Biology subjects

Stone, B.

Publications and source records attributed to Stone, B..

7 recordsLinked to original sources

bioRxiv2026

Apparent generalism in Pseudomonas aeruginosa is underpinned by Convergent, Cryptic Specialization

Microbes that span environmental reservoirs and diverse human infections are often described as generalists or as ubiquitous, yet ecological theory predicts generalism should be unstable when specialists outperform within any one niche. Here we show that Pseudomonas aeruginosas apparent ecological breadth reflects convergent, cryptic specialism (CCS) - repeatable, environment-linked genomic differentiation that is not confined to deep lineages - rather than strict specialism or generalism. An analysis of 6,627 genomes with source-environment metadata reveals that environments are broadly dispersed across the phylogeny, inconsistent with lineage-locked specialization. Despite this shallow phylogenetic structure, genome content predicted environment-of-isolation across nine genotype-discernible environments, including under cross-validation that blocks phylogenetic relatedness. Interpretable feature profiles recovered both shared and environment-specific signals, including genomic signatures distinguishing distinct chronic and acute human infections. Finally, phenotypes from 47 diverse strains clustered more strongly by environmental source than by phylogenetic relatedness. Together, these results indicate that widely distributed bacterial "generalists" can comprise mixtures of cryptic, convergent specialists. By mapping genotype-defined ecological structure, our approach can identify when apparent generalists harbor hidden structure relevant to infection risk.

microbiology↗

bioRxiv2025

An Amygdalar Oscillatory Switch Governs Valence Assignment

Reward pursuit and punishment avoidance are among the most fundamental behaviors necessary for survival. The binary valuation of an experience as either positive or negative - "valence assignment" - is imperative for successful navigation of a regularly updating environment. Mounting evidence highlights the critical role of valence responsive basolateral amygdala (BLA) ensembles in coding valence information. However, how BLA ensembles are recruited to drive real-time valence assignment remains elusive. Here, we show locus coeruleus (LC)-derived norepinephrine coordinates this neural computational process via modulatory control over network-organizing BLA parvalbumin-expressing (PV) interneuron activity. Specifically, optogenetic activation of LC to BLA noradrenergic terminals (LC-BLANE) drives real-time negative valence assignment and suppression of BLA fast gamma oscillatory activity via BLA interneuronal 1a adrenergic receptor signaling. Conversely, positive valence assignment also requires BLA PV interneuron activity but is associated with an enhancement of local fast gamma power. Together, these converging data highlight a PV-driven amygdalar oscillatory switch that governs valence assignment.

neuroscience↗

bioRxiv2025

Specialist Generalist Trade Offs in Microbial Growth Rates Across Soil Habitats

Microbial ecological strategies are shaped by a fundamental trade-off: is it better to specialize and thrive in a narrow niche or generalize and persist across diverse environments? In soils, this trade-off is particularly relevant in the rhizosphere and detritusphere, where microorganisms encounter distinct resource inputs from living and decaying roots. Using H {superscript 1} O quantitative stable isotope probing (qSIP), we measured in situ bacterial and fungal growth rates in the rhizosphere, the root detritusphere, and in the combined presence of rhizosphere + root detritus to test whether specialists--microbes growing in a single habitat--grow faster than generalists that persist across multiple environments. Specialists grew consistently faster than generalists, suggesting a trade-off between the breadth of environmental conditions a microorganism can tolerate and its ability to grow quickly in a specific habitat. This cost to broad niche adaptation was apparent for bacteria, but growth rates of fungal saprotrophs varied little between specialists and generalists, reflecting how fundamental differences in life-history strategies between bacteria and fungi can shape microbial responses to resource availability and habitat heterogeneity. Net relatedness and nearest taxon indices indicated total bacterial communities were phylogenetically clustered while specialist and generalist communities were phylogenetically random, suggesting that functional traits, not lineage, best predict ecological strategy. In annual grassland soils, fast-growing specialists may dominate ecosystem processes when resources abound, and slow-growing generalists may sustain element transformations when conditions shift; understanding this interplay is key to predicting soil-carbon trajectories.

microbiology↗

bioRxiv2024

Metrics based on habitat area and condition are poor proxies for invertebrate biodiversity

There is increasing demand for standardised, easy-to-use metrics to assess progress towards achieving biodiversity targets and the effectiveness of ecological compensation schemes. Biodiversity metrics based on combining habitat area and habitat condition scores are proliferating rapidly, but there is limited evidence on how they relate to ecological outcomes. Here, we test the relationship between the statutory biodiversity metric used for Biodiversity Net Gain (BNG) in England -- and as the basis for new biodiversity credit systems around the world -- and invertebrate richness, abundance, and community composition. We find that the combined area-condition BNG metric does not capture the value of arable farmland and grassland sites for invertebrate biodiversity: invertebrate communities were highly variable across sites that had the same type and condition under the BNG metric. We found no reliable relationship between scores under the metric and either invertebrate abundance or species richness, with the risk of the metric undervaluing sites of high invertebrate value. Our results highlight the need to incorporate factors beyond habitat type and condition into site evaluations, and to complement metric use with species-based surveys.

ecology↗

bioRxiv2024

Early life stress influences epilepsy outcomes in mice

Stress is a common seizure trigger that has been implicated in worsening epilepsy outcomes. The neuroendocrine response to stress is mediated by the hypothalamic-pituitary-adrenal (HPA) axis and HPA axis dysfunction worsens epilepsy outcomes, increasing seizure burden, behavioral comorbidities, and risk for sudden unexpected death in epilepsy (SUDEP) in mice. Early life stress (ELS) reprograms the HPA axis into adulthood, impacting both the basal and stress-induced activity. Thus, we propose that ELS may influence epilepsy outcomes by influencing the function of the HPA axis. To test this hypothesis, we utilized the maternal separation paradigm and examined the impact on seizure susceptibility. We show that ELS exerts a sex dependent effect on seizure susceptibility in response to acute administration of the chemoconvulsant, kainic acid, which is associated with an altered relationship between seizure activity and HPA axis function. To further examine the impact of ELS on epilepsy outcomes, we utilized the intrahippocampal kainic acid model of chronic epilepsy in mice previously exposed to maternal separation. We find that the relationship between corticosterone levels and the extent of epileptiform activity is altered in mice subjected to ELS. We demonstrate that ELS impacts behavioral outcomes associated with chronic epilepsy in a sex-dependent manner, with females being more affected. We also observe reduced mortality (presumed SUDEP) in female mice subjected to ELS, consistent with previous findings suggesting a role for HPA axis dysfunction in SUDEP risk. These data demonstrate for the first time that ELS influences epilepsy outcomes and suggest that previous life experiences may impact the trajectory of epilepsy.

neuroscience↗

bioRxiv2024

Sex-dependent effects of early life stress on network and behavioral states.

BackgroundAdverse childhood experiences (ACEs) are associated with numerous detriments in health, including increased vulnerability to psychiatric illnesses. Early life stress (ELS) in rodents has been shown to effectively model several of the behavioral and endocrine impacts of ACEs and has been utilized to investigate the underlying mechanisms contributing to disease. However, the precise neural mechanisms responsible for mediating the impact of ELS on vulnerability to psychiatric illnesses remain largely unknown. MethodsWe use behavior, immunoassay, in vivo LFP recording, histology, and patch clamp to describe the effects of ELS on stress behaviors, endocrinology, network states, protein expression, and cellular physiology in male and female mice. ResultsWe demonstrate that a murine maternal separation (MS) ELS model causes sex-dependent alterations in behavioral and hormonal responses following an acute stressor. Local field potential (LFP) recordings in the basolateral amygdala (BLA) and frontal cortex (FC) reveal similar sex-dependent alterations at baseline, in response to acute ethological stress, and during fear memory extinction, supporting a large body of literature demonstrating that these network states contribute to stress reactivity and vulnerability to psychiatric illnesses. Sex differences were accompanied by altered physiology of BLA principal neurons in males and BLA PV interneurons in females. ConclusionsCollectively, these results implicate novel, sex-dependent mechanisms through which ACEs may impact psychiatric health, involving altered cellular physiology and network states involved in emotional processing.

neuroscience↗

bioRxiv2023

Experience-dependent information routing through the basolateral amygdala

The basolateral amygdala (BLA) is an emotional processing hub and is well-established to influence both positive and negative valence processing. Selective engagement of a heterogeneous cell population in the BLA is thought to contribute to this flexibility in valence processing. However, how this process is impacted by previous experiences which influence valence processing is unknown. Here we demonstrate that previous positive (EE) or negative (chronic unpredictable stress) experiences differentially influence the activity of specific populations of BLA principal neurons projecting to either the nucleus accumbens core or bed nucleus of the stria terminalis. Using chemogenetic manipulation of these projection-specific neurons we can mimic or occlude the effects of chronic unpredictable stress or enriched environment on valence processing to bidirectionally control avoidance behaviors and stress-induced helplessness. These data demonstrate that previous experiences influence the responsiveness of projection-specific BLA principal neurons, biasing information routing through the BLA, to govern valence processing.

neuroscience↗