitation, with the goal of evaluating A. alternata as it currently stands based on taxonomic best practice. Given the recombination detected among isolates of A. alternata, different symbiotic associations in this species should not be considered phylogenetically informative.

Culturable fungal endophyte communities of primary successional plants on Mount St. Helens, WA, USA

Background

While a considerable amount of research has explored plant community composition in primary successional systems, little is known about the microbial communities inhabiting these pioneer plant species. Fungal endophytes are ubiquitous within plants, and may play major roles in early successional ecosystems. Specifically, endophytes have been shown to affect successional processes, as well as alter host stress tolerance and litter decomposition dynamics—both of which are important components in harsh environments where soil organic matter is still scarce.

Results

To determine possible contributions of fungal endophytes to plant colonization patterns, we surveyed six of the most common woody species on the Pumice Plain of Mount St. Helens (WA, USA; Lawetlat'la in the Cowlitz language; created during the 1980 eruption)—a model primary successional ecosystem—and found low colonization rates (< 15%), low species richness, and low diversity. Furthermore, while endophyte community composition did differ among woody species, we found only marginal evidence of temporal changes in community composition over a single field season (July–September).

Conclusions

Our results indicate that even after a post-eruption period of 40 years, foliar endophyte communities still seem to be in the early stages of community development, and that the dominant pioneer riparian species Sitka alder (Alnus viridis ssp. sinuata) and Sitka willow (Salix sitchensis) may be serving as important microbial reservoirs for incoming plant colonizers.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-01974-2.

Ecological generalism drives hyperdiversity of secondary metabolite gene clusters in xylarialean endophytes

Although secondary metabolites are typically associated with competitive or pathogenic interactions, the high bioactivity of endophytic fungi in the Xylariales, coupled with their abundance and broad host ranges spanning all lineages of land plants and lichens, suggests that enhanced secondary metabolism might facilitate symbioses with phylogenetically diverse hosts. Here, we examined secondary metabolite gene clusters (SMGCs) across 96 Xylariales genomes in two clades (Xylariaceae s.l. and Hypoxylaceae), including 88 newly sequenced genomes of endophytes and closely related saprotrophs and pathogens. We paired genomic data with extensive metadata on endophyte hosts and substrates, enabling us to examine genomic factors related to the breadth of symbiotic interactions and ecological roles. All genomes contain hyperabundant SMGCs; however, Xylariaceae have increased numbers of gene duplications, horizontal gene transfers (HGTs) and SMGCs. Enhanced metabolic diversity of endophytes is associated with a greater diversity of hosts and increased capacity for lignocellulose decomposition. Our results suggest that, as host and substrate generalists, Xylariaceae endophytes experience greater selection to diversify SMGCs compared with more ecologically specialised Hypoxylaceae species. Overall, our results provide new evidence that SMGCs may facilitate symbiosis with phylogenetically diverse hosts, highlighting the importance of microbial symbioses to drive fungal metabolic diversity.

Fungal Endophytes and Their Role in Agricultural Plant Protection against Pests and Pathogens

Virtually all examined plant species harbour fungal endophytes which asymptomatically infect or colonize living plant tissues, including leaves, branches, stems and roots. Endophyte-host interactions are complex and span the mutualist-pathogen continuum. Notably, mutualist endophytes can confer increased fitness to their host plants compared with uncolonized plants, which has attracted interest in their potential application in integrated plant health management strategies. In this review, we report on the many benefits that fungal endophytes provide to agricultural plants against common non-insect pests such as fungi, bacteria, nematodes, viruses, and mites. We report endophytic modes of action against the aforementioned pests and describe why this broad group of fungi is vitally important to current and future agricultural practices. We also list an extensive number of plant-friendly endophytes and detail where they are most commonly found or applied in different studies. This review acts as a general resource for understanding endophytes as they relate to potential large-scale agricultural applications.

Drivers and implications of distance decay differ for ectomycorrhizal and foliar endophytic fungi across an anciently fragmented landscape

Fungal communities associated with plants often decrease in similarity as the distance between sampling sites increases (i.e., they demonstrate distance decay). In the southwestern USA, forests occur in highlands separated from one another by warmer, drier biomes with plant and fungal communities that differ from those at higher elevations. These disjunct forests are broadly similar in climate to one another, offering an opportunity to examine drivers of distance decay in plant-associated fungi across multiple ecologically similar yet geographically disparate landscapes. We examined ectomycorrhizal and foliar endophytic fungi associated with a dominant forest tree (Pinus ponderosa) in forests across ca. 550 km of geographic distance from northwestern to southeastern Arizona (USA). Both guilds of fungi showed distance decay, but drivers differed for each: ectomycorrhizal fungi are constrained primarily by dispersal limitation, whereas foliar endophytes are constrained by specific environmental conditions. Most ectomycorrhizal fungi were found in only a single forested area, as were many endophytic fungi. Such regional-scale perspectives are needed for baseline estimates of fungal diversity associated with forest trees at a landscape scale, with attention to the sensitivity of different guilds of fungal symbionts to decreasing areas of suitable habitat, increasing disturbance, and related impacts of climate change.

Methodological Approaches Frame Insights into Endophyte Richness and Community Composition

Isolating microbes is vital to study microbiomes, but insights into microbial diversity and ecology can be constrained by recalcitrant or unculturable strains. Culture-free methods (e.g., next-generation sequencing, NGS) have become popular in part because they detect greater richness than culturing alone. Both approaches are used widely to characterize microfungi within healthy leaves (foliar endophytes), but methodological differences among studies can constrain large-scale insights into endophyte ecology. We examined endophytes in a temperate plant community to quantify how certain methodological factors, such as the choice of cultivation media for culturing and storage period after leaf collection, affect inferences regarding endophyte communities; how such effects vary among plant taxa; and how complementary culturing and NGS can be when subsets of the same plant tissue are used for each. We found that endophyte richness and composition from culturing were consistent across five media types. Insights from culturing and NGS were largely robust to differences in storage period (1, 5, and 10 days). Although endophyte richness, composition, and taxonomic diversity identified via culturing vs. NGS differed markedly, both methods revealed host-structured communities. Studies differing only in cultivation media or storage period thus can be compared to estimate endophyte richness, composition, and turnover at scales larger than those of individual studies alone. Our data show that it is likely more important to sample more host species, rather than sampling fewer species more intensively, to quantify endophyte diversity in given locations, with the richest insights into endophyte ecology emerging when culturing and NGS are paired.

Maternal effects shape the seed mycobiome in Quercus petraea

The tree seed mycobiome has received little attention despite its potential role in forest regeneration and health. The aim of the present study was to analyze the processes shaping the composition of seed fungal communities in natural forests as seeds transition from the mother plant to the ground for establishment. We used metabarcoding approaches and confocal microscopy to analyze the fungal communities of seeds collected in the canopy and on the ground in four natural populations of sessile oak (Quercus petraea). Ecological processes shaping the seed mycobiome were inferred using joint species distribution models. Fungi were present in seed internal tissues, including the embryo. The seed mycobiome differed among oak populations and trees within the same population. Its composition was largely influenced by the mother, with weak significant environmental influences. The models also revealed several probable interactions among fungal pathogens and mycoparasites. Our results demonstrate that maternal effects, environmental filtering and biotic interactions all shape the seed mycobiome of sessile oak. They provide a starting point for future research aimed at understanding how maternal genes and environments interact to control the vertical transmission of fungal species that could then influence seed dispersal and germination, and seedling recruitment.

The Impact of Pine Wood Nematode Infection on the Host Fungal Community

Pine wilt disease (PWD), caused by pinewood nematode (PWN) Bursaphelenchus xylophilus, is globally one of the most destructive diseases of pine forests, especially in China. However, little is known about the effect of PWD on the host microbiome. In this study, the fungal community and functional structures in the needles, roots, and soil of and around Pinus thunbergii naturally infected by PWN were investigated by using high-throughput sequencing coupled with the functional prediction (FUNGuild). The results showed that fungal richness, diversity, and evenness in the needles of diseased trees were significantly lower than those of healthy ones (p < 0.05), whereas no differences were found in the roots and soil. Principal coordinate analysis (PCoA) showed that the fungal community and functional structures significantly differed only in the needles of diseased and healthy trees, but not in the soil and roots. Functionally, the saprotrophs had a higher abundance in the needles of diseased trees, whereas symbiotrophs abundance was higher in the needles of healthy trees (linear discriminant analysis (LDA) > 2.0, p < 0.05). These results indicated that PWN infection primarily affected the fungal community and functional structures in the needles of P. thunbergii, but not the roots and soil.

Seed Banks as Incidental Fungi Banks: Fungal Endophyte Diversity in Stored Seeds of Banana Wild Relatives

Seed banks were first established to conserve crop genetic diversity, but seed banking has more recently been extended to wild plants, particularly crop wild relatives (CWRs) (e.g., by the Millennium Seed Bank (MSB), Royal Botanic Gardens Kew). CWRs have been recognised as potential reservoirs of beneficial traits for our domesticated crops, and with mounting evidence of the importance of the microbiome to organismal health, it follows that the microbial communities of wild relatives could also be a valuable resource for crop resilience to environmental and pathogenic threats. Endophytic fungi reside asymptomatically inside all plant tissues and have been found to confer advantages to their plant host. Preserving the natural microbial diversity of plants could therefore represent an important secondary conservation role of seed banks. At the same time, species that are reported as endophytes may also be latent pathogens. We explored the potential of the MSB as an incidental fungal endophyte bank by assessing diversity of fungi inside stored seeds. Using banana CWRs in the genus Musa as a case-study, we sequenced an extended ITS-LSU fragment in order to delimit operational taxonomic units (OTUs) and used a similarity and phylogenetics approach for classification. Fungi were successfully detected inside just under one third of the seeds, with a few genera accounting for most of the OTUs-primarily Lasiodiplodia, Fusarium, and Aspergillus-while a large variety of rare OTUs from across the Ascomycota were isolated only once. Fusarium species were notably abundant-of significance in light of Fusarium wilt, a disease threatening global banana crops-and so were targeted for additional sequencing with the marker EF1α in order to delimit species and place them in a phylogeny of the genus. Endophyte community composition, diversity and abundance was significantly different across habitats, and we explored the relationship between community differences and seed germination/viability. Our results show that there is a previously neglected invisible fungal dimension to seed banking that could well have implications for the seed collection and storage procedures, and that collections such as the MSB are indeed a novel source of potentially useful fungal strains.

Sareomycetes: more diverse than meets the eye

Since its resurrection, the resinicolous discomycete genus Sarea has been accepted as containing two species, one with black apothecia and pycnidia, and one with orange. We investigate this hypothesis using three ribosomal (nuITS, nuLSU, mtSSU) regions from and morphological examination of 70 specimens collected primarily in Europe and North America. The results of our analyses support separation of the traditional Sarea difformis s.lat. and Sarea resinae s.lat. into two distinct genera, Sarea and Zythia. Sarea as circumscribed is shown to conservatively comprise three phylospecies, with one corresponding to Sarea difformis s.str. and two, morphologically indistinguishable, corresponding to the newly combined Sarea coeloplata. Zythia is provisionally maintained as monotypic, containing only a genetically and morphologically variable Z. resinae. The new genus Atrozythia is erected for the new species A. klamathica. Arthrographis lignicola is placed in this genus on molecular grounds, expanding the concept of Sareomycetes by inclusion of a previously unknown type of asexual morph. Dating analyses using additional marker regions indicate the emergence of the Sareomycetes was roughly concurrent with the diversification of the genus Pinus, suggesting that this group of fungi emerged to exploit the newly-available resinous ecological niche supplied by Pinus or another, extinct group of conifers. Our phylogeographic studies also permitted us to study the introductions of these fungi to areas where they are not native, including Antarctica, Cape Verde, and New Zealand and are consistent with historical hypotheses of introduction.

Double lives: transfer of fungal endophytes from leaves to woody substrates

Fungal endophytes are a ubiquitous feature of plants, yet for many fungi the benefits of endophytism are still unknown. The Foraging Ascomycete (FA) hypothesis proposes that saprotrophic fungi can utilize leaves both as dispersal vehicles and as resource havens during times of scarcity. The presence of saprotrophs in leaf endophyte communities has been previously observed but their ability to transfer to non-foliar saprobic substrates has not been well investigated. To assess this ability, we conducted a culture study by placing surface-sterilized leaves from a single tropical angiosperm tree (Nectandra lineatifolia) directly onto sterile wood fragments and incubating them for 6 weeks. Fungi from the wood were subsequently isolated in culture and identified to the genus level by ITS sequences or morphology. Four-hundred and seventy-seven fungal isolates comprising 24 taxa were cultured from the wood. Of these, 70.8% of taxa (82.3% of isolates) belong to saprotrophic genera according to the FUNGuild database. Furthermore, 27% of OTUs (6% of isolates) were basidiomycetes, an unusually high proportion compared to typical endophyte communities. Xylaria flabelliformis, although absent in our original isolations, formed anamorphic fruiting structures on the woody substrates. We introduce the term viaphyte (literally, "by way of plant") to refer to fungi that undergo an interim stage as leaf endophytes and, after leaf senescence, colonize other woody substrates via hyphal growth. Our results support the FA hypothesis and suggest that viaphytism may play a significant role in fungal dispersal.

Fungal communities living within leaves of native Hawaiian dicots are structured by landscape-scale variables as well as by host plants

A phylogenetically diverse array of fungi live within healthy leaf tissue of dicotyledonous plants. Many studies have examined these endophytes within a single plant species and/or at small spatial scales, but landscape-scale variables that determine their community composition are not well understood, either across geographic space, across climatic conditions, or in the context of host plant phylogeny. Here, we evaluate the contributions of these variables to endophyte beta diversity using a survey of foliar endophytic fungi in native Hawaiian dicots sampled across the Hawaiian archipelago. We used Illumina technology to sequence fungal ITS1 amplicons to characterize foliar endophyte communities across five islands and 80 host plant genera. We found that communities of foliar endophytic fungi showed strong geographic structuring between distances of 7 and 36 km. Endophyte community structure was most strongly associated with host plant phylogeny and evapotranspiration, and was also significantly associated with NDVI, elevation and solar radiation. Additionally, our bipartite network analysis revealed that the five islands we sampled each harboured significantly specialized endophyte communities. These results demonstrate how the interaction of factors at large and small spatial and phylogenetic scales shapes fungal symbiont communities.

Pyrophilous fungi detected after wildfires in the Great Smoky Mountains National Park expand known species ranges and biodiversity estimates

Following a late fall wildfire in 2016 in the Great Smoky Mountains National Park, pyrophilous fungi in burn zones were documented over a 2-y period with respect to burn severity and phenology. Nuc rDNA internal transcribed spacer (ITS1-5.8S-ITS2 = ITS) barcodes were obtained to confirm morphological evaluations. Forty-one taxa of Ascomycota and Basidiomycota were identified from burn sites and categorized as fruiting only in response to fire or fruiting enhanced by fire. Twenty-two species of Pezizales (Ascomycota) were among the earliest to form ascomata in severe burn zones, only one of which had previously been documented in the Great Smoky Mountains National Park. Nineteen species of Basidiomycota, primarily Agaricales, were also documented. Among these, only five species (Coprinellus angulatus, Gymnopilus decipiens, Lyophyllum anthracophilum, Pholiota carbonicola, and Psathyrella pennata) were considered to be obligate pyrophilous taxa, but fruiting of two additional taxa (Hygrocybe conica and Mycena galericulata) was clearly enhanced by fire. Laccaria trichodermophora was an early colonizer of severe burn sites and persisted through the winter of 2017 and into spring and summer of 2018, often appearing in close association with Pinus pungens seedlings. Fruiting of pyrophilous fungi peaked 4-6 mo post fire then diminished, but some continued to fruit up to 2.5 y after the fire. In all, a total of 27 previously unrecorded taxa were added to the All Taxa Biodiversity Inventory (ATBI) database (~0.9%). Most pyrophilous fungi identified in this study are either cosmopolitan or have a Northern Hemisphere distribution, but cryptic endemic lineages were detected in Anthracobia and Sphaerosporella. One new combination, Hygrocybe spadicea var. spadicea f. odora, is proposed.

Secret lifestyles of pyrophilous fungi in the genus Sphaerosporella

PREMISE

Pyrophilous fungi form aboveground fruiting structures (ascocarps) following wildfires, but their ecology, natural history, and life cycles in the absence of wildfires are largely unknown. Sphaerosporella is considered to be pyrophilous. This study explores Sphaerosporella ascocarp appearance following a rare 2016 wildfire in the Great Smoky Mountains National Park (GSMNP), compares the timing of ascocarp formation with recovery of Sphaerosporella DNA sequences in soils, and explores the association of Sphaerosporella with post-fire Table Mountain pine (Pinus pungens) seedlings.

METHODS

Burned sites in the GSMNP were surveyed for pyrophilous fungal ascocarps over 2 years. Ascocarps, mycorrhizae, and endophyte cultures were evaluated morphologically and by Sanger sequencing of the nuclear ribosomal ITS gene region (fungal barcode; Schoch et al., 2012). DNA from soil cores was subjected to Illumina sequencing.

RESULTS

The timing and location of post-fire Sphaerosporella ascocarp formation was correlated with recovery of Sphaerosporella DNA sequences in soils. Genetic markers (fungal barcode) of Sphaerosporella were also recovered from mycorrhizal root tips and endophyte cultures from seedlings of Pinus pungens.

CONCLUSIONS

This study demonstrates that Sphaerosporella species, in the absence of fire, are biotrophic, forming both mycorrhizal and endophytic associations with developing Pinus pungens seedlings and may persist in nature in the absence of wildfire as a conifer symbiont. We speculate that Sphaerosporella may fruit only after the host plant is damaged or destroyed and that after wildfires, deep roots, needle endophytes, or heat-resistant spores could serve as a source of soil mycelium.

Mollisiaceae: An overlooked lineage of diverse endophytes

Mollisia is a taxonomically neglected discomycete genus (Helotiales, Leotiomycetes) of commonly encountered saprotrophs on decaying plant tissues throughout temperate regions. The combination of indistinct morphological characters, more than 700 names in the literature, and lack of reference DNA sequences presents a major challenge when working with Mollisia. Unidentified endophytes, including strains that produced antifungal or antiinsectan secondary metabolites, were isolated from conifer needles in New Brunswick and placed with uncertainty in Phialocephala and Mollisia, necessitating a more comprehensive treatment of these genera. In this study, morphology and multigene phylogenetic analyses were used to explore the taxonomy of Mollisiaceae, including Mollisia, Phialocephala, and related genera, using new field collections, herbarium specimens, and accessioned cultures and sequences. The phylogeny of Mollisiaceae was reconstructed and compared using the nuc internal transcribed spacer rDNA (ITS) barcode and partial sequences of the 28S nuc rDNA (LSU) gene, largest subunit of RNA polymerase II (RPB1), DNA topoisomerase I (TOP1), and the hypothetical protein Lipin/Ned1/Smp2 (LNS2). The results show that endophytism is common throughout the Mollisiaceae lineage in a diverse range of hosts but is infrequently attributed to Mollisia because of a paucity of reference sequences. Generic boundaries within Mollisiaceae are poorly resolved and based on phylogenetic evidence the family included species placed in Acephala, Acidomelania, Barrenia, Bispora, Cheirospora, Cystodendron, Fuscosclera, Hysteronaevia, Loramyces, Mollisia, Neopyrenopeziza, Obtectodiscus, Ombrophila, Patellariopsis, Phialocephala, Pulvinata, Tapesia (=Mollisia), and Trimmatostroma. Taxonomic novelties included the description of five novel Mollisia species and five novel Phialocephala species and the synonymy of Fuscosclera with Phialocephala, Acidomelania with Mollisia, and Loramycetaceae with Mollisiaceae.

Tryblidiopsis magnesii sp. nov. from Picea glauca in Eastern Canada

Tryblidiopsis pinastri (Leotiomycetes, Rhytismatales) was described from Picea abies in Europe and was also thought to occur on North American Picea. However, previously published sequences of Picea foliar endophytes from Eastern Canada suggested the presence of at least two cryptic Tryblidiopsis species, distinct from T. pinastri and other known species. Our subsequent sampling of Tryblidiopsis ascomata from dead attached Picea glauca branches resulted in the collection of a putatively undescribed species previously isolated as a P. glauca endophyte. Morphological evidence combined with phylogenetic analyses based on nuclear ribosomal internal transcribed spacer (ITS) and large subunit ribosomal (LSU) DNA sequences support the distinctiveness of this species, described here as T. magnesii.

Gene deletion of Corynespora cassiicola cassiicolin Cas1 suppresses virulence in the rubber tree

Corynespora cassiicola is an ascomycete fungus causing important damages in a wide range of plant hosts, including rubber tree. The small secreted protein cassiicolin is suspected to play a role in the onset of the disease in rubber tree, based on toxicity and gene expression profiles. However, its exact contribution to virulence, compared to other putative effectors, remains unclear. We created a deletion mutant targeting the cassiicolin gene Cas1 from the highly aggressive isolate CCP. Wild-type CCP and mutant ccpΔcas1 did not differ in terms of mycelium growth, sporulation, and germination rate in vitro. Cas1 gene deletion induced a complete loss of virulence on the susceptible clones PB260 and IRCA631, as revealed by inoculation experiments on intact (non-detached) leaves. However, residual symptoms persisted when inoculations were conducted on detached leaves, notably with longer incubation times. Complementation with exogenous cassiicolin restored the mutant capacity to colonize the leaf tissues. We also compared the toxicity of CCP and ccpΔcas1 culture filtrates, through electrolyte leakage measurements on abraded detached leaves, over a range of clones as well as an F1 population derived from the cross between the clones PB260 (susceptible) and RRIM600 (tolerant). On average, filtrate toxicity was lower but not fully suppressed in ccpΔcas1 compared to CCP, with clone-dependent variations. The two QTL, previously found associated with sensitivity to CPP filtrate or to the purified cassiicolin, were no longer detected with the mutant filtrate, while new QTL were revealed. Our results demonstrate that: (1) cassiicolin is a necrotrophic effector conferring virulence to the CCP isolate in susceptible rubber clones and (2) other effectors produced by CCP contribute to residual filtrate toxicity and virulence in senescing/wounded tissues. These other effectors may be involved in saprotrophy rather than necrotrophy.

Leaves of Indoor Ornamentals Are Biodiversity and Functional Hotspots for Fungi

Leaf-inhabiting fungi are an important, but often overlooked component of molecular biodiversity studies. To understand their diversity and function in relation to plant species and climate, the phyllospheres of 14 phylogenetically diverse ornamental plant species were analyzed under different controlled greenhouse conditions. We found unexpectedly high fungal diversity (H' = 2.8-6.5), OTU numbers (449-1050) and abundances (103-106 CFU cm-2 leaf surface) associated with all plants studied indoors. Despite experimental limitations, the composition of fungal communities were inclined toward a plant species-dependent pattern compared to the ambient climatic variables. Most detected fungi were patho- and saprotrophs showing a yeast-like growth morphology and were associated to the groups of endophytes and potential plant pathogens in a plant species-specific manner. A representative strain collection showed that 1/3 of the tested fungi (mainly Penicillium, Cladosporium, and Cryptococcus spp.) were able to inhibit mycelial growth and 2/3 inhibit sporulation of the plant pathogen Botrytis cinerea by the production of antifungal volatile organic compounds (VOCs) completely. This study indicates that plant leaves harbor a stable phyllosphere fungal diversity in diverse microclimates and enrich distinctive functional guilds.

RNA-based analyses reveal fungal communities structured by a senescence gradient in the moss Dicranum scoparium and the presence of putative multi-trophic fungi

Diverse plant-associated fungi are thought to have symbiotrophic and saprotrophic states because they can be isolated from both dead and living plant tissues. However, such tissues often are separated in time and space, and fungal activity at various stages of plant senescence is rarely assessed directly in fungal community studies. We used fungal ribosomal RNA metatranscriptomics to detect active fungal communities across a natural senescence gradient within wild-collected gametophytes of Dicranum scoparium (Bryophyta) to understand the distribution of active fungal communities in adjacent living, senescing and dead tissues. Ascomycota were active in all tissues across the senescence gradient. By contrast, Basidiomycota were prevalent and active in senescing and dead tissues. Several fungi were detected as active in living and dead tissues, suggesting their capacity for multi-trophy. Differences in community assembly detected by metatranscriptomics were echoed by amplicon sequencing of cDNA and compared to culture-based inferences and observation of fungal fruit bodies in the field. The combination of amplicon sequencing of cDNA and metatranscriptomics is promising for studying symbiotic systems with complex microbial diversity, allowing for the simultaneous detection of their presence and activity.

Broad-spectrum inhibition of Phytophthora infestans by fungal endophytes

Phytophthora infestans is a devastating pathogen of tomato and potato. It readily overcomes resistance genes and applied agrochemicals and hence even today causes large yield losses. Fungal endophytes provide a largely unexplored avenue of control of Phy. infestans. Not only do endophytes produce a wide array of bioactive metabolites, they may also directly compete with and defeat pathogens in planta. Here, we tested 12 fungal endophytes isolated from different plant species in vitro for their production of metabolites with anti- Phytophthora activity. Four well-performing isolates were evaluated for their ability to suppress nine isolates of Phy. infestans on agar medium and in planta. Two endophytes reliably inhibited all Phy. infestans isolates on agar medium, of which Phoma eupatorii isolate 8082 was the most promising. It nearly abolished infection by Phy. infestans in planta. Our data indicate a role for the production of anti-Phytophthora compounds by the fungus and/or an enhanced plant defense response, as evident by an enhanced anthocyanin production. Here, we present a potential biocontrol agent, which can inhibit a broad-spectrum of Phy. infestans isolates. Such broadly acting inhibition is ideal, because it allows for effective control of genetically diverse isolates and may slow the adaptation of Phy. infestans.

Cytotoxic and Noncytotoxic Metabolites from Teratosphaeria sp. FL2137, a Fungus Associated with Pinus clausa

A new naphthoquinone, teratosphaerone A (1), four new naphthalenones, namely, teratosphaerone B (2), structurally related to 1, iso-balticol B (3), iso-balticol B-4,9-acetonide (4), and (+)-balticol C (5), a new furanonaphthalenone, (3a S,9 R,9a S)-1(9a),3(3a),9-hexahydromonosporascone (6), and the known metabolite monosporascone (7) were isolated from Teratosphaeria sp. FL2137, a fungal strain inhabiting the internal tissue of recently dead but undecomposed foliage of Pinus clausa. The structures of 1-6 were elucidated on the basis of their spectroscopic data including 2D NMR, and absolute configurations of 2, 3, and 6 were determined by the modified Mosher's ester method. When evaluated in a panel of five tumor cell lines, metabolites 1 and 7 isolated from a cytotoxic fraction of the extract exhibited moderate selectivity for metastatic breast adenocarcinoma cell line MDA-MB-231. Of these, 1 showed cytotoxicity to this cell line with an IC₅₀ of 1.2 ± 0.1 μM.

Negative plant-phyllosphere feedbacks in native Asteraceae hosts - a novel extension of the plant-soil feedback framework

Over the past 25 years, the plant-soil feedback (PSF) framework has catalyzed our understanding of how belowground microbiota impact plant fitness and species coexistence. Here, we apply a novel extension of this framework to microbiota associated with aboveground tissues, termed 'plant-phyllosphere feedback (PPFs)'. In parallel greenhouse experiments, rhizosphere and phyllosphere microbiota of con- and heterospecific hosts from four species were independently manipulated. In a third experiment, we tested the combined effects of soil and phyllosphere feedback under field conditions. We found that three of four species experienced weak negative PSF whereas, in contrast, all four species experienced strong negative PPFs. Field-based feedback estimates were highly negative for all four species, though variable in magnitude. Our results suggest that phyllosphere microbiota, like rhizosphere microbiota, can potentially mediate plant species coexistence via negative feedbacks. Extension of the PSF framework to the phyllosphere is needed to more fully elucidate plant-microbiota interactions.