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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 541 records · Page 30Linked to original sources
bioRxiv2026

Ecological Drivers of Nontuberculous Mycobacteria in Aquatic Systems: Biodiversity, Niche Competition, and Pathogen Emergence

Microbial diversity remains largely unexplored across environments and scales, notably because at local scales many microbial taxa exist under a dormant state. Microbial biogeography is shaped by edaphic and ecological drivers, and shifts in microbial community composition are frequently associated with host community structure and health. Nontuberculous mycobacteria represent a striking example of environmental microorganisms with opportunistic pathogenic potential. Unfortunately, data on their diversity, distribution, and ecological interactions in aquatic environments remain limited. However, understanding competition for niche space and the role of abiotic and biotic factors shaping their biogeography is crucial for predicting disease emergence and transmission. Here we aimed at i) identifying microhabitat abiotic and biotic drivers influencing their distribution, ii) assessing the predictability of their diversity and distribution across continents, and iii) examining potential exclusion or associations between pathogenic and nonpathogenic mycobacterial species. By deploying an eDNA-based metabarcoding approach from freshwater samples collected in urban and rural sites in French Guiana and Cote dIvoire, we have boosted our understanding of environmental mycobacteria ecology by highlighting the influence of habitat type, abiotic factors, and microbial interactions on mycobacterial distribution. In addition, the detection of pathogenic species further highlighted the importance of environmental reservoirs in mycobacterial disease transmission.

ecology↗
bioRxiv2026

Seasonal dynamics in the trophic ecology and condition of a marine, benthic mesopredator, the southern stingray, Hypanus americanus

Mesopredators contribute to food web stability and as such, understanding their trophic ecology can help to predict potential consequences of ongoing ecosystem modification. Here, multi-tissue carbon and nitrogen stable isotope analysis ({delta}13C and {delta}15N) and biochemical blood parameters ({beta}-hydroxybutyrate, glucose, lactate, and osmolality) were used to assess sex, size, spatial and seasonal differences in trophic ecology and condition of southern stingrays, Hypanus americanus, in Bimini, The Bahamas. Stingrays exhibited a dietary preference for molluscs and annelids, with an ontogenetic shift towards lower {delta}13C with increasing body size indicating a shift towards more mangrove associated prey. Nitrogen isotope values showed minimal seasonal changes, but higher {delta}15N values in males indicated foraging at a higher trophic level than females. Blood {beta}-hydroxybutyrate concentrations and osmolality revealed a similar energetic state and condition between sex, size, location and season. Our results advance our understanding of the seasonal trophic ecology of a benthic, marine mesopredator and identify the southern stingray as an important trophic link in seagrass and mangrove habitats in Bimini.

ecology↗
bioRxiv2026

Spatial distribution of ticks and tick-borne pathogens in central Hokkaido, Japan and associated ecological factors revealed by intensive short-term survey in 2024

Tick-borne pathogens are transmitted by tick bites to cause infectious diseases in humans and domestic animals. To anticipate the occurrence of tick-borne diseases, it is required to understand high resolution distribution of infection risk and associated ecological factors. The aim of the present study is to reveal the spatial distribution of ticks and ticks infected with pathogens in central Hokkaido, Japan. Adult and nymphal ticks were collected with a constant effort at 171 sites from 13 May to 26 June 2024, followed by screening tick-borne pathogens. The potential suitable habitats of seven tick species and the endemic tick-borne pathogens in the study area (i.e. tick-borne encephalitis virus, Yezo virus, Beiji nairovirus, Lyme disease group borreliae, and relapsing fever group borreliae) were predicted using ecological niche modeling. Ixodes persulcatus and Ixodes ovatus were identified as the primary ticks to determine the distributions of all the pathogens. Besides, the predicted suitable habitats were specific to each pathogen/tick species. Among the environmental variables considered for modeling, snow depth appeared to significantly contribute to the distribution differences between ticks and pathogens. The findings of this study expand our understanding of the spatial risk distribution of tick-borne pathogen infections and its ecological context.

ecology↗
bioRxiv2026

Feeding Ecology and Behavioral Adaptations Shape Injury Patterns in Central European Ants

Injuries are common in animals and represent a major threat to individual survival. They can result from inter- or intraspecific conflict, predation, or pugnacious prey. Despite their potential ecological and evolutionary importance, injury patterns remain poorly documented in animal populations. To test whether a species feeding ecology or habitat can predict injury patterns, we quantified injury rates and affected body regions among native ant species collected from different habitats in Bavaria, Germany. Specimens were sampled using pitfall traps, which proved to be an efficient method for injury assessment. Injury rates varied substantially among species and genera, ranging from 0% to 38%. Predatory ant species exhibited higher frequencies of leg injuries, whereas omnivorous species were more frequently injured at the antennae. The distribution of injuries likely reflects both foraging ecology and species-specific wound care behaviors, with a high frequency of trochanter injuries potentially indicating prior amputation events to cope with infected leg injuries, as observed in Lasius alienus. Our findings demonstrate that injury propensity and distribution are shaped by feeding habits and behavioral adaptations, providing comparative evidence that the costs and management of injuries vary systematically among ant species. Our study thus highlights injuries as a measurable axis of selection that may have contributed to the emergence of wound care and other forms of social immunity in ants.

ecology↗
bioRxiv2026

Bridging the gaps between field-based ecology and remote sensing to estimate plant functional diversity: a systematic review

Understanding plant functional diversity across scales requires integrating field-based ecology and remote sensing, yet these disciplines differ in how traits are studied. We evaluated the conceptual and methodological convergence between these disciplines. Our results reveal that field-based ecology has undergone longer conceptual development and covers a broader range of traits, while remote sensing has experienced rapid growth driven by technological advances. Both disciplines are increasingly converging on similar concepts. However, major gaps in empirical coverage persist across biomes in both disciplines. Although plant-dominated ecosystems have been extensively studied, extreme ecosystems remain undersampled. While there is considerable diversity in the definition "functional traits", both disciplines converge on using a similar set of traits, reflecting their central role in plant strategies and spectral detectability. Our synthesis underscores the potential for methodological synergy. Harmonizing trait definitions, scaling assumptions, and computational steps involved in estimating plant functional diversity are crucial for building a unified, multiscale framework for biodiversity monitoring in ecosystems undergoing biodiversity loss and climate change. TeaserA synthesis of how field ecology and remote sensing can be aligned to monitor plant functional diversity across scales.

ecology↗
bioRxiv2026

Tipping Points and Emergent Phases of Species Diversity in Mutualistic Ecological Networks under Global Warming

Global warming poses a severe threat to ecosystem resilience and biodiversity, potentially driving species loss, declining diversity, and ecosystem collapse. Accurately predicting tipping points of ecological resilience under global warming remains a fundamental challenge. Here, we develop a theoretical framework to identify climate-induced tipping points in mutualistic ecological networks, capturing critical transitions under warming scenarios. We show that rising temperatures, increasing intraspecific competition, and deteriorating mutualistic interaction can drive ecosystems through three distinct dynamical phases of species diversity: stable full coexistence, stable partial coexistence, and total extinction. Notably, ecosystems with low species abundances are particularly vulnerable, facing heightened risks of diversity loss and extinction. Moreover, the warming rate modulates these transitions, as slower warming grants endangered species a window of time within which to adjust and attenuate the loss of resilience. Applying this framework to assess various emission mitigation pathways, we find that "pollute first, clean up later" scenarios pose a threat to biodiversity, leading to irreversible biodiversity losses even after subsequent emission reductions. Our findings offer critical insights into the timing and mechanisms of ecological tipping points under climate change and underscore the urgency of proactive mitigation strategies.

ecology↗
bioRxiv2026

Repeated trends in altitudinal gradients of diversity: how habitat filtering and biotic interactions structure ecological communities

Understanding how biodiversity is structured along tropical elevational gradients requires disentangling the relative roles of regional evolutionary history and local processes shaping ecological assemblies. Here, Ithomiini butterfly communities were studied along repeated elevational gradients in two Neotropical regions with contrasting evolutionary histories: the Amazonian Andes and the Guiana Shield. The study tested whether similar elevational patterns of taxonomic, mimetic, and phylogenetic structure emerge despite distinct regional species pools, and whether abiotic and biotic factors contribute to shaping these patterns. Despite marked regional differences in overall richness, consistent elevational patterns emerged across both regions. Taxonomic and mimetic richness increased with elevation and were accompanied by stronger phylogenetic clustering, indicating that similar habitat filtering processes operate along altitudinal gradients irrespective of regional context. Phylogenetic {beta}-diversity was predominantly driven by lineage turnover, particularly in the Andes, highlighting the role of elevational gradients in promoting replacement of phylogenetically distinct lineages rather than simple species loss. These shared patterns suggest that altitude has a strong and repeatable effect on community structure, with habitat filtering acting locally on regionally distinct species pool. Abiotic factors such as temperature appeared to constrain species distributions at broad spatial scales, whereas biotic interactions acted more locally. In particular, butterfly diversity was positively associated with potential host plant richness and predation pressure, indicating that ecological interactions can further shape local community composition once broad-scale environmental constraints are accounted for. By integrating phylogenetic structure, biotic interactions, and environmental gradients across regions with contrasting evolutionary histories, this study shows how regional species pools and local ecological filtering jointly shape tropical biodiversity and highlights that similar elevational assembly processes could arise independently across the Neotropics.

ecology↗
bioRxiv2026

Characterizing Industrial Pond Ecology Timeline in DISCOVR Cultivation Trials for Early Detection of Pond Crashes

For sustainable algal biomass cultivation, we need substantial improvement in annualized productivity by reducing the frequency of crop failure and improved growth in open raceway pond systems. In this study, high-performing strains were identified and optimized for biomass productivity. We utilized next-generation sequencing methods to quantify the ecological features of open raceway systems cultivated at in Arizona. We utilized data from several months of cultivation runs to construct a rich time-series of the ecology dynamics using amplicon sequencing and used custom anomaly detection, "PondSentry", for the early prediction of pond crashes. PondSentry uses tensor decomposition of higher-order joint moments to detect incipient anomalies in multivariate data and displays significant improvements from standard knowledge-based anomaly detection methods. The PondSentry strategy identifies signs of deteriorating pond health at an average of three days before an actual crash event, with rank order of the ecological features plausible for crop failures driven by organisms such as Amoeboaphelidium occidentale FD01. These findings are independently confirmed with PCR and microscopy studies at an Arizona cultivation site. PondSentrys time-series-based anomaly detection of crashes provides a suitable monitoring strategy for eukaryotic crash agents in unialgal culture. The early warnings can be used to time interventions or harvests to prevent biomass loss. The PondSentry strategy strengthens the role of data science and data-driven methods in algal cultivation and can increase the feasibility of algal-biomass based products.

ecology↗
bioRxiv2026

Single-cell sequencing reveals genome streamlining and functional diversity in ecologically dominant marine protists

A large fraction of marine protists, particularly the smallest ones, belong to uncultured lineages that lack genomic data, limiting insights into their ecological roles and evolutionary strategies. Here, we generated 325 single-cell amplified genomes (SAGs) from 2-5 {micro}m planktonic protists, which resulted in 147 genomes from dominant marine species at varying levels of completeness (40 of them >50%). These genomes matched the in situ community, with Prymnesiophyceae, Mamiellophyceae and Chrysophyceae dominating pigmented cells and MAST, Choanoflagellata and Picozoa prevailing among heterotrophic colourless cells. This resource allowed us to describe the genomic architecture of marine protist species, and revealed a pronounced genome streamlining in ecologically successful lineages. Comparative analyses highlighted unique functions enriched in photosynthetic and heterotrophic taxa (including motility, signal transduction, digestion and secondary metabolism), and revealed a broad distribution of gene families with adaptive traits such as polyketide synthases and rhodopsins. This large-scale single-cell genomics dataset provides a mechanistic foundation for investigating functional diversity, ecological strategies and genome evolution in the ocean.

ecology↗
bioRxiv2026

Convergent gliding, divergent ecology: Environmental drivers of gliding vertebrates in Southeast Asia

Gliding has evolved repeatedly across vertebrates and is often regarded as a classic example of convergent evolution associated with arboreal habitats. However, it remains unclear whether convergent locomotion corresponds to shared ecological responses across taxa. In this study, we investigated the distribution patterns and environmental drivers of gliding vertebrates in Southeast Asia using occurrence records and environmental variables representing climate and forest structure. We analyzed five major groups, including flying lemurs, flying squirrels, gliding lizards, gliding snakes, and gliding frogs, using presence-background logistic regression models. Across taxa, temperature seasonality showed consistently negative effects, while canopy height showed positive effects, indicating a shared association with climatically stable environments and well-developed vertical forest structure. In contrast, other environmental variables exhibited substantial taxon-specific variation. For example, elevation showed a strong negative effect only in gliding snakes, suggesting a tendency toward lowland habitats, whereas precipitation variables had limited explanatory power for gliding frogs. These results demonstrate that, despite the convergent evolution of gliding locomotion, ecological responses to environmental factors are not uniform across vertebrate taxa. Instead, species distributions are shaped by a combination of shared functional constraints and lineage-specific ecological traits. Our findings highlight the importance of vertical forest structure and suggest that habitat alteration affecting canopy structure may disproportionately impact certain taxa.

ecology↗
bioRxiv2026

Ecological constraints to mirror life

Our biosphere exhibits remarkable diversity yet is constrained by universal organizational principles, including molecular homochirality. Advances in synthetic biology have raised the possibility of engineering alternative life forms based on mirror-image biomolecules, prompting both technological interest and biosecurity concerns. While current discussions of mirror life largely emphasize molecular feasibility and cellular function, its potential establishment in natural environments remains poorly understood. Here, we develop a theoretical framework to assess the invasion potential of mirror organisms within existing ecosystems. Using population-level models that incorporate resource competition, metabolic constraints, and ecological network interactions, we show that mirror life might face severe limitations arising from both nutrient incompatibility and competitive exclusion by established biota. In particular, the reliance on rare or achiral substrates and the asymmetry of interactions with natural organisms constrain growth and persistence across a broad range of ecological conditions. These results highlight the importance of ecological constraints in evaluating the risks and feasibility of synthetic life.

ecology↗
bioRxiv2026

Least Component Analysis reveals ecological constraints in microbial communities

How microbial communities maintain robust and reproducible ecological functions despite their extraordinary taxonomic diversity remains an open question. Here we show that functional organization in microbial communities can be uncovered by repurposing Principal Component Analysis to focus on directions of lowest variance in taxon abundance data, rather than maximal variance. These least-variance components are statistically significant and correspond to ecological constraints on taxon abundances that are consistently fulfilled across samples. Using consumer-resource models, we show that these constraints arise from resource-mediated interactions and express biomass conservation, effectively grouping taxa into producer and consumer guilds. We validate this interpretation in simulated communities and experimental systems under competition and cross-feeding. Finally, we show that low-variance structure is ubiquitous in natural microbial communities and reveals a sparse network of taxa with disproportionate influence on community structure. Together, our results establish low-variance components as indicators of ecological constraints linking taxonomic diversity to functional organization.

ecology↗
bioRxiv2026

Virome-mediated ecological firewalls govern pathogen eradication in the gut microbiome

Microbiome recovery after antibiotic-induced dysbiosis is often unpredictable, and the ecological mechanisms governing successful gut microbiome restoration remain unclear. Here we introduce a novel dynamical model of bacteria-phage-pathogen interactions to examine how gut virome reshapes gut microbiome states. The model identifies pathogen eradication thresholds and shows that recovery is strongly history-dependent, with bistability allowing either clearance or persistence depending on past conditions. Viral adsorption rates strongly regulate invasion probability and recurrence susceptibility, while microbial diversity enhances stability. Furthermore, we identify an ecological "firewall" mechanism in which the resident microbiome maintains a standing virome community that suppresses pathogen invasion and stabilizes healthy microbiome. These results reveal general ecological principles governing virus-mediated microbiome recovery and inform the design of virome-based therapeutic strategies.

ecology↗
bioRxiv2026

Memory stabilizes complex ecological systems but delays full restoration

Memory effects--defined as the capacity of system states to exert long-lasting influence on subsequent dynamics--are widely recognized as central features of complex living systems. In ecological systems, however, their consequences for stability and recovery dynamics remain poorly understood. To fill this gap, we develop a general theoretical framework that incorporates memory into the dynamics of species-rich ecological systems with complex interaction structures. Our analyses reveal that memory effects expand the stability domain, enabling systems that would otherwise be unstable to persist following perturbations, particularly in cases where instability involves oscillatory behavior. At the same time, memory can accelerate short-term recovery, allowing systems to return more rapidly toward equilibrium in the early stages after perturbation. These apparent benefits, however, come at a cost: memory effects markedly slow long-term recovery, thereby delaying full restoration, as memory retains the influence of past perturbations and hinders a full return to equilibrium. We further support these results by integrating empirical data into the framework. Together, these results reveal fundamental trade-offs mediated by memory--enhanced stability and faster short-term recovery at the expense of delayed full restoration--highlighting the dual role of memory in shaping resilience in complex ecological systems and, more broadly, complex living systems.

ecology↗
bioRxiv2026

Emergent feasibility in random ecological systems with higher-order interactions

A recurring lesson from random ecological models is that coexistence is hard to come by: in the Generalized Lotka-Volterra (GLV) model with pairwise interactions, the probability that randomly sampled parameters admit a positive (feasible) equilibrium - a necessary condition for coexistence - is exactly 1/2n in n species, vanishing rapidly with diversity. This rarity is often read as evidence that coexistence demands specific ecological mechanisms. Real interactions, however, are rarely strictly pairwise: any nonlinear dependence of one species growth rate on anothers abundance, Taylor-expanded, generates higher-order interactions (HOIs) of increasing degree. Treating the interaction order d as a knob that indexes this nonlinearity, we map the random GLV with HOIs onto the Kostlan-Shub-Smale class of random polynomial systems and approximate the probability of feasibility (Pf ) analytically. We find a phase transition at d = 4: below this threshold, Pf decays with diversity as in the pairwise case; above it, the exponential proliferation of equilibria outpaces the probability that any given equilibrium is feasible, and the probability of feasibility increases with n, approaching one. The transition appears to be universal across symmetric coefficient distributions, but vanishes when sign symmetry of the parameter distribution is broken. This work uncovers a route by which feasibility emerges from nonlinearity alone, with no fine-tuning of parameters and no appeal to specific ecological mechanisms.

ecology↗
bioRxiv2026

Biological and ecological insights from a rare underwater footage of the white shark (Carcharodon carcharias) in the Mediterranean Sea

The white shark Carcharodon carcharias (Linnaeus, 1758) is one of the most iconic and threatened marine predators globally and is listed as critically endangered by the IUCN in the Mediterranean Sea, where populations are primarily affected by fishing pressure and the degradation of critical habitats. Available information on Mediterranean white sharks mostly relies on fishing interactions and opportunistic surface records, thereby limiting evaluations on the species ecology. Here, we report an exceptionally rare underwater encounter with this species, documented by divers involved in an expedition aimed at removing ghost fishing gear from a World War II shipwreck in the Strait of Sicily (SoS), central Mediterranean. Given the exceptional nature of this observation, we analysed the video footage in detail with the aim of providing morphological information and novel insights into the species ecology. The footage analysis also allowed close observations on behavioural aspects and on interspecific and parasitic associations, thus providing information that is rarely achievable through surface sightings or from captured individuals, which historically represent the majority of records for this species in the region. To contextualize this observation within the SoS--an area suggested to function as a nursery and reproductive ground for the species--we also provide an updated compilation of records reported in the scientific literature over the last decade, adding 18 new records to existing datasets. This study highlights the value of shipwrecks as observation sites for rare and elusive species, and underscores the importance of non-invasive, video-based approaches in advancing knowledge of a species whose ecology in the Mediterranean remains poorly understood.

ecology↗
bioRxiv2026

Linking automated image analysis to ecological inference: high-throughput monitoring of soil fauna

1 - Automated in situ sensors - e.g., buried scanners - are transforming biodiversity monitoring by generating data at spatio-temporal resolutions unattainable through traditional sampling, including in cryptic environments such as soil that have remained largely inaccessible to existing methods. However, extracting ecologically meaningful information from these data streams requires substantial image processing effort that currently constitutes a critical bottleneck, particularly when the signal-to-noise ratio is low and annotated training data are scarce. 2 - Standard end-to-end deep learning detection pipelines offer unsatisfactory results due to the lack of training data and heterogeneity of the taxa of interest. We explore the potential of combining traditional computer vision algorithms with state-of-the-art deep learning models to build an efficient raw data processing pipelines from limited annotation effort. Specifically, based on the observation that the background barely changes, we focus on the differences between two consecutive images to turn the initial detection problem (with very low signal) into a simpler classification problem, which we solve by fine-tuning foundation models on limited annotated data. 3 - Our approach significantly reduces the annotation effort, allowing us to release an open dataset with about 600 soil scans and more than 8 000 labeled invertebrate occurrences across nine taxa. Using this dataset to train our models, we obtained population count estimates with relative errors ranging from 10% to 61% across taxa over a three-month period. Ecological validation through a land-use stability analysis showed full directional congruence between automated and expert-annotated classifications across all nine taxa examined, with effect-size discrepancies proportional to per-taxon classification accuracy. 4 - These results demonstrate that combining domain-specific heuristics with fine-tuned foundation models provides an effective and data-efficient strategy for automating ecological image processing workflows in low-signal, data-scarce contexts. The validated pipeline removes the manual annotation bottleneck that has historically limited scanner-based soil monitoring to short observational windows and restricted taxonomic scope, opening the way for continuous, large-scale tracking of soil invertebrate community dynamics at resolutions previously unachievable.

ecology↗
bioRxiv2026

The hidden multiverse of ecological roles in Fungi

Ecological roles are treated as discrete, bounded units of biological organization, even as evidence shows that many taxa are versatile, performing more than one of them. Each record of versatility represents a boundary crossing, yet current categorical paradigms prevent this cumulative evidence from reshaping the roles themselves. We solve this by introducing the ecological multiverse, a self-correcting framework that turns boundary crossings into a network of role connectivity. Applied to Fungi, the multiverse recasts the major form of plant pathogenicity from an isolated disease role into a central hub linking much of fungal functional space, especially benign plant symbioses and decomposition. By exposing this topology, the multiverse transforms categorical views of ecological function into a dynamic map, revealing pathways of role change as organisms and knowledge evolve.

ecology↗