Missing checkerboards? An absence of competitive signal in Alnus-associated ectomycorrhizal fungal communities

Maintenance of host specialisation gradients in ectomycorrhizal symbionts

Many fungi that form ectomycorrhizas exhibit a degree of host specialisation, and individual trees are frequently colonised by communities of mycorrhizal fungi comprising species that fall on a gradient of specialisation along genetic, functional and taxonomic axes of variation. By contrast, arbuscular mycorrhizal fungi exhibit little specialisation. Here, we propose that host tree root morphology is a key factor that gives host plants fine-scale control over colonisation and therefore opportunities for driving specialisation and speciation of ectomycorrhizal fungi. A gradient in host specialisation is likely driven by four proximate mechanistic 'filters' comprising partner availability, signalling recognition, competition for colonisation, and symbiotic function (trade, rewards and sanctions), and the spatially restricted colonisation seen in heterorhizic roots enables these mechanisms, especially symbiotic function, to be more effective in driving the evolution of specialisation. We encourage manipulation experiments that integrate molecular genetics and isotope tracers to test these mechanisms, alongside mathematical simulations of eco-evolutionary dynamics in mycorrhizal symbioses.

Structure of plant-associated microeukaryotes in roots and leaves of aquatic and terrestrial plants revealed by blocking peptide-nucleic acid (PNA) amplification

Studies of plant-microbe interactions, including mutualistic, antagonistic, parasitic, or commensal microbes, have greatly benefited our understanding of ecosystem functioning. New molecular identification tools have increasingly revealed the association patterns between microorganisms and plants. Here, we integrated long-read PacBio single-molecule sequencing technology with a blocking protein-nucleic acid (PNA) approach to minimise plant amplicons in a survey of plant-eukaryotic microbe relationships in roots and leaves of different aquatic and terrestrial plants to determine patterns of organ, host, and habitat preferences. The PNA approach reduced the samples' relative amounts of plant reads and did not distort the fungal and other microeukaryotic composition. Our analyses revealed that the eukaryotic microbiomes associated with leaves and roots of aquatic plants exhibit a much larger proportion of non-fungal microorganisms than terrestrial plants, and leaf and root microbiomes are similar. Terrestrial plants had much stronger differentiation of leaf and root microbiomes and stronger partner specificity than aquatic plants.

Fungal Endophytes of Alnus incana ssp. rugosa and Alnus alnobetula ssp. crispa and Their Potential to Tolerate Heavy Metals and to Promote Plant Growth

Soil contamination by metals is of particular interest, given that their retention times within the profile can be indefinite. Thus, phytostabilization can be viewed as a means of limiting metal toxicity in soils. Due to their ability to grow on contaminated soils, alders have repeatedly been used as key species in phytostabilization efforts. Alder ability to grow on contaminated sites stems, in part, from its association with microbial endophytes. This work emphasizes the fungal endophytes populations associated with Alnus incana ssp. rugosa and Alnus alnobetula ssp. crispa (previously A. viridis ssp. crispa) under a phytostabilization angle. Fungal endophytes were isolated from alder trees that were growing on or near disturbed environments; their tolerances to Cu, Ni, Zn, and As, and acidic pH (4.3, 3, and 2) were subsequently assessed. Cryptosporiopsis spp. and Rhizoscyphus spp. were identified as fungal endophytes of Alnus for the first time. When used as inoculants for alder, some isolates promoted plant growth, while others apparently presented antagonistic relationships with the host plant. This study reports the first step in finding the right fungal endophytic partners for two species of alder used in phytostabilization of metal-contaminated mining sites.

Ectomycorrhizal and endophytic fungi associated with Alnus glutinosa growing in a saline area of central Poland

Alnus glutinosa (black alder) is a mycorrhizal pioneer tree species with tolerance to high concentrations of salt in the soil and can therefore be considered to be an important tree for the regeneration of forests areas devastated by excessive salt. However, there is still a lack of information about the ectomycorrhizal fungi (EMF) associated with mature individuals of A. glutinosa growing in natural saline conditions. The main objective of this study was to test the effect of soil salinity and other physicochemical parameters on root tips colonized by EMF, as well as on the species richness and diversity of an EMF community associated with A. glutinosa growing in natural conditions. We identified a significant effect of soil salinity (expressed as electrical conductivity: EC_e and EC_1:5) on fungal taxa but not on the total level of EM fungal colonization on roots. Increasing soil salinity promoted dark-coloured EMF belonging to the order Thelephorales (Tomentella sp. and Thelephora sp.). These fungi are also commonly found in soils polluted with heavy-metal. The ability of these fungi to grow in contaminated soil may be due to the presence of melanine, a natural dark pigment and common wall component of the Thelephoraceae that is known to act as a protective interface between fungal metabolism and biotic and abiotic environmental stressors. Moreover, increased colonization of fungi belonging to the class of Leotiomycetes and Sordiomycetes, known as endophytic fungal species, was observed at the test sites, that contained a larger content of total phosphorus. This observation confirms the ability of commonly known endophytic fungi to form ectomycorrhizal structures on the roots of A. glutinosa under saline stress conditions.

Networks Depicting the Fine-Scale Co-Occurrences of Fungi in Soil Horizons

Fungi in soil play pivotal roles in nutrient cycling, pest controls, and plant community succession in terrestrial ecosystems. Despite the ecosystem functions provided by soil fungi, our knowledge of the assembly processes of belowground fungi has been limited. In particular, we still have limited knowledge of how diverse functional groups of fungi interact with each other in facilitative and competitive ways in soil. Based on the high-throughput sequencing data of fungi in a cool-temperate forest in northern Japan, we analyzed how taxonomically and functionally diverse fungi showed correlated fine-scale distributions in soil. By uncovering pairs of fungi that frequently co-occurred in the same soil samples, networks depicting fine-scale co-occurrences of fungi were inferred at the O (organic matter) and A (surface soil) horizons. The results then led to the working hypothesis that mycorrhizal, endophytic, saprotrophic, and pathogenic fungi could form compartmentalized (modular) networks of facilitative, antagonistic, and/or competitive interactions in belowground ecosystems. Overall, this study provides a research basis for further understanding how interspecific interactions, along with sharing of niches among fungi, drive the dynamics of poorly explored biospheres in soil.

Competitive avoidance not edaphic specialization drives vertical niche partitioning among sister species of ectomycorrhizal fungi

Soil depth partitioning is thought to promote the diversity of ectomycorrhizal (EM) fungal communities, but little is known about whether it is controlled by abiotic or biotic factors. In three bioassay experiments, we tested the role of vertical soil heterogeneity in determining the distributions and competitive outcomes of the EM sister species Rhizopogon vinicolor and Rhizopogon vesiculosus. We planted Pseudotsuga menziesii seedlings into soils that were either a homogenized mix of upper and lower depths or vertically stratified combinations mimicking natural field conditions. We found that both species colonized the upper or lower soil depths in the absence of competition, suggesting that their distributions were not limited by abiotic edaphic factors. In competition within homogeneous soils, R. vesiculosus completely excluded colonization by R. vinicolor, but R. vinicolor was able to persist when soils were stratified. The amount of colonization by R. vinicolor in the stratified soils was also significantly correlated with the number of multilocus genotypes present. Taken together, our findings suggest that the differential vertical distributions of R. vinicolor and R. vesiculosus in natural settings are probably attributable to competition rather than edaphic specialization, but that soil heterogeneity may play a key role in promoting EM fungal diversity.

Ectomycorrhizal fungal spore bank recovery after a severe forest fire: some like it hot

After severe wildfires, pine recovery depends on ectomycorrhizal (ECM) fungal spores surviving and serving as partners for regenerating forest trees. We took advantage of a large, severe natural forest fire that burned our long-term study plots to test the response of ECM fungi to fire. We sampled the ECM spore bank using pine seedling bioassays and high-throughput sequencing before and after the California Rim Fire. We found that ECM spore bank fungi survived the fire and dominated the colonization of in situ and bioassay seedlings, but there were specific fire adapted fungi such as Rhizopogon olivaceotinctus that increased in abundance after the fire. The frequency of ECM fungal species colonizing pre-fire bioassay seedlings, post-fire bioassay seedlings and in situ seedlings were strongly positively correlated. However, fire reduced the ECM spore bank richness by eliminating some of the rare species, and the density of the spore bank was reduced as evidenced by a larger number of soil samples that yielded uncolonized seedlings. Our results show that although there is a reduction in ECM inoculum, the ECM spore bank community largely remains intact, even after a high-intensity fire. We used advanced techniques for data quality control with Illumina and found consistent results among varying methods. Furthermore, simple greenhouse bioassays can be used to determine which fungi will colonize after fires. Similar to plant seed banks, a specific suite of ruderal, spore bank fungi take advantage of open niche space after fires.