Harzianic acid exerts antimicrobial activity against Gram-positive bacteria and targets the cell membrane

The thermophilic fungus Oidiodendron flavum is a saprobe that is commonly isolated from soil. Here, we identified a Gram-positive bacteria-selective antimicrobial secondary metabolite from this fungal species, harzianic acid (HA). Using Bacillus subtilis strain 168 combined with dynamic bacterial morphology imaging, we found that HA targeted the cell membrane. To further study the antimicrobial activity of HA, we isolated an HA-resistant strain, Bacillus subtilis strain M9015, and discovered that the mutant had more translucent colonies than the wild type strain, showed cross resistance to rifampin, and harbored five mutations in the coding region of four distinct genes. Further analysis of these genes indicated that the mutation in atpE might be responsible for the translucency of the colonies, and mutation in mdtR for resistance to both HA and rifampin. We conclude that HA is an antimicrobial agent against Gram-positive bacteria that targets the cell membrane.

Several Characteristics of Oidiodendron maius G.L. Barron Important for Heather Plants' Controlled Mycorrhization

Oidiodendron maius G.L. Barron is a recognized fungal species capable of forming ericoid mycorrhiza with various positive effects on host plants; therefore, newly found and previously uncharacterized O. maius strains may be valuable for heather plants' controlled mycorrhization. Characteristics of the O. maius F3860 strain were studied, i.e., mycelium growth on various nutrient media and the ability to secrete auxins and enzymes. O. maius F3860 grew rapidly on malt extract agar and potato dextrose agar. It was also able to grow on nutrient media suitable for heather plant cultivation. The presence of the flavonoids rutin and quercetin increased the mycelium growth rate compared to the control, starting from the 8th to the 13th days of cultivation. The ability to secrete auxins was confirmed with bioassay and thin-layer chromatography, and their content, as well as phytase activity, was estimated spectrophotometrically. Both in nutrient media with tryptophan and without it, O. maius F3860 secreted about 6 μg IAA/mL growth medium. O. maius F3860 possessed extracellular phytase, protease, and phenol oxidase activities. The investigation indicates O. maius F3860's promise for heather seedling inoculation as an approach to increase their fitness.

Old-growth Acer macrophyllum trees host a unique suite of arbuscular mycorrhizal fungi and other root-associated fungal taxa in their canopy soil environment

Canopy soils occur on tree branches throughout the temperate rainforests of the Pacific Northwest Coast and are recognized as a defining characteristic of these ecosystems. Certain tree species extend adventitious roots into these canopy soil environments. Yet, research on adventitious root-associated fungi remains limited. Our study used microscopy to compare fungal colonization intensity between canopy and forest floor roots of old-growth bigleaf maple (Acer macrophyllum) trees. Subsequently, two high-throughput sequencing platforms were used to explore the spatial and seasonal variation of root-associated fungi between the two soil environments over one year. We found that canopy and forest floor roots had similar colonization intensity and were associating with a diversity of arbuscular mycorrhizal fungi and other potential symbionts, many of which were resolved to species level. Soil environment and seasonality affected root-associated fungal community composition, and several fungal species were indicative of the canopy soil environment. In Washington State's (USA) temperate old-growth rainforests, these canopy soil environments host a unique suite of root-associated fungi. The presence of arbuscular mycorrhizae provides further evidence that adventitious roots form fungal associations to exploit canopy soils for resources, and there may be novel relationships forming with other fungi. These soils may be providing a redundancy compartment (i.e., "nutrient reserve"), imparting a resiliency to disturbances for certain old-growth trees.

Discovery of plastic-degrading microbial strains isolated from the alpine and Arctic terrestrial plastisphere

Increasing plastic production and the release of some plastic in to the environment highlight the need for circular plastic economy. Microorganisms have a great potential to enable a more sustainable plastic economy by biodegradation and enzymatic recycling of polymers. Temperature is a crucial parameter affecting biodegradation rates, but so far microbial plastic degradation has mostly been studied at temperatures above 20°C. Here, we isolated 34 cold-adapted microbial strains from the plastisphere using plastics buried in alpine and Arctic soils during laboratory incubations as well as plastics collected directly from Arctic terrestrial environments. We tested their ability to degrade, at 15°C, conventional polyethylene (PE) and the biodegradable plastics polyester-polyurethane (PUR; Impranil®); ecovio® and BI-OPL, two commercial plastic films made of polybutylene adipate-co-terephthalate (PBAT) and polylactic acid (PLA); pure PBAT; and pure PLA. Agar clearing tests indicated that 19 strains had the ability to degrade the dispersed PUR. Weight-loss analysis showed degradation of the polyester plastic films ecovio® and BI-OPL by 12 and 5 strains, respectively, whereas no strain was able to break down PE. NMR analysis revealed significant mass reduction of the PBAT and PLA components in the biodegradable plastic films by 8 and 7 strains, respectively. Co-hydrolysis experiments with a polymer-embedded fluorogenic probe revealed the potential of many strains to depolymerize PBAT. Neodevriesia and Lachnellula strains were able to degrade all the tested biodegradable plastic materials, making these strains especially promising for future applications. Further, the composition of the culturing medium strongly affected the microbial plastic degradation, with different strains having different optimal conditions. In our study we discovered many novel microbial taxa with the ability to break down biodegradable plastic films, dispersed PUR, and PBAT, providing a strong foundation to underline the role of biodegradable polymers in a circular plastic economy.

Ericoid mycorrhizal fungi as biostimulants for improving propagation and production of ericaceous plants

The mutualistic relationship between mycorrhizal fungi and plant roots is a widespread terrestrial symbiosis. The symbiosis enables plants to better adapt to adverse soil conditions, enhances plant tolerance to abiotic and biotic stresses, and improves plant establishment and growth. Thus, mycorrhizal fungi are considered biostimulants. Among the four most common types of mycorrhizae, arbuscular mycorrhiza (AM) and ectomycorrhiza (EcM) have been more intensively studied than ericoid mycorrhiza (ErM) and orchidaceous mycorrhiza (OrM). ErM fungi can form symbiotic relationships with plants in the family Ericaceae. Economically important plants in this family include blueberry, bilberry, cranberry, and rhododendron. ErM fungi are versatile as they are both saprotrophic and biotrophic. Increasing reports have shown that they can degrade soil organic matter, resulting in the bioavailability of nutrients for plants and microbes. ErM fungi can synthesize hormones to improve fungal establishment and plant root initiation and growth. ErM colonization enables plants to effective acquisition of mineral nutrients. Colonized plants are able to tolerate different abiotic stresses, including drought, heavy metals, and soil salinity as well as biotic stresses, such as pathogen infections. This article is intended to briefly introduce ErM fungi and document their beneficial effects on ericaceous plants. It is anticipated that the exploration of this special group of fungi will further improve our understanding of their value of symbiosis to ericaceous plants and ultimately result in the application of valuable species or strains for improving the establishment and growth of ericaceous plants.

Thrombolytic Potential of Micromycetes from the Genus Tolypocladium, Obtained from White Sea Soils: Screening of Producers and Exoproteinases Properties

Thrombotherapy is an important approach in treatment of various diseases associated with pathologies of the cardiovascular and human hemostasis systems. Screening for producers of modern, specific, and safe thrombolytic substances is an important task for medicine and biotechnology. The aim of this study was to characterize thrombolytic potential of seven strains of micromycete belonging to the genus Tolypocladium, which was obtained from White Sea soils. The Tolypocladium inflatum 62a strain was considered the most promising producer of thrombolytic agent activities suitable for possible use in thrombotherapy or diagnostics of hemostasis pathologies. It demonstrated a high radial growth rate and was characterized not only by a sufficiently high value of enzymatic index in media with fibrin and fibrinogen but also by the highest specificity for fibrillar proteins among all strains. The preparation obtained from it demonstrated pronounced thrombolytic effectiveness and substrate specificity.

Molecular and Morphological Characteristics of a New Species Collected from an Insect (Cicindela transbaicalica) in Korea

To exploit insect-derived fungi, insects were collected from seven different regions in Korea, including Gyeongbuk, Goryeong, and several fungi were isolated from them. A fungal strain designated 21-64-D was isolated from riparian tiger beetle (Cicindela transbaicalica) and morphologically identified as a species belonging to the genus Oidiodendron. Phylogenetic analysis using the nucleotide sequences of internal transcribed spacer (ITS) regions and the partial sequence of the large subunit of the nuclear ribosomal RNA (LSU) gene revealed the distinct phylogenetic position of the isolate among recognized Oidiodendron species including its closest neighbors O. chlamydosporicum, O. citrinum, O. maius, and O. pilicola. The hyphal and conidial morphology of the strain, particularly club-shaped hyphae, clearly differentiated it from its close relatives. Results indicated that 21-64-D is a novel species in the genus Oidiodendron, for which the name Oidiodendron clavatum sp. nov. is proposed.

Apothecial Ancestry, Evolution, and Re-Evolution in Thelebolales (Leotiomycetes, Fungi)

Simple Summary

Leotiomycetes is one of the most speciose classes of the phylum Ascomycota (Fungi). Its species are mainly apothecioid, paraphysate, and possess active ascospore discharge. Thelebolales are a distinctive order of the Leotiomycetes class whose members have mostly closed ascomata, evanescent asci, and thus passively dispersed ascospores. Within the order, a great diversity of peridia have evolved as adaptations to different dispersal strategies. The genus Thelebolus is an exceptional case of ascomatal evolution within the order. Its species are the most diverse in functional traits, encompassing species with closed ascomata and evanescent asci, and species with open ascomata, active ascospore discharge, and paraphyses. Open ascomata were previously suggested as the ancestral state in the genus, these ascomata depend on mammals and birds as dispersal agents. In our work, we used morphological and phylogenetic methods, as well as the reconstruction of ancestral traits for ascomatal type, asci dehiscence, the presence or absence of paraphyses, and ascospore features to explore evolution within Thelebolales. We demonstrate the apothecial ancestry in Thelebolales and propose a new hypothesis about the evolution of the open ascomata in Thelebolus involving a process of re-evolution where the active dispersal of ascospores appears independently twice within the order. A new family, Holwayaceae, is proposed within Thelebolales, comprising three genera: Holwaya, Patinella, and Ramgea.

Abstract

Closed cleistothecia-like ascomata have repeatedly evolved in non-related perithecioid and apothecioid lineages of lichenized and non-lichenized Ascomycota. The evolution of a closed, darkly pigmented ascoma that protects asci and ascospores is conceived as either an adaptation to harsh environmental conditions or a specialized dispersal strategy. Species with closed ascomata have mostly lost sterile hymenial elements (paraphyses) and the capacity to actively discharge ascospores. The class Leotiomycetes, one of the most speciose classes of Ascomycota, is mainly apothecioid, paraphysate, and possesses active ascospore discharge. Lineages with closed ascomata, and their morphological variants, have evolved independently in several families, such as Erysiphaceae, Myxotrichaceae, Rutstroemiaceae, etc. Thelebolales is a distinctive order in the Leotiomycetes class. It has two widespread families (Thelebolaceae, Pseudeurotiaceae) with mostly closed ascomata, evanescent asci, and thus passively dispersed ascospores. Within the order, closed ascomata dominate and a great diversity of peridia have evolved as adaptations to different dispersal strategies. The type genus, Thelebolus, is an exceptional case of ascomatal evolution within the order. Its species are the most diverse in functional traits, encompassing species with closed ascomata and evanescent asci, and species with open ascomata, active ascospore discharge, and paraphyses. Open ascomata were previously suggested as the ancestral state in the genus, these ascomata depend on mammals and birds as dispersal agents. In this scheme, species with closed ascomata, a lack of paraphyses, and passive ascospore discharge exhibit derived traits that evolved in adaptation to cold ecosystems. Here, we used morphological and phylogenetic methods, as well as the reconstruction of ancestral traits for ascomatal type, asci dehiscence, the presence or absence of paraphyses, and ascospore features to explore evolution within Thelebolales. We demonstrate the apothecial ancestry in Thelebolales and propose a new hypothesis about the evolution of the open ascomata in Thelebolus, involving a process of re-evolution where the active dispersal of ascospores appears independently twice within the order. We propose a new family, Holwayaceae, within Thelebolales, that retains the phenotypic features exhibited by species of Thelebolus, i.e., pigmented capitate paraphyses and active asci discharge with an opening limitation ring.

Site and land-use associations of soil bacteria and fungi define core and indicative taxa

Soil microbial diversity has major influences on ecosystem functions and services. However, due to its complexity and uneven distribution of abundant and rare taxa, quantification of soil microbial diversity remains challenging and thereby impeding its integration into long-term monitoring programs. Using metabarcoding, we analyzed soil bacterial and fungal communities at 30 long-term soil monitoring sites from the three land-use types arable land, permanent grassland, and forest with a yearly sampling between snowmelt and first fertilization over five years. Unlike soil microbial biomass and alpha-diversity, microbial community compositions and structures were site- and land-use-specific with CAP reclassification success rates of 100%. The temporally stable site core communities included 38.5% of bacterial and 33.1% of fungal OTUs covering 95.9% and 93.2% of relative abundances. We characterized bacterial and fungal core communities and their land-use associations at the family-level. In general, fungal families revealed stronger land-use associations as compared to bacteria. This is likely due to a stronger vegetation effect on fungal core taxa, while bacterial core taxa were stronger related to soil properties. The assessment of core communities can be used to form cultivation-independent reference lists of microbial taxa, which may facilitate the development of microbial indicators for soil quality and the use of soil microbiota for long-term soil biomonitoring.

High Fungal Diversity but Low Seasonal Dynamics and Ectomycorrhizal Abundance in a Mountain Beech Forest

Forests on steep slopes constitute a significant proportion of European mountain areas and are important as production and protection forests. This study describes the soil fungal community structure in a European beech-dominated mountain forest stands in the Northern Calcareous Alps and investigates how it is determined by season and soil properties. Samples were collected at high spatial resolution in an area of ca. 100 m × 700 m in May (spring) and August (summer). Illumina MiSeq high-throughput sequencing of the ITS2-region revealed distinct patterns for the soil fungal communities. In contrast to other studies from temperate European beech forest stands, Ascomycota dominated the highly diverse fungal community, while ectomycorrhizal fungi were of lower abundance. Russulaceae, which are often among the dominant ectomycorrhizal fungi associated with European beech, were absent from all samples. Potentially plant pathogenic fungi were more prevalent than previously reported. Only subtle seasonal differences were found between fungal communities in spring and summer. Especially, dominant saprotrophic taxa were largely unaffected by season, while slightly stronger effects were observed for ectomycorrhizal fungi. Soil characteristics like pH and organic carbon content, on the other hand, strongly shaped abundant taxa among the saprotrophic fungal community.

First Speleomycological Study on the Occurrence of Psychrophilic and Psychrotolerant Aeromycota in the Brestovská Cave (Western Tatras Mts., Slovakia) and First Reports for Some Species at Underground Sites

Most underground ecosystems are heterotrophic, fungi in these objects are dispersed in the air in the form of spores, and they may be potentially hazardous to mammals. Research in underground sites has focused on mesophilic airborne fungi and only a few concerned cold-adapted species. Therefore, the goal of our research was the first report of psychrophilic and psychrotolerant aeromycota in the Brestovská Cave using culture-based techniques with genetic and phenotypic identification. Plates with PDA medium containing sampled biological material were incubated at 8 ± 0.5 °C. The density of mycobiota inside the cave ranged from 37.4 to 71 CFU 1 m-3 of air and 63.3 CFU 1 m-3 of air outside the cave. Thus, the level of fungal spores did not exceed the standards for the mycological quality of the air. A total of 18 species were isolated during the study, and some species may be potentially dangerous to people with weakened immune system. All fungal species were present inside the cave and only seven of them were outside. Cladosporium cladosporioides dominated in the external air samples and Mortierella parvispora was cultured most frequently from internal air samples. To our knowledge, this is the first discovery of the fungal species such as Coniothyrium pyrinum, Cystobasidium laryngis, Filobasidium wieringae, Leucosporidium drummii, M. parvispora, Mrakia blollopis, Nakazawaea holstii, and Vishniacozyma victoriae in the air inside the underground sites. Moreover, C. pyrinum, C. laryngis, L. drummii, M. blollopis, and N. holstii have never been detected in any component of the underground ecosystems. There are possible reasons explaining the detection of those species, but global warming is the most likely.

Soil stabilisation for DNA metabarcoding of plants and fungi. Implications for sampling at remote locations or via third-parties

Storage of soil samples prior to metagenomic analysis presents a problem. If field sites are remote or if samples are collected by third parties, transport to analytical laboratories may take several days or even weeks. The bulk of such samples and requirement for later homogenisation precludes the convenient use of a stabilisation buffer, so samples are usually cooled or frozen during transit. There has been limited testing of the most appropriate storage methods for later study of soil organisms by eDNA approaches. Here we tested a range of storage methods on two contrasting soils, comparing these methods to the control of freezing at -80 °C, followed by freeze-drying. To our knowledge, this is the first study to examine the effect of storage conditions on eukaryote DNA in soil, including both viable organisms (fungi) and DNA contained within dying/dead tissues (plants). For fungi, the best storage regimes (closest to the control) were storage at 4 °C (for up to 14 d) or active air-drying at room temperature. The worst treatments involved initial freezing, followed by thawing which led to significant later spoilage. The key spoilage organisms were identified as Metarhizium carneum and Mortierella spp., with a general increase in saprotrophic fungi and reduced abundances of mycorrhizal/biotrophic fungi. Plant data showed a similar pattern, but with greater variability in community structure, especially in the freeze-thaw treatments, probably due to stochastic variation in substrates for fungal decomposition, algal proliferation and some seed germination. In the absence of freeze drying facilities, samples should be shipped refrigerated, but not frozen if there is any risk of thawing.

Pygmaeomycetaceae, a new root-associated family in Mucoromycotina from the pygmy pine plains

A new genus, Pygmaeomyces, and two new species are described based on phylogenetic analyses and phenotypic and ecological characters. The species delimitation was based on concordance of gene genealogies. The Pygmaeomyces cultures were isolated from the roots of mountain laurel (Kalmia latifolia) and pitch pine (Pinus rigida) from the acidic and oligotrophic New Jersey pygmy pine plains; however, they likely have a broader distribution because their internal transcribed spacer (ITS) sequences have high similarity to a number of environmental sequences from multiple independent studies. Based on the phylogeny and phenotypic characters, a new family, Pygmaeomycetaceae, is proposed to accommodate this new lineage in Mucoromycotina. Pygmaeomycetaceae corresponds to Clade GS23, which was identified based on a sequence-only soil fungal survey and was believed to be a distinct new class. Compared with the culture-based methods, we observed that sequence-only analyses tend to overestimate the taxonomic level. Results from this work will facilitate ecological and evolutionary studies on root-associated fungi.

Antifungal Norditerpene Oidiolactones from the Fungus Oidiodendron truncatum, a Potential Biocontrol Agent for White-Nose Syndrome in Bats

White-nose syndrome (WNS) is a devastating disease of hibernating bats caused by the fungus Pseudogymnoascus destructans. We obtained 383 fungal and bacterial isolates from the Soudan Iron Mine, an important bat hibernaculum in Minnesota, then screened this library for antifungal activity to develop biological control treatments for WNS. An extract from the fungus Oidiodendron truncatum was subjected to bioassay-guided fractionation, which led to the isolation of 14 norditerpene and three anthraquinone metabolites. Ten of these compounds were previously described in the literature, and here we present the structures of seven new norditerpene analogues. Additionally, this is the first report of 4-chlorophyscion from a natural source, previously identified as a semisynthetic product. The compounds PR 1388 and LL-Z1271α were the only inhibitors of P. destructans (MIC = 7.5 and 15 μg/mL, respectively). Compounds were tested for cytotoxicity against fibroblast cell cultures obtained from Myotis septentrionalis (northern long eared bat) and M. grisescens (gray bat) using a standard MTT viability assay. The most active antifungal compound, PR 1388, was nontoxic toward cells from both bat species (IC₅₀ > 100 μM). We discuss the implications of these results in the context of the challenges and logistics of developing a substrate treatment or prophylactic for WNS.

Diversity of xerotolerant and xerophilic fungi in honey

Fungi can colonize most of the substrata on Earth. Honey, a sugary food produced by bees (and other insects) has been studied little in terms of its fungal diversity. We have surveyed and evaluated the presence of xerotolerant and xerophilic fungi in a set of honey bee samples collected from across Spain. From 84 samples, a total of 104 fungal strains were isolated, and morphologically and phylogenetically characterized. We identified 32 species distributed across 16 genera, most of them belonging to the ascomycetous genera Aspergillus, Bettsia, Candida, Eremascus, Monascus, Oidiodendron, Penicillium, Skoua, Talaromyces and Zygosaccharomyces. As a result of this survey, eight new taxa are proposed: i.e. the new family Helicoarthrosporaceae, two new genera, Helicoarthrosporum and Strongyloarthrosporum in Onygenales; three new species of Eurotiales, Talaromyces affinitatimellis, T. basipetosporus, and T. brunneosporus; and two new species of Myxotrichaceae, Oidiodendron mellicola, and Skoua asexualis.

Intensive tropical land use massively shifts soil fungal communities

Soil fungi are key players in nutrient cycles as decomposers, mutualists and pathogens, but the impact of tropical rain forest transformation into rubber or oil palm plantations on fungal community structures and their ecological functions are unknown. We hypothesized that increasing land use intensity and habitat loss due to the replacement of the hyperdiverse forest flora by nonendemic cash crops drives a drastic loss of diversity of soil fungal taxa and impairs the ecological soil functions. Unexpectedly, rain forest conversion was not associated with strong diversity loss but with massive shifts in soil fungal community composition. Fungal communities clustered according to land use system and loss of plant species. Network analysis revealed characteristic fungal genera significantly associated with different land use systems. Shifts in soil fungal community structure were particularly distinct among different trophic groups, with substantial decreases in symbiotrophic fungi and increases in saprotrophic and pathotrophic fungi in oil palm and rubber plantations in comparison with rain forests. In conclusion, conversion of rain forests and current land use systems restructure soil fungal communities towards enhanced pathogen pressure and, thus, threaten ecosystem health functions.

Network hubs in root-associated fungal metacommunities

BACKGROUND

Although a number of recent studies have uncovered remarkable diversity of microbes associated with plants, understanding and managing dynamics of plant microbiomes remain major scientific challenges. In this respect, network analytical methods have provided a basis for exploring "hub" microbial species, which potentially organize community-scale processes of plant-microbe interactions.

METHODS

By compiling Illumina sequencing data of root-associated fungi in eight forest ecosystems across the Japanese Archipelago, we explored hubs within "metacommunity-scale" networks of plant-fungus associations. In total, the metadata included 8080 fungal operational taxonomic units (OTUs) detected from 227 local populations of 150 plant species/taxa.

RESULTS

Few fungal OTUs were common across all the eight forests. However, in each of the metacommunity-scale networks representing northern four localities or southern four localities, diverse mycorrhizal, endophytic, and pathogenic fungi were classified as "metacommunity hubs," which were detected from diverse host plant taxa throughout a climatic region. Specifically, Mortierella (Mortierellales), Cladophialophora (Chaetothyriales), Ilyonectria (Hypocreales), Pezicula (Helotiales), and Cadophora (incertae sedis) had broad geographic and host ranges across the northern (cool-temperate) region, while Saitozyma/Cryptococcus (Tremellales/Trichosporonales) and Mortierella as well as some arbuscular mycorrhizal fungi were placed at the central positions of the metacommunity-scale network representing warm-temperate and subtropical forests in southern Japan.

CONCLUSIONS

The network theoretical framework presented in this study will help us explore prospective fungi and bacteria, which have high potentials for agricultural application to diverse plant species within each climatic region. As some of those fungal taxa with broad geographic and host ranges have been known to promote the survival and growth of host plants, further studies elucidating their functional roles are awaited.

Ericoid plant species and Pinus sylvestris shape fungal communities in their roots and surrounding soil

Root-colonizing fungi can form mycorrhizal or endophytic associations with plant roots, the type of association depending on the host. We investigated the differences and similarities of the fungal communities of three boreal ericoid plants and one coniferous tree, and identified the community structure of fungi utilizing photosynthates from the plants studied. The fungal communities of roots and soils of Vaccinium myrtillus, Vaccinium vitis-idaea, Calluna vulgaris and Pinus sylvestris were studied in an 18-month-long experiment where the plants were grown individually in natural substrate. Photosynthates utilizing fungi were detected with DNA stable-isotope probing using ¹³ CO₂ (¹³ C-DNA-SIP). The results indicated that the plants studied provide different ecological niches preferred by different fungal species. Those fungi which dominated the community in washed roots had also the highest ¹³ C-uptake. In addition, a common root endophyte without confirmed mycorrhizal status also obtained ¹³ C from all the plants, indicating close plant-association of this fungal species. We detect several fungal species inhabiting the roots of both ericoid mycorrhizal and ectomycorrhizal plants. Our results highlight that the ecological role of co-occurrence of fungi with different life styles (e.g. mycorrhizal or endophytic) in plant root systems should be further investigated.

Root-Associated Fungi Shared Between Arbuscular Mycorrhizal and Ectomycorrhizal Conifers in a Temperate Forest

Arbuscular mycorrhizal and ectomycorrhizal symbioses are among the most important drivers of terrestrial ecosystem dynamics. Historically, the two types of symbioses have been investigated separately because arbuscular mycorrhizal and ectomycorrhizal plant species are considered to host discrete sets of fungal symbionts (i.e., arbuscular mycorrhizal and ectomycorrhizal fungi, respectively). Nonetheless, recent studies based on high-throughput DNA sequencing technologies have suggested that diverse non-mycorrhizal fungi (e.g., endophytic fungi) with broad host ranges play roles in relationships between arbuscular mycorrhizal and ectomycorrhizal plant species in forest ecosystems. By analyzing an Illumina sequencing dataset of root-associated fungi in a temperate forest in Japan, we statistically examined whether co-occurring arbuscular mycorrhizal (Chamaecyparis obtusa) and ectomycorrhizal (Pinus densiflora) plant species could share non-mycorrhizal fungal communities. Among the 919 fungal operational taxonomic units (OTUs) detected, OTUs in various taxonomic lineages were statistically designated as “generalists,” which associated commonly with both coniferous species. The list of the generalists included fungi in the genera Meliniomyces, Oidiodendron, Cladophialophora, Rhizodermea, Penicillium, and Mortierella. Meanwhile, our statistical analysis also detected fungi preferentially associated with Chamaecyparis (e.g., Pezicula) or Pinus (e.g., Neolecta). Overall, this study provides a basis for future studies on how arbuscular mycorrhizal and ectomycorrhizal plant species interactively drive community- or ecosystem-scale processes. The physiological functions of the fungi highlighted in our host-preference analysis deserve intensive investigations for understanding their roles in plant endosphere and rhizosphere.

Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists

Some soil fungi in the Leotiomycetes form ericoid mycorrhizal (ERM) symbioses with Ericaceae. In the harsh habitats in which they occur, ERM plant survival relies on nutrient mobilization from soil organic matter (SOM) by their fungal partners. The characterization of the fungal genetic machinery underpinning both the symbiotic lifestyle and SOM degradation is needed to understand ERM symbiosis functioning and evolution, and its impact on soil carbon (C) turnover. We sequenced the genomes of the ERM fungi Meliniomyces bicolor, M. variabilis, Oidiodendron maius and Rhizoscyphus ericae, and compared their gene repertoires with those of fungi with different lifestyles (ecto- and orchid mycorrhiza, endophytes, saprotrophs, pathogens). We also identified fungal transcripts induced in symbiosis. The ERM fungal gene contents for polysaccharide-degrading enzymes, lipases, proteases and enzymes involved in secondary metabolism are closer to those of saprotrophs and pathogens than to those of ectomycorrhizal symbionts. The fungal genes most highly upregulated in symbiosis are those coding for fungal and plant cell wall-degrading enzymes (CWDEs), lipases, proteases, transporters and mycorrhiza-induced small secreted proteins (MiSSPs). The ERM fungal gene repertoire reveals a capacity for a dual saprotrophic and biotrophic lifestyle. This may reflect an incomplete transition from saprotrophy to the mycorrhizal habit, or a versatile life strategy similar to fungal endophytes.

A New Oidiodendron maius Strain Isolated from Rhododendron fortunei and its Effects on Nitrogen Uptake and Plant Growth

A new mycorrhizal fungal strain was isolated from hair roots of Rhododendron fortunei Lindl. grown in Huading Forest Park, Zhejiang Province, China. Morphological characterization and internal transcribed spacer rDNA analysis suggested that it belongs to Oidiodendron maius Barron, and we designated it as strain Om19. Methods for culturing Om19 were established, and the ability of Om19 to form mycorrhizae on R. fortunei was evaluated in a peat-based substrate. Microscopic observations showed hyaline hyphae on the surface of hair roots and crowded hyphal complexes (hyphal coils) inside root cortical cells of R. fortunei after inoculation, indicating that the roots were well colonized by Om19. In a second experiment, fresh and dry weight of R. fortunei 2 months after Om19 inoculation were greater than uninoculated plants, and the total nitrogen absorbed by plants inoculated with Om19 was greater than the uninoculated controls. qRT-PCR analysis of five genes related to N uptake and metabolism (two nitrate transporters, an ammonium transporter, glutamine synthetase, and glutamate synthase) showed that these genes were highly upregulated with twofold to ninefold greater expression in plants inoculated with Om19 compared to uninoculated plants. In the third experiment, Om19 was inoculated into the peat-based substrate for growing Formosa azalea (Rhododendron indica 'Formosa'). 'Formosa' azalea plants grown in the inoculated substrate had larger canopies and root systems compared to uninoculated plants. Our results show that Om19 could be an important microbial tool for improving production of Rhododendron plants.

Network modules and hubs in plant-root fungal biomes

Terrestrial plants host phylogenetically and functionally diverse groups of below-ground microbes, whose community structure controls plant growth/survival in both natural and agricultural ecosystems. Therefore, understanding the processes by which whole root-associated microbiomes are organized is one of the major challenges in ecology and plant science. We here report that diverse root-associated fungi can form highly compartmentalized networks of coexistence within host roots and that the structure of the fungal symbiont communities can be partitioned into semi-discrete types even within a single host plant population. Illumina sequencing of root-associated fungi in a monodominant south beech forest revealed that the network representing symbiont-symbiont co-occurrence patterns was compartmentalized into clear modules, which consisted of diverse functional groups of mycorrhizal and endophytic fungi. Consequently, terminal roots of the plant were colonized by either of the two largest fungal species sets (represented by Oidiodendron or Cenococcum). Thus, species-rich root microbiomes can have alternative community structures, as recently shown in the relationships between human gut microbiome type (i.e., 'enterotype') and host individual health. This study also shows an analytical framework for pinpointing network hubs in symbiont-symbiont networks, leading to the working hypothesis that a small number of microbial species organize the overall root-microbiome dynamics.

In vitro decomposition of Sphagnum by some microfungi resembles white rot of wood

The abilities of some ascomycetes (Myxotrichaceae) from a Sphagnum bog in Alberta to degrade cellulose, phenolics, and Sphagnum tissue were compared with those of two basidiomycetes. Most Myxotrichaceae degraded cellulose and tannic acid, and removed cell-wall components simultaneously from Sphagnum tissues, whereas the basidiomycetes degraded cellulose and insoluble phenolics, and preferentially removed the polyphenolic matrix from Sphagnum cell walls. Mass losses from Sphagnum varied from up to 50% for some ascomycetes to a maximum of 35% for the basidiomycetes. The decomposition of Sphagnum by the Myxotrichaceae was analogous to the white rot of wood and indicates that these fungi have the potential to cause significant mineralization of carbon in bogs.