Fire as a driver of fungal diversity - A synthesis of current knowledge

Small-scale fire refugia increase soil bacterial and fungal richness and increase community cohesion nine years after fire

Small-scale variation in wildfire behavior may cause large differences in belowground bacterial and fungal communities with consequences for belowground microbial diversity, community assembly, and function. Here we combine pre-fire, active-fire, and post-wildfire measurements in a mixed-conifer forest to identify how fine-scale wildfire behavior, unburned refugia, and aboveground forest structure are associated with belowground bacterial and fungal communities nine years after wildfire. We used fine-scale mapping of small (0.9-172.6 m2) refugia to sample soil-associated burned and refugial microbial communities. Richness was higher in refugia for bacteria (+19 %) and fungi (+31 %) and in all functional guilds relative to burned soils. Refugial communities had greater proportions of saprotrophic and lower proportions of pathogenic fungi relative to burned soils. Composition differed in burned areas and refugia and was most strongly associated with small-scale fire behavior, aboveground live tree basal area, and tree mortality. Refugial communities had more connected association networks and fewer facilitative interactions relative to burned soils - supporting both the stress-gradient hypothesis and the conclusion that refugial communities may have greater resistance to future disturbance. Small-scale differences in wildfire behavior and effects can have long-term impacts on belowground microbes, highlighting the need to assess neighborhood effects at spatial scales that influence microbes.

Fuel accumulation shapes post-fire fuel decomposition through soil heating effects on plants, fungi, and soil chemistry

Forty percent of terrestrial ecosystems require recurrent fires driven by feedbacks between fire and plant fuels. The accumulation of fine fuels in these ecosystems play a key role in fire intensity, which alters soil nutrients and shapes soil microbial and plant community responses to fire. Changes to post-fire plant fuel production are well known to feed back to future fires, but post-fire decomposition of new fuels is poorly understood. Our study sought to quantify how pre-fire fuel loading influenced post-fire fuel decomposition through soil abiotic properties, as well as plant and soil fungal communities. Prior to spring prescribed burns, we manipulated fine fuel loads in plots, both near (<10 m) and away (>10 m) from overstory pines, to modify soil heating in an old-growth longleaf pine savanna. We then assessed how fuel load and soil heating influenced post-fire plant fuel decomposition through changes to soil chemistry, vegetation, and fungi. Burning larger fuel loads made fires hotter, burn longer, and more completely combusted fuels. In these plots, decomposition of newly deposited fine fuels was slower in the eight months following fire. Decomposition changes from greater soil heating were mediated by greater shifts to postfire plant (2 and 4 months postfire) and fungal communities (4 and 6 months postfire). Soil properties (C: N ratios, soil pH, and P) controlled postfire decomposition throughout the year, but weakly responded to soil heating differences from fuels. Since the mechanisms for fuel effects on decomposition change over time, fire timing may be a future target for understanding fire feedbacks to fuel decomposition. Integrating these feedbacks with fuel production responses across fire-dependent ecosystems can help managers better set prescribed fire intervals and predict responses to reintroducing burning in fire-suppressed ecosystems.

Prescribed fire regimes influence responses of fungal and bacterial communities on new litter substrates in a brackish tidal marsh

Processes modifying newly deposited litter substrates should affect fine fuels in fire-managed tidal marsh ecosystems. Differences in chemical composition and dynamics of litter should arise from fire histories that generate pyrodiverse plant communities, tropical cyclones that deposit wrack as litter, tidal inundation that introduces and alters sediments and microbes, and interactions among these different processes. The resulting diversity and dynamics of available litter compounds should affect microbial (fungal and bacterial) communities and their roles in litter substrate dynamics and ecosystem responses over time. We experimentally examined effects of differences in litter types produced by different fire regimes and litter loads (simulating wrack deposition) on microbial community composition and changes over time. We established replicated plots at similar elevations within frequent tidal-inundation zones of a coastal brackish Louisiana marsh. Plots were located within blocks with different prescribed fire regimes. We deployed different measured loads of new sterilized litter collected from zones in which plots were established, then re-measured litter masses at subsequent collection times. We used DNA sequencing to characterize microbial communities, indicator families, and inferred ecosystem functions in litter subsamples. Differences in fire regimes had large, similar effects on fungal and bacterial indicator families and community compositions and were associated with alternate trajectories of community development over time. Both microbial and plant community compositional patterns were associated with fire regimes, but in dissimilar ways. Differences in litter loads introduced differences in sediment accumulation associated with tidal inundation that may have affected microbial communities. Our study further suggests that fire regimes and tropical cyclones, in the context of frequent tidal inundation, may interactively generate substrate heterogeneities and alter microbial community composition, potentially modifying fine fuels and hence subsequent fires. Understanding microbial community compositional and functional responses to fire regimes and tropical cyclones should be useful in management of coastal marsh ecosystems.

Disaster Plant Pathology: Smart Solutions for Threats to Global Plant Health from Natural and Human-Driven Disasters

Disaster plant pathology addresses how natural and human-driven disasters impact plant diseases and the requirements for smart management solutions. Local to global drivers of plant disease change in response to disasters, often creating environments more conducive to plant disease. Most disasters have indirect effects on plant health through factors such as disrupted supply chains and damaged infrastructure. There is also the potential for direct effects from disasters, such as pathogen or vector dispersal due to floods, hurricanes, and human migration driven by war. Pulse stressors such as hurricanes and war require rapid responses, whereas press stressors such as climate change leave more time for management adaptation but may ultimately cause broader challenges. Smart solutions for the effects of disasters can be deployed through digital agriculture and decision support systems supporting disaster preparedness and optimized humanitarian aid across scales. Here, we use the disaster plant pathology framework to synthesize the effects of disasters in plant pathology and outline solutions to maintain food security and plant health in catastrophic scenarios. We recommend actions for improving food security before and following disasters, including (i) strengthening regional and global cooperation, (ii) capacity building for rapid implementation of new technologies, (iii) effective clean seed systems that can act quickly to replace seed lost in disasters, (iv) resilient biosecurity infrastructure and risk assessment ready for rapid implementation, and (v) decision support systems that can adapt rapidly to unexpected scenarios. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Drought legacy interacts with wildfire to alter soil microbial communities in a Mediterranean climate-type forest

Mediterranean forest ecosystems will be increasingly affected by hotter drought and more frequent and severe wildfire events in the future. However, little is known about the longer-term responses of these forests to multiple disturbances and the forests' capacity to maintain ecosystem function. This is particularly so for below-ground organisms, which have received less attention than those above-ground, despite their essential contributions to forest function. We investigated rhizosphere microbial communities in a resprouting Eucalyptus marginata forest, southwestern Australia, that had experienced a severe wildfire four years previously, and a hotter drought eight years previously. Our aim was to understand how microbial communities are affected over longer-term trajectories by hotter drought and wildfire, singularly, and in combination. Fungal and bacterial DNA was extracted from soil samples, amplified, and subjected to high throughput sequencing. Richness, diversity, composition, and putative functional groups were then examined. We found a monotonic decrease in fungal, but not bacterial, richness and diversity with increasing disturbance with the greatest changes resulting from the combination of drought and wildfire. Overall fungal and bacterial community composition reflected a stronger effect of fire than drought, but the combination of both produced the greatest number of indicator taxa for fungi, and a significant negative effect on the abundance of several fungal functional groups. Key mycorrhizal fungi, fungal saprotrophs and fungal pathogens were found at lower proportions in sites affected by drought plus wildfire. Wildfire had a positive effect on bacterial hydrogen and bacterial nitrogen recyclers. Fungal community composition was positively correlated with live tree height. These results suggest that microbial communities, in particular key fungal functional groups, are highly responsive to wildfire following drought. Thus, a legacy of past climate conditions such as hotter drought can be important for mediating the responses of soil microbial communities to subsequent disturbance like wildfire.

Smut fungus (Langdonia walkerae) incidence is lower in two bunchgrass species (Aristida stricta and A. beyrichiana) after fires early in the year

PREMISE

In frequently burned southeastern USA pine-grassland communities, wiregrass (Aristida stricta and A. beyrichiana) are dominant bunchgrasses whose flowers are infected during flowering by a smut fungus (Langdonia walkerae). We hypothesized that because prescribed fire timing affects wiregrass flowering patterns, it could affect smut incidence (occurrence of smut on plants) and severity of infection in inflorescences and spikelets. Because soil order could influence plant susceptibility, we hypothesized that these patterns would differ between soil orders. We hypothesized differences between species as representative of geographic variation in this ecosystem.

METHODS

We surveyed the incidence and severity of L. walkerae in wiregrass populations (85 populations at 14 sites) that had been prescription burned at different times during the previous year. We used binomial regressions to test whether incidence and severity differed by burn day, soil order, or species, with site as a random effect.

RESULTS

Fires that occurred in the winter were associated with significantly lower incidence than fires later in the year (as the months progressed into summer). Plants growing on Spodosol soils were significantly less likely to be infected than those on other soils. More variation in incidence, however, was explained by site, suggesting that site-specific characteristics were important. Smut severity in inflorescences and spikelets was greater overall in populations of A. stricta than in southern populations (A. beyrichiana).

CONCLUSIONS

Our findings indicate that fire timing and soil order affect L. walkerae incidence in wiregrass plants, but neither appears to be associated with greater severity. Patterns of smut infection are related to site history and geographic variation.

Dispersal of microbes from grassland fire smoke to soils

Wildland fire is increasingly recognized as a driver of bioaerosol emissions, but the effects that smoke-emitted microbes have on the diversity and community assembly patterns of the habitats where they are deposited remain unknown. In this study, we examined whether microbes aerosolized by biomass burning smoke detectably impact the composition and function of soil sinks using lab-based mesocosm experiments. Soils either containing the native microbial community or presterilized by γ-irradiation were inundated with various doses of smoke from native tallgrass prairie grasses. Smoke-inundated, γ-irradiated soils exhibited significantly higher respiration rates than both smoke-inundated, native soils and γ-irradiated soils exposed to ambient air only. Microbial communities in γ-irradiated soils were significantly different between smoke-treated and control soils, which supports the hypothesis that wildland fire smoke can act as a dispersal agent. Community compositions differed based on smoke dose, incubation time, and soil type. Concentrations of phosphate and microbial biomass carbon and nitrogen together with pH were significant predictors of community composition. Source tracking analysis attributed smoke as contributing nearly 30% of the taxa found in smoke-inundated, γ-irradiated soils, suggesting smoke may play a role in the recovery of microbial communities in similar damaged soils. Our findings demonstrate that short-distance microbial dispersal by biomass burning smoke can influence the assembly processes of microbial communities in soils and has implications for a broad range of subjects including agriculture, restoration, plant disease, and biodiversity.

The Impact of Post-Fire Smoke on Plant Communities: A Global Approach

Smoke is one of the fire-related cues that can alter vegetation communities' compositions, by promoting or excluding different plant species. For over 30 years, smoke-derived compounds have been a hot topic in plant and crop physiology. Research in this field was initiated in fire-prone areas in Australia, South Africa and some countries of both Americas, mostly with Mediterranean-type climates. Then, research extended to regions with moderate climates, like Central European countries; this was sometimes determined by the fact that in those regions, extensive prescribed or illegal burning (swailing) occurs. Hence, this review updates information about the effects of smoke compounds on plant kingdoms in different regions. It also focuses on research advances in the field of the physiological effects of smoke chemicals, mostly karrikins, and attempts to gather and summarize the current state of research and opinions on the roles of such compounds in plants' lives. We finish our review by discussing major research gaps, which include issues such as why plants that occur in non-fire-prone areas respond to smoke chemicals. Have recent climate change and human activities increased the risk of wildfires, and how may these affect local plant communities through physiologically active smoke compounds? Is the response of seeds to smoke and smoke compounds an evolutionarily driven trait that allows plants to adapt to the environment? What can we learn by examining post-fire smoke on a large scale?

Testing the contribution of dispersal to microbial succession following a wildfire

IMPORTANCE

Identifying the mechanisms underlying microbial community succession is necessary for predicting how microbial communities, and their functioning, will respond to future environmental change. Dispersal is one mechanism expected to affect microbial succession, yet the difficult nature of manipulating microorganisms in the environment has limited our understanding of its contribution. Using a dispersal exclusion experiment, this study isolates the specific effect of environmental dispersal on bacterial and fungal community assembly over time following a wildfire. The work demonstrates the potential to quantify dispersal impacts on soil microbial communities over time and test how dispersal might further interact with other assembly processes in response to environmental change.

Fire shapes fungal guild diversity and composition through direct and indirect pathways

Fire has shaped global ecosystems for millennia by directly killing organisms and indirectly altering habitats and resources. All terrestrial ecosystems, including fire-prone ecosystems, rely on soil-inhabiting fungi, where they play vital roles in ecological processes. Yet our understanding of how fire regimes influence soil fungi remains limited and our knowledge of these interactions in semiarid landscapes is virtually absent. We collected soil samples and vegetation measurements from sites across a gradient in time-since-fire ages (0-75 years-since-fire) and fire frequency (burnt 0-5 times during the recent 29-year period) in a semiarid heathland of south-eastern Australia. We characterized fungal communities using ITS amplicon-sequencing and assigned fungi taxonomically to trophic guilds. We used structural equation models to examine direct, indirect and total effects of time-since-fire and fire frequency on total fungal, ectomycorrhizal, saprotrophic and pathogenic richness. We used multivariate analyses to investigate how total fungal, ectomycorrhizal, saprotrophic and pathogenic species composition differed between post-fire successional stages and fire frequency classes. Time-since-fire was an important driver of saprotrophic richness; directly, saprotrophic richness increased with time-since-fire, and indirectly, saprotrophic richness declined with time-since-fire (resulting in a positive total effect), mediated through the impact of fire on substrates. Frequently burnt sites had lower numbers of saprotrophic and pathogenic species. Post-fire successional stages and fire frequency classes were characterized by distinct fungal communities, with large differences in ectomycorrhizal species composition. Understanding the complex responses of fungal communities to fire can be improved by exploring how the effects of fire flow through ecosystems. Diverse fire histories may be important for maintaining the functional diversity of fungi in semiarid regions.

Larger presence of ectomycorrhizae detected from pygmy pine ecotype in the fire-frequent pine barrens ecosystem

Pine barrens ecosystem has acidic, sandy, and nutrient-poor soil and is prone to drought and fire. In the New Jersey Pine Barrens, the predominant pitch pine (Pinus rigida) consists of two ecotypes: the regular pitch pines with heights of 4.6-12 m, and the pygmy pines of low stature (1.2-1.8 m) in the New Jersey Pine Plains. Previous ecological studies suggested that the dwarf pines in the Pine Plains that are embedded within the Pine Barrens were an evolutionary adaptation to frequent fire. Pines are obligate ectomycorrhizal (EcM) mutualists, and their root mycobiota may contribute to stress protection and plant health. However, information on the mycobiota associated with plants in the pine barrens ecosystem is lacking. To have a holistic understanding of the evolution and adaptation in this stressed environment, we used both culture-independent metabarcoding and culture-based method to characterize the mycobiota from soil and root of the two ecotypes and to identify core mycobiota. We found that Agaricomycetes, Leotiomycetes, and Mucoromycotina are predominant fungi in the New Jersey Pine Barrens ecosystem, which is rich in root mutualistic fungi. We observed that the pygmy pine roots had significantly higher density of EcM tips than the regular pine roots. This was corroborated by our metabarcoding analysis, which showed that the pygmy pine trees had higher ratio of ectomycorrhiza-forming fungi than the regular-statured pines. We hypothesize that symbiotrophic EcM fungi associated with pygmy pines are capable of mitigating high fire stress in the Pine Plains.

What If Root Nodules Are a Guesthouse for a Microbiome? The Case Study of Acacia longifolia

Acacia longifolia is one of the most aggressive invaders worldwide whose invasion is potentiated after a fire, a common perturbation in Mediterranean climates. As a legume, this species establishes symbioses with nitrogen-fixing bacteria inside root nodules; however, the overall microbial diversity is still unclear. In this study, we addressed root nodules' structure and biodiversity through histology and Next-Generation Sequencing, targeting 16S and 25S-28S rDNA genes for bacteria and fungi, respectively. We wanted to evaluate the effect of fire in root nodules from 1-year-old saplings, by comparing unburnt and burnt sites. We found that although having the same general structure, after a fire event, nodules had a higher number of infected cells and greater starch accumulation. Starch accumulated in uninfected cells can be a possible carbon source for the microbiota. Regarding diversity, Bradyrhizobium was dominant in both sites (ca. 77%), suggesting it is the preferential partner, followed by Tardiphaga (ca. 9%), a non-rhizobial Alphaproteobacteria, and Synechococcus, a cyanobacteria (ca. 5%). However, at the burnt site, additional N-fixing bacteria were included in the top 10 genera, highlighting the importance of this process. Major differences were found in the mycobiome, which was diverse in both sites and included genera mostly described as plant endophytes. Coniochaeta was dominant in nodules from the burnt site (69%), suggesting its role as a facilitator of symbiotic associations. We highlight the presence of a large bacterial and fungal community in nodules, suggesting nodulation is not restricted to nitrogen fixation. Thus, this microbiome can be involved in facilitating A. longifolia invasive success.

All boreal forest successional stages needed to maintain the full suite of soil biodiversity, community composition, and function following wildfire

Wildfire is a natural disturbance in boreal forest systems that has been predicted to increase in frequency, intensity, and extent due to climate change. Most studies tend to assess the recovery of one component of the community at a time but here we use DNA metabarcoding to simultaneously monitor soil bacteria, fungi, and arthropods along an 85-year chronosequence following wildfire in jack pine-dominated ecosites. We describe soil successional and community assembly processes to better inform sustainable forest management practices. Soil taxa showed different recovery trajectories following wildfire. Bacteria shared a large core community across stand development stages (~ 95-97% of their unique sequences) and appeared to recover relatively quickly by crown closure. By comparison fungi and arthropods shared smaller core communities (64-77% and 68-69%, respectively) and each stage appeared to support unique biodiversity. We show the importance of maintaining a mosaic ecosystem that represents each stand development stage to maintain the full suite of biodiversity in soils following wildfire, especially for fungi and arthropods. These results will provide a useful baseline for comparison when assessing the effects of human disturbance such as harvest or for assessing the effects of more frequent wildfire events due to climate change.

Tumor heterogeneity: preclinical models, emerging technologies, and future applications

Heterogeneity describes the differences among cancer cells within and between tumors. It refers to cancer cells describing variations in morphology, transcriptional profiles, metabolism, and metastatic potential. More recently, the field has included the characterization of the tumor immune microenvironment and the depiction of the dynamics underlying the cellular interactions promoting the tumor ecosystem evolution. Heterogeneity has been found in most tumors representing one of the most challenging behaviors in cancer ecosystems. As one of the critical factors impairing the long-term efficacy of solid tumor therapy, heterogeneity leads to tumor resistance, more aggressive metastasizing, and recurrence. We review the role of the main models and the emerging single-cell and spatial genomic technologies in our understanding of tumor heterogeneity, its contribution to lethal cancer outcomes, and the physiological challenges to consider in designing cancer therapies. We highlight how tumor cells dynamically evolve because of the interactions within the tumor immune microenvironment and how to leverage this to unleash immune recognition through immunotherapy. A multidisciplinary approach grounded in novel bioinformatic and computational tools will allow reaching the integrated, multilayered knowledge of tumor heterogeneity required to implement personalized, more efficient therapies urgently required for cancer patients.

Recovery of the soil fungal microbiome after steam disinfection to manage the plant pathogen Fusarium solani

Soil disinfection using high temperatures via steam is a promising approach to manage plant pathogens, pests, and weeds. Soil steaming is a viable option for growers who are moving away from dependence on chemical soil fumigants, especially in plant nursery or high tunnel environments. However, there are few studies that investigate how soil steaming causes substantial disturbance to the soil by killing both target pathogens and other soil biota. Steaming treatments also change the trajectory of the soil microbiome as it reassembles over time. Growers are interested in the health of soils after using steam-disinfection, especially if a virulent pathogen colonizes the soil and then flourishes in a situation where there are very few microbes to suppress its growth. Should recruitment of a virulent pathogen occur in the soil, this could have devasting effects on seed germination, seedling establishment and survival. Beneficial microbes are often used to prevent the colonization of plant pathogens, especially after a soil-steaming event. Here, we experimentally test how soil fungal communities assemble after steaming disinfection. We introduce to steam-treated soil Fusarium solani, an important fungal pathogen of soybean and Trichoderma harzianum, a known beneficial fungus used for soilborne pathogen suppression. Results show that F. solani significantly affects the relative abundance and diversity of the soil fungal microbiome, however, T. harzianum does not mitigate the amount of F. solani in the steam treated soil. Within the T. harzianum microbial addition, the soil fungal communities were similar to the control (steaming only). This result suggests inoculating the soil with T. harzianum does not drastically alter the assembly trajectory of the soil fungal microbiome. Other soil amendments such as a combination of Trichoderma spp. or other genera could suppress F. solani growth and shift soil microbiome composition and function post-steaming, however, more experimental research is needed.

Rapid bacterial and fungal successional dynamics in first year after chaparral wildfire

The rise in wildfire frequency and severity across the globe has increased interest in secondary succession. However, despite the role of soil microbial communities in controlling biogeochemical cycling and their role in the regeneration of post-fire vegetation, the lack of measurements immediately post-fire and at high temporal resolution has limited understanding of microbial secondary succession. To fill this knowledge gap, we sampled soils at 17, 25, 34, 67, 95, 131, 187, 286, and 376 days after a southern California wildfire in fire-adapted chaparral shrublands. We assessed bacterial and fungal biomass with qPCR of 16S and 18S and richness and composition with Illumina MiSeq sequencing of 16S and ITS2 amplicons. Fire severely reduced bacterial biomass by 47%, bacterial richness by 46%, fungal biomass by 86%, and fungal richness by 68%. The burned bacterial and fungal communities experienced rapid succession, with 5-6 compositional turnover periods. Analogous to plants, turnover was driven by "fire-loving" pyrophilous microbes, many of which have been previously found in forests worldwide and changed markedly in abundance over time. Fungal secondary succession was initiated by the Basidiomycete yeast Geminibasidium, which traded off against the filamentous Ascomycetes Pyronema, Aspergillus, and Penicillium. For bacteria, the Proteobacteria Massilia dominated all year, but the Firmicute Bacillus and Proteobacteria Noviherbaspirillum increased in abundance over time. Our high-resolution temporal sampling allowed us to capture post-fire microbial secondary successional dynamics and suggest that putative tradeoffs in thermotolerance, colonization, and competition among dominant pyrophilous microbes control microbial succession with possible implications for ecosystem function.

Diversity of genomic adaptations to the post-fire environment in Pezizales fungi points to crosstalk between charcoal tolerance and sexual development

Wildfires drastically impact the soil environment, altering the soil organic matter, forming pyrolyzed compounds, and markedly reducing the diversity of microorganisms. Pyrophilous fungi, especially the species from the orders Pezizales and Agaricales, are fire-responsive fungal colonizers of post-fire soil that have historically been found fruiting on burned soil and thus may encode mechanisms of processing these compounds in their genomes. Pyrophilous fungi are diverse. In this work, we explored this diversity and sequenced six new genomes of pyrophilous Pezizales fungi isolated after the 2013 Rim Fire near Yosemite Park in California, USA: Pyronema domesticum, Pyronema omphalodes, Tricharina praecox, Geopyxis carbonaria, Morchella snyderi, and Peziza echinospora. A comparative genomics analysis revealed the enrichment of gene families involved in responses to stress and the degradation of pyrolyzed organic matter. In addition, we found that both protein sequence lengths and G + C content in the third base of codons (GC3) in pyrophilous fungi fall between those in mesophilic/nonpyrophilous and thermophilic fungi. A comparative transcriptome analysis of P. domesticum under two conditions - growing on charcoal, and during sexual development - identified modules of genes that are co-expressed in the charcoal and light-induced sexual development conditions. In addition, environmental sensors such as transcription factors STE12, LreA, LreB, VosA, and EsdC were upregulated in the charcoal condition. Taken together, these results highlight genomic adaptations of pyrophilous fungi and indicate a potential connection between charcoal tolerance and fruiting body formation in P. domesticum.