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bioRxiv2023

Scattered differentiation of unlinked loci across the genome underlines ecological divergence of the selfing grass Brachypodium stacei

Ecological divergence without geographic isolation, as an early speciation process that may lead finally to reproductive isolation through natural selection, remains one of the most interesting issues in evolutionary biology. However, the patterns of the underlying genetic divergences across the genome vary between different groups. Here we report that Brachypodium stacei, an inbreeding grass species, has been involved in sympatric ecological divergence without geographic isolation. Genomic, transcriptomic, and metabolomic analyses suggest that diploid B. stacei diverged sympatrically in two slopes with contrasting biomes at Evolution Canyon I (ECI), Mount Carmel, Israel, where gene flow has continued freely but reduced with the time. This ecological divergence involved the scattered divergence of many unlinked loci across the total genome that include both coding and non-coding regions. We also identified significantly differential expressions of ABA signaling pathway genes, and contrasting metabolome composition between the arid-vs forest-adapted B. stacei ECI populations. These results suggest that many small loci involved in environmental responses act additively to account for the ecological usages of this species in contrasted environments with gene flow. SignificanceEcological divergence provides evidence for the origin of species through natural selection that has governed evolutionists attention since Darwin. In this study, we present multiple-omics analyses of two plant populations growing sympatrically in contrasted environments and revealed their distinct differentiation across all examined data. These two populations share the most recent ancestor compared with other populations and their divergence started in the early Holocene. We revealed that gene flow had continued but with a progressive reduction over time. The genetic divergences are scattered across the total genome involving many unlinked coding and non-coding regions. These findings highlight the significance of natural selection in the ecological divergence that may finally lead to species formation without geographic isolation.

evolutionary biology↗

bioRxiv2023

Ecological drift during colonization drives within- and between-host heterogeneity in animal symbiont populations

Host-associated microbiomes vary greatly in composition both within and between host individuals, providing the raw material for natural selection to act on host-microbe associations. Nonetheless, the drivers of compositional heterogeneity in host-associated microbiomes have only rarely been examined. To understand how this heterogeneity arises, we utilize the squash bug, Anasa tristis, and its bacterial symbionts in the genus Caballeronia. We artificially modulate symbiont bottleneck size and strain diversity during colonization to demonstrate the significance of ecological drift, which causes stochastic fluctuations in community composition. Consistent with predictions from the neutral theory of biodiversity, ecological drift alone can account for heterogeneity in symbiont community composition between hosts, even when two strains are nearly genetically identical. When acting on competing, unrelated strains, ecological drift can maintain symbiont genetic diversity among different hosts by stochastically determining the dominant strain within each host. Finally, ecological drift mediates heterogeneity in isogenic symbiont populations even within a single host, along a consistent gradient running the anterior-posterior axis of the symbiotic organ. Our results demonstrate that symbiont population structure across scales does not necessarily require host-mediated selection, but emerges as a result of ecological drift acting on both isogenic and unrelated competitors. Our findings illuminate the processes that might affect symbiont transmission, coinfection, and population structure in nature, which can drive the evolution of host-microbe symbiosis and microbe-microbe interactions within host-associated microbiomes.

microbiology↗

bioRxiv2023

Lineage maintenance due to assortative mating but not ecological divergence in a sympatric sibling species pair

The combination of differential adaptation to ecological niches and the development of reproductive barriers are considered helpful for maintaining co-existing species. In the absence of one of these elements, species boundaries are expected to breakdown. The tephritid fruit fly species pair, Bactrocera tryoni and B. neohumeralis, have significant overlap in geographic range and host use, with time of day of male mating the only known difference in their mating systems. Using a combination of ecological (seasonal abundance, host use and habitat use) and genomic data, we tested the differing roles of competition and assortative mating on the maintenance of the species boundaries in this species pair. Genome-wide SNP analyses found strong genetic differentiation between the species with no evidence for hybridization in the field. Most outlier SNPs were restricted to narrow regions towards the centromeres and telomeres of chromosomes and high nucleotide diversity rates were observed throughout the chromosomes of both species. Enrichment of annotation terms indicated an overabundance of genes with the abnormal neuroanatomy term. Terms of interest associated with sleep and circadian rhythm, potentially important to the allochronic reproductive barrier, were non-enriched. Ecological data found limited evidence for ecological differentiation between the two species based on significant positive correlations between species numbers trapped at different times of the year, trapped in different habitats within a region, or when reared from fruit. Our study highlights the significance of assortative mating over ecological differentiation for sympatric maintenance of the B. tryoni/B. neohumeralis sibling pair.

evolutionary biology↗

bioRxiv2023

A culture-based approach to study ecological interactions among the microbial species of the human scalp.

The human scalp hosts an unusually low diversity microbiota dominated by three species: Cutibacterium acnes, Staphylococcus epidermidis, and Malassezia restricta, where characteristic shifts in species frequencies are associated with seborrheic dermatitis and dandruff. In order to better understand this important community, here we study the ecological interactions between these scalp species. We establish a new experimental model system that supports the growth of all three species in vitro and allows one to selectively enumerate each species from co-culture. Our work reveals the potential for strong ecological interactions within the scalp community. In particular, C. acnes greatly benefits from the presence of M. restricta, but harms it in return (exploitation), while S. epidermidis suppresses both M. restricta and C. acnes. Our data suggest that the shifts in composition seen in compromised scalps are influenced by ecological interactions between species. We argue that the scalp microbiome should be viewed as an ecological system where species interactions have the potential to contribute to health outcomes. ImportanceOur bodies are home to diverse communities of microorganisms, our microbiome, which can be critical for health and wellbeing. The human scalp hosts a relatively simple community dominated by three species: two bacteria, Cutibacterium acnes and Staphylococcus epidermidis, and one fungus, Malassezia restricta. Both dandruff and seborrheic dermatitis are strongly associated with characteristic shifts in the frequencies of these three species. However, how these species affect one another and behave as a community remains poorly understood. Here, we develop a simple experimental system to empirically study how these three species interact and affect one another for the first time. We find that S. epidermidis greatly suppresses the growth of the other species, while C. acnes specifically exploits M. restricta. Our work suggests that the human scalp is an ecological system in which species interactions have the potential to affect health outcomes.

microbiology↗

bioRxiv2023

Ecological tradeoffs lead to complex evolutionary trajectories and sustained diversity on dynamic fitness landscapes

The course and outcome of evolution are critically determined by the fitness landscape, which maps genotype to fitness. Most theory has considered static fitness landscapes or fitness landscapes that fluctuate according to abiotic environmental changes. In the presence of biotic interactions between coexisting genotypes, the fitness landscape becomes dynamic and frequency-dependent. Here, we introduce a fitness landscape model that incorporates ecological interactions between individuals in a population. In the model, fitness is determined by individuals competing for resources according to a set of traits they possess. An individuals genotype determines the trait values through a Rough Mount Fuji fitness landscape model, allowing for tunable epistasis (i.e., non-additive gene interaction) and trait correlations (i.e., whether there are tradeoffs or synergies in the ability to use resources). Focusing on the effects of epistasis and trait correlations, we quantify the resulting eco-evolutionary dynamics under simulated Wright-Fisher dynamics (i.e., including genetic drift, mutation, and selection under the assumption of a constant population size) on the dynamics fitness landscape in comparison with a similar, static, fitness landscape model without ecological interactions. Whereas the non-ecological model ultimately leads to the maintenance of one main geno-type in the population, evolution in the ecological model can lead to the long-term coexistence of several genotypes at intermediate frequencies across much of the parameter range. Including ecological interactions increases steady-state diversity whenever the trait correlations are not too strong. However, strong epistasis can hinder coexistence, and additive genotype-phenotype maps yield the highest haplotype diversity at the steady state. Interestingly, we frequently observe long-term coexistence also in the absence of induced trade-offs in the ability to consume resources. In summary, our simulation study presents a new dynamic fitness landscape model that highlights the complex eco-evolutionary consequences of a (finite) genotype-phenotype-fitness map in the presence of biotic interactions.

evolutionary biology↗

bioRxiv2023

Complex allometric relationships and ecological factors shape the development and evolution of eye size in the modular visual system of spiders

Eye size affects many aspects of visual function, most notably including contrast sensitivity and achievable spatial resolution, but eyes are costly to grow and maintain. The allometry of eyes can provide insight to this trade-off in the context of visual ecology, but to date, this has mainly been explored in species that have a single pair of eyes of equal size. By contrast, animals possessing larger visual systems can exhibit variable eye sizes within individuals. Spiders have up to four pairs of eyes whose size often varies, but their ontogenetic, static, and evolutionary allometry has not yet been studied in a comparative context. We report variable evolutionary and developmental dynamics in eye size across 1098 individuals in 39 species and 8 families, indicating selective pressures and constraints driving the evolution of different eye pairs and lineages. We observed variation in the relationship between eye and body size not only between taxa and visual ecologies, but between eye pairs within species, indicating that growth dynamics are variable and can be divergently adapted in particular eye pairs. Supplementing our sampling with a phylogenetically comprehensive dataset recently published by Wolff et al. (2022), we confirmed these findings across more than 400 species, found that ecological factors such as visual hunting, web building, and diurnality can also impact eye diameter, and identified significant allometric shifts across spider phylogeny using an unbiased approach, many of which coincide with ecological changes such as visual pursuit hunting strategies. This study represents the first detailed comparative exploration of visual allometry in spiders, revealing striking differences in eye growth not only between families but also within species. Our findings shed light on the relationship between spider visual systems and their diverse ecologies, and how spiders exploit the modular nature of their visual systems to balance selective pressures and optical and energetic constraints.

evolutionary biology↗

bioRxiv2024

Modeling tumors as species-rich ecological communities

Many advanced cancers resist therapeutic intervention. This process is fundamentally related to intra-tumor heterogeneity: multiple cell populations, each with different mutational and phenotypic signatures, coexist within a tumor and its metastatic nodes. Like species in an ecosystem, many cancer cell populations are intertwined in a complex network of ecological interactions. Most mathematical models of tumor ecology, however, cannot account for such phenotypic diversity nor are able to predict its consequences. Here we propose that the Generalized Lotka-Volterra model (GLV), a standard tool to describe complex, species-rich ecological communities, provides a suitable framework to describe the ecology of heterogeneous tumors. We develop a GLV model of tumor growth and discuss how its emerging properties, such as outgrowth and multistability, provide a new understanding of the disease. Additionally, we discuss potential extensions of the model and their application to three active areas of cancer research, namely phenotypic plasticity, the cancer-immune interplay and the resistance of metastatic tumors to treatment. Our work outlines a set of questions and a tentative road map for further research in cancer ecology.

cancer biology↗

bioRxiv2024

Socio-ecological context modulates significance of territorial contest competition in Drosophila prolongata

The intensity and direction of sexual selection is intricately linked to the social and ecological context. Both operational sex ratios (OSRs) and population densities can affect the ability of males to monopolize resources and mates, and thus the form and intensity of sexual selection on them. Here, we studied how the mating system of the promiscuous and strongly sexually dimorphic fruit fly Drosophila prolongata responds to changes in the OSR and population density. We recorded groups of flies over five days and quantified territory occupancy, mating success, and competitive fertilization success. Although sexual selection was stronger under male-biased than even OSRs but unrelated to density, realized selection on morphological traits was higher under even OSRs and increased with density. Larger and more territorial males achieved both higher mating success and competitive fertilization success, but only under even OSRs. Our combined results also support a shift in the mating system from territorial contest competition to scramble competition under male-biased OSRs and potentially at low density, where there was no clear contribution of the measured traits to reproductive success. Our study emphasizes the limitations of traditional selection metrics and the role of the socio-ecological context in predicting adaptation to a changing environment. SignificanceMating systems are complex and dynamic, adapting to ongoing ecological change. Studies often assume that changes in the socio-ecological context alter the intensity of sexual selection on traits indicating individual fitness, but our work on Drosophila prolongata challenges this view. By manipulating operational sex ratio and population density, and jointly investigating territorial behavior and both pre- and post-mating reproductive success over several days, we reveal the plastic mating strategies in this fly. This dynamism underscores the limitations of static classifications and the importance of studying selection across diverse socio-ecological contexts. This broader perspective advances our understanding of the tight connections between environmental change, population demographics, and the evolutionary process.

evolutionary biology↗

bioRxiv2024

Drivers of ecological success for Escherichia coli vary among human gut microbiome samples from different individuals

Gut microbial community composition varies from one person to another. Potentially, this means the ecological interactions experienced by individual strains or species also vary among microbiomes of different people. However, testing this directly in human microbiomes and identifying ecological drivers involved is challenging. Here, we use replicated anaerobic microcosms to quantify variability of population growth for a key commensal species among microbiome samples from different individuals, and to identify underlying intra- and interspecific interactions. In a reciprocal transplant experiment, both absolute and relative growth performance of different Escherichia coli strains varied among gut microbiome samples from healthy individuals. This was partly explained by intraspecific competition: ecological success of individual E. coli strains was associated with displacement of resident conspecifics. However, the determinants of E. coli growth varied among samples. In one microbiome sample with a distinctive taxonomic composition, culture acidification by resident microbes impaired growth of all E. coli strains. We identified a strain of Clostridium butyricum contributing to this effect, and showed that transferring it into other microbiomes predictably altered pH, fermentation product profiles (butyrate accumulation and acetate/lactate depletion) and population growth of other species including E. coli, thereby reshaping overall taxonomic composition. Our results suggest natural inter-individual gut microbiome variation translates to variable ecological interactions with incoming bacteria, but these dynamics can be manipulated by a generalizable interspecies interaction. Significance statementGut-microbiome variation among healthy individuals is widely documented, yet its impact on the success of incoming bacterial strains and its implications for microbiome-targeted interventions remain unclear. Here, we test this experimentally by cultivating stool samples from healthy individuals and transplanting strains across samples. We reveal a functional relationship between microbiome variation and growth performance of individual strains. This underscores the challenge of predicting colonization outcomes. Yet, we identify a taxon contributing to the distinct functional profile of one of the samples, and show that its transplantion into other microbiome samples reproducibly alters key properties, including pH and population growth of other bacteria, revealing a common ecological control point. These findings advance our ability to explain and manipulate human gut-microbiome variation.

microbiology↗

bioRxiv2024

Spatiotemporal dynamics of non-ecological speciation in rubyspot damselflies (Hetaerina spp.)

Non-ecological speciation is a common mode of speciation which occurs when allopatric lineages diverge in the absence of pronounced ecological differences. Yet, relative to other speciation mechanisms, non-ecological speciation remains understudied. Numerous damselfly clades are characterized as non-adaptive radiations (the result of several rounds of non-ecological speciation), but there are few damselfly lineages for which we have a detailed understanding of the spatiotemporal dynamics of divergence. Recent phylogeographic analyses demonstrate that American rubyspot damselflies (Hetaerina americana sensu lato) actually comprise at least two cryptic lineages that coexist sympatrically across most of Mexico. To broaden our understanding of the dynamics of diversification to other rubyspot lineages, we investigated the phylogeographic history of smoky rubyspot damselflies (Hetaerina titia) using genomic data collected across Central and North America. Unexpectedly, we found evidence of reproductive isolation between the highly genetically differentiated Pacific and Atlantic lineages of H. titia in a narrow secondary contact zone on the Isthmus of Tehuantepec, Mexico. We then fit models of historical demography to both H. americana sensu lato and H. titia to place these comparisons in a temporal context. Our findings indicate that Pacific and Atlantic lineages of H. titia split more recently than the broadly sympatric lineages within H. americana sensu lato, supporting key assumptions of the non-ecological speciation model and demonstrating that these two pairs of sister lineages are at different stages of the speciation cycle.

evolutionary biology↗

bioRxiv2025

Ecological niche differentiation mediates near complete premating reproductive isolation within the Gladiolus carneus (Iridaceae) species complex.

Background and aimsEcological niche differentiation is well associated with intraspecific divergence of functional traits, which may lead to the evolution of premating reproductive isolation. However, the link between the ecological niches, trait divergence, and premating isolation remains poorly understood. This is particularly pertinent in hyper-diverse areas such as the Cape Floristic Region (CFR) of South Africa, where fine-scale ecological heterogeneity has been hypothesised as a major driver of speciation. Using the polymorphic geophyte Gladiolus carneus, endemic to the CFR, we test whether ecological niche differentiation mediates premating reproductive isolation. MethodsWe first tested whether newly and previously described Gladiolus carneus varieties were distinct based on their floral and vegetative morphology. Next, we documented each varietys abiotic niche, flowering phenology and pollination niche and further tested whether any resulting niche differentiation causes premating reproductive isolation. Key resultsSeven morphologically distinct varieties were identified, of which two of these are newly documented. Using niche modelling and multivariate analyses, we found that these varieties occupied distinct abiotic niches, resulting in strong ecogeographic isolation. They also had distinct flowering times, causing varying strengths of phenological isolation. For the pollinator niche, we found that all sampled populations had a single highly effective functional pollinator; however, at the variety level, there were no consistent trends leading to varying strengths in pollinator-mediated isolation. Across all varieties, ecogeographic isolation was the strongest gene flow barrier, which combined with phenological and pollinator-mediated isolation, causes near complete premating reproductive isolation. ConclusionsThese results suggest that ecological niche differentiation between Gladiolus carneus varieties may be contributing to incipient speciation within the species complex and further suggests that ecological niche differentiation may be a major driver of speciation in the hyper-diverse Cape Floristic Region.

evolutionary biology↗

bioRxiv2025

Ecological opportunity and the onset of polyploid niche expansion waves

Polyploidy, the presence of more than two sets of chromosomes, has evolved many times across the tree of life, yet we still do not know why some polyploid lineages persist while most go extinct. The establishment of polyploid populations is often reported to be associated with harsh environmental conditions, and stress tolerance in particular, which have led to the widespread view that polyploidy-specific niche requirements are key to their persistence at ecological and evolutionary timescales. Here, we reevaluate this perspective through a classical mathematical model of polyploid establishment, for which we provide new analytical and numerical results, along with an empirical case study. We show that simple eco-evolutionary processes at the margins of diploid range-expansion waves, more specifically ecological drift and dispersal limitation, can be sufficient to allow polyploid populations to carve out their own space, without any a priori adaptive advantage over their diploid ancestors. Our modelling effort reveals three key insights. First, polyploids most readily gain a foothold at the low-density front of a diploid range expansion wave, where ecological drift is strongest. Second, limited dispersal accelerates spatial clustering of polyploid organisms through assortative mating. Third, once spatially segregated, diploid and polyploid populations experience different environments, so natural selection can drive niche divergence. We illustrate these interconnected principles by simulating the phylogeographic history of a well-documented autopolyploid complex of Neobatrachus Australian burrowing frogs. Altogether, our results provide a neutral baseline against which the ecological consequences of polyploidization can be readily detected and inferred within natural populations. Significance statementPolyploidy, having multiple copies of the entire set of chromosomes, underpins major innovations in both animals and plants and fuels biodiversity. Yet, why some polyploid lineages are successful while others fail remains unclear. Our study shows that simple eco-evolutionary forces, specifically ecological drift at the edge of an expanding range and limited dispersal, can enable polyploids to establish and become geographically separated from their diploid relatives, even without any inherent adaptive benefits. This spatial segregation then exposes each cytotype to distinct environments, setting the stage for natural selection to operate. Our neutral theoretical framework helps biologists disentangle when polyploidy itself drives adaptation and when success is just a matter of being in the right place at the right time.

evolutionary biology↗

bioRxiv2025

Unwelcome guests: characterizing the ecological niche of insertion sequences within prokaryotic genomes

Insertion sequences (ISs) are widespread prokaryotic transposable elements, often regarded as genomic parasites that primarily cause deleterious mutations. However, they can also promote adaptive changes. These antagonistic properties make their overall impact on prokaryotic evolution difficult to grasp. Here, we address this challenge by leveraging the framework of transposon ecology to analyze IS occurrences across and within 30,499 prokaryotic genomes. Combining phylogenomics with multi-scale genomic analysis, quantitative ecology, and mathematical modeling, we provide evidence that although genomes generally provide sufficient resources for IS coexistence, universal mechanisms shape their occurrence and chromosomal distribution across genomes. These include: (i) the preferential localization of ISs within highly variable and GC-heterogeneous chromosomal regions of genomic plasticity (RGPs), which act as the primary reservoir of IS niches; (ii) a linear scaling between IS abundance and niche size, with an average of 5.4 additional accessible insertion sites per IS; (iii) a dependence of IS occurrence on the presence of other ISs, suggesting a form of group behavior; (iv) the accumulation of AT-rich sequences in both coding and non-coding regions up to 100 kb surrounding ISs, indicative of ecological isolation; and (v) the spatial partitioning of mobile genetic elements around ISs, reminiscent of ecological niche differentiation. Besides these general principles, we also uncover niche specificities associated with particular IS families, hinting at regulatory mechanisms that modulate IS activity. Altogether, this comprehensive transposon ecology approach offers new insights and avenues for understanding IS-host interactions and genome evolution, moving beyond traditional host-centric perspectives.

genomics↗

bioRxiv2025

Copy number variation facilitates rapid toggling between ecological strategies

A central question in evolutionary biology is how different types of mutations shape ecological strategy. Whereas both single nucleotide variants (SNVs) and copy number variants (CNVs) can alter gene dosage, it remains unclear whether CNVs confer unique adaptive advantages. Here, we show that CNVs do not mediate adaptive tracking in fluctuating environments, but instead act as reversible toggles between ecological strategies. Using a dual-fluorescent CNV reporter system in Saccharomyces cerevisiae, we tracked CNV dynamics at two transporter loci during long-term evolution under static and fluctuating nitrogen limitation. CNVs arose with high repeatability in static conditions but showed dampened or divergent dynamics in fluctuating environments, suggesting they do not track environmental change. Instead, we found that the ratio of copy number between the two loci, but not copy number at either locus alone, predicted ecological strategy: imbalanced CNV ratios defined specialists, while balanced ratios defined generalists. Evolution in static environments favored specialists whereas fluctuating environments favored generalists. Applying this framework to over 3,000 sequenced yeast genomes, we found generalist CNV signatures in both wild and domesticated strains, but specialist signatures exclusively in domesticated strains. These findings introduce a generalizable framework for predicting ecological strategy from genome structure, positioning CNV ratios as a molecular signature of niche breadth across evolutionary and ecological contexts.

evolutionary biology↗

bioRxiv2025

Adaptive radiation along ecological and morphological lines of least resistance in Cyprinodon pupfishes

Adaptive radiation results in part from ecological opportunity in a new environment, but it is unclear how pre-existing constraints in the founding population may limit this process. Genetic lines of least resistance, and by proxy morphological variance, are known to limit adaptive divergence, but ecological variance is rarely investigated. Here we test whether ecological or morphological lines of least resistance in generalist populations may have constrained the directions of species divergence in two independent Caribbean adaptive radiations of Cyprinodon pupfishes. We find almost universal congruence between the major multivariate dimensions of intraspecific craniofacial and dietary variance within generalist populations and the major axes of interspecific divergence within each adaptive radiation. This is surprising given that we document unique trophic specialists within each radiation, including a bivalve-specialist, zooplanktivore, molluscivore/ostracod-specialist, and scale-eating specialist, while nearly all generalist populations were observed to feed rarely on these same resources. We conclude that pre-existing genetic constraints within each founding generalist population, resulting in dimensions of greater ecological and morphological variance, may partially constrain and predict the directions of species divergence and dietary specialization during adaptive radiation. We also provide a new framework for examining ecological lines of least resistance.

evolutionary biology↗

bioRxiv2025

Comparative Characterization Reveals Conserved and Divergent Ecological Traits of Oral Corynebacteria

Corynebacteria are abundant members of the oral microbiome and increasingly recognized as key structural organizers of supragingival biofilms. Despite their prevalence, the ecological roles and phenotypic traits of many oral corynebacterial species remain poorly defined. Here, we isolated and characterized two new strains, Corynebacterium durum JJ2 and Corynebacterium argentoratense MB1, and compared them with reference strains Corynebacterium durum JJ1 and Corynebacterium matruchotii ATCC14266. Phenotypic assays revealed that C. durum strains displayed robust aggregation, thick biofilm formation, and extensive extracellular polymeric substance (EPS) networks, whereas C. argentoratense and C. matruchotii formed thinner biofilms with minimal EPS production. All four strains secreted extracellular membrane vesicles (EMVs) capable of inducing chain elongation in Streptococcus sanguinis, underscoring a conserved interspecies signaling function. Genomic analysis demonstrated close relatedness between C. durum and C. matruchotii, while C. argentoratense was more distantly related, with a reduced genome, fewer metabolic pathways, and absence of nitrate reductase genes, consistent with its inability to grow under anaerobic conditions. These findings suggest that C. argentoratense may represent a less specialized or transient inhabitant of the oral cavity, whereas C. durum and C. matruchotii are well adapted to the oral niche. Together, this study expands our understanding of phenotypic diversity, metabolic capacity, and interspecies interactions among oral corynebacteria, highlighting their potential importance as biofilm organizers and contributors to oral microbial ecology. ImportanceOral Corynebacteria contribute to the structural and ecological stability of supragingival communities. Yet, their species-level functions remain poorly defined. By isolating and characterizing new strains of Corynebacterium durum and Corynebacterium argentoratense, and comparing them with reference strains including C. matruchotii, we provide new insight into their phenotypic diversity, metabolic capacity, and ecological roles. Our results demonstrate that C. durum strains form robust biofilms enriched in extracellular polymeric substances, while C. argentoratense produces thinner biofilms and lacks the genomic features required for anaerobic growth, suggesting a less specialized or transient role in the oral cavity. Importantly, we show that extracellular membrane vesicles secreted by all tested strains promote chain elongation in Streptococcus sanguinis, highlighting a conserved mechanism of interspecies communication. These findings advance our understanding of how oral corynebacteria contribute to biofilm organization and microbial homeostasis, and position them as critical but understudied players in oral microbial ecology.

microbiology↗

bioRxiv2025

From ecology to evolution: plasmid- and colicin-mediated persistence of antibiotic resistant Escherichia coli in gulls

Antimicrobial resistance in wildlife is an emerging concern within the One Health concept. Gulls, due to their synanthropic behaviour and long-distance migration, are recognised as vectors and secondary reservoirs of resistant bacteria. These birds can facilitate the environmental spread of resistant strains across ecosystem boundaries. Understanding their role in shaping microbial communities is essential for assessing the broader ecological impact. This study investigates the persistence and competitive dynamics of cephalosporin-resistant Escherichia coli in Caspian gulls captured at their breeding colony at a water reservoir and subsequently monitored in captivity for three months, representing the longest in vivo experiment of its kind conducted on wild birds. We observed sustained colonization and long-term shedding of resistant E. coli throughout the entire study, marking the longest documented carriage of resistant bacteria in wild birds to date. Notably, rapid dissemination of various E. coli sequence types (STs) with CTX-M-1 was observed, with ST11138 rapidly outcompeting other strains, including the initially dominant ST11893. Genomic analyses revealed that ST11138 harboured F24:A-:B1 and IncI1/ST3/CTX-M-1 plasmids encoding colicins and corresponding immunity genes, likely conferring a competitive advantage. Our findings underscore the role of bacteriocin-mediated interactions in shaping microbial communities and highlight the importance of plasmid-encoded traits in the persistence of resistant strains in wildlife. Importantly, our findings underscore the ecological novelty of longitudinal in vivo tracking of AMR persistence in natural hosts and highlight the need to consider ecological and microbiome-level interactions when assessing the environmental dimension of AMR under the One Health concept. ImportanceAntimicrobial resistance in wildlife is an emerging concern within the One Health framework, with gulls recognized as important vectors and secondary reservoirs of resistant bacteria. Due to their synanthropic behaviour and long-distance migration, these birds can facilitate the spread of resistant strains across ecosystems. However, the role of wildlife in resistance dynamics remains underexplored, especially in long-term, natural settings. Our study is unique in its scope and duration, representing the longest in vivo experiment of its kind conducted on wild birds. By capturing these processes in live hosts under naturalistic conditions and across an extended period, our study provides rare and ecologically grounded insights into how antimicrobial resistance is maintained outside clinical or laboratory settings. Our findings show sustained colonization and long-term shedding of resistant E. coli, with strain ST11138 outcompeting others. Genomic analyses reveal plasmid-encoded traits, highlighting the novel ecological and evolutionary mechanisms underlying resistance maintenance in wildlife.

microbiology↗

bioRxiv2025

How to catch flies in the city (fast): Citizen Science on Drosophila ecology helps to raise awareness for biodiversity in urban environments

To efficiently mitigate biodiversity loss both robust ecological data and broader societal engagement are needed. Citizen science offers a pathway to address these dual challenges by combining data collection with public involvement. Here, we introduce the citizen science project Vienna City Fly, conducted at the Natural History Museum Vienna (NHMW), which used fruit flies (Drosophila) as a model organism group for urban biodiversity research and public engagement. Participants deployed standardized traps across Vienna, enabling systematic sampling and active participation in research, which resulted in hundreds of fly collections, thousands of sampled fly specimens and new insights into the biodiversity and ecology of the collected fly species, demonstrating the feasibility of large-scale ecological research through public collaboration. To assess motivational drivers and perceived impacts of participation, we conducted an online survey (N=59) using the validated psychometric MORFEN-CS scale. Survey results revealed that nature conservation values and the intention to contribute to biodiversity conservation emerged as the strongest drivers of engagement, complemented by sociopolitical responsibility and citizen science-based motivations. Reported outcomes include knowledge gain (61%), more positive attitude toward study organisms (50%), and increased awareness of biodiversity (30%). Satisfaction was very high, with 85% rating their experience at the top of the scale and all participants expressing willingness to join future citizen science projects. Recruitment occurred mainly via social networks, and the sample of participants was highly educated, indicating limits to inclusivity and reach. Our findings demonstrate that citizen science can contribute to robust ecological data collection while gaining knowledge and awareness. Natural history museums, as trusted institutions, play a key role in facilitating such initiatives. Overall, Drosophila research proves to be a suitable field for citizen science, combining accessibility with strong potential for advancing ecological and biodiversity research as well as public engagement in urban biodiversity research.

scientific communication and education↗