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.

Life in the Midwater: The Ecology of Deep Pelagic Animals.

The water column of the deep ocean is dark, cold, low in food, and under crushing pressures, yet it is full of diverse life. Due to its enormous volume, this mesopelagic zone is home to some of the most abundant animals on the planet. Rather than struggling to survive, they thrive-owing to a broad set of adaptations for feeding, behavior, and physiology. Our understanding of these adaptations is constrained by the tools available for exploring the deep sea, but this tool kit is expanding along with technological advances. Each time we apply a new method to the depths, we gain surprising insights about genetics, ecology, behavior, physiology, diversity, and the dynamics of change. These discoveries show structure within the seemingly uniform habitat, limits to the seemingly inexhaustible resources, and vulnerability in the seemingly impervious environment. To understand midwater ecology, we need to reimagine the rules that govern terrestrial ecosystems. By spending more time at depth-with whatever tools are available-we can fill the knowledge gaps and better link ecology to the environment throughout the water column.

The Pelagic Species Trait Database, an open data resource to support trait-based ocean research.

Trait-based frameworks are increasingly used for predicting how ecological communities respond to ongoing global change. As species range shifts result in novel encounters between predators and prey, identifying prey 'guilds', based on a suite of shared traits, can distill complex species interactions, and aid in predicting food web dynamics. To support advances in trait-based research in open-ocean systems, we present the Pelagic Species Trait Database, an extensive resource documenting functional traits of 529 pelagic fish and invertebrate species in a single, open-source repository. We synthesized literature sources and online resources, conducted morphometric analysis of species images, as well as laboratory analyses of trawl-captured specimens to collate traits describing 1) habitat use and behavior, 2) morphology, 3) nutritional quality, and 4) population status information. Species in the dataset primarily inhabit the California Current system and broader NE Pacific Ocean, but also includes pelagic species known to be consumed by top ocean predators from other ocean basins. The aim of this dataset is to enhance the use of trait-based approaches in marine ecosystems and for predator populations worldwide.

Harnessing a mesopelagic predator as a biological sampler reveals taxonomic and vertical resource partitioning among three poorly known deep-sea fishes.

Pelagic predators are effective biological samplers of midtrophic taxa and are especially useful in deep-sea habitats where relatively mobile taxa frequently avoid observation with conventional methods. We examined specimens sampled from the stomachs of longnose lancetfish, Alepisaurus ferox, to describe the diets and foraging behaviors of three common, but poorly known deep-sea fishes: the hammerjaw (Omosudis lowii, n = 79, 0.3-92 g), juvenile common fangtooth (Anoplogaster cornuta, n = 91, 0.6-22 g), and juvenile Al. ferox (n = 138, 0.3-744 g). Diet overlap among the three species was high, with five shared prey families accounting for 63 ± 11% of the total prey mass per species. However, distinct differences in foraging strategies and prey sizes were evident. Resource partitioning was greatest between An. cornuta that specialized on small (mean = 0.13 ± 0.11 g), shallow-living hyperiid amphipods and O. lowii that specialized on large (mean = 0.97 ± 0.45 g), deep-dwelling hatchetfishes. Juvenile Al. ferox foraged on a high diversity of prey from both shallow and deep habitats. We describe the foraging ecologies of three midtrophic fish competitors and demonstrate the potential for biological samplers to improve our understanding of deep-sea food webs.

Coastal upwelling drives ecosystem temporal variability from the surface to the abyssal seafloor.

Long-term biological time series that monitor ecosystems across the ocean's full water column are extremely rare. As a result, classic paradigms are yet to be tested. One such paradigm is that variations in coastal upwelling drive changes in marine ecosystems throughout the water column. We examine this hypothesis by using data from three multidecadal time series spanning surface (0 m), midwater (200 to 1,000 m), and benthic (~4,000 m) habitats in the central California Current Upwelling System. Data include microscopic counts of surface plankton, video quantification of midwater animals, and imaging of benthic seafloor invertebrates. Taxon-specific plankton biomass and midwater and benthic animal densities were separately analyzed with principal component analysis. Within each community, the first mode of variability corresponds to most taxa increasing and decreasing over time, capturing seasonal surface blooms and lower-frequency midwater and benthic variability. When compared to local wind-driven upwelling variability, each community correlates to changes in upwelling damped over distinct timescales. This suggests that periods of high upwelling favor increase in organism biomass or density from the surface ocean through the midwater down to the abyssal seafloor. These connections most likely occur directly via changes in primary production and vertical carbon flux, and to a lesser extent indirectly via other oceanic changes. The timescales over which species respond to upwelling are taxon-specific and are likely linked to the longevity of phytoplankton blooms (surface) and of animal life (midwater and benthos), which dictate how long upwelling-driven changes persist within each community.

Towards a North Pacific Ocean long-term monitoring program for plastic pollution: A review and recommendations for plastic ingestion bioindicators.

Marine debris is now a ubiquitous component of the Anthropocene global ocean. Plastic ingestion by marine wildlife was first reported in the 1960s and since that time, roughly one thousand marine species have been reported to consume this debris. This study focuses on plastic ingestion by marine invertebrates and vertebrates in the North Pacific Ocean. Specifically, we reviewed the scientific literature to assess the scope of the problem, identified key bioindicator species, and proposed guidelines for future monitoring of plastic debris in North Pacific marine ecosystems. Our meta-analysis confirmed that the North Pacific is among the most polluted ocean regions globally; roughly half of all fish and seabird specimens and more than three-quarters of sea turtles and bivalve specimens examined in this region had consumed plastic. While there are not enough standardized data to assess if these ingestion rates are changing, sampling standardization and reporting of methods are improving over time. Using a rubric-evaluation approach, we evaluated 352 species for their potential to serve as bioindicators of the prevalence of plastic pollution in the North Pacific. This analysis revealed a suite of 12 bioindicator species candidates which sample a variety of ecosystem components and cover a wide range of plastic size classes. Thus, we contend that these bioindicator candidates provide a key foundation for developing a comprehensive plastic monitoring program in the region. To enhance the utility of these bioindicators, we developed a framework for standardized data collection to minimize methodological variability across different studies and to facilitate the assessment of temporal trends over space and time. Tracking plastic ingestion by these bioindicators will help to assess the effectiveness of mitigation actions in the region, a critical step to evaluate progress towards sustainability and improved ocean health in the 21st century.

Characterizing the secret diets of siphonophores (Cnidaria: Hydrozoa) using DNA metabarcoding.

Siphonophores (Cnidaria: Hydrozoa) are abundant and diverse gelatinous predators in open-ocean ecosystems. Due to limited access to the midwater, little is known about the diets of most deep-dwelling gelatinous species, which constrains our understanding of food-web structure and nutrient flow in these vast ecosystems. Visual gut-content methods can rarely identify soft-bodied rapidly-digested prey, while observations from submersibles often overlook small prey items. These methods have been differentially applied to shallow and deep siphonophore taxa, confounding habitat and methodological biases. DNA metabarcoding can be used to assess both shallow and deep species' diets under a common methodological framework, since it can detect both small and gelatinous prey. We (1) further characterized the diets of open-ocean siphonophores using DNA metabarcoding, (2) compared the prey detected by visual and molecular methods to evaluate their technical biases, and (3) evaluated tentacle-based predictions of diet. To do this, we performed DNA metabarcoding analyses on the gut contents of 39 siphonophore species across depths to describe their diets, using six barcode regions along the 18S gene. Taxonomic identifications were assigned using public databases combined with local zooplankton sequences. We identified 55 unique prey items, including crustaceans, gelatinous animals, and fish across 47 siphonophore specimens in 24 species. We reported 29 novel predator-prey interactions, among them the first insights into the diets of nine siphonophore species, many of which were congruent with the dietary predictions based on tentilla morphology. Our analyses detected both small and gelatinous prey taxa underrepresented by visual methods in species from both shallow and deep habitats, indicating that siphonophores play similar trophic roles across depth habitats. We also reveal hidden links between siphonophores and filter-feeders near the base of the food web. This study expands our understanding of the ecological roles of siphonophores in the open ocean, their trophic roles within the 'jelly-web', and the importance of their diversity for nutrient flow and ecosystem functioning. Understanding these inconspicuous yet ubiquitous predator-prey interactions is critical to predict the impacts of climate change, overfishing, and conservation policies on oceanic ecosystems.

Global data set for nitrogen and carbon stable isotopes of tunas.

Nitrogen and carbon stable isotope data sets are commonly used to assess complex population to ecosystem responses to natural or anthropogenic changes at regional to global spatial scales, and monthly to decadal timescales. Measured in the tissues of consumers, nitrogen isotopes (δ15 N) are primarily used to estimate trophic position while carbon isotopes (δ13 C) describe habitat associations and feeding pathways. Models of both δ15 N and δ13 C values and their associated variance can be used to estimate likely dietary contributions and niche width and provide inferences about consumer movement and migration. Stable isotope data have added utility when used in combination with other empirical data sets (e.g., stomach content, movement tracking, bioregionalization, contaminant, or fisheries data) and are increasingly relied upon in food web and ecosystem models. While numerous regional studies publish tables of mean δ15 N and δ13 C values, limited individual records have been made available for wider use. Such a deficiency has impeded full utility of the data, which otherwise would facilitate identification of macroscale patterns. The data provided here consist of 4,498 records of individuals of three tuna species, Thunnus alalunga, T. obesus, and T. albacares sampled from all major ocean basins from 2000 to 2015. For each individual tuna, we provide a record of the following: species name, sampling date, sampling location, tuna length, muscle bulk and baseline corrected δ15 N values, and muscle bulk and, where available, lipid corrected δ13 C values. We provide these individual records to support comparative studies and more robust modeling projects seeking to improve understanding of complex marine ecosystem dynamics and their responses to a changing environment. There are no copyright restrictions for research and/or teaching purposes. Users are requested to acknowledge their use of the data in publications, research proposals, websites, and other outlets following the citation instructions in Class III, Section B.

Author Correction: The vertical distribution and biological transport of marine microplastics across the epipelagic and mesopelagic water column.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Trends in tuna carbon isotopes suggest global changes in pelagic phytoplankton communities.

Considerable uncertainty remains over how increasing atmospheric CO2 and anthropogenic climate changes are affecting open-ocean marine ecosystems from phytoplankton to top predators. Biological time series data are thus urgently needed for the world's oceans. Here, we use the carbon stable isotope composition of tuna to provide a first insight into the existence of global trends in complex ecosystem dynamics and changes in the oceanic carbon cycle. From 2000 to 2015, considerable declines in δ13 C values of 0.8‰-2.5‰ were observed across three tuna species sampled globally, with more substantial changes in the Pacific Ocean compared to the Atlantic and Indian Oceans. Tuna recorded not only the Suess effect, that is, fossil fuel-derived and isotopically light carbon being incorporated into marine ecosystems, but also recorded profound changes at the base of marine food webs. We suggest a global shift in phytoplankton community structure, for example, a reduction in 13 C-rich phytoplankton such as diatoms, and/or a change in phytoplankton physiology during this period, although this does not rule out other concomitant changes at higher levels in the food webs. Our study establishes tuna δ13 C values as a candidate essential ocean variable to assess complex ecosystem responses to climate change at regional to global scales and over decadal timescales. Finally, this time series will be invaluable in calibrating and validating global earth system models to project changes in marine biota.

Differences in the trophic ecology of micronekton driven by diel vertical migration.

Many species of micronekton perform diel vertical migrations (DVMs), which ultimately contributes to carbon export to the deep sea. However, not all micronekton species perform DVM, and the nonmigrators, which are often understudied, have different energetic requirements that might be reflected in their trophic ecology. We analyze bulk tissue and whole animal stable nitrogen isotopic compositions (δ 15N values) of micronekton species collected seasonally between 0 and 1250 m depth to explore differences in the trophic ecology of vertically migrating and nonmigrating micronekton in the central North Pacific. Nonmigrating species exhibit depth-related increases in δ 15N values mirroring their main prey, zooplankton. Higher variance in δ 15N values of bathypelagic species points to the increasing reliance of deeper dwelling micronekton on microbially reworked, very small suspended particles. Migrators have higher δ 15N values than nonmigrators inhabiting the epipelagic zone, suggesting the consumption of material during the day at depth, not only at night when they migrate closer to the surface. Migrating species also appear to eat larger prey and exhibit a higher range of variation in δ 15N values seasonally than nonmigrators, likely because of their higher energy needs. The dependence on material at depth enriched in 15N relative to surface particles is higher in migratory fish that ascend only to the lower epipelagic zone. Our results confirm that stark differences in the food habits and dietary sources of micronekton species are driven by vertical migrations.

The vertical distribution and biological transport of marine microplastics across the epipelagic and mesopelagic water column.

Plastic waste has been documented in nearly all types of marine environments and has been found in species spanning all levels of marine food webs. Within these marine environments, deep pelagic waters encompass the largest ecosystems on Earth. We lack a comprehensive understanding of the concentrations, cycling, and fate of plastic waste in sub-surface waters, constraining our ability to implement effective, large-scale policy and conservation strategies. We used remotely operated vehicles and engineered purpose-built samplers to collect and examine the distribution of microplastics in the Monterey Bay pelagic ecosystem at water column depths ranging from 5 to 1000 m. Laser Raman spectroscopy was used to identify microplastic particles collected from throughout the deep pelagic water column, with the highest concentrations present at depths between 200 and 600 m. Examination of two abundant particle feeders in this ecosystem, pelagic red crabs (Pleuroncodes planipes) and giant larvaceans (Bathochordaeus stygius), showed that microplastic particles readily flow from the environment into coupled water column and seafloor food webs. Our findings suggest that one of the largest and currently underappreciated reservoirs of marine microplastics may be contained within the water column and animal communities of the deep sea.

Improving Marine Ecosystem Models with Biochemical Tracers.

Empirical data on food web dynamics and predator-prey interactions underpin ecosystem models, which are increasingly used to support strategic management of marine resources. These data have traditionally derived from stomach content analysis, but new and complementary forms of ecological data are increasingly available from biochemical tracer techniques. Extensive opportunities exist to improve the empirical robustness of ecosystem models through the incorporation of biochemical tracer data and derived indices, an area that is rapidly expanding because of advances in analytical developments and sophisticated statistical techniques. Here, we explore the trophic information required by ecosystem model frameworks (species, individual, and size based) and match them to the most commonly used biochemical tracers (bulk tissue and compound-specific stable isotopes, fatty acids, and trace elements). Key quantitative parameters derived from biochemical tracers include estimates of diet composition, niche width, and trophic position. Biochemical tracers also provide powerful insight into the spatial and temporal variability of food web structure and the characterization of dominant basal and microbial food web groups. A major challenge in incorporating biochemical tracer data into ecosystem models is scale and data type mismatches, which can be overcome with greater knowledge exchange and numerical approaches that transform, integrate, and visualize data.

Deep pelagic food web structure as revealed by in situ feeding observations.

Food web linkages, or the feeding relationships between species inhabiting a shared ecosystem, are an ecological lens through which ecosystem structure and function can be assessed, and thus are fundamental to informing sustainable resource management. Empirical feeding datasets have traditionally been painstakingly generated from stomach content analysis, direct observations and from biochemical trophic markers (stable isotopes, fatty acids, molecular tools). Each approach carries inherent biases and limitations, as well as advantages. Here, using 27 years (1991-2016) of in situ feeding observations collected by remotely operated vehicles (ROVs), we quantitatively characterize the deep pelagic food web of central California within the California Current, complementing existing studies of diet and trophic interactions with a unique perspective. Seven hundred and forty-three independent feeding events were observed with ROVs from near-surface waters down to depths approaching 4000 m, involving an assemblage of 84 different predators and 82 different prey types, for a total of 242 unique feeding relationships. The greatest diversity of prey was consumed by narcomedusae, followed by physonect siphonophores, ctenophores and cephalopods. We highlight key interactions within the poorly understood 'jelly web', showing the importance of medusae, ctenophores and siphonophores as key predators, whose ecological significance is comparable to large fish and squid species within the central California deep pelagic food web. Gelatinous predators are often thought to comprise relatively inefficient trophic pathways within marine communities, but we build upon previous findings to document their substantial and integral roles in deep pelagic food webs.

Carbon, Nitrogen, and Mercury Isotope Evidence for the Biogeochemical History of Mercury in Hawaiian Marine Bottomfish.

The complex biogeochemical cycle of Hg makes identifying primary sources of fish tissue Hg problematic. To identify sources and provide insight into this cycle, we combined carbon (δ13C), nitrogen amino acid (δ15NPhe), and Hg isotope (Δ199Hg, Δ201Hg, δ202Hg) data for six species of Hawaiian marine bottomfish. Results from these isotopic systems identified individuals within species that likely fed from separate food webs. Terrestrial freshwater inputs to coastal sediments were identified as the primary source of tissue Hg in the jack species, Caranx ignobilis, which inhabit shallow marine ecosystems. Thus, coastal C. ignobilis were a biological vector transporting Hg from freshwater environments into marine ecosystems. Depth profiles of Hg isotopic compositions for bottomfish (excludung C. ignobilis) were similar, but not identical, to profiles for open-ocean pelagic fishes, suggesting that in both settings inorganic Hg, which was ultimately transformed to monomethylmercury (MeHg) and bioaccumulated, was dominantly from a single source. However, differences between pelagic fish and bottomfish profiles were attributable to mass-dependent fractionation in the benthos prior to incorporation into the food web. Results also confirmed that bottomfish relied, at least in part, on a benthic food web and identified the incorporation of deeper water oceanic MeHg sources into deeper water sediments prior to food web uptake and transfer.

From the surface to the seafloor: How giant larvaceans transport microplastics into the deep sea.

Plastic waste is a pervasive feature of marine environments, yet little is empirically known about the biological and physical processes that transport plastics through marine ecosystems. To address this need, we conducted in situ feeding studies of microplastic particles (10 to 600 µm in diameter) with the giant larvacean Bathochordaeus stygius. Larvaceans are abundant components of global zooplankton assemblages, regularly build mucus "houses" to filter particulate matter from the surrounding water, and later abandon these structures when clogged. By conducting in situ feeding experiments with remotely operated vehicles, we show that giant larvaceans are able to filter a range of microplastic particles from the water column, ingest, and then package microplastics into their fecal pellets. Microplastics also readily affix to their houses, which have been shown to sink quickly to the seafloor and deliver pulses of carbon to benthic ecosystems. Thus, giant larvaceans can contribute to the vertical flux of microplastics through the rapid sinking of fecal pellets and discarded houses. Larvaceans, and potentially other abundant pelagic filter feeders, may thus comprise a novel biological transport mechanism delivering microplastics from surface waters, through the water column, and to the seafloor. Our findings necessitate the development of tools and sampling methodologies to quantify concentrations and identify environmental microplastics throughout the water column.

Mercury sources and trophic ecology for Hawaiian bottomfish.

In Hawaii, some of the most important commercial and recreational fishes comprise an assemblage of lutjanids and carangids called bottomfish. Despite their importance, we know little about their trophic ecology or where the mercury (Hg) that ultimately resides in their tissue originates. Here we investigated these topics, by analyzing muscle samples for mercury content, nitrogen, carbon, and amino acid specific nitrogen isotope ratios in six species distributed across different depths from the Northwestern Hawaiian Islands (NWHI) and the Main Hawaiian Islands (MHI). Fishes had different sources of nitrogen and carbon, with isotopic values suggesting benthic food sources for shallow nearshore species. High trophic position lutjanids that foraged in deeper water, benthic environments generally had higher Hg levels. Model results also suggested that benthic Hg methylation was an important source of Hg for shallow benthic feeders, while deepwater sources of mercury may be important for those with a diet that derives, at least in part, from the pelagic environment. Further, despite the lack of freshwater sources of Hg in the NWHI, statistical models explaining the variation in tissue Hg in the MHI and NWHI were nearly identical, suggesting freshwater Hg inputs were not a major source of Hg in fish tissue.

Tracing the biosynthetic source of essential amino acids in marine turtles using delta13C fingerprints.

Plants, bacteria, and fungi produce essential amino acids (EAAs) with distinctive patterns of delta13C values that can be used as naturally occurring fingerprints of biosynthetic origin of EAAs in a food web. Because animals cannot synthesize EAAs and must obtain them from food, their tissues reflect delta13C(EAA) patterns found in diet, but it is not known how microbes responsible for hindgut fermentation in some herbivores influence the delta13C values of EAAs in their hosts' tissues. We examined whether distinctive delta13C fingerprints of hindgut flora are evident in the tissues of green turtles (Chelonia mydas), which are known to be facultative hindgut fermenters. We determined delta13C(EAA) values in tissues of green turtles foraging herbivorously in neritic habitats of Hawaii and compared them with those from green, olive ridley, and loggerhead turtles foraging carnivorously in oceanic environments of the central and southeast Pacific Ocean. Results of multivariate statistical analysis revealed two distinct groups that could be distinguished based on unique delta13C(EAA) patterns. A three-end-member predictive linear discriminant model indicated that delta13C(EAA) fingerprints existed in the tissues of carnivorous turtles that resembled patterns found in microalgae, which form the base of an oceanic food web, whereas herbivorous turtles derive EAAs from a bacterial or seagrass source. This study demonstrates the capacity for delta13C fingerprinting to establish the biosynthetic origin of EAAs in higher consumers, and that marine turtles foraging on macroalgal diets appear to receive nutritional supplementation from bacterial symbionts in their digestive system.