Method or madness: does OTU delineation bias our perceptions of fungal ecology?

This is the author's manuscript. The definitive version is available at www.newphytologist.co

Deciphering the relative contributions of multiple functions within plant-microbe symbioses

This is the publisher's version, also available electronically from http://www.esajournals.org/doi/abs/10.1890/09-1858.1For microbial symbioses with plants, such as mycorrhizas, we typically quantify either the net effects of one partner on another or a single function a symbiont provides. However, many microbial symbioses provide multiple functions to plants that vary based on the microbial species or functional group, plant species, and environment. Here we quantified the relative contributions of multiple functions provided by arbuscular mycorrhizal (AM) fungi to symbiont-mediated changes in plant biomass. We used two published data sets, one that measured multiple functions (pathogen protection and nutrient uptake) on a single plant and one that measured a single function (pathogen protection) on multiple plants. Using structural equation modeling, we observed strong variation in the functional pathways by which AM fungi altered plant growth; changes in plant biomass were associated with different functions (and different AM fungal functional groups) for the different plant species. Utilizing this methodology across multiple partners and environments will allow researchers to gauge the relative importance of functions they isolate and, perhaps more importantly, those they did not consider. This baseline information is essential for establishing the specific mechanisms by which microbial symbioses influence plant diversity and to more effectively utilize these organisms in agriculture, restoration and conservation

Indigenous Arbuscular Mycorrhizal Fungal Assemblages Protect Grassland Host Plants from Pathogens

Plant roots can establish associations with neutral, beneficial and pathogenic groups of soil organisms. Although it has been recognized from the study of individual isolates that these associations are individually important for plant growth, little is known about interactions of whole assemblages of beneficial and pathogenic microorganisms associating with plants

Silicon accumulation suppresses arbuscular mycorrhizal fungal colonisation in the model grass Brachypodium distachyon

Purpose Silicon (Si) accumulation by grasses alleviates diverse biotic and abiotic stresses. Despite this important functional role, we have limited understanding of how root microbial symbionts, such as arbuscular mycorrhizal (AM) fungi, affect Si uptake and even less about how Si supply and accumulation affect AM fungal colonisation. Our objective was to determine the nature of this two–way interaction in the model grass, Brachypodium distachyon. Methods We grew B. distachyon with five levels of Si supplementation using wild-type plants and a mutant (Bdlsi1-1) that has little capacity for Si uptake. Half of the plants were colonised by AM fungi; half were free of AM fungi. We measured Si accumulation, AM fungal colonisation, leaf carbon (C), nitrogen (N) and phosphorus (P) concentrations. Results AM fungi did not affect Si accumulation, although small increases occurred when root mass was included as a covariate. Si supplemented soil promoted plant growth and P uptake. Si accumulation suppressed colonisation by AM fungi and C concentrations in wild type but not in Bdlsi1-1 plants. Si concentrations were negatively correlated with C and N concentrations, with correlations being stronger in wild-type plants than Bdlsi1-1 plants. Conclusions Our results indicate that Si accumulation in the plant, rather than Si availability in the soil, underpinned reduced AMF colonisation. We propose that Si accumulation is unlikely to be impacted by AM fungi in plants with inherently high Si accumulation, but Si accumulation may suppress AM fungal colonisation in such plants

Soil physico-chemical properties are critical for predicting carbon storage and nutrient availability across Australia

Soil carbon and nutrient availability play crucial roles in ecosystem sustainability, and they are controlled by the interaction of climatic, biotic, and soil physico-chemical variables. Although soil physico-chemical properties have been recognized as vital variables for predicting soil organic carbon (SOC) and nutrients, their relative influence across broad geographical scales has yet to be evaluated when simultaneously considering many other drivers. Using boosted regression tree and structural equation modelling analyses of observations from topsoil (0-10 cm) and subsoil (20-30 cm) at 628 sites across Australia, we investigated the effects and relative influence of climate (mean annual temperature and aridity index), plant productivity, soil biodiversity (bacterial and fungal richness), and soil physical (clay and silt) and chemical (pH and iron) properties on SOC content and nutrient availability (i.e. nitrogen, phosphorus, and potassium). Among these variables, we found that soil physico-chemical properties primarily predicted the continent-scale SOC storage and nutrient availability. In contrast, climate, plant productivity, and soil biodiversity played relatively small roles. The importance of physico-chemical properties was evident across soil depths and ecosystem types (i.e. tropical, temperate, arid, and cropland). Our findings point to the need to better understand the role of soil physico-chemical properties in soil carbon and nutrient cycling and including these variables in predictions of SOC and nutrient dynamics at the ecosystem to continental scale

The mycobiome of Australian tree hollows in relation to the Cryptococcus gattii and C. neoformans species complexes

Cryptococcosis is a fungal infection caused by members of the Cryptococcus gattii and C. neoformans species complexes. The C. gattii species complex has a strong environmental association with eucalypt hollows (particularly Eucalyptus camaldulensis), which may present a source of infection. It remains unclear whether a specific mycobiome is required to support its environmental survival and growth. Conventional detection of environmental Cryptococcus spp. involves culture on differential media, such as Guizotia abyssinica seed agar. Next-generation sequencing (NGS)-based culture-independent identification aids in contextualising these species in the environmental mycobiome. Samples from 23 Australian tree hollows were subjected to both culture- and amplicon-based metagenomic analysis to characterize the mycobiome and assess relationships between Cryptococcus spp. and other fungal taxa. The most abundant genera detected were Coniochaeta, Aspergillus, and Penicillium, all being commonly isolated from decaying wood. There was no correlation between the presence of Cryptococcus spp. in a tree hollow and the presence of any other fungal genus. Some differences in the abundance of numerous taxa were noted in a differential heat tree comparing samples with or without Cryptococcus-NGS reads. The study expanded the known environmental niche of the C. gattii and C. neoformans species complexes in Australia with detections from a further five tree species. Discrepancies between the detection of Cryptococcus spp. using culture or NGS suggest that neither is superior per se and that, rather, these methodologies are complementary. The inherent biases of amplicon-based metagenomics require cautious interpretation of data through consideration of its biological relevance

Environmental and geographical factors structure soil microbial diversity in New Caledonian ultramafic substrates: A metagenomic approach

Soil microorganisms play key roles in ecosystem functioning and are known to be influenced by biotic and abiotic factors, such as plant cover or edaphic parameters. New Caledonia, a biodiversity hotspot located in the southwest Pacific, is one-third covered by ultramafic substrates. These types of soils are notably characterised by low nutrient content and high heavy metal concentrations. Ultramafic outcrops harbour diverse vegetation types and remarkable plant diversity. In this study, we aimed to assess soil bacterial and fungal diversity in New Caledonian ultramafic substrates and to determine whether floristic composition, edaphic parameters and geographical factors affect this microbial diversity. Therefore, four plant formation types at two distinct sites were studied. These formations represent different stages in a potential chronosequence. Soil cores, according to a given sampling procedure, were collected to assess microbial diversity using a metagenomic approach, and to characterise the physico-chemical parameters. A botanical inventory was also performed. Our results indicated that microbial richness, composition and abundance were linked to the plant cover type and the dominant plant species. Furthermore, a large proportion of Ascomycota phylum (fungi), mostly in non-rainforest formations, and Planctomycetes phylum (bacteria) in all formations were observed. Interestingly, such patterns could be indicators of past disturbances that occurred on different time scales. Furthermore, the bacteria and fungi were influenced by diverse edaphic parameters as well as by the interplay between these two soil communities. Another striking finding was the existence of a site effect. Differences in microbial communities between geographical locations may be explained by dispersal limitation in the context of the biogeographical island theory. In conclusion, each plant formation at each site possesses is own microbial community resulting from multiple interactions between abiotic and biotic factors. (Résumé d'auteur

Deterministic processes vary during community assembly for ecologically dissimilar taxa

The continuum hypothesis states that both deterministic and stochastic processes contribute to the assembly of ecological communities. However, the contextual dependency of these processes remains an open question that imposes strong limitations on predictions of community responses to environmental change. Here we measure community and habitat turnover across multiple vertical soil horizons at 183 sites across Scotland for bacteria and fungi, both dominant and functionally vital components of all soils but which differ substantially in their growth habit and dispersal capability. We find that habitat turnover is the primary driver of bacterial community turnover in general, although its importance decreases with increasing isolation and disturbance. Fungal communities, however, exhibit a highly stochastic assembly process, both neutral and non-neutral in nature, largely independent of disturbance. These findings suggest that increased focus on dispersal limitation and biotic interactions are necessary to manage and conserve the key ecosystem services provided by these assemblages

Reciprocal effects of silicon supply and endophytes on silicon accumulation and Epichloë colonization in grasses

Cool season grasses associate asymptomatically with foliar Epichloë endophytic fungi in a symbiosis where Epichloë spp. protects the plant from a number of biotic and abiotic stresses. Furthermore, many grass species can accumulate large quantities of silicon (Si), which also alleviates a similar range of stresses. While Epichloë endophytes may improve uptake of minerals and nutrients, their impact on Si is largely unknown. Likewise, the effect of Si availability on Epichloë colonization remains untested. To assess the bidirectional relationship, we grew tall fescue (Festuca arundinacea) and perennial ryegrass (Lolium perenne) hydroponically with or without Si. Grasses were associated with five different Epichloë endophyte strains [tall fescue: AR584 or wild type (WT); perennial ryegrass: AR37, AR1, or WT] or as Epichloë-free controls. Reciprocally beneficial effects were observed for tall fescue associations. Specifically, Epichloë presence increased Si concentration in the foliage of tall fescue by at least 31%, regardless of endophyte strain. In perennial ryegrass, an increase in foliar Si was observed only for plants associated with the AR37. Epichloë promotion of Si was (i) independent of responses in plant growth, and (ii) positively correlated with endophyte colonization, which lends support to an endophyte effect independent of their impacts on root growth. Moreover, Epichloë colonization in tall fescue increased by more than 60% in the presence of silicon; however, this was not observed in perennial ryegrass. The reciprocal benefits of Epichloë-endophytes and foliar Si accumulation reported here, especially for tall fescue, might further increase grass tolerance to stress

β-diversity in temperate grasslands is driven by stronger environmental filtering of plant species with large genomes

Elucidating mechanisms underlying community assembly and biodiversity patterns is central to ecology and evolution. Genome size (GS) has long been hypothesized to potentially affect species' capacity to tolerate environmental stress and might therefore help drive community assembly. However, its role in driving β-diversity (i.e., spatial variability in species composition) remains unclear. We measured GS for 161 plant species and community composition across 52 sites spanning a 3200-km transect in the temperate grasslands of China. By correlating the turnover of species composition with environmental dissimilarity, we found that resource filtering (i.e., environmental dissimilarity that includes precipitation, and soil nitrogen and phosphorus concentrations) affected β-diversity patterns of large-GS species more than small-GS species. By contrast, geographical distance explained more variation of β-diversity for small-GS than for large-GS species. In a 10-year experiment manipulating levels of water, nitrogen, and phosphorus, adding resources increased plant biomass in species with large GS, suggesting that large-GS species are more sensitive to the changes in resource availability. These findings highlight the role of GS in driving community assembly and predicting species responses to global change