Belgium

The physiological mechanisms that underpin aquatic ectotherms’ ability to tolerate elevated temperatures have been long studied but remain largely unresolved due to the historical reductionism that has dominated biology for decades. However, recent advances in omics approaches are enabling us to acquire more comprehensive portraits of the way physiological systems function, have evolved and will respond to future environmental challenges. Particularly, integrated multi-omics analyses can provide an in-depth characterisation of the physiological status of organisms living under different environmental conditions. Polar marine ectotherms face important physiological challenges with the progression of ocean warming. Here we compared (as an ideal study system) the multi-omics response of an Arctic clam species to its more eurythermal temperate counterpart to a gradient of seven temperatures mimicking acute thermal conditions and marine heatwaves exposed under laboratory conditions. We measured survival after 12 days of exposure and sampled three tissues (gills, mantle, posterior adductor muscle), on which we performed targeted metabolomics (focussing particularly on energy metabolism) and untargeted lipidomics. Multivariate analyses combined with breakpoint analyses helped show that the lower tolerance observed under elevated temperatures in the Arctic species is underpinned by a limited ability for metabolomic rewiring, when compared to its temperate counterpart. The latter may rely on the activation of DNA repair and cell-signaling pathways. Further, we present the results for our lipidomic profiling and its multi-omics integration with metabolomics data to acquire a greater mechanistic understanding of the sensitivities of polar and temperate marine species to ocean warming.

SEB Conference 2025

Integrating metabolomics and lipidomics approaches to investigate the sensitivity of marine ectotherms from different climatic regimes to marine heatwaves

mollusks

marine ectotherms

lipidomics

marine heatwaves

metabolomics

multi-omics

climate change

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Temperature shapes phenotypic variation through effects at different levels and time-scales; changes in phenotype frequencies due to natural selection and changes in phenotype expression due to phenotypic plasticity. In particular, the temperature experienced during development can determine the production of distinct adult phenotypes from the same genotype; a phenomenon called thermal developmental plasticity. This plasticity can match phenotype to ecological conditions and help organisms to cope with environmental heterogeneity, including differences between alternating seasons. I will use two insect models of seasonal plasticity to illustrate the importance of thermal plasticity in studies of variation in organismal phenotypes, and of the impact of climate change in natural populations. Temperature (T) during development affects a series of adult traits which impact their fitness. Some of these traits are fixed throughout adult life (e.g. body size and pigmentation) while others can still respond to adult environmental conditions (e.g. behaviour and immunity). I will present date documenting these effects and how thermal plasticity depends on genetic (G) and environmental (E) context. These GxT and ExT interactions will affect how thermally plastic populations might cope and adapt to temperature perturbation.

Context-dependence of thermal plasticity in insects

Species with short lifespans (e.g. weeks) experience environmental heterogeneity, both spatially and temporarily, including seasonal changes that occur across generations. Balancing selection, a process that maintains genetic diversity within populations by shifting allele frequencies as environmental conditions change, may facilitate rapid adaptation to fluctuating environments. Understanding the genomic and physiological mechanisms driving fast adaptive responses in organisms can improve our ability to predict whether and how taxa may adapt to human-led climate change. In this study, we leverage a wild population of the copepod Eurytemora affinis from the Baltic Sea (Kiel, Germany) to identify the genomic and physiological responses to rapid environmental change. Copepods were collected at four timepoints from spring to summer of 2024 and common-gardened over three generations to two experimental temperature regimes simulating the local seasonal sea surface conditions (7o C and 16o C). We measured metabolic and feeding rates, and key fitness traits: growth and number of eggs per female. Additionally, whole-genome sequencing of 30 pooled individuals, collected in both spring and summer was used to identify rapid adaptation over a 13-year time period (2009, 2011, 2015, 2022). We found nearly 1,000 loci consistently responding to seasonal variation across all years, indicating ongoing rapid evolution via balancing selection. Cold-adapted populations from our common-garden experiments had lower energy requirements and outperformed warm-adapted populations in growth and fecundity in all but one collection, highlighting potential trade-offs in adaptation to fluctuating environments. These findings provide strong evidence of rapid evolutionary responses to seasonal change, affecting the physiological performance of Eurytemora affinis.

Exploring the genomic and physiological basis of adaptation to seasonal variation in the copepod Eurytemora affinis

Artificial light at night (ALAN) is an emerging environmental stressor in urban aquatic ecosystems, increasingly co-occurring with chemical pollutants. Light pollution disrupts circadian rhythms in various organisms, affecting essential biological processes such as reproduction, hormone regulation, and stress responses. However, its long-term and transgenerational effects remain understudied. This study assessed ALAN’s impact on zebrafish (Danio rerio) reproduction and offspring development. Adult zebrafish were exposed to either 0 or 10 lux during the night for 10 weeks, with reproductive output assessed biweekly. Egg viability at 0 and 24 hours was recorded, and F1 embryos were exposed to the same light conditions. Embryo development was monitored for 120 hours post-fertilization (hpf), evaluating mortality, hatching success, malformations, and heart rate at 48 hpf. To assess transgenerational effects, offspring from both exposure groups underwent acute exposure to 3,4-dichloroaniline (3,4-DCA) (0.375–6 mg/L) under control light conditions (0 lux). Results indicate that ALAN-exposed adults laid fewer and lower-quality eggs than controls. Additionally, parental ALAN exposure significantly increased offspring heart rate, regardless of their own light exposure. Offspring from ALAN-exposed parents also exhibited heightened sensitivity to 3,4-DCA, with increased mortality at 1.5 and 3 mg/L. These findings highlight ALAN as a key environmental stressor affecting zebrafish reproduction, development, and transgenerational responses to pollutants. This study underscores the need to integrate light pollution into ecotoxicological risk assessments and consider its ecological implications for aquatic ecosystems.

Lights out: Transgenerational effects of artificial light at night on zebrafish

Transactional scaffolding (TS) is an innovation that has recently been applied to the pedagogic approach in a first year (SCQF7) module in Comparative Anatomy and Physiology at Edinburgh Napier University. The technique aims to enhance self-actualisation of new HE learners by increasing engagement with virtual learning environments (VLE) and improved self-knowledge of attendance and engagement; with the goal of promoting connections between theory and practice.The idea of TS has grown out of the work of Salmon (2019) and Smith (2023). Salmon (2019) promotes the idea of strongly structured learning within VLE. Whilst the findings of Smith (2023) showed that for most learners the strongest motivational factors to study are transactional. Many learners are slow to engage in self-actuation activities unless they see how these contribute to their achievement of their intended qualification and graduate destination.Transactional scaffolding harnesses data from VLE engagement and attendance monitoring to allow learners to unlock access to learning material and summative assessments. Crucially, the approach provides opportunities for learners to latterly compensate for earlier poor engagement and is relatively unlaborious for academic staff and requires no dedicated administrative support. It allows learners to confidentially rank themselves within the cohort in terms of attendance, engagement and progress within a single online environment.The initial intervention appears to have significantly improved student evaluation of the investigated module compared with previous cohorts. Overall student satisfaction increased from 89% in 2023 to 98% in 2024. Student attendance at on-line learning events improved from 10% to 95%.

Transactional scaffolding improves learning engagement within blended learning environments in  Scottish Higher Education

Significant progress has been made in the field of plant genomics, as demonstrated by the increased use of high-throughput methodologies that enable the characterization of multiple genome-wide molecular phenotypes. These findings have provided valuable insights into plant traits and their underlying genetic mechanisms, particularly in model plant species. Nonetheless, effectively leveraging them to make accurate predictions represents a critical step in crop genomic improvement. We present AgroNT, a foundational large language model trained on genomes from 48 plant species with a predominant focus on crop species. We show that AgroNT can obtain state-of-the-art predictions for regulatory annotations, promoter/terminator strength, tissue-specific gene expression, and prioritize functional variants. We conduct a large-scale in silico saturation mutagenesis analysis on cassava to evaluate the regulatory impact of over 10 million mutations and provide their predicted effects as a resource for variant characterization. Finally, we propose the use of the diverse datasets compiled here as the Plants Genomic Benchmark (PGB), providing a comprehensive benchmark for deep learning-based methods in plant genomic research.

A foundational large language model for edible plant genomes

Bittersweet nightshade (Solanum dulcamara) plants produce a large variety of steroidal glycosides (SGs). Minor chemical differences, for example the level of saturation in the steroidal moiety, are associated with differences in resistance to herbivores and pathogens. Liquid Chromatography-quadrupole Time of Flight – Mass Spectrometry metabolomic analyses showed that both total leaf SG levels and SG diversity are associated with herbivore preference and leaf damage. We analysed the metabolomes of leaves and roots of selected chemotypes with saturated and unsaturated SG profiles in their leaves. In addition, we assessed the expression a GLYCOALKALOID METABOLISM25 (GAME25) homologue. In tomato, GAME25 is coding for a short-chain dehydrogenase responsible for the reduction of the C-5,6 double bond in dehydrotomatidine, which results in the formation of tomatidine. We found that differences in leaf SG chemodiversity were associated with the expression of SdGAME25. In contrast to leaves, roots of the same saturated and unsaturated individuals were more similar in their SG profiles and SdGAME25 expression levels. This implies that leaf and root SG chemodiversity in S. dulcamara are under differential selection pressures by aboveground and belowground interactions with herbivores and pathogens. In a common garden experiment, we manipulated the frequencies of these two S. dulcamara chemotypes to create different levels of SG plot chemodiversity. We found that both fruit and seed production as well as herbivore damage were affected by individual and plot diversity level. This suggest that herbivores as well as herbivore community composition may maintain chemodiversity as observed in natural S. dulcamara populations.

One beast's host plant is another beast's poison. Ecological consequences of steroidal glycoside diversity in Solanum dulcamara

Coffee trees (Coffea spp.)are highly susceptible to changes in environmental conditions and agricultural practices. Concurrently, it is also one of the most valued, consumed and traded crops worldwide due to its economic relevance and health effects. Coffee drink is recognized for its psychostimulant effects and antioxidant properties, which are linked to its chemical composition, rich in alkaloids, phenolic compounds and diterpenes. These bioactive compounds are not only associated with beneficial health effects but also play an important role in ecological interactions and plant performance. From the quality perspective, the chemical composition of unroasted green beans and the accumulation of non-volatile and bioactive compounds will determine the sensorial profile and value in the market. Reversely, their relative composition is highly influenced by the genetic background, geographical origin, corresponding environmental growing conditions, agricultural practices and post-harvesting processing. Aiming to underscore the complex interplay between all these factors, we employed metabolomics to access the content of major coffee's bioactive compounds in Brazilian specialty coffee beans produced in different locations. De-pulping processing increased the sensory score by 1.5% and the content of chlorogenic acid derivatives by 5.8%. Altitude, ferulic acid,p-coumaric acid, sweetness, and acidity were predictors distinguishing the samples. Higher-quality coffees were linked to higher-altitude regions and increased soil organic carbon stock. Theobromine, theophylline, ferulic acid, and p-coumaric acid were linked with sustainable management practices and coffee quality. These findings provide novel insights for coffee quality assessment with a focus on their bioactive compounds and sustainable agricultural practices.

Metabolomics-based approach to distinguish specialty coffee beans from different origins and processing practices based on their bioactive chemical profile

Photosynthesis is a vital driver of plant growth and, under well-watered conditions, is inherently shaped by environmental factors such as light, temperature and CO2 . Recent advances in sensor technology and plant cuvette design enable detailed, real-time monitoring and modelling of dynamic photosynthetic responses under controlled conditions. These insights are not only key to mechanistic understanding but also serve as inspiration for optimizing plant growth in novel plant production systems. Yet, plant growth involves more than just the fixation of atmospheric carbon. It is a biophysical process also strongly governed by plant-water relations. Next-generation measurements and growth models must incorporate the dynamics of water transport and the crucial role of internal water storage pools in sustaining turgor pressure, especially under changing environmental conditions. This turgor-driven perspective is essential to fully understand how growth occurs, particularly under drought stress. To further complete this picture, we must also consider the often-overlooked recycling of internally respired CO₂, which becomes increasingly relevant under drought stress when stomatal closure limits atmospheric CO₂ uptake. Together, these processes highlight the intricate interplay between carbon and water relations in plants. Plants grow in a carbon-water world, and bridging the gap between controlled-environment experiments and real-world conditions requires embracing this complexity.

Plant growth on the bridge between carbon assimilation and water dynamics

In Plant Factories with Artificial Lighting (PFAL), the photoperiod can be reduced to save electricity, but a large daily reduction leads to a decrease in plant growth and Light Use Efficiency (LUE). The reduction in plant growth is linked to the decrease in the total amount of light provided to the plant, known as the Daily Light Integral (DLI). The loss in LUE is linked to photoperiod duration and the plant's circadian rhythm. When the photoperiod matches the circadian rhythm, plants enter circadian resonance, maximizing LUE because photosynthetic capacity and light availability are synchronized. When the photoperiod is reduced, the circadian resonance state can be disrupted, altering LUE. To better characterize the link between photoperiod duration and LUE, we carried out two experiments, in which we studied the carbohydrate contents, photosynthesis, stomatal conductance and photosystem II efficiency. In the first experiment, lettuces were grown under a photoperiod inducing a periodic 4-hour mismatch with the circadian rhythm. This mismatch did not disrupt the circadian regulation of stomatal conductance, photosystem II efficiency, or sugar metabolism. In the second experiment, larger periodic mismatches of 6 and 12 hours were induced to reduce energy consumption by 12.5% or 25%. The 12.5% modality was the better compromise between agronomical parameters and energy savings. With 25% energy savings, the circadian regulation of stomatal conductance was altered, leading to a significant reduction in LUE. These findings highlight the need to consider circadian rhythms in photoperiod management within PFAL to optimize LUE and reduce energy consumption.

Circadian rhythm and photosynthesis in controlled environment agriculture: limits and opportunities

Some sacoglossan sea slugs are able to acquire and retain chloroplasts from their algal prey, enabling them to use light energy for the synthesis of organic compounds, a process known as kleptoplasty. However, the lifespan of these stolen chloroplasts (kleptoplasts) is limited and these sea slugs require regular feeding to maintain high levels of photosynthetic activity. Lipids, essential molecules for cell membrane stability, energy storage, and signaling, are key to chloroplast retention and functionality within the host animal cells. This study used advanced lipidomics techniques (C18-LC-HR-MS & MS/MS) to investigate lipid profile shifts associated with the decline in photosynthetic capacity of kleptoplastidic sea slugs under different feeding and starvation conditions. In the sea slugs Elysia viridis and Elysia crispata, glycolipids – exclusive to chloroplast membranes – declined noticeably in the absence of algal food sources. The rate of decline was different in E. viridis depending on the algal species previously consumed, indicating that the chloroplast donor plays a crucial role in chloroplast retention. Furthermore, sterols from both plant and animal sources increased in sea slugs experiencing reduced photosynthetic capacity, likely due to chloroplast degradation and stress-induced lipid synthesis. These findings revealed how kleptoplastidic sea slugs adapt their lipid metabolism to environmental stress, shedding light on their strategies to cope with fluctuations in algal availability and photosynthetic capacity

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Context-dependence of thermal plasticity in insects

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