Biology subjects

Adrian-Kalchhauser, I.

Publications and source records attributed to Adrian-Kalchhauser, I..

11 recordsLinked to original sources

bioRxiv2026

Early-life conditions shape baseline immune gene expression, but not pathogen-induced immune activation, in brown trout

Early-life environment and parental background can shape immune phenotypes, but whether such differences persist during infection and influence the immune response remains unclear. We used single-cell RNA sequencing to characterize kidney immune responses in brown trout (Salmo trutta) from three origins differing in parental history and early rearing: wild parents with offspring reared in the wild; wild parents with offspring reared in a hatchery; and hatchery parents with offspring reared in a hatchery. All fish originated from the same river and showed no detectable genetic population structure. Fish were exposed to Tetracapsuloides bryosalmonae, the causative agent of proliferative kidney disease, and analyzed 25 days later alongside unexposed controls. Across 18 scRNA-seq datasets, we identified 30 cell clusters and found a clear transcriptional imprint of developmental and parental history in the resting immune system. In unexposed fish, origin was associated with pronounced differences in gene expression, particularly in B cells. When fish were subsequently exposed to the pathogen and developed subclinical infections, both immune-cell composition and transcriptional state experienced pronounced changes: T cells increased in relative abundance, while B cells, neutrophils and proliferating progenitors showed the strongest transcriptional responses, consistent with an active but controlled subclinical response. Strikingly, the strong origin-dependent differences present before exposure largely disappeared after infection. Fish from all three backgrounds converged on a shared transcriptional response, and genes associated with origin showed little overlap with those responding to infection. Thus, at single-cell resolution in vivo, we identify infection-induced transcriptional convergence across distinct environmental and parental backgrounds. Our findings show that substantial baseline immune variation can persist under resting conditions yet be overridden by pathogen exposure, constraining distinct immune states towards a common response.

immunology↗

bioRxiv2026

Persistent maternal memory, transient offspring effects: the temporal and sex-specific architecture of heritable heat-stress responses in zebrafish

Environmental experiences can influence subsequent generations, yet little is known about the dynamics of such molecular memories across time, reproduction events, and offspring development. Here we provide a temporal map of the transmission of environmental information through egg provisioning and its phenotypic consequences in zebrafish. Specifically, we follow the effects of a 2-week heat wave across successive matings and two unexposed generations along a complete adult-to-egg-to-adult experimental trajectory, assessing gonad responses, maternal RNA, embryo survival, larval behaviour, adult stress resistance and liver transcriptomes. We find that oocyte maternal RNA retained a pronounced heat-shock signature across several weeks and multiple spawning events, with selected functional components persisting into oocytes of the next generation. Somatic responses followed a fundamentally different trajectory: effects on liver transcription were sex- and timepoint-specific, with minor intergenerational signatures of energy metabolism and metabolic stress in males. Parental heat exposure also altered offspring survival, larval behaviour and thermal tolerance, with progressively weakened effects across successive reproductive events and across generations. Our results reveal distinct temporal dynamics of environmental memory in the germline vs the developing and adult soma, with persistent molecular information in maternal provisioning coexisting with progressively fading offspring phenotypes. Such selective retention and loss of parental information align with theoretical predictions about the progressively declining value of inherited information and may determine the dynamics of cross-generational population-level responses to extreme events.

evolutionary biology↗

bioRxiv2025

Single-cell RNA sequencing reveals influences of rearing environment on cellular immunity in brown trout (Salmo trutta)

Vertebrate immune systems exhibit striking evolutionary diversity, yet our understanding remains biased toward mammalian models. Here, we generate a single-cell atlas of immune cells from the ecologically and economically important salmonid Salmo trutta (brown trout), a lineage characterized by an ancestral whole-genome duplication (WGD). Profiling over 83,000 kidney-derived immune cells, we resolved 34 transcriptionally distinct populations, identified core immune lineages, and uncovered novel markers in neutrophils, macrophages, T- and B-cells. We detected pervasive transcriptional divergence between WGD-derived ohnologue pairs, indicating putative sub- and neofunctionalization in immune gene regulation. We further show that the transcriptional identity of immune cells is shaped by rearing history: fish raised in hatcheries--whether for one or multiple generations--showed shifts in immune gene expression across cell types. These included genes involved in G protein-coupled receptor signalling, a process which has previously been implicated in domestication. Our findings provide insight into the evolution of vertebrate immunity and raise concerns about the immunological fitness of hatchery-reared fish released into the wild.

immunology↗

bioRxiv2025

Success factors for inter- and transdisciplinary research. Lessons from a decade of studies on invasive aquatic species.

Ecological research for environmental management occupies a unique and demanding space at the interface of societal needs and academic research. Projects in this space must reconcile stakeholder involvement and real-world applicability with academic requirements such as disciplinary excellence and career advancement. Here, we present a post-hoc account of a 12-year inter- and transdisciplinary research initiative on the management of invasive gobies in central Europe. Based on a synthesis of inputs, outputs, and outcomes, we distill facilitating conditions that increased the likelihood of the project reaching its goals across political, administrative, societal, institutional, team, and individual levels. Rather than "success factors" in a deterministic sense, these are conditions and practices that created a favorable environment for both academic and applied outcomes. The interaction of these domains created windows of opportunity that could be seized for both scientific progress and societal impact. By reflecting from the perspective of natural scientists directly engaged in such a project, we aim to complement existing social science frameworks with an insider view of the lived realities of inter- and transdisciplinary collaboration. Our retrospective can inform policy makers, funders, and institutions seeking to create enabling environments for interface research, and may support fellow natural scientists in proactively preparing the ground for their own initiatives.

scientific communication and education↗

bioRxiv2024

Towards an eco-epidemiological framework for managing freshwater crayfish communities confronted with crayfish plague

Wildlife diseases figure prominently among the main causes of biodiversity loss worldwide. Especially fungal and fungus-like pathogens are on the rise, wreaking havoc across the tree of life by threatening species persistence and destabilizing ecosystems. A worrisome example are freshwater crayfish species in Eurasia and Oceania, facing the dual challenge of introduced competitive crayfish species and an introduced water mold (Aphanomyces astaci) causing crayfish plague. A. astaci locally extinguishes susceptible native crayfish populations, while non-native individuals (mostly from North America) remain largely unaffected. Despite its significant impact and its [~]150 years of presence in Europe, studies and disease management recommendations for crayfish plague that are firmly rooted in epidemiological theory are scarce. Here, we present a practical eco-epidemiological framework to understand how multi-species crayfish communities react to crayfish plague introductions. The framework is based on the observation that the dynamics of crayfish communities are mainly determined by life-history characteristics, within- and among-species competition, effects of generalist predators (including fishing), and host-pathogen interactions. From this ecological and epidemiological context, we derive fundamental epidemiological metrics, single-host species and community-level basic reproduction numbers (R0). We investigate how host species densities affect the likelihood of a disease outbreak in a crayfish community, and we demonstrate that a communitys R0 value is simply the sum of the communitys single-host species R0 values, adjusted for competition and predation. We further demonstrate how R0 can be used to guide preventative and mitigation actions for crayfish communities. For example, we show how R0 expressions - even without a detailed parametrization - can be used to construct regional risk rankings for different crayfish communities, for an effective allocation of resources to local conservation plans. Our eco-epidemiological framework will also be of interest to the management of other aquatic host-pathogen systems with water-borne pathogen transmission as the main route of pathogen spread.

ecology↗

bioRxiv2023

An adaptable, user-friendly score sheet to monitor welfare in experimental fish

Fish are increasingly used as experimental animals across research fields. Currently, a quarter of all experimental animals used in Europe are fish. Less than 20% of these are standard model species. Welfare assessments for experimental fish are in their infancy compared to rodents. This can be attributed to the diversity of species used, the relative recency of fish as go-to model for research, and challenges to assess welfare and pain in non-vocal underwater species. The lack of guidelines and tools presents a challenge for researchers (particularly, for newcomers), for ethics committees, and for implementing refinement measures. Here, we present an adaptable, user-friendly score sheet for fish. The parameters contained in the excel tool are based on a literature review, have been validated by expert interviews, and evaluated by a fish pathologist. The tool allows to score individuals as well as groups, calculates summary scores and visualizes trends. We provide the underlying literature, give use examples and provide instructions on the adaptation and use of the score sheet. We hope that this tool will empower researchers to include welfare assessment in their routines, foster discussions on fish welfare parameters among scientists, facilitate interactions with ethics committees, and most importantly, enable the refinement of fish experiments.

animal behavior and cognition↗

bioRxiv2023

Analysis of a European general wildlife health surveillance program: chances, challenges and recommendations

In the context of a One Health perspective general wildlife health surveillance (GWHS) gains importance worldwide, as pathogen transmission among wildlife, domestic animals and humans raises health, conservation and economic concerns. However, GWHS programs operate in the face of legal, geographical, financial, or administrative conditions. The present study uses a multi-tiered approach to understand the current characteristics, strengths and gaps of a European GWHS that operates in a fragmented legislative and multi-stakeholder environment. The aim is to support the implementation or improvement of other GWHS systems by managers, surveillance experts, and administrations. To assess the current state of wildlife health investigations and trends within the GWHS, we analyzed 20 years of wildlife diagnostic data, conducted an online survey and phone interviews with official field partners (hunting administrators, game wardens and hunters), and performed a time-per-task analysis. Firstly, we found that infectious disease dynamics, the level of public awareness for specific diseases, research activities and increasing population sizes of in depth-monitored protected species, together with biogeographical and political boundaries all impacted case numbers and can present unexpected challenges to a GWHS. Secondly, we found that even a seemingly comprehensive GWHS can feature pronounced information gaps, with underrepresentation of common or easily recognizable diseases, blind spots in non-hunted species and only a fraction of discovered carcasses being submitted. Thirdly, we found that substantial amounts of wildlife health data may be available at local hunting administrations or disease specialist centers, but outside the reach of the GWHS and its processes. In conclusion, we recommend that fragmented and federalist GWHS programs like the one addressed require a central, consistent and accessible collection of wildlife health data. Also, considering the growing role of citizen observers in environmental research, we recommend using online reporting systems to harness decentrally available information and fill wildlife health information gaps.

zoology↗

bioRxiv2022

High nucleotide diversity accompanies differential DNA methylation in naturally diverging populations

Epigenetic mechanisms such as DNA methylation (DNAme) are thought to comprise an invaluable adaptive toolkit in the early stages of local adaptation, especially when genetic diversity is constrained. However, the link between genetic diversity and DNAme has been scarcely examined in natural populations, despite its potential to shed light on the evolutionary forces acting on methylation state. Here, we analysed reduced-representation bisulfite sequencing and whole genome pool-seq data from marine and freshwater stickleback populations to examine the relationship between DNAme variation (between- and within-population), and nucleotide diversity in the context of freshwater adaptation. We find that sites that are differentially methylated between populations have higher underlying standing genetic variation, with diversity higher among sites that gained methylation in freshwater than those that lost it. Strikingly, while nucleotide diversity is generally lower in the freshwater population as expected from a population bottleneck, this is not the case for sites which lost methylation which instead have elevated nucleotide diversity in freshwater compared to marine. Subsequently, we show that nucleotide diversity is higher among sites with ancestrally variable methylation and also positively correlates with the sensitivity to environmentally induced methylation change. Both suggest that as selection on the control of methylation state becomes relaxed, so too does selection against mutations at the sites themselves. Increased epigenetic variance in a population is therefore likely to precede genetic diversification.

evolutionary biology↗

bioRxiv2022

Detecting aquatic pathogens with field-compatible dried qPCR assays

Field-ready qPCR assays with a long shelf-life support monitoring programs for emerging aquatic pathogens and enable quick conservation and management decisions. Here, we develop, validate, and test the shelf-life of qPCR assays targeting Gyrodactylus salaris and Aphanomyces astaci with lyophilization and air-drying.

microbiology↗

bioRxiv2022

Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems

Recirculating aquaculture systems (RAS) heavily depend on microbial communities to maintain water quality. These communities therefore influence the growth, development, and welfare of farmed fish. With the increasing socio-economic role of fish farming e.g. regarding food security, an in-depth understanding of aquaculture microbial communities is also relevant from a management perspective. However, the data situation regarding the composition of microbial communities within RAS is patchy. Since this is partly ascribed to method choices, there clearly is a need for accurate, standardized, and user-friendly methods to study microbial communities in aquaculture systems. Here, we compare the performance of 16S amplicon sequencing, Pac-Bio long-read amplicon sequencing, and amplification-free shotgun metagenomics in the characterization of microbial communities in two commercial-size RAS fish farms. We show that, even though primer choice affects read quality, diversity, and assigned taxa, distinct primer pairs uncover similar spatio-temporal patterns between sample types, farms, and time points. We find that long-read amplicons underperform regarding quantitative resolution of spatio-temporal patterns, but allow for species-level identification of functional services and pathogens. Finally, shotgun metagenomics data identified fungi, viruses, and bacteriophages, opening avenues for an exploration of natural approaches regarding antipathogenic treatments. Overall, the datasets agreed on major prokaryotic players. In conclusion, different sequencing approaches yield overlapping and highly complementary results, with each contributing data no other approach could. Such a tiered approach therefore constitutes a practical and cost-effective strategy for obtaining the maximum amount of information on aquaculture microbial communities. These data could lead to better farm management practices and at the same time inform basic research on community evolution dynamics.

microbiology↗

bioRxiv2019

Evolved for success in novel environments: the round goby genome

Since the beginning of global trade, hundreds of species have colonized territories outside of their native range. Some of these species proliferate at the expense of native ecosystems, i.e., have become invasive. Invasive species constitute powerful in situ experimental systems to study fast adaptation and directional selection on short ecological timescales. They also present promising case studies for ecological and evolutionary success in novel environments.\n\nWe seize this unique opportunity to study genomic substrates for ecological success and adaptability to novel environments in a vertebrate. We report a highly contiguous long-read based genome assembly for the most successful temperate invasive fish, the benthic round goby (Neogobius melanostomus), and analyse gene families that may promote its impressive ecological success.\n\nOur approach provides novel insights from the large evolutionary scale to the small species-specific scale. We describe expansions in specific cytochrome P450 enzymes, a remarkably diverse innate immune system, an ancient duplication in red light vision accompanied by red skin fluorescence, evolutionary patterns in epigenetic regulators, and the presence of genes that may have contributed to the round gobys capacity to invade cold and salty waters.\n\nA recurring theme across all analyzed gene families are gene expansions. This suggests that gene duplications may promote ecological flexibility, superior performance in novel environments, and underlie the impressive colonization success of the round goby. Gobiidae generally feature fascinating adaptations and are excellent colonizers. Further long-read genome approaches across the goby family may reveal whether the ability to conquer new habitats relates more generally to gene copy number expansions.

ecology↗