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bioRxiv2026

Widespread SARS-CoV-2 infection in free-ranging Neotropical bats suggests repeated human-to-bat spillback

Bats harbor exceptional coronavirus diversity and are considered ancestral sources of several human pathogens. As SARS-CoV-2 transitioned from pandemic emergence to global endemicity in humans, concern has shifted from wildlife-to-human spillover toward reverse zoonosis. However, infection of free-ranging bat populations under natural conditions has not previously been demonstrated. Here, we report widespread detection of SARS-CoV-2 RNA in wild Neotropical bats sampled across Andean and Amazonian ecosystems of Southern Ecuador. RT-qPCR screening of 126 individuals, representing nine taxa, detected SARS-CoV-2 RNA in 34.12% of bats across multiple sites. Partial to near-complete viral genomes recovered from five individuals showed >99% nucleotide identity to contemporary human SARS-CoV-2 lineages and clustered within multiple global phylogenetic clades. Mixed-effects modeling revealed pronounced species-level heterogeneity, a positive association between elevation and infection probability, and higher infection probability in females compared with males. The close phylogenetic affinity of bat-derived genomes to circulating human variants and their distribution across multiple lineages suggest repeated anthropogenic spillback rather than sustained bat-specific circulation. These results expand current understanding of the ecological footprint of the COVID-19 pandemic and highlight the importance of integrating wildlife surveillance into long-term One Health strategies for emerging infectious diseases.

microbiology↗

bioRxiv2026

Linking continuous behavior to aesthetic enjoyment in a walkable virtual-reality museum tour: effects of agency and a painting-level analysis framework

Museum visits typically follow curator-defined routes that constrain how visitors shape their own experience, yet choice is widely held to heighten engagement, autonomy, and enjoyment. Virtual reality (VR) offers a setting in which to study these processes because it combines ecological immersion with precise, continuous behavioral measurement. We investigated (i) whether VR- derived behavioral signals are associated with self-reported enjoyment during a virtual museum tour, and (ii) whether the level of agency afforded to visitors influences enjoyment. Forty-eight adults completed a room-scale, life-size VR tour (8 * 4 m) of seven paintings from the Tel Aviv Museum of Art, each accompanied by a synchronized audio guide. Synchronized gaze and head- position streams were logged continuously (50 Hz) and segmented into painting-level viewing episodes using a trial-and-tile pipeline that intersects each painting's trial interval with an empirically defined spatial window in front of the canvas. Participants were randomly assigned to one of three agency conditions, Active (choice before every artwork), Semi-Active (choice for the first three), or Passive (fixed route),while the artwork sequence was held identical. Self- reported enjoyment at the tour and painting levels did not differ reliably across agency conditions. Among VR-derived measures, gaze engagement during the audio guide showed the clearest (though modest) association with painting-level liking, whereas locomotion and pacing measures were weak and inconsistent predictors. Agency nonetheless reliably modulated several gaze- and time-based viewing measures. The findings reveal a dissociation between subjective enjoyment and the micro-structure of viewing, and establish a reusable framework for full-tour, painting-level behavioral analysis in immersive settings.

neuroscience↗

bioRxiv2026

Polystyrene Microplastics Accelerate Antibiotic Resistance Evolution and Exacerbate Pathogenicity in Acinetobacter Baumannii

Microplastics are pervasive environmental contaminants and are increasingly detected in contexts relevant to human health, yet their effects on antimicrobial resistance, host-pathogen interactions, and infection outcomes remain poorly understood. Here, we show that exposure to polystyrene microplastics alters both antibiotic resistance evolution and pathogenic behavior in Acinetobacter baumannii, a leading cause of multidrug-resistant hospital-acquired infections. Using experimental evolution under antibiotic selection, we demonstrate that microplastic exposure accelerates resistance emergence across multiple antibiotic classes. Although microplastic exposure did not uniformly enhance biofilm formation, it modestly impaired macrophage-mediated bacterial clearance, suggesting broader effects on bacterial adaptation and host interaction. In vivo, microplastic-associated infection resulted in more severe disease, characterized by increased lung tissue damage and reduced survival in a murine model of A. baumannii pneumonia. Together, these findings identify microplastics as ecological modifiers of bacterial adaptation, linking widespread plastic pollution to enhanced antimicrobial resistance and worsened infectious disease outcomes.

microbiology↗

bioRxiv2026

The histone demethylase Kdm5 and the ARGONAUTE proteins Piwi and Aubergine regulate female abdominal pigmentation in Drosophila melanogaster

Insect pigmentation is an ecologically critical trait influencing many physiological processes. In Drosophila melanogaster, abdominal pigmentation is sexually dimorphic: males have fully pigmented posterior segments, while females exhibit a posterior melanin stripe. Pigmentation relies on the expression of pigmentation genes that encode enzymes involved in pigment synthesis. These genes are tightly regulated during pupal and young adult stages. To expand the gene regulatory network of pigmentation genes, we conducted an RNAi screen using the yellow-Gal4 driver, expressed during the pupal stage in abdominal epidermis. One of the candidates from this screen, Kdm5, encodes a histone demethylase erasing the H3K4me3 histone mark catalyzed by the histone methyl-transferase Trithorax (Trx). We show that Kdm5 down-regulation reduces abdominal pigmentation, mimicking trx down-regulation. Kdm5 activates melanin production through regulation of the pigmentation gene tan. Transcriptomic analyses reveal that Kdm5 and Trx share many targets in pupal abdominal epidermis, including piRNA pathway components such as piwi and aubergine. These piRNA components, originally associated with transposon silencing in the germline, also function in some somatic tissues such as the nervous system, the fat body or the gut. We demonstrate that Piwi and Aubergine participate in female abdominal pigmentation establishment, without evident piRNA production. We also show that Kdm5 and Piwi act not only in pupal abdominal epidermis but also in pupal fat body. This study therefore expands the regulatory network of pigmentation genes. It identifies a new somatic function for Kdm5 and Piwi and reveals a role for pupal fat body in female abdominal pigmentation regulation.

genetics↗

bioRxiv2026

Detection of Stress in Naturalistic Settings Through Passive Mobile Sensing

Unobtrusive stress detection using wearable sensors could enable scalable, continuous mental-health monitoring. However, stress is an inherently subjective state that can only be inferred indirectly from physiological signals, making generalizable detection in naturalistic settings challenging. Although prior work has focused on improving model performance, it remains unclear whether wearable physiology supports a shared cross-individual mapping to subjective stress or whether this relationship is fundamentally person-specific. We evaluated feature-based and deep-learning models across multiple physiological modalities using ecological momentary assessment (EMA) as the reference standard, comparing within- and between-individual modeling approaches. Within-individual models achieved modest but consistent improvements in stress detection, whereas between-individual models consistently failed to generalize, yielding negative R2 values despite multimodal fusion and high-capacity architectures. Error analyses revealed regression to the mean, reduced sensitivity to high-stress states, and residual associations with general physiological activation, highlighting the limited stress specificity of wearable physiology. These findings suggest that wearable stress detection is fundamentally a personalized inference problem and that future systems should prioritize individual adaptation and contextual modeling over universal stress predictors.

neuroscience↗

bioRxiv2026

Red and blue light cues drive contrasting remodeling of lipophilic metabolites and photophysiology in natural benthic diatom biofilms

Intertidal mudflats are low hydrodynamic energy environments hosting microphytobenthic communities that experience strong spatiotemporal variability in light regimes, including changes in spectral quality and light intensity that can lead to cellular photooxidative stress. To cope with these fluctuations, autotrophs exhibit diverse and highly plastic adaptations that are often species-dependent and shaped by their ecological niches. This study investigates photophysiological responses and metabolic remodeling in a diatom assemblage originating from a natural winter microphytobenthic biofilm under contrasting red and blue light intensities. To this end, photosynthetic parameters were monitored alongside changes in lipophilic metabolites, including untargeted lipids and lipophilic pigments. While few metabolites showed temporal remodeling, rapid and contrasting changes were observed within 30 minutes in response to both spectral quality and light intensity. Red light treatments induced broader remodeling of lipophilic metabolites than blue light, whereas blue light appeared to have a greater impact on photosynthetic parameters. Moreover, red light induced xanthophyll-cycle responses comparable to those observed under blue light at equivalent incident intensity. We discuss these metabolic responses in relation to diatom photoadaptive strategies, placing these findings within the intertidal environmental framework. This work further underlines the importance of understanding rapid metabolic plasticity in coping with light fluctuations, providing new insights into the photoregulatory strategies of natural microphytobenthic communities.

cell biology↗

bioRxiv2026

Accurate detection of metagenomic strain-level associations using average nucleotide identity with StrainSpy

Genetic variation among microbial strains of the same species can profoundly influence their phenotypes, ecological functions, and impacts on human health. Traditionally, the relative abundance of a species has been used to identify associations between the microbiome and disease. However, this approach overlooks intra-species genetic variation and is susceptible to spurious correlations arising from the compositional nature of abundance data and microbial load. Fast, k-mer-based algorithms can now accurately estimate strain-level Average Nucleotide Identity (ANI) in metagenomes. Despite its value as an orthogonal metric for strain-level analysis, methods for conducting ANI-based association studies remain limited. To address this, we developed StrainSpy, a statistical algorithm that identifies associations between containment ANI and variables of interest across a wide range of study designs, including longitudinal and multi-cohort designs. Re-analysis of a study examining gut microbiota recovery in 12 healthy adults following antibiotic exposure revealed novel strain-level associations, including a reduction in strain-level diversity despite species persistence. Applying StrainSpy to a multi-cohort analysis of 3,414 colorectal cancer metagenomes identified novel strain-level associations with colorectal cancer. However, in a separate collection of microbiome-immunotherapy studies, no individual strain was consistently associated across cohorts. Importantly, across both datasets, StrainSpy informed containment ANI-based machine learning models achieved comparable accuracy to traditional abundance-based methods. StrainSpy is publicly available as an R package github.com/gtonkinhill/strainspy.

microbiology↗

bioRxiv2026

Structural basis for catalytic and inhibitory divergence between archaeal and bacterial ammonia monooxygenases

Ammonia oxidation initiates nitrification and is closely linked to microbial N2O production. Ammonia monooxygenase (AMO) catalyzes the first and rate-limiting step of nitrification and is widespread across evolutionarily distinct ammonia-oxidizing archaea (AOA) and bacteria (AOB). The ocean is the largest biome for AOA and AOB, which have distinct ecological niches and markedly different sensitivities to nitrification inhibitors. However, the lack of archaeal AMO structures and inhibitor-bound AMO complexes has hindered mechanistic understanding of the architectural, catalytic, and inhibitory divergence between these two enzyme systems. Here, we report high-resolution cryo-electron microscopy (cryo-EM) structures of marine archaeal AMO captured in active and inactivated states within its native membrane environment, together with inhibitor-bound structures of estuarine bacterial AMO. Archaeal AMO forms an unexpected cup-shaped homotrimer composed of eight subunits per protomer and exhibits substantial architectural divergence from bacterial AMO. Integrated structural, biochemical, kinetic, and computational analyses reveal distinct periplasmic architectures, copper-center organization, and hydrophobic channels between archaeal and bacterial AMOs for ammonium acquisition, catalysis and inhibitor response. These findings provide a structural and mechanistic framework for understanding how archaeal and bacterial AMOs have diverged to distinct ammonia-oxidizing strategies and inhibitor susceptibilities across environmentally important ammonia oxidizers.

molecular biology↗

bioRxiv2026

Phylogeny and Species Delimitation in Isoxylosteum, a Lonicera Clade Endemic to the Himalayan-Tibetan-Hengduan Region

The Himalayan-Tibetan-Hengduan (HTH) region is the richest biodiversity hotspot for high-elevation plants. However, owing to its remote and physically challenging topography as well as the trans-national nature of the region, many taxonomic problems in the area remain unresolved, particularly in the Himalaya. This, in turn, has impeded our understanding of the assembly of its extraordinary high-elevation flora. Here, we resolve phylogenetic relationships and delimit species in a distinctive clade of honeysuckles that is endemic to the HTH, the Isoxylosteum clade of Lonicera, using restriction-site associated DNA sequencing (RADseq) and morphological data. Five species complexes of Isoxylosteum have standardly been recognized. Three of these complexes are highly variable and have been divided into several varieties or species each. Phylogenetic, population structure, and morphological analyses of leaf and floral traits from samples collected across the range of the clade support the recognition of five species, including a species that has most often been recognized as a variety of L. rupicola (L. rupicola var. minuta). Instead, we find that it is sister to L. spinosa. This is surprising because the geographic range of L. minuta is contiguous with the other varieties of L. rupicola in the northern Hengduan region but widely separated from L. spinosa whose range lies mainly to the west of the Tibetan plateau. On close examination we find that several morphological and ecological traits also support a closer relation of L. minuta to L. spinosa. None of the other eight previously recognized varieties and species were supported. Floral traits showed high discriminatory power, correctly classifying 89% of samples to species. By comparison, leaf dimensions classified species with 59% accuracy. Our results identify diagnostic morphological apomorphies for each recognized species and major clade and provide a revised taxonomic framework for Isoxylosteum.

evolutionary biology↗

bioRxiv2026

Increased substrate complexity drives re-diversification and functional reorganization in simplified methanogenic consortia

Anaerobic digestion is a sustainable process for methane production that relies on complex microbial networks. While simplified enriched consortia offer a promising strategy to improve process control, excessive simplification can disrupt key functions and microbial partnerships, reducing community resilience. In this study, we investigated whether simplified methanogenic communities could re-diversify and maintain methane production when exposed to more complex substrates, namely butyrate and glucose. We also evaluated the effect of vitamin and amino acid supplementation on sustaining key methanogens and beneficial microbial partners. Three methanogenic communities were monitored over three months for methane production and microbial diversity while receiving butyrate and/or glucose, with different vitamin or amino acid supplements. Exposure to more complex substrates successfully restored the diversity of acidogenic and acetogenic populations, even after prolonged feeding with simple substrates, highlighting both the resilience of the simplified communities and the ecological importance of low-abundance taxa. However, the transition reduced process stability and methane production, likely due to substrate overloading. The results further suggest that substrate complexification should be introduced stepwise, promoting acetogenesis before acidogenesis. This fundamental study brings new light on which factors must be considered in the long-term goal of designing tailored-made consortia for anaerobic digestion.

bioengineering↗

bioRxiv2013

Sap flow through petioles and petioles reveals leaf-level responses to light and vapor pressure deficit in the tropical tree Tabebuia rosea (Bignoniaceae)

Continuous measurements of sap flow have been widely used to measure water flux through tree stems and branches. However, these measurements lack the resolution necessary for determining fine-scale, leaf-level responses to environmental variables. We used the heat ratio method to measure sap flow rates through leaf petioles and leaflet petiolules of saplings of the tropical tree Tabebuia rosea (Bignoniaceae) to determine how leaf and leaflet sap flow responds to variation in light and vapor pressure deficit (VPD). We found that in the morning sap flow rates to east-facing leaves increased 26 minutes before adjacent west-facing leaves. Although leaves had higher integrated sap flow than their largest leaflet, this difference was not proportional to the difference in leaf area, which could be due to lower conduit area in petiolules than in petioles. In contrast to measurements on main stems, integrated daily sap flow was negatively correlated with daily mean VPD. Furthermore, leaves exhibited previously undescribed patterns of hysteresis in the sap flow-VPD and sap flow-PAR relationships. When hysteresis in the sap flow-PAR relationship was clockwise, the sap flow-VPD relationship was also clockwise; however, when hysteresis in the sap flow-PAR relationship was counterclockwise, the sap flow-VPD relationship displayed an intersected loop. These pattern differences highlight how substantially leaf-level processes may vary within a canopy and how leaf-level processes may not scale predictably to the stem level.

Ecology↗

bioRxiv2013

Linking indices for biodiversity monitoring to extinction risk theory

Biodiversity indices often combine data from different species when used in monitoring programs. Heuristic properties can suggest preferred indices, but we lack objective ways to discriminate between indices with similar heuristics. Biodiversity indices can be evaluated by determining how well they reflect management objectives that a monitoring program aims to support. For example, the Convention on Biological Diversity requires reporting about extinction rates, so simple indices that reflect extinction risk would be valuable. Here we develop three biodiversity indices that are based on simple models of population viability that relate extinction risk to abundance. The first index is based on the geometric mean abundance of species. A second uses a more general power mean. A third integrates both the geometric mean abundance and trend. These indices require the same data as previous indices, but they also relate directly to extinction risk. Field data for butterflies and woodland plants, and experimental studies of protozoan communities show that the indices correlate with local extinction rates. Applying the index based on the geometric mean to global data on changes in avian abundance suggests that the average extinction probability of birds has increased approximately 1% from 1970 to 2009.

Ecology↗

bioRxiv2013

The Effectiveness of China’s National Forest Protection Program and National-level Nature Reserves, 2000 to 2010: PREPRINT

There is profound interest in knowing the degree to which Chinas institutions are capable of protecting its natural forests and biodiversity in the face of economic and political change. Chinas two most important forest protection policies are its National Forest Protection Program (NFPP) and its National-level Nature Reserves (NNRs). The NFPP was implemented in 17 provinces starting in the year 2000 in response to deforestation-caused flooding. We used MODIS data (MOD13Q1) to estimate forest cover and forest loss across mainland China, and we report that 1.765 million km2 or 18.7% of mainland China was covered in forest (12.3%, canopy cover > 70%) and woodland (6.4%, 40% [≤] canopy cover < 70%) in 2000. By 2010, a total of 480,203 km2 of forest + woodland was lost, amounting to an annual deforestation rate of 2.7%. The forest-only loss was 127,473 km2, or 1.05% annually. The three most rapidly deforested provinces were outside NFPP jurisdiction, in the southeast. Within the NFPP provinces, the annual forest + woodland loss rate was 2.26%, and the forest-only rate was 0.62%. Because these loss rates are likely overestimates, China appears to have achieved, and even exceeded, its NFPP target of reducing deforestation to 1.1% annually in the target provinces. We also assemble the first-ever polygon dataset for Chinas forested NNRs (n = 237), which covered 74,030 km2 in 2000. Conventional unmatched and covariate-matching analyses both find that about two-thirds of Chinas NNRs exhibit effectiveness in protecting forest cover and that within-NNR deforestation rates are higher in provinces that have higher overall deforestation.

Ecology↗

bioRxiv2013

Mechanism of β-Aminobutyric Acid-Induced Resistance in Wheat to the Grain Aphid, Sitobion avenae

The non-protein amino acid {beta}-aminobutyric acid (BABA) could induce plant resistance to a broad spectrum of biotic and abiotic stresses. However, BABA-induced plant resistance to insects is less well-studied, especially its underlying mechanism. In this research, we applied BABA to wheat seedlings and tested its effects on Sitobion avenae. When applied as a soil drench, BABA significantly reduced weight of S. avenae, whereas foliar spray and seed treatment had no such effects. BABA-mediated suppression of S. avenae growth is dose dependent and could last at least for 7 days. The aminobutyric acid concentration in phloem sap of BABA-treated plants accumulated to high levels and increased with BABA concentrations applied. Moreover, after 10 days of treatment, the aminobutyric acid content in BABA-treated plants was still higher than that in control treatment. S. avenae could not discriminate artificial diet containing BABA from standard diet, indicating that BABA itself is not a deterrent to this aphid. Also S. avenae did not show preference for control plants or BABA-treated plants. Consistent with choice test results, S. avenae had similar feeding activities on control and BABA-treated plants, suggesting that BABA did not induce antifeedants in wheat seedlings. In addition, aminobutyric acid concentration in S. avenae feeding on BABA-treated plants was significantly higher than those feeding on control palnts. S. avenae growth rate was reduced on artificial diet containing BABA, indicating direct toxic effects of BABA to this aphid. These results suggest that BABA application could enhance wheat plant resistance to S. avenae and the mechanism is possibly due to direct toxicity of high BABA contents in plant phloem.

Ecology↗

bioRxiv2013

Broad-scale spatial patterns of canopy cover and pond morphology affect the structure of a Neotropical amphibian metacommunity

Spatial and environmental processes influence species composition at distinct scales. Previous studies suggested that the landscape-scale distribution of larval anurans is influenced by environmental gradients related to adult breeding site selection, such as pond canopy cover, but not water chemistry. However, the combined effects of spatial, pond morphology, and water chemistry variables on metacommunity structure of larval anurans have not been analyzed. We used a partial redundancy analysis with variation partitioning to analyze the relative influence of pond morphology (e.g., depth, area, and aquatic vegetation), water chemistry, and spatial variables on a tadpole metacommunity from southeastern Brazil. We predict that the metacommunity will be spatially structured at broad spatial scales, while environmental variables, mainly related to adult habitat selection, would play a larger role at fine spatial scales. We found that broad-scale spatial patterns of pond canopy cover and pond morphology strongly influenced metacommunity structure. Additionally, species composition was spatially autocorrelated at short distances. We suggest that the reproductive behavior of adult anurans is driving tadpole metacommunity dynamics, since pond morphology, but not water chemistry affects breeding site selection by adults. Our results contribute to the understanding of amphibian species diversity in tropical environments.

Ecology↗

bioRxiv2013

Assessing the Use of Antiviral Treatment to Control Influenza

Vaccines are the cornerstone of influenza control policy, but can suffer from several drawbacks. Seasonal influenza vaccines are prone to production problems and low efficacies, while pandemic vaccines are unlikely to be available in time to slow a rapidly spreading global outbreak. Antiviral therapy was found to be beneficial during the influenza A(H1N1)pdm09 pandemic even with limited use; however, antiviral use has decreased further since then. We seek to determine the role antiviral therapy can play in pandemic and seasonal influenza control on the population level, and to find optimized strategies for more efficient use of treatment. Using an age-structured contact network model for an urban population, we find that while a conservative antiviral therapy strategy cannot replace a robust influenza vaccine, it can play a role in reducing attack rates and eliminating outbreaks.

Ecology↗

bioRxiv2013

Black rhinoceros demography should be stage, not age, based.

Biologically meaningful and standardized definitions of life stages are essential for demographic studies, especially for endangered and intensively managed species such as rhinoceros. Focusing on the black rhinoceros Diceros bicornis, we argue that standardized biological definitions of calf, subadult, and adult, rather than age classes, provide the appropriate basis for black rhinoceros demography. Age classes do not correlate well with the risks of mortality nor characterize, at least for females, the attainment of reproductive maturity. Black rhinoceros demography based on age classes, typical of existing literature, obscures the significance of studies of mortality and fecundity. Comparison of studies also requires standardized definitions. We propose biologically meaningful definitions of life stages appropriate for the demography of the black rhinoceros and encourage the community of rhinoceros researchers to reach consensus on standardized, demographically appropriate definitions for adoption for each rhinoceros species.

Ecology↗

bioRxiv2014

Expertly validated models suggest responses to climate change are related to species traits: a phylogenetically-controlled analysis of the Order Lagomorpha

Climate change during the last five decades has impacted significantly on natural ecosystems and the rate of current climate change is of great concern among conservation biologists. Species Distribution Models (SDMs) have been used widely to project changes in species bioclimatic envelopes under future climate scenarios. Here, we aimed to advance this technique by assessing future changes in the bioclimatic envelopes of an entire mammalian Order, the Lagomorpha, using a novel framework for model validation based jointly on subjective expert evaluation and objective model evaluation statistics. SDMs were built using climatic, topographical and habitat variables for all 87 species under past and current climate scenarios. Expert evaluation and Kappa values were used to validate past and current distribution models and only those deemed modellable through our framework were projected under future climate scenarios (58 species). We then used phylogenetically-controlled regressions to test whether species traits were correlated with predicted responses to climate change. Climate change will impact more than two-thirds of the Lagomorpha, with leporids (rabbits, hares and jackrabbits) likely to undertake poleward shifts with little overall change in range extent, whilst pikas are likely to show extreme shifts to higher altitudes associated with marked range declines, including the likely extinction of Kozlovs Pika (Ochotona koslowi). Smaller-bodied species were more likely to exhibit range contractions and elevational increases, but showing little poleward movement, and fecund species were more likely to shift latitudinally and elevationally. Our results suggest that species traits may be important indicators of future climate change and we believe multi-species approaches, as demonstrated here, are likely to lead to more effective mitigation measures and conservation management.

Ecology↗

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