We surveyed endophytic fungal communities in leaves of a single tree species (Metrosideros polymorpha) across wide environmental gradients (500–5,500 mm of rain/y; 10–22 °C mean annual temperature) spanning short geographic distances on Mauna Loa Volcano, Hawai’i. Using barcoded amplicon pyrosequencing at 13 sites (10 trees/site; 10 leaves/tree), we found very high levels of diversity within sites (a mean of 551 ± 134 taxonomic units per site). However, among-site diversity contributed even more than did within-site diversity to the overall richness of more than 4,200 taxonomic units observed in M. polymorpha, and this among-site variation in endophyte community composition correlated strongly with temperature and rainfall. These results are consistent with suggestions that foliar endophytic fungi are hyperdiverse. They further suggest that microbial diversity may be even greater than has been assumed and that broad-scale environmental controls such as temperature and rainfall can structure eukaryotic microbial diversity. Appropriately constrained study systems across strong environmental gradients present a useful means to understand the environmental factors that structure the diversity of microbial communities.

https://www.pnas.org/content/pnas/109/32/13022.full.pdf

Fungal endophyte communities reflect environmental structuring across a Hawaiian landscape

This article is a Commentary on Mark et al. (2020), 227: 1362–1375.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.16630

Lichens redefined as complex ecosystems.

Lichenicolous fungi represent a highly specialized and successful group of organisms that live exclusively on lichens, most commonly as host-specific parasites, but also as broad-spectrum pathogens, saprotrophs or commensals. We present here the most recent update to the classification of lichenicolous fungi in the Ascomycota and Basidiomycota to genus level, arranged phylogenetically according to published classifications. For each genus, all known lichenicolous taxa (obligately lichenicolous taxa, lichenicolous lichens, and facultatively lichenicolous taxa) are listed, along with information about types, synonyms, pertinent literature and whether or not molecular data are available for any of the listed species. The number of accepted lichenicolous fungi is now 2319, with 2000 obligately lichenicolous species, subspecies or varieties, 257 lichenicolous lichens and 62 facultatively lichenicolous taxa. These species are found in 10 different classes of Fungi (Ascomycota and Basidiomycota), 55 orders, 115 families and 397 genera. The 2319 total taxa is an increase from the 1559 total species reported in the last published catalogue in 2003, and a larger number than the approximately 1800 reported in the most recent online checklist (www.lichenicolous.net) posted in January 2018. Of the total number of taxa, 2219 (96%) are ascomycetes and 100 (4%) are basidiomycetes. Of the 397 genera containing lichenicolous species, c. 50% (198) are entirely lichenicolous. In addition, six families (Abrothallaceae, Adelococcaceae, Cyphobasidiaceae, Obryzaceae, Polycoccaceae, Sarcopyreniaceae) and two orders (Abrothallales, Cyphobasidiales) are entirely lichenicolous. Sequence information is available for lichenicolous species in 128 (32%) of the 397 genera containing lichenicolous species, and in 56 (28%) of the 198 entirely lichenicolous genera. Many species are known from only one host lichen, but it is likely that broader host ecologies will be discovered as new sequence information is obtained from ongoing microbiome studies. Phaeopyxis Rambold & Triebel is considered as a new synonym of Bachmanniomyces D.Hawksw., resulting in five new combinations B. australis (Rambold & Triebel) Diederich & Pino-Bodas (≡ P. australis), B. carniolicus (Arnold) Diederich & Pino-Bodas (≡ Biatora carniolica), B. muscigenae (Alstrup & E.S.Hansen) Diederich & Pino-Bodas (≡ P. muscigenae), B. punctum (A.Massal.) Diederich & Pino-Bodas (≡ Nesolechia punctum) and B. varius (Coppins, Rambold & Triebel) Diederich & Pino-Bodas (≡ P. varia). As a consequence of a phylogenetic analysis including new sequences, Dactylospora Korb. is regarded as a new synonym of Sclerococcum Fr. : Fr., resulting in one new name (S. acarosporicola Ertz & Diederich) and 46 new combinations. Sclerococcaceae Reblova, Unter. & W.Gams is considered as a new synonym of Dactylosporaceae Bellem. & Hafellner. The new Sclerococcum ophthalmizae Coppins is described. Sclerophyton occidentale Herre is lectotypified on the lichenicolous fungus present in the type specimen and becomes a younger synonym of Sclerococcum parasiticum. A replacement name is Arthonia polydactylonis Diederich & Ertz (≡ A. ceracea). Further new combinations are Abrothallus lobariae (Diederich & Etayo) Diederich & Ertz (≡ Phoma lobariae), A. psoromatis (Zhurb. & U. Braun) Diederich & Zhurb. (≡ P. psoromatis), Asteroglobulus pyramidalis (Etayo) Diederich (≡ Cornutispora pyramidalis), Didymocyrtis grumantiana (Zhurb. & Diederich) Zhurb. & Diederich (≡ Phoma grumantiana), Epithamnolia atrolazulina (Etayo) Diederich (≡ Hainesia atrolazulina), Gyalolechia epiplacynthium (Etayo) Diederich (≡ Fulgensia epiplacynthium), Nesolechia doerfeltii (Alstrup & P.Scholz) Diederich (≡ Phacopsis doerfeltii), N. falcispora (Triebel & Rambold) Diederich (≡ P. falcispora), N. oxyspora var. fusca (Triebel & Rambold) Diederich (≡ P. oxyspora var. fusca), Preussia peltigerae (Brackel) Diederich (≡ Sporormiella peltigerae), Scutula curvispora (D.Hawksw. & Miądl.) Diederich (≡ Libertiella curvispora), S. didymospora (D.Hawksw. & Miądl.) Diederich (≡ L. didymospora), Stigmidium haesitans (Nyl.) Diederich (≡ Verrucaria haesitans), and S. parvum (Henssen) Diederich (≡ Pharcidia parvum).

The 2018 classification and checklist of lichenicolous fungi, with 2000 non-lichenized, obligately lichenicolous taxa

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.

https://www.mdpi.com/1999-4907/10/1/42/pdf

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

Numerous plant pathogens, rhizosphere symbionts, and endophytic bacteria and yeasts produce the important phytohormone indole-3-acetic acid (IAA), often with profound effects on host plants. However, to date IAA production has not been documented among foliar endophytes -- the diverse guild of primarily filamentous Ascomycota that live within healthy, above-ground tissues of all plant species studied thus far. Recently bacteria that live within hyphae of endophytes (endohyphal bacteria) have been detected, but their effects have not been studied previously. Here we show not only that IAA is produced in vitro by a foliar endophyte (here identified as Pestalotiopsis aff. neglecta, Xylariales), but that IAA production is enhanced significantly when the endophyte hosts an endohyphal bacterium (here identified as Luteibacter sp., Xanthomonadales). Both the endophyte and the endophyte/bacterium complex appear to rely on an L-tryptophan dependent pathway for IAA synthesis. The bacterium can be isolated from the fungus when the symbiotic complex is cultivated at 36°C. In pure culture the bacterium does not produce IAA. Culture filtrate from the endophyte-bacterium complex significantly enhances growth of tomato in vitro relative to controls and to filtrate from the endophyte alone. Together these results speak to a facultative symbiosis between an endophyte and endohyphal bacterium that strongly influences IAA production, providing a new framework in which to explore endophyte-plant interactions.

/pdf/endohyphal-bacterium-enhances-production-of-indole-3-acetic-4nma59ab9h.pdf

Endohyphal bacterium enhances production of indole-3-acetic acid by a foliar fungal endophyte.

 Premise of the study: Endophytic and endolichenic fungi occur in healthy tissues of plants and lichens, respectively, playing potentially important roles in the ecology and evolution of their hosts. However, previous sampling has not comprehensively evaluated the biotic, biogeographic, and abiotic factors that structure their communities.  Methods: Using molecular data we examined the diversity, composition, and distributions of 4154 endophytic and endolichenic Ascomycota cultured from replicate surveys of ca. 20 plant and lichen species in each of fiNorth American sites (Madrean coniferous forest, Arizona; montane semideciduous forest, North Carolina; scrub forest, Florida; Beringian tundra and forest, western Alaska; subalpine tundra, eastern central Alaska).  Key results: Endolichenic fungi were more abundant and diverse per host species than endophytes, but communities of endophytes were more diverse overall, refl ecting high diversity in mosses and lycophytes. Endophytes of vascular plants were largely distinct from fungal communities that inhabit mosses and lichens. Fungi from closely related hosts from different regions were similar in higher taxonomy, but differed at shallow taxonomic levels. These differences refl ected climate factors more strongly than geographic distance alone.  Conclusions: Our study provides a fi rst evaluation of endophytic and endolichenic fungal associations with their hosts at a continental scale. Both plants and lichens harbor abundant and diverse fungal communities whose incidence, diversity, and composition refl ect the interplay of climatic patterns, geographic separation, host type, and host lineage. Although culture-free methods will inform future work, our study sets the stage for empirical assessments of ecological specifi city, metabolic capability, and comparative genomics.

Host and geographic structure of endophytic and endolichenic fungi at a continental scale

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Host and geographic structure of endophytic and endolichenic fungi at a continental scale