The Endophytic Mycobiome of European Ash and Sycamore Maple Leaves - Geographic Patterns, Host Specificity and Influence of Ash Dieback

What are the 100 most cited fungal genera?

The global diversity of fungi has been estimated between 2 to 11 million species, of which only about 155 000 have been named. Most fungi are invisible to the unaided eye, but they represent a major component of biodiversity on our planet, and play essential ecological roles, supporting life as we know it. Although approximately 20 000 fungal genera are presently recognised, the ecology of most remains undetermined. Despite all this diversity, the mycological community actively researches some fungal genera more commonly than others. This poses an interesting question: why have some fungal genera impacted mycology and related fields more than others? To address this issue, we conducted a bibliometric analysis to identify the top 100 most cited fungal genera. A thorough database search of the Web of Science, Google Scholar, and PubMed was performed to establish which genera are most cited. The most cited 10 genera are Saccharomyces, Candida, Aspergillus, Fusarium, Penicillium, Trichoderma, Botrytis, Pichia, Cryptococcus and Alternaria. Case studies are presented for the 100 most cited genera with general background, notes on their ecology and economic significance and important research advances. This paper provides a historic overview of scientific research of these genera and the prospect for further research. Citation: Bhunjun CS, Chen YJ, Phukhamsakda C, Boekhout T, Groenewald JZ, McKenzie EHC, Francisco EC, Frisvad JC, Groenewald M, Hurdeal VG, Luangsa-ard J, Perrone G, Visagie CM, Bai FY, Błaszkowski J, Braun U, de Souza FA, de Queiroz MB, Dutta AK, Gonkhom D, Goto BT, Guarnaccia V, Hagen F, Houbraken J, Lachance MA, Li JJ, Luo KY, Magurno F, Mongkolsamrit S, Robert V, Roy N, Tibpromma S, Wanasinghe DN, Wang DQ, Wei DP, Zhao CL, Aiphuk W, Ajayi-Oyetunde O, Arantes TD, Araujo JC, Begerow D, Bakhshi M, Barbosa RN, Behrens FH, Bensch K, Bezerra JDP, Bilański P, Bradley CA, Bubner B, Burgess TI, Buyck B, Čadež N, Cai L, Calaça FJS, Campbell LJ, Chaverri P, Chen YY, Chethana KWT, Coetzee B, Costa MM, Chen Q, Custódio FA, Dai YC, Damm U, de Azevedo Santiago ALCM, De Miccolis Angelini RM, Dijksterhuis J, Dissanayake AJ, Doilom M, Dong W, Alvarez-Duarte E, Fischer M, Gajanayake AJ, Gené J, Gomdola D, Gomes AAM, Hausner G, He MQ, Hou L, Iturrieta-González I, Jami F, Jankowiak R, Jayawardena RS, Kandemir H, Kiss L, Kobmoo N, Kowalski T, Landi L, Lin CG, Liu JK, Liu XB, Loizides M, Luangharn T, Maharachchikumbura SSN, Makhathini Mkhwanazi GJ, Manawasinghe IS, Marin-Felix Y, McTaggart AR, Moreau PA, Morozova OV, Mostert L, Osiewacz HD, Pem D, Phookamsak R, Pollastro S, Pordel A, Poyntner C, Phillips AJL, Phonemany M, Promputtha I, Rathnayaka AR, Rodrigues AM, Romanazzi G, Rothmann L, Salgado-Salazar C, Sandoval-Denis M, Saupe SJ, Scholler M, Scott P, Shivas RG, Silar P, Souza-Motta CM, Silva-Filho AGS, Spies CFJ, Stchigel AM, Sterflinger K, Summerbell RC, Svetasheva TY, Takamatsu S, Theelen B, Theodoro RC, Thines M, Thongklang N, Torres R, Turchetti B, van den Brule T, Wang XW, Wartchow F, Welti S, Wijesinghe SN, Wu F, Xu R, Yang ZL, Yilmaz N, Yurkov A, Zhao L, Zhao RL, Zhou N, Hyde KD, Crous PW (2024). What are the 100 most cited fungal genera? Studies in Mycology 108: 1-411. doi: 10.3114/sim.2024.108.01.

Unraveling endophytic diversity in dioecious Siraitia grosvenorii: implications for mogroside production

Host and tissue-specificity of endophytes are important attributes that limit the endophyte application on multiple crops. Therefore, understanding the endophytic composition of the targeted crop is essential, especially for the dioecious plants where the male and female plants are different. Here, efforts were made to understand the endophytic bacterial composition of the dioecious Siraitia grosvenorii plant using 16S rRNA amplicon sequencing. The present study revealed the association of distinct endophytic bacterial communities with different parts of male and female plants. Roots of male and female plants had a higher bacterial diversity than other parts of plants, and the roots of male plants had more bacterial diversity than the roots of female plants. Endophytes belonging to the phylum Proteobacteria were abundant in all parts of male and female plants except male stems and fruit pulp, where the Firmicutes were most abundant. Class Gammaproteobacteria predominated in both male and female plants, with the genus Acinetobacter as the most dominant and part of the core microbiome of the plant (present in all parts of both, male and female plants). The presence of distinct taxa specific to male and female plants was also identified. Macrococcus, Facklamia, and Propionibacterium were the distinct genera found only in fruit pulp, the edible part of S. grosvenorii. Predictive functional analysis revealed the abundance of enzymes of secondary metabolite (especially mogroside) biosynthesis in the associated endophytic community with predominance in roots. The present study revealed bacterial endophytic communities of male and female S. grosvenorii plants that can be further explored for monk fruit cultivation, mogroside production, and early-stage identification of male and female plants. KEY POINTS: • Male and female Siraitia grosvenorii plants had distinct endophytic communities • The diversity of endophytic communities was specific to different parts of plants • S. grosvenorii-associated endophytes may be valuable for mogroside biosynthesis and monk fruit cultivation.

Taxonomic analysis reveals host preference of rare fungi in endophytes of Vitis vinifera from the Czech Republic

This paper represents the results of screening a diversity of fungal endophytes associated with Vitis vinifera leaves and canes in the Czech Republic. The characterization of strains is based on morphological and phylogenetic analyses of ITS, EF1α and TUB2 sequence data. Our strain selection covers 16 species and seven orders belonging to Ascomycota and Basidiomycota. Together with ubiquitous fungi, we report on several poorly known plant-associated fungi, Angustimassarina quercicola (= A. coryli, a synonym proposed in this study) and Pleurophoma pleurospora. Other species, such as Didymella negriana, D. variabilis, Neosetophoma sp. (species identical or sister to N. rosae), Phragmocamarosporium qujingensis and Sporocadus rosigena, have so far been little known and rarely found, but are frequent on V. vinifera in different parts of the world and obviously belong to a microbiota with a strong preference for this plant. Detailed taxonomical identification allowed us to identify species with apparent stable associations with V. vinifera, for which further interactions with V. vinifera can be expected. Our study is the first to focus on V. vinifera endophytes in Central Europe and expands the knowledge about their taxonomy, ecology and geography.

Comparison of Fungal Genera Isolated from Cucumber Plants and Rhizosphere Soil by Using Various Cultural Media

Plant endophytic fungi and rhizosphere soil fungi are often reported as biocontrol agents against plant pathogens or with plant growth promotion potential. Four treatments were performed in field and greenhouse experiments where cucumber plants were inoculated with Trichoderma harzianum and Fusarium oxysporum in 2022. The roots, stems and leaves of cucumber plants and their rhizosphere soil were collected twice individually from the field and greenhouse for isolation of cucumber endophytic and rhizosphere soil fungi. All fungal strains were identified through sequence similarity of the ITS1-5.8s-ITS2 rDNA region. The potato dextrose agar (PDA) media yielded the highest number of genera isolated from cucumber plants, rhizosphere soil and both compared to other media. There were no significant differences among the four media for the isolation of all cucumber endophytic fungi. However, in the roots, the number of endophytic fungi isolated by MRBA was significantly higher than that isolated on malt extract agar (MEA), while in the stems, the number of fungi isolated with PDA was significantly higher than that isolated with Martin's rose bengal agar medium (MRBA). PDA had significantly higher isolation efficiency for the rhizosphere soil fungi than MRBA. The 28 fungal genera had high isolation efficiency, and the endophytic Trichoderma strains were significantly more isolated by MEA than those of MRBA. It is suggested that PDA can be used as a basic medium, and different cultural media can be considered for specific fungal genera.

Fungal succession in decomposing ash leaves colonized by the ash dieback pathogen Hymenoscyphus fraxineus or its harmless relative Hymenoscyphus albidus

Introduction

The ascomycete Hymenoscyphus fraxineus, originating from Asia, is currently threatening common ash (Fraxinus excelsior) in Europe, massive ascospore production from the saprotrophic phase being a key determinant of its invasiveness.

Methods

To consider whether fungal diversity and succession in decomposing leaf litter are affected by this invader, we used ITS-1 metabarcoding to profile changes in fungal community composition during overwintering. The subjected ash leaf petioles, collected from a diseased forest and a healthy ash stand hosting the harmless ash endophyte Hymenoscyphus albidus, were incubated in the forest floor of the diseased stand between October 2017 and June 2018 and harvested at 2-3-month intervals.

Results

Total fungal DNA level showed a 3-fold increase during overwintering as estimated by FungiQuant qPCR. Petioles from the healthy site showed pronounced changes during overwintering; ascomycetes of the class Dothideomycetes were predominant after leaf shed, but the basidiomycete genus Mycena (class Agaricomycetes) became predominant by April, whereas H. albidus showed low prevalence. Petioles from the diseased site showed little change during overwintering; H. fraxineus was predominant, while Mycena spp. showed increased read proportion by June.

Discussion

The low species richness and evenness in petioles from the diseased site in comparison to petioles from the healthy site were obviously related to tremendous infection pressure of H. fraxineus in diseased forests. Changes in leaf litter quality, owing to accumulation of host defense phenolics in the pathogen challenged leaves, and strong saprophytic competence of H. fraxineus are other factors that probably influence fungal succession. For additional comparison, we examined fungal community structure in petioles collected in the healthy stand in August 2013 and showing H. albidus ascomata. This species was similarly predominant in these petioles as H. fraxineus was in petioles from the diseased site, suggesting that both fungi have similar suppressive effects on fungal richness in petiole/rachis segments they have secured for completion of their life cycle. However, the ability of H. fraxineus to secure the entire leaf nerve system in diseased forests, in opposite to H. albidus, impacts the general diversity and successional trajectory of fungi in decomposing ash petioles.

Fungi associated with woody tissues of Acer pseudoplatanus in forest stands with different health status concerning sooty bark disease (Cryptostroma corticale)

From 2018 to 2020, Germany experienced periods of exceptional weather conditions. Extremely high summer temperatures and precipitation deficits induced stress and mortality in forest trees. Acer pseudoplatanus (sycamore) was one of the affected tree species. Symptoms of sooty bark disease (SBD) and severe damage of entire stands, both caused by the fungal species Cryptostroma corticale, were reported more frequently. To explore the non-symptomatic distribution of C. corticale, wood cores from visibly healthy sycamore stems were sampled and all outgrowing fungi were identified and recorded. In total, 50 trees, aged 30–65 years, were sampled at five different forest stands, from which 91 endophytic filamentous morphotypes could be isolated. The fungal endophytic community in the woody tissue of the sycamore trees varied greatly at the different sites and between the trees. The number of isolated morphotypes at the different sites ranged from 13 to 44 and no morphotype was found at all sites. At 1.20-m stem height, 3.3 fungi could be isolated from woody tissue per tree on average. The most abundant species isolated from visibly healthy sycamore in regard to both occurrence at the studied sites and continuity was C. corticale. It was recorded at four of the studied forest stands, from 26% of all studied sycamore trees, and had a frequency of 7.85% relative to the 293 isolated filamentous strains that were isolated. The second most abundant species was Xylaria longipes followed by Lopadostoma turgidum. In this study clear evidence for the endophytic lifestyle of C. corticale is presented which thus appears to be spread further than expected based on visible SBD symptoms.

Traces of Hymenoscyphus fraxineus in Northeastern Europe Extend Further Back in History than Expected

Herbaria are a promising but still poorly applied information source for retrospective microbiological studies. In order to find any evidence of the virulent European origin of ash dieback agent Hymenoscyphus fraxineus and other fungal pathogens, we analyzed 109 leaf samples from three different Estonian botanical herbaria, sampled during 171 years from 20 ash species and cultivars, using a PacBio third-generation sequencing of the fungal internal transcribed spacer ITS1-5.8S-ITS2 ribosomal DNA region. We identified a large amount of saprotrophic fungi naturally colonizing ash leaves. Hymenoscyphus fraxineus colonized a Fraxinus chinensis subsp. rhynchophylla specimen and a F. chinensis specimen collected from Tallinn Botanic Garden in July 1978 and July 1992, respectively. The samples originated from trees grown in this garden from seeds collected from Shamora, Far-East Russia, in 1961 and from a Beijing botanical garden in eastern China in 1985, respectively. Repeated subsequent DNA extraction, real-time quantitative PCR, and Sanger and Illumina sequencing confirmed our findings of these apparently oldest cases of the ash dieback agent in Europe. These results show that H. fraxineus evidently was present in Estonia 19 years earlier than our previous data from fungal herbaria documented and 14 years before the first visible damage of ash trees was registered in Poland. Because we found no evidence of the saprotrophic H. albidus from earlier mycological and botanical herbarium specimens, the presence of H. albidus in Estonia remains questionable.

Pyrenochaeta fraxinina as colonizer of ash and sycamore petioles, its morphology, ecology, and phylogenetic connections

Pyrenochaeta fraxinina was first described in 1913 from the state of New York (USA) on petioles of Fraxinus sp. Since then, the species has not been reported from North America and reports from the other regions of the world are very sparse. The results of this study on P. fraxinina are based on the material collected in various regions of Poland from 2012 to 2019. The material comprised 2700 previous year’s leaf petioles of Fraxinus excelsior and 1970 petioles or leaf residues of eight other deciduous tree species. As a result, the occurrence of pycnidial conidiomata of P. fraxinina was confirmed on F. excelsior (3.4% of petioles), F. mandshurica (1.5%), F. pennsylvanica (3.2%), and Acer pseudoplatanus (2.0%). The morphology of the microstructures was described based on the fresh material and compared with the holotype of P. fraxinina. The optimal temperature for the growth of the fungus in vitro was estimated as 20 °C. The analyses based on ITS-LSU rDNA sequences and a protein coding sequence of TUB2 and RPB2 genes showed that P. fraxinina isolates form a well-supported clade in the phylogenetic trees. The species proved to be closely related to Nematostoma parasiticum (asexual morph Pyrenochaeta parasitica), a species occurring on Abies alba in connection with needle browning disease. Interactions between P. fraxinina and the ash dieback pathogen, Hymenoscyphus fraxineus, were analyzed in vivo on ash petioles and in vitro in dual cultures. Among 93 petioles of F. excelsior, for which P. fraxinina conidiomata were detected, 26 were also colonized by H. fraxineus. Mostly, these two fungi occurred separately, colonizing different sections of a petiole. For all dual cultures, both fungi, P. fraxinina and H. fraxineus, showed growth inhibition toward the counterpartner. The role of P. fraxinina as a saprotrophic competitor toward H. fraxineus in ash petioles is discussed.

Host Specificity and Seasonal Variation in the Colonization of Tubakia sensu lato Associated with Evergreen Oak Species in Eastern Japan

Foliar fungal endophytes are ubiquitous and hyperdiverse, and tend to be host-specific among dominant forest tree species. The fungal genus Tubakia sensu lato is comprised of foliar pathogens and endophytes that exhibit host preference for Quercus and other Fagaceae species. To clarify interspecific differences in ecological characteristics among Tubakia species, we examined the endophyte communities of seven evergreen Quercus spp. at three sites in eastern Japan during summer and winter. Host tree species was the most significant factor affecting endophyte community composition. Tubakia species found at the study sites were divided into five specialists and three generalists according to their relative abundance in each host species and their host ranges. Specialists were dominant on their own host in summer, and their abundance declined in winter. To test the hypothesis that generalists are more widely adapted to their environment than specialists, we compared their spore germination rates at different temperatures. Spores of generalist Tubakia species were more tolerant of colder temperatures than were spores of specialist Tubakia species, supporting our hypothesis. Seasonal and site variations among Tubakia species were also consistent with our hypothesis. Host identity and ecology were significantly associated with endophyte community structure.

Culturable Endophytic Fungi in Fraxinus excelsior and Their Interactions with Hymenoscyphus fraxineus

The species diversity of culturable endophytic fungi was studied in the leaves and twigs of symptomatic and asymptomatic Fraxinus excelsior trees. Endophytic mycobiota was dominated by Ascomycota species, with Pleosporales (44.17%) and Diaporthales (23.79%) endophytes being the most frequently observed in the tree samples. The number of endophytic isolates and species richness varied depending on the sampling date (May and October) and tissue location. Of the 54 species identified based on ITS sequences, 14 were classified as dominant. The most frequently isolated species were Diaporthe eres, followed by Alternaria alternata, Dothiorella gregaria, and Fraxinicola fraxini. The inhibitory effect of 41 species (75 isolates) of endophytes on the radial growth of a Hymenoscyphus fraxineus isolate was studied under in vitro conditions (dual cultures). The radial growth of H. fraxineus was the most inhibited by four endophytic fungi from twigs (Fusarium lateritium, Didymella aliena, Didymella macrostoma, and Dothiorella gregaria). The inhibitory effect of the four isolates was also studied under in planta conditions. The isolates artificially inoculated into the trunks of ash trees reduced the length of necroses formed by H. fraxineus co-inoculated in the same trunks. This effect depended on the isolate, and the inhibition was most prominent only on trunks inoculated with F. lateritium and D. aliena. Although the total length of necrotic lesions formed by the H. fraxineus infection was shorter in the ash trunks co-inoculated with the endophytes, the difference was not significant.

The Native Hymenoscyphus albidus and the Invasive Hymenoscyphus fraxineus Are Similar in Their Necrotrophic Growth Phase in Ash Leaves

The populations of European ash and its harmless fungal associate Hymenoscyphus albidus are in decline owing to ash dieback caused by the invasive Hymenoscyphus fraxineus, a fungus that in its native range in Asia is a harmless leaf endophyte of local ash species. To clarify the behavior of H. albidus and its spatial and temporal niche overlap with the invasive relative, we used light microscopy, fungal species-specific qPCR assays, and PacBio long-read amplicon sequencing of the ITS1-5.8S-ITS2 region to examine fungal growth and species composition in attached leaves of European ash. The plant material was collected from a healthy stand in central Norway, where ash saplings in late autumn showed leaflet vein necrosis like that commonly related to H. fraxineus. For reference, leaflet samples were analyzed from stands with epidemic level of ash dieback in southeastern Norway and Estonia. While H. albidus was predominant in the necrotic veins in the healthy stand, H. fraxineus was predominant in the diseased stands. Otherwise, endophytes with pathogenic potential in the genera Venturia (anamorph Fusicladium), Mycosphaerella (anamorph Ramularia), and Phoma, and basidiomycetous yeasts formed the core leaflet mycobiome both in the healthy and diseased stands. In necrotic leaf areas with high levels of either H. albidus or H. fraxineus DNA, one common feature was the high colonization of sclerenchyma and phloem, a region from which the ascomata of both species arise. Our data suggest that H. albidus can induce necrosis in ash leaves, but that owing to low infection pressure, this first takes place in tissues weakened by autumn senescence, 1-2 months later in the season than what is characteristic of H. fraxineus at an epidemic phase of ash dieback. The most striking difference between these fungi would appear to be the high fecundity of H. fraxineus. The adaptation to a host that is phylogenetically closely related to European ash, a tree species with high occurrence frequency in Europe, and the presence of environmental conditions favorable to H. fraxineus life cycle completion in most years may enable the build-up of high infection pressure and challenge of leaf defense prior to autumn senescence.

Long-term soil warming alters fine root dynamics and morphology, and their ectomycorrhizal fungal community in a temperate forest soil

Climate warming is predicted to affect temperate forests severely, but the response of fine roots, key to plant nutrition, water uptake, soil carbon, and nutrient cycling is unclear. Understanding how fine roots will respond to increasing temperature is a prerequisite for predicting the functioning of forests in a warmer climate. We studied the response of fine roots and their ectomycorrhizal (EcM) fungal and root-associated bacterial communities to soil warming by 4°C in a mixed spruce-beech forest in the Austrian Limestone Alps after 8 and 14 years of soil warming, respectively. Fine root biomass (FRB) and fine root production were 17% and 128% higher in the warmed plots, respectively, after 14 years. The increase in FRB (13%) was not significant after 8 years of treatment, whereas specific root length, specific root area, and root tip density were significantly higher in warmed plots at both sampling occasions. Soil warming did not affect EcM exploration types and diversity, but changed their community composition, with an increase in the relative abundance of Cenoccocum at 0-10 cm soil depth, a drought-stress-tolerant genus, and an increase in short- and long-distance exploration types like Sebacina and Boletus at 10-20 cm soil depth. Warming increased the root-associated bacterial diversity but did not affect their community composition. Soil warming did not affect nutrient concentrations of fine roots, though we found indications of limited soil phosphorus (P) and potassium (K) availability. Our findings suggest that, in the studied ecosystem, global warming could persistently increase soil carbon inputs due to accelerated fine root growth and turnover, and could simultaneously alter fine root morphology and EcM fungal community composition toward improved nutrient foraging.

Current Insight into Traditional and Modern Methods in Fungal Diversity Estimates

Fungi are an important and diverse component in various ecosystems. The methods to identify different fungi are an important step in any mycological study. Classical methods of fungal identification, which rely mainly on morphological characteristics and modern use of DNA based molecular techniques, have proven to be very helpful to explore their taxonomic identity. In the present compilation, we provide detailed information on estimates of fungi provided by different mycologistsover time. Along with this, a comprehensive analysis of the importance of classical and molecular methods is also presented. In orderto understand the utility of genus and species specific markers in fungal identification, a polyphasic approach to investigate various fungi is also presented in this paper. An account of the study of various fungi based on culture-based and cultureindependent methods is also provided here to understand the development and significance of both approaches. The available information on classical and modern methods compiled in this study revealed that the DNA based molecular studies are still scant, and more studies are required to achieve the accurate estimation of fungi present on earth.

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.

Weeds harbor an impressive diversity of fungi, which offers possibilities for biocontrol

The use of herbicides for weed control is very common, but some of them represent a threat to human health, are environmentally detrimental and stimulate herbicide resistance. Therefore, using microorganisms as natural herbicides appears as a promising alternative. The mycoflorae colonizing different species of symptomatic and asymptomatic weeds were compared to characterize the possible mycoherbicidal candidates associated with symptomatic weeds. A collection of 475 symptomatic and asymptomatic plants belonging to 23 weed species was established. A metabarcoding approach based on amplification of the internal transcribed spacer (ITS) region combined with high-throughput amplicon sequencing revealed the diversity of fungal communities hosted by these weeds: 542 fungal genera were identified. The variability of the composition of fungal communities revealed a dispersed distribution of taxa governed neither by geographical location nor by the botanical species, suggesting a common core displaying non-specific interactions with host plants. Beyond this core, specific taxa were more particularly associated with symptomatic plants. Some of these, such as Alternaria, Blumeria, Cercospora, Puccinia, are known pathogens, while others such as Sphaerellopsis, Vishniacozyma and Filobasidium are not, at least on crops, and constitute new tracks to be followed in the search for mycoherbicidal candidates. IMPORTANCE: This approach is original because the diversity of weed-colonizing fungi has rarely been studied before. Furthermore, targeting both the ITS1 and ITS2 regions to characterize the fungal communities i) highlighted the complementarity of these two regions, ii) revealed a great diversity of weed-colonizing fungi, and iii) allowed for the identification of potential mycoherbicides, among which unexpected genera.

Fungal endophytes in Fraxinus excelsior petioles and their in vitro antagonistic potential against the ash dieback pathogen Hymenoscyphus fraxineus

Fungal endophytes were isolated from 250 asymptomatic leaf petioles of Fraxinus excelsior collected from trees showing symptoms of ash dieback in five forest sites in southern Poland. Fungal isolations yielded 1646 colonies representing 97 taxa, including 92 Ascomycota and 5 Basidiomycota species. The most common Ascomycota comprised Nemania serpens (38.0 % of colonized petioles), Diaporthe eres (33.6 %), Venturia fraxini (26.4 %), Diaporthe sp. 1 (20.4 %), Alternaria sp. 1 (14.8 %), Colletotrichum acutatum (14.8 %), Nemania diffusa (14.0 %), Colletotrichum gloeosporioides (12.4 %) and Colletotrichum sp. (12.4 %). The occurrence of all these taxa except Alternaria sp. 1 was significantly different between the studied forest sites. Two yeast species, Vishniacozyma foliicola (4.8 %) and Cystobasidium pinicola (2.8 %), dominated among the Basidiomycota endophytes detected. All the fungal endophytes were tested in dual culture antagonistic assays against two strains of Hymenoscyphus fraxineus, resulting in the development of four interaction types. The interactions included the physical contact of co-partners' mycelia (41.8 %), development of an inhibition zone (47.4 %), growth of endophyte mycelia over H. fraxineus colonies (9.3 %) and growth of H. fraxineus mycelia over endophyte colonies (1.5 %). The strongest antibiotic activity against H. fraxineus, measured by the width of the inhibition zone, was observed for Cytospora pruinosa, Fusarium lateritium, Phoma sp. 2, Pleosporales sp. 2 and Thielavia basicola. A variety of morphophysiological deformations of H. fraxineus hyphae were observed under endophyte pressure: spiral twist of the hyphae, formation of cytoplasmic extrusions, development of torulose hyphae and excessive lateral branching of the hyphae. The strongest antagonistic effects, coupled with the potential to overgrow H. fraxineus colonies, was shown by Clonostachys rosea, Nemania diffusa, N. serpens, Peniophora cinerea, Rosellinia corticium and Xylaria polymorpha. Some of these species were able to attack H. fraxineus hyphae in a mycoparasitic manner. The antagonistic activities included the physical penetration of H. fraxineus hyphae, dissolution of hyphal cell walls, disappearance of pigmentation, disintegration of hyphae and degradation of other fungal structures. In contrast, one of the most commonly detected endophytes in ash leaves, Venturia fraxini, did not show in vitro antagonistic potential against H. fraxineus. Finally, we discuss the potential of the detected fungal endophytes to combat H. fraxineus invasion, the cause of ash decline in Europe.

The Occurrence of Apiognomonia hystrix and Its Pathogenicity towards Acer pseudoplatanus and Fraxinus excelsior under Field Conditions

Apiognomonia hystrix is an ascomycetous fungus within Diaporthales that is found on maples and to a lesser extent on other hardwood trees in Europe, Northern America and Asia. To date, varying opinions on the species’ status as a cause of plant diseases have been expressed. In this study, we present the results of analyses conducted from 2012–2017 at forest sites in Poland on the occurrence of A. hystrix on Acer pseudoplatanus and Fraxinus excelsior and the pathogenicity of this fungus towards both tree species. For the sycamore leaves, A. hystrix conidiomata were detected in connection with 19.2% of galls caused by Dasineura vitrina, 20.4% of galls caused by Drisina glutinosa and 67.9% of extensive vein-associated necroses. The A. hystrix colonization of galls caused by both midge species resulted in statistically significantly larger necroses. On European ash leaves, conidiomata of A. hystrix occurred in connection with 0.8% of Dasineura fraxinea galls. Perithecia of A. hystrix were detected on overwintered leaf petioles in 8.1% of A. pseudoplatanus and 1.2% of F. excelsior samples. Twelve representative cultures were characterized molecularly by barcoding three marker genes (ITS, ACT, CAL). Results of phylogenetic analyses indicate that A. hystrix isolates are genetically variable, and three lineages are distinguishable. Eight isolates, including four originating from sycamore and four from European ash, were used to determine A. hystrix pathogenicity. Among the 48 A. pseudoplatanus petioles inoculated with A. hystrix, 41 developed necrotic lesions after 8 weeks, with the average necrosis length caused by particular isolates ranging from 14.5 to 67.2 mm. None of the 48 inoculated F. excelsior petioles developed necrotic lesions. Finally, selected aspects of A. hystrix morphology on natural substrates and in vitro are discussed in this paper, as well as the species’ potential to cause disease symptoms.

Fungi Detected in the Previous Year’s Leaf Petioles of Fraxinus excelsior and Their Antagonistic Potential against Hymenoscyphus fraxineus

Studies on fungal communities in the previous year’s leaf petioles of Fraxinus excelsior found in litter in five ash stands in southern Poland were made in 2017. Fungi were identified on the basis of isolation from 300 surface sterilized leaf petioles and by in situ inventory of fruit bodies (on 600 petioles, in spring and autumn). Identification was based on morphology of colonies and fruit bodies, and sequencing of ITS region of the rRNA gene cluster. In total, 2832 isolates from 117 taxa (Ascomycota—100; Basidiomycota—15; Mucoromycota—2 taxa) were obtained with the isolation method. The most frequent taxa (with frequency >10%) were: Nemania serpens, Hymenoscyphus fraxineus, Alternaria sp. 1, Boeremia sp., Helotiales sp. 1, Epicoccum nigrum, Venturia fraxini, Fusarium sp., Fusarium lateritium, Nemania diffusa, Typhula sp. 2 (in descending order). In total, 45 taxa were detected with the in situ inventory method. Eleven taxa were classified as dominant: Hymenoscyphus fraxineus, Venturia fraxini, Leptosphaeria sp. 2, Cyathicula fraxinophila, Typhula sp. 2, Hypoderma rubi, Pyrenopeziza petiolaris, Cyathicula coronata, Hymenoscyphus scutula, Leptosphaeria sclerotioides and Hymenoscyphus caudatus. Among 202 leaf petioles colonized by H. fraxineus, 177 petioles also showed fructification of 26 other fungi. All the isolated saprotrophs were tested in dual-culture assay for antagonism to two strains of H. fraxineus. Three interaction types were observed: type A, mutual direct contact, when the two fungi meet along the contact line (occurred with 43.3% of test fungi); type B, with inhibition zone between colonies (with 46.9% of test fungi); type C, when the test fungus overgrows the colony of H. fraxineus (with 9.8% of test fungi). The possible contribution of the fungal saprotrophs in limiting of the expansion of H. fraxineus in ash leaf petioles, which may result in reduction in the inoculum of ash dieback causal agent, is discussed.

Seasonal Dynamics of Fungi Associated with Healthy and Diseased Pinus sylvestris Needles in Northern Europe

The relationship between the ecological success of needle pathogens of forest trees and species richness of co-inhabiting endophytic fungi is poorly understood. One of the most dangerous foliar pathogens of pine is Dothistroma septosporum, which is a widely spread threat to northern European forests. We sampled two Pinus sylvestris sites in Estonia and two in Norway in order to analyse the relations between the abundance of D. septosporum and overall fungal richness, specific fungal species composition, time of season, needle age and position in the canopy. In both countries, the overall species richness of fungi was highest in autumn, showing a trend of increase with needle age. The overall species richness in the second-year needles in Estonia and third-year needles in Norway was similar, suggesting that a critical colonization threshold for needle shed in P. sylvestris is breached earlier in Estonia than in Norway. The fungal species richness in P. sylvestris needles was largely affected by Lophodermium conigenum. Especially in older needles, the relative abundance of L. conigenum was significantly higher in spring compared to summer or autumn. The timing of recruitment and colonization mechanisms of different foliage endophytes are shortly discussed.

Assessing Genotypic and Environmental Effects on Endophyte Communities of Fraxinus (Ash) Using Culture Dependent and Independent DNA Sequencing

Fraxinus excelsior populations are in decline due to the ash dieback disease Hymenoscyphus fraxineus. It is important to understand genotypic and environmental effects on its fungal microbiome to develop disease management strategies. To do this, we used culture dependent and culture independent approaches to characterize endophyte material from contrasting ash provenances, environments, and tissues (leaves, roots, seeds). Endophytes were isolated and identified using nrITS, LSU, or tef DNA loci in the culture dependent assessments, which were mostly Ascomycota and assigned to 37 families. Few taxa were shared between roots and leaves. The culture independent approach used high throughput sequencing (HTS) of nrITS amplicons directly from plant DNA and detected 35 families. Large differences were found in OTU diversity and community composition estimated by the contrasting approaches and these data need to be combined for estimations of the core endophyte communities. Species richness and Shannon index values were highest for the leaf material and the French population. Few species were shared between seed and leaf tissue. PCoA and NMDS of the HTS data showed that seed and leaf microbiome communities were highly distinct and that there was a strong influence of Fraxinus species identity on their fungal community composition. The results will facilitate a better understanding of ash fungal ecology and are a step toward identifying microbial biocontrol systems to minimize the impact of the disease.

Water pre-filtration methods to improve environmental DNA detection by real-time PCR and metabarcoding

Environmental DNA (eDNA) analysis is a novel approach for biomonitoring and has been mostly used in clear water. It is difficult to detect eDNA in turbid water as filter clogging occurs, and environmental samples contain various substances that inhibit the polymerase chain reaction (PCR) and affect the accuracy of eDNA analysis. Therefore, we applied a pre-filtration method to better detect the fish species (particularly pale chub, Opsariichthys platypus) present in a water body by measuring eDNA in environmental samples containing PCR inhibitors. Upon conducting 12S rRNA metabarcoding analysis (MiFish), we found that pre-filtration did not affect the number or identities of fish species detected in our samples, but pre-filtration through pore sizes resulted in significantly reduced variance among replicate samples. Additionally, PCR amplification was improved by the pre-filtration of environmental samples containing PCR inhibitors such as humic substances. Although this study may appear to be a conservative and ancillary experiment, pre-filtration is a simple technique that can not only improve the physical properties of water, such as turbidity, but also the quality of eDNA biomonitoring.

Drivers of richness and community composition of fungal endophytes of tree seeds

Recent studies revealed a high diversity of fungal endophytes in traded tree seeds, including potential plant pathogens. The factors determining richness and composition of seed mycobiomes are poorly understood, but might be an important determinant for tree health. We assessed the relative impact of host identity, site, several site-specific environmental factors, and whether the host was sampled in its native or non-native distribution range, on the richness and composition of fungal seed endophytes of nine tree species across 15 sites in Europe and North America. Our results show that fungal richness was affected by host identity, but not by environmental variables or host distribution range. Fungal community composition was primarily driven by host identity, and to a lesser extent by environment. Around 25% of the 2147 amplicon sequence variants (ASVs) were generalists appearing on both continents and in both gymnosperms and angiosperms. Around 63% of the ASVs appeared in only gymnosperms or angiosperms, and 33% of the ASVs were associated with a single host species, while none were found in all tree species. Our results suggest that although seed trade might facilitate movements of fungi, their establishment and spread in the new environment might be limited by host availability.

Analyzing Ash Leaf-Colonizing Fungal Communities for Their Biological Control of Hymenoscyphus fraxineus

The invasive ascomycete Hymenoscyphus fraxineus has been threatening Fraxinus excelsior populations throughout Europe for over two decades. Since the infection and first colonization by the pathogen occurs in leaves, leaf-colonizing microorganisms have been discussed as a barrier and as possible biocontrol agents against the disease. To identify fungal groups with health-supporting potential, we compared the fungal microbiota of compound leaves from susceptible and tolerant ash trees in four ash stands with high H. fraxineus exposure. The fungal communities were analyzed both culture-independently by ITS2 amplicon sequencing and by the taxonomic classification of 1,704 isolates using matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) or sequencing of the entire ITS region. The fungal community structure did not show significant differences depending on the health status. However, for several OTUs and a MALDI group, a significantly higher abundance was found in tolerant ash trees. Thus, the yeast Papiliotrema flavescens was significantly increased and accounted for 12.3% of the mycobiome of tolerant ashes (OTU0003), and it had also a distinctly higher abundance among the isolates. The filamentous ascomycete Sarocladium strictum was increased 24-fold among the isolates of tolerant trees, but its abundance was comparably low. An in vitro screening for the growth inhibition of the pathogen via cocultivation resulted in 28 yeast-like isolates and 79 filamentous fungi with antagonistic activity. A statistical cocultivation test on two H. fraxineus strains confirmed six of the yeast-like isolates that suppressed H. fraxineus significantly, from 39-50%, two of them through a fungicidal effect. The highest inhibition rates among the yeasts were found for three isolates belonging to Aureobasidium pullulans and P. flavescens. The cocultivation test of the filamentous isolates revealed higher effects compared to the yeasts. Four isolates showed significant inhibition of both H. fraxineus strains with a rate of 72-100%, and five further isolates inhibited only one H. fraxineus strain significantly. The most effective isolates were members of the genus Cladosporium. During the next step, in planta tests will be necessary to verify the efficacy of the antagonistic isolates and to assess their suitability as biocontrol agents.

The Relationship between Fungal Diversity and Invasibility of a Foliar Niche-The Case of Ash Dieback

European ash (Fraxinus excelsior) is threatened by the invasive ascomycete Hymenoscyphus fraxineus originating from Asia. Ash leaf tissues serve as a route for shoot infection but also as a sporulation substrate for this pathogen. Knowledge of the leaf niche partitioning by indigenous fungi and H. fraxineus is needed to understand the fungal community receptiveness to the invasion. We subjected DNA extracted from unwashed and washed leaflets of healthy and diseased European ash to PacBio sequencing of the fungal ITS1-5.8S-ITS2 rDNA region. Leaflets from co-inhabiting rowan trees (Sorbus aucuparia) served as a reference. The overlap in leaflet mycobiomes between ash and rowan was remarkably high, but unlike in rowan, in ash leaflets the sequence read proportion, and the qPCR-based DNA amount estimates of H. fraxineus increased vigorously towards autumn, concomitant with a significant decline in overall fungal richness. The niche of ash and rowan leaves was dominated by epiphytic propagules (Vishniacozyma yeasts, the dimorphic fungus Aureobasidion pullulans and the dematiaceous hyphomycete Cladosporium ramotenellum and H. fraxineus), and endophytic thalli of biotrophs (Phyllactinia and Taphrina species), the indigenous necrotroph Venturia fraxini and H. fraxineus. Mycobiome comparison between healthy and symptomatic European ash leaflets revealed no significant differences in relative abundance of H. fraxineus, but A. pullulans was more prevalent in symptomatic trees. The impacts of host specificity, spatiotemporal niche partitioning, species carbon utilization profiles and life cycle traits are discussed to understand the ecological success of H. fraxineus in Europe. Further, the inherent limitations of different experimental approaches in the profiling of foliicolous fungi are addressed.

GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies

Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultivated and wild plants and pathogenicity. The high importance of fungi in ecosystem processes contrasts with the incompleteness of our understanding of the patterns of fungal biogeography and the environmental factors that drive those patterns. To reduce this gap of knowledge, we collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface at https://globalfungi.com . The GlobalFungi database contains over 600 million observations of fungal sequences across > 17 000 samples with geographical locations and additional metadata contained in 178 original studies with millions of unique nucleotide sequences (sequence variants) of the fungal internal transcribed spacers (ITS) 1 and 2 representing fungal species and genera. The study represents the most comprehensive atlas of global fungal distribution, and it is framed in such a way that third-party data addition is possible.

A Comparative Analysis of Ash Leaf-Colonizing Bacterial Communities Identifies Putative Antagonists of Hymenoscyphus fraxineus

In the last few years, the alarming spread of Hymenoscyphus fraxineus, the causal agent of ash dieback, has resulted in a substantial threat to native ash stands in central and northern Europe. Since leaves and leaf petioles are the primary infection sites, phyllosphere microorganisms are presumed to interact with the pathogen and are discussed as a source of biocontrol agents. We studied compound leaves from susceptible and visible infection-free trees in four ash stands with a high likelihood of infection to assess a possible variation in the bacterial microbiota, depending on the health status of the trees. The bacterial community was analyzed by culture-independent 16S rRNA gene amplicon sequencing and through the isolation and taxonomic classification of 2,589 isolates using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The bacterial community structure did not show significant differences. However, a set of amplicon sequence variants (ASVs) and MALDI groups belonging to Luteimonas, Aureimonas, Pseudomonas, Bacillus, and Paenibacillus were distinctly increased in tolerant trees, which may be associated with the ability of the tree to resist the pathogen. The most obvious differences were observed for Luteimonas, a genus that is also exclusively present in the healthy core microbiome. In a first in vitro screen of antagonists, approximately 11% of total isolates suppressed the growth of H. fraxineus, but a statistical test with two different H. fraxineus strains confirmed only the antagonistic activity of 8% of these isolates. The antagonistic isolates were assigned to Bacillus velezensis, Pantoea vagans, and Pseudomonas caspiana. Overall, our study provides a set of isolates or phylogenetic groups that might be involved in the process that prevents the penetration and spread of H. fraxineus. In the next step, in planta experiments are required with a longer period of exposure to H. fraxineus to evaluate effective isolates or consortia of isolates acting through direct antagonism or competition or indirectly by inducing resistance.

Adaptation of subpopulations of the Norway spruce needle endophyte Lophodermium piceae to the temperature regime

Lophodermium piceae represents the most common Norway spruce needle endophyte. The aim of this study was to find out whether subpopulations of L. piceae in climatically different environments (in which Norway spruce occurs natively) are adapted to local thermal conditions. L. piceae's ability for thermal adaptation was investigated by determining growth rates of 163 isolates in vitro at four different temperatures: 2, 6, 20 and 25 °C. Isolates were obtained between 1995 and 2010 from apparently healthy needles sampled in Finland, Poland, Switzerland, Italy and southeastern Siberia. The sampling sites represent seven climatically distinct locations. Results were evaluated in relation to the age and geographic origin of the isolate, in addition to the highest and lowest average monthly temperature of the sampling location. We found a significant correlation between the growth rate and the age of the isolate at 25 °C. Variation in growth rates between subpopulations was low compared to within subpopulations. Only at 2 °C did statistically significant differences between the average growth rates of subpopulations emerge. These results suggest that L. piceae covers the whole distribution area of Norway spruce but that generally the thermal reaction norm of its subpopulations has not changed according to local temperature ranges, despite high contrast in thermal conditions across this vast area. Therefore, it would appear that the thermal environment is not a crucial factor in assessing the fitness of this fungal species within the native range of Norway spruce.

Interactions and Coadaptation in Plant Metaorganisms

Plants associate with a wide diversity of microorganisms. Some microorganisms engage in intimate associations with the plant host, collectively forming a metaorganism. Such close coexistence with plants requires specific adaptations that allow microorganisms to overcome plant defenses and inhabit plant tissues during growth and reproduction. New data suggest that the plant immune system has a broader role beyond pathogen recognition and also plays an important role in the community assembly of the associated microorganism. We propose that core microorganisms undergo coadaptation with their plant host, notably in response to the plant immune system allowing them to persist and propagate in their host. Microorganisms, which are vertically transmitted from generation to generation via plant seeds, putatively compose highly adapted species and may have plant-beneficial functions. The extent to which plant domestication has impacted the underlying genetics of plant-microbe associations remains poorly understood. We propose that the ability of domesticated plants to select and maintain advantageous microbial partners may have been affected. In this review, we discuss factors that impact plant metaorganism assembly and function. We underline the importance of microbe-microbe interactions in plant tissues, as they are still poorly studied but may have a great impact on plant health.

Forest Tree Microbiomes and Associated Fungal Endophytes: Functional Roles and Impact on Forest Health

Terrestrial plants including forest trees are generally known to live in close association with microbial organisms. The inherent features of this close association can be commensalism, parasitism or mutualism. The term “microbiota” has been used to describe this ecological community of plant-associated pathogenic, mutualistic, endophytic and commensal microorganisms. Many of these microbiota inhabiting forest trees could have a potential impact on the health of, and disease progression in, forest biomes. Comparatively, studies on forest tree microbiomes and their roles in mutualism and disease lag far behind parallel work on crop and human microbiome projects. Very recently, our understanding of plant and tree microbiomes has been enriched due to novel technological advances using metabarcoding, metagenomics, metatranscriptomics and metaproteomics approaches. In addition, the availability of massive DNA databases (e.g., NCBI (USA), EMBL (Europe), DDBJ (Japan), UNITE (Estonia)) as well as powerful computational and bioinformatics tools has helped to facilitate data mining by researchers across diverse disciplines. Available data demonstrate that plant phyllosphere bacterial communities are dominated by members of only a few phyla (Proteobacteria, Actinobacteria, Bacteroidetes). In bulk forest soil, the dominant fungal group is Basidiomycota, whereas Ascomycota is the most prevalent group within plant tissues. The current challenge, however, is how to harness and link the acquired knowledge on microbiomes for translational forest management. Among tree-associated microorganisms, endophytic fungal biota are attracting a lot of attention for their beneficial health- and growth-promoting effects, and were preferentially discussed in this review.