The European flat oyster (Ostrea edulis) is an ecosystem engineer that structures reef habitats and is a major focus of restoration efforts across Europe, yet its biological rhythms in its habitat remain unknown. These rhythms synchronize physiology with environmental cycles, indicating ecological adaptation. Here, we investigated behavioral, physiological, and molecular rhythms in O. edulis, as well as their environmental drivers. Using high-resolution valvometry, we monitored valve activity and shell growth over 540-days in the German Bight (Helgoland), along with environmental variables such as photoperiod, temperature, underwater sound, and food availability. Monthly gene expression profiling of clock-related genes was also performed. O. edulis displayed coordinated daily, tidal, lunar, semilunar, and annual rhythms, mainly driven by photoperiod and temperature. This integrative chronobiological approach reveals a multiple rhythm system in O. edulis, highlighting both adaptive capacity and vulnerability to anthropogenic pressures, and providing key indicators for the conservation and restoration of oyster reef habitats.

Abstract Human-induced global climate change and other anthropogenic stressors are fundamentally altering our oceans. Understanding the ecological and societal implications of these changes is critical for developing mitigation strategies and conservation measures. However, major components of the marine pelagic ecosystem remain poorly understood. This is true for euphausiids (“krill”), which are a crucial part of marine food webs and play an important role in elemental cycling, including in the biological carbon pump, but for which we know surprisingly little. In this review, we first provide an overview of the ecological and socio-economic value of krill, highlighting their function in marine food webs and biogeochemical cycling. Next, we describe what is currently known regarding the response of krill to climate change and other anthropogenic stressors, focusing on changes in their biogeography, physiology, life history, as well as the impacts of krill fishing and their association with pathogens and parasites. We identify five key gaps in our current knowledge of krill: (1) the effects of krill on food web dynamics and stability, (2) the effects of changing predator and/or prey communities on krill populations, (3) the identification of important krill habitats, (4) the understanding of vertical and horizontal range shifts, and (5) the combined effects of multiple climate change and other anthropogenic stressors on krill. We also highlight the krill species, regions, and habitats that are understudied. Finally, we propose strategies to improve our understanding of this ecologically important taxonomic group, including the sustained funding for time series; implementation of novel research technologies; expanding research on understudied species and regions; and creating a global community of krill researchers.

Theme 5 examines the impacts of human activities in Antarctica, including exploring human impacts such as scientific operations, tourism, shipping, local and global pollution, and krill fisheries. interact with climate change to inform environmental policy within and beyond the Antarctic Treaty System. Local pressures generate chemical and plastic pollution, black carbon, underwater noise, wildlife disturbance, invasive species, and antimicrobial resistance, affecting ecosystem resilience. The theme seeks to quantify and monitor anthropogenic pressures through standardized, internationally coordinated protocols spanning chemical, biological, ecological, and cultural dimensions during InSync. Key topics include pollutants and plastics, underwater soundscapes, tourism impacts, fishery ecosystem effects and management, environmental DNA and antimicrobial resistance, marine pollution impacts and climate feedback, and the cultural legacies of historic expeditions. Approaches combine harmonized sampling, long-term monitoring, remote sensing, in situ observations, and modelling to identify hotspots and cumulative impacts. By integrating open-access data across disciplines, Theme 5 advances predictive risk assessment, science-based mitigation, and conservation strategies to detect anthropogenic signatures and strengthen the protection of Antarctic ecosystems.

Antarctic krill (Euphausia superba) is the central prey species in the Southern Ocean food web, supporting the largest and fastest-growing fishery in the region, managed by the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR). Climate change is threatening krill populations and their predators, while current catch limits do not take into account climate variability or krill population dynamics. In 2024, CCAMLR was unable to renew its spatial catch limits, highlighting the urgent need for improved management of the krill fishery to prevent any harm to the Southern Ocean ecosystem. To address this, we propose a management framework that integrates variability in krill recruitment and key pathways between spawning and nursery areas-a krill stock hypothesis-to inform decisions on catch limits and conservation measures. Implementing this approach will require targeted data collection, which we propose can be achieved through a multisector collaborative network that combines traditional and new technologies, including the use of fishing vessels as data collection platforms. We use case studies to demonstrate how fisheries can contribute to data collection while promoting sustainable management. A major challenge in this effort is securing long-term funding for data collection, which is critical for managing climate-sensitive populations of high commercial interest. We therefore recommend using the industry as a source of funding, research platform and data provider, alongside national research funding opportunities. Given the fundamental role of krill in the Southern Ocean ecosystem, its decline would have cascading effects on predators and essential ecosystem services.

Field observations during summer-fall of 2018 in the Antarctic Peninsula region provided the first morphological evidence that under certain environmental conditions, Salpa thompsoni blastozooid development can deviate from its traditional sequential protogynous hermaphroditism (SPH). Early male testis development at female blastozooid stages points to a wide-spread overlapping protogynous hermaphroditism (OPH) in regions where warm Antarctic Circumpolar Current waters mix with colder Antarctic Coastal waters. Our findings highlight the importance of the environmental setting in determining the reproductive pathway in S. thompsoni. OPH was observed in cooler and less productive waters, while SPH occured in both warmer and cooler productive waters. It appears that food availability may offset the effect of decreasing water temperatures for warm-water S. thompsoni reproductive development. It is plausible that OPH may permit the establishment of the S. thompsoni populations in the high Antarctic under the warming trend in the Southern Ocean by allowing for more efficient reproduction.

Understanding diet composition is essential for unravelling trophic interactions in aquatic ecosystems. DNA metabarcoding, utilising various variable regions of the 18S rRNA gene, is increasingly employed to investigate zooplankton diet composition. However, accurate results depend on rapid inactivation of digestive enzymes and DNA nucleases through proper sample processing and preservation. In this study, we compare the prey communities of Antarctic krill retrieved from the 18S variable regions V4 and V7 and assess how different processing treatments affect the detected prey composition of both krill and salps. Our findings highlight the critical importance of prompt sample processing for species with highly efficient digestive enzymes, such as krill, to preserve rapidly digested prey, including gelatinous plankton. Comparative analyses of the V4 and V7 regions revealed significantly different prey communities within the same krill samples, indicating that these regions may not be suitable for direct comparisons within or across studies. To complement molecular approaches, we also analyse fatty acids (FA) as trophic markers which provide insights into dietary habits over both short and long time scales. By comparing FA signals from stomach and tissue samples of the same krill and salp individuals, we identified significant differences in trophic markers representing different plankton groups. These findings emphasise the necessity of separating digestive tract from tissue to distinguish between short- and long-term diet signals. Furthermore, integrating FA analysis with metabarcoding offers valuable insights into zooplankton digestion efficiency across taxonomic levels. This combined approach enhances our understanding of zooplankton feeding ecology and trophic interactions in marine ecosystems.

Marine organisms exhibit a multitude of biological rhythms synchronized with the interactions of the sun-, earth-, and moon cycles. However, the biological rhythms in bivalves remain poorly studied. This study focuses on the native European flat oyster (Ostrea edulis), an endangered species of coastal ecosystems and a key organism in restoring of biogenic reef habitats. We aim to determine whether a molecular endogenous circadian rhythm exists in O. edulis and to characterize its daily expression. To address these questions, the oysters’ valve behavior, as an output of the circadian clock expression, was recorded under different light conditions and free-running regimes using non-invasive valvometry. This work demonstrates the existence of a circadian clock mechanism that generates a labile behavioral circadian oscillation under free-running conditions. In light: dark conditions, a diel rhythm appears nocturnal, synchronizable to a shift of light phase, and remains unmodified whether the oysters are fed or not. This rhythm anticipates light: dark changes, indicating its endogenous origin. Finally, when exposed to artificial light at night the daily behavior is disrupted. This study characterizes the circadian behavioral rhythm of O. edulis’s as plastic and labile. This plasticity would be advantageous in terms of ecological adaptability but increases sensitivity to anthropogenic pressures such as light pollution.

[This corrects the article DOI: 10.1371/journal.pone.0286036.].

Calanus finmarchicus is an important, extensively studied zooplankton species in the North Atlantic. Many studies have explored its abundance and life cycle, but basin-wide relationships between its vertical distribution and environment during the feeding season remain poorly known. We conducted a meta-analysis of stage-specific vertical distribution and its relationships with environmental variables (temperature, salinity, irradiance, chlorophyll-a) in the epipelagic layer (0–200 m) of the North Atlantic during spring and summer (21 March to 21 September). Fitting a GAM model, we analyzed data from 47 years (1971–2018) with the aim to discern common, stage-specific responses to environment across the area. Highest abundances were observed in the upper 50 m in spring (at 5°C) and summer (at 7.5°C). The timing of the phytoplankton bloom emerged as a key driver determining vertical distribution, with all stages found shallower during the seasonal surface Chl.-a maximum. Contrary to reports of mismatch with global warming, the data indicated a region-wide match of spring bloom and Calanus. In the coldest areas of its habitat (< 1°C), the copepods stayed closer to surface, potentially to fulfill development, while in warmest areas (>10°C), early stages stayed deeper likely to avoid warm surface waters.

Antarctic krill is a species with fundamental importance for the Southern Ocean ecosystem. Their large biomass and synchronized movements, like diel vertical migration (DVM), significantly impact ecosystem structure and the biological carbon pump. Despite decades of research, the mechanistic basis of DVM remains unclear. Circadian clocks help organisms anticipate daily environmental changes, optimizing adaptation. In this study, we used a recently developed activity monitor to record swimming activity of individual, wild-caught krill under various light conditions and across different seasons. Our data demonstrate how the krill circadian clock, in combination with light, drives a distinct bimodal pattern of swimming activity, which could facilitate ecologically important behavioral patterns, such as DVM. Rapid damping and flexible synchronization of krill activity indicate that the krill clock is adapted to a life at high latitudes and seasonal activity recordings suggest a clock-based mechanism for the timing of seasonal processes. Our findings advance our understanding of biological timing and high-latitude adaptation in this key species.

Circadian clocks enable organisms to synchronize their biological processes to environmental daily cycles, thereby increasing species fitness. Components of the molecular clock are conserved across many taxa, though their structure and function can vary. In this study, we aim to investigate the circadian clock of the European flat oyster Ostrea edulis, an endangered species with a pivotal role in biogenic reef ecosystems. Phylogenetic and protein domain analyses were performed to identify orthologues of core clock and clock-associated genes (OeClock, OeBmal1, OePeriod, OeTimeless, OeCryptochrome2, OeRev-erb, OeRor, OeDoubletime, OeClockWorkOrange, OeShaggy), a gene related to melatonin synthesis (OeHiomt) and genes involved in light perception (OeCryptochrome1, OeOpsin4). As a functional output of the clock, we observed daily and circadian rhythms in valve behaviour recorded under light:dark and constant dark conditions. In parallel, gene expression analyses in two tissues under similar light regimes revealed tissue-specific rhythms, suggesting the presence of a functional and plastic endogenous circadian system in O. edulis. These findings offer a first molecular work for deeper exploration of the circadian clock functioning in O. edulis, providing essential resources to investigate its evolutionary adaptation to cyclic environments, and inform restoration and conservation strategies of this threatened species.

Despite the increasing importance of salps and the recognition of their role as important players in food webs and biogeochemical cycles, their life cycle characteristics and physiology remain mysterious. This uncertainty encourages oversimplifying modeling approaches, leading to inaccuracies that may affect population dynamics results. This lack of knowledge is critical, making it difficult to adequately assess their sensitivity to global warming and their impact on ecosystems if their abundance and distribution change with rising seawater temperatures. Therefore, we generated a de novo transcriptome of Salpa fusiformis to further investigate the physiological processes involved in the life cycle of salps. We examined differentially expressed genes between both reproductive forms, blastozooids and oozoids, and detected a general form-specific difference among Salpa. Furthermore, we identified mainly temporally driven processes (energy delivery, cell communication, spermatogenesis) by studying gene expression profiles of different developmental stages of blastozooids of Salpa fusiformis. A life cycle that physiologically prepares blastozooids during the potential reproductive period, regardless of their fertilization status, may favor rapid response to favorable conditions and formation of salp blooms. Understanding the processes involved will contribute to a better assessment of their sensitivity to environmental change and support the implementation of their role in ecosystem models. In addition, the generated transcriptome was used to select and validate a set of potential reference genes for future qPCR applications. This will facilitate molecular studies of tunicates generally and stimulate future physiological studies on salps.

Rapid climate change threatens the relatively pristine environment of the Southern Ocean. The effects on biogeochemical cycles and their subsequent consequences for the organisms in this area are of significant interest. Antarctic krill, Euphausia superba, is the dominant species in the Antarctic ecosystem and a vital component of the Southern Ocean food web. Its metabolism is influenced by the feeding regime, which is governed by environmental conditions. However, little is yet known about the metabolome of Antarctic krill. Here, we investigated metabolite classes that can serve as tracers for documenting variations in the metabolic and biochemical status of krill. To this end, we utilised targeted metabolomics to analyse coenzyme A thioesters, amino acids, B vitamins, and respiratory quinones in the digestive system of Antarctic krill, sampled during two campaigns in the Antarctic summer and autumn. A significant proportion of the detected coenzyme A thioesters were associated with the β-oxidation of fatty acids and, consequently, with lipid metabolism. Propionyl-CoA was particularly abundant in samples from the digestive gland, while malonyl- and succinyl-CoA were more prevalent in stomach and hindgut samples. 3-Hydroxy-3-methylglutaryl-CoA, an intermediate in the metabolism of branched amino acids and the biosynthesis of isoprenoids, occurred almost exclusively in the summer samples. Analyzing the free amino acids, very high levels of the non-proteinogenic amino acid sarcosine were found, which possibly serves as an osmolyte for the Antarctic krill and/or plays a role in its digestive process. Among the B vitamins, there were seasonal fluctuations, particularly in B1 and B5. The respiratory quinones exhibited more homogeneous patterns, with UQ10:10 as the dominant representative. These seasonal and organ-dependent variations in the composition of the different metabolite classes can serve as a reference point in future studies to better assess the influence of changing conditions in Antarctic waters.

Antarctic krill is a keystone species in the Antarctic marine ecosystem and the target of a growing fishery. Given the ecological importance of krill, concerns have been raised about potential negative impacts of fishing on the Southern Ocean ecosystem. Resource-efficient approaches to fisheries monitoring are particularly valuable in this context due to the high costs associated with data collection in Antarctica. In this study, we trained a segmentation model (U-Net) to extract dives of air-breathing krill predators from more than 30,000 h of active acoustic data collected by three krill fishing vessels over six years. We were able to characterize the temporal and spatial dynamics of predator-vessel co-occurrences, which aligned well with the findings from more costly tracking studies. For example, we found that encounters with whales consistently peaked in autumn around the Antarctic Peninsula, when whales are building up fat reserves for their migration to breeding grounds. We also demonstrated that protection measures, introduced to protect breeding penguins at the Antarctic Peninsula, have simply shifted penguin-vessel encounters to the South Orkney Islands, where the affected colonies are not currently monitored. Our approach, results, and application example demonstrate how acoustic data from fishing vessels can provide important information to support fisheries management. As a by-product of fishing operations, these data are cost-effective, offering unique temporal and spatial coverage and providing a useful basis for rapid, low-level assessments of the fishery's interaction with the wider ecosystem. This is particularly important given the unpredictable dynamics of krill fishery management decision-making.

BACKGROUND:The Antarctic krill Euphausia superba is a keystone species in the Southern Ocean ecosystem. This crustacean has an ancestral clock whose main components have been identified and characterized in the past few years. However, the second feedback loop, modulating clock gene expression through two transcription factors, VRI and PDP1, has yet to be described. The presence of this second regulatory mechanism is suggested by the identification of its negative component, vrille, at the transcriptional level. RESULTS:Here, we describe the second feedback loop of krill by identifying the positive component, pdp1, and functionally characterizing both pdp1 and vrille. Starting from the online transcriptome database KrillDB2, we identified and cloned three putative pdp1 sequences which were subsequently analyzed for tissue expression and functional activity using luciferase assays, individually and in combination with two vrille isoforms. Among the pdp1 isoforms, Espdp1_3 displayed higher expression levels in relevant circadian districts than the other two. Furthermore, EsPDP1_3 and EsVRI_2 exhibited the expected positive and negative regulation of the V/P-box in our in vitro system. Finally, Espdp1_3 and Esvrille also showed rhythmic expression in light-dark cycles, supporting their involvement in the regulation of the main circadian clock of the Antarctic krill. CONCLUSIONS:This study expands our knowledge about the molecular architecture of the Antarctic krill circadian clock by defining the components that take part in the modulation of clock expression, establishing a second feedback loop.

Annual rhythms are observed in living organisms with numerous ecological implications. In the zooplanktonic copepod Calanus finmarchicus, such rhythms are crucial regarding its phenology, body lipid accumulation, and global carbon storage. Climate change drives annual biological rhythms out of phase with the prevailing environmental conditions with yet unknown but potentially catastrophic consequences. However, the molecular dynamics underlying phenology are still poorly described. In a rhythmic analysis of C. finmarchicus annual gene expression, results reveal that more than 90% of the transcriptome shows significant annual rhythms, with abrupt and dramatic upheaval between the active and diapause life cycle states. This work explores the implication of the circadian clock in the annual timing, which may control epigenetic mechanisms to profoundly modulate gene expression in response to calendar time. Results also suggest an increased light sensitivity during diapause that would ensure the photoperiodic entrainment of the endogenous annual clock.

Salps have attracted attention as zooplankton organisms that may be able to expand their habitat range and increase their ecological importance in the face of ongoing global warming. Due to their gelatinous nature, unique feeding strategy, and reproductive ecology such changes could have profound impacts on regional marine ecosystems. While their role in the regional carbon cycle is receiving attention, our knowledge of their physiology and life cycle is still limited. This knowledge gap is mainly due to their fragile gelatinous nature, which makes it difficult to capture and maintain intact specimen in the laboratory. We present here a modified kreisel tank system that has been tested onboard a research vessel with the Southern Ocean salp Salpa thompsoni and at a research station with Salpa fusiformis and Thalia democratica from the Mediterranean Sea. Successful maintenance over days to weeks allowed us to obtain relative growth and developmental rates comparable to in situ field samples of S. thompsoni and S. fusiformis, and provided insights into previously unknown features of their life cycle (e.g., testes development). Our results show that traditional methods of estimating growth, such as cohort analysis, may lead to a general overestimation of growth rates and neglect individual strategies (e.g., shrinkage), which can affect the results and conclusions drawn from population dynamic models. By providing a starting point for the successful maintenance of different species, comparable experiments on the physiology of salps is made possible. This will contribute to refining model parameters and improving the reliability of the predictions.

Krill are vital as food for many marine animals but also impacted by global warming. To learn how they and other zooplankton may adapt to a warmer world we studied local adaptation in the widespread Northern krill (Meganyctiphanes norvegica). We assemble and characterize its large genome and compare genome-scale variation among 74 specimens from the colder Atlantic Ocean and warmer Mediterranean Sea. The 19 Gb genome likely evolved through proliferation of retrotransposons, now targeted for inactivation by extensive DNA methylation, and contains many duplicated genes associated with molting and vision. Analysis of 760 million SNPs indicates extensive homogenizing gene-flow among populations. Nevertheless, we detect signatures of adaptive divergence across hundreds of genes, implicated in photoreception, circadian regulation, reproduction and thermal tolerance, indicating polygenic adaptation to light and temperature. The top gene candidate for ecological adaptation was nrf-6, a lipid transporter with a Mediterranean variant that may contribute to early spring reproduction. Such variation could become increasingly important for fitness in Atlantic stocks. Our study underscores the widespread but uneven distribution of adaptive variation, necessitating characterization of genetic variation among natural zooplankton populations to understand their adaptive potential, predict risks and support ocean conservation in the face of climate change. Marine life depends on zooplankton like krill, but it's uncertain how these species will respond to a warming ocean. This study of genome variation in the Northern krill uncovered many gene variants that could be crucial for environmental adaptation and support stock assessment under climate change.

Understanding and managing the response of marine ecosystems to human pressures including climate change requires reliable large-scale and multi-decadal information on the state of key populations. These populations include the pelagic animals that support ecosystem services including carbon export and fisheries. The use of research vessels to collect information using scientific nets and acoustics is being replaced with technologies such as autonomous moorings, gliders, and meta-genetics. Paradoxically, these newer methods sample pelagic populations at ever-smaller spatial scales, and ecological change might go undetected in the time needed to build up large-scale, long time series. These global-scale issues are epitomised by Antarctic krill ( Euphausia superba ), which is concentrated in rapidly warming areas, exports substantial quantities of carbon and supports an expanding fishery, but opinion is divided on how resilient their stocks are to climatic change. Based on a workshop of 137 krill experts we identify the challenges of observing climate change impacts with shifting sampling methods and suggest three tractable solutions. These are to: improve overlap and calibration of new with traditional methods; improve communication to harmonise, link and scale up the capacity of new but localised sampling programs; and expand opportunities from other research platforms and data sources, including the fishing industry. Contrasting evidence for both change and stability in krill stocks illustrates how the risks of false negative and false positive diagnoses of change are related to the temporal and spatial scale of sampling. Given the uncertainty about how krill are responding to rapid warming we recommend a shift towards a fishery management approach that prioritises monitoring of stock status and can adapt to variability and change.