Deep-sea predator niche segregation revealed by combined cetacean biologging and eDNA analysis of cephalopod prey

Advective Transport Drives Environmental DNA Dispersal in an Estuary

Environmental DNA (eDNA) is increasingly used for species detection and biodiversity monitoring in estuary and marine environments. The dynamic nature of these environments affects eDNA distribution relative to its source organisms, complicating the interpretation of eDNA observations and challenging the field sampling design. Here, an eDNA fate and transport model, built on an ocean model with Lagrangian particle tracking, provided a spatiotemporal estimate of the rapidly diluted eDNA shed by rare targets in an estuary environment before sampling. Based on the predicted particle densities, over 70% of the preselected stations detected the target eDNA. Despite potential variations in source strength and patchy distributions, the model explained approximately 40% of the observed variation in eDNA abundance; by comparison, eDNA concentration was uncorrelated with straight-line distance from the source or with a simplified oceanographic model. Our study revealed the extent of advective transport in shaping eDNA distribution and abundance and demonstrated the utility of ocean models and particle tracking in integrating marine eDNA observations with degradation, transport, and dilution processes; thus, it suggests broader applications to enhance understanding of eDNA signals and dispersal and optimize sampling strategies in other estuarine or marine environments.

Design and Validation of an Open-Close Device for Integrated Environmental DNA Sampling Detects A Depth Gradient in Indian Ocean Deep-Sea Fish Assemblages

Advances in methods for collecting environmental DNA (eDNA) are revolutionizing biomonitoring capabilities. The goal of this study was to leverage existing survey technology to design and test an eDNA sampler that captures an integrated eDNA sample over the length of a deep-water transect. We manufactured a 300 × 100 × 100 mm mountable, open-ended box made of high-density polyethylene that could be attached to the frame of a preexisting deep tow camera system. The box (OCD; open-close device) was equipped with an actuator that attached to hinged doors at both ends, enabling it to be opened and closed remotely at depths up to 6000 m through preexisting communications, thereby exposing the internal chamber to the surrounding water upon activation. A sterile active carbon sponge was inserted into the internal chamber for eDNA capture during each deployment. The OCD sampler was field tested during a voyage to the Gascoyne Marine Park region off northwest Australia. We compared three different methods for processing the captured eDNA from the sampler: filtering OCD water, extracting eDNA from sponge pieces, and filtering sponge rinse water. Using fish as our example organism, we also compared the identities of fishes from eDNA detections with bottom trawl survey data collected during the same survey, and the known regional species pool, to confirm the eDNA identifications were plausible. A large number of fishes (193 taxa, from 87 families) were detected, and the majority were found within their expected depth ranges (> 75%), and in the trawl catches (60%). We discuss design and manufacturing lessons, ideas for increased eDNA capture efficiency for improved methodologies in sample processing, and how to establish appropriate field controls. We also discuss how this technology could advance our scientific understanding in ocean studies in terms of ecological metrics provided and the trade-offs compared to other sampling tools.

Environmental DNA as a complementary tool for biodiversity monitoring: A multi-technique and multi-trophic approach to investigate cetacean distribution and feeding ecology

The use of environmental DNA (eDNA) to assess the presence of biological communities has emerged as a promising monitoring tool in the marine conservation landscape. Moreover, advances in Next-Generation Sequencing techniques, such as DNA metabarcoding, enable multi-species detection in mixed samples, allowing the study of complex ecosystems such as oceanic ones. We aimed at using these molecular-based techniques to characterize cetacean communities, as well as potential prey on the northern coast of Mainland Portugal. During four seasonal campaigns (summer 2021 to winter 2022/2023), seawater samples were collected along with visual records of cetacean occurrence. The eDNA isolated from 64 environmental samples was sequenced in an Illumina platform, with universal primers targeting marine vertebrates. Five cetacean species were identified by molecular detection: common dolphin (Delphinus delphis), bottlenose dolphin (Tursiops truncatus), Risso's dolphin (Grampus griseus), harbor porpoise (Phocoena phocoena) and fin whale (Balaenoptera physalus). Overall, except for the latter (not sighted during the campaigns), this cetacean community composition was similar to that obtained through visual monitoring, and the complementary results suggest their presence in the region all year round. In addition, the positive molecular detections of Balaenoptera physalus are of special relevance since there are no records of this species reported on scientific bibliography in the area. The detection of multiple known prey of the identified dolphins indicates an overlap between predator and prey in the study area, which suggests that these animals may use this coastal area for feeding purposes. While this methodological approach remains in a development stage, the present work highlights the benefits of using eDNA to study marine communities, with specific applications for research on cetacean distribution and feeding ecology.

Integrated approaches for comprehensive cetacean research and conservation in the East China Sea

This study thoroughly examines three cetacean monitoring methods and assessing their advantages and limitations, establishing a foundational basis for comprehensive information on composition, distribution, and behavior. While real-time and non-invasive, visual surveys favor surface-active cetaceans and are weather-dependent. Local ecological knowledge supplements insights into group behavior. Environmental DNA (eDNA) analysis efficiently detects species like the narrow-ridged finless porpoise (Neophocaena asiaeorientalis) and common bottlenose dolphin (Tursiops truncatus), offering non-invasive, and spatially adept monitoring. Furthermore, eDNA provides prey species information, revealing the narrow-ridged finless porpoise's winter migration to deeper waters due to prey distribution. The study identifies prevalent prey species, like the Japanese Anchovy (Engraulis japonicus) and Osbeck's grenadier anchovy (Coilia mystus), offering insights into the porpoise's feeding ecology and adaptation to changing prey availability in winter. This study systematically compares diverse methodologies employed in cetacean surveys, thereby yielding a comprehensive understanding of cetacean distribution, behavior, and feeding ecology.

Using low volume eDNA methods to sample pelagic marine animal assemblages

Environmental DNA (eDNA) is an increasingly useful method for detecting pelagic animals in the ocean but typically requires large water volumes to sample diverse assemblages. Ship-based pelagic sampling programs that could implement eDNA methods generally have restrictive water budgets. Studies that quantify how eDNA methods perform on low water volumes in the ocean are limited, especially in deep-sea habitats with low animal biomass and poorly described species assemblages. Using 12S rRNA and COI gene primers, we quantified assemblages comprised of micronekton, coastal forage fishes, and zooplankton from low volume eDNA seawater samples (n = 436, 380-1800 mL) collected at depths of 0-2200 m in the southern California Current. We compared diversity in eDNA samples to concurrently collected pelagic trawl samples (n = 27), detecting a higher diversity of vertebrate and invertebrate groups in the eDNA samples. Differences in assemblage composition could be explained by variability in size-selectivity among methods and DNA primer suitability across taxonomic groups. The number of reads and amplicon sequences variants (ASVs) did not vary substantially among shallow (<200 m) and deep samples (>600 m), but the proportion of invertebrate ASVs that could be assigned a species-level identification decreased with sampling depth. Using hierarchical clustering, we resolved horizontal and vertical variability in marine animal assemblages from samples characterized by a relatively low diversity of ecologically important species. Low volume eDNA samples will quantify greater taxonomic diversity as reference libraries, especially for deep-dwelling invertebrate species, continue to expand.

Bioenergetic modelling of a marine top predator's responses to changes in prey structure

Determining how animals allocate energy, and how external factors influence this allocation, is crucial to understand species' life history requirements and response to disturbance. This response is driven in part by individuals' energy balance, prey characteristics, foraging behaviour and energy required for essential functions. We developed a bioenergetic model to estimate minimum foraging success rate (FSR), that is, the lowest possible prey capture rate for individuals to obtain the minimum energy intake needed to meet daily metabolic requirements, for female sperm whale (Physeter macrocephalus). The model was based on whales' theoretical energetic requirements using foraging and prey characteristics from animal-borne tags and stomach contents, respectively. We used this model to simulate two prey structure change scenarios: (1) decrease in mean prey size, thus lower prey energy content and (2) decrease in prey size variability, reducing the variability in prey energy content. We estimate the whales need minimum of ~14% FSR to meet their energetic requirements, and energy intake is more sensitive to energy content changes than a decrease in energy variability. To estimate vulnerability to prey structure changes, we evaluated the compensation level required to meet bioenergetic demands. Considering a minimum 14% FSR, whales would need to increase energy intake by 21% (5-35%) and 49% (27-67%) to compensate for a 15% and 30% decrease in energy content, respectively. For a 30% and 50% decrease in energy variability, whales would need to increase energy intake by 13% (0-23%) and 24% (10-35%) to meet energetic demands, respectively. Our model demonstrates how foraging and prey characteristics can be used to estimate impact of changing prey structure in top predator energetics, which can help inform bottom-up effects on marine ecosystems. We showed the importance of considering different FSR in bioenergetics models, as it can have decisive implications on estimates of energy acquired and affect the conclusions about top predator's vulnerability to possible environmental fluctuations.

Atlantic Oceanic Squids in the "Grey Speciation Zone"

Cryptic species complexes represent an important challenge for the adequate characterization of Earth's biodiversity. Oceanic organisms tend to have greater unrecognized cryptic biodiversity since the marine realm was often considered to lack hard barriers to genetic exchange. Here, we tested the effect of several Atlantic and Mediterranean oceanic barriers on 16 morphospecies of oceanic squids of the orders Oegopsida and Bathyteuthida using three mitochondrial and one nuclear molecular marker and five species delimitation methods. Number of species recognized within each morphospecies differed among different markers and analyses, but we found strong evidence of cryptic biodiversity in at least four of the studied species (Chtenopteryx sicula, Chtenopteryx canariensis, Ancistrocheirus lesueurii, and Galiteuthis armata). There were highly geographically structured units within Helicocranchia navossae that could either represent recently diverged species or population structure. Although the species studied here can be considered relatively passive with respect to oceanic currents, cryptic speciation patterns showed few signs of being related to oceanic currents. We hypothesize that the bathymetry of the egg masses and duration of the paralarval stage might influence the geographic distribution of oceanic squids. Because the results of different markers and different species delimitation methods are inconsistent and because molecular data encompassing broad geographic sampling areas for oceanic squids are scarce and finding morphological diagnostic characters for early life stages is difficult, it is challenging to assess the species boundaries for many of these species. Thus, we consider many to be in the "grey speciation zone." As many oceanic squids have cosmopolitan distributions, new studies combining genomic and morphological information from specimens collected worldwide are needed to correctly assess the actual oceanic squid biodiversity.

Field physiology in the aquatic realm: ecological energetics and diving behavior provide context for elucidating patterns and deviations

Comparative physiology has developed a rich understanding of the physiological adaptations of organisms, from microbes to megafauna. Despite extreme differences in size and a diversity of habitats, general patterns are observed in their physiological adaptations. Yet, many organisms deviate from the general patterns, providing an opportunity to understand the importance of ecology in determining the evolution of unusual adaptations. Aquatic air-breathing vertebrates provide unique study systems in which the interplay between ecology, physiology and behavior is most evident. They must perform breath-hold dives to obtain food underwater, which imposes a physiological constraint on their foraging time as they must resurface to breathe. This separation of two critical resources has led researchers to investigate these organisms' physiological adaptations and trade-offs. Addressing such questions on large marine animals is best done in the field, given the difficulty of replicating the environment of these animals in the lab. This Review examines the long history of research on diving physiology and behavior. We show how innovative technology and the careful selection of research animals have provided a holistic understanding of diving mammals' physiology, behavior and ecology. We explore the role of the aerobic diving limit, body size, oxygen stores, prey distribution and metabolism. We then identify gaps in our knowledge and suggest areas for future research, pointing out how this research will help conserve these unique animals.

Quantification by droplet digital PCR and species identification by metabarcoding of environmental (e)DNA from Blainville's beaked whales, with assisted localization from an acoustic array

Detection and identification of species, subspecies or stocks of whales, dolphins and porpoises at sea remain challenging, particularly for cryptic or elusive species like beaked whales (Family: Ziphiidae). Here we investigated the potential for using an acoustically assisted sampling design to collect environmental (e)DNA from beaked whales on the U.S. Navy's Atlantic Undersea Test and Evaluation Center (AUTEC) in The Bahamas. During 12 days of August 2019, we conducted 9 small-boat surveys and collected 56 samples of seawater (paired subsamples of 1L each, including controls) using both a spatial collection design in the absence of visual confirmation of whales, and a serial collection design in the proximity of whales at the surface. There were 7 sightings of whales, including 11 Blainville's beaked whales (Mesoplodon densirostris). All whales were located initially with the assistance of information from a bottom-mounted acoustic array available on the AUTEC range. Quantification by droplet digital (dd)PCR from the four spatial design collections showed no samples of eDNA above the threshold of detection and none of these 20 samples yielded amplicons for conventional or next-generation sequencing. Quantification of the 31 samples from four serial collections identified 11 likely positive detections. eDNA barcoding by conventional sequencing and eDNA metabarcoding by next-generation sequencing confirmed species identification for 9 samples from three of the four serial collections. We further resolved five intra-specific variants (i.e., haplotypes), two of which showed an exact match to previously published haplotypes and three that have not been reported previously to the international repository, GenBank. A minimum spanning network of the five eDNA haplotypes, with all other published haplotypes of Blainville's beaked whales, suggested the potential for further resolution of differences between oceanic populations.

Trapped DNA fragments in marine sponge specimens unveil North Atlantic deep-sea fish diversity

Sponges pump water to filter feed and for diffusive oxygen uptake. In doing so, trace DNA fragments from a multitude of organisms living around them are trapped in their tissues. Here we show that the environmental DNA retrieved from archived marine sponge specimens can reconstruct the fish communities at the place of sampling and discriminate North Atlantic assemblages according to biogeographic region (from Western Greenland to Svalbard), depth habitat (80-1600 m), and even the level of protection in place. Given the cost associated with ocean biodiversity surveys, we argue that targeted and opportunistic sponge samples - as well as the specimens already stored in museums and other research collections - represent an invaluable trove of biodiversity information that can significantly extend the reach of ocean monitoring.

Ultrasensitive and on-site eDNA detection for the monitoring of crown-of-thorns starfish densities at the pre-outbreak stage using an electrochemical biosensor

The coral reef crisis has significantly intensified over the last decades, mainly due to severe outbreaks of crown-of-thorns starfish (COTS). Current ecological monitoring has failed to detect COTS densities at the pre-outbreak stage, thus preventing early intervention. In this work, we developed an effective electrochemical biosensor modified by a MoO₂/C nanomaterial, as well as a specific DNA probe that could detect trace COTS environmental DNA (eDNA) at a lower detection limit (LOD = 0.147 ng/μL) with excellent specificity. The reliability and accuracy of the biosensor were validated against the standard methods by an ultramicro spectrophotometer and droplet digital PCR (p > 0.05). The biosensor was then utilized for the on-site analysis of seawater samples from SYM-LD and SY sites in the South China Sea. For the SYM-LD site suffering an outbreak, the COTS eDNA concentrations were 0.33 ng/μL (1 m, depth) and 0.26 ng/μL (10 m, depth), respectively. According to the ecological survey, the COTS density was 500 ind/hm² at the SYM-LD site, verifying the accuracy of our measurements. At the SY site, COTS eDNA was also detected at 0.19 ng/μL, but COTS was not found by the traditional survey. Hence, larvae were possibly present in this region. Therefore, this electrochemical biosensor could be used to monitor COTS populations at the pre-outbreak stages, and potentially serve as a revolutionary early warning method. We will continue to improve this method for picomolar or even femtomolar detection of COTS eDNA.

Energetic connectivity of diverse elasmobranch populations - implications for ecological resilience

Understanding the factors shaping patterns of ecological resilience is critical for mitigating the loss of global biodiversity. Throughout aquatic environments, highly mobile predators are thought to serve as important vectors of energy between ecosystems thereby promoting stability and resilience. However, the role these predators play in connecting food webs and promoting energy flow remains poorly understood in most contexts. Using carbon and nitrogen isotopes, we quantified the use of several prey resource pools (small oceanic forage, large oceanics, coral reef, and seagrass) by 17 species of elasmobranch fishes (n = 351 individuals) in The Bahamas to determine their functional diversity and roles as ecosystem links. We observed remarkable functional diversity across species and identified four major groups responsible for connecting discrete regions of the seascape. Elasmobranchs were responsible for promoting energetic connectivity between neritic, oceanic and deep-sea ecosystems. Our findings illustrate how mobile predators promote ecosystem connectivity, underscoring their functional significance and role in supporting ecological resilience. More broadly, strong predator conservation efforts in developing island nations, such as The Bahamas, are likely to yield ecological benefits that enhance the resilience of marine ecosystems to combat imminent threats such as habitat degradation and climate change.

Estimating energetic intake for marine mammal bioenergetic models

Bioenergetics is the study of how animals achieve energetic balance. Energetic balance results from the energetic expenditure of an individual and the energy they extract from their environment. Ingested energy depends on several extrinsic (e.g prey species, nutritional value and composition, prey density and availability) and intrinsic factors (e.g. foraging effort, success at catching prey, digestive processes and associated energy losses, and digestive capacity). While the focus in bioenergetic modelling is often on the energetic costs an animal incurs, the robust estimation of an individual's energy intake is equally critical for producing meaningful predictions. Here, we review the components and processes that affect energy intake from ingested gross energy to biologically useful net energy (NE). The current state of knowledge of each parameter is reviewed, shedding light on research gaps to advance this field. The review highlighted that the foraging behaviour of many marine mammals is relatively well studied via biologging tags, with estimates of success rate typically assumed for most species. However, actual prey capture success rates are often only assumed, although we note studies that provide approaches for its estimation using current techniques. A comprehensive collation of the nutritional content of marine mammal prey species revealed a robust foundation from which prey quality (comprising prey species, size and energy density) can be assessed, though data remain unavailable for many prey species. Empirical information on various energy losses following ingestion of prey was unbalanced among marine mammal species, with considerably more literature available for pinnipeds. An increased understanding and accurate estimate of each of the components that comprise a species NE intake are an integral part of bioenergetics. Such models provide a key tool to investigate the effects of disturbance on marine mammals at an individual and population level and to support effective conservation and management.

The global depth range of marine fishes and their genetic coverage for environmental DNA metabarcoding

The bathymetric and geographical distribution of marine species represent a key information in biodiversity conservation. Yet, deep-sea ecosystems are among the least explored on Earth and are increasingly impacted by human activities. Environmental DNA (eDNA) metabarcoding has emerged as a promising method to study fish biodiversity but applications to the deep-sea are still scarce. A major limitation in the application of eDNA metabarcoding is the incompleteness of species sequences available in public genetic databases which reduces the extent of detected species. This incompleteness by depth is still unknown. Here, we built the global bathymetric and geographical distribution of 10,826 actinopterygian and 960 chondrichthyan fish species. We assessed their genetic coverage by depth and by ocean for three main metabarcoding markers used in the literature: teleo and MiFish-U/E. We also estimated the number of primer mismatches per species amplified by in silico polymerase chain reaction which influence the probability of species detection. Actinopterygians show a stronger decrease in species richness with depth than Chondrichthyans. These richness gradients are accompanied by a continuous species turnover between depths. Fish species coverage with the MiFish-U/E markers is higher than with teleo while threatened species are more sequenced than the others. "Deep-endemic" species, those not ascending to the shallow depth layer, are less sequenced than not threatened species. The number of primer mismatches is not higher for deep-sea species than for shallower ones. eDNA metabarcoding is promising for species detection in the deep-sea to better account for the 3-dimensional structure of the ocean in marine biodiversity monitoring and conservation. However, we argue that sequencing efforts on "deep-endemic" species are needed.

Key questions in marine mammal bioenergetics

Bioenergetic approaches are increasingly used to understand how marine mammal populations could be affected by a changing and disturbed aquatic environment. There remain considerable gaps in our knowledge of marine mammal bioenergetics, which hinder the application of bioenergetic studies to inform policy decisions. We conducted a priority-setting exercise to identify high-priority unanswered questions in marine mammal bioenergetics, with an emphasis on questions relevant to conservation and management. Electronic communication and a virtual workshop were used to solicit and collate potential research questions from the marine mammal bioenergetic community. From a final list of 39 questions, 11 were identified as 'key' questions because they received votes from at least 50% of survey participants. Key questions included those related to energy intake (prey landscapes, exposure to human activities) and expenditure (field metabolic rate, exposure to human activities, lactation, time-activity budgets), energy allocation priorities, metrics of body condition and relationships with survival and reproductive success and extrapolation of data from one species to another. Existing tools to address key questions include labelled water, animal-borne sensors, mark-resight data from long-term research programs, environmental DNA and unmanned vehicles. Further validation of existing approaches and development of new methodologies are needed to comprehensively address some key questions, particularly for cetaceans. The identification of these key questions can provide a guiding framework to set research priorities, which ultimately may yield more accurate information to inform policies and better conserve marine mammal populations.

Risso's dolphins perform spin dives to target deep-dwelling prey

Foraging decisions of deep-diving cetaceans can provide fundamental insight into food web dynamics of the deep pelagic ocean. Cetacean optimal foraging entails a tight balance between oxygen-conserving dive strategies and access to deep-dwelling prey of sufficient energetic reward. Risso's dolphins (Grampus griseus) displayed a thus far unknown dive strategy, which we termed the spin dive. Dives started with intense stroking and right-sided lateral rotation. This remarkable behaviour resulted in a rapid descent. By tracking the fine-scale foraging behaviour of seven tagged individuals, matched with prey layer recordings, we tested the hypothesis that spin dives are foraging dives targeting deep-dwelling prey. Hunting depth traced the diel movement of the deep scattering layer, a dense aggregation of prey, that resides deep during the day and near-surface at night. Individuals shifted their foraging strategy from deep spin dives to shallow non-spin dives around dusk. Spin dives were significantly faster, steeper and deeper than non-spin dives, effectively minimizing transit time to bountiful mesopelagic prey, and were focused on periods when the migratory prey might be easier to catch. Hence, whereas Risso's dolphins were mostly shallow, nocturnal foragers, their spin dives enabled extended and rewarding diurnal foraging on deep-dwelling prey.

Friend or foe: Risso's dolphins eavesdrop on conspecific sounds to induce or avoid intra-specific interaction

The detection and use of emitters' signals by unintended receivers, i.e., eavesdropping, represents an important and often low-cost way for animals to gather information from their environment. Acoustic eavesdropping can be a key driver in mediating intra- and interspecific interactions (e.g., cooperation, predator-prey systems), specifically in species such as cetaceans that use sound as a primary sensory modality. While most cetacean species produce context-specific sounds, little is known about the use of those sounds by potential conspecific eavesdroppers. We experimentally tested the hypothesis that a social cetacean, Risso's dolphin (Grampus griseus), is able to gather biologically relevant information by eavesdropping on conspecific sounds. We conducted playback experiments on free-ranging dolphins using three context-specific sounds stimuli and monitored their horizontal movement using visual or airborne focal follow observations. We broadcasted natural sequences of conspecific foraging sounds potentially providing an attractive dinner bell signal (n = 7), male social sounds simulating a risk of forthcoming agonistic interaction (n = 7) and female-calf social sounds representing no particularly threatening context (n = 7). We developed a quantitative movement response score and tested whether animals changed their direction of horizontal movement towards or away from the playback source. Dolphins approached the foraging and the social female-calf sounds whereas they avoided the social male sounds. Hence, by acoustically eavesdropping on conspecifics, dolphins can discriminate between social and behavioural contexts and anticipate potential threatening or beneficial situations. Eavesdropping and the ensuing classification of 'friend or foe' can thus shape intra-specific social interactions in cetaceans.