Ericoid mycorrhizal root fungi and their multicopper oxidases from a temperate forest shrub

Deciphering mycobiota and its functional dynamics in root hairs of Rhododendron campanulatum D. Don through Next-gen sequencing

The Himalayas provide unique opportunities for the extension of shrubs beyond the upper limit of the tree. However, little is known about the limitation of the biotic factors belowground of shrub growth at these cruising altitudes. To fill this gap, the present study deals with the documentation of root-associated microbiota with their predicted functional profiles and interactions in the host Rhododendron campanulatum, a krummholz species. While processing 12 root samples of R. campanulatum from the sites using Omics we could identify 134 root-associated fungal species belonging to 104 genera, 74 families, 39 orders, 17 classes, and 5 phyla. The root-associated microbiota members of Ascomycota were unambiguously dominant followed by Basidiomycota. Using FUNGuild, we reported that symbiotroph and pathotroph as abundant trophic modes. Furthermore, FUNGuild revealed the dominant prevalence of the saptroptroph guild followed by plant pathogens and wood saprotrophs. Alpha diversity was significantly different at the sites. The heatmap dendrogram showed the correlation between various soil nutrients and some fungal species. The study paves the way for a more in-depth exploration of unidentified root fungal symbionts, their interactions and their probable functional roles, which may serve as an important factor for the growth and conservation of these high-altitude ericaceous plants.

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.

Ericoid shrubs shape fungal communities and suppress organic matter decomposition in boreal forests

Mycorrhizal fungi associated with boreal trees and ericaceous shrubs are central actors in organic matter (OM) accumulation through their belowground carbon allocation, their potential capacity to mine organic matter for nitrogen (N) and their ability to suppress saprotrophs. Yet, interactions between co-occurring ectomycorrhizal fungi (EMF), ericoid mycorrhizal fungi (ERI), and saprotrophs are poorly understood. We used a long-term (19 yr) plant functional group manipulation experiment with removals of tree roots, ericaceous shrubs and mosses and analysed the responses of different fungal guilds (assessed by metabarcoding) and their interactions in relation to OM quality (assessed by mid-infrared spectroscopy and nuclear magnetic resonance) and decomposition (litter mesh-bags) across a 5000-yr post-fire boreal forest chronosequence. We found that the removal of ericaceous shrubs and associated ERI changed the composition of EMF communities, with larger effects occurring at earlier stages of the chronosequence. Removal of shrubs was associated with enhanced N availability, litter decomposition and enrichment of the recalcitrant OM fraction. We conclude that increasing abundance of slow-growing ericaceous shrubs and the associated fungi contributes to increasing nutrient limitation, impaired decomposition and progressive OM accumulation in boreal forests, particularly towards later successional stages. These results are indicative of the contrasting roles of EMF and ERI in regulating belowground OM storage.

The functional role of ericoid mycorrhizal plants and fungi on carbon and nitrogen dynamics in forests

Ericoid mycorrhizal (ErM) shrubs commonly occur in forest understories and could therefore alter arbuscular (AM) and/or ectomycorrhizal (EcM) tree effects on soil carbon and nitrogen dynamics. Specifically, ErM fungi have extensive organic matter decay capabilities, and ErM plant and fungal tissues have high concentrations of secondary compounds that can form persistent complexes in the soil. Together, these traits could contribute to organic matter accumulation and inorganic nutrient limitation. These effects could also differ in AM- vs EcM-dominated stands at multiple scales within and among forest biomes by, for instance, altering fungal guild interactions. Most work on ErM effects in forests has been conducted in boreal forests dominated by EcM trees. However, ErM plants occur in c. 96, 69 and 29% of boreal, temperate and tropical forests, respectively. Within tropical montane forests, the effects of ErM plants could be particularly pronounced because their traits are more distinct from AM than EcM trees. Because ErM fungi can function as free-living saprotrophs, they could also be more resilient to forest disturbances than obligate symbionts. Further consideration of ErM effects within and among forest biomes could improve our understanding of how cooccurring mycorrhizal types interact to collectively affect soil carbon and nitrogen dynamics under changing conditions.

Diversity of putative ericoid mycorrhizal fungi increases with soil age and progressive phosphorus limitation across a 4.1-million-year chronosequence

Ericaceous plants rely on ericoid mycorrhizal fungi for nutrient acquisition. However, the factors that affect the composition and structure of fungal communities associated with the roots of ericaceous plants remain largely unknown. Here, we use a 4.1-million-year (myr) soil chronosequence in Hawaii to test the hypothesis that changes in nutrient availability with soil age determine the diversity and species composition of fungi associated with ericoid roots. We sampled roots of a native Hawaiian plant, Vaccinium calycinum, and used DNA metabarcoding to quantify changes in fungal diversity and community composition. We also used a fertilization experiment at the youngest and oldest sites to assess the importance of nutrient limitation. We found an increase in diversity and a clear pattern of species turnover across the chronosequence, driven largely by putative ericoid mycorrhizal fungi. Fertilization with nitrogen at the youngest site and phosphorus at the oldest site reduced fungal diversity, suggesting a direct role of nutrient limitation. Our results also reveal the presence of novel fungal species associated with Hawaiian Ericaceae and suggest a greater importance of phosphorus availability for communities of ericoid mycorrhizal fungi than is generally assumed.

Greater local diversity under older species pools may arise from enhanced competitive equivalence

Ecological communities typically contain more species when located within geologically older regions. This pattern is traditionally attributed to the long-term accumulation of species in the regional species pool, with local species interactions playing a minor role. We provide evidence suggesting a more important role of local species interactions than generally assumed. We assembled 320 communities of root-associated fungi under 80 species pools, varying species pool richness and the mean age of the sites from which the fungi were collected across a 4-myr soil chronosequence. We found that local diversity increased more with increasing species pool richness when species were from older sites. We also found that older species pools had lower functional and phylogenetic diversity, indicating greater competitive equivalence among species. Our results suggest that older regions have higher local richness not simply because older pools are more speciose but also because species have evolved traits that allow them to locally co-occur.

Mycorrhizal types differ in ecophysiology and alter plant nutrition and soil processes

Mycorrhizal fungi benefit plants by improved mineral nutrition and protection against stress, yet information about fundamental differences among mycorrhizal types in fungi and trees and their relative importance in biogeochemical processes is only beginning to accumulate. We critically review and synthesize the ecophysiological differences in ectomycorrhizal, ericoid mycorrhizal and arbuscular mycorrhizal symbioses and the effect of these mycorrhizal types on soil processes from local to global scales. We demonstrate that guilds of mycorrhizal fungi display substantial differences in genome-encoded capacity for mineral nutrition, particularly acquisition of nitrogen and phosphorus from organic material. Mycorrhizal associations alter the trade-off between allocation to roots or mycelium, ecophysiological traits such as root exudation, weathering, enzyme production, plant protection, and community assembly as well as response to climate change. Mycorrhizal types exhibit differential effects on ecosystem carbon and nutrient cycling that affect global elemental fluxes and may mediate biome shifts in response to global change. We also note that most studies performed to date have not been properly replicated and collectively suffer from strong geographical sampling bias towards temperate biomes. We advocate that combining carefully replicated field experiments and controlled laboratory experiments with isotope labelling and -omics techniques offers great promise towards understanding differences in ecophysiology and ecosystem services among mycorrhizal types.

Assembly processes of trophic guilds in the root mycobiome of temperate forests

Root-associated mycobiomes (RAMs) link plant and soil ecological processes, thereby supporting ecosystem functions. Understanding the forces that govern the assembly of RAMs is key to sustainable ecosystem management. Here, we dissected RAMs according to functional guilds and combined phylogenetic and multivariate analyses to distinguish and quantify the forces driving RAM assembly processes. Across large biogeographic scales (>1,000 km) in temperate forests (>100 plots), RAMs were taxonomically highly distinct but composed of a stable trophic structure encompassing symbiotrophic, ectomycorrhizal (55%), saprotrophic (7%), endotrophic (3%) and pathotrophic fungi (<1%). Taxonomic community composition of RAMs is explained by abiotic factors, forest management intensity, dominant tree family (Fagaceae, Pinaceae) and root resource traits. Local RAM assemblies are phylogenetically clustered, indicating stronger habitat filtering on roots in dry, acid soils and in conifer stands than in other forest types. The local assembly of ectomycorrhizal communities is driven by forest management intensity. At larger scales, root resource traits and soil pH shift the assembly process of ectomycorrhizal fungi from deterministic to neutral. Neutral or weak deterministic assembly processes are prevalent in saprotrophic and endophytic guilds. The remarkable consistency of the trophic composition of the RAMs suggests that temperate forests attract fungal assemblages that afford functional resilience under the current range of climatic and edaphic conditions. At local scales, the filtering processes that structure symbiotrophic assemblies can be influenced by forest management and tree selection, but at larger scales, environmental cues and host resource traits are the most prevalent forces.

Ecological responses to forest age, habitat, and host vary by mycorrhizal type in boreal peatlands

Despite covering vast areas of boreal North America, the ecological factors structuring mycorrhizal fungal communities in peatland forests are relatively poorly understood. To assess how these communities vary by age (younger vs. mature), habitat (fen vs. bog), and host (conifer trees vs. ericaceous shrub), we sampled the roots of two canopy trees (Larix laricina and Picea mariana) and an ericaceous shrub (Ledum groenlandicum) at four sites in northern Minnesota, USA. To characterize the specific influence of host co-occurrence on mycorrhizal fungal community structure, we also conducted a greenhouse bioassay using the same three hosts. Root samples were assessed using Illumina-based high-throughput sequencing (HTS) of the ITS1 rRNA gene region. As expected, we found that the relative abundance of ectomycorrhizal fungi was high on both Larix and Picea, whereas ericoid mycorrhizal fungi had high relative abundance only on Ledum. Ericoid mycorrhizal fungal richness was significantly higher in mature forests, in bogs, and on Ledum hosts, while ectomycorrhizal fungal richness did not differ significantly across any of these three variables. In terms of community composition, ericoid mycorrhizal fungi were more strongly influenced by host while ectomycorrhizal fungi were more influenced by habitat. In the greenhouse bioassay, the presence of Ledum had consistently stronger effects on the composition of ectomycorrhizal, ericoid, and ericoid-ectomycorrhizal fungal communities than either Larix or Picea. Collectively, these results suggest that partitioning HTS-based datasets by mycorrhizal type in boreal peatland forests is important, as their responses to rapidly changing environmental conditions are not likely to be uniform.

First evidence of Pezoloma ericae in Australia: using the Biomes of Australia Soil Environments (BASE) to explore the Australian phylogeography of known ericoid mycorrhizal and root-associated fungi

The prominent ericoid mycorrhizal fungus, Pezoloma ericae, has not been found in Australia to date. In the present study, internal transcribed spacer (ITS) data from the Biomes of Australia Soil Environments (BASE) was searched for evidence of P. ericae and other known ericoid mycorrhizal and root-associated taxa. ITS sequences with high identity to P. ericae, Meliniomyces bicolor, Meliniomyces variabilis, Cairneyella sp. 2, Cadophora finlandica and Woollsia mycorrhizal fungus VI were identified and their distribution in Australia visualised. This is the first evidence that P. ericae, M. bicolor and M. variabilis very likely occur on the Australian continent and provides a set of locations from which to seek isolates for further characterisation. The presence of P. ericae in South America, South Africa, and now Australia suggests a broad and ancient Gondwanan distribution for this well-studied species.

Changes of soil bacterial activities and functions after different N additions in a temperate forest

It has been shown that different nitrogen (N) addition led to various influences on soil microbial activities in forest ecosystems; however, the changes of bacteria were still unclear. In this work, inorganic N (NH₄NO₃) and organic N (urea and glycine) were fertilized with different ratios (5:0, 1:4, 3:2, 2:3, and 1:4) on temperate forest soils, while fungicide (cycloheximide) was simultaneously added on half of each treatment to inhibit fungal activities (leaving only bacteria). After a 3-year field experiment, soil samples were harvested, then microbial enzymatic activities involved in carbon (C), and N and phosphorus (P) cycles were determined. Under laboratory conditions, four purified bacteria which were isolated from sample site had been inoculated in sterilized soils under different N types and enzymatic activities were assayed after 90-day incubation. The results showed that cellulase and polyphenol oxidase activities of non-fungicide-added treatments increased after N addition and greater organic N accelerated the increases. However, these enzymatic activities of fungicide-added treatments were not significantly influenced by N addition and N types. It may be due to the insufficient ability of bacteria to synthesize enough enzymes to decompose complex organic C (such as cellulose and lignin) into available compound, although N-limitation was alleviated. Alkaline phosphatase activities increased after N addition in both non-fungicide-added and fungicide-added treatments, and the acceleration on bacterial alkaline phosphatase activities was even greater. Furthermore, organic N showed at least 2.5 times promotion on bacteria alkaline phosphatase than those of inorganic N, which indicated greater alleviation of bacterial P-limitation after the addition of organic N. All the results indicated that soil bacteria may be seriously limited by soil available C but become the dominant decomposer of the complex P compounds after N addition, particularly greater organic N.

First record of Rhizoscyphus ericae in Southern Hemisphere's Ericaceae

Ericoid mycorrhiza is arguably the least investigated mycorrhizal type, particularly when related to the number of potential hosts and the ecosystems they inhabit. Little is known about the global distribution of ericoid mycorrhizal (ErM) fungi, and this holds true even for the prominent ErM mycobiont Rhizoscyphus ericae. Earlier studies suggested R. ericae might be low in abundance or absent in the roots of Southern Hemisphere's Ericaceae, and our previous investigations in two Argentine Patagonian forests supported this view. Here, we revisited the formerly investigated area, albeit at a higher altitude, and screened fungi inhabiting hair roots of Gaultheria caespitosa and Gaultheria pumila at a treeless alpine site using the same methods as previously. We obtained 234 isolates, most of them belonging to Ascomycota. In contrast to previous findings, however, among 37 detected operational taxonomic units (OTUs), OTU 1 (=R. ericae s. str.) comprised the highest number of isolates (87, ∼37 %). Most of the OTUs and isolates belonged to the Helotiales, and 82.5 % of isolates belonged to OTUs shared between both Gaultheria species. At the alpine site, ericoid mycorrhizal fungi dominated, followed by dark septate endophytes and aquatic hyphomycetes probably acting as root endophytes. Our results suggest that the distribution of R. ericae is influenced, among others, by factors related to altitude such as soil type and presence/absence and type of the neighboring vegetation. Our study is the first report on R. ericae colonizing Ericaceae roots in the Southern Hemisphere and extends the known range of this prominent ErM species to NW Patagonia.

A Thermostable Bilirubin-Oxidizing Enzyme from Activated Sludge Isolated by a Metagenomic Approach

A gene coding for a multicopper oxidase (BopA) was identified through the screening of a metagenomic library constructed from wastewater treatment activated sludge. The recombinant BopA protein produced in Escherichia coli exhibited oxidation activity toward 2,2′-azino-bis-(3-ethylbenzothiazoline-6-sulfonate) (ABTS) in the presence of copper, suggesting that BopA is laccase. A bioinformatic analysis of the bopA gene sequence indicated that it has a phylogenetically bacterial origin, possibly derived from a bacterium within the phylum Deinococcus-Thermus. Purified BopA exhibited maximum activity at pH 7.5 with bilirubin as its substrate and was found to be active over a markedly broad pH range from 6 to 11. It also showed notable thermostability; its activity remained intact even after a heat treatment at 90°C for 60 min. This enzyme is a thermostable-bilirubin oxidase that exhibits markedly higher thermostability than that previously reported for laccases.

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.

Is the root-colonizing endophyte Acremonium strictum an ericoid mycorrhizal fungus?

In previous investigations, we found that Acremonium strictum (strain DSM 100709) developed intracellular structures with similarity to mycelia of ericoid mycorrhizal fungi in the rhizodermal cells of flax plants and in hair roots of Rhododendron plantlets. A. strictum had also been isolated from roots of ericaceous salal plants and was described as an unusual ericoid mycorrhizal fungus (ERMF). As its mycorrhizal traits were doubted, we revised the hypothesis of a mycorrhizal nature of A. strictum. A successful synthesis of mycorrhiza in hair roots of inoculated ericaceous plants was a first step of evidence, followed by fluorescence microscopy with FUN(®)1 cell stain to observe the vitality of the host cells at the early infection stage. In inoculation trials with in vitro-raised mycorrhiza-free Rhododendron plants in axenic liquid culture and in greenhouse substrate culture, A. strictum was never observed in living hair root cells. As compared to the ERMF Oidiodendron maius and Rhizoscyphus ericae that invaded metabolically active host cells and established a symbiotic unit, A. strictum was only found in cells that were dead or in the process of dying and in the apoplast. In conclusion, A. strictum does not behave like a common ERMF-if it is one at all. A comparison of A. strictum isolates from ericaceous and non-ericaceous hosts could reveal further identity details to generalize or specify our findings on the symbiotic nature of A. strictum. At least, the staining method enables to discern between true mycorrhizal and other root endophytes-a tool for further studies.

Root-associated fungi of Vaccinium carlesii in subtropical forests of China: intra- and inter-annual variability and impacts of human disturbances

Ericoid mycorrhiza (ERM) are expected to facilitate establishment of ericaceous plants in harsh habitats. However, diversity and driving factors of the root-associated fungi of ericaceous plants are poorly understood. In this study, hair-root samples of Vaccinium carlesii were taken from four forest types: old growth forests (OGF), secondary forests with once or twice cutting (SEC I and SEC II), and Cunninghamia lanceolata plantation (PLF). Fungal communities were determined using high-throughput sequencing, and impacts of human disturbances and the intra- and inter-annual variability of root-associated fungal community were evaluated. Diverse fungal taxa were observed and our results showed that (1) Intra- and inter-annual changes in root-associated fungal community were found, and the Basidiomycota to Ascomycota ratio was related to mean temperature of the sampling month; (2) Human disturbances significantly affected structure of root-associated fungal community of V. carlesii, and two secondary forest types were similar in root-associated fungal community and were closer to that of the old growth forest; (3) Plant community composition, edaphic parameters, and geographic factors significantly affected root-associated fungal communities of V. carlesii. These results may be helpful in better understanding the maintenance mechanisms of fungal diversity associated with hair roots of ERM plants under human disturbances.

Is the prominent ericoid mycorrhizal fungus Rhizoscyphus ericae absent in the Southern Hemisphere's Ericaceae? A case study on the diversity of root mycobionts in Gaultheria spp. from northwest Patagonia, Argentina

Ericaceae diversity hotspots are in the mountains of the Neotropics and Papua New Guinea, South Africa's fynbos and Southeast Asia but majority of references to their root mycobionts come from the Northern Hemisphere. Here, typical cultivable ericoid mycorrhizal (ErM) fungi comprise Rhizoscyphus ericae, Meliniomyces variabilis, and Oidiodendron maius. It is however unclear whether this is true also for the Southern Hemisphere. Our study focused on cultivable mycobionts from hair roots of Gaultheria mucronata and Gaultheria poeppigii (Ericaceae) from two natural forests in NW Patagonia, Argentina, differing in mycorrhizal preferences of their tree dominants. We detected 62 well-defined OTUs mostly belonging to Helotiales and Hypocreales; the most frequent were Phialocephala fortinii s. l., Pochonia suchlasporia, and Ilyonectria radicicola. Only one out of 257 isolates showed ITS nrDNA similarity to members of the R. ericae aggregate (REA) but was not conspecific with R. ericae, and only five isolates were conspecific with O. maius. Microscopic observations showed that the screened roots were frequently colonized in a manner differing from the pattern typically produced by R. ericae and O. maius. A re-synthesis experiment with selected isolates showed that only O. maius formed colonization resembling ericoid mycorrhiza. Amplification of root fungal DNA with REA-specific and Sebacinaceae-specific primers showed that REA mycobionts were present in some of the screened samples while Sebacinaceae were present in all samples. These results suggest that Gaultheria spp. from NW Patagonia form ericoid mycorrhizae predominantly with the difficult-to-cultivate Sebacinaceae while the incidence of REA is relatively low and may be masked by other most likely non-mycorrhizal cultivable mycobionts.

Effects of different types of N deposition on the fungal decomposition activities of temperate forest soils

Nitrogen (N) deposition significantly affects soil microbial activities and litter decomposition processes in forest ecosystems. However, the changes in soil fungi during litter decomposition remain unclear. In this study, ammonium nitrate was selected as inorganic N (IN), whereas urea and glycine were selected as organic N (ON). N fertilizer with different IN-to-ON ratios (1:4, 2:3, 3:2, 4:1, and 5:0) was mixed in equal amounts and then added to temperate forest soils. Half of each treatment was simultaneously added with streptomycin to inhibit soil bacteria. The activities of enzymes involved in litter decomposition (invertase, β-glucosidase, cellulase, polyphenol oxidase, and phosphatase) were assayed after a three-year field experiment. The results showed that enzymatic activities were inhibited by IN addition but accelerated by ON addition in the non-antibiotic addition treatments. An increase in ON in the mixed N fertilizer also shifted enzymatic activities from N inhibition to N stimulation. Similarly, in the antibiotic addition treatments, fungal activities revealed the same trends, but they were seriously inhibited by IN and significantly accelerated by ON. These results indicated that soil fungi were more sensitive to N deposition, particularly to ON. A large amount of ON may convert soil microbial communities into a fungi-dominated system. However, excessive ON deposition (20% IN+80% ON) caused N saturation and repressed fungal activities. These results suggested that soil fungi were sensitive to N type and that different IN-to-ON ratios may induce diverse ecological effects on soil fungi.