Biology subjects

Glassman, S. I.

Publications and source records attributed to Glassman, S. I..

18 recordsLinked to original sources

bioRxiv2026

Burn intensity regulates post-fire effects on soil N2O emissions: A grassland soil pyrocosm study

Post-fire soil emissions of nitric oxide (NO) and nitrous oxide (N2O) are important ecosystem nitrogen (N) loss pathways, but their flux dynamics vary widely across studies, making generalizations challenging. Natural variation in burn intensity--or heat energy released during combustionm--may help resolve this variability by mediating the soil physicochemical and biological drivers of these emissions. Here, we used an experimental "pyrocosm" system to evaluate how varying burn intensity influences post-fire NO and N2O emissions using soil from a Southern California grassland across 18 weeks. Over several months, we measured soil NO and N2O fluxes alongside soil pH, extractable nitrate (NO3-) and ammonium (NH4+), net NH4+ production, net nitrification, soil carbon (C) pools, microbial biomass C, and the potential activities of five extracellular hydrolytic enzymes under Control, Low- (100.1 {+/-} 20.0 oC peak soil temperature at 5 cm depth), and High-intensity (243.8 {+/-} 7.4 oC peak soil temperature at 5 cm depth) burns. Soil NO emissions were not significantly affected by burn intensity. In contrast, N2O emissions tripled under low burn intensity relative to unburned controls, but did not differ from controls at high burn intensity. This stimulation of N2O emission under low burn intensity was driven by increased denitrification, as supported by elevated soil pH and labile C availability, and an 88% reduction in net nitrification that signaled active NO3- consumption. Under high burn intensity, however, severe loss of microbial biomass, soil C, and NO3- constrained denitrification, with rising hydrolytic enzyme activities over time suggesting C limitation. Together, these findings demonstrate that post-fire N2O emissions reflect a fire intensity-dependent balance between microbial mortality and resource limitation, helping to explain divergent N emissions across ecosystems.

ecology↗

bioRxiv2026

Wildfires drive trade-offs in ammonia-oxidizing groups and promote denitrification to increase soil emissions of nitric oxide (NO) and nitrous oxide (N2O) in California chaparral

Wildfires can promote trade-offs in soil nitrifier and denitrifier communities that affect post-fire nitrogen (N) cycling and emissions of nitric oxide (NO), nitrous oxide (N2O), and dinitrogen (N2). For example, by increasing soil pH and ammonium (NH4+), wildfires could increase the abundance of ammonia-oxidizing bacteria (AOB) over archaea (AOA). Because AOB and AOA process N differently, nitrifier trade-offs may affect N emissions and nitrate (NO3-) supply with downstream effects on denitrifier activity, leading us to ask: Do trade-offs between AOA and AOB abundance and shifts in denitrifying processes influence N emissions over time after wildfire? We selectively inhibited AOA and AOB communities from soil collected over four seasonal time points one year before and after a chaparral wildfire and used stable isotopes to parse denitrifier contributions to N2O emissions. Over one year after the wildfire, soil pH increased from 6.1 to 7.0, soil extractable NH4+ increased 30-fold, NO3- increased 5-fold, and NO2- increased 9-fold. AOB amoA gene copy numbers increased 20-fold one year after fire, while AOA abundance remained unchanged. Post-fire soil NO emissions increased 63-fold over one year, with varied contributions from all nitrifier groups. Soil N2O emissions peaked eight months after fire (2271 {+/-} 634 ng N2O-N g-1 soil), with increased contributions from AOA. Wildfire increased {delta}15NSPN2O and {delta}15NbulkN2O values, suggesting increased N2O reduction to N2. Overall, wildfire increased AOB abundance relative to AOA, promoting nitrification activity and providing intermediates to denitrifiers to increase emissions of NO and N2O for up to one year after fire.

ecology↗

bioRxiv2026

Microbial association networks reveal hidden keystone taxa and cross-kingdom interactions after dryland wildfires

How wildfires reorganize soil microbial interactions is a key knowledge gap, particularly for drylands that cover nearly 40% of Earths surface and face increasing wildfire frequency with global change. We compared bacterial, fungal, and cross-kingdom association networks across four timepoints from 2 weeks to 3 years post-fire in two California dryland systems: a high-intensity chaparral shrubland fire and a low-intensity Eastern Joshua tree desert fire, using nearly identical sampling designs and molecular workflows. Wildfire increased bacterial-fungal associations more than bacterial or fungal interactions in both systems, with burned plots consistently shifting toward cooperative over competitive associations. Bacterial-fungal interactions also increased in burned relative to unburned desert plots, suggesting fire promoted microbial associations in desert soils. Although microbial richness declined by up to 61% one year after chaparral wildfire but remained unchanged in the desert, network clustering declined in both systems, indicating reduced community resilience independent of richness loss. Pyrophilous bacteria, including Massilia and Noviherbaspirillum, emerged as keystone taxa after chaparral wildfire, while generalist bacteria and the putatively pyrophilous Pyronemataceae fungus Pseudotricharina structured desert burned networks. Cross-kingdom network analysis revealed shifts in post-fire microbiomes invisible to traditional diversity metrics, highlighting bacterial-fungal interactions and keystone taxa as drivers of dryland post-fire succession.

microbiology↗

bioRxiv2026

Differential impacts of fall versus spring prescribed burns on microbial biomass, richness, and composition in young mixed conifer forests

Prescribed burns aim to restore ecological processes and mitigate high-severity wildfire risks. Historically, California wildfires occur in summer or fall, but due to limited burning opportunities, prescribed burns occur in fall and spring. Yet, whether the burn season affects ecological outcomes is largely unknown. Here, we test prescribed burn season impacts on soil burn severity, bacterial and fungal abundance, richness, and composition as assessed with 16S and 18S qPCR and 16S and ITS2 Illumina MiSeq. We implemented a Before-After-Control-Impact design with 9 California montane mixed conifer forest stands (4 fall, 4 spring, 1 unburned control). We assessed resilience by collecting 6 sub-samples per stand at 6 time points ranging from pre-fire to 3 days, 1 and 6 months, and 1 and 2 years after fall and spring burns. Fall burns significantly reduced bacterial and fungal abundance and richness, whereas spring burns did not. Indeed, at 24 days after fall burns compared to pre-fire, bacterial and fungal richness were reduced by 24-30%, with richness of ectomycorrhizal fungi reduced by 45% and saprobic fungi by 28%. After the fall burn, fungal richness recovered within a year and fungal abundance within 6 months, whereas bacterial abundance and richness recovered in 2 years. Bacterial and fungal communities experienced compositional turnovers after both burns, with the emergence of several genera of "fire-loving" pyrophilous bacteria (Massilia, Paenibacillus) and fungi (Geminibasidium, Pyronema, Neurospora). Our findings suggest that, although seasonal differences were evident, both fall and spring prescribed burns mitigate wildfire impacts while promoting the succession of pyrophilous microbes.

microbiology↗

bioRxiv2025

Strain-Level Adaptation of Pyrophilous Bacteria through Gene Fragmentation and Horizontal Gene Transfer

Wildfires reshape soil carbon (C) and nitrogen (N) dynamics by generating pyrogenic organic matter (PyOM) and selecting for pyrophilous "fire-loving" bacteria, yet the genomic mechanisms underpinning their post-fire adaptations are largely unknown. We combined comparative genomics of 16 pyrophilous bacteria spanning three phyla with bioassays and transcriptome profiling following PyOM exposure to test whether post-fire conditions promote genomic innovation within bacterial populations. Pyrophilous bacterial isolates exhibited genomic novelty through gene fragmentation, horizontal gene transfer (HGT), and plasmid-mediated operon expansion, enriching aromatic C degradation and N acquisition genes relative to non-pyrophilous sister taxa. Plasmid-encoded PyOM metabolism genes showed evidence of HGT across pyrophilous bacterial orders and cross-kingdom with pyrophilous fungi. Bioassays revealed overflow organic acid production associated with variation in tricarboxylic acid cycle genes, potentially moderating elevated post-fire soil pH and facilitating microbial succession. Our findings reveal how fire selects for bacterial genomic innovation and illuminate microbial evolution in extreme environments.

microbiology↗

bioRxiv2025

Wildfire alters nitrogen cycling to increase soil emissions of nitric oxide (NO) and the heterogeneity of nitrous oxide (N2O) in California chaparral

Wildfires can disrupt ecosystem nitrogen (N) cycling by combusting vegetation biomass N and depositing ash that is rich in ammonium (NH4+) onto soils. Post-fire increases in NH4+ and soil physicochemical changes may promote further N loss by stimulating microbially-driven emissions of nitric oxide (NO) and nitrous oxide (N2O)--trace gases that alter air quality and climate. We hypothesized that soil NO and N2O emissions would increase with the flush of post-fire N availability and would be highest in soils that burned at medium severity due to the combination of high soil N availability and persistence of microbial activity. To test this, we established nine plots (6 burned; 3 unburned) and sampled soils seasonally over three years after wildfire in a chaparral shrubland in Southern California, USA. Wildfire significantly increased soil extractable NH4+ by an average of 10 {micro}g NH4+-N g soil-1, soil extractable NO3- by 8 {micro}g NO3--N, and soil pH by 0.5 units. Post-fire soil NO emissions significantly increased by an average 74 ng NO-N g-1 (cumulative 40-h incubations) over three years, with the highest emissions measured in year one from plots that burned at medium and high severities. No significant effects of burning were detectable for N2O emissions over three years (average {+/-} standard error; 224 {+/-} 107 ng N2O-N g-1 soil in burned plots and 30 {+/-} 17 ng N2O-N g-1 soil in unburned plots); however, we observed high fluxes only from soils that burned at medium and high severities (N2O > 3500 ng N2O-N g-1 soil). Isotopic characterization of N2O from high-emitting soils indicated contributions from diverse sources and increased N2O reduction to N2. Overall, the occurrence of high N2O fluxes and accelerated NO emissions post fire indicate wildfires interact with soil N cycling to promote burn-severity-sensitive gaseous N losses long after wildfires are extinguished.

ecology↗

bioRxiv2025

Mojave Desert microbial communities show high resistance and resilience over three years despite widespread plant mortality following the Dome Fire

O_LIHigh severity desert fires are uncommon but typically chart a new successional trajectory altering plant communities for at least 65 years. These aboveground vegetation shifts can have large implications for belowground microbial communities that maintain soil structure and nutrient cycling. High severity wildfires in forests or shrublands can severely reduce microbial species richness and biomass and alter microbiomes for decades but impacts on desert soil microbiomes are virtually unknown. C_LIO_LIThe 2020 Mojave Desert Dome Fire burned 43,273 acres of Eastern Joshua tree (Yucca jaegeriana) habitat, burning roughly 1 million trees. To track aboveground and belowground impacts of the Dome Fire, we established 9 plots (6 burned; 3 unburned) and sampled 4 subsamples per plot for 5 time points ranging from 2 weeks to 3 years post-fire. We measured initial ash depth as a proxy of soil burn severity and assessed plant mortality, plant richness, soil chemical characteristics, estimated soil microbial biomass with qPCR, and microbial richness and composition with Illumina MiSeq of 16S and ITS2 amplicons. C_LIO_LIBelowground communities were highly diverse, containing 25,444 bacterial, 269 archaeal, and 6,683 fungal ASVs amplicon sequence variants (ASVs) or microbial taxa. We identified at least 65 plant species and saw 80% Eastern Joshua tree mortality in burned plots over three years, with reduced plant richness post-fire except an abundance of annual herbs at 1-year post-fire, yet the fire did not significantly reduce microbial biomass or richness at any time point. C_LIO_LIMicrobial communities for both bacteria and fungi showed small but significant changes, enriching for pyrophilous microbes in burned plots. We identified increases of pyrophilous microbes such as Tumebacillus, Massilia, Noviherbaspirillum bacteria and Pseudotricharina, Penicillium, Coniochaeta and Naganishia fungi. C_LIO_LISynthesis: We present the first comprehensive above and belowground examination following a natural desert wildfire including Archaea, Bacteria, and Fungi. Despite the widespread mortality of Eastern Joshua trees across 3 years, microbial biomass, richness, and community composition were mostly resistant to change, like microbial responses to low-intensity fast-moving grassland fires. Despite high resistance overall, wildfire still increased several pyrophilous bacterial and fungal taxa common after high severity shrubland and forest wildfires. C_LI

microbiology↗

bioRxiv2025

Gene Duplication, Horizontal Gene Transfer, and Trait Trade-offs Drive Evolution of Post-Fire Resource Acquisition in Pyrophilous Fungi

Wildfires significantly alter soil carbon (C) and nitrogen (N), reducing microbial richness and biomass, while selecting for "fire-loving" pyrophilous microbes that drive post-fire nutrient cycling. However, the genomic strategies and functional trade-offs (balancing gains in one trait with costs in another) underlying the traits that enable pyrophilous microbes to survive and thrive post-fire are virtually unknown. We hypothesized that pyrophilous fungi employ specialized genomic adaptations for C and N cycling, with evolutionary trade-offs between traits governing aromatic C degradation, N acquisition pathways, and rapid growth. To test these hypotheses, we performed complementary comparative genomics, transcriptomics after pyrogenic organic matter amendment, and growth rate bioassays for 18 pyrophilous fungi from five Ascomycota (Eurotiales, Pleosporales, Sordariales, Coniochaetales, and Pezizales) and three Basidiomycota (Agaricales, Holtermaniales, and Geminibasidiales) orders isolated from burned soils. We found a dramatic trait trade-off between fast growth and number of genes responsible for aromatic C degradation, implying burned environments select for metabolically costly genes despite their evolutionary cost. We used the comparative genomics framework to evaluate genomic signatures of evolution and found that either gene duplication and somatic mutation, or recombination via sexual reproduction, were the primary drivers of fungal genomic variation in aromatic C degradation and N acquisition genes. Finally, we identified cross-kingdom bacterial to fungal horizontal gene transfer as a secondary strategy producing novel aromatic C degradation genes. Overall, we found that trait trade-offs and genome evolutionary strategies are key drivers that may predict the persistence and contribution of pyrophilous fungi to global C and N cycling. Significance statementWildfires affect large tracts of the terrestrial biosphere, and while much is understood about plant adaptations to fire, here we uncovered for the first time genomic adaptations in fungi that can be modeled to predict impacts on global C and N cycling. We tested theorized trait trade-offs, and showed with genomics and bioassays how evolutionary trade-offs, like prioritizing aromatic C degradation at the expense of rapid growth, enable pyrophilous fungi to thrive post-fire. Further, we advance fungal genomics, and reveal the importance of mechanisms like gene duplication, sexual reproduction, and cross-kingdom horizontal gene transfer for enabling adaptation and evolutionary diversification in fungi. Finally, we identify fungi that may be useful inoculants to enhance recovery of polluted or burned soils.

genomics↗

bioRxiv2025

Eastern Joshua tree arbuscular mycorrhizal fungal mycobiomes largely consistent across roots, soils, and seasons

The Mojave Desert is home to iconic Joshua trees threatened by climate change. Most desert plants form mutually beneficial partnerships with arbuscular mycorrhizal fungi (AMF), yet the AMF of the Eastern Joshua tree (Yucca jaegeriana) remain completely uncharacterized. We tested how Y. jaegeriana AMF spore abundance, richness, and composition varied when sampling 20 trees across 4 seasons from roots versus soils. We confirmed root colonization via staining, assessed spore abundance via microscopy, and used Illumina MiSeq to sequence AMF virtual taxa (VT) with WANDA AML2 primers. We identified 12 spore morphotypes and 47 VTs across 5 families within Glomeromycotina and the most abundant VT Glomus VTX00294 appeared in 87% of soil and root samples. The majority of VTs (26/47) were present across all seasons and were shared among soil and roots (38/47) with more VTs unique to soil. In soil, per tree mean spore abundance and AMF richness was lowest in Summer but consistent across other seasons with richness ranging from 8.8 to 11.5 VTs and mean root richness consistent across seasons. We conclude that sampling from soils rather than roots and any season other than Summer will yield the most diverse AMF communities.

microbiology↗

bioRxiv2024

Evaluating Best Practices for Isolating Pyrophilous Bacteria and Fungi from Burned Soil

A live microbial culture is invaluable to assess traits and functions, yet culturing immediately from fresh soil is logistically challenging and media selection is not trivial. Deeper ecological understanding of pyrophilous microbes and their traits is hampered by a lack of culture-based work causing researchers to rely heavily on community sequence analysis. To improve our understanding of isolating pyrophilous bacteria and fungi after wildfires from burned soil, we tested which: 1) soil storage method and 2) media retained highest genera richness and highest culturable viability as measured by CFUs retained. We tested four soil storage methods (dried, refrigerated at 4{degrees}C, stored at -80{degrees}C with or without glycerol) using a well-homogenized soil sample, plated microbes on rich media, and compared to fresh soil obtained 6 months after a severe California shrubland wildfire. From the fresh soils, we tested 3 media types: rich (Lysogeny Broth (LB) for bacteria; Malt Yeast Agar (MYA) for fungi), oligotrophic (Reasoners 2 Agar (R2A)) and media made from pyrogenic organic matter (PyOM). For bacteria, storing soil frozen at -80{degrees}C without glycerol yielded the highest genera richness and with glycerol preserved the most species. For fungi, storing soil at -80{degrees}C without glycerol preserved the most species but preserved equivalent richness of genera as fresh and 4{degrees}C soil. R2A yielded the highest bacterial and fungal genus richness but some species of interest were only captured with PyOM. Using a combination of these storage and media methods along with a few additional techniques (mushroom cultivation, smoke cultivation, etc.) from 2018-2022, we cultured >500 isolates (286 bacteria; 258 fungi) after 7 California wildfires for testing pyrophilous microbial traits. ImportanceFires are increasing in frequency and severity across the globe, making the understanding of the traits of the pyrophilous microbes that survive and thrive post-fire and influence post-fire ecosystem regeneration critical and pressing. Yet, our ability to characterize the traits of pyrophilous microbes through genomics, transcriptomics, and phenotypic assays is hampered by lack of organisms in culture. Here, we debut a new medium created from pyrogenic organic matter that helps to cultivate fastidious pyrophilous microbes, and also describe a large-scale culture collection of pyrophilous bacteria and fungi (>500 isolates) that can be used for future collaborative research. We comprehensively test how soil storage and media type affect the cultivation of both bacteria and fungi, and for the first time, we test the best method to store soil to retain fungal diversity. Our work can be applied to improve culture collections of fastidious microbes from a variety of environments.

microbiology↗

bioRxiv2024

Chaparral wildfire shifts the functional potential for soil pyrogenic organic matter and nitrogen cycling

Wildfires reshape soil microbiomes and chemistry, enhancing nitrogen availability and leaving behind pyrogenic organic matter (PyOM), a difficult to degrade carbon substrate potentially used by pyrophilous or "fire-loving" microbes. Understanding whether pyrophilous bacteria can metabolize post-fire resources is critical for predicting the fate of both carbon and nitrogen. We explored how secondary succession of pyrophilous bacteria align with changes in functional gene composition, particularly genes related to PyOM degradation and microbial nitrogen metabolism using shotgun metagenomics on 30 burned and unburned soils collected at 17, 25, 34, 131, and 376 days after a high-severity wildfire in a fire-adapted chaparral in Southern California. In burned soils, genes for PyOM degradation increased over time by 167% and for inorganic nitrogen cycling by 117%, while unburned soils showed no significant changes. Genes encoding catechol and protocatechuate, intermediates in the PyOM degradation pathway, indicate that the easier-to-degrade ortho-cleavage pathways consistently dominated the burned plots. These pathways co-occurred with genes for nitrification and nitrogen retention, including assimilatory and dissimilatory nitrate reduction to ammonia (DNRA). We also identified 446 bacterial metagenome-assembled genomes (MAGs) and linked gene profiles to dominant taxa and found that increases in genes for PyOM and nitrogen cycling paralleled the dominance of pyrophilous Massilia and Noviherbaspirillum, which encoded distinct pathways for PyOM and inorganic nitrogen use over time. Together, these findings reveal previously unrecognized functional shifts in bacterial communities over a high-resolution successional timeline, providing insights into the long-term impact of fire on microbial-mediated ecosystem processes that shape soil carbon and nitrogen dynamics.

microbiology↗

bioRxiv2021

Bacterial and fungal communities experience rapid succession during the first year following a wildfire in a California chaparral.

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.

microbiology↗

bioRxiv2021

Prescribed versus wildfire impacts on exotic plants and soil microbes in California grasslands

O_LIPrescribed fire is often used as a management tool to decrease exotic plant cover and increase native plant cover in grasslands. These changes may also be mediated by fire impacts on soil microbial communities, which drive plant productivity and function. Yet, the ecological effects of prescribed burns compared to wildfires on either plant or soil microbial composition remain unclear. C_LIO_LIHere, we investigated the impacts of a spring prescribed fire versus a fall wildfire on plant cover and community composition and bacterial and fungal richness, abundance, and composition in a California grassland. We used qPCR of 16S and 18S to assess impacts on bacterial and fungal abundance and Illumina MiSeq of 16S and ITS2 to assess impacts on bacterial and fungal richness and composition. C_LIO_LIWildfire had stronger impacts than prescribed fire on microbial communities and both fires had similar impacts on plants with both prescribed and wildfire reducing exotic plant cover but neither reducing exotic plant richness. Fungal richness declined after the wildfire but not prescribed fire, but bacterial richness was unaffected by either. Yet increasing char levels in both fire types resulted in reduced bacterial and fungal biomass, and both fire types slightly altered bacterial and fungal composition. C_LIO_LIExotic and native plant diversity differentially affected soil microbial diversity, with native plant diversity leading to increased arbuscular mycorrhizal fungal richness while exotic plant diversity better predicted bacterial richness. However, the remainder of the soil microbial communities were more related to aspects of soil chemistry including cation exchange capacity, organic matter, pH and phosphorous. C_LIO_LISynthesis and applications. Understanding the different ecological effects of prescribed fires and wildfires on plant and soil communities are key to enhancing a prevalent management action and to guide potential management opportunities post wildfires. Our coupled plant and soil community sampling allowed us to capture the sensitivity of the fungal community to fire and highlights the importance of potentially incorporating management actions such as soil or fungal amendments to promote this critical community that mediates native plant performance. C_LI

ecology↗

bioRxiv2021

Mega-fire in Redwood Tanoak Forest Reduces Bacterial and Fungal Richness and Selects for Pyrophilous Taxa and Traits that are Phylogenetically Conserved

Mega-fires of unprecedented size, intensity, and socio-economic impacts have surged globally due to climate change, fire suppression, and development. Soil microbiomes are critical for post-fire plant regeneration and nutrient cycling, yet how mega-fires impact the soil microbiome remains unclear. We had a serendipitous opportunity to obtain pre- and post-fire soils from the same sampling locations because the 2016 Soberanes Fire, a mega-fire burning >500 Km2, burned with high severity throughout several of our established redwood-tanoak plots. This makes our study the first to examine microbial fire response in redwood-tanoak forests. We re-sampled soils immediately post-fire from two burned plots and one unburned plot to elucidate the effect of mega-fire on soil microbiomes. We used Illumina MiSeq sequencing of 16S and ITS1 to determine that both bacterial and fungal richness were reduced by 38-70% in burned plots, with richness unchanged in the unburned plot. Fire altered composition by 27% for bacteria and 24% for fungi, whereas the unburned plots experienced no change in fungal and negligible change in bacterial composition. We observed several pyrophilous taxa previously observed in Pinaceae forests, indicating that these microbes are likely general fire-responders across forest types. Further, the pyrophilous taxa that positively responded to fire were phylogenetically conserved, suggesting shared evolutionary traits. For bacteria, fire selected for increased Firmicutes and Actinobacteria. For fungi, fire selected for the Ascomycota classes Pezizomycetes and Eurotiomycetes and for a Basidiomycota class of heat-resistant Geminibasidiomycete yeasts. We hypothesize that microbes share analogous fire response to plants and propose a trait-based conceptual model of microbial response to fire that builds from Grimes Competitor-Stress tolerator-Ruderal framework (C-S-R) and its recent applications to microbes. Using this framework and established literature on several microbial species, we hypothesize some generalizable principals to predict which microbial taxa will respond to fire.

ecology↗

bioRxiv2020

High resilience of the mycorrhizal community to prescribed seasonal burnings in a Mediterranean woodland

Fire effects on ecosystems range from destruction of aboveground vegetation to direct and indirect effects on belowground microorganisms. Although variation in such effects is expected to be related to fire severity, another potentially important and poorly understood factor is the effects of fire seasonality on soil microorganisms. We carried out a large-scale field experiment examining the effects of spring versus autumn burns on the community composition of soil fungi in a typical Mediterranean woodland. Although the intensity and severity of our prescribed burns were largely consistent between the two burning seasons, we detected differential fire season effects on the composition of the soil fungal community, driven by changes in the saprotrophic fungal guild. The community composition of ectomycorrhizal fungi, assayed both in pine seedling bioassays and from soil sequencing, appeared to be resilient to the variation inflicted by seasonal fires. Since changes in the soil saprotrophic fungal community can directly influence carbon emission and decomposition rates, we suggest that regardless of their intensity and severity, seasonal fires may cause changes in ecosystem functioning. DeclarationsO_ST_ABSFundingC_ST_ABSThis research was co-supported by the United States-Israel Binational Science Foundation (BSF Grant 2012081) and Tel-Hai College. Conflicts of interest/Competing interestsWe declare no conflicts of interest and that this material has not been submitted for publication elsewhere. Ethics approvalNot applicable Consent to participateNot applicable Consent for publicationNot applicable Availability of data and materialSequences were submitted to the National Center for Biotechnology Information Sequence Read Archive under accession numbers SRRXXX{square}SRRXXX. Code availabilityNot applicable Authors contributionsOO HS TB YO YC conceived and designed the experiment. SSL YA HM AT performed the experiment. SIG provided the pipeline scripts, and guidance in bioinformatics work and analyses. SLL OO HS wrote the paper and analyzed the data, and all authors contributed substantially to revisions.

ecology↗

bioRxiv2019

Soil microbial communities associated with giant sequoia: How does the world’s largest tree affect some of the world’s smallest organisms?

Giant sequoia (Sequoiadendron giganteum) is an iconic conifer that lives in relic populations on the western slopes of the California Sierra Nevada. In these settings it is unusual among the dominant trees in that it associates with arbuscular mycorrhizal fungi rather than ectomycorrhizal fungi. However, it is unclear whether differences in microbial associations extends more broadly to non-mycorrhizal components of the soil microbial community. To address this question we characterized microbiomes associated with giant sequoia and co-occurring sugar pine (Pinus lambertiana) by sequencing 16S and ITS1 of the bulk soil community at two groves with distinct parent material. We found tree-associated differences were apparent despite a strong grove effect. Bacterial/archaeal richness was greater beneath giant sequoia than sugar pine, with a unique core community that was double the size. The tree species also harbored compositionally distinct fungal communities. This pattern depended on grove but was associated with a consistently elevated relative abundance of Hygrocybe species beneath giant sequoia. Compositional differences between host trees correlated with soil pH, calcium availability, and soil moisture. We conclude that the effects of giant sequoia extend beyond mycorrhizal mutualists to include the broader community, and that some but not all host tree differences are grove-dependent.

ecology↗

bioRxiv2019

Native and invasive populations of the ectomycorrhizal death cap Amanita phalloides are highly sexual but dispersal limited

The authors have withdrawn this manuscript and do not wish it to be cited. As we have moved more deeply into population genomics, we have discovered the analyses we initially used do not answer our questions well. We are recalibrating and intend to submit a new manuscript in the future. If you have any questions, please contact the corresponding author.

microbiology↗

bioRxiv2018

Ecological patterns are robust to use of exact sequence variants versus operational taxonomic units

Recent controversy focuses on the best method for delineating microbial taxa, based on either traditional operational taxonomic units (OTUs) or exact sequence variants (ESVs) of marker gene sequences. We sought to test if the binning approach (ESVs versus OTUs) affected the ecological conclusions of a large field study. The dataset included sequences of both bacteria (16S) and fungi (ITS), across multiple environments diverging markedly in abiotic conditions, over three collection times. Despite quantitative differences in microbial richness, we found that all alpha- and beta-diversity metrics were highly positively correlated (r > 0.90) between samples analyzed with both approaches. Moreover, the community composition of the dominant taxa did not vary between approaches. Consequently, statistical inferences were nearly indistinguishable. Thus, we conclude that for typical alpha- and beta-diversity analyses, OTU or ESV methods will likely reveal similar ecological results and determining which method to employ will depend on the question at hand.

microbiology↗