Host-microbiome interactions
Using the water flea Daphnia magna as model organism
How do tiny microbes shape the survival of their hosts in a changing world? Our research investigates how gut microbiota influence the ability of aquatic organisms to cope with stressors such as low oxygen and toxic cyanobacteria, two major challenges in freshwater ecosystems under climate change. Through controlled microbiome transplant experiments in Daphnia magna, we uncover how microbial history, host genotype, and epigenetic mechanisms interact to affect fitness and resilience. By linking microbiome composition, functional profiles, and metabolites to host performance, we aim to reveal the hidden role of microbial partners in rapid acclimation and adaptation.
- By performing reciprocal gut microbiome transplants under normoxic and hypoxic conditions, we showed that prior microbial exposure to hypoxia increases host survival in low-oxygen environments (Coone, Bisschop, et al., Journal of Evolutionary Biology, 2023 PDF)
- Using a fully factorial microbiome transplant experiment, we demonstrated that host performance and DNA methylation depend on microbiota origin and diet toxicity, revealing genotype-microbiome matching and environmental history as key drivers of stress resilience in Daphnia magna (Bisschop, Goel, et al., The ISME Journal, 2025 PDF)
Experimental Evolution
using spider mites as model species
Experimental evolution is research following the evolution of certain populations across generations. This is a great tool to unravel evolutionary processes, as the initial state and the novel conditions of the populations are known. Ecological and evolutionary dynamics can furthermore be monitored in time in multiple replicates.
Using Tetranychus urticae or the two-spotted spider mite as model organism, we addressed several questions concerning both the spatial- and the community-context of ecological specialisation. Some findings are listed below.
- Interspecific competition may counteract the detrimental effect of high dispersal from an ancestral population towards a novel challenging environment (Alzate, Bisschop, et al., 2017 PDF).
- Unsuccessful ghost species can induce a long-term effect on the performance of other members in the community (Bisschop et al., 2020 PDF).
- A heterogeneous environment can facilitate adaptation to a harsh environment by providing an evolutionary stepping stone (Bisschop et al., 2019 PDF).
- Using a population dynamics model, I provided evidence that adaptation may either positively or negatively affect carrying capacity, depending on the ecological conditions leading to variation in adaptation (Bisschop et al., 2022 PDF) - Recognized by The American Naturalist Society as the runner-up for the Student Paper Award for 2023.
- Using an individual based eco-evolutionary model, we showed that community-wide evolutionary rescue under environmental deterioration leads to rapid loss of rare species due to competition and limited beneficial mutations (van Eldijk, Bisschop, et al., 2020 PDF)
This work is part of a joint research project between the research group of Dries Bonte (Ghent University) and Rampal Etienne (University of Groningen), supported by the U4 Society University network.
Computer vision in ecological and evolutionary research
Can we objectively quantify animal patterns?
We use computer vision to analyze large image datasets of organisms and habitats, enabling automated detection and measurement of traits that matter for evolution. By combining image-processing tools with AI-based vision transformer models (DINOv2), our framework extracts detailed color and structural features from photographs. More specifically, this approach will help us study pattern polymorphism in Anolis lizards and understand how these variations relate to adaptation. But it will also provide a scalable method applicable to other species.
This is in collaboration with Jonathan Goldenberg.
Repeatability of Evolution
Origins Center
The relative contribution of selection, genetic drift, and mutation will affect the predictability of adaptive evolution. This is affected by several factors that may influence each other: the effective population size, the strength of selection and the initial allele frequency. The smaller the effective population size, the higher the importance of random genetic drift, which will decrease the predictability. The larger the selection strength, the more predictable the system's behaviour is. If the beneficial allele is already available at a high frequency in the population, the predictability of adaptive evolution increases.
This project is a collaboration of several research institutes in The Netherlands and Belgium in which we aim to turn evolutionary biology in a more predictive science using experimental evolution with Caenorhabditis elegans.
Wortel et al., 2023 PDF; Bisschop, Blankers et al., 2022 PDF; Bisschop et al., bioRxiv preprint
Can species richness influence fitness and genetic evolution?
Together with Cyrus A. Mallon and Rampal S. Etienne, we investigate how species richness and higher order effects influence both fitness and genetic evolution. For this, we used a synthetic bacterial ecosystem with four different bacterial species (Mallon et al., in preparation).
Field work
Borneo & South-Africa
In 2018, Kasper Hendriks and I collaborated to collect micro land snails on limestone outcrops in Sabah (Malaysian Borneo). These species were sampled to investigate correlations between the snails, their diet, and their microbiome (Hendriks et al., 2019 PDF).
- We found positive relationships between the microbiome and both the host community and the diet. Besides, these correlations were strongly affected by the environment, especially by anthropogenic activity and habitat size (Hendriks, Bisschop, et al., Ecology, 2020 PDF)
- By metabarcoding gut contents of 658 land snails from Malaysian Borneo, we showed that species share much of their plant diet but differ greatly in diet richness, mainly linked to body size, highlighting how noncompetitive factors shape coexistence in tropical snail communities (Hendriks, Bisschop, et al., Journal of Molluscan studies, 2021 PDF).
In 2019, I joined a field work trip to South-Africa with Jonathan Goldenberg and Federico Massetti as part of a large-scale project investigating the evolution and the thermal properties of the coloured integument of the endemic cordylid lizards. This project contributed to foresee the resilience of ectotherms to climate change and initiated a collaboration to explore how colour brightness influences resilience not only in cordylids but also across other squamate groups.
Some of our findings:
- By analysing brightness in 126 viper species, we showed that substrate thermal properties strongly shape ventral coloration evolution, favouring brighter ventra in hot, conductive habitats for efficient heat transfer (Goldenberg et al., Communications Biology, 2021 PDF)
- By critically reviewing ecological rules, we demonstrated that predictions linking body size and colouration to thermoregulation often fail under climate change, advocating for a micro-environmental perspective over geographic rules (Goldenberg et al., OIKOS, 2022 PDF)
- By mechanistically modelling body temperature of colour-polyphenic lizards under current and future climates, we showed that darker populations may gain activity time and benefit from warming, emphasising the need to account for population-level variation in climate change responses (Mader et al., Functional Ecology, 2022 PDF)
- By examining melanistic morphs in two snake species across Italy, we found that climate-driven variation in melanism reflects opposing selective pressures for thermoregulation and UV protection (Goldenberg et al., Ecology and Evolution, 2024)
- Using a global dataset of 1249 squamates, we showed that habitat openness consistently drives brightness evolution, with brighter colours favoured in open habitats and evolutionary rates tracking global aridification events (Goldenberg et al., Nature Communications, 2025 PDF)
