Biology subjects

Homyak, P. M.

Publications and source records attributed to Homyak, P. M..

7 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

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

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↗

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↗