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Crust-like Sebacinaceae , comprising the genera Helvellosebacina , Sebacina , and Tremelloscypha , represent the only ectomycorrhizal lineage within the Sebacinaceae family. However, species delimitation within this group remains challenging because of their cryptic lifestyles, inconspicuous morphological traits, and limited taxonomic annotation. To address these limitations, we investigated crust-like Sebacinaceae in Asia by integrating two datasets: specimen-derived (barcoding) sequence data and root-associated metabarcoding data. A high diversity of crust-like Sebacinaceae species was uncovered, most of which did not match any previously described taxa. Multigene phylogenetic analyses (ITS, LSU, and rpb2) based on basidiomata identified eleven distinct species, of which six are proposed here as new to science. In parallel, metabarcoding data revealed additional crust-like Sebacinaceae species and confirmed their ectomycorrhizal association with Pinus and Quercus species. These findings advance our understanding of crust-like Sebacinaceae diversity and ecology in previously unexplored regions.

The successful conversion of plant production systems from conventional resource-exhausting to sustainable strategies depends on knowledge-based management of environmental factors. Root-inhabiting fungi came more and more into focus because their hyphae connect in ideal manner resources and challenges of the surrounding with the plant. A paradigm for such root endophytes is presented by the basidiomycete Piriformospora indica. This fungus possesses a broad host spectrum and positively affects different aspects of plant performance. This so far unique combination of attributes makes P. indica and its close relatives among the Sebacinales very interesting tools for cultivation of various crops. This review will outline the different aspects required to apply this root endophyte in agri- and horticulture concerning plant growth, plant nutrition and plant defence or tolerance thereby explaining what is known about the biological basis for the observed effects. Open questions and challenges for successful inoculum production and application will be discussed.

Orchid mycorrhizal (OrM) symbionts play a key role in the growth of orchids, but the temporal variation and habitat partitioning of these fungi in roots and soil remain unclear. Temporal changes in root and rhizosphere fungal communities of Cypripedium calceolus, Neottia ovata and Orchis militaris were studied in meadow and forest habitats over the vegetation period by using 454 pyrosequencing of the full internal transcribed spacer (ITS) region. The community of typical OrM symbionts differed by plant species and habitats. The root fungal community of N. ovata changed significantly in time, but this was not observed in C. calceolus and O. militaris. The rhizosphere community included a low proportion of OrM symbionts that exhibited a slight temporal turnover in meadow habitats but not in forests. Habitat differences in OrM and all fungal associates are largely attributable to the greater proportion of ectomycorrhizal fungi in forests. Temporal changes in OrM fungal communities in roots of certain species indicate selection of suitable fungal species by plants. It remains to be elucidated whether these shifts depend on functional differences inside roots, seasonality, climate or succession.

Mycorrhizal fungi are essential for the survival of orchid seedlings under natural conditions. The distribution of these fungi in soil can constrain the establishment and resulting spatial arrangement of orchids at the local scale, but the actual extent of occurrence and spatial patterns of orchid mycorrhizal (OrM) fungi in soil remain largely unknown. We addressed the fine-scale spatial distribution of OrM fungi in two orchid-rich Mediterranean grasslands by means of high-throughput sequencing of fungal ITS2 amplicons, obtained from soil samples collected either directly beneath or at a distance from adult Anacamptis morio and Ophrys sphegodes plants. Like ectomycorrhizal and arbuscular mycobionts, OrM fungi (tulasnelloid, ceratobasidioid, sebacinoid and pezizoid fungi) exhibited significant horizontal spatial autocorrelation in soil. However, OrM fungal read numbers did not correlate with distance from adult orchid plants, and several of these fungi were extremely sporadic or undetected even in the soil samples containing the orchid roots. Orchid mycorrhizal ‘rhizoctonias’ are commonly regarded as unspecialized saprotrophs. The sporadic occurrence of mycobionts of grassland orchids in host-rich stands questions the view of these mycorrhizal fungi as capable of sustained growth in soil.

Aims The use of rootstock is effective at protecting plants from soil-borne diseases, however, the underlying mechanisms remain to be elucidated. Methods In this study, the root-associated microbiomes and root exudate profiles of rootstock (grafted) and self-rooted (ungrafted) watermelon plants grown in plastic shelters heavily infected with Fusarium oxysporum f. sp. niveum (FON) were characterized. Results We showed that grafting markedly controlled Fusarium wilt disease, greatly reduced FON abundance in the rhizoplane and endosphere, and improved microbial diversity across rhizosphere to endosphere in continuous cropping soils. We further found that grafting significantly changed the composition of root-associated microbiomes, improved microbial association network complexity, and had potential beneficial bacterial taxa like Streptomycetales and Sphingomonadales, and fungal taxa like Capnodiales and Sebacinales significantly enriched in grafted watermelon. The grafted watermelon also possessed a distinct root exudate profile from the ungrafted watermelon and rootstock plants, with organic acids (potential autotoxins) significantly depleted but more plant defense-related metabolites such as organosulfur compounds and benzenoids enriched in comparison to ungrafted watermelon. Conclusion Together, our results suggest that grafting facilitates plant disease resistance potentially by direct antagonism effect through root exudates and indirectly by shaping the protective root-associated microbiomes.

The Serendipitaceae family was erected in 2016 to accommodate the Sebacinales ‘group B’ clade, which contains peculiar species of cultivable root–associated fungi involved in symbiotic associations with a wide range of plant species. Here we report the isolation of a new Serendipita species which was obtained from protocorms of the terrestrial orchid Epidendrum fulgens cultivated in a greenhouse. This species is described based on phylogenetic analysis and on its microscopic and ultrastructural features in pure culture and in association with the host’s protocorms. Its genome size was estimated using flow cytometry, and its capacity to promote the germination of E. fulgens seeds and to associate with roots of Arabidopsis thaliana was also investigated. Serendipita restingae sp. nov. is closely related to Serendipita sp. MAFF305841, isolated from Microtis rara (Orchidaceae), from which it differs by 14.2% in the ITS region and by 6.5% in the LSU region. It produces microsclerotia formed of non-monilioid hyphae, a feature that was not reported for the Sebacinales hitherto. Serendipita restingae promoted the germination of E. fulgens seeds, forming typical mycorrhizal pelotons within protocorm cells. It was also able to colonize the roots of Arabidopsis thaliana under in vitro conditions. Arabidopsis plants grown in association with S. restingae increased their biomass more than fourfold. Serendipita restingae is the first Serendipitaceae species described for the Americas.

There is increasing evidence that microbes play a key role in some plant invasions. A diverse and widespread but little understood group of plant-associated microbes are the fungal root endophytes of the order Sebacinales. They are associated with exotic populations of invasive knotweed (Reynoutria ssp.) in Europe, but their effects on the invaders are unknown. We used the recently isolated Sebacinales root endophyte Serendipita herbamans to experimentally inoculate invasive knotweed and study root colonisation and effects on knotweed growth under different environmental conditions. We verified the inoculation success and fungal colonisation through immunofluorescence microscopy and qPCR. We found that S. herbamans strongly colonized invasive knotweed in low-nutrient and shade environments, but much less under drought or benign conditions. At low nutrients, the endophyte had a positive effect on plant growth, whereas the opposite was true under shaded conditions. Our study demonstrates that the root endophyte S. herbamans has the potential to colonize invasive knotweed fine roots and impact its growth, and it could thus also play a role in natural populations. Our results also show that effects of fungal endophytes on plants can be strongly environment-dependent, and may only be visible under stressful environmental conditions.

Crust-like Sebacinaceae , comprising the genera Helvellosebacina , Sebacina , and Tremelloscypha , represent the only ectomycorrhizal lineage within the Sebacinaceae family. However, species delimitation within this group remains challenging because of their cryptic lifestyles, inconspicuous morphological traits, and limited taxonomic annotation. To address these limitations, we investigated crust-like Sebacinaceae in Asia by integrating two datasets: specimen-derived (barcoding) sequence data and root-associated metabarcoding data. A high diversity of crust-like Sebacinaceae species was uncovered, most of which did not match any previously described taxa. Multigene phylogenetic analyses (ITS, LSU, and rpb 2) based on basidiomata identified eleven distinct species, of which six are proposed here as new to science. In parallel, metabarcoding data revealed additional crust-like Sebacinaceae species and confirmed their ectomycorrhizal association with Pinus and Quercus species. These findings advance our understanding of crust-like Sebacinaceae diversity and ecology in previously unexplored regions.

Mixotrophy (MX, also called partial mycoheterotrophy) in plants is characterized by isotopic abundances that differ from those of autotrophs. Previous studies have evaluated mycoheterotrophy in MX plants associated with fungi of similar ecological characteristics, but little is known about the differences in the relative abundances of 13C and 15N in an orchid species that associates with several different mycobionts species. Since the chlorophyllous orchid Cremastra variabilis Nakai associates with various fungi with different ecologies, we hypothesized that it may change its relative abundances of 13C and 15N depending on the associated mycobionts. We investigated mycobiont diversity in the chlorophyllous orchid C. variabilis together with the relative abundance of 13C and 15N and morphological underground differentiation (presence or absence of a mycorhizome with fungal colonization). Rhizoctonias (Tulasnellaceae, Ceratobasidiaceae, Sebacinales) were detected as the main mycobionts. High differences in δ13C values (– 34.7  to – 27.4 ‰) among individuals were found, in which the individuals associated with specific Psathyrellaceae showed significantly high relative abundance of 13C. In addition, Psathyrellaceae fungi were always detected on individuals with mycorhizomes. In the present study, MX orchid association with non-rhizoctonia saprobic fungi was confirmed, and the influence of mycobionts on morphological development and on relative abundance of 13C and 15N was discovered. Cremastra variabilis may increase opportunities to gain nutrients from diverse partners, in a bet-hedging plasticity that allows colonization of various environmental conditions.