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

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

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

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

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

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

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

Myristate and the ecology of AM fungi : significance, opportunities, applications and challenges

A recent study by Sugiura and coworkers reported the nonsymbiotic growth and spore production of an arbuscular mycorrhizal (AM) fungus, Rhizophagus irregularis, when the fungus received an external supply of certain fatty acids, myristates (C:14). This discovery follows the insight that AM fungi receive fatty acids from their hosts when in symbiosis. If this result holds up and can be repeated under nonsterile conditions and with a broader range of fungi, it has numerous consequences for our understanding of AM fungal ecology, from the level of the fungus, at the plant community level, and to functional consequences in ecosystems. In addition, myristate may open up several avenues from a more applied perspective, including improved fungal culture and supplementation of AM fungi or inoculum in the field. We here map these potential opportunities, and additionally offer thoughts on potential risks of this potentially new technology. Lastly, we discuss the specific research challenges that need to be overcome to come to an understanding of the potential role of myristate in AM ecology

A review of peer-review for Pedobiologia: Journal of Soil Ecology

Peer-review is an integral part of the scientific process, but getting a sufficient number of busy scientists to provide constructive reviews on a manuscript can be a challenge. The majority of individuals that we polled have had experience in the last two years with having manuscripts rejected and then submitting them elsewhere and/or with receiving invitations to review the same manuscript for different journals. Many experienced these events multiple times in that period. Authors who have had manuscripts rejected from journals after review have the opportunity to improve their manuscripts in light of reviewer comments. However unless the next journal to receive the manuscript has the technical means to transfer reviews from the previous journal, most journals treat these submissions as if they had not undergone peer review. Providing authors the option to submit responses to previous reviewer comments with details about how the manuscript has been revised since rejection from the previous journal is a practical means to increase the efficiency of peer review, requiring fewer reviews and leading to more rapid publication. Pedobiologia – Journal of Soil Ecology invites authors to include previous reviewer reports and detailed responses with new submissions

Unpredictable assembly of arbuscular mycorrhizal fungal communities

In their analysis of arbuscular mycorrhizal fungal communities sampled from roots collected around the globe, Davison et al. (2015, Science 349: 970) demonstrated that these fungi exhibit low endemism and suggested that their biogeography is largely determined by local environmental conditions. Here, we show that, within similar environments, these communities are largely unpredictable based on environmental conditions and exhibit patterns that are either consistent with neutral models of community assembly or are more stochastic than what models based on environmental filtering, niche-based assembly, or neutrality would predict. We also show that the degree of unpredictability is related to geography and the characteristics of the host plant, suggesting opportunities for future research to understand assembly processes in mycorrhizal fungal communities