Diel vertical migration (DVM) is the largest mass-movement of animals on Earth, with profound ecological and biogeochemical consequences. DVM has mostly been studied in the open ocean; however, at steep slopes, pelagic animals including vertical migrators must contend with the seafloor, emphasizing the importance of understanding DVM in these prevalent, critical habitats. Here we used active acoustics in combination with video to conduct a detailed study of the interactions of vertical migrators with the steep wall of a submarine canyon during their sunrise descent. We found regular and frequent, high-density sunrise aggregations of animals consistent with seafloor blocking of descending vertical migrators across all seasons. While topographic blocking was thought to be primarily caused by nighttime advection of migrators over shallows by prevailing currents, here the occurrence of this phenomenon was observed to be largely independent of oceanographic drivers including advection as measured by an ADCP, providing evidence that behavior plays an important role. Advection, season, upwelling, and other environmental factors were found to impact specific characteristics of sunrise aggregations but not likelihood of occurrence. Given its intensity and prevalence, topographic blocking likely creates high-quality, predictable foraging opportunities for a large diversity of predators and influences the abundance and habitat use of predators in the area. The steep slopes of this canyon, as with any abrupt bathymetry, juxtapose the deep and the shallow, the benthic and the pelagic, and the offshore and nearshore. Thus, topographic blocking may be prevalent in other steep canyons and at steep bathymetry more generally.

Appendicularia comprises 70 marine, invertebrate, chordate species. Appendicularians play important ecological and evolutionary roles, yet their morphological disparity remains understudied. Most appendicularians are small, develop rapidly, and with a stereotyped cell lineage, leading to the hypothesis that Appendicularia derived progenetically from an ascidian-like ancestor. Here, we describe the detailed anatomy of the central nervous system of Bathochordaeus stygius, a giant appendicularian from the mesopelagic. We show that the brain consists of a forebrain with on average smaller and more uniform cells and a hindbrain, in which cell shapes and sizes vary to a greater extent. Cell count for the brain was 102. We demonstrate the presence of three paired brain nerves. Brain nerve 1 traces into the epidermis of the upper lip region and consists of several fibers with some supportive bulb cells in its course. Brain nerve 2 innervates oral sensory organs and brain nerve 3 innervates the ciliary ring of the gill slits and lateral epidermis. Brain nerve 3 is asymmetric, with the right nerve consisting of two neurites originating posterior to the left one that contains three neurites. Similarities and differences to the anatomy of the brain of the model species Oikopleura dioica are discussed. We interpret the small number of cells in the brain of B. stygius as an evolutionary trace of miniaturization and conclude that giant appendicularians evolved from a small, progenetic ancestor that secondarily increased in size within Appendicularia.

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.

Gill parasites of coleoid cephalopods are frequently observed during remotely operated vehicle (ROV) dives in the Monterey Submarine Canyon. However, little knowledge exists on the identity of the parasite species or their effects on the cephalopod community. With the help of ROV-collected specimens and in situ footage from the past 27 years, we report on their identity, prevalence and potential infection strategy. Gill parasites were genetically and morphologically identified from collected specimens of Chiroteuthis calyx , Vampyroteuthis infernalis and Gonatus spp . In situ prevalence was estimated from video footage for C. calyx , Galiteuthis spp., Taonius spp. and Japetella diaphana , enabled by their transparent mantle tissue. The most common parasite was identified as Hochbergia cf. moroteuthensis , a protist of unresolved taxonomic ranking. We provide the first molecular data for this parasite and show a sister group relationship to the dinoflagellate genus Oodinium . Hochbergia cf. moroteuthensis was most commonly observed in adult individuals of all species and was sighted year round over the analyzed time period. In situ prevalence was highest in C. calyx (75%), followed by Galiteuthis spp. (29%), Taonius spp. (27%) and J. diaphana (7%). A second parasite, not seen on the in situ footage, but occurring within the gills of Gonatus berryi and Vampyroteuthis infernalis , could not be found in the literature or be identified through DNA barcoding. The need for further investigation is highlighted, making this study a starting point for unravelling ecological implications of the cephalopod-gill-parasite system in deep pelagic waters.

Many animals build complex structures to aid in their survival, but very few are built exclusively from materials that animals create 1 , 2 . In the midwaters of the ocean, mucoid structures are readily secreted by numerous animals, and serve many vital functions 3 , 4 . However, little is known about these mucoid structures owing to the challenges of observing them in the deep sea. Among these mucoid forms, the ‘houses’ of larvaceans are marvels of nature 5 , and in the ocean twilight zone giant larvaceans secrete and build mucus filtering structures that can reach diameters of more than 1 m 6 . Here we describe in situ laser-imaging technology 7 that reconstructs three-dimensional models of mucus forms. The models provide high-resolution views of giant larvacean houses and elucidate the role that house structure has in food capture and predator avoidance. Now that tools exist to study mucus structures found throughout the ocean, we can shed light on some of nature’s most complex forms.

Diel vertical migrations (DVM) by zooplankton and nekton are driven by the selective advantage of avoiding visually cued predators near the surface during the hours of daylight. And just as there is a second set of predators that occupy the migrators’ dark daytime depths, there is also a diverse suite of predators that comprise a gauntlet of threats during the migrations. Here we examine these migrations from the perspective of the migrators, to enumerate the kinds of predatory threats they face and to assess the threat potential of various predator types. The study is based on thousands of hours of in situ observations and measurements of the mesopelagic community in Monterey Bay, California, conducted chiefly by remotely operated vehicles (ROVs). We provide accounts of some predator/prey interactions, and we introduce a means to calculate the threat potential of specific predators, based on MBARI’s long-term time-series of quantitative video surveys.

Several species of small, red, deep-sea Trachymedusae have been described and then re-described over the past 20 years, leading to some confusion in the scientific literature. This paper provides an overview of three genera (Benthocodon, Crossota, and Pectis) in the family Rhopalonematidae (Cnidaria: Hydrozoa) that have been observed and examined both in the field and in the laboratory. Twenty years of in situ observations in Monterey Bay indicate that two of the genera, Benthocodon and Pectis, are often associated with the benthic boundary layer and can occur in dense patches. They have been observed resting on soft sediments with their subumbrellar surface down but are also found swimming up to several 100 m above the bottom. Individuals in the genus Crossota tend to be solitary and more pelagic in nature. Although Crossota may be found near the bottom as well, down to depths of 4,000 m, they have not been observed resting on the bottom. The three genera are morphologically similar and difficult to distinguish from each other. As a group, they are small (< 5 cm) and sometimes darkly pigmented, making in situ identifications challenging. We show that these three genera can be differentiated morphologically and we provide a key to the genera and species common in Monterey Bay. Further, the genera differ in their depth distribution and behavior. Molecular genetics suggest that the genera and species are distinct from each other but that their taxonomy needs revision. This paper reviews the generic characteristics along with species identifications and provides images and video (Supplementary Material) that may be helpful in identification.

Coevolution is a process through which two interactive systems mutually influence each other's development. Midwater research and remotely operated vehicle technology are two such interactive systems, and at the Monterey Bay Aquarium Research Institute they have been coevolving for 30 years. As the technology has matured, the scope, scale, and complexity of the research has also advanced, particularly in such areas as observing animal behavior and in situ experimentation, which were virtually impossible before we gained direct access to the environment. Here we examine midwater research domains and the technologies that enable them: how new instrumentation enables in situ respiration and fluid dynamics measurements; how imaging and data handling systems build data sets that allow long-term analyses of seasonal, episodic, and anthropogenic environmental changes; and how variable ballast and thruster controls have allowed us to make close-up observations and conduct delicate experimental manipulations without disturbing the animals we are studying. The coevolution continues and future developments will focus on integrating diverse sensor systems to provide new perspectives for midwater ecology, and on automating research processes to expand the scale of operations, improve efficiency, and promote technology transfer.

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.

To accurately assess the impacts of climate change on our planet, modeling of oceanic systems and understanding how atmospheric carbon is transported from surface waters to the deep benthos are required. The biological pump drives the transport of carbon through the ocean's depths, and the rates at which carbon is removed and sequestered are often dependent on the grazing abilities of surface and midwater organisms. Some of the most effective and abundant midwater grazers are filter-feeding invertebrates. Although the impact of smaller, near-surface filter feeders is generally known, efforts to quantify the impact of deeper filter feeders, such as giant larvaceans, have been unsuccessful. Giant larvaceans occupy the upper 400 m of the water column, where they build complex mucus filtering structures that reach diameters greater than 1 m. Because of the fragility of these structures, direct measurements of filtration rates require in situ methods. Hence, we developed DeepPIV, an instrument deployed from a remotely operated vehicle that enables the direct measurement of in situ filtration rates. The rates measured for giant larvaceans exceed those of any other zooplankton filter feeder. Given these filtration rates and abundance data from a 22-year time series, the grazing impact of giant larvaceans far exceeds previous estimates, with the potential for processing their 200-m principal depth range in Monterey Bay in as little as 13 days. Technologies such as DeepPIV will enable more accurate assessments of the long-term removal of atmospheric carbon by deep-water biota.

Larvaceans in the genus Bathochordaeus are large, often abundant filter feeders found throughout much of the world ocean. The first described species, Bathochordaeus charon, was reported over 100 years ago by Chun. However in the time since, few specimens have matched Chun’s original description, resulting in ambiguity on the validity of B. charon as a species.

Bathochordaeus mcnutti sp. nov. is described from the mesopelagic northeast Pacific Ocean (Monterey Bay, California, USA). Larvaceans in the genus Bathochordaeus are large, often abundant zooplankters found throughout much of the world ocean, but until recently it was unclear whether more than a single species of Bathochordaeus existed. Using remotely operated vehicles, we have made hundreds of in situ observations, compiled two decades of time-series data, and carefully collected enough specimens to determine that three species of Bathochordaeus occur in Monterey Bay: B. charon (Chun), B. stygius (Garstang), and B. mcnutti sp. nov. Bathochordaeus mcnutti is readily distinguished from its two congeners by the distinct blue outline visible around the periphery of its tail, and by other aspects of its morphology, ecology, and genetics. The abundance of larvaceans means they are ecologically important as particle processors. Species within the genus, Bathochordaeus, comprise the largest of described larvaceans.

A small ROV was used to collect plankton, make video surveys and take hydrographic measurements in close proximity to six free-drifting, Antarctic icebergs. The icebergs studied ranged in size from <0.5 to >32km in length. Large icebergs have a greater scale of influence than do smaller ones and iceberg-mediated differences in the hydrographic characteristics of their surrounding water depend on the scale sampled. Irrespective of size, temperature generally decreased in close proximity to an iceberg while salinity increased. Chlorophyll a was often lower in the surface waters near the iceberg, relative to the surface waters further away. Tabular icebergs typically had 3 distinct underwater features: shelf, side and bottom. Ablation pockets were a common feature of subsurface ice. The ice itself is a dynamic and seemingly harsh environment with relatively few macrofauna living on it. Those that do inhabit the ice face are either highly specialized or highly mobile. Species composition of zooplankton within 40m of an iceberg did not change relative to distance. However, biomass was generally greater within 5m of an iceberg than it was 15 to 40m distant.

Recent warming in the Antarctic has led to increased production of icebergs; however, the ecological effects of icebergs on pelagic communities within the Southern Ocean have not been well-studied. We used a 10m2 MOCNESS to collect macrozooplankton and micronekton in the upper 300m of the water column near free-drifting icebergs in the Atlantic sector of the Southern Ocean during three seasons: December 2005 (late spring), June 2008 (late fall) and March-April 2009 (late summer). Communities were dominated in all three seasons by Antarctic krill (Euphausia superba) and salps (Salpa thompsoni), which collectively comprised 60-95% of the community wet biomass in most cases. During our spring and summer cruises, mean biomass was elevated by 3.1-4.3x at a distance of 0.37km from large icebergs vs. 9.26km away. These differences were not statistically significant, and no trend in biomass with distance was apparent in samples from fall 2008, when total biomass was an order of magnitude lower. Biomass levels near icebergs during Dec 2005 and Mar-Apr 2009 were comparable to values reported from marginal ice zones, suggesting that waters around icebergs support macrozooplankton and micronekton communities comparable in magnitude to those in some of the most productive areas of the Southern Ocean. Sample variance also was significantly higher within 1.85km of icebergs during Dec 2005 and Mar-Apr 2009, reflecting increased patchiness on scales sampled by the MOCNESS (20–40×103m3 filtered per sample). This pattern was not significant during Jun 2008. Large predatory medusae were observed within 1.85km of icebergs and in Iceberg Alley, an area through which icebergs pass frequently, but were virtually absent in areas remote from icebergs. Small euphausiids showed an inverse distribution, with low densities in areas populated by large medusae. A shift in community composition from a near-iceberg assemblage dominated by herbivores to a carnivore-dominated community in Iceberg Alley may reflect a transition from bottom-up to top-down control with increasing distance and time. Body sizes of dominant species varied seasonally but did not show consistent trends with distance from icebergs. Concentrations of photosynthetic pigments in the guts of E. superba and S. thompsoni corresponded broadly to patterns in surface chlorophyll a concentrations and were comparable to maximum gut pigment concentrations measured in animals collected from highly productive marginal ice zones. Our results suggest that the macrozooplankton and micronekton assemblages near free-drifting icebergs can be quantitatively and qualitatively different from those in surrounding, iceberg-free waters, perhaps due to both bottom-up and top-down processes as well as physical forcing by the passage of a large object through the upper ocean.

We used a quiet, deep-diving remotely operated vehicle (ROV) to conduct oblique, quantitative video transects of the bathypelagic fauna at depths between 1000 and 3500m at a site over the Monterey Submarine Canyon, in the eastern North Pacific off central California. Fifteen such dives were made over a two-year period. Analyses of the video data revealed a rich and diverse fauna dominated by gelatinous animals. In particular, the holopelagic polychaete Poeobius meseres was an important detritivore in the upper half of this depth range. As Poeobius abundance eventually declined with increasing depth, larvacean abundance increased. In contrast, the relative numbers of crustacean grazers, principally copepods and mysids, remained relatively constant with depth. Medusae were most abundant and most diverse among the gelatinous predators, which also included ctenophores, and siphonophores. Chaetognaths occurred chiefly in the upper half of the depth range. While there is considerable overlap, the bathypelagic fauna can be separated into upper (1000 to 2300m) and lower (2400 to 3300m) zones, as well as a distinct and populous benthic boundary layer. Within the overall bathypelagic community is a complex web of trophic links involving gelatinous predators that feed on both gelatinous and hard-bodied particle feeders, as well as on each other. The amount of organic carbon contained in this jelly web is substantial but its ecological fate is uncertain. The assessment of bathypelagic communities will be important for establishing baselines to conserve deep pelagic biodiversity within high-seas protected areas.

Ephyrae of Aurelia labiata given dissolved organic matter (DOM) in seawater had higher carbon content than starved ephyrae. DOM-fed ephyrae of Chrysaora colorata did not have significantly higher carbon content than starved ephyrae, although the mean trend was higher. DOM-fed ephyrae of A. labiata developed aberrant morphologies similar to starved ephyrae, and neither starved nor DOM-fed ephyrae of either species developed into medusae. In addition to higher carbon content, there was evidence for DOM utilization by A. labiata shown through uptake of and increased ammonium production after exposure to a fluorescently labeled lysine polymer.

An unresolved issue in ocean science is the discrepancy between the food requirements of the animals living on the deep sea floor and their food supply, as measured by sediment traps. A 10-year time-series study of the water column off Monterey Bay, California, revealed that the discarded mucus feeding structures of giant larvaceans carry a substantial portion of the upper ocean's productivity to the deep seabed. These abundant, rapidly sinking, carbon-rich vectors are not detected by conventional,sampling methods and thus have not been included in calculations of vertical nutrient flux or in oceanic carbon budgets.

We demonstrate an attentional selection and tracking system for processing video streams from remotely operated underwater vehicles (ROVs). The system identifies and tracks potentially interesting visual events spanning multiple frames based on low-level properties of salient objects, which are associated with those events. If video frames contain interesting frames, they are labeled “interesting”, otherwise they are labeled “boring”. By marking the interesting events and omitting boring frames in the output stream, we augment the productivity of human video annotators, or, alternatively, provide input for a subsequent object classification algorithm.