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During polar nights of 2012 and 2017, bioluminescence (BL) potential surveys demonstrated high emissions at depths around and below 100 m at offshore stations to the north of a Svalbard fjord (Rijpfjorden). We demonstrated that the highest bioluminescent emissions for offshore stations are located at depths below depths of modelled/ambient light intensities corresponding to the reported irradiance thresholds for the behavioral light sensitivity of krill and copepods, and suggest that behavioral light sensitivity is one of the reasons for high values of BL potential observed below 100 m at offshore stations. In order to understand sources of bioluminescent taxa responsible for the observed high values of BL potential in offshore waters, we have investigated the origin and pathways of water masses circulating to the north, offshore of the fjord Rijpfjorden by using a hydrodynamic model. For both 2012 and 2017, the model water masses mostly originate from the west, where the Atlantic water is flowing northward, then along the shelf and shelf slope of northern Svalbard, and to the offshore of the fjord. This indicates that the advection of zooplankton by North Atlantic Water is one possible source of bioluminescent organisms offshore of northern Svalbard. In 2012, water masses also originated from the inflow through Hinlopen trench and strait, while, in 2017, the offshore water was advected and upwelled into the fjord on time scales less than 10 days, and after that there was a recirculation back from the fjord to offshore on time scales larger than 10 days. This recirculation from the fjord might be another source of bioluminescent organisms in the offshore waters.

During polar nights in January 2012 and 2017, significantly higher bioluminescence (BL) potential emissions in the upper 50 m were observed in the fjord Rijpfjorden (Svalbard, Norway) in comparison to offshore stations (located on the shelf-break, shelf-slope areas and in the deeper water). The objective of this paper is to better understand why, during two polar nights (separated by 5 years), the values of BL potential in the northern Svalbard fjord are higher than at offshore stations, and what the role of advection is in observed elevated BL potential values in the top 50 m of the fjord. To address the above objective, we applied the same BL potential modeling approach and strategies during polar nights for both 2012 and 2017. For both years, advection of BL potential from offshore (including upwelling along the shelf, shelf-slope) produced an increase of BL potential in the fjord area, in spite of the introduction of mortality in bioluminescent organisms. Observations of BL potential indicated high emissions at depths below 100 m at offshore stations for both polar nights. Our modeling studies demonstrated that these high values of BL potential below 100 m are upwelled and advected to the top 50 m of the fjord. We demonstrated that upwelling and advection of these deep high BL potential values (and therefore, upwelling and advection of corresponding bioluminescent taxa) from offshore areas are dominant factors in observed BL potential dynamics in the top 50 m in the fjord.

Anthropogenic noise is increasingly recognized as a potentially significant stressor for marine animals. Beaked whales, deep-diving cephalopod predators, have been disproportionally present in atypical mass stranding events coincident with military sonar exercises, while frequently disturbed populations that do not strand may have reductions in fitness. We present in situ measures of prey availability, a key factor affecting fitness, for 2 distinct populations of Mesoplodon densirostris: one on a US Navy range in The Bahamas and one nearby in an area less exposed to sonar. The variables most strongly correlated with beaked whale habitat use were related to the distribution of deep-sea squid (mode spacing, peak depth, and 100 m scale variability). All squid metrics were more favorable for beaked whales at the less exposed site than those on the range. To develop a generalized functional relationship between prey resources and beaked whale habitat use, data from The Bahamas were combined with comparable data from another Navy range and the larger beaked whale, Ziphius cavirostris. A power-law relationship was observed between a normalized metric of prey quality and whale habitat use. A critical threshold in prey characteristics, below which beaked whales appear unlikely to be successful, but above which small changes in resource availability enable large gains for predators, was observed. This implies that modest changes in the behavior of individual whales associated with disturbance can have consequential population effects. Our results elucidate the ecological realities of these elusive and sensitive beaked whales, and the importance of environmental context in effective spatial planning for the deep sea.

Bioluminescence (BL) potential observations registered high BL potential emissions during the polar night of January 2012 at the mouth of a fjord Rijpfjorden (northern Svalbard, Norway). Notably, observations of BL potential at this location were significantly higher in the upper 50 m than observed BL potential at offshore stations located on the shelf-slope areas and in the deeper water off northern Svalbard. In the present paper, we address questions as to why the values of BL potential in the fjord are higher than at offshore stations and what the role of advection is in the observed elevation of BL potential values in the fjord in comparison to offshore stations. We utilized the ensemble approach when changes in BL potential are modeled with the advection-diffusion-source (ADS) model, and the focus is on modeling and predictions of a large ensemble of averaged values of BL potential over a specific domain of interest at the fjord mouth. Results of the modeling have demonstrated increases in ensemble members with BL potential values larger than or equal to the specific threshold in comparison to corresponding ensemble members in the initial distribution. Even when we introduced mortality rates in our simulations (values from 0.1 to 0.3 day−1), increases in ensemble members with higher than the threshold value were more than 3.7 times larger in comparison to ensemble members in the initial distribution. The interpretation of our results is that during the polar night, the fjord represents an area where bioluminescent organisms from offshore aggregate through advection and mixing.

Group formation in animals is a widespread phenomenon driven by food acquisition, reproduction, and defense. Life in the ocean is characteristically aggregated into horizontally extensive layers as a result of strong vertical gradients in the environment. Each day, animals in high biomass aggregations called “deep scattering layers” migrate vertically, comprising the largest net animal movement on earth. This movement is commonly thought of as a predator avoidance tactic, however, the aggregation of animals into layers has been viewed as an incidental outcome of similar responses by many individuals to the risk of visual predation coupled with the location of resources including food and oxygen rather than active, socially mediated congregation for defense purposes. Here, using a newly adapted autonomous vehicle to measure individual characteristics, we provide the first measures of the internal layer structure, demonstrating that these features are made up of many topologically scaled, mono-specific aggregations, or “schools” rather than an indiscriminate mix of sizes and species. Schools responded to predators using behavior much like flash compression while neighboring aggregations increased their spacing to maintain coherent layers. Rather than simply an incidental outcome, the formation of layers of life in the sea is a highly organized process driven, at least in part, by biotic pressures for cohesion with broad adaptive significance for the myriad species that inhabit these ubiquitous features. These observations highlight the range of spatial scales we must examine in order to understand the strong impacts these high-biomass layers have on ecological and biogeochemical processes in the sea.

Results from first observational program of bioluminescence (BL) potential in the Delaware Bay area are presented. During the field program July 30–August 1, 2015, the satellite Visible Infrared Imaging Radiometer Suite (VIIRS) imagery shows the development of the submesoscale filament with elevated chlorophyll-a in the area of interaction of lighter water masses of the Bay outflow with denser upwelled water. We have shown that ageostrophic secondary circulation (ASC) cells contributed to the development of this filament. Analysis of BL potential observations have shown elevated values of BL potential in the area of the submesoscale filament. Analysis of observed temperature, salinity, sigma-t, and BL potential along the stations crossing the Bay mouth have shown a presence of a strong frontal structure separating colder, more saline, denser offshore water from the bay water masses. Over 3 days of sampling, this frontal structure moved onshore to the entrance of the bay, and brought offshore BL plankton communities with higher values of BL potential. We compared two surveys (at the end of July and in the middle of August) of water masses located in the area where the buoyant outflow of the Delaware Coastal Current is turned around and taken to the north up the shelf by upwelling favorable winds. Analysis of observations shows that the survey at the end of July has fresher water masses (due to higher river runoff before and during survey) and higher values of BL potential in comparison to the survey at the middle of August.

How much light isa vailable for biological processes during Polar Night? This question appears simple enough. But the reality is that conventional light sen- sors for measuring visible light (~350 to ~700 nm) have not been sensitive enough to answer it. Beyond this technical challenge, “light” is a general term that must be qualified in terms of “light climate” before it has meaning for biological systems. In this chapter, we provide an answer to the question posed above and explore aspects of light climate during Polar Night with relevance to biology, specifically, how Polar Night is defined by solar elevation, atmospheric light in Polar Night and its propaga- tion underwater, bioluminescence in Polar Night and the concept of Polar Night as a deep-sea analogue, light pollution, and future perspectives. This chapter focuses on the quantity and quality of light present during Polar Night, while subsequent chapters in this volume focus on specific biological effects of this light for algae (Chap. “Marine Micro- and Macroalgae in the Polar Night”), zooplankton (Chaps.“Zooplankton in the Polar Night” and “Biological Clocks and Rhythms in Polar Organisms”), and fish (Chap. “Fish Ecology in the Polar Night”).

Observations of hydrodynamics along with optical and acoustical water characteristics in a tropical fringing reef environment reveal a distinct signature associated with flow characteristics and tidal conditions. Flow conditions are dominated by tidal forcing with an offshore component from the reef flat during ebb. Measurements span variable wave conditions enabling identification of wave effects on optical and acoustical water properties. High-frequency acoustic backscatter (6 MHz) is strongly correlated with tidal forcing increasing with offshore directed flow and modulated by wave height, indicating dominant hydrodynamic influence. Backscatter at 300 and 1200 kHz is predominantly diurnal suggesting a biological component. Optical backscatter is closely correlated with high-frequency acoustic backscatter across the range of study conditions. Acoustic backscatter frequency dependence is used along with changes in optical properties to interpret particle-size variations. Changes across wave heights suggest shifts in particle-size distributions with increases in relative concentrations of smaller particles for larger wave conditions. Establishing a connection between the physical processes of a fringing tropical reef and the resulting acoustical and optical signals allows for interpretation and forecasting of the remote sensing response of these phenomena over larger scales.

Acoustic echo sounders designed to map and discriminate organisms in the water column have primarily been deployed on ships. Because of acoustic attenuation of higher frequencies used to detect and discriminate micronekton and nekton, this has effectively restricted the range of this information to the upper water column. In an effort to overcome these range limitations by reducing the distance between the transducer and the targets of interest, dual-frequency (38 and 120 kHz) split-beam echo sounders were integrated into a Remote Environmental Monitoring Units (REMUS) 600 autonomous underwater vehicle (AUV), effectively doubling the range of quantitative acoustic data into the mesopelagic zone (600–1200 m). Data from the first set of missions in a range of conditions revealed that the AUV provided a stable platform for the echo sounders and improved vertical and horizontal positional accuracy over echo sounders towed by ships. In comparison to hull-mounted echo sounders, elimination of ship noise and surface bubbles provided a 17- and 19-dBW decrease in the noise floor for the 38- and 120-kHz echo sounders, respectively, effectively increasing the sampling range by 30%–40%. The extended depth range also increased the resolution of the acoustic horizontal footprint from 37–40 to 0.6–3.7 m, enabling discrimination of individual targets at depth. Also developed here is novel onboard echo sounder data processing and autonomy to allow sampling not feasible in a surface ship or towed configuration. Taken together, these data demonstrate an effective new tool for examining the biology of animals in the mesopelagic zone (600–1200 m) in ways previously only possible in the upper ocean.

Source at https://doi.org/10.1007/s00300-018-2278-5. Under-ice blooms of phytoplankton in the Chukchi Sea have been observed, with strong implications for our understanding of the production regimes in the Arctic Ocean. Using a combination of satellite remote sensing of phytoplankton biomass, in situ observations under sea ice from an autonomous underwater vehicle (AUV), and in vivo photophysiology, we examined the composition, magnitude and origin of a bloom detected beneath the sea ice Northwest of Svalbard (Southern Yermak Plateau) in May 2010. In situ concentration of up to 20 mg chlorophyll a [Chl a] m−3, were dominated by the northern planktonic spring species of diatoms, Thalassiosira nordenskioeldii, T. antarctica var. borealis, Chaetoceros socialis species complex and Fragilariopsis oceanica. These species were also found south of the marginal ice zone (MIZ). Cells in the water column under the sea ice were typically high-light acclimated, with a mean light saturation index (Ek) of 138 μmol photons m−2 s−1 and a ratio between photoprotective carotenoids (PPC) and Chl a (w:w) of 0.2. Remotely sensed data of [Chl a] showed a 32,000 km2 bloom developing south of the MIZ. In effect, our data suggest that the observed under-ice bloom was in fact a bloom developed in open waters south of the ice edge, and that a combination of northward-flowing water masses and southward drifting sea ice effectively positioned the bloom under the sea ice. This have implications for our general understanding of under-ice blooms, suggesting that their origin and connection with open water may be different in different regions of the Arctic.

In June 2011, a 9 day oceanographic survey was conducted over the East Flower Garden Bank, a coral reef, located on the outer shelf in the northwestern Gulf of Mexico. Current, temperature, conductivity, and microstructure measurements were collected to characterize flow evolution, turbulence, and mixing over the bank. During the experiment, the flow was highly stratified, subcritical (Froude number below 0.4), hydrostatic, and nonlinear with rotational effects being important. Observations showed that flow structure, turbulence, and mixing were highly dependent on the direction and strength of the current; thus, they varied spatially and temporarily. Responses resulting from interactions between the free-stream flow and the obstacle were significantly different on the upstream and downstream sides of the bank. Blocking and diverging of the flow just below the bank height was observed on the upstream side. On the downstream side, a wake with imbedded vortices developed. Moreover, turbulence was amplified over the bank top and on its downstream side. Turbulent dissipation rates were as high as 1026 W kg21 and resulted in measured rates of energy dissipation and mixing by turbulence per unit width as high as 40 W m21. Mixing in the downstream side was elevated with eddy diffusivities reaching 1023 m2 s21, well above a typical value of 1025 m2 s21 commonly found in the ocean thermocline and over shelves with flat topography. On the upstream side, estimated eddy diffusivities were close to that for the ocean thermocline, i.e., they were generally less than 0.531024 m2 s21.

Colored Dissolved Organic Matter (CDOM) is an important optical constituent in seawater, which significantly attenuates the violet to blue portion of visible light. Thus, CDOM reduces the radiation energy available to phytoplankton and affects remote-sensing signals. We present data from two cruises transecting the Polar Front from Atlantic to Arctic waters in the Barents Sea, in 2007 and 2008. The latter took place during the spring bloom of phytoplankton in May (0.2-3) and the former during August (max. [Chl a]-3). Absorption by CDOM at 443nm ranged from 0.004 to 0.080m -1 during May and from 0.006 to 0.162m -1 during August. Surprisingly, CDOM absorption differed little across the Polar Front, but was higher during August than during May (P-1 (mean=0.015nm -1) including both cruises, and varied little across the Front (P>0.05). The CDOM remote sensing product from GlobColour correlated well with sampled data (R 2=0.73) during May. However, during August the satellite product performed poorly (R 2=0.02) due to extensive scattering caused by coccolithophorids in the Atlantic Water. The CDOM pool was of autochthonous (marine) origin as characterized from its S vs. absorption relationship. Modeling showed that CDOM, on average, contributed equally to the light absorption as did phytoplankton (at 1mg Chl a m -3), and thereby reduces the amount of light available for primary production.

[1] The network comprising 61 high-frequency radar systems along the U.S. West Coast (USWC) provides a unique, high resolution, and broad scale view of ocean surface circulation. Subinertial alongshore surface currents show poleward propagating signals with phase speeds of O(10) and O(100–300) km d −1 that are consistent with historical in situ observations off the USWC and that can be possibly interpreted as coastally trapped waves (CTWs). The propagating signals in the slow mode are partly observed in southern California, which may result from scattering and reflection of higher-mode CTWs due to curvature of shoreline and bathymetry near Point Conception, California. On the other hand, considering the order of the phase speed in the slow mode, the poleward propagating signals may be attributed to alongshore advection or pressure-driven flows. A statistical regression of coastal winds at National Data Buoy Center buoys on the observed surface currents partitions locally and remotely wind-forced components, isolates footprints of the equatorward propagating storm events in winter off the USWC, and shows the poleward propagating signals year round.

The complex dynamics associated with coastal buoyant plumes make it difficult to document the interactions between light availability, phytoplankton carbon fixation, and biomass accumulation. Using real-time data, provided by satellites and high frequency radar, we adaptively sampled a low salinity parcel of water that was exported from the Hudson river estuary in April 2005. The water was characterized by high nutrients and high chlorophyll concentrations. The majority of the low salinity water was re-circulated within a nearshore surface feature for 5 days during which nitrate concentrations dropped 7-fold, the maximum quantum yield for photosynthesis dropped 10-fold, and primary productivity rates decreased 5-fold. Associated with the decline in nitrate was an increase in phytoplankton biomass. The phytoplankton combined with the Colored Dissolved Organic Matter (CDOM) and non-algal particles attenuated the light so the 1% light level ranged between 3 and 10 m depending on the age of the plume water. As the plume was 10–15 m thick, the majority of the phytoplankton were light-limited. Vertical mixing within the plume was high as indicated by the dispersion of injected of rhodamine dye. The mixing within the buoyant plume was more rapid than phytoplankton photoacclimation processes. Mixing rates within the plume was the critical factor determining overall productivity rates within the turbid plume.

Quantifying the fine-scale movement patterns and habitat use of active fishes has historically been challenging due to their scope of movement or the labor intensive nature of actively tracking potentially wide-ranging species. This project focuses on improving the localization accuracy and temporal resolution of an acoustically tagged fish by filtering the position measurements received from an acoustic receiver array. Using the k-means clustering algorithm, data sets are broken into groups which have similar fish speeds and yaw rates to yield a discrete number of movement behaviors characterized by the mean and standard deviation of speed and yaw. Next, a Particle Filter state estimator is proposed, in which position and speed state estimates of particles are used to calculate the most likely motion behavior, which in turn is used as a first order motion model to propagate the particle's fish state estimates forward in time. These predicted particle states are compared with the position measurements and then resampled as done with most Particle Filters. Offline processing of a shovelnose guitarfish (Rhinobatos productus) data set shows that the estimation of the fish's location is improved during periods of time when no measurements could be obtained when compared with two common filtering approaches.

We targeted a habitat used differentially by deep-diving, air-breathing predators to empirically sample their prey's distributions off southern California. Fine-scale measurements of the spatial variability of potential prey animals from the surface to 1 200 m were obtained using conventional fisheries echosounders aboard a surface ship and uniquely integrated into a deep-diving autonomous vehicle. Significant spatial variability in the size, composition, total biomass, and spatial organization of biota was evident over all spatial scales examined and was consistent with the general distribution patterns of foraging Cuvier's beaked whales ( Ziphius cavirostris ) observed in separate studies. Striking differences found in prey characteristics between regions at depth, however, did not reflect differences observed in surface layers. These differences in deep pelagic structure horizontally and relative to surface structure, absent clear physical differences, change our long-held views of this habitat as uniform. The revelation that animals deep in the water column are so spatially heterogeneous at scales from 10 m to 50 km critically affects our understanding of the processes driving predator–prey interactions, energy transfer, biogeochemical cycling, and other ecological processes in the deep sea, and the connections between the productive surface mixed layer and the deep-water column.

A correlation between genome size and cell volume has been observed across diverse assemblages of eukaryotes. We examined this relationship in diatoms (Bacillariophyceae), a phylum in which cell volume is of critical ecological and biogeochemical importance. In addition to testing whether there is a predictive relationship across extant species, we tested whether evolutionary divergences in genome size were correlated with evolutionary divergences in cell size (using independent contrasts). We estimated total DNA content for 16 diatom species using a flow cytometer and estimated cell volumes using critical dimensions with scaling equations. Our independent contrast analyses indicated a significant correlated evolution between genome size and cell volume. We then explored the evolutionary and ecological implications of this evolutionary relationship. Diatom cell volume is an important component of the global carbon cycle; therefore, understanding the mechanisms that drive diatom genome evolution has both evolutionary and ecological importance.

Bioluminescence is reported in members of 18 dinoflagellate genera. Species of dinoflagellates are known to have different bioluminescent signatures, making it difficult to assess the presence of particular species in the water column using optical tools, particularly when bioluminescent populations are in nonbloom conditions. A "universal" oligonucleotide primer set, along with species and genus-specific primers specific to the luciferase gene were developed for the detection of bioluminescent dinoflagellates. These primers amplified luciferase sequences from bioluminescent dinoflagellate cultures and from environmental samples containing bioluminescent dinoflagellate populations. Novel luciferase sequences were obtained for strains of Alexandrium cf. catenella (Whedon et Kof.) Balech and Alexandrium fundyense Balech, and also from a strain of Gonyaulax spinifera (Clap. et Whitting) Diesing, which produces bioluminescence undetectable to the naked eye. The phylogeny of partial luciferase sequences revealed five significant clades of the dinoflagellate luciferase gene, suggesting divergence among some species and providing clues on their molecular evolution. We propose that the primers developed in this study will allow further detection of low-light-emitting bioluminescent dinoflagellate species and will have applications as robust indicators of dinoflagellate bioluminescence in natural water samples.

Before man hunted the large baleen whales to near extinction by the end of the nineteenth century, Arctic ecosystems were strongly influenced by these large predators. Their main prey were zooplankton, among which the calanoid copepod species of the genus Calanus, long considered key elements of polar marine ecosystems, are particularly abundant. These herbivorous zooplankters display a range of adaptations to the highly seasonal environments of the polar oceans, most notably extensive energy reserves and seasonal migrations to deep waters where the non-feeding season is spent in diapause. Classical work in marine ecology has suggested that slow growth, long lifespan and large body size in zooplankton are specific adaptations to life in cold waters with short and unpredictable feeding seasons. Here, we challenge this understanding and, by using an analogy from the evolutionary and contemporary history of the avocado, argue that predation pressure by the now nearly extinct baleen whales was an important driving force in the evolution of life history diversity in the Arctic Calanus complex.

This study examines the composition and activity of the planktonic community during the polar night in the high Arctic Kongsfjord, Svalbard. Our results are the first published evidence of bioluminescence among zooplankton during the Arctic polar night. The observations were collected by a bathyphotometer detecting bioluminescence, integrated into an autonomous underwater vehicle, to determine the concentration and intensity of bioluminescent flashes as a function of time of day and depth. To further understand community dynamics and composition, plankton nets were used to collect organisms passing through the bathyphotometer along with traditional vertical net tows. Additionally, using a moored bathyphotometer closed to the sampling site, the bioluminescence potential itself was shown not to have a diurnal or circadian rhythm. Rather, our results provide evidence for a diel vertical migration of bioluminescent zooplankton that does not correspond to any externally detectable changes in illumination.

Sound is a key sense for animals in the ocean, including humans. The integration of passive and active acoustics in behavioral and ecosystem studies has revealed much about how ocean systems work. Here, I will discuss how the integration of echosounders with various passive acoustic approaches has contributed to our understanding to the biology and ecology of marine mammals. For example, explaining the habitat selection of beaked whales, the foraging ecology, behavior, and communication of spinner dolphins, and the ability of dolphin sonar to discriminate fish species. Careful integration of passive and active acoustics has also contributed to sonar signal design and processing approaches. A recent study of Risso’s dolphins using passive acoustic recording tags on the dolphins themselves and echosounders deployed from a ship and an underwater vehicle provided new insights into how these animals make foraging decisions, what information is available to them and when, and how changes in their prey over space and time affect their foraging behavior. The combination of passive and active acoustics is providing insight into the ecology and dynamics of predator and prey at the scale of the individual and the population.Sound is a key sense for animals in the ocean, including humans. The integration of passive and active acoustics in behavioral and ecosystem studies has revealed much about how ocean systems work. Here, I will discuss how the integration of echosounders with various passive acoustic approaches has contributed to our understanding to the biology and ecology of marine mammals. For example, explaining the habitat selection of beaked whales, the foraging ecology, behavior, and communication of spinner dolphins, and the ability of dolphin sonar to discriminate fish species. Careful integration of passive and active acoustics has also contributed to sonar signal design and processing approaches. A recent study of Risso’s dolphins using passive acoustic recording tags on the dolphins themselves and echosounders deployed from a ship and an underwater vehicle provided new insights into how these animals make foraging decisions, what information is available to them and when, and how changes in their prey over spac...

Significant avoidance of acoustically detected zooplankton was observed in response to a profiling instrument package. Avoidance decreased acoustic scattering from zooplankton averaged over the entire profile by more than a factor of 2, while the maximum avoidance decreased zooplankton acoustic scattering by a factor of 15 over the depth of some discrete scattering layers. Experimental manipulation of the profiler and its instruments revealed that an open-path fluorometer was triggering the avoidance. Avoidance occurred at an average of 8 m below the profiler with a range between 2 and 13 m. Effect range was positively correlated with the average attenuation coefficient of light over the effect range and consistently resulted in avoidance when light levels of approximately 0.013 micro umol photons m(-2) s(-1) were received by the zooplankton. These results have important implications for the analysis of zooplankton data collected from platforms carrying open-path fluorometers and may also warrant careful interpretation of optical measurements from these packages.

This study combined measurements from multiple platforms with acoustic instruments on moorings and on a ship and optics on a profiler and an autonomous underwater vehicle (AUV) to examine the relationships between fluorescent, bioluminescent, and acoustically scattering layers in Monterey Bay during nighttime hours in July and August of 2006 and May of 2008. We identified thin bioluminescent layers that were strongly correlated with acoustic scattering at the same depth but were part of vertically broad acoustic features, suggesting layers of unique composition inside larger biomass features. These compositional thin layers nested inside larger biomass features may be a common ecosystem component and are likely to have significant ecological impacts but are extremely difficult to identify as most approaches capable of the vertical scales of measurement necessary for the identification of sub-meter scale patterns assess bulk properties rather than specific layer composition. Measurements of multiple types of thin layers showed that the depth offset between thin phytoplankton and zooplankton layers was highly variable with some layers found at the same depth but others found up to 16 m apart. The vertical offset between phytoplankton and zooplankton thin layers was strongly predicted by the fraction of the water column fluorescence contained within a thin phytoplankton layer. Thin zooplankton layers were only vertically associated with thin phytoplankton layers when the phytoplankton in a layer accounted for more than about 18–20% of the water column chlorophyll. Trophic interactions were likely occurring between phytoplankton and zooplankton thin layers but phytoplankton thin layers were exploited by zooplankton only when they represented a large fraction of the available phytoplankton, suggesting zooplankton have some knowledge of the available food over the entire water column. The horizontal extent of phytoplankton layers, discussed in the second paper in this series, is likely an important factor contributing to this selective exploitation by zooplankton. The pattern of vertical offset between phytoplankton and zooplankton layers was consistent between studies in different years and using different combinations of platforms, indicating the importance of the relationship between zooplankton layers and the fraction of phytoplankton within a layer at night within Monterey Bay. These results highlight the value of integrating measurements of various types of organisms to understand thin layers processes and the importance of assessing ecological interactions in plankton thin layers within the context of the properties of the entire water column, like the animals themselves do.

The degree of layered organization of planktonic organisms in coastal systems impacts trophic interactions, the vertical availability of nutrients, and many biological rate processes. While there is reasonable characterization of the vertical structure of these phenomena, the extent and horizontal length scale of variation has rarely been addressed. Here we extend the examination of the vertical scale in the first paper of the series to the horizontal scale with combined shipboard acoustic measurements and bio-optic measurements taken on an autonomous underwater vehicle. Measurements were made in Monterey Bay, CA from 2002 to 2008 for the bio-optical parameters and during 2006 for acoustic scattering measurements. The combined data set was used to evaluate the horizontal decorrelation length scales of the bio-optical and acoustic scattering layers themselves. Because biological layers are often decoupled from the physical structure of the water column, assessment of the variance within identified layers was appropriate. This differs from other studies in that physical parameters were not used as a basis for the layer definition. There was a significant diel pattern to the decorrelation length scale for acoustic layers with the more abundant nighttime layers showing less horizontal variability despite their smaller horizontal extent. A significant decrease in the decorrelation length scale was found in bio-optical parameters over six years of study, coinciding with a documented shift in the plankton community. Results highlight the importance of considering plankton behavior and time of day with respect to scale when studying layers, and the challenges of sampling these phenomena.

Bioluminescence spans all oceanic dimensions and has evolved many times—from bacteria to fish—to powerfully influence behavioral and ecosystem dynamics. New methods and technology have brought great advances in understanding of the molecular basis of bioluminescence, its physiological control, and its significance in marine communities. Novel tools derived from understanding the chemistry of natural light-producing molecules have led to countless valuable applications, culminating recently in a related Nobel Prize. Marine organisms utilize bioluminescence for vital functions ranging from defense to reproduction. To understand these interactions and the distributions of luminous organisms, new instruments and platforms allow observations on individual to oceanographic scales. This review explores recent advances, including the chemical and molecular, phylogenetic and functional, community and oceanographic aspects of bioluminescence.

One of the key challenges in the development and implementation of ocean observatories is sustained observations over relevant temporal and spatial scales. Autonomous underwater vehicles (AUVs) have demonstrated their potential for synoptic spatial coverage of regions of scientific and strategic interest. The range and duration of these systems are limited, however, to the capabilities of a single charge. A few efforts have been made to develop docking systems for propeller-driven vehicles; however, these systems are not applicable for buoyancy-driven gliders and cannot be universally applied to AUVs. Here the authors introduce an alternative strategy for AUV docking, demonstrate feasibility with a series of field tests using a remotely operated vehicle (ROV) to remotely recover an AUV, and comment on the scalability within the framework of the evolving global ocean observatory initiatives. Implementation of simple strategies such as this has the potential to reduce the chronic problem of undersampling in the ocean and may facilitate addressing some outstanding scientific questions related to the ocean.

Ecosystem function will in large part be determined by functional groups present in biological communities. The simplest distinction with respect to functional groups of an ecosystem is the differentiation between primary and secondary producers. A challenge thus far has been to examine these groups simultaneously with sufficient temporal and spatial resolution for observations to be relevant to the scales of change in coastal oceans. This study takes advantage of general differences in the bioluminescence flash kinetics between planktonic dinoflagellates and zooplankton to measure relative abundances of the two groups within the same-time space volume. This novel approach for distinguishing these general classifications using a single sensor is validated using fluorescence data and exclusion experiments. The approach is then applied to data collected from an autonomous underwater vehicle surveying >500 km in Monterey Bay and San Luis Obispo Bay, CA during the summers of 2002–2004. The approach also reveals that identifying trophic interaction between the two planktonic communities may also be possible.

This issue is devoted to recent developments of autonomous and Lagrangian platforms and sensors (ALPS) and their uses for solving a broad range of interdisciplinary aquatic problems. The collective papers treat a variety of problems that generally require measurements spanning a continuum of temporal and spatial scales. ALPS platforms in this issue include surface drifters, profiling and other types of subsurface floats, gliders, unmanned boats, autonomous underwater vehicles, and instrumented animals. ALPS platforms can provide access in difficult environments (e.g., under ice and in high-sea states). They are also important for emerging networked ocean and lake observing systems that require continuous measurements and near-real-time data. This introductory paper provides historical perspectives, background, motivation for the issue, and a tabular summary of papers in the present collection.

The potential for using synergistic combinations of measurements from autonomous underwater vehicles (AUVs) and output from three-dimensional numerical models for studying the central California coastal region is demonstrated. Two case studies are used to illustrate the approach. In the first, propeller-driven AUV observations revealed a subsurface salinity minimum in northern Monterey Bay. A Regional Ocean Modeling System (ROMS) reanalysis of the three-dimensional flow in the region suggested an offshore source for this water and particular propagation pathways from the south and west into the bay. In the second case study, the effectiveness of assimilating observations in improving the ROMS reanalysis fields is investigated. A significant improvement, especially in the salinity fields, is demonstrated through a single glider deployed outside the intensive observational domain. These results suggest that investigation of more sophisticated techniques for using data and models together is warranted. Such techniques include increasing model resolution in areas of interest identified by observing platforms and using model-based “targeted observing” techniques to identify areas of uncertainty in the flow to guide placement of observational assets.

Bioluminescence is reported in members of 18 dinoflagellate genera. Species of dinoflagellates are known to have different bioluminescent signatures, making it difficult to assess the presence of particular species in the water column using optical tools, particularly when bioluminescent populations are in nonbloom conditions. A ‘‘universal’’ oligonucleotide primer set, along with species and genus-specific primers specific to the luciferase gene were developed for the detection of bioluminescent dinoflagellates. These primers amplified luciferase sequences from bioluminescent dinoflagellate cultures and from environmental samples containing bioluminescent dinoflagellate populations. Novel luciferase sequences were obtained for strains of Alexandrium cf. catenella (Whedon et Kof.) Balech and Alexandrium fundyense Balech, and also from a strain of Gonyaulax spinifera (Clap. et Whitting) Diesing, which produces bioluminescence undetectable to the naked eye. The phylogeny of partial luciferase sequences revealed five significant clades of the dinoflagellate luciferase gene, suggesting divergence among some species and providing clues on their molecular evolution. We propose that the primers developed in this study will allow further detection of low-light-emitting bioluminescent dinoflagellate species and will have applications as robust indicators of dinoflagellate bioluminescence in natural water samples.

A correlation between genome size and cell volume has been observed across diverse assemblages of eukaryotes. We examined this relationship in diatoms (Bacillariophyceae), a phylum in which cell volume is of critical ecological and biogeochemical importance. In addition to testing whether there is a predictive relationship across extant species, we tested whether evolutionary divergences in genome size were correlated with evolutionary divergences in cell size (using independent contrasts). We estimated total DNA content for 16 diatom species using a flow cytometer and estimated cell volumes using critical dimensions with scaling equations. Our independent contrast analyses indicated a significant correlated evolution between genome size and cell volume. We then explored the evolutionary and ecological implications of this evolutionary relationship. Diatom cell volume is an important component of the global carbon cycle; therefore, understanding the mechanisms that drive diatom genome evolution has both evolutionary and ecological importance.

Patchiness or spatial variability is ubiquitous in marine systems. With increasing anthropogenic impacts to coastal resources and coastal systems being disproportionately large contributors to ocean productivity, identifying the spatial scales of this patchiness, particularly in coastal waters, is of critical importance to understand coastal ecosystem dynamics. The current work focuses on fine scale structure in three coastal regions. More specifically, we utilize variogram analyses to identify sub-kilometer scales of variability in biological and physical parameters measured by an autonomous underwater vehicle (AUV) in the Mid-Atlantic Bight, Monterey Bay, and in San Luis Obispo Bay between 2001 and 2004. Critical scales of variability in density, turbidity, fluorescence, and bioluminescence are examined as a function of depth and distance offshore. Furthermore, the effects of undersampling are assessed using predictive error analysis. Results indicate the presence of scales of variability ranging from 10s to 100s of meters and provide valuable insight for sampling design and resource allocation for future studies.

Bioluminescence commonly influences pelagic trophic interactions at mesopelagic depths. Here we characterize a vertical gradient in structure of a generally low species diversity bioluminescent community at shallower epipelagic depths during the polar night period in a high Arctic fjord with in situ bathyphotometric sampling. Bioluminescence potential of the community increased with depth to a peak at 80 m. Community composition changed over this range, with an ecotone at 20–40 m where a dinoflagellate-dominated community transitioned to dominance by the copepod Metridia longa. Coincident at this depth was bioluminescence exceeding atmospheric light in the ambient pelagic photon budget, which we term the bioluminescence compensation depth. Collectively, we show a winter bioluminescent community in the high Arctic with vertical structure linked to attenuation of atmospheric light, which has the potential to influence pelagic ecology during the light-limited polar night. © The Author(s) 2016. This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

Climate-driven sympatry may lead to competition for food resources between species. Rapid warming in the West Antarctic Peninsula (WAP) is coincident with increasing gentoo penguin and decreasing Adélie penguin populations, suggesting that competition for food may exacerbate the Adélie penguin decline. On fine scales, we tested for foraging competition between these species during the chick-rearing period by comparing their foraging behaviors with the distribution of their prey, Antarctic krill. We detected krill aggregations within the horizontal and vertical foraging ranges of Adélie and gentoo penguins and found that krill selected for habitats that balance the need to consume food and avoid predation. In overlapping Adélie and gentoo penguin foraging areas, four gentoo penguins switched foraging behavior by foraging at deeper depths, a strategy which limits competition with Adélie penguins. This suggests that climate-driven sympatry does not necessarily result in competitive exclusion of Adélie penguins by gentoo penguins. Contrary to a recent theory, which suggests that increased competition for krill is one of the major drivers of Adélie penguin population declines, we suggest that declines in Adélie penguins along the WAP are more likely due to direct and indirect climate impacts on their life histories.

New technology has led to new opportunities for a holistic environmental monitoring approach adjusted to purpose and object of interest. The proposed integrated environmental mapping and monitoring (IEMM) concept, presented in this paper, describes the different steps in such a system from mission of survey to selection of parameters, sensors, sensor platforms, data collection, data storage, analysis and to data interpretation for reliable decision making. The system is generic; it can be used by authorities, industry and academia and is useful for planning- and operational phases. In the planning process the systematic approach is also ideal to identify areas with gap of knowledge. The critical stages of the concept is discussed and exemplified by two case studies, one environmental mapping and one monitoring case. As an operational system, the IEMM concept can contribute to an optimised integrated environmental mapping and monitoring for knowledge generation as basis for decision making.