Molecular fingerprint of gilthead seabream physiology in response to pollutant mixtures in the wild

The increase in trace element concentrations in the aquatic environment due to anthropogenic activities, urges the need for their monitoring and potential toxicity, persistence, bioaccumulation, and biomagnification at different trophic levels. Gilthead seabream is a species of commercial importance in the Mediterranean Sea, both for the aquaculture and fisheries sectors, however very little is known about their trace element contamination accumulation and the resulting effect on their health status. In the present study, 135 juveniles were collected from seven coastal lagoons known to be essential nursery areas for this species. We measured seventeen different inorganic contaminants at the individual level in fish muscle (namely Al, As, Be, Bi, Cd, Cr, Cu, Hg, Li, Ni, Pb, Rb, Sb, Sr, Ti, Tl and Zn). Our results revealed the accumulation of multiple trace elements in individuals and distinct contamination signatures between lagoons which might lead to contrasted quality as nurseries for juveniles of numerous ecologically and economically relevant fish species in addition to seabreams. We further evaluated the potential adverse effect of these complex contamination mixtures on the liver (the main organ implicated in the metabolism of xenobiotics) and red muscle (a highly metabolic organ) using a proteomic approach. Alterations in cellular organization pathways and protein transport were detected in both tissues (albeit they were not similarly regulated). Chromosome organization and telomere maintenance in the liver appeared to be affected by contaminant mixture which could increase mortality, age-related disease risk and shorter lifetime expectancy for these juveniles. Red muscle proteome also demonstrated an upregulation of pathways involved in metabolism in response to contamination which raises the issue of potential energy allocation trade-offs between the organisms' main functions such as reproduction and growth. This study provides new insights into the cellular and molecular responses of seabreams to environmental pollution and proposed biomarkers of health effects of trace elements that could serve as a starting point for larger-scale biomonitoring programs.

Unidirectional trans-Atlantic gene flow and a mixed spawning area shape the genetic connectivity of Atlantic bluefin tuna

The commercially important Atlantic bluefin tuna (Thunnus thynnus), a large migratory fish, has experienced notable recovery aided by accurate resource assessment and effective fisheries management efforts. Traditionally, this species has been perceived as consisting of eastern and western populations, spawning respectively in the Mediterranean Sea and the Gulf of Mexico, with mixing occurring throughout the Atlantic. However, recent studies have challenged this assumption by revealing weak genetic differentiation and identifying a previously unknown spawning ground in the Slope Sea used by Atlantic bluefin tuna of uncertain origin. To further understand the current and past population structure and connectivity of Atlantic bluefin tuna, we have assembled a unique dataset including thousands of genome-wide single-nucleotide polymorphisms (SNPs) from 500 larvae, young of the year and spawning adult samples covering the three spawning grounds and including individuals of other Thunnus species. Our analyses support two weakly differentiated but demographically connected ancestral populations that interbreed in the Slope Sea. Moreover, we also identified signatures of introgression from albacore (Thunnus alalunga) into the Atlantic bluefin tuna genome, exhibiting varied frequencies across spawning areas, indicating strong gene flow from the Mediterranean Sea towards the Slope Sea. We hypothesize that the observed genetic differentiation may be attributed to increased gene flow caused by a recent intensification of westward migration by the eastern population, which could have implications for the genetic diversity and conservation of western populations. Future conservation efforts should consider these findings to address potential genetic homogenization in the species.

Industrial fisheries have reversed the carbon sequestration by tuna carcasses into emissions

To limit climate warming to 2°C above preindustrial levels, most economic sectors will need a rapid transformation toward a net zero emission of CO2 . Tuna fisheries is a key food production sector that burns fossil fuel to operate but also reduces the deadfall of large-bodied fish so the capacity of this natural carbon pump to deep sea. Yet, the carbon balance of tuna populations, so the net difference between CO2 emission due to industrial exploitation and CO2 sequestration by fish deadfall after natural mortality, is still unknown. Here, by considering the dynamics of two main contrasting tuna species (Katsuwonus pelamis and Thunnus obesus) across the Pacific since the 1980s, we show that most tuna populations became CO2 sources instead of remaining natural sinks. Without considering the supply chain, the main factors associated with this shift are exploitation rate, transshipment intensity, fuel consumption, and climate change. Our study urges for a better global ocean stewardship, by curbing subsidies and limiting transshipment in remote international waters, to quickly rebuild most pelagic fish stocks above their target management reference points and reactivate a neglected carbon pump toward the deep sea as an additional Nature Climate Solution in our portfolio. Even if this potential carbon sequestration by surface unit may appear low compared to that of coastal ecosystems or tropical forests, the ocean covers a vast area and the sinking biomass of dead vertebrates can sequester carbon for around 1000 years in the deep sea. We also highlight the multiple co-benefits and trade-offs from engaging the industrial fisheries sector with carbon neutrality.

Metabarcoding confirms the opportunistic foraging behaviour of Atlantic bluefin tuna and reveals the importance of gelatinous prey

Studies of the diet, feeding habits and trophic activity of top marine predators are essential for understanding their trophodynamics. The main direct method used for such studies thus far has been morphological inventories of stomach contents. This approach presents limitations such as missing gelatinous prey, which are usually digested too quickly to be detectable. Here, we analysed the stomachs of 48 Atlantic bluefin tuna (Thunnus thynnus, approximately 15 to 60 kg, including juveniles and adult fishes) collected from the Mediterranean Sea through the metabarcoding of two gene regions (cytochrome c oxidase subunit I (COI) and the ribosomal 18S-V1V2 region). The identified prey taxa and their relative read abundances (RRAs) estimated using COI results were in line with the findings of morphologically based inventories simultaneously performed on the same set of tuna samples. In both cases (and with the same rankings), the prey taxa included anchovy (Engraulis encrasicolus, here detected in more than 80% of samples, RRA = 43%), sardine (Sardina pilchardus, also approximately 80%, RRA = 30%), sprat (Sprattus sprattus, approximately 66%, RRA = 8%), mackerel (Scomber colias, approximately 44%, RRA = 7%) and cephalopods (approximately 15%, RRA = 1.4%). Another striking result was the detection, based on 18S (with which vertebrates were detected as the most abundant group, RRA = 61.6%), of a high prevalence and diversity of gelatinous organisms (RRA = 27.1%), including cnidarians (6.7%), salps (11.7%), and ctenophores (8.7%), the latter increasing with the size of the predator. These results thus support the hypothesis of the role of gelatinous prey in the diet of Atlantic bluefin tuna, suggesting that this species is even more generalist and opportunistic than previously thought. This study further confirms that DNA metabarcoding can be a powerful tool for assessing the diet and trophodynamics of top marine predators.

Is starvation a cause of overmortality of the Mediterranean sardine?

Animal mortality is difficult to observe in marine systems, preventing a mechanistic understanding of major drivers of fish population dynamics. In particular, starvation is known to be a major cause of mortality at larval stages, but adult mortality is often unknown. In this study, we used a laboratory food-deprivation experiment, on wild caught sardine Sardina pilchardus from the Gulf of Lions. This population is interesting because mean individual phenotype shifted around 2008, becoming dominated by small, young individuals in poor body condition, a phenomenon that may result from declines in energy availability. Continuous monitoring of body mass loss and metabolic rate in 78 captive food-deprived individuals revealed that sardines could survive for up to 57 days on body reserves. Sardines submitted to long-term caloric restriction prior to food-deprivation displayed adaptive phenotypic plasticity, reducing metabolic energy expenditure and enduring starvation for longer than sardines that had not been calorie-restricted. Overall, entry into critical fasting phase 3 occurred at a body condition of 0.72. Such a degree of leanness has rarely been observed over 34 years of wild population monitoring. Still, the proportion of sardines below this threshold has doubled since 2008 and is maximal in January and February (the peak of the reproductive season), now reaching almost 10 % of the population at that time. These results indicate that the demographic changes observed in the wild may result in part from starvation-related adult mortality at the end of the winter reproductive period, despite adaptive plastic responses.

Changes in foraging mode caused by a decline in prey size have major bioenergetic consequences for a small pelagic fish

Global warming is causing profound modifications of aquatic ecosystems and one major outcome appears to be a decline in adult size of many fish species. Over the last decade, sardine populations in the Gulf of Lions (NW Mediterranean Sea) have shown severe declines in body size and condition as well as disappearance of the oldest individuals, which could not be related to overfishing, predation pressure or epizootic diseases. In this study, we investigated whether this situation reflects a bottom-up phenomenon caused by reduced size and availability of prey that could lead to energetic constraints. We fed captive sardines with food items of two different sizes eliciting a change in feeding mode (filter-feeding on small items and directly capturing larger ones) at two different rations for several months, and then assessed their muscle bioenergetics to test for changes in cellular function. Feeding on smaller items was associated with a decline in body condition, even at high ration, and almost completely inhibited growth by comparison to sardines fed large items at high ration. Sardines fed on small items presented specific mitochondrial adjustments for energy sparing, indicating a major bioenergetic challenge. Moreover, mitochondria from sardines in poor condition had low basal oxidative activity but high efficiency of ATP production. Notably, when body condition was below a threshold value of 1.07, close to the mean observed in the wild, it was directly correlated with basal mitochondrial activity in muscle. The results show a link between whole-animal condition and cellular bioenergetics in the sardine, and reveal physiological consequences of a shift in feeding mode. They demonstrate that filter-feeding on small prey leads to poor growth, even under abundant food and an increase in the efficiency of ATP production. These findings may partially explain the declines in sardine size and condition observed in the wild.

Satellite-based indicator of zooplankton distribution for global monitoring

This study investigates the association between an index of mesozooplankton biomass, derived from the Continuous Plankton Recorder survey and satellite-derived productivity fronts in the North Atlantic. While chlorophyll-a content (CHL) is commonly described as a proxy for phytoplankton biomass, the size of productivity fronts estimated from the horizontal gradient of CHL appears to be directly linked to mesozooplankton biomass. Our results suggest that the lifespan of productivity fronts, which ranges from weeks to months, meets the time requirement of mesozooplankton to develop. The proposed indicator describes the daily distribution of mesozooplankton's suitable feeding habitat. It also provides a coherent interpretation of the productivity front development with respect to phytoplankton activity (CHL values) and potential predation by higher trophic levels. Since mesozooplankton are essential for feeding at higher trophic levels, this satellite-derived indicator delivers essential information for research and policy. An unanticipated positive trend of the indicator from 2003 to 2017 is observed at a basin scale under the current effects of climate change, with regional peaks in relatively poorly productive areas. Such monitoring indicator is potentially important to advances in marine food web modelling, fisheries science and the dynamic management of oceans towards sustainability.

Body reserves mediate trade-offs between life-history traits: new insights from small pelagic fish reproduction

Limited resources in the environment prevent individuals from simultaneously maximizing all life-history traits, resulting in trade-offs. In particular, the cost of reproduction is well known to negatively affect energy investment in growth and maintenance. Here, we investigated these trade-offs during contrasting periods of high versus low fish size and body condition (before/after 2008) in the Gulf of Lions. Female reproductive allocation and performance in anchovy (Engraulis encrasicolus) and sardine (Sardina pilchardus) were examined based on morphometric historical data from the 1970s and from 2003 to 2015. Additionally, potential maternal effects on egg quantity and quality were examined in 2014/2015. After 2008, the gonadosomatic index increased for sardine and remained steady for anchovy, while a strong decline in mean length at first maturity indicated earlier maturation for both species. Regarding maternal effects, for both species egg quantity was positively linked to fish size but not to fish lipid reserves, while the egg quality was positively related to lipid reserves. Atresia prevalence and intensity were rather low regardless of fish condition and size. Finally, estimations of total annual numbers of eggs spawned indicated a sharp decrease for sardine since 2008 but a slight increase for anchovy during the last 5 years. This study revealed a biased allocation towards reproduction in small pelagic fish when confronted with a really low body condition. This highlights that fish can maintain high reproductive investment potentially at the cost of other traits which might explain the present disappearance of old and large individuals in the Gulf of Lions.

Body reserves mediate trade-offs between life-history traits: new insights from small pelagic fish reproduction

Limited resources in the environment prevent individuals from simultaneously maximizing all life-history traits, resulting in trade-offs. In particular, the cost of reproduction is well known to negatively affect energy investment in growth and maintenance. Here, we investigated these trade-offs during contrasting periods of high versus low fish size and body condition (before/after 2008) in the Gulf of Lions. Female reproductive allocation and performance in anchovy (Engraulis encrasicolus) and sardine (Sardina pilchardus) were examined based on morphometric historical data from the 1970s and from 2003 to 2015. Additionally, potential maternal effects on egg quantity and quality were examined in 2014/2015. After 2008, the gonadosomatic index increased for sardine and remained steady for anchovy, while a strong decline in mean length at first maturity indicated earlier maturation for both species. Regarding maternal effects, for both species egg quantity was positively linked to fish size but not to fish lipid reserves, while the egg quality was positively related to lipid reserves. Atresia prevalence and intensity were rather low regardless of fish condition and size. Finally, estimations of total annual numbers of eggs spawned indicated a sharp decrease for sardine since 2008 but a slight increase for anchovy during the last 5 years. This study revealed a biased allocation towards reproduction in small pelagic fish when confronted with a really low body condition. This highlights that fish can maintain high reproductive investment potentially at the cost of other traits which might explain the present disappearance of old and large individuals in the Gulf of Lions.

Co-Occurrence and Habitat Use of Fin Whales, Striped Dolphins and Atlantic Bluefin Tuna in the Northwestern Mediterranean Sea

Different dolphin and tuna species have frequently been reported to aggregate in areas of high frontal activity, sometimes developing close multi-species associations to increase feeding success. Aerial surveys are a common tool to monitor the density and abundance of marine mammals, and have recently become a focus in the search for methods to provide fisheries-independent abundance indicators for tuna stock assessment. In this study, we present first density estimates corrected for availability bias of fin whales (Balaenoptera physalus) and striped dolphins (Stenella coeruleoalba) from the Golf of Lions (GoL), compared with uncorrected estimates of Atlantic bluefin tuna (ABFT; Thunnus thynnus) densities from 8 years of line transect aerial surveys. The raw sighting data were further used to analyze patterns of spatial co-occurrence and density of these three top marine predators in this important feeding ground in the Northwestern Mediterranean Sea. These patterns were investigated regarding known species-specific feeding preferences and environmental characteristics (i. e. mesoscale activity) of the survey zone. ABFT was by far the most abundant species during the surveys in terms of schools and individuals, followed by striped dolphins and fin whales. However, when accounted for availability bias, schools of dolphins and fin whales were of equal density. Direct interactions of the species appeared to be the exception, but results indicate that densities, presence and core sighting locations of striped dolphins and ABFT were correlated. Core sighting areas of these species were located close to an area of high mesoscale activity (oceanic fronts and eddies). Fin whales did not show such a correlation. The results further highlight the feasibility to coordinate research efforts to explore the behaviour and abundance of the investigated species, as demanded by the Marine Strategy Framework Directive (MSFD).

Spatial structure and distribution of small pelagic fish in the northwestern Mediterranean Sea

Understanding the ecological and anthropogenic drivers of population dynamics requires detailed studies on habitat selection and spatial distribution. Although small pelagic fish aggregate in large shoals and usually exhibit important spatial structure, their dynamics in time and space remain unpredictable and challenging. In the Gulf of Lions (north-western Mediterranean), sardine and anchovy biomasses have declined over the past 5 years causing an important fishery crisis while sprat abundance rose. Applying geostatistical tools on scientific acoustic surveys conducted in the Gulf of Lions, we investigated anchovy, sardine and sprat spatial distributions and structures over 10 years. Our results show that sardines and sprats were more coastal than anchovies. The spatial structure of the three species was fairly stable over time according to variogram outputs, while year-to-year variations in kriged maps highlighted substantial changes in their location. Support for the McCall's basin hypothesis (covariation of both population density and presence area with biomass) was found only in sprats, the most variable of the three species. An innovative method to investigate species collocation at different scales revealed that globally the three species strongly overlap. Although species often co-occurred in terms of presence/absence, their biomass density differed at local scale, suggesting potential interspecific avoidance or different sensitivity to local environmental characteristics. Persistent favourable areas were finally detected, but their environmental characteristics remain to be determined.

Effects of stochasticity in early life history on steepness and population growth rate estimates: an illustration on Atlantic bluefin tuna

The intrinsic population growth rate (r) of the surplus production function used in the biomass dynamic model and the steepness (h) of the stock-recruitment relationship used in age-structured population dynamics models are two key parameters in fish stock assessment. There is generally insufficient information in the data to estimate these parameters that thus have to be constrained. We developed methods to directly estimate the probability distributions of r and h for the Atlantic bluefin tuna (Thunnus thynnus, Scombridae), using all available biological and ecological information. We examined the existing literature to define appropriate probability distributions of key life history parameters associated with intrinsic growth rate and steepness, paying particular attention to the natural mortality for early life history stages. The estimated probability distribution of the population intrinsic growth rate was weakly informative, with an estimated mean r = 0.77 (±0.53) and an interquartile range of (0.34, 1.12). The estimated distribution of h was more informative, but also strongly asymmetric with an estimated mean h = 0.89 (±0.20) and a median of 0.99. We note that these two key demographic parameters strongly depend on the distribution of early life history mortality rate (M(0)), which is known to exhibit high year-to-year variations. This variability results in a widely spread distribution of M(0) that affects the distribution of the intrinsic population growth rate and further makes the spawning stock biomass an inadequate proxy to predict recruitment levels.

Spatio-temporal patterns of key exploited marine species in the Northwestern Mediterranean Sea

This study analyzes the temporal variability/stability of the spatial distributions of key exploited species in the Gulf of Lions (Northwestern Mediterranean Sea). To do so, we analyzed data from the MEDITS bottom-trawl scientific surveys from 1994 to 2010 at 66 fixed stations and selected 12 key exploited species. We proposed a geostatistical approach to handle zero-inflated and non-stationary distributions and to test for the temporal stability of the spatial structures. Empirical Orthogonal Functions and other descriptors were then applied to investigate the temporal persistence and the characteristics of the spatial patterns. The spatial structure of the distribution (i.e. the pattern of spatial autocorrelation) of the 12 key species studied remained highly stable over the time period sampled. The spatial distributions of all species obtained through kriging also appeared to be stable over time, while each species displayed a specific spatial distribution. Furthermore, adults were generally more densely concentrated than juveniles and occupied areas included in the distribution of juveniles. Despite the strong persistence of spatial distributions, we also observed that the area occupied by each species was correlated to its abundance: the more abundant the species, the larger the occupation area. Such a result tends to support MacCall's basin theory, according to which density-dependence responses would drive the expansion of those 12 key species in the Gulf of Lions. Further analyses showed that these species never saturated their habitats, suggesting that they are below their carrying capacity; an assumption in agreement with the overexploitation of several of these species. Finally, the stability of their spatial distributions over time and their potential ability to diffuse outside their main habitats give support to Marine Protected Areas as a potential pertinent management tool.

Ecosystem oceanography for global change in fisheries

Overexploitation and climate change are increasingly causing unanticipated changes in marine ecosystems, such as higher variability in fish recruitment and shifts in species dominance. An ecosystem-based approach to fisheries attempts to address these effects by integrating populations, food webs and fish habitats at different scales. Ecosystem models represent indispensable tools to achieve this objective. However, a balanced research strategy is needed to avoid overly complex models. Ecosystem oceanography represents such a balanced strategy that relates ecosystem components and their interactions to climate change and exploitation. It aims at developing realistic and robust models at different levels of organisation and addressing specific questions in a global change context while systematically exploring the ever-increasing amount of biological and environmental data.

Spatio-temporal dynamics of species richness in coastal fish communities

Determining patterns of change in species richness and the processes underlying the dynamics of biodiversity are of key interest within the field of ecology, but few studies have investigated the dynamics of vertebrate communities at a decadal temporal scale. Here, we report findings on the spatio-temporal variability in the richness and composition of fish communities along the Norwegian Skagerrak coast having been surveyed for more than half a century. Using statistical models incorporating non-detection and associated sampling variance, we estimate local species richness and changes in species composition allowing us to compute temporal variability in species richness. We tested whether temporal variation could be related to distance to the open sea and to local levels of pollution. Clear differences in mean species richness and temporal variability are observed between fjords that were and were not exposed to the effects of pollution. Altogether this indicates that the fjord is an appropriate scale for studying changes in coastal fish communities in space and time. The year-to-year rates of local extinction and turnover were found to be smaller than spatial differences in community composition. At the regional level, exposure to the open sea plays a homogenizing role, possibly due to coastal currents and advection.

Ecological responses to recent climate change

There is now ample evidence of the ecological impacts of recent climate change, from polar terrestrial to tropical marine environments. The responses of both flora and fauna span an array of ecosystems and organizational hierarchies, from the species to the community levels. Despite continued uncertainty as to community and ecosystem trajectories under global change, our review exposes a coherent pattern of ecological change across systems. Although we are only at an early stage in the projected trends of global warming, ecological responses to recent climate change are already clearly visible.

Cycles and trends in cod populations

Year-to-year fluctuations in fish stocks are usually attributed to variability in recruitment, competition, predation, and changes in catchability. Trends in abundance, in contrast, are usually ascribed to human exploitation and large-scale environmental changes. In this study, we demonstrate, through statistical modeling of survey data (1921-1994) of cod from the Norwegian Skagerrak coast, that both short- and long-term variability may arise from the same set of age-structured interactions. Asymmetric competition and cannibalism between cohorts generate alternating years of high and low abundance. Intercohort interactions also resonate the recruitment variability so that long-term trends are induced. The coupling of age-structure and variable recruitment should, therefore, be considered when explaining both the short- and long-term fluctuations displayed by the coastal cod populations. Resonant effects may occur in many marine populations that exhibit this combination of traits.

Global climate change and phenotypic variation among red deer cohorts

The variability of two fitness-related phenotypic traits (body weight and a mandibular skeletal ratio) was analysed among cohorts and age-classes of red deer in Norway. Phenotypic variation among cohorts was pronounced for calves, yearlings and reproductively mature adults. Fluctuations in cohort-specific mean body weights and skeletal ratios of adults correlated with global climatic variation in winter conditions influenced by the North Atlantic Oscillation while cohorts were in utero. Red deer born following warm winters were smaller than those born after cold winters, and this inter-cohort variability persisted into adulthood. Phenotypic variation among cohorts of red deer influenced by climate change may pose consequences for fitness of cohorts since body size and condition contribute to reproductive success and survival in male and female red deer. In particular, the recent trend of increasingly warm winters in northern Europe and Scandinavia may lead to reduced body size and fecundity of red deer, and perhaps other ungulates, in those areas.