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bioRxiv2026

Environmental sensing capacity predicts bacterial ecological strategies and environmental preferences

The ability to sense environmental variation is a prerequisite for ecological success. Sensor domains enable bacteria to detect nutrients, neighboring organisms, and physicochemical conditions, but whether variation in these sensing systems reflects ecological specialization remains unresolved. Here, we analyzed sensor domains across 51,343 bacterial genomes and 255 soil metagenomes spanning a climatic gradient to determine whether sensory repertoires encode bacterial ecological strategies and environmental preferences. Sensory repertoires exhibited strong phylogenetic conservatism and revealed signatures of genome streamlining, indicating that environmental sensing reflects trade-offs associated with maintaining sensory complexity. Taxa occupying environmentally heterogeneous habitats, particularly free-living aerobic generalists, encoded the largest sensory repertoires, consistent with selection for expanded environmental information processing. To link sensory function with ecological adaptation, we mapped experimentally-characterized ligand-binding motifs (LBMs) across genomes and metagenomes. Distinct LBM profiles discriminated host-associated and free-living taxa, aerobic and anaerobic lineages, and generalists and non-generalists, revealing a tight coupling between sensory capacity and ecological strategy. Across soil communities, motifs associated with osmoprotection and oxygen sensing were consistently enriched under increasing aridity, linking sensory function to environmental filtering in natural ecosystems. These findings identify environmental sensing as an important organizational axis of bacterial trait-based ecology that integrates evolutionary history, ecological lifestyle, and adaptation to local conditions. Environmental sensing should be considered for predicting microbial niches and responses to environmental change.

ecology↗

bioRxiv2026

An ecological model of masting reproduction matches empirical dynamics

Masting, characterized by highly variable, synchronized, and intermittent seed or fruit production, represents a common reproductive strategy among perennial plants and has profound ecological consequences. Resource provisioning and pollen limitation have long been viewed as central physiological mechanisms underlying this strategy, recent empirical evidence also highlights the role of weather cues in initiating and synchronizing reproductive effort. Drawing on mechanisms that drive periodicity in disease dynamics, this study proposes an alternative proximate mechanism for masting. We develop and analyze a stage-structured population growth model in which developmental delays create population-level cycles, and demographic stochasticity adds individual-level variation; together, yielding masting-like patterns. We compare the behaviour of this novel model with that of the widely used resource budget model and empirically observed patterns of masting in perennial plants. To quantify and compare model outputs and empirical observations, we employ three continuous metrics of masting that capture volatility, synchrony, and periodicity. Our study provides an alternative proximate mechanism for masting. Comparison of this novel mechanism and the established resource-budget model to empirical time-series reveals that both represent realistic yet distinct forms of masting reproduction. Together, these models provide a foundation for further exploration of the conditions under which this reproductive strategy can evolve. Beyond masting, our results highlight the general importance of life-history timing and demographic stochasticity in shaping population ecology.

ecology↗

bioRxiv2026

Convergent stochastic assembly governs reef biofilm microbiomes across ecologically distinct benthic substrates

Understanding the processes that shape microbial biodiversity and community structure is a key objective of the field of microbial ecology. The processes driving assembly of benthic biofilm bacteria on functionally important reef substrates, such as crustose coralline algae (CCA) and calcium carbonate, are not well understood, despite their critical contributions to the maintenance of biodiversity and ecosystem function on reefs. To characterize the patterns of community assembly and biogeography on these substrates, climax biofilm bacterial communities from 11 reef sites were collected, and full 16S small subunit rRNA genes were sequenced. Though CCA- and carbonate-associated communities demonstrated different diversity, composition, and correlations with environmental conditions, communities on both substrates were assembled according to similar processes. Stochastic processes dominated assembly on both substrates, primarily drift with moderate influence from dispersal limitation and selection. Sub-communities of habitat generalists and specialists, as well as rare and abundant taxa, experienced disparate patterns of assembly that remained consistent between substrates, highlighting the importance of individual taxa traits in shaping community assembly. These results provide insight into the factors shaping benthic biofilm bacterial assembly and biogeography in a tropical reef ecosystem and contribute to understanding of reef resilience in the face of environmental change.

ecology↗

bioRxiv2026

A strong-to-weak interaction shift during microbiome succession is coupled to colonizer-dependent antimicrobial resistance

The outcome of ecological succession is often attributed to the characteristics of the invader or the resident community, but rarely to how the community's interaction network reorganizes during assembly. Here, we track intraspecific lineage dynamics and infer time-resolved community interaction networks using Dynamic Covariance Mapping during ecological invasion of the mouse gut by a chromosomally barcoded, spectinomycin-resistant Escherichia coli K12 colonizer. The network is initially dominated by strong, predominantly inhibitory interactions, but as community diversity recovers, the distribution of interaction strengths contracts toward zero, producing a community increasingly dominated by weak and near-neutral interactions. The dominant eigenvalue of the DCM-inferred interaction matrix moves toward marginal stability predicted for dynamically assembling ecological networks. This pattern replicates across eight independent mice in two experimental cohorts, at both inter- and intra-species resolution. The ecological transition coincides with the reproducible resurgence of Paenibacillaceae to high relative abundance and persistent coexistence with E. coli under continued spectinomycin pressure. Whole-genome sequencing of recovered Paenibacillus macerans isolates identifies recurrent mutations in ribosomal protein S5 region associated with spectinomycin binding and strongly implicating this variant in resistance. Strikingly, under antibiotic pressure but without E. coli K12 invasion, resident Paenibacillaceae never blooms, indicating that expansion of the resistant population depends on the ecological context established by the colonizer. These findings show that gut microbiome succession is accompanied by a reproducible transition from strong toward weak interactions and link this network reorganization to the colonizer-dependent ecological benefit of antimicrobial resistance.

ecology↗

bioRxiv2026

Both environmental filtering and intraspecific variation shape small mammals' elementomes

The biogeochemical niche hypothesis (BNH) proposes the multi-elemental composition of organisms - their elementome - as a new ecological dimension. However, which ecological factors shape elementome assembly remains little known, especially in animals. Here, we studied the mandibular elementome of two sympatric small mammals - Apodemus flavicollis and Clethrionomys glareolus - to assess how intraspecific variability (ontogenetic changes in body mass and sex under the vertebrate bone hypothesis; VBH) and environmental filtering (season and habitat) shape essential and non-essential elementome assembly. Species showed moderate elementome segregation and seasonal niche partitioning, with implications for coexistence. Ontogenetic body mass predicted elemental variation and calcium substitution, with several hypermetric scalings in autumn indicating strong departures from mass-invariant homeostasis. Finally, our results suggest a dichotomy: essential elementomes were mainly driven by intraspecific variation, whereas non-essential elementomes were rather shaped by environmental filtering. Our results position animal elementomes as an integrative ecological dimension linking organismal biology, species interactions, and environmental filtering across individuals, populations, and species.

ecology↗

bioRxiv2026

Resource supply dynamics control stability and chaos in complex ecosystems

Ecological interactions are often mediated by feedbacks between organisms and their resource environments. Yet, how resource supply dynamics dictate collective dynamical phases of an ecosystem remains unclear. Here, we analyse a generalised consumer--resource model with non-reciprocal interactions to demonstrate that self-renewing versus externally-supplied resources yield fundamentally different dynamical phase diagrams. As interactions become increasingly non-reciprocal, ecosystems relying on self-renewing resources transition from stable dynamics to chaos and ultimately to infeasibility. By contrast, ecosystems with externally-supplied resources remain stable over a broader parameter range and transition to infeasibility without experiencing an intervening chaotic phase. Using the cavity method, we derive a unified stability condition applicable to a broad class of resource supply functions, explaining why externally-supplied resources can expand the stable region. We show that stability hinges crucially on the susceptibility of resources to perturbations, which depends strongly on their supply. Further, we show that external resource supply suppresses chaos in the unstable region by drastically reducing the susceptibility of resources closest to extinction. Our findings demonstrate that resource dynamics fundamentally reshape the accessible dynamical behaviours of an ecosystem, with implications for interpreting microbial community experiments.

ecology↗

bioRxiv2026

AWET -- Arthropod Weight Estimation Tool

Arthropods drive essential ecosystem processes such as pollination, decomposition, and nutrient cycling and are widely used as indicators of ecosystem condition and function. Among various arthropod-derived metrics, body weight is a key variable in functional ecology and frequently assessed as dry body weight. However, drying arthropod specimens limits the samples future potential for research, as it prevents further processing such as trait measurements or species identification. Here, we present AWET (Arthropod Weight Estimation Tool), an open-source application for automated estimation of individual fresh body weight and extraction of morphometric measurements from standardized images of pre-sorted arthropod samples. AWET combines automated image analysis with taxon-specific allometric regression models to estimate fresh body weight while simultaneously quantifying body length, width, area, and specimen abundance. The software operates with standard imaging equipment, requires no machine-learning-based classification or segmentation, and allows users to define taxonomic groupings according to their objectives. By preserving specimens for downstream analyses while processing large numbers of individuals within milliseconds, AWET provides an efficient, non-destructive, and cost-effective workflow for high-throughput arthropod phenotyping. The software is a practical and expandable tool for biodiversity monitoring projects investigating changes in arthropod biomass, abundance and individual morphometric measures.

ecology↗

bioRxiv2026

Deep sequencing artificially inflates estimates of microbial diversity

Sequencing artifacts challenge accuracy and reproducibility when quantifying microbial diversity. To track error propagation in microbiome analyses, we analyze no-diversity amplicons, which are amplified from host genes with limited genetic diversity or from synthetic spike-ins. We find that sequencing at greater than 104 reads exponentially increased no-diversity amplicon sequence variant (ASV) richness, with hundreds of ASVs observed per sample. This striking pattern was shared with microbial amplicons (16S rRNA, ITS, gyrB, rpoB), which revealed inflated Shannon diversity with an increase in read counts for both the community and within taxa. Comparing sequencing error profiles between no-diversity and microbial amplicons showed that truncating reads to shorter lengths and use of the AVITI Element platform can mitigate, but not abolish, the impacts of artificial inflation; we recommend caution when read depths vary orders of magnitude between samples. Overall, utilizing no-diversity amplicons can help optimize parameters to improve estimates of microbial diversity.

ecology↗

bioRxiv2026

From concentration to export: resource contrasts and bee traits shape pollinator spillover to crops

Floral plantings can either concentrate bees or export them to adjacent crops, yet the ecological conditions influencing these outcomes remain unclear. Here, we develop a mathematical model as proof of concept for our previous integrative hypothesis: concentrator and exporter outcomes can arise as alternative, context-dependent outcomes of the same underlying resource-selection process. Using bees as a model and focusing specifically on spillover from floral plantings to crops, we identified resource-specific thresholds separating concentration- and export-favoring conditions. Our model translates differences in relative patch attractiveness into context-dependent concentration and export outcomes and generates resource-specific, testable predictions about the conditions favoring pollinator movement into crops. In our simulations, the concentrator-exporter transition occurred at a lower flowering-intensity contrast than at pollen or nectar contrasts, which suggests that flowering intensity may provide an initial cue for bee movement, whereas nectar and pollen rewards refine or sustain bee responses once crops are perceived as attractive. Spillover thresholds differed among resource contrasts, whereas response steepness varied across bee-trait and community scenarios. Under the model's trait-sensitivity formulation, predicted spillover probability responded more strongly to flowering contrast for specialists than for generalists; colony size amplified this response, whereas bee richness dampened it. Together, these patterns show how flowering and resource contrasts interact with bee traits and community context to shape predicted spillover. Our results confirm that the concentrator and exporter hypotheses can be understood as context-dependent outcomes of the same ecological process rather than as mutually exclusive alternatives. Experimental tests of the predicted thresholds conducted in the field could reveal when and where floral plantings are most likely to promote bee spillover to crops, potentially supporting crop pollination.

ecology↗

bioRxiv2026

Beyond Single-Metric Assessments: Uncovering Masked Butterfly Declines via Multi-Scalar Analysis in Central Alberta

1. This study analyzed 21 years (2000-2025) of butterfly count data from Central Alberta, integrated with intensive 5-year (2021-2025) high-resolution intra-seasonal sampling. 2. Long-term macro-scale analysis revealed a significant decline in Shannon Diversity, a change that remained obscured when relying solely on traditional metrics of species richness and evenness. 3. This diversity decline was primarily driven by the severe, long-term collapse of the native Common Ringlet (Coenonympha tullia). 4. Four other dominant species--Cabbage White (Pieris rapae), Clouded Sulphur (Colias eriphyle), European Skipper (Thymelicus lineola), and Common Wood Nymph (Cercyonis pegala)--maintained long-term population stability, though their abundances were significantly constrained by extreme winter minimum temperatures and rapid spring warming. 5. High-resolution intra-seasonal analysis (2021-2025) demonstrated that community indices and species-specific abundances were strongly limited by daily weather, particularly wind velocity and temperature. 6. These findings illustrate that while traditional metrics like richness and evenness are fundamental to community ecology, they provide incomplete insights when applied in isolation; they are most effective when utilized as part of a complementary, multi-scalar framework. 7. This study highlights the necessity of coupling multi-decadal historical datasets with high-frequency, fine-scale sampling to accurately identify the mechanisms of community turnover that simpler metrics may overlook. 8. The results underscore the critical importance of standardized citizen science monitoring in quantifying environmental impacts and establishing conservation priorities for terrestrial insect groups.

ecology↗

bioRxiv2026

City life: airborne DNA metagenomic biodiversity monitoring reveals dynamic changes across time and space

Airborne environmental DNA can capture biodiversity across the tree of life, but low sample biomass makes rapid, untargeted detection technically challenging. We combined 45-min air collection, nanopore sequencing and real-time taxonomic analysis in a shotgun metagenomic workflow capable of producing results within 3 hours. Across 77 samples from 13 London sites, including a year of weekly sampling at the Natural History Museum Wildlife Garden, we detected 1,916 species spanning bacteria, fungi, plants and animals. Communities varied spatially and seasonally, shifting from plant dominance in spring to ascomycete dominance in summer and basidiomycete dominance in late autumn and winter. Plant read abundance increased with upwind vegetation, linking airborne signals to surrounding habitat. Detection of catalogued garden plants depended on reference availability, dispersal biology, plant size and proximity to the collector. Together, these findings establish airborne shotgun metagenomics as a platform for rapid, repeated and scalable biodiversity assessment across space and time.

ecology↗

bioRxiv2026

Structural characteristics of important daily movement corridors for waterbirds in urban areas: A case study on Black-headed Gulls

Landscape management facilitating animal movement is essential for sustaining urban wildlife populations and ecosystem services. Although linear vegetation corridors effectively conserve terrestrial animal movements, it remains unclear which landscape elements serve as pathways for aquatic organisms. Urban waterbirds frequently utilize rivers, but the specific characteristics that render certain river segments crucial as movement corridors have yet to be elucidated. This study aims to identify the characteristics of river segments functioning as critical corridors based on waterbird movement strategies. We tracked the movement behaviors of the Black-headed Gull (Chroicocephalus ridibundus), a river-dependent species in daily movements, and identified key movement corridors in highly urbanized Tokyo, Japan. Using GPS tracking data from gulls, we evaluated how river sinuosity and surrounding feature heights influenced tendencies to follow rivers across various temporal scales and perceptual ranges. Furthermore, we predicted and mapped these tendencies across individual river segments in central Tokyo. Gulls tended to fly along river segments with tall features during instantaneous to mid-term decision-making. In contrast, they utilized straight channels for long-term decisions. Although results varied slightly depending on the spatial scale they can perceive, this overarching trend remained consistent. Furthermore, our model predicted that the lower reaches of the Sumida River serve as critical movement corridors. This predictive tendency was also highly robust across all time scales. While straightened river segments with high feature heights may provide unsuitable habitats for diverse taxa, we emphasize their ecological value and argue that they should be conserved as essential movement corridors for waterbirds.

ecology↗

bioRxiv2026

Division of labor and low temperatures predict geographic variation in thermal tolerance of a North American paper wasp (Mischocyttarus mexicanus cubicola)

The biogeographic study of organismal thermal performance is fundamental to our understanding of how climate drives evolution. However, despite highly social insects being popular models for such studies, biogeographic comparisons of thermal functional traits seldom consider division of labor. Individuals within cooperative societies can operate in different microclimates, exposing different task groups to different selection pressures. Here we present a study of how thermal tolerance limits in a social paper wasp vary broadly across temperate and subtropical climates in eastern North America, testing whether division of labor between foundresses and non-reproductive workers generates adaptive variation in thermal performance within the colony. Cold tolerance rather than heat tolerance varied more predictably with environmental temperatures across latitudes, with temperate populations experiencing bouts of winter cold coma, unlike in subtropical populations. Within colonies, reproductive foundresses were also more cold-tolerant than workers, enabling them to remain mobile at cooler periods of early spring during crucial tasks of nest construction, before workers emerge. Together, these results broaden our understanding of how climate shapes thermal performance on both biogeographic and social scales.

ecology↗

bioRxiv2026

Geometric causes of species rarity

Understanding the limits of species distributions is a central objective of biogeography and macroecology and has become increasingly important as climate change drives rapid shifts in geographic ranges. Species range sizes follow a highly skewed frequency distribution, with most species occupying ranges orders of magnitude smaller than those of the most widespread species. Range sizes also exhibit pronounced geographic patterns, with small-ranged species concentrated near continental margins and other geographic boundaries. No universally accepted explanation has been proposed for these patterns. Here we present a simple geometric model showing that species range size patterns emerge from the random placement of dispersal barriers within continental domains. The model predicts both the observed frequency distribution and the spatial distribution of range sizes across amphibians, birds, and mammals. It therefore provides a first-order explanation for global patterns of species rarity and can be refined by incorporating elevational barriers and spatial variation in species richness. Our findings suggest that species range size is constrained by the geometry of dispersal barriers and the geographic domain, with proximity to domain boundaries acting as a primary determinant of species rarity. These results have important implications for understanding species' evolutionary potential and vulnerability to extinction.

ecology↗

bioRxiv2026

A Computational Re-evaluation of Spatial Trials for Zoonotic Tuberculosis Control: Model Misspecification, Diagnostic Miss-classification, and the Illusion of Wildlife Culling Efficacy

1. Wildlife reservoir management frequently relies on the Randomised Badger Culling Trial's (RBCT) trade-off hypothesis, which posits that reductions in cattle herd infections are offset by a perturbation effect driven by disrupted host dispersal. This paper evaluates the computational and epidemiological robustness of this historical trial, which serves as the foundational empirical experiment guiding zoonotic tuberculosis (Mycobacterium bovis) control policies. 2. Using generalized linear mixed models with a generalized Poisson error distribution to explicitly address historical data overdispersion, this study contrasts traditional parametric inference against exact cluster-constrained permutation tests across distinct operational definitions of disease incidence. 3. Non-parametric diagnostics reveal that previously reported treatment and perturbation effects render as statistical artifacts under exact non-parametric permutation. Inside culling zones, parametric significance fails to withstand exact permutation verification due to extreme data leverage in localized cluster blocks. 4. Crucially, when diagnostic misclassification biases are eliminated by analysing total reactor datasets, all apparent culling effects disappear, and information criteria overwhelmingly favour nested null architectures. Unconfirmed reactors likely represent true biological infections missed by low-sensitivity post-mortem macro-necropsy, proving that host removal tracks observation noise rather than genuine zoonotic transmission pathways. 5. Finally, empirical scaling conducted in this study identifies a novel mathematical saturation effect, demonstrating that this sub-linear scaling is an operational artifact of unmodelled herd-level disease recurrence over time. 6. Policy implications. Because current zoonotic tuberculosis intervention frameworks are built upon a structurally misspecified statistical model, they have driven large-scale veterinary policies resulting in substantial, unevidenced ecological and economic interventions while failing to provide genuine public health, animal health, or disease control benefits.

ecology↗

bioRxiv2026

Soils from different landscape elements diverge in response to multiple global change factors

Global change factors (GCFs) are known to affect terrestrial ecosystems across a range of land-use types, including farmlands, grasslands, and forests. However, it remains unclear whether different landscape elements within the same region respond differently to the same global change pressures. Here, we investigated this question using four soils collected from co-located farmland, grassland, pine forest, and oak forest, representing distinct landscape elements under the same regional climatic conditions. Each soil was exposed to one of six individual GCFs, warming, drought, nitrogen deposition, salinity, microplastics, and antibiotics, as well as to all six factors combined. We found that landscape elements exhibited strongly divergent responses to the same GCFs. The effects on soil functions also varied among soils under combined stress, with responses diverging from different null-model predictions depending on soils and response variable. Moreover, landscape-element specific response patterns became more pronounced under multiple concurrent stressors. Overall, our findings show that landscape heterogeneity represents a mosaic of different capacities to resist and respond to global change, even under shared climatic and geographic conditions. Global change assessments and ecosystem models should therefore better account for landscape-level heterogeneity, and management strategies aimed at enhancing ecosystem resilience should be tailored to individual landscape elements.

ecology↗

bioRxiv2026

Burning down the mouse: Effects of wildfire and post-fire reseeding on Sin Nombre virus prevalence in its reservoir host

Worldwide, physical habitats and biological communities are being reshaped by wildfire. Such changes have obvious potential to alter pathogen ecology, yet few studies, outside of those focused on ectoparasites, have tested the effects of wildfire on pathogen prevalence in wildlife. Even fewer have focused on the impacts of strategies for post-fire remediation on pathogen circulation. Here, we investigated the effect of wildfire and wildfire mitigation on the prevalence and viral load of Sin Nombre virus (SNV) infection in its reservoir host, the western deer mouse, using a study design of matched burned, unburned, and post-burn reseeded sites in northern New Mexico. In total, we screened 411 individual deer mice for SNV via RT-qPCR and analyzed the effect of wildfire and wildfire mitigation on relative mouse abundance, individual infection probability, site-level prevalence and viral load. Relative abundance was highest at reseeded sites, and model selection indicated that habitat structure, particularly the gradient from closed canopy to open-herbaceous habitat, was consistently associated with increased relative abundance. Similarly, SNV prevalence was significantly higher in reseeded sites than either burned or unburned sites but did not differ in burned versus unburned sites. Viral load did not differ between burn history types, and zero-inflated gamma hurdle models did not identify any strong predictors of viral load. Serendipitously, we were also able to investigate the impacts of an El Nino Southern Oscillation (ENSO) cycle on patterns of infection in a subsample of sites that were studied during and one year after an ENSO year and found that SNV prevalence increased significantly post-ENSO. Both reseeding and ENSO deliver resource pulses that can support increases in mouse density and thereby enhance SNV transmission. The impacts of post-fire management practices on SNV prevalence in its reservoir host that were revealed in this study should be considered when implementing such strategies and when utilizing treated areas.

ecology↗

bioRxiv2026

Historical squid biomass increase is not explained by rising temperature but rather by loss of top predators.

Squid abundance has been reported to increase globally between 1970 and 2010. This increase has been hypothesized to result from two primary factors: the loss of top predators due to overfishing and rising ocean temperatures. The decline in apex predators may lead to the expansion of squid populations either through reduced predation pressure or diminished competition with juvenile predators. Concurrently, increased temperatures could enhance the somatic growth rates of squid, thereby accelerating their population growth. However, empirically disentangling the impacts of predator loss and temperature on squid biomass remains challenging, especially in a food-web context. In this study, we used a size- and trait-based model of upper trophic levels that resolves the ecosystem structure -- biomass and trophic interactions of fish and squid -- for varying depth, temperature, and secondary production, to investigate two hypotheses of the historical expansion of squid, i.e., the effects of predator depletion from fishing and rising temperatures on squid biomass. Our model reveals that intensified fishing of squid predators -- specifically large demersal fish in shelf systems and large pelagic fish in open oceans -- leads to a slight increase in squid biomass. Conversely, elevated temperatures are associated with a decline in squid biomass. This temperature-driven reduction in biomass is attributed to an increased metabolism of squids beyond the available food supply. If historic overfishing on large marine predators continues to be curtailed, we expect a corresponding reduction in global squid biomass and fisheries potential, which could be further exacerbated by rising temperatures.

ecology↗