Enigmatic Sebacinales

Bacterial and fungal communities in sub-Arctic tundra heaths are shaped by contrasting snow accumulation and nutrient availability

Climate change is affecting winter snow conditions significantly in northern ecosystems but the effects of the changing conditions for soil microbial communities are not well-understood. We utilized naturally occurring differences in snow accumulation to understand how the wintertime subnivean conditions shape bacterial and fungal communities in dwarf shrub-dominated sub-Arctic Fennoscandian tundra sampled in mid-winter, early, and late growing season. Phospholipid fatty acid (PLFA) and quantitative PCR analyses indicated that fungal abundance was higher in windswept tundra heaths with low snow accumulation and lower nutrient availability. This was associated with clear differences in the microbial community structure throughout the season. Members of Clavaria spp. and Sebacinales were especially dominant in the windswept heaths. Bacterial biomass proxies were higher in the snow-accumulating tundra heaths in the late growing season but there were only minor differences in the biomass or community structure in winter. Bacterial communities were dominated by members of Alphaproteobacteria, Actinomycetota, and Acidobacteriota and were less affected by the snow conditions than the fungal communities. The results suggest that small-scale spatial patterns in snow accumulation leading to a mosaic of differing tundra heath vegetation shapes bacterial and fungal communities as well as soil carbon and nutrient availability.

Fallopia japonica and Impatiens glandulifera are colonized by species-poor root-associated fungal communities but have minor impacts on soil properties in riparian habitats

Fallopia japonica and Impatiens glandulifera are major plant invaders on a global scale that often become dominant in riparian areas. However, little is known about how these species affect interactions in soil–plant systems. The aim of this study was to investigate the impact of both species on abiotic and biotic soil properties, with a special focus on fungi. We investigated eight sites along small streams invaded by F. japonica and I. glandulifera, respectively, and compared each with nearby sites dominated by the native species Urtica dioica. Three different types of samples were collected: bulk soil, rhizosphere soil and roots from invasive and native stands at each site. Bulk soil samples were analysed for soil physicochemical, microbial properties (soil microbial respiration and ergosterol) and soil arthropod abundance (Acari and Collembola). Soil respiration was also evaluated in rhizosphere samples. The fungal community composition of both bulk soil and roots were analysed using a metabarcoding approach. Soil physicochemical properties as well as soil microbial activity, fungal biomass and soil fungal operational unit taxonomic unit (OTU) richness did not differ between invaded and native riparian habitats, indicating only minor belowground impacts of the two invasive plant species. Soil microbial activity, fungal biomass and soil fungal OTU richness were rather related to the soil physicochemical properties. In contrast, Acari abundance decreased by 68% in the presence of F. japonica, while Collembola abundance increased by 11% in I. glandulifera sites. Moreover, root-associated fungal communities differed between the invasive and native plants. In F. japonica roots, fungal OTU richness of all investigated ecological groups (mycorrhiza, endophytes, parasites, saprobes) were lower compared to U. dioica. However, in I. glandulifera roots only the OTU richness of mycorrhiza and saprobic fungi was lower. Overall, our findings show that F. japonica and I. glandulifera can influence the abundance of soil arthropods and are characterized by lower OTU richness of root-associated fungi.

Co-occurring epiphytic orchids have specialized mycorrhizal fungal niches that are also linked to ontogeny

Mycorrhizal symbiosis has been related to the coexistence and community assembly of coexisting orchids in few studies despite their obligate dependence on mycorrhizal partners to establish and survive. In hyper-diverse environments like tropical rain forests, coexistence of epiphytic orchids may be facilitated through mycorrhizal fungal specialization (i.e., sets of unique and dominant mycorrhizal fungi associated with a particular host species). However, information on the role of orchid mycorrhizal fungi (OMF) in niche differentiation and coexistence of epiphytic orchids is still scarce. In this study, we sought to identify the variation in fungal preferences of four co-occurring epiphytic orchids in a tropical rainforest in Costa Rica by addressing the identity and composition of their endophytic fungal and OMF communities across species and life stages. We show that the endophytic fungal communities are formed mainly of previously recognized OMF taxa, and that the four coexisting orchid species have both a set of shared mycorrhizal fungi and a group of fungi unique to an orchid species. We also found that adult plants keep the OMF of the juvenile stage while adding new mycobionts over time. This study provides evidence for the utilization of specific OMF that may be involved in niche segregation, and for an aggregation mechanism where adult orchids keep initial fungal mycobionts of the juvenile stage while adding others.

Molinia caerulea alters forest Quercus petraea seedling growth through reduced mycorrhization

Oak regeneration is jeopardized by purple moor grass, a well-known competitive perennial grass in the temperate forests of Western Europe. Below-ground interactions regarding resource acquisition and interference have been demonstrated and have led to new questions about the negative impact of purple moor grass on ectomycorrhizal colonization. The objective was to examine the effects of moor grass on root system size and ectomycorrhization rate of oak seedlings as well as consequences on nitrogen (N) content in oak and soil. Oak seedlings and moor grass tufts were planted together or separately in pots under semi-controlled conditions (irrigated and natural light) and harvested 1 year after planting. Biomass, N content in shoot and root in oak and moor grass as well as number of lateral roots and ectomycorrhizal rate in oak were measured. Biomass in both oak shoot and root was reduced when planting with moor grass. Concurrently, oak lateral roots number and ectomycorrhization rate decreased, along with a reduction in N content in mixed-grown oak. An interference mechanism of moor grass is affecting oak seedlings performance through reduction in oak lateral roots number and its ectomycorrhization, observed in conjunction with a lower growth and N content in oak. By altering both oak roots and mycorrhizas, moor grass appears to be a species with a high allelopathic potential. More broadly, these results show the complexity of interspecific interactions that involve various ecological processes involving the soil microbial community and need to be explored in situ.

Host generalists dominate fungal communities associated with alpine knotweed roots: a study of Sebacinales

Bistorta vivipara is a widespread herbaceous perennial plant with a discontinuous pattern of distribution in arctic, alpine, subalpine and boreal habitats across the northern Hemisphere. Studies of the fungi associated with the roots of B. vivipara have mainly been conducted in arctic and alpine ecosystems. This study examined the fungal diversity and specificity from root tips of B. vivipara in two local mountain ecosystems as well as on a global scale. Sequences were generated by Sanger sequencing of the internal transcribed spacer (ITS) region followed by an analysis of accurately annotated nuclear segments including ITS1-5.8S-ITS2 sequences available from public databases. In total, 181 different UNITE species hypotheses (SHs) were detected to be fungi associated with B. vivipara, 73 of which occurred in the Bavarian Alps and nine in the Swabian Alps-with one SH shared among both mountains. In both sites as well as in additional public data, individuals of B. vivipara were found to contain phylogenetically diverse fungi, with the Basidiomycota, represented by the Thelephorales and Sebacinales, being the most dominant. A comparative analysis of the diversity of the Sebacinales associated with B. vivipara and other co-occurring plant genera showed that the highest number of sebacinoid SHs were associated with Quercus and Pinus, followed by Bistorta. A comparison of B. vivipara with plant families such as Ericaceae, Fagaceae, Orchidaceae, and Pinaceae showed a clear trend: Only a few species were specific to B. vivipara and a large number of SHs were shared with other co-occurring non-B. vivipara plant species. In Sebacinales, the majority of SHs associated with B. vivipara belonged to the ectomycorrhiza (ECM)-forming Sebacinaceae, with fewer SHs belonging to the Serendipitaceae encompassing diverse ericoid-orchid-ECM-endophytic associations. The large proportion of non-host-specific fungi able to form a symbiosis with other non-B. vivipara plants could suggest that the high fungal diversity in B. vivipara comes from an active recruitment of their associates from the co-occurring vegetation. The non-host-specificity suggests that this strategy may offer ecological advantages; specifically, linkages with generalist rather than specialist fungi. Proximity to co-occurring non-B. vivipara plants can maximise the fitness of B. vivipara, allowing more rapid and easy colonisation of the available habitats.

The fungal root endophyte Serendipita vermifera displays inter-kingdom synergistic beneficial effects with the microbiota in Arabidopsis thaliana and barley

Plant root-associated bacteria can confer protection against pathogen infection. By contrast, the beneficial effects of root endophytic fungi and their synergistic interactions with bacteria remain poorly defined. We demonstrate that the combined action of a fungal root endophyte from a widespread taxon with core bacterial microbiota members provides synergistic protection against an aggressive soil-borne pathogen in Arabidopsis thaliana and barley. We additionally reveal early inter-kingdom growth promotion benefits which are host and microbiota composition dependent. Using RNA-sequencing, we show that these beneficial activities are not associated with extensive host transcriptional reprogramming but rather with the modulation of expression of microbial effectors and carbohydrate-active enzymes.

The Potential of Rhizoctonia-Like Fungi for the Biological Protection of Cereals against Fungal Pathogens

The use of biological control is becoming a common practice in plant production. One overlooked group of organisms potentially suitable for biological control are Rhizoctonia-like (Rh-like) fungi. Some of them are capable of forming endophytic associations with a large group of higher plants as well as mycorrhizal symbioses. Various benefits of endophytic associations were proved, including amelioration of devastating effects of pathogens such as Fusarium culmorum. The advantage of Rh-like endophytes over strictly biotrophic mycorrhizal organisms is the possibility of their cultivation on organic substrates, which makes their use more suitable for production. We focused on abilities of five Rh-like fungi isolated from orchid mycorrhizas, endophytic fungi Serendipita indica, Microdochium bolleyi and pathogenic Ceratobasidium cereale to inhibit the growth of pathogenic F. culmorum or Pyrenophora teres in vitro. We also analysed their suppressive effect on wheat infection by F. culmorum in a growth chamber, as well as an effect on barley under field conditions. Some of the Rh-like fungi affected the growth of plant pathogens in vitro, then the interaction with plants was tested. Beneficial effect was especially noted in the pot experiments, where wheat plants were negatively influenced by F. culmorum. Inoculation with S. indica caused higher dry shoot biomass in comparison to plants treated with fungicide. Prospective for future work are the effects of these endophytes on plant signalling pathways, factors affecting the level of colonization and surviving of infectious particles.

Serendipita restingae sp. nov. (Sebacinales): an orchid mycorrhizal agaricomycete with wide host range

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.

Community composition of arctic root-associated fungi mirrors host plant phylogeny

The number of plant species regarded as non-mycorrhizal increases at higher latitudes, and several plant species in the High-Arctic Archipelago Svalbard have been reported as non-mycorrhizal. We used the rRNA ITS2 and 18S gene markers to survey which fungi, as well as other micro-eukaryotes, were associated with roots of 31 arctic plant species not usually regarded as mycorrhizal in Svalbard. We assessed to what degree the root-associated fungi showed any host preference and whether the phylogeny of the plant hosts may mirror the composition of root-associated fungi. Fungal communities were largely structured according to host plant identity and to a less extent by environmental factors. We observed a positive relationship between the phylogenetic distance of host plants and the distance of fungal community composition between samples, indicating that the evolutionary history of the host plants plays a major role for which fungi colonize the plant roots. In contrast to the ITS2 marker, the 18S rRNA gene marker showed that chytrid fungi were prevalently associated with plant roots, together with a wide spectrum of amoeba-like protists and nematodes. Our study confirms that arbuscular mycorrhizal (AM) fungi are present also in arctic environments in low abundance.

Evaluation of genome size and quantitative features of the dolipore septum as taxonomic predictors for the Serendipita 'williamsii' species complex

Despite multiple taxonomic revisions, several uncertainties at the genus and species level remain to be resolved within the Serendipitaceae family (Sebacinales). This volatile classification is attributed to the limited number of available axenic cultures and the scarcity of useful morphological traits. In the current study, we attempted to discover alternative taxonomic markers not relying on DNA sequences to differentiate among the closely related members of our Congolese Serendipita isolate collection and the reference strains S. indica (syn. Piriformospora indica) and S. williamsii (syn. P. williamsii). We demonstrated that nuclear distribution across hyphal cells and genome size (determined by flow cytometry) did not have enough resolving power, but quantitative and qualitative variations in the ultrastructure of the dolipore septa investigated by transmission electron microscopy did provide useful markers. Multivariate analysis revealed that subtle differences in ultrastructural characteristics of the parenthesome and the attached endoplasmic reticulum are most relevant when studying this fungal group. Moreover, the observed clustering pattern showed that there might be more diversity amongst the Congolese isolates within the S. 'williamsii' species complex than previously anticipated based on molecular data. Altogether, our results provide novel perspectives on the use of integrative approaches to support sebacinoid and Serendipitaceae taxonomy.

Share the wealth: Trees with greater ectomycorrhizal species overlap share more carbon

The mutualistic symbiosis between forest trees and ectomycorrhizal fungi (EMF) is among the most ubiquitous and successful interactions in terrestrial ecosystems. Specific species of EMF are known to colonize specific tree species, benefitting from their carbon source, and in turn, improving their access to soil water and nutrients. EMF also form extensive mycelial networks that can link multiple root-tips of different trees. Yet the number of tree species connected by such mycelial networks, and the traffic of material across them, are just now under study. Recently we reported substantial belowground carbon transfer between Picea, Pinus, Larix and Fagus trees in a mature forest. Here, we analyze the EMF community of these same individual trees and identify the most likely taxa responsible for the observed carbon transfer. Among the nearly 1,200 EMF root-tips examined, 50%-70% belong to operational taxonomic units (OTUs) that were associated with three or four tree host species, and 90% of all OTUs were associated with at least two tree species. Sporocarp 13 C signals indicated that carbon originating from labelled Picea trees was transferred among trees through EMF networks. Interestingly, phylogenetically more closely related tree species exhibited more similar EMF communities and exchanged more carbon. Our results show that belowground carbon transfer is well orchestrated by the evolution of EMFs and tree symbiosis.

Is the Distribution of Two Rare Orchis Sister Species Limited by Their Main Mycobiont?

As orchids rely on their mycorrhizal fungi for nutrient supply, their spatial range is dependent on the distribution of orchid mycorrhizal (OM) fungi. We addressed possible correlations between mycorrhizal specificity and the geographic distribution of orchids and OM fungi in three populations of the rare sister species Orchis patens and O. canariensis. Metabarcoding of the fungal ITS2 region indicated that, although adult plants of either species were colonized by several ceratobasidioid, tulasnelloid, sebacinoid and serendipitoid fungi, the mycobiont spectra were dominated by Tulasnella helicospora (which occurred in 100% of examined plants with high read numbers), which is a globally distributed fungus. In vitro assays with a T. helicospora isolate obtained from O. patens indicated the effectiveness of this OM fungus at germinating seeds of its native host. At a local scale, higher read numbers for T. helicospora were found in soil samples collected underneath O. patens roots than at locations unoccupied by the orchid. Although these findings suggest that the geographical pattern of the main fungal symbiont does not limit the distribution of O. patens and O. canariensis at this scale, the actual causal link between orchid and OM fungal occurrence/abundance still needs to be better understood.

Oak displays common local but specific distant gene regulation responses to different mycorrhizal fungi

BACKGROUND

Associations of tree roots with diverse symbiotic mycorrhizal fungi have distinct effects on whole plant functioning. An untested explanation might be that such effect variability is associated with distinct impacts of different fungi on gene expression in local and distant plant organs. Using a large scale transcriptome sequencing approach, we compared the impact of three ectomycorrhizal (EMF) and one orchid mycorrhizal fungi (OMF) on gene regulation in colonized roots (local), non-colonized roots (short distance) and leaves (long distance) of the Quercus robur clone DF159 with reference to the recently published oak genome. Since different mycorrhizal fungi form symbiosis in a different time span and variable extents of apposition structure development, we sampled inoculated but non-mycorrhizal plants, for which however markedly symbiotic effects have been reported. Local root colonization by the fungi was assessed by fungal transcript analysis.

RESULTS

The EMF induced marked and species specific effects on plant development in the analysed association stage, but the OMF did not. At local level, a common set of plant differentially expressed genes (DEG) was identified with similar patterns of responses to the three EMF, but not to the OMF. Most of these core DEG were down-regulated and correspond to already described but also new functions related to establishment of EMF symbiosis. Analysis of the fungal transcripts of two EMF in highly colonized roots also revealed onset of a symbiosis establishment. In contrast, in the OMF, the DEG were mainly related to plant defence. Already at short distances, high specificities in transcriptomic responses to the four fungi were detected, which were further enhanced at long distance in leaves, where almost no common DEG were found between the treatments. Notably, no correlation between phylogeny of the EMF and gene expression patterns was observed.

CONCLUSIONS

Use of clonal oaks allowed us to identify a core transcriptional program in roots colonized by three different EMF, supporting the existence of a common EMF symbiotic pathway. Conversely, the specific responses in non-colonized organs were more closely related to the specific impacts of the different of EMF on plant performance.

Sebacinoids within rhizospheric fungal communities associated with subsistence farming in the Congo Basin: a needle in each haystack

The unique ecosystem of the Congolese rainforest has only scarcely been explored for its plant-fungal interactions. Here, we characterized the root fungal communities of field-grown maize and of Panicum from adjacent borders in the Congo Basin and assessed parameters that could shape them. The soil properties indicated that comparable poor soil conditions prevailed in fields and borders, illustrating the low input character of local subsistence farming. The rhizosphere fungal communities, dominated by ascomycetous members, were structured by plant species, slash-and-burn practices and soil P, pH and C/N ratio. Examining fungi with potential plant growth-promoting abilities, the glomeromycotan communities appeared to be affected by the same parameters, whereas the inconspicuous symbionts of the order Sebacinales seemed less susceptible to environmental and anthropogenic factors. Notwithstanding the low abundances at which they were detected, sebacinoids occurred in 87% of the field samples, implying that they represent a consistent taxon within indigenous fungal populations across smallholder farm sites. Pending further insight into their ecosystem functionality, these data suggest that Sebacinales are robust root inhabitants that might be relevant for on-farm inoculum development within sustainable soil fertility management in the Sub-Saharan region.

An improved growth medium for enhanced inoculum production of the plant growth-promoting fungus Serendipita indica

BACKGROUND

The plant endophytic fungus Serendipita indica colonizes roots of a wide range of plant species and can enhance growth and stress resistance of these plants. Due to its ease of axenic cultivation and its broad host plant range including the model plant Arabidopsis thaliana and numerous crop plants, it is widely used as a model fungus to study beneficial fungus-root interactions. In addition, it was suggested to be utilized for commercial applications, e.g. to enhance yield in barley and other species. To produce inoculum, S. indica is mostly cultivated in a complex Hill-Käfer medium (CM medium), however, growth in this medium is slow, and yield of chlamydospores, which are often used for plant root inoculation, is relatively low.

RESULTS

We tested and optimized a simple vegetable juice-based medium for an enhanced yield of fungal inoculum. The described vegetable juice (VJ) medium is based on commercially available vegetable juice and is easy to prepare. VJ medium was superior to the currently used CM medium with respect to biomass production in liquid medium and hyphal growth on agar plates. Using solid VJ medium supplemented with sucrose (VJS), a high amount of chlamydospores developed already after 8 days of cultivation, producing significantly more spores than on CM medium. Use of VJ medium is not restricted to S. indica, as it also supported growth of two pathogenic fungi often used in plant pathology experiments: the ascomycete Fusarium graminearum, the causal agent of Fusarium head blight disease on wheat and barley, and Verticillium longisporum, the causal agent of verticillium wilt.

CONCLUSIONS

The described VJ medium is recommended for streamlined and efficient production of inoculum for the plant endophytic fungus Serendipita indica and might prove superior for the propagation of other fungi for research purposes.

Notes, outline and divergence times of Basidiomycota

The Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.

The inconspicuous gatekeeper: endophytic Serendipita vermifera acts as extended plant protection barrier in the rhizosphere

In nature, beneficial and pathogenic fungi often simultaneously colonise plants. Despite substantial efforts to understand the composition of natural plant-microbe communities, the mechanisms driving such multipartite interactions remain largely unknown. Here we address how the interaction between the beneficial root endophyte Serendipita vermifera and the pathogen Bipolaris sorokiniana affects fungal behaviour and determines barley host responses using a gnotobiotic soil-based split-root system. Fungal confrontation in soil resulted in induction of B. sorokiniana genes involved in secondary metabolism and a significant repression of genes encoding putative effectors. In S. vermifera, genes encoding hydrolytic enzymes were strongly induced. This antagonistic response was not activated during the tripartite interaction in barley roots. Instead, we observed a specific induction of S. vermifera genes involved in detoxification and redox homeostasis. Pathogen infection but not endophyte colonisation resulted in substantial host transcriptional reprogramming and activation of defence. In the presence of S. vermifera, pathogen infection and disease symptoms were significantly reduced despite no marked alterations of the plant transcriptional response. The activation of stress response genes and concomitant repression of putative effector gene expression in B. sorokiniana during confrontation with the endophyte suggest a reduction of the pathogen's virulence potential before host plant infection.

Scavenging organic nitrogen and remodelling lipid metabolism are key survival strategies adopted by the endophytic fungi, Serendipita vermifera and Serendipita bescii to alleviate nitrogen and phosphorous starvation in vitro

Serendipitaceae represents a diverse fungal group in the Basidiomycota that includes endophytes and lineages that repeatedly evolved ericoid, orchid and ectomycorrhizal lifestyle. Plants rely upon both nitrogen and phosphorous, for essential growth processes, and are often provided by mycorrhizal fungi. In this study, we investigated the cellular proteome of Serendipita vermifera MAFF305830 and closely related Serendipita vermifera subsp. bescii NFPB0129 grown in vitro under (N) ammonium and (P) phosphate starvation conditions. Mycelial growth pattern was documented under these conditions to correlate growth-specific responses to nutrient starvation. We found that N-starvation accelerated hyphal radial growth, whereas P-starvation accelerated hyphal branching. Additionally, P-starvation triggers an integrated starvation response leading to remodelling of lipid metabolism. Higher abundance of an ammonium transporter known to serve as both an ammonium sensor and stimulator of hyphal growth was detected under N-starvation. Additionally, N-starvation led to strong up-regulation of nitrate, amino acid, peptide, and urea transporters, along with several proteins predicted to have peptidase activity. Taken together, our finding suggests S. bescii and S. vermifera have the metabolic capacity for nitrogen assimilation from organic forms of N compounds. We hypothesize that the nitrogen metabolite repression is a key regulator of such organic N assimilation.

Serendipita indica E5'NT modulates extracellular nucleotide levels in the plant apoplast and affects fungal colonization

Extracellular adenosine 5′‐triphosphate (eATP) is an essential signaling molecule that mediates different cellular processes through its interaction with membrane‐associated receptor proteins in animals and plants. eATP regulates plant growth, development, and responses to biotic and abiotic stresses. Its accumulation in the apoplast induces ROS production and cytoplasmic calcium increase mediating a defense response to invading microbes. We show here that perception of extracellular nucleotides, such as eATP, is important in plant–fungus interactions and that during colonization by the beneficial root endophyte Serendipita indica eATP accumulates in the apoplast at early symbiotic stages. Using liquid chromatography–tandem mass spectrometry, and cytological and functional analysis, we show that S. indica secrets SiE5′NT, an enzymatically active ecto‐5′‐nucleotidase capable of hydrolyzing nucleotides in the apoplast. Arabidopsis thaliana lines producing extracellular SiE5′NT are significantly better colonized, have reduced eATP levels, and altered responses to biotic stresses, indicating that SiE5′NT functions as a compatibility factor. Our data suggest that extracellular bioactive nucleotides and their perception play an important role in fungus–root interactions and that fungal‐derived enzymes can modify apoplastic metabolites to promote fungal accommodation.

Non-targeted Colonization by the Endomycorrhizal Fungus, Serendipita vermifera, in Three Weeds Typically Co-occurring with Switchgrass

Serendipita vermifera (=Sebacina vermifera; isolate MAFF305830) is a mycorrhizal fungus originally isolated from the roots of an Australian orchid that we have previously shown to be beneficial in enhancing biomass yield and drought tolerance in switchgrass, an important bioenergy crop for cellulosic ethanol production in the United States. However, almost nothing is known about how this root-associated fungus proliferates and grows through the soil matrix. Such information is critical to evaluate the possibility of non-target effects, such as unintended spread to weedy plants growing near a colonized switchgrass plant in a field environment. A microcosm experiment was conducted to study movement of vegetative mycelia of S. vermifera between intentionally inoculated switchgrass (Panicum virgatum L.) and nearby weeds. We constructed size-exclusion microcosms to test three different common weeds, large crabgrass (Digitaria sanguinalis L.), Texas panicum (Panicum texanum L.), and Broadleaf signalgrass (Brachiaria platyphylla L.), all species that typically co-occur in Southern Oklahoma and potentially compete with switchgrass. We report that such colonization of non-target plants by S. vermifera can indeed occur, seemingly via co-mingled root systems. As a consequence of colonization, significant enhancement of growth was noted in signalgrass, while a mild increase (albeit not significant) was evident in crabgrass. Migration of the fungus seems unlikely in root-free bulk soil, as we failed to see transmission when the roots were kept separate. This research is the first documentation of non-targeted colonization of this unique root symbiotic fungus and highlights the need for such assessments prior to deployment of biological organisms in the field.

Does warming by open-top chambers induce change in the root-associated fungal community of the arctic dwarf shrub Cassiope tetragona (Ericaceae)?

Climate change may alter mycorrhizal communities, which impact ecosystem characteristics such as carbon sequestration processes. These impacts occur at a greater magnitude in Arctic ecosystems, where the climate is warming faster than in lower latitudes. Cassiope tetragona (L.) D. Don is an Arctic plant species in the Ericaceae family with a circumpolar range. C. tetragona has been reported to form ericoid mycorrhizal (ErM) as well as ectomycorrhizal (ECM) symbioses. In this study, the fungal taxa present within roots of C. tetragona plants collected from Svalbard were investigated using DNA metabarcoding. In light of ongoing climate change in the Arctic, the effects of artificial warming by open-top chambers (OTCs) on the fungal root community of C. tetragona were evaluated. We detected only a weak effect of warming by OTCs on the root-associated fungal communities that was masked by the spatial variation between sampling sites. The root fungal community of C. tetragona was dominated by fungal groups in the Basidiomycota traditionally classified as either saprotrophic or ECM symbionts, including the orders Sebacinales and Agaricales and the genera Clavaria, Cortinarius, and Mycena. Only a minor proportion of the operational taxonomic units (OTUs) could be annotated as ErM-forming fungi. This indicates that C. tetragona may be forming mycorrhizal symbioses with typically ECM-forming fungi, although no characteristic ECM root tips were observed. Previous studies have indicated that some saprophytic fungi may also be involved in biotrophic associations, but whether the saprotrophic fungi in the roots of C. tetragona are involved in biotrophic associations remains unclear. The need for more experimental and microscopy-based studies to reveal the nature of the fungal associations in C. tetragona roots is emphasized.

Local-scale spatial structure and community composition of orchid mycorrhizal fungi in semi-natural grasslands

Orchid mycorrhizal (OrM) fungi play a crucial role in the ontogeny of orchids, yet little is known about how the structure of OrM fungal communities varies with space and environmental factors. Previous studies suggest that within orchid patches, the distance to adult orchids may affect the abundance of OrM fungi. Many orchid species grow in species-rich temperate semi-natural grasslands, the persistence of which depends on moderate physical disturbances, such as grazing and mowing. The aim of this study was to test whether the diversity, structure and composition of OrM fungal community are influenced by the orchid patches and management intensity in semi-natural grasslands. We detected putative OrM fungi from 0 to 32 m away from the patches of host orchid species (Orchis militaris and Platanthera chlorantha) in 21 semi-natural calcareous grasslands using pyrosequencing. In addition, we assessed different ecological conditions in semi-natural grasslands but primarily focused on the effect of grazing intensity on OrM fungal communities in soil. We found that investigated orchid species were mostly associated with Ceratobasidiaceae and Tulasnellaceae and, to a lesser extent, with Sebacinales. Of all the examined factors, the intensity of grazing explained the largest proportion of variation in OrM fungal as well as total fungal community composition in soil. Spatial analyses showed limited evidence for spatial clustering of OrM fungi and their dependence on host orchids. Our results indicate that habitat management can shape OrM fungal communities, and the spatial distribution of these fungi appears to be weakly structured outside the orchid patches.

Long-Term Enrichment of Stress-Tolerant Cellulolytic Soil Populations following Timber Harvesting Evidenced by Multi-Omic Stable Isotope Probing

Soil management is vital for maintaining the productivity of commercial forests, yet the long-term impact of timber harvesting on soil microbial communities remains largely a matter of conjecture. Decomposition of plant biomass, comprised mainly of lignocellulose, has a broad impact on nutrient cycling, microbial activity and physicochemical characteristics of soil. At "Long-term Soil Productivity Study" sites in California dominated by Ponderosa pine, we tested whether clear-cut timber harvesting, accompanied by varying degrees of organic matter (OM) removal, affected the activity and structure of the cellulose-degrading microbial populations 16 years after harvesting. Using a variety of experimental approaches, including stable isotope probing with 13C-labeled cellulose in soil microcosms, we demonstrated that harvesting led to a decrease in net respiration and cellulolytic activity. The decrease in cellulolytic activity was associated with an increased relative abundance of thermophilic, cellulolytic fungi (Chaetomiaceae), coupled with a decreased relative abundance of cellulolytic bacteria, particularly members of Opitutaceae, Caulobacter, and Streptomycetaceae. In general, harvesting led to an increase in stress-tolerant taxa (i.e., also non-cellulolytic taxa), though our results indicated that OM retention mitigated population shifts via buffering against abiotic changes. Stable-isotope probing improved shotgun metagenome assembly by 20-fold and enabled the recovery of 10 metagenome-assembled genomes of cellulolytic bacteria and fungi. Our study demonstrates the putative cellulolytic activity of a number of uncultured taxa and highlights the mineral soil layer as a reservoir of uncharacterized diversity of cellulose-degraders. It also and contributes to a growing body of research showing persistent changes in microbial community structure in the decades following forest harvesting.

Fine-scale spatial distribution of orchid mycorrhizal fungi in the soil of host-rich grasslands

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.

Experimental evidence of ericoid mycorrhizal potential within Serendipitaceae (Sebacinales)

The Sebacinales are a monophyletic group of ubiquitous hymenomycetous mycobionts which form ericoid and orchid mycorrhizae, ecto- and ectendomycorrhizae, and nonspecific root endophytic associations with a wide spectrum of plants. However, due to the complete lack of fungal isolates derived from Ericaceae roots, the Sebacinales ericoid mycorrhizal (ErM) potential has not yet been tested experimentally. Here, we report for the first time isolation of a serendipitoid (formerly Sebacinales Group B) mycobiont from Ericaceae which survived in pure culture for several years. This allowed us to test its ability to form ericoid mycorrhizae with an Ericaceae host in vitro, to describe its development and colonization pattern in host roots over time, and to compare its performance with typical ErM fungi and other serendipitoids derived from non-Ericaceae hosts. Out of ten serendipitoid isolates tested, eight intracellularly colonized Vaccinium hair roots, but only the Ericaceae-derived isolate repeatedly formed typical ericoid mycorrhiza morphologically identical to ericoid mycorrhiza commonly found in naturally colonized Ericaceae, but yet different from ericoid mycorrhiza formed in vitro by the prominent ascomycetous ErM fungus Rhizoscyphus ericae. One Orchidaceae-derived isolate repeatedly formed abundant hyaline intracellular microsclerotia morphologically identical to those occasionally found in naturally colonized Ericaceae, and an isolate of Serendipita (= Piriformospora) indica produced abundant intracellular chlamydospores typical of this species. Our results confirm for the first time experimentally that some Sebacinales can form ericoid mycorrhiza, point to their broad endophytic potential in Ericaceae hosts, and suggest possible ericoid mycorrhizal specificity in Serendipitaceae.

New mutualistic fungal endophytes isolated from poplar roots display high metal tolerance

This study aimed to isolate, identify, and characterise metal-tolerant fungi colonising poplar roots at a metal-contaminated phytoremediation site. Poplar roots were colonised by arbuscular mycorrhizal, ectomycorrhizal, and endophytic fungi, and the species were determined by ITS molecular analyses. Eight different isolates were successfully isolated into pure culture. Three isolates belonging to the Helotiales (P02, P06) and the Serendipita vermifera species (P04) were highly tolerant to metals (Cd, Zn, Pb, and Cu) compared to the mycorrhizal Hebeloma isolates. The three isolates degraded complex carbohydrates, such as xylan and cellulose, indicating that they could partially degrade root cell walls and penetrate into cells. This hypothesis was confirmed by further in vitro re-synthesis experiments, which showed that the three isolates colonised root tissues of poplar plantlets whereas two of them formed microsclerotia-like structures. Taken together, these results suggest an endophytic lifestyle of these isolates. This is the first evidence of S. vermifera as a root endophyte of poplar. A new endophytic putative species belonging to the Helotiales and closely related to Leohumicola is also reported. Interestingly, and when compared to mock-inoculated plants, both P06 and P04 isolates increased the number of root tips of inoculated poplar plantlets in vitro. Moreover, the S. vermifera P04 isolate also increased the shoot biomass. The results are discussed in relation to the potential use of endophytic strains for tree-based phytoremediation of metal-contaminated sites.

Fungal endophytes for sustainable crop production

This minireview highlights the importance of endophytic fungi for sustainable agriculture and horticulture production. Fungal endophytes play a key role in habitat adaptation of plants resulting in improved plant performance and plant protection against biotic and abiotic stresses. They encode a vast variety of novel secondary metabolites including volatile organic compounds. In addition to protecting plants against pathogens and pests, selected fungal endophytes have been used to remove animal toxicities associated with fungal endophytes in temperate grasses, to create corn and rice plants that are tolerant to a range of biotic and abiotic stresses, and for improved management of post-harvest control. We argue that practices used in plant breeding, seed treatments and agriculture, often caused by poor knowledge of the importance of fungal endophytes, are among the reasons for the loss of fungal endophyte diversity in domesticated plants and also accounts for the reduced effectiveness of some endophyte strains to confer plant benefits. We provide recommendations on how to mitigate against these negative impacts in modern agriculture.

Microbially Mediated Plant Salt Tolerance and Microbiome-based Solutions for Saline Agriculture

Soil salinization adversely affects plant growth and has become one of the major limiting factors for crop productivity worldwide. The conventional approach, breeding salt-tolerant plant cultivars, has often failed to efficiently alleviate the situation. In contrast, the use of a diverse array of microorganisms harbored by plants has attracted increasing attention because of the remarkable beneficial effects of microorganisms on plants. Multiple advanced '-omics' technologies have enabled us to gain insights into the structure and function of plant-associated microbes. In this review, we first focus on microbe-mediated plant salt tolerance, in particular on the physiological and molecular mechanisms underlying root-microbe symbiosis. Unfortunately, when introducing such microbes as single strains to soils, they are often ineffective in improving plant growth and stress tolerance, largely due to competition with native soil microbial communities and limited colonization efficiency. Rapid progress in rhizosphere microbiome research has revived the belief that plants may benefit more from association with interacting, diverse microbial communities (microbiome) than from individual members in a community. Understanding how a microbiome assembles in the continuous compartments (endosphere, rhizoplane, and rhizosphere) will assist in predicting a subset of core or minimal microbiome and thus facilitate synthetic re-construction of microbial communities and their functional complementarity and synergistic effects. These developments will open a new avenue for capitalizing on the cultivable microbiome to strengthen plant salt tolerance and thus to refine agricultural practices and production under saline conditions.

Non-specific symbiotic germination of Cynorkis purpurea (Thouars) Kraezl., a habitat-specific terrestrial orchid from the Central Highlands of Madagascar

Orchids, particularly terrestrial taxa, rely mostly on basidiomycete fungi in the Cantharellales and Sebacinales that trigger the process of seed germination and/or initiate the full development of the seedling. During the course of development, orchids may associate with the same fungus, or they may enlist other types of fungi for their developmental needs leading to resilience in a natural setting. This study examined in vitro seed germination and seedling developmental behavior of Cynorkis purpurea, a terrestrial orchid from the Central Highlands of Madagascar. This species is mostly restricted to gallery forests in the Itremo Massif, in moist substrate between rocks bordering streams. The main objective was to understand the influence of diverse mycorrhizal fungi on seed germination and further development of C. purpurea. The study aims to compare symbiotic versus asymbiotic germination and seedling development with seeds and fungi collected from a 13-km(2) area in the Itremo region. Seeds collected from the wild were sown with diverse orchid mycorrhizal fungi (OMF) spanning 12 operational taxonomic units (OTUs) in three genera (Tulasnella, Ceratobasidium, and Sebacina) acquired from different habitats. Treatments were assessed in terms of the percentage of germinated seeds and fully developed seedlings against those in asymbiotic control media treatments. Overall, OMF significantly improved seedling development within the 12-week experiment period. Sebacina as a genus was the most effective at promoting seedling development of C. purpurea, as well as having the ability to enter into successful symbiotic relationships with orchids of different life forms; this new knowledge may be especially useful for orchid conservation practiced in tropical areas like Madagascar. A Sebacina isolate from an epiphytic seedling of Polystachya concreta was the most effective at inducing rapid seedling development and was among the five that outperformed fungi isolated from roots of C. purpurea. C. purpurea was found to be a mycorrhizal generalist, despite its specific habitat preference, highlighting the complex interaction between the plant, fungi, and the environment. The potential impact on conservation strategies of understanding the requirements for orchid seed germination and development by identifying and using OMF from diverse sources is discussed in detail.

Sebacinales - one thousand and one interactions with land plants

20 I 21 II 21 III 23 IV 29 V 33 VI 35 36 36 References 36 SUMMARY: Root endophytism and mycorrhizal associations are complex derived traits in fungi that shape plant physiology. Sebacinales (Agaricomycetes, Basidiomycota) display highly diverse interactions with plants. Although early-diverging Sebacinales lineages are root endophytes and/or have saprotrophic abilities, several more derived clades harbour obligate biotrophs forming mycorrhizal associations. Sebacinales thus display transitions from saprotrophy to endophytism and to mycorrhizal nutrition within one fungal order. This review discusses the genomic traits possibly associated with these transitions. We also show how molecular ecology revealed the hyperdiversity of Sebacinales and their evolutionary diversification into two sister families: Sebacinaceae encompasses mainly ectomycorrhizal and early-diverging saprotrophic species; the second family includes endophytes and lineages that repeatedly evolved ericoid, orchid and ectomycorrhizal abilities. We propose the name Serendipitaceae for this family and, within it, we transfer to the genus Serendipita the endophytic cultivable species Piriformospora indica and P. williamsii. Such cultivable Serendipitaceae species provide excellent models for root endophytism, especially because of available genomes, genetic tractability, and broad host plant range including important crop plants and the model plant Arabidopsis thaliana. We review insights gained with endophytic Serendipitaceae species into the molecular mechanisms of endophytism and of beneficial effects on host plants, including enhanced resistance to abiotic and pathogen stress.

Deciphering endophyte behaviour: the link between endophyte biology and efficacious biological control agents

Endophytes associate with the majority of plant species found in natural and managed ecosystems. They are regarded as extremely important plant partners that provide improved stress tolerance to the host compared with plants that lack this symbiosis. Fossil records of endophytes date back more than 400 million years, implicating these microorganisms in host plant adaptation to habitat transitions. However, it is only recently that endophytes, and their bioactive products, have received meaningful attention from the scientific community. The benefits some endophytes can confer on their hosts include plant growth promotion and survival through the inhibition of pathogenic microorganisms and invertebrate pests, the removal of soil contaminants, improved tolerance of low fertility soils, and increased tolerance of extreme temperatures and low water availability. Endophytes are extremely diverse and can exhibit many different biological behaviours. Not all endophyte technologies have been successfully commercialised. Of interest in the development of the next generation of plant protection products is how much of this is due to the biology of the particular endophytic microorganism. In this review, we highlight selected case studies of endophytes and discuss their lifestyles and behavioural traits, and discuss how these factors contribute towards their effectiveness as biological control agents.

Spatial and niche-based ecological processes drive the distribution of endophytic Sebacinales in soil and root of grassland communities

The interest in endophytic sebacinalean communities has been increasing during the last decade due to the increased knowledge about their symbiotic life style and potential role for ecosystem functioning. Although they are present in many ecosystems, their abundance in individual plant roots is very limited. This fact affects their study: they are difficult to isolate and to detect in root DNA samples. To advance knowledge of the forces that shape their distribution, we approached the parallel study of sebacinalean communities in roots and soil of grassland. Using a small-scale spatially explicit sampling design, we analysed the contribution of spatial position, soil properties, plant community and phylogenetic components to the variation of sebacinalean communities. The results revealed the presence of 11 operational taxonomic units (OTUs) and a high coincidence between root and soil communities: on an average a single-OTU per sample was recorded for both sample types. Spatial distance was found to mainly drive the distribution of Sebacinales in soil, whereas phylogenetic plus environmental signatures mainly drove their presence in roots. Independently of the sample type, we found clear evidence of environmental filtering caused by soil pH which, furthermore, seemed to control the presence of a specialized sebacinalean OTU.

Divergence Times and Phylogenetic Patterns of Sebacinales, a Highly Diverse and Widespread Fungal Lineage

Patterns of geographic distribution and composition of fungal communities are still poorly understood. Widespread occurrence in terrestrial ecosystems and the unique richness of interactions of Sebacinales with plants make them a target group to study evolutionary events in the light of nutritional lifestyle. We inferred diversity patterns, phylogenetic structures and divergence times of Sebacinales with respect to their nutritional lifestyles by integrating data from fossil-calibrated phylogenetic analyses. Relaxed molecular clock analyses indicated that Sebacinales originated late Permian within Basidiomycota, and their split into Sebacinaceae and Serendipitaceae nom. prov. likely occurred during the late Jurassic and the early Cretaceous, coinciding with major diversifications of land plants. In Sebacinaceae, diversification of species with ectomycorrhizal lifestyle presumably started during the Paleocene. Lineage radiations of the core group of ericoid and cavendishioid mycorrhizal Sebacinales started probably in the Eocene, coinciding with diversification events of their hosts. The diversification of Sebacinales with jungermannioid interactions started during the Oligocene, and occurred much later than the diversification of their hosts. Sebacinales communities associated either with ectomycorrhizal plants, achlorophyllous orchids, ericoid and cavendishioid Ericaceae or liverworts were phylogenetically clustered and globally distributed. Major Sebacinales lineage diversifications started after the continents had drifted apart. We also briefly discuss dispersal patterns of extant Sebacinales.

Sebacina vermifera: a unique root symbiont with vast agronomic potential

The Sebacinales belong to a taxonomically, ecologically, and physiologically diverse group of fungi in the Basidiomycota. While historically recognized as orchid mycorrhizae, recent DNA studies have brought to light both their pandemic distribution and the broad spectrum of mycorrhizal types they form. Indeed, ecological studies using molecular-based methods of detection have found Sebacinales fungi in field specimens of bryophytes (moss), pteridophytes (fern) and all families of herbaceous angiosperms (flowering plants) from temperate, subtropical and tropical regions. These natural host plants include, among others, liverworts, wheat, maize and Arabidopsis thaliana, the model plant traditionally viewed as non-mycorrhizal. The orchid mycorrhizal fungus Sebacina vermifera (MAFF 305830) was first isolated from the Australian orchid Cyrtostylis reniformis. Research performed with this strain clearly indicates its plant growth promoting abilities in a variety of plants, while demonstrating a lack of specificity that rivals or even surpasses that of arbuscular mycorrhizae. Indeed, these traits thus far appear to characterize a majority of strains belonging to the so-called "clade B" within the Sebacinales (recently re-classified as the Serendipitaceae), raising numerous basic research questions regarding plant-microbe signaling and the evolution of mycorrhizal symbioses. Further, given their proven beneficial impact on plant growth and their apparent but cryptic ubiquity, sebacinoid fungi should be considered as a previously hidden, but amenable and effective microbial tool for enhancing plant productivity and stress tolerance.

Ectomycorrhizal fungal communities of Coccoloba uvifera (L.) L. mature trees and seedlings in the neotropical coastal forests of Guadeloupe (Lesser Antilles)

We studied belowground and aboveground diversity and distribution of ectomycorrhizal (EM) fungal species colonizing Coccoloba uvifera (L.) L. (seagrape) mature trees and seedlings naturally regenerating in four littoral forests of the Guadeloupe island (Lesser Antilles). We collected 546 sporocarps, 49 sclerotia, and morphotyped 26,722 root tips from mature trees and seedlings. Seven EM fungal species only were recovered among sporocarps (Cantharellus cinnabarinus, Amanita arenicola, Russula cremeolilacina, Inocybe littoralis, Inocybe xerophytica, Melanogaster sp., and Scleroderma bermudense) and one EM fungal species from sclerotia (Cenococcum geophilum). After internal transcribed spacer (ITS) sequencing, the EM root tips fell into 15 EM fungal taxa including 14 basidiomycetes and 1 ascomycete identified. Sporocarp survey only weakly reflected belowground assessment of the EM fungal community, although 5 fruiting species were found on roots. Seagrape seedlings and mature trees had very similar communities of EM fungi, dominated by S. bermudense, R. cremeolilacina, and two Thelephoraceae: shared species represented 93 % of the taxonomic EM fungal diversity and 74 % of the sampled EM root tips. Furthermore, some significant differences were observed between the frequencies of EM fungal taxa on mature trees and seedlings. The EM fungal community composition also varied between the four investigated sites. We discuss the reasons for such a species-poor community and the possible role of common mycorrhizal networks linking seagrape seedlings and mature trees in regeneration of coastal forests.

Mutualistic root endophytism is not associated with the reduction of saprotrophic traits and requires a noncompromised plant innate immunity

During a compatible interaction, the sebacinoid root-associated fungi Piriformospora indica and Sebacina vermifera induce modification of root morphology and enhance shoot growth in Arabidopsis thaliana. The genomic traits common in these two fungi were investigated and compared with those of other root-associated fungi and saprotrophs. The transcriptional responses of the two sebacinoid fungi and of Arabidopsis roots to colonization at three different symbiotic stages were analyzed by custom-designed microarrays. We identified key genomic features characteristic of sebacinoid fungi, such as expansions for gene families involved in hydrolytic activities, carbohydrate-binding and protein-protein interaction. Additionally, we show that colonization of Arabidopsis correlates with the induction of salicylic acid catabolism and accumulation of jasmonate and glucosinolates (GSLs). Genes involved in root developmental processes were specifically induced by S. vermifera at later stages during interaction. Using different Arabidopsis indole-GSLs mutants and measurement of secondary metabolites, we demonstrate the importance of the indolic glucosinolate pathway in the growth restriction of P. indica and S. vermifera and we identify indole-phytoalexins and specifically indole-carboxylic acids derivatives as potential key players in the maintenance of a mutualistic interaction with root endophytes.

Temporal patterns of orchid mycorrhizal fungi in meadows and forests as revealed by 454 pyrosequencing

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.

Temporal variation in mycorrhizal diversity and carbon and nitrogen stable isotope abundance in the wintergreen meadow orchid Anacamptis morio

Many adult orchids, especially photoautotrophic species, associate with a diverse range of mycorrhizal fungi, but little is known about the temporal changes that might occur in the diversity and functioning of orchid mycorrhiza during vegetative and reproductive plant growth. Temporal variations in the spectrum of mycorrhizal fungi and in stable isotope natural abundance were investigated in adult plants of Anacamptis morio, a wintergreen meadow orchid. Anacamptis morio associated with mycorrhizal fungi belonging to Tulasnella, Ceratobasidium and a clade of Pezizaceae (Ascomycetes). When a complete growing season was investigated, multivariate analyses indicated significant differences in the mycorrhizal fungal community. Among fungi identified from manually isolated pelotons, Tulasnella was more common in autumn and winter, the pezizacean clade was very frequent in spring, and Ceratobasidium was more frequent in summer. By contrast, relatively small variations were found in carbon (C) and nitrogen (N) stable isotope natural abundance, A. morio samples showing similar (15)N enrichment and (13)C depletion at the different sampling times. These observations suggest that, irrespective of differences in the seasonal environmental conditions, the plant phenological stages and the associated fungi, the isotopic content in mycorrhizal A. morio remains fairly constant over time.

Culturable fungal endophytes in roots of Enkianthus campanulatus (Ericaceae)

Roots of plants in the genus Enkianthus, which belongs to the earliest diverging lineage in the Ericaceae, are commonly colonized by arbuscular mycorrhizal (AM) fungi. We documented the community of fungal root endophytes associated with Enkianthus species using a culture-based method for better understanding the members of root-colonizing fungi, except for AM fungi. Fungal isolates were successfully obtained from 610 out of 3,599 (16.9 %) root segments. Molecular analysis of fungal cultures based on ribosomal internal transcribed spacer (ITS) sequences yielded 63 operational taxonomical units (OTUs: 97 % sequence similarity cutoff) from 315 representative isolates. Further phylogenetic analysis showed that most (296 isolates) belonged to Ascomycota and were either members of Helotiales (Dermataceae, Hyaloscyphaceae, Phialocephala and Rhizoscyphus ericae aggregate), Oidiodendron, or other Pezizomycotina. Twenty-three out of 63 OTUs, which mainly consisted of Leotiomycetes, showed high similarities with reference sequences derived from roots of other ericaceous plants such as Rhododendron. The results indicated that Enkianthus houses variable root mycobionts including putative endophytic and mycorrhizal fungi in addition to AM fungi.