3D intrusions transport active surface microbial assemblages to the dark ocean

Subtropical oceans contribute significantly to global primary production, but the fate of the picophytoplankton that dominate in these low-nutrient regions is poorly understood. Working in the subtropical Mediterranean, we demonstrate that subduction of water at ocean fronts generates 3D intrusions with uncharacteristically high carbon, chlorophyll, and oxygen that extend below the sunlit photic zone into the dark ocean. These contain fresh picophytoplankton assemblages that resemble the photic-zone regions where the water originated. Intrusions propagate depth-dependent seasonal variations in microbial assemblages into the ocean interior. Strikingly, the intrusions included dominant biomass contributions from nonphotosynthetic bacteria and enrichment of enigmatic heterotrophic bacterial lineages. Thus, the intrusions not only deliver material that differs in composition and nutritional character from sinking detrital particles, but also drive shifts in bacterial community composition, organic matter processing, and interactions between surface and deep communities. Modeling efforts paired with global observations demonstrate that subduction can flux similar magnitudes of particulate organic carbon as sinking export, but is not accounted for in current export estimates and carbon cycle models. Intrusions formed by subduction are a particularly important mechanism for enhancing connectivity between surface and upper mesopelagic ecosystems in stratified subtropical ocean environments that are expanding due to the warming climate.

Deep-pelagic fishes: Demographic instability in a stable environment

Demographic histories are frequently a product of the environment, as populations expand or contract in response to major environmental changes, often driven by changes in climate. Meso- and bathy-pelagic fishes inhabit some of the most temporally and spatially stable habitats on the planet. The stability of the deep-pelagic could make deep-pelagic fishes resistant to the demographic instability commonly reported in fish species inhabiting other marine habitats, however the demographic histories of deep-pelagic fishes are unknown. We reconstructed the historical demography of 11 species of deep-pelagic fishes using mitochondrial and nuclear DNA sequence data. We uncovered widespread evidence of population expansions in our study species, a counterintuitive result based on the nature of deep-pelagic ecosystems. Frequency-based methods detected potential demographic changes in nine species of fishes, while extended Bayesian skyline plots identified population expansions in four species. These results suggest that despite the relatively stable nature of the deep-pelagic environment, the fishes that reside here have likely been impacted by past changes in climate. Further investigation is necessary to better understand how deep-pelagic fishes, by far Earth's most abundant vertebrates, will respond to future climatic changes.

Biological information on a rare pelagic fish, black ruff Centrolophus niger, caught in Icelandic waters: Distribution, feeding, and otoliths

Black ruff (Centrolophus niger) is a rare and poorly studied species found in both the Atlantic and Pacific Oceans and also in the Mediterranean Sea. It is sporadically caught south of Iceland during the annual International Ecosystem Summer Survey of the Nordic Seas. In total, 43 specimens were caught from 2009 to 2021, of which 41 specimens were caught during 2017-2021. All specimens, except one, were caught using a pelagic trawl (cod-end mesh-size: 50 mm) close to the surface (trawl depth: 0-35 m) with in situ temperature ranging from 9 to 13°C. The area south of Iceland is characterized by having warmer temperatures than other areas around the island, which might be indicative of a northern limit for the distribution of black ruff. The fish were primarily in the range of 29-46 cm with a few larger individuals up to 71 cm. Fourteen fish, caught in 2017 and 2021, were dissected to gather biological information on this species. These fish were all juveniles with no obvious sign of gonad development. Correlations between total length, fork length, and standard length are presented. Otoliths were thin and delicate with a length of ~13-16 mm, and otolith size (length, width, and area) was correlated with fish size. Much of the stomach content was at an advanced stage of digestion, but some contents could be identified and consisted of invertebrates, primarily of the orders Amphipoda and Calanoida with some unidentified fish also present.

A new genus and species of oceanic planktonic Tisbidae (Crustacea, Copepoda, Harpacticoida) with enlarged modified eyes

Both sexes of a new monotypic genus of Tisbidae (Copepoda, Harpacticoida) are described from the epi- or mesopelagic zone in the Kuroshio region, Japan. Gyoromeguttatumgen. et sp. nov. belongs to a monophyletic lineage of deepwater holoplanktonic genera defined by a suite of characters. Within this clade, Gyoromegen. nov. appears most closely related to Neotisbella Boxshall, 1979. The most distinguishable feature of G.guttatumgen. et sp. nov. is the presence of large, paired, frontal modified eyes, each consisting of a baculiform ocellus, a globular (Gicklhorn's?) organ, and a semi-parabolic plate. The taxonomic position of Tisbespinulosa Bradford & Wells, 1983 is discussed and a key to the six meso- and bathypelagic tisbid species is provided. Confusion surrounding earlier literature reports of supernumerary elements on the caudal ramus in some harpacticoid taxa is clarified. Secondary modifications of ocellar components of the typical naupliar eye in the Harpacticoida are reviewed. It is suggested that the development of specialized eyes in G.guttatumgen. et sp. nov. may provide a means for detecting bioluminescent food particles in oligotrophic pelagic environments. The large, vaulted prosome indicates the species is an opportunistic macrophage that has adopted gorging as a feeding strategy.

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 photic-aphotic divide is a strong ecological and evolutionary force determining the distribution of ciliates (Alveolata, Ciliophora) in the ocean

The bulk of knowledge on marine ciliates is from shallow and/or sunlit waters. We studied ciliate diversity and distribution across epi- and mesopelagic oceanic waters, using DNA metabarcoding and phylogeny-based metrics. We analyzed sequences of the 18S rRNA gene (V4 region) from 369 samples collected at 12 depths (0-1000 m) at the Bermuda Atlantic Time-series Study site of the Sargasso Sea (North Atlantic) monthly for 3 years. The comprehensive depth and temporal resolutions analyzed led to three main findings. First, there was a gradual but significant decrease in alpha-diversity (based on Faith's phylogenetic diversity index) from surface to 1000-m waters. Second, multivariate analyses of beta-diversity (based on UniFrac distances) indicate that ciliate assemblages change significantly from photic to aphotic waters, with a switch from Oligotrichea to Oligohymenophorea prevalence. Third, phylogenetic placement of sequence variants and clade-level correlations (EPA-ng and GAPPA algorithms) show Oligotrichea, Litostomatea, Prostomatea, and Phyllopharyngea as anti-correlated with depth, while Oligohymenophorea (especially Apostomatia) have a direct relationship with depth. Two enigmatic environmental clades include either prevalent variants widely distributed in aphotic layers (the Oligohymenophorea OLIGO5) or subclades differentially distributed in photic versus aphotic waters (the Discotrichidae NASSO1). These results settle contradictory relationships between ciliate alpha-diversity and depth reported before, suggest functional changes in ciliate assemblages from photic to aphotic waters (with the prevalence of algivory and mixotrophy vs. omnivory and parasitism, respectively), and indicate that contemporary taxon distributions in the vertical profile have been strongly influenced by evolutionary processes. Integration of DNA sequences with organismal data (microscopy, functional experiments) and development of databases that link these sources of information remain as major tasks to better understand ciliate diversity, ecological roles, and evolution in the ocean.

Microbial functional diversity across biogeochemical provinces in the central Pacific Ocean

Enzymes catalyze key reactions within Earth's life-sustaining biogeochemical cycles. Here, we use metaproteomics to examine the enzymatic capabilities of the microbial community (0.2 to 3 µm) along a 5,000-km-long, 1-km-deep transect in the central Pacific Ocean. Eighty-five percent of total protein abundance was of bacterial origin, with Archaea contributing 1.6%. Over 2,000 functional KEGG Ontology (KO) groups were identified, yet only 25 KO groups contributed over half of the protein abundance, simultaneously indicating abundant key functions and a long tail of diverse functions. Vertical attenuation of individual proteins displayed stratification of nutrient transport, carbon utilization, and environmental stress. The microbial community also varied along horizontal scales, shaped by environmental features specific to the oligotrophic North Pacific Subtropical Gyre, the oxygen-depleted Eastern Tropical North Pacific, and nutrient-rich equatorial upwelling. Some of the most abundant proteins were associated with nitrification and C1 metabolisms, with observed interactions between these pathways. The oxidoreductases nitrite oxidoreductase (NxrAB), nitrite reductase (NirK), ammonia monooxygenase (AmoABC), manganese oxidase (MnxG), formate dehydrogenase (FdoGH and FDH), and carbon monoxide dehydrogenase (CoxLM) displayed distributions indicative of biogeochemical status such as oxidative or nutritional stress, with the potential to be more sensitive than chemical sensors. Enzymes that mediate transformations of atmospheric gases like CO, CO₂, NO, methanethiol, and methylamines were most abundant in the upwelling region. We identified hot spots of biochemical transformation in the central Pacific Ocean, highlighted previously understudied metabolic pathways in the environment, and provided rich empirical data for biogeochemical models critical for forecasting ecosystem response to climate change.

Uncertainties of particulate organic carbon concentrations in the mesopelagic zone of the Atlantic ocean

Measurements of particulate organic carbon (POC) in the open ocean provide grounds for estimating oceanic carbon budgets and for modelling carbon cycling. The majority of the published POC measurements have been collected at the sea surface. Thus, POC stocks in the upper layer of the water column are relatively well constrained. However, our understanding of the POC distribution and its dynamics in deeper areas is still modest due to insufficient POC measurements. Moreover, the uncertainty of published POC estimates is not always quantified, and neither is it fully understood. In this study, we determined the POC concentrations of samples collected in the upper 500 m during an Atlantic Meridional Transect and described a method for quantifying its experimental uncertainties using duplicate measurements. The analysis revealed that the medians of the total experimental uncertainties associated with our POC concentrations in the productive and mesopelagic zones were 2(±2) mg/m 3 and 3(±1) mg/m 3, respectively. In relative terms, these uncertainties corresponded to ∼12% and ∼35% of POC concentrations, respectively. We modelled the POC uncertainty in order to identify its main causes. This model however could explain only ∼19% of the experimental POC uncertainty. Potential sources of the unexplained uncertainty are discussed.

The Functional and Ecological Significance of Deep Diving by Large Marine Predators

Many large marine predators make excursions from surface waters to the deep ocean below 200 m. Moreover, the ability to access meso- and bathypelagic habitats has evolved independently across marine mammals, reptiles, birds, teleost fishes, and elasmobranchs. Theoretical and empirical evidence suggests a number of plausible functional hypotheses for deep-diving behavior. Developing ways to test among these hypotheses will, however, require new ways to quantify animal behavior and biophysical oceanographic processes at coherent spatiotemporal scales. Current knowledge gaps include quantifying ecological links between surface waters and mesopelagic habitats and the value of ecosystem services provided by biomass in the ocean twilight zone. Growing pressure for ocean twilight zone fisheries creates an urgent need to understand the importance of the deep pelagic ocean to large marine predators.

Visual gene expression reveals a cone to rod developmental progression in deep-sea fishes

Vertebrates use cone cells in the retina for colour vision and rod cells to see in dim light. Many deep-sea fishes have adapted to their environment to have only rod cells in the retina, while both rod and cone genes are still preserved in their genomes. As deep-sea fish larvae start their lives in the shallow, and only later submerge to the depth, they have to cope with diverse environmental conditions during ontogeny. Using a comparative transcriptomic approach in 20 deep-sea fish species from eight teleost orders, we report on a developmental cone-to-rod switch. While adults mostly rely on rod opsin (RH1) for vision in dim light, larvae almost exclusively express middle-wavelength-sensitive ("green") cone opsins (RH2) in their retinas. The phototransduction cascade genes follow a similar ontogenetic pattern of cone- followed by rod-specific gene expression in most species, except for the pearleye and sabretooth (Aulopiformes), in which the cone cascade remains dominant throughout development. By inspecting the whole genomes of five deep-sea species (four of them sequenced within this study: Idiacanthus fasciola, Chauliodus sloani; Stomiiformes; Coccorella atlantica, and Scopelarchus michaelsarsi; Aulopiformes), we found that deep-sea fish possess one or two copies of the rod RH1 opsin gene, and up to seven copies of the cone RH2 opsin genes in their genomes, while other cone opsin classes have been mostly lost. Our findings hence provide molecular evidence for a limited opsin gene repertoire and a conserved vertebrate pattern whereby cone photoreceptors develop first and rod photoreceptors are added only at later developmental stages.

Processing Mixed Mesopelagic Biomass from the North-East Atlantic into Aquafeed Resources; Implication for Food Safety

Aquaculture produces most of the world's seafood and is a valuable food source for an increasing global population. Low trophic mesopelagic biomasses have the potential to sustainably supplement aquafeed demands for increased seafood production. The present study is a theoretical whole-chain feed and food safety assessment on ingredients from mesopelagic biomass and the resulting farmed fish fed these ingredients, based on analysis of processed mesopelagic biomass. Earlier theoretical estimations have indicated that several undesirable compounds (e.g., dioxins and metals and fluoride) would exceed the legal maximum levels for feed and food safety. Our measurements on processed mesopelagic biomasses show that only fluoride exceeds legal feed safety limits. Due to high levels of fluoride in crustaceans, their catch proportion will dictate the fluoride level in the whole biomass and can be highly variable. Processing factors are established that can be used to estimate the levels of undesirables in mesopelagic aquafeed ingredients from highly variable species biomass catches. Levels of most the studied undesirables (dioxins, PCBs, organochlorine pesticides, brominated flame retardant, metals, metalloids) were generally low compared to aquafeed ingredients based on pelagic fish. Using a feed-to-fillet aquaculture transfer model, the use of mesopelagic processed aquafeed ingredients was estimated to reduce the level of dioxins and PCBs by ~30% in farmed seafood such as Atlantic salmon.

Functional traits explain trophic allometries of cephalopods

Individual body size strongly influences the trophic role of marine organisms and the structure and function of marine ecosystems. Quantifying trophic position-individual body size relationships (trophic allometries) underpins the development of size-structured ecosystem models to predict abundance and the transfer of energy through ecosystems. Trophic allometries are well studied for fishes but remain relatively unexplored for cephalopods. Cephalopods are important components of coastal, oceanic and deep-sea ecosystems, and they play a key role in the transfer of biomass from low trophic positions to higher predators. It is therefore important to resolve cephalopod trophic allometries to accurately represent them within size-structured ecosystem models. We assessed the trophic positions of cephalopods in an oceanic pelagic (0-500 m) community (sampled by trawling in a cold-core eddy in the western Tasman Sea), comprising 22 species from 12 families, using bulk tissue stable isotope analysis and amino acid compound-specific stable isotope analysis. We assessed whether ontogenetic trophic position shifts were evident at the species-level and tested for the best predictor of community-level trophic allometry among body size, taxonomy and functional grouping (informed by fin and mantle morphology). Individuals in this cephalopod community spanned two trophic positions and fell into three functional groups on an activity level gradient: low, medium and high. The relationship between trophic position and ontogeny varied among species, with the most marked differences evident between species from different functional groups. Activity-level-based functional group and individual body size are best explained by cephalopod trophic positions (marginal R²  = 0.43). Our results suggest that the morphological traits used to infer activity level, such as fin-to-mantle length ratio, fin musculature and mantle musculature are strong predictors of cephalopod trophic allometries. Contrary to established theory, not all cephalopods are voracious predators. Low activity level cephalopods have a distinct feeding mode, with low trophic positions and little-to-no ontogenetic increases. Given the important role of cephalopods in marine ecosystems, distinct feeding modes could have important consequences for energy pathways and ecosystem structure and function. These findings will facilitate trait-based and other model estimates of cephalopod abundance in the changing global ocean.

Undesirables in Mesopelagic Species and Implications for Food and Feed Safety-Insights from Norwegian Fjords

The increase in the global population demands more biomass from the ocean as future food and feed, and the mesopelagic species might contribute significantly. In the present study, we evaluated the food and feed safety of six of the most abundant mesopelagic species in Norwegian fjords. Trace elements (i.e., arsenic, cadmium, mercury, and lead), organic pollutants (i.e., dioxins, furans, dioxin-like polychlorinated biphenyls, and polybrominated flame-retardants), and potentially problematic lipid compounds (i.e., wax esters and erucic acid) were analyzed and compared to existing food and feed maximum levels and intake recommendations. Furthermore, contaminant loads in processed mesopelagic biomass (protein, oil, and fish meal) was estimated using worst-case scenarios to identify possible food and feed safety issues. While most undesirables were low considering European food legislation, we identified a few potential food safety issues regarding high levels of fluoride in Northern krill, wax esters in glacier lanternfish, and long-chain monounsaturated fatty acids in silvery lightfish. Our estimates in processed biomass indicated high levels of undesirable trace elements in the protein fraction, frequently exceeding the maximum levels for feed ingredients. However, in fish meal, almost no exceedances were seen. In the oil fraction, dioxins and furans were above the maximum levels, given for food and feed ingredients. The present study is crucial to enable an evaluation of the value of these species; however, more data is needed before proceeding with large-scale harvesting of mesopelagic biomass.

Nutrient Composition of Demersal, Pelagic, and Mesopelagic Fish Species Sampled Off the Coast of Bangladesh and Their Potential Contribution to Food and Nutrition Security-The EAF-Nansen Programme

Fish is a major part of the Bangladeshi diet, but data on the nutrient composition of marine fish species are sparse. Mesopelagic fish may be a new potential resource of food and nutrients; however, nutrient composition data are lacking. The aim of this study was to provide nutrient composition data of fish species sampled off the coast of Bangladesh and determine their potential contribution to recommended nutrient intakes (RNI). Seven species from the pelagic, mesopelagic, and demersal zones were sampled from the coast of Bangladesh with Dr. Fridtjof Nansen in 2018. Three pooled samples containing 15-840 individuals from each species were analysed at the Institute of Marine Research, Norway. The demersal species contained substantially lower concentrations of nearly all nutrients, whereas the mesopelagic species generally were more nutrient dense. All species, except for the demersal species Bombay duck (9% dry matter), were found to contribute ≥100% to the RNI of vitamin B₁₂, eicosapentaenoic acid, docosahexaenoic acid, and selenium. All species, except for the demersal fish species, contributed ≥25% to the RNI of six or more nutrients. The data presented in this paper are an important contribution to the Bangladeshi food composition table and contribute to the understanding of fish as an important source of micronutrients.

Mesopelagic Species and Their Potential Contribution to Food and Feed Security-A Case Study from Norway

The projected increase in global population will demand a major increase in global food production. There is a need for more biomass from the ocean as future food and feed, preferentially from lower trophic levels. In this study, we estimated the mesopelagic biomass in three Norwegian fjords. We analyzed the nutrient composition in six of the most abundant mesopelagic species and evaluated their potential contribution to food and feed security. The six species make up a large part of the mesopelagic biomass in deep Norwegian fjords. Several of the analyzed mesopelagic species, especially the fish species Benthosema glaciale and Maurolicus muelleri, were nutrient dense, containing a high level of vitamin A1, calcium, selenium, iodine, eicopentaenoic acid (EPA), docosahexaenoic acid (DHA) and cetoleic acid. We were able to show that mesopelagic species, whose genus or family are found to be widespread and numerous around the globe, are nutrient dense sources of micronutrients and marine-based ingredients and may contribute significantly to global food and feed security.

Solving the plastic problem: From cradle to grave, to reincarnation

Plastic packaging accounts for 36% of all plastics made, but amounts to 47% of all plastic waste; 90% of all plastic items are used once and then discarded, which corresponds to around 50% of the total mass of plastics manufactured. Evidence for the ubiquity of microplastic pollution is accumulating rapidly, and wherever such material is sought, it seems to be found. Thus, microplastics have been identified in Arctic ice, the air, food and drinking water, soils, rivers, aquifers, remote maintain regions, glaciers, the oceans and ocean sediments, including waters and deep sea sediments around Antarctica, and within the deepest marine trenches of the Earth. They have also been detected in the bodies of animals, including humans, and as being passed along the hierarchy of food chains, up to marine top predators. Evidence has also been presented that microplastics are able to cross different life stages of mosquito that use different habitats - larva (feeding) to pupa (non-feeding) to adult terrestrial (flying) - and therefore can be spread from aquatic systems by flying insects. The so-called 'missing plastic problem' appears to be, in part, due to limitations in sampling methods, that is, many of the very small microplastic particles may simply escape capture in the trawl nets that are typically employed to collect them, but have been evidenced in grab-sampling experiments. Moreover, it is simply not possible to measure entirely through the vast, oceanic volumes of the oceans. It can, however, be concluded with some confidence that the majority of the plastic is not located at the sea surface, and indeed, several different sinks have been proposed for microplastics, including the sea floor and sediments, the ocean column itself, ice sheets, glaciers and soils. The treatment of land with sewage sludge is also thought to make a significant contribution of microplastics to soil. A substantial amount of airborne microparticulate pollution is created by the abrasion of tyres on road surfaces (and other 'non-exhaust' sources), meaning that even electric vehicles are not 'clean' in this regard, despite their elimination of tailpipe PM_2.5 and PM₁₀ emissions. The emergence of nanoplastics in the environment poses a new set of potential threats, although any impacts on human health are not yet known, save, as indicated from model studies. While improved design, manufacture, collection, reuse, repurposing and reprocessing/recycling of plastic items are necessary, overwhelmingly, a curbing in the use of plastic materials in the first place is demanded, particularly from single-use packaging. However, plastic pollution is just one element in the overall matrix of a changing climate ('the world's woes') and must be addressed as part of an integrated consideration of how we use all resources, fossil and otherwise, and the need to change our expectations, goals and lifestyles. In this effort, the role of deglobalisation/relocalisation may prove critical: thus, food and other necessities might be produced more on the local than the global scale, with smaller inputs of fossil fuels for transportation and other purposes, water and fertilisers, along with a marked reduction in the need for plastic packaging.

Solving the plastic problem: From cradle to grave, to reincarnation

Plastic packaging accounts for 36% of all plastics made, but amounts to 47% of all plastic waste; 90% of all plastic items are used once and then discarded, which corresponds to around 50% of the total mass of plastics manufactured. Evidence for the ubiquity of microplastic pollution is accumulating rapidly, and wherever such material is sought, it seems to be found. Thus, microplastics have been identified in Arctic ice, the air, food and drinking water, soils, rivers, aquifers, remote maintain regions, glaciers, the oceans and ocean sediments, including waters and deep sea sediments around Antarctica, and within the deepest marine trenches of the Earth. They have also been detected in the bodies of animals, including humans, and as being passed along the hierarchy of food chains, up to marine top predators. Evidence has also been presented that microplastics are able to cross different life stages of mosquito that use different habitats - larva (feeding) to pupa (non-feeding) to adult terrestrial (flying) - and therefore can be spread from aquatic systems by flying insects. The so-called 'missing plastic problem' appears to be, in part, due to limitations in sampling methods, that is, many of the very small microplastic particles may simply escape capture in the trawl nets that are typically employed to collect them, but have been evidenced in grab-sampling experiments. Moreover, it is simply not possible to measure entirely through the vast, oceanic volumes of the oceans. It can, however, be concluded with some confidence that the majority of the plastic is not located at the sea surface, and indeed, several different sinks have been proposed for microplastics, including the sea floor and sediments, the ocean column itself, ice sheets, glaciers and soils. The treatment of land with sewage sludge is also thought to make a significant contribution of microplastics to soil. A substantial amount of airborne microparticulate pollution is created by the abrasion of tyres on road surfaces (and other 'non-exhaust' sources), meaning that even electric vehicles are not 'clean' in this regard, despite their elimination of tailpipe PM2.5 and PM10 emissions. The emergence of nanoplastics in the environment poses a new set of potential threats, although any impacts on human health are not yet known, save, as indicated from model studies. While improved design, manufacture, collection, reuse, repurposing and reprocessing/recycling of plastic items are necessary, overwhelmingly, a curbing in the use of plastic materials in the first place is demanded, particularly from single-use packaging. However, plastic pollution is just one element in the overall matrix of a changing climate ('the world's woes') and must be addressed as part of an integrated consideration of how we use all resources, fossil and otherwise, and the need to change our expectations, goals and lifestyles. In this effort, the role of deglobalisation/relocalisation may prove critical: thus, food and other necessities might be produced more on the local than the global scale, with smaller inputs of fossil fuels for transportation and other purposes, water and fertilisers, along with a marked reduction in the need for plastic packaging.

Mesoscale eddies release pelagic sharks from thermal constraints to foraging in the ocean twilight zone

New dynamic approaches to managing marine fisheries promise more effective management in a changing climate. However, they require detailed knowledge of the links between oceanographic features and marine megafauna. Here, we demonstrate that satellite tracking of animal movements, combined with ocean remote sensing and numerical models, can provide this critical information for the most exploited pelagic shark in the Atlantic Ocean. We find that this predator dives deep in warm, swirling water masses called eddies that have traditionally been considered ocean “deserts.” Sharks use these warm features as a conduit to forage in the ocean twilight zone, a region of the deep ocean that contains the largest fish biomass on Earth, highlighting the importance of these deep ocean prey resources.

Mesoscale eddies are critical components of the ocean’s “internal weather” system. Mixing and stirring by eddies exerts significant control on biogeochemical fluxes in the open ocean, and eddies may trap distinctive plankton communities that remain coherent for months and can be transported hundreds to thousands of kilometers. Debate regarding how and why predators use fronts and eddies, for example as a migratory cue, enhanced forage opportunities, or preferred thermal habitat, has been ongoing since the 1950s. The influence of eddies on the behavior of large pelagic fishes, however, remains largely unexplored. Here, we reconstruct movements of a pelagic predator, the blue shark (Prionace glauca), in the Gulf Stream region using electronic tags, earth-observing satellites, and data-assimilating ocean forecasting models. Based on >2,000 tracking days and nearly 500,000 high-resolution time series measurements collected by 15 instrumented individuals, we show that blue sharks seek out the interiors of anticyclonic eddies where they dive deep while foraging. Our observations counter the existing paradigm that anticyclonic eddies are unproductive ocean “deserts” and suggest anomalously warm temperatures in these features connect surface-oriented predators to the most abundant fish community on the planet in the mesopelagic. These results also shed light on the ecosystem services provided by mesopelagic prey. Careful consideration will be needed before biomass extraction from the ocean twilight zone to avoid interrupting a key link between planktonic production and top predators. Moreover, robust associations between targeted fish species and oceanographic features increase the prospects for effective dynamic ocean management.

Complete mitochondrial DNA genomes for two northeast Pacific mesopelagic fishes, the Mexican lampfish (Triphoturus mexicanus) and black-belly dragonfish (Stomias atriventer)

Mesopelagic fishes are an important component of marine ecosystems, providing an important link between lower and higher trophic levels. This group of fishes is also highly abundant and make up a large portion of the marine vertebrate biomass. Here we report on the full mitochondrial sequences for two common mesopelagic fishes from the southern California bight: the Mexican lampfish Triphoturus mexicanus (Actinopterygii: Myctophidae) and the black-belly dragonfish Stomias atriventer (Actinopterygii: Stomiidae). Triphoturus mexicanus showed previously reported gene rearrangements for the Myctophidae. Phylogenetic analysis grouped S. atriventer with other Stomiiformes and T. mexicanus within the Myctophiformes.

Two eyes for two purposes: in situ evidence for asymmetric vision in the cockeyed squids Histioteuthis heteropsis and Stigmatoteuthis dofleini

The light environment of the mesopelagic realm of the ocean changes with both depth and viewer orientation, and this has probably driven the high diversity of visual adaptations found among its inhabitants. The mesopelagic 'cockeyed' squids of family Histioteuthidae have unusual eyes, as the left and right eyes are dimorphic in size, shape and sometimes lens pigmentation. This dimorphism may be an adaptation to the two different sources of light in the mesopelagic realm, with the large eye oriented upward to view objects silhouetted against the dim, downwelling sunlight and the small eye oriented slightly downward to view bioluminescent point sources. We used in situ video footage from remotely operated vehicles in the Monterey Submarine Canyon to observe the orientation behaviour of 152 Histioteuthis heteropsis and nine Stigmatoteuthis dofleini We found evidence for upward orientation in the large eye and slightly downward orientation in the small eye, which was facilitated by a tail-up oblique body orientation. We also found that 65% of adult H. heteropsis (n = 69) had yellow pigmentation in the lens of the larger left eye, which may be used to break the counterillumination camouflage of their prey. Finally, we used visual modelling to show that the visual returns provided by increasing eye size are much higher for an upward-oriented eye than for a downward-oriented eye, which may explain the development of this unique visual strategy.This article is part of the themed issue 'Vision in dim light'.

Vertical gradients in species richness and community composition across the twilight zone in the North Pacific Subtropical Gyre

Although metazoan animals in the mesopelagic zone play critical roles in deep pelagic food webs and in the attenuation of carbon in midwaters, the diversity of these assemblages is not fully known. A metabarcoding survey of mesozooplankton diversity across the epipelagic, mesopelagic and upper bathypelagic zones (0-1500 m) in the North Pacific Subtropical Gyre revealed far higher estimates of species richness than expected given prior morphology-based studies in the region (4,024 OTUs, 10-fold increase), despite conservative bioinformatic processing. Operational taxonomic unit (OTU) richness of the full assemblage peaked at lower epipelagic-upper mesopelagic depths (100-300 m), with slight shoaling of maximal richness at night due to diel vertical migration, in contrast to expectations of a deep mesopelagic diversity maximum as reported for several plankton groups in early systematic and zoogeographic studies. Four distinct depth-stratified species assemblages were identified, with faunal transitions occurring at 100 m, 300 m and 500 m. Highest diversity occurred in the smallest zooplankton size fractions (0.2-0.5 mm), which had significantly lower % OTUs classified due to poor representation in reference databases, suggesting a deep reservoir of poorly understood diversity in the smallest metazoan animals. A diverse meroplankton assemblage also was detected (350 OTUs), including larvae of both shallow and deep living benthic species. Our results provide some of the first insights into the hidden diversity present in zooplankton assemblages in midwaters, and a molecular reappraisal of vertical gradients in species richness, depth distributions and community composition for the full zooplankton assemblage across the epipelagic, mesopelagic and upper bathypelagic zones.

Chasing after Non-cyanobacterial Nitrogen Fixation in Marine Pelagic Environments

Traditionally, cyanobacterial activity in oceanic photic layers was considered responsible for the marine pelagic dinitrogen (N₂) fixation. Other potentially N₂-fixing bacteria and archaea have also been detected in the pelagic water column, however, the activity and importance of these non-cyanobacterial diazotrophs (NCDs) remain poorly constrained. In this perspective we summarize the N₂ fixation rates from recently published studies on photic and aphotic layers that have been attributed to NCD activity via parallel molecular measurements, and discuss the status, challenges, and data gaps in estimating non-cyanobacterial N₂ fixation NCNF in the ocean. Rates attributed to NCNF have generally been near the detection limit thus far (<1 nmol N L⁻¹ d⁻¹). Yet, if considering the large volume of the dark ocean, even low rates of NCNF could make a significant contribution to the new nitrogen input to the ocean. The synthesis here shows that nifH transcription data for NCDs have been reported in only a few studies where N₂ fixation rates were detected in the absence of diazotrophic cyanobacteria. In addition, high apparent diversity and regional variability in the NCDs complicate investigations of these communities. Future studies should focus on further investigating impacts of environmental drivers including oxygen, dissolved organic matter, and dissolved inorganic nitrogen on NCNF. Describing the ecology of NCDs and accurately measuring NCNF rates, are critical for a future evaluation of the contribution of NCNF to the marine nitrogen budget.

SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter

Deep-ocean regions beyond the reach of sunlight contain an estimated 615 Pg of dissolved organic matter (DOM), much of which persists for thousands of years. It is thought that bacteria oxidize DOM until it is too dilute or refractory to support microbial activity. We analyzed five single-amplified genomes (SAGs) from the abundant SAR202 clade of dark-ocean bacterioplankton and found they encode multiple families of paralogous enzymes involved in carbon catabolism, including several families of oxidative enzymes that we hypothesize participate in the degradation of cyclic alkanes. The five partial genomes encoded 152 flavin mononucleotide/F420-dependent monooxygenases (FMNOs), many of which are predicted to be type II Baeyer-Villiger monooxygenases (BVMOs) that catalyze oxygen insertion into semilabile alicyclic alkanes. The large number of oxidative enzymes, as well as other families of enzymes that appear to play complementary roles in catabolic pathways, suggests that SAR202 might catalyze final steps in the biological oxidation of relatively recalcitrant organic compounds to refractory compounds that persist.IMPORTANCE Carbon in the ocean is massively sequestered in a complex mixture of biologically refractory molecules that accumulate as the chemical end member of biological oxidation and diagenetic change. However, few details are known about the biochemical machinery of carbon sequestration in the deep ocean. Reconstruction of the metabolism of a deep-ocean microbial clade, SAR202, led to postulation of new biochemical pathways that may be the penultimate stages of DOM oxidation to refractory forms that persist. These pathways are tied to a proliferation of oxidative enzymes. This research illuminates dark-ocean biochemistry that is broadly consequential for reconstructing the global carbon cycle.

Manta birostris, predator of the deep? Insight into the diet of the giant manta ray through stable isotope analysis

The characterization of diet for the giant manta ray Manta birostris has been problematic given their large-scale movement patterns and the difficulty in obtaining stomach contents from this species. The large majority of existing information is based on observational data limited to feeding events at the sea surface during daylight. Recently discovered aggregation sites for the giant manta ray off mainland Ecuador are some of the most accessible to date and provide a unique opportunity for researchers to gather much needed information on this elusive species. To assess how important surface zooplankton is to giant manta ray diet, we conducted stable isotope analysis (¹⁵N and ¹³C) on M. birostris muscle and surface zooplankton. Trophic position estimates placed M. birostris overall at a secondary consumer level of approximately 3.4 but there was large variation in δ¹⁵N and δ¹³C values among individuals. Manta birostris muscle tissue δ¹³C values were also not consistent with this species feeding predominantly on surface zooplankton and suggest that the majority of dietary intake is of mesopelagic origin. Given the conservative life history and fisheries pressure on large planktivores, knowledge of their trophic role and foraging strategies is essential to better understand their ecology and develop effective conservation measures.

Prokaryotic Responses to Ammonium and Organic Carbon Reveal Alternative CO2 Fixation Pathways and Importance of Alkaline Phosphatase in the Mesopelagic North Atlantic

To decipher the response of mesopelagic prokaryotic communities to input of nutrients, we tracked changes in prokaryotic abundance, extracellular enzymatic activities, heterotrophic production, dark dissolved inorganic carbon (DIC) fixation, community composition (16S rRNA sequencing) and community gene expression (metatranscriptomics) in 3 microcosm experiments with water from the mesopelagic North Atlantic. Responses in 3 different treatments amended with thiosulfate, ammonium or organic matter (i.e., pyruvate plus acetate) were compared to unamended controls. The strongest stimulation was found in the organic matter enrichments, where all measured rates increased >10-fold. Strikingly, in the organic matter treatment, the dark DIC fixation rates-assumed to be related to autotrophic metabolisms-were equally stimulated as all the other heterotrophic-related parameters. This increase in DIC fixation rates was paralleled by an up-regulation of genes involved in DIC assimilation via anaplerotic pathways. Alkaline phosphatase was the metabolic rate most strongly stimulated and its activity seemed to be related to cross-activation by nonpartner histidine kinases, and/or the activation of genes involved in the regulation of elemental balance during catabolic processes. These findings suggest that episodic events such as strong sedimentation of organic matter into the mesopelagic might trigger rapid increases of originally rare members of the prokaryotic community, enhancing heterotrophic and autotrophic carbon uptake rates, ultimately affecting carbon cycling. Our experiments highlight a number of fairly unstudied microbial processes of potential importance in mesopelagic waters that require future attention.

Trophic interactions of fish communities at midwater depths enhance long-term carbon storage and benthic production on continental slopes

Biological transfer of nutrients and materials between linked ecosystems influences global carbon budgets and ecosystem structure and function. Identifying the organisms or functional groups that are responsible for nutrient transfer, and quantifying their influence on ecosystem structure and carbon capture is an essential step for informed management of ecosystems in physically distant, but ecologically linked areas. Here, we combine natural abundance stable isotope tracers and survey data to show that mid-water and bentho-pelagic-feeding demersal fishes play an important role in the ocean carbon cycle, bypassing the detrital particle flux and transferring carbon to deep long-term storage. Global peaks in biomass and diversity of fishes at mid-slope depths are explained by competitive release of the demersal fish predators of mid-water organisms, which in turn support benthic fish production. Over 50% of the biomass of the demersal fish community at depths between 500 and 1800 m is supported by biological rather than detrital nutrient flux processes, and we estimate that bentho-pelagic fishes from the UK-Irish continental slope capture and store a volume of carbon equivalent to over 1 million tonnes of CO2 every year.

Attenuation of sinking particulate organic carbon flux through the mesopelagic ocean

The biological carbon pump, which transports particulate organic carbon (POC) from the surface to the deep ocean, plays an important role in regulating atmospheric carbon dioxide (CO2) concentrations. We know very little about geographical variability in the remineralization depth of this sinking material and less about what controls such variability. Here we present previously unpublished profiles of mesopelagic POC flux derived from neutrally buoyant sediment traps deployed in the North Atlantic, from which we calculate the remineralization length scale for each site. Combining these results with corresponding data from the North Pacific, we show that the observed variability in attenuation of vertical POC flux can largely be explained by temperature, with shallower remineralization occurring in warmer waters. This is seemingly inconsistent with conclusions drawn from earlier analyses of deep-sea sediment trap and export flux data, which suggest lowest transfer efficiency at high latitudes. However, the two patterns can be reconciled by considering relatively intense remineralization of a labile fraction of material in warm waters, followed by efficient downward transfer of the remaining refractory fraction, while in cold environments, a larger labile fraction undergoes slower remineralization that continues over a longer length scale. Based on the observed relationship, future increases in ocean temperature will likely lead to shallower remineralization of POC and hence reduced storage of CO2 by the ocean.

Microbial gardening in the ocean's twilight zone: detritivorous metazoans benefit from fragmenting, rather than ingesting, sinking detritus: fragmentation of refractory detritus by zooplankton beneath the euphotic zone stimulates the harvestable production of labile and nutritious microbial biomass

Sinking organic particles transfer ∼10 gigatonnes of carbon into the deep ocean each year, keeping the atmospheric CO₂ concentration significantly lower than would otherwise be the case. The exact size of this effect is strongly influenced by biological activity in the ocean's twilight zone (∼50–1,000 m beneath the surface). Recent work suggests that the resident zooplankton fragment, rather than ingest, the majority of encountered organic particles, thereby stimulating bacterial proliferation and the deep-ocean microbial food web. Here we speculate that this apparently counterintuitive behaviour is an example of ‘microbial gardening’, a strategy that exploits the enzymatic and biosynthetic capabilities of microorganisms to facilitate the ‘gardener's’ access to a suite of otherwise unavailable compounds that are essential for metazoan life. We demonstrate the potential gains that zooplankton stand to make from microbial gardening using a simple steady state model, and we suggest avenues for future research.

Vertical ecology of the pelagic ocean: classical patterns and new perspectives

Applications of acoustic and optical sensing and intensive, discrete-depth sampling, in concert with collaborative international research programmes, have substantially advanced knowledge of pelagic ecosystems in the 17 years since the 1996 Deepwater Fishes Symposium of the Fisheries Society of the British Isles. Although the epipelagic habitat is the best-known, and remote sensing and high-resolution modelling allow near-synoptic investigation of upper layer biophysical dynamics, ecological studies within the mesopelagic and deep-demersal habitats have begun to link lower and upper trophic level processes. Bathypelagic taxonomic inventories are far from complete, but recent projects (e.g. MAR-ECO and CMarZ, supported by the Census of Marine Life programme) have quantitatively strengthened distribution patterns previously described for fishes and have provided new perspectives. Synthesis of net and acoustic studies suggests that the biomass of deep-pelagic fishes may be two to three orders of magnitude greater than the total global commercial fisheries landings. Discrete-depth net sampling has revealed relatively high pelagic fish biomass below 1000 m in some regions, and that gelatinous zooplankton may be key energy vectors for deep-pelagic fish production. Lastly, perhaps, the most substantive paradigm shift is that vertical connectivity among fishes across classical depth zones is prevalent- suggesting that a whole-water column approach is warranted for deep ocean conservation and management.

First in situ observations of the deep-sea squid Grimalditeuthis bonplandi reveal unique use of tentacles

The deep-sea squid Grimalditeuthis bonplandi has tentacles unique among known squids. The elastic stalk is extremely thin and fragile, whereas the clubs bear no suckers, hooks or photophores. It is unknown whether and how these tentacles are used in prey capture and handling. We present, to our knowledge, the first in situ observations of this species obtained by remotely operated vehicles (ROVs) in the Atlantic and North Pacific. Unexpectedly, G. bonplandi is unable to rapidly extend and retract the tentacle stalk as do other squids, but instead manoeuvres the tentacles by undulation and flapping of the clubs' trabecular protective membranes. These tentacle club movements superficially resemble the movements of small marine organisms and suggest the possibility that G. bonplandi uses aggressive mimicry by the tentacle clubs to lure prey, which we find to consist of crustaceans and cephalopods. In the darkness of the meso- and bathypelagic zones the flapping and undulatory movements of the tentacle may: (i) stimulate bioluminescence in the surrounding water, (ii) create low-frequency vibrations and/or (iii) produce a hydrodynamic wake. Potential prey of G. bonplandi may be attracted to one or more of these as signals. This singular use of the tentacle adds to the diverse foraging and feeding strategies known in deep-sea cephalopods.

Five in situ observations of live oarfish Regalecus glesne (Regalecidae) by remotely operated vehicles in the oceanic waters of the northern Gulf of Mexico

As part of the SERPENT Project, five observations of apparently healthy oarfish Regalecus glesne by remotely operated vehicles are reported from the northern Gulf of Mexico. Regalecus glesne were observed between 2008 and 2011 at depths from within the epipelagic and mesopelagic zones. These observations include the deepest verified record of R. glesne (463-492 m) and the first record of an arthropod ectoparasite (isopod).

Influences of El Niño on assemblages of mesopelagic fish larvae along the Pacific coast of Baja California Sur

Seasonal assemblages of mesopelagic fish larvae and changes related with environmental factors (plankton biomass, sea surface temperature anomaly, upwelling, and the multivariate El Niño index) were investigated. From 1982 to 1987, 16 oceanographic cruises were carried out along the Pacific coast of Baja California Sur, Mexico. Larvae of 42 mesopelagic fish taxa were collected. Larval abundance was highly variable during the studied period, but summer months coincided with higher abundance (>200 larvae under 10 m²). Larval assemblages were dominated by three of the most common species of tropical (Vinciguerria lucetia, Diogenichthys laternatus) and subtropical affinity (Triphoturus mexicanus). A group of species of tropical affinity (Diplophos proximus, Diaphus pacificus, Benthosema panamense) was useful for distinguishing the 1982-84 El Niño event, and an assemblage of larvae of temperate affinity (Symbolophorus californiensis, Melamphaes lugubris, Bathylagus ochotensis, Leuroglossus stilbius, Protomyctophum crockeri) characterized 'normal' years (mid-1984 to mid-1987).