Biology subjects

Allison, S. D.

Publications and source records attributed to Allison, S. D..

9 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

A life-history axis of resource acquisition in bacteria: depolymerisation versus uptake

Microbial decomposition of complex organic matter is a major control on the global carbon cycle, and its efficiency hinges on how microbes acquire resources. Decomposition requires costly extracellular enzymes to break down complex polymers, whereas the resulting soluble products are captured far more cheaply through membrane transporters. How microbes balance investment between these two processes is a fundamental axis of microbial life history, yet it has remained difficult to quantify across their vast diversity. Using genomic repertoires for carbohydrate depolymerisation and uptake, we developed a simple ratio distinguishing depolymerisation-optimised from uptake-optimised strategies, and applied it to more than 249,000 environmental and host-associated bacterial genomes. These strategies were strongly phylogenetically structured and differed by habitat, with uptake-optimised bacteria unexpectedly more prevalent in diffusion-limited soils than in aquatic environments. In an 18-month field-scale plant litter decomposition experiment, uptake-optimised bacteria dominated during early decomposition, when fungi were more abundant and strongly expressed hydrolytic enzymes, shifting towards depolymerisation-optimised bacteria at later stages. A simple genomic ratio therefore captures ecologically meaningful resource-acquisition strategies that vary with phylogeny, habitat and successional stage. The balance of these strategies could shape community-level extracellular enzyme investment, with consequences for decomposition and carbon cycling.

microbiology↗

bioRxiv2026

The response of leaf litter bacterial communities to simulated drought depends on temperature

Microbial communities regulate carbon and nitrogen (N) cycling, yet their long-term responses to chronic global changes remain unclear. Using 12 years of grassland litter samples from the Loma Ridge Global Change Experiment in Irvine, California, we tested whether interactions between experimental drought and N deposition, and previously observed temporal variability are driven by background climatic conditions, including precipitation and temperature. Consistent with short-term studies, drought and N addition had relatively small effects on bacterial community composition compared to pronounced seasonal and interannual variability, with drought-by-year interactions explaining more variation than drought alone. Seasonal shifts were largely driven by short-term fluctuations in rainfall and temperature, whereas the substantial interannual variability in community composition was not captured by site-level climate metrics. Contrary to expectations, drought effects were influenced more by background temperature than precipitation, with the strongest effects observed in cooler years. Lastly, a bacterial taxons sensitivity to climate variability under ambient conditions did not predict its response to chronic drought. Together, our findings show that bacterial responses to drought are temporally dynamic and influenced by background temperature, underscoring the need for long-term longitudinal studies of soil microbial communities to better predict microbial responses under future global change. ImportanceMicrobial responses to global change, particularly drought and nitrogen addition, are often inferred from short-term studies (< 2 years), yet natural temporal variability may overshadow experimental effects. Using a 12-year dataset of grassland leaf litter communities, we show that temporal variability, both seasonal and interannual, exert a stronger influence on bacterial community composition than chronic drought or nitrogen deposition. These findings challenge assumptions about the magnitude of drought effects, particularly in naturally drought-affected ecosystem such as California grasslands and highlight the importance of long-term datasets for predicting microbial responses to climate change. By demonstrating that bacterial communities are strongly shaped by background climatic variability (baseline precipitation and temperature independent of imposed chronic treatments) and may be buffered to sustained drought, this work improves forecasts of ecosystem responses and informs the design of global change experiments and restoration strategies in future research studies.

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

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↗

bioRxiv2024

Bacterial population-level trade-offs between drought tolerance and resource acquisition traits impact decomposition

Microbes drive fundamental ecosystem processes such as decomposition. Environmental stressors are known to affect microbes, their fitness, and the ecosystem functions that they perform, yet understanding the causal mechanisms behind this influence has been difficult. We used leaf litter on soil surface as a model in situ system to assess changes in bacterial genomic traits and decomposition rates over 18 months with drought as a stressor. We hypothesized that genome-scale trade-offs due to investment in stress tolerance traits under drought reduce the capacity for bacterial populations to carry out decomposition; and that these population-level trade-offs scale up to impact emergent community traits thereby reducing decomposition rates. We observed drought tolerance mechanisms that were heightened in bacterial populations under drought, identified as higher gene copy numbers in metagenome-assembled genomes. A subset of populations under drought had reduced carbohydrate-active enzyme genes which suggested - as a trade-off - a decline in decomposition capabilities. These trade-offs were taxonomically structured as distinct patterns appeared in populations across families. We show that trait-tradeoffs in bacterial populations under drought could scale up to reduce overall decomposition capabilities and litter decay rates. Using a trait-based approach to assess the population ecology of soil bacteria, we demonstrate genome-level trade-offs in response to drought with consequences for decomposition rates.

ecology↗

bioRxiv2019

Physiological adaptations of leaf litter microbial communities to long-term drought

Drought represents a significant stress to soil microorganisms and is known to reduce microbial activity and organic matter decomposition in Mediterranean ecosystems. However, we still lack a detailed understanding of the drought stress adaptations of microbial decomposers. We hypothesised that drought causes greater microbial allocation to stress tolerance relative to growth pathways. Here we present metatranscriptomic and metabolomic data on the physiological response of in situ microbial communities on plant leaf litter to long-term drought and pulse wetting in Californian grass and shrub ecosystems. Wetting litter after a long dry summer caused only subtle shifts in gene expression. On grass litter, communities from the decade-long ambient and reduced precipitation treatments had distinct functional profiles. The most discernable physiological adaptations to drought were production or uptake of compatible solutes to maintain cellular osmotic balance, and synthesis of capsular and extracellular polymeric substances as a mechanism to retain water. The results show a clear functional response to drought in grass litter communities with greater allocation to survival relative to growth that could affect decomposition under drought. In contrast, communities on chemically more diverse and complex shrub litter had smaller physiological differences in response to long-term drought but higher investment in resource acquisition traits across treatments, suggesting that the functional response to drought is constrained by substrate quality. Our findings suggest, for the first time in a field setting, a trade-off between microbial drought stress tolerance, resource acquisition and growth traits in leaf litter microbial communities.

microbiology↗

bioRxiv2018

Soil microbial communities with greater investment in resource acquisition have lower growth yield

Resource acquisition and growth yield are fundamental traits of microorganisms that have consequences for ecosystem functioning. However, there is a lack of empirical observations linking these traits. Using a landscape-scale survey of temperate near-neutral pH soils, we show tradeoffs in key community-level parameters linked to these traits. Increased investment into extracellular enzymes was associated with reduced growth yield; this reduction was linked more to carbon than nitrogen acquisition enzymes suggesting smaller stoichiometric constraints on community metabolism in examined soils.

ecology↗

bioRxiv2018

Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change

Microorganisms are critical in terrestrial carbon cycling because their growth, activity and interactions with the environment largely control the fate of recent plant carbon inputs, as well as the stability of assimilated carbon (Gleixner, 2013; Schimel and Schaeffer, 2012). Soil carbon stocks reflect a balance between microbial decomposition and stabilization of organic carbon. The balance can shift under altered environmental conditions (Davidson and Janssens, 2006), and new research suggests that knowledge of microbial physiology may be critical for projecting changes in soil carbon and improving the prognosis of climate change feedbacks (Allison et al., 2010; Bradford et al., 2016; Liang et al., 2017; Wieder et al., 2015). Still, predicting the ecosystem implications of microbial processes remains a challenge. Here we argue that this challenge can be m ...

ecology↗