Biology subjects

Alexander, J. M.

Publications and source records attributed to Alexander, J. M..

11 recordsLinked to original sources

bioRxiv2026

Linking plant-soil feedback with resource competition to understand plant coexistence

1. Plant-soil feedback (PSF) is increasingly recognized as an important mechanism influencing plant coexistence, but most studies have examined PSF in isolation under controlled conditions. Under natural conditions, PSF operates together with other processes such as resource competition, yet how these processes jointly shape plant coexistence across environmental gradients remains poorly understood. 2. We combined field and greenhouse experiments to assess the contribution of PSF to plant coexistence at low- and high-elevation sites in the Swiss Alps. In the field, we quantified total niche and fitness differences and predicted interaction outcomes for nine plant species pairs, integrating PSF, resource competition, and other processes. In a complementary greenhouse experiment, we used soil microbial communities conditioned during the field experiment to isolate PSF-driven niche and fitness differences for the same species pairs. 3. PSF alone generated strong fitness differences but weak niche differences in the greenhouse experiment, predominantly predicting competitive exclusion. Interaction outcomes predicted from PSF alone corresponded poorly with those in the field, suggesting that PSF in isolation poorly explain plant coexistence under natural conditions. Nevertheless, PSF-driven niche and fitness differences were related to those quantified in the field, which were likely driven largely by resource competition, suggesting that PSF may contribute to coexistence by reinforcing or counteracting other ecological processes. These relationships varied between elevations, highlighting the context dependence of PSF contributions to coexistence. 4. Synthesis. Our study shows that the impacts of plant-soil feedback on plant coexistence cannot be understood from their effects in isolation. Instead, their contribution depends on how they interact with other ecological processes and on the environmental context in which these processes operate. Together, our findings emphasize the need to move beyond studying PSF in isolation towards quantifying how it combines with other mechanisms that drives coexistence under natural conditions.

ecology↗

bioRxiv2026

Neutrophils rapidly release nucleoli-stored IFNα during infection

Type I interferons (IFN-I) are critical for antiviral defense but can drive severe pathology when dysregulated. Excess IFN-I is associated with prominent neutrophil accumulation; however, the contribution of neutrophils to IFN-I overproduction remains underexplored. In all cell types previously studied, IFN-I is synthesized de novo following sensing of microbial or host-derived inflammatory stimuli. Contrary to this paradigm, we find that neutrophils express IFN during development and store it in the nucleolus, a membrane-less intranuclear condensate classically functioning in ribosome biogenesis. TLR-mediated bacterial sensing induces a nucleolar stress response in neutrophils that triggers rapid release of nucleoli-stored IFN independent of de novo protein synthesis. These findings reveal that neutrophils have repurposed the nucleolus as a cytokine storage and secretory organelle, identify the first naturally occurring immunoregulatory function of nucleolar stress, and provide insight into the relationship between detrimental IFN-I levels and neutrophil accumulation.

immunology↗

bioRxiv2024

Darwin's Naturalization Conundrum explained by gradients of environmental stress and disturbance

Darwins Naturalization Conundrum (DNC) states that non-native species closely related to the native community are either more likely to succeed because shared adaptations help them overcome environmental filtering, or less likely to succeed because of strong competition with their native relatives. Despite extensive research, no general patterns have so far emerged. One reason may be that the relative importance of competition and environmental filtering depends on environmental conditions. To test this hypothesis, we conducted a global assessment of DNC examining patterns of phylogenetic relatedness of non-native plant species to the native community along gradients of elevation and anthropogenic disturbance in mountains. Phylogenetic distance of non-native to native species decreased with increasing elevation and in disturbed plant communities. Our results help resolve DNC by showing that the environmental context sets expectations for patterns of relatedness between non-native and native species and helps illuminate the ecological and evolutionary processes generating these patterns.

ecology↗

bioRxiv2024

Functional traits predict outcomes of current and novel competition under warmer climate

Functional traits offer a potential avenue to generalize and forecast the impacts of changing competition on plant communities, including changing outcomes of competition among species that currently interact (current competition) or that will interact in the future following range shifts (novel competition). However, it remains unclear how well traits explain variation in the outcomes of current and novel competition, as well as the underlying processes determining coexistence or competitive exclusion, under changing climate. Here, we conducted a field experiment in which pairs of high and low-elevation species interacted in three sites across an elevation gradient in the Swiss Alps. For each species pair, we quantified the population-level outcomes of competition (invasion growth rates), relative fitness differences and niche overlap and related these to 15 functional traits that were measured in each site. Most traits were significantly associated with invasion growth rates at the low elevation, where species had greater relative fitness differences, but these associations were much weaker towards higher elevations. This appears to be because traits, particularly those associated with light competition, captured species relative fitness differences at lower elevations, but not at the high elevation site. Greater relative fitness differences towards lower elevations suggest that climate warming may increase the likelihood of competitive exclusion of species that are poor competitors for light. In addition, novel competitors tended to show greater niche overlap than current competitors, leading to stronger overall competitive effects. But in general, trait differences predicted competitive outcomes of novel and current competitors similarly well, suggesting that traits can be used to predict interactions between species that do not yet interact. Our study reinforces the importance of considering changing interactions for predicting species responses to climate change and provides experimental evidence supporting the usefulness of functional trait differences in forecasting the impacts of future plant interactions under changing climate.

ecology↗

bioRxiv2023

Deep learning to extract the meteorological by-catch of wildlife cameras

Microclimate - proximal climatic variation at scales of meters and minutes - can exacerbate or mitigate the impacts of climate change on biodiversity. However, most microclimate studies are temperature-centric, and do not consider meteorological factors such as sunshine, hail and snow. Meanwhile, remote cameras have become a primary tool to monitor wild plants and animals, even at micro-scales, with deep learning tools to rapidly convert images into ecological data. However, deep learning applications for wildlife imagery have focused exclusively on living subjects. Here, we identify an overlooked opportunity to extract latent, yet ecologically relevant, meteorological information. We produce an annotated image dataset of micrometeorological conditions across 49 wildlife cameras in South Africas Maloti-Drakensberg and the Swiss Alps. We train ensemble deep learning models to classify conditions as overcast, sunshine, hail or snow. Our best model achieves 91.7% accuracy on test cameras not seen during training. Furthermore, we show how effective accuracy is raised to 96% by disregarding 14.1% of classifications where ensemble member models did not reach a consensus. Unlike previous studies we test model performance in remote and novel locations, distinguishing overcast and sunny conditions in Svalbard, Norway with 79.3% accuracy (93.9% consensus accuracy). Our model rapidly classifies sunshine, snow and hail in almost 2 million unlabeled images. Resulting micrometeorological data illustrated common seasonal patterns of summer hailstorms and autumn snowfalls across mountains in the northern and southern hemispheres. However, daily patterns of sunshine and shade diverged between sites, impacting daily temperature cycles. Crucially, we leverage micrometeorological data to demonstrate that (1) experimental warming using open-top chambers shortens early snow events in autumn, and (2) image-derived sunshine marginally outperforms sensor-derived temperature when predicting bumblebee foraging. These methods generate novel micrometeorological variables in synchrony with biological recordings, enabling new insights from an increasingly global network of wildlife cameras.

ecology↗

bioRxiv2023

Leaf metabolic traits reveal hidden dimensions of plant form and function

The plant metabolome encompasses the biochemical mechanisms through which evolutionary and ecological processes shape plant form and function1,2. However, while the metabolome should thus be an important component of plant life-history variation3, we know little about how it varies across the plant kingdom. Here, we use the plant functional trait concept4 - a powerful framework for describing plant form and function5-7 - to interpret leaf metabolome variation among 457 tropical and 339 temperate plant species. Distilling metabolite chemistry into five discriminant metabolic functional traits reveals that plants vary along two major axes of leaf metabolic specialization - a leaf chemical defense spectrum and an expression of leaf longevity. These axes are qualitatively consistent for tropical and temperate species, with many trait combinations being viable. However, axes of leaf metabolic specialization vary orthogonally to life-history strategies described by widely used functional traits5-7, while being at least equally important to them. Our findings question classical trait6 and plant defense8 theory that predicts relationships between the leaf chemical phenotype, plant productivity, and pace of life. Moreover, we show that metabolic functional traits describe unique dimensions of plant life-history variation that are complementary to, and independent from, those captured by existing plant functional traits.

ecology↗

bioRxiv2022

Unravelling drivers of local adaptation through Evolutionary Functional-Structural Plant modelling

O_LILocal adaptation to contrasting environmental conditions along environmental gradients is a widespread phenomenon in plant populations, yet we lack a mechanistic understanding of how individual agents of selection contribute to local adaptation. C_LIO_LIHere, we developed a novel evolutionary functional-structural plant (E-FSP) model that simulates local adaptation of virtual plants along an environmental gradient. First, we validate the model by testing if it can recreate two elevational ecotypes of Dianthus carthusianorum occurring in the Swiss Alps. Second, we use the E-FSP model to disentangle the relative contribution of abiotic (temperature) and biotic (competition and pollination) selection pressures to elevational adaptation in D. carthusianorum. C_LIO_LIThe model reproduced the qualitative differences between the elevational ecotypes in two phenological (germination and flowering time) and one morphological trait (stalk height), as well as qualitative differences in four performance variables that emerge from GxE interactions (flowering time, number of stalks, rosette area and seed production). Our results suggest that elevational adaptation in D. carthusianorum is predominantly driven by the abiotic environment. C_LIO_LIOur approach shows how E-FSP models incorporating physiological, ecological and evolutionary mechanisms can be used in combination with experiments to examine hypotheses about patterns of adaptation observed in the field. C_LI

evolutionary biology↗

bioRxiv2022

Microbial invasion of a toxic medium is facilitated by a resident community but inhibited as the community co-evolves

Predicting whether microbial invaders will colonize an environment is critical for managing natural and engineered ecosystems, and controlling infectious disease. Invaders often face competition by resident microbes. But how invasions play out in communities dominated by facilitative interactions is less clear. We previously showed that growth medium toxicity can promote facilitation between four bacterial species, as species that cannot grow alone rely on others to survive. Following the same logic, here we allowed other bacterial species to invade the four-species community, and found that invaders could more easily colonize a toxic medium when the community was present. In a more benign environment instead, invasive species that could survive alone colonized more successfully when the residents were absent. Next, we asked whether early colonists could exclude future ones through a priority effect, by inoculating the invaders into the resident community only after its members had co-evolved for 44 weeks. Compared to the ancestral community, the co-evolved resident community was more competitive toward invaders, and less affected by them. Our experiments show how communities may assemble by facilitating one another in harsh, sterile environments, but that arriving after community members have co-evolved can limit invasion success.

microbiology↗

bioRxiv2022

Competition contributes to both warm and cool range edges

Competition plays an important role in shaping species spatial distributions. However, it remains unclear where and how competition regulates species range limits. In a field experiment with plants originating from low and high elevations and conducted across an elevation gradient in the Swiss Alps, we find that both lowland and highland species can better persist in the presence of competition within than beyond their elevation ranges, suggesting that competition helps set both lower and upper elevation range limits of these species. Furthermore, the reduced ability of pairs of lowland or highland species to coexist beyond their range edges is mainly driven by diminishing niche differences; changes in both niche differences and relative fitness differences drive weakening competitive dominance of lowland over highland species with increasing elevation. These results highlight the need to account for competitive interactions and investigate underlying coexistence mechanisms to understand current and future species distributions.

ecology↗

bioRxiv2021

Lowland plant migrations into alpine ecosystems amplify soil carbon loss under climate warming

Climate warming is releasing carbon from soils around the world1-3, constituting a positive climate feedback. Warming is also causing species to expand their ranges into new ecosystems4-9. Yet, in most ecosystems, whether range expanding species will amplify or buffer expected soil carbon loss is unknown10. Here we used two whole-community transplant experiments and a follow-up glasshouse experiment to determine whether the establishment of herbaceous lowland plants in alpine ecosystems influences soil carbon content under warming. We found that warming (transplantation to low elevation) led to a negligible decrease in alpine soil carbon content, but its effects became significant and 52% {+/-} 31% (mean {+/-} 95% CIs) larger after lowland plants were introduced at low density into the ecosystem. We present evidence that decreases in soil carbon content likely occurred via lowland plants increasing rates of root exudation, soil microbial respiration and CO2 release under warming. Our findings suggest that warming-induced range expansions of herbaceous plants have the potential to alter climate feedbacks from this system, and that plant range expansions among herbaceous communities may be an overlooked mediator of warming effects on carbon dynamics.

ecology↗

bioRxiv2018

Live-Cell Imaging Reveals Enhancer-dependent Sox2 Transcription in the Absence of Enhancer Proximity

Enhancers are important regulatory elements that can control gene activity across vast genetic distances. However, the underlying nature of this regulation remains obscured because it has been difficult to observe in living cells. Here, we visualize the spatial organization and transcriptional output of the key pluripotency regulator Sox2 and its essential enhancer Sox2 Control Region (SCR) in living embryonic stem cells (ESCs). We find that Sox2 and SCR show no evidence of enhanced spatial proximity and that spatial dynamics of this pair is limited over tens of minutes. Sox2 transcription occurs in short, intermittent bursts in ESCs and, intriguingly, we find this activity demonstrates no association with enhancer proximity, suggesting that direct enhancer-promoter contacts do not drive contemporaneous Sox2 transcription. Our study establishes a framework for interrogation of enhancer function in living cells and supports an unexpected mechanism for enhancer control of Sox2 expression that uncouples transcription from enhancer proximity.

genetics↗