Microbial eukaryotes (protists) are important contributors to marine biogeochemistry and play essential roles as both producers and consumers in marine ecosystems. Among protists, mixotrophs—those that use both heterotrophy and autotrophy to satisfy their energy requirements—are especially important to primary production in oligotrophic regions where nutrient availability is otherwise limiting. For instance, acantharians accomplish mixotrophy by hosting Phaeocystis spp. as endosymbionts. Despite their ecological importance, Acantharea-Phaeocystis symbioses are understudied due to host fragility and inability to survive in culture. We investigated the evolution and ecological functioning of these symbioses by sequencing single-cell transcriptomes from sixteen acantharians. Since hosts harbor multiple Phaeocystis species, we prepared transcriptomes for the two most common symbiont species available in culture—P. cordata and P. jahnii—and evaluated differential gene expression between symbiotic and free-living cells. Results indicate photosynthesis genes are upregulated in symbiosis for both symbiont species, suggesting symbionts are photosynthesizing at elevated rates within hosts. However, biosynthesis and metabolism of storage carbohydrates and lipids are downregulated in symbiosis, indicating that extra energy captured through elevated photosynthesis is not retained. Symbiont gene expression suggests symbionts relinquish fixed carbon as small organonitrogen compounds, such as amides and amino acids, while receiving host-supplied nitrogen as urea and ammonium. Importantly, genes associated with protein kinase signaling pathways that promote cell proliferation are deactivated in symbionts. Manipulation of these pathways may prevent symbionts from overgrowing hosts and therefore represents a key component of maintaining the symbiosis. This study illuminates mechanisms of host control and nutrient transfer in an important microbial symbiosis in oligotrophic waters.

MAJOR POINTS: 1) The Barents and GIN basins are warming rapidly and exhibiting strong strong interannual variability. 2) While interannual variability of heat content in the GIN Seas is controlled by Atlantic water transport, we show interannual variability of heat content in the Barents is controlled by surface flux (see also Schlichtholtz et al 2011). 3) Interannual variations in surface flux are the result of variations in wintertime latent heat loss resulting from intrusions of warm moist air from the south. 4) (not shown) these variations also control winter sea ice cover.

Internal waves and vortical mode are ubiquitous in the ocean, providing a conduit for energy transfer from tides and wind-driven circulation to fine- and micro-scale turbulence associated with internal-wave breaking and dissipation. Numerical simulations of a Garrett-Munk internal-wave field are used to study the interactions between internal waves and vortical mode, and the generation of turbulent mixing events and semi-permanent finestructure (vortical mode). Regions of reduced stratification are found to occupy between ~5% and 25% of the model domain, depending on the strength of the anomalies. Decomposition of 3-dimensional model fields into linear internal-wave and vortical-mode components shows that both influence stratification, with ~88% of the anomalies due to linear internal waves and ~40% due to vortical mode, the overlap in percentiles representing regions that are a combination of the two. The time evolution of anomalies is examined, from the initial generation to eventual dissipation. Results further describe the preconditions of these regions, including their relation to a subcritical Richardson number and overturning / mixing events as quantified via Thorpe scales and turbulent dissipation rate.

Alterations in the ocean and polar and mountain cryosphere from climate change have the potential for far-reaching impacts on ecosystems and human systems all over the world. The IPCC Special Report on Ocean and Cryosphere in a Changing Climate (SROCC) was prepared in response to proposals of member governments and observer organisations for Special Reports assessing highly policy-relevant issues. This report focuses on observed and projected changes in the ocean and cryosphere; impacts, vulnerability and risks to ecosystems and human systems, as well as adaptation options. The SROCC is structured in six chapters: Framing and context of the report; high mountain areas; polar regions; sea level rise and implications for low lying islands, coasts and communities; changing ocean, marine ecosystems, and dependent communities; extremes, abrupt changes and managing risks; together with an integrative cross-chapter box on low-lying islands and coasts. Over 100 scientists from 36 countries led the assessment of the latest scientific knowledge in more than two years of intense work. This presentation will provide some background information, an overview on the milestones during report development and focus on the key messages from the report’s Summary for Policymakers.

This study is motivated by the observation that after a wave breaking event in the ocean, the residual surface foam left in the wake of the breaker rapidly cools down. The relationship between the cooling foam and the characteristics of the breaking wave such as bubble plume dynamics, visible surface foam, and energy dissipation is investigated experimentally. Previous studies have suggested that the decay time of the visible foam can be used to determine the dynamics of the subsurface bubble plume, and to estimate the energy dissipation by the breaking process. But the foam decay process can be greatly affected by the surfactant concentration in the ocean and this effect need to be accounted for independently. We present a new approach that utilizes the thermal signature of the cooling foam to infer the breaking characteristics and is less sensitive to surfactant concentration. The experiments are conducted in a wave flume that is equipped with a piston-type wavemaker and is filled with salt water. In order to study the effects of surfactants on the cooling of the residual foam, two sets of experiments are carried out; In the first set clean salt water is used and in the second set, Triton X-100 at a concentration of approximately 200 mg/L is added to the water. Breaking waves are generated using the focusing wavepacket technique and are designed to cover a wide range of slopes and breaking intensities. The bubble plume and the surface foam are imaged using visible cameras and the surface temperature is captured using an IR camera with an overlapping field of view with the visible foam camera. It is observed that the average temperature of the foam initially increases after the passage of a breaking wave due to the disruption of the cool skin layer, but the foam starts to cool down soon after the bubble plume has subsided, and the foam regeneration is not sustained by the bubbles anymore. It is found that the time from the start of the breaking process to the onset of cooling of the foam (τcool) scales with the decay time of the bubble plume (τplume), energy dissipation, and the wavepacket slope of the breakers. It is also observed that the foam decay time is prolonged greatly by the presence of additional surfactants (consistent with the literature), but the bubble plume decay time and the onset of cooling of the foam are not significantly affected.

The West Florida Shelf (WFS) is an extremely important area for both commercial and recreational fisheries. However, the lack of habitat maps in this area makes planning fisheries independent monitoring surveys difficult, and hinders the ability to manage and monitor fish stocks and ecosystems over time. As of 2015, only 5% of the WFS had been mapped in high resolution using a multibeam echosounder with little effort expended to infer and verify habitat type. In 2015, The Continental Shelf Characterization, Assessment, and Mapping Project (C-SCAMP) began using a multibeam echosounder and towed underwater video to map benthic habitats and improve our understanding of fish-habitat relationships on the WFS. For this study, high resolution multibeam bathymetry and co-registered backscatter data were collected and processed. A portion of these areas were then “ground-truthed” using towed video transects to assess habitat type and identify fish. Habitat maps were created using a statistical classification model that predicts benthic habitat type based on the acoustic signature. Progress towards a unified habitat map of the West Florida Shelf will be presented including habitat interpretation of multibeam surfaces collected by other groups prior to this project, particularly focusing on those within Marine Protected Areas. Applications of the resultant habitat maps for fisheries management will be demonstrated and discussed.

ESA is building on almost 15 years of continuous Fiducial Reference Measurements (FRM) from UK-funded shipborne radiometers by establishing a service to provide historic and ongoing FRM measurements to the wider SST community through an International SST FRM Radiometer Network (ships4sst). The ships4sst is open for partners around the world, currently compromising of partners from the UK (University of Southampton, Rutherford Appleton Laboratory, Space ConneXions), Denmark (Danish Meteorological Institute) and France (Ifremer) and will not only collect Shipborne radiometer data but also use the data to validate SLSTR and other satellite SST products with the Felyx MDB tool. Included in the service is a long term data archive of the FRM datasets at Ifremer where the data will be stored in the ships4sst netCDF L2R format. We will show examples of the ships4sst data and demonstrate its use with the newest SLSTR validation results from the ships4sst network regions, showing that SLSTR performs at least as well as its predecessor AATSR. We will also show results of the SLSTR A and B units during the Sentinel-3 tandem phase in 2018 by using triple collocations on the ships4sst FRM data and the SLSTR units on Sentinel 3 A and B.

The need for extended and comprehensive ocean observations is ever-growing. Global challenges such as changing climate, pollution and sustainable resource management demand for a thorough data base and models to provide the basis for enhanced decision taking. These endeavors are costly and can only be achieved to enough extend if an efficient collaboration of all the stakeholders involved can be realized. One foundation for this needed collaboration is represented by the large amount of research and development projects and assessment initiatives in which researchers from scientific institutions and representatives from the private sector work together globally. For over more than a decade we have gathered experience as a sensor manufacturing start-up and as part of a globally active technology corporation. Collaboration with scientists and joint projects resemble essential elements during all stages of this business development. Although the nature of the collaborations can vary (educational project, basic research, targeted development, technology assessment, etc.), all these alliances should have in common that they are carried out with maximum efficiency. This means that the intersectoral partners should contribute according to their strengths, be clear on their individual interests to be able to prepare a win-win setting and be willing to partner on eye level. Besides generalized reflections on science-industry collaboration (e.g. motivations and benefits for the different type of actors), this contribution will highlight and present exemplary results from past and ongoing global project collaborations, i.e. initiatives from the USA and Europe. These examples might include development, assessment and application work on chemical analyzers for the determination of total alkalinity and pH, sensors for dissolved CO2, CH4 or O2, scientific echo sounders, sensor integrations on modern mobile platforms or lander-based observation and monitoring systems.

Insights from half a century investigating seafloor hydrothermal circulation on Earth can inform exploration on other Ocean Worlds. Early data/models for Earth provided useful predictions for flow at rift axes, but interpretations of the distribution of subseafloor circulation were revised significantly as data and simulations improved. Lessons learned for Earth systems elucidate how investigators might assess hydrothermal processes on other Ocean Worlds. Basin-scale morphology and heat flow indicate whether conduction explains the flux or cooling by seawater advection occurs. Detailed sonar mapping reveals areas where high flux is most likely. Seismicity patterns suggest different modes of circulation: East Pacific circulation is mapped via microseismicity within porous basaltic crust; Regional seismicity in the Atlantic highlights detachment-dominated rift segments, where faults channel circulation, sometimes within peridotite blocks that react with seawater. Exothermic serpentinization, also inferred for the lower ocean crust near subduction zones, should impart detectable temperature (T) signals. High-T/-flux circulation may be recognized with remote sensing (sonar, thermistors, chemical sensors, cameras) at the seafloor whereas low-T/-flux systems are difficult to identify. Modeling examines factors that influence hydrothermal circulation. Early models were simple single-pass cases; later data and more complex models show circulation includes multi-pass convection that can be 3D, unstable, and strongly guided by permeability patterns. Borehole observatories reveal heterogeneity in fluid chemistry and crustal microbiology. Interpreting Ocean World hydrothermal conditions will be challenging, but some fundamental inferences for Earth’s seafloor hydrothermal systems have proven robust. Early studies generated testable hypotheses, advanced instrumentation and simulations, and helped focus interdisciplinary discovery.

Quantifying mixing rates in the Arctic Ocean is critical to our ability to predict heat flux, freshwater distribution, and circulation. However, turbulence measurements in the Arctic are sparse, and cannot characterize the high spatiotemporal variability typical of ocean mixing. Using year-round temperature and salinity data from Ice-Tethered Profiler (ITP) instruments between 2004 and 2018, we apply a finescale parameterization to obtain pan-Arctic estimates of turbulent dissipation and mixing rates at unprecedented space-time resolution. Building on previous work that used ITP data to identify double-diffusive staircases and analyze the associated convective mixing, we apply the finescale parameterization only where these step-like thermohaline structures are not present and mixing is expected to be internal wave-dominated. We find that the inferred wave-driven dissipation and mixing rates are generally low, but highly variable in both space and time, displaying significant regional differences between the shelves and central basins, as well as a small seasonal cycle. We detect no statistically significant interannual trend in mixing rate estimates over the period examined, with the exception of a small increase in the Canada Basin immediately below the mixed layer. The joint consideration of turbulent dissipation rates and stratification imply varied Arctic Ocean mixing regimes, which are most often not appropriately characterized as isotropic turbulence. Where justified, we infer turbulent heat fluxes out of the Atlantic Water layer that are mostly small, but also exhibit a distinct regional dependence.

Accurately measuring CO2 system variables in the ocean is necessary not only to estimate carbon fluxes, but also to understand changes in seawater chemistry and its effect on marine organisms. Total alkalinity (AT) is one of the most commonly used parameters to characterize the marine CO2 system, but compared to the other measureable CO2 system variables, the measurement of AT necessarily titrates all bases present in seawater, and not just those of interest (carbonate and bicarbonate). While the majority of non-CO2 bases in seawater are identified and easily accounted for, there is extensive evidence for unidentified bases (excess alkalinity, AX) at levels exceeding the uncertainty of the AT measurement. Failure to account for these unidentified bases in a quantitatively meaningful way will lead to errors in interpreting AT as a CO2 system variable. Few methods estimating AX are presented with uncertainty estimates, and none have so far dealt with the uncertainty in the total boron content (BT), the second largest acid-base system in the ocean following the CO2 system. I will describe an open-cell titration approach that can, together with equilibrium modelling, quantify AX as a combination of one or several acid-base systems with apparent total concentration(s) (XT) and acid dissociation constant(s) (KX). The method includes titration of a seawater sample with a strong acid to estimate AT, followed by quantitative removal of CO2. The sample is then titrated with a strong base, and data from this “back-titration” can be used to quantify AX. An uncertainty assessment is provided that includes systematic errors and effects of CO2 contamination, supplemented by colorimetric measurements of BT. This work provides realistic uncertainties of AT measurements made in areas suspected of having a high presence of unidentified acid-base systems, thus contributing to a more accurate assessment of changes in marine CO2 chemistry and speciation in many environments.

Turbulent flow in surface layer, the top few meters in the ocean, tends to exhibit consistent and repeatable characteristics, and useful empirical laws can be formed to shed light on turbulence parameterization. Here, Monin-Obukhov similarity theory (MOST), developed for the atmospheric surface layer, is examined for the ocean surface layer. Using data collected from several moored surface flux buoys, we consider the relationship between surface fluxes and subsurface temperature gradients under a wide range of stability conditions. Large deviations from MOST predictions are found in our analysis, with smaller observed temperature gradients under both stable and unstable forcing. We hypothesize that these are attributed to the presence of Langmuir structures through interaction of Eulerian current with Stokes drift, which is not included in traditional Monin-Obukhov formulation. We examine the ability of recent Langmuir turbulence closure models to predict the observed differences.

The assessment of planktonic organisms is a prevailing task in marine ecology and oceanography as planktons form the principal food source for consumers at higher trophic levels. Reliable estimates on the production at the lowermost trophic levels are thus an integral part for the management of marine ecosystems. Traditional plankton sampling and analysis are limited in their spatial and temporal context of the organisms’ environment, which are often critical clues to a biologist for its habitation. In addition, ship-based sampling as described leads to a high level of uncertainty in the estimation, since point measurements that are intermittent in space and time are used (Reid et al 2003; Lermusiaux 2006; Vannier 2018). A disruptive change in approach to tackle this problem is currently taking place, enabled by the use of autonomous robots (Henthorn et al 2006) and augmented by visual sensing for real-time analysis (Ohman et al 2019; AILARON 2019). Approaches providing taxonomy estimates from time-series image analysis (Sosik and Olson 2008) or via computer simulations (Roberts and Jaffe 2007), with the recent advances in deep learning, enabled by the computational power of multicore CPUs and GPUs, made possible processing and classification of large datasets while learning higher level representations. Enhanced traditional machine learning methods are driven by multiple kernel learning, where general features are combined with robust features and new types from multiple views are defined in order to generate multiple classifiers (Py et al 2016; Dai et al 2016; Lee et al 2016; Moniruzzaman et al 2017). In this paper, we present recent DL methods for microscopic organisms’ identification and classification. A proposed DL architecture (cf. figure 2) reported an accuracy of 95% as opposed to (90% - 93% cf. table 2) achieved by the state-of-the-art networks: ZooplanktoNet, VGGNet, AlexNet, ResNet, and GoogleNet, while training over a labeled dataset of extracted objects from images of plankton organisms captured in-situ (cf. table 1). COAPNet is embedded into a light-weight autonomous vehicle (LAUV) for real-time in-situ plankton taxa identification and classification. The LAUV in turn utilizes the feedback from the image analysis to constantly update a probability density map that further enables an adaptive sampling process.

Zooplankton is a key ecological component of aquatic ecosystems. Studying and monitoring the spatial distribution and temporal variability of zooplankton is vital to understanding their community composition and its relation to climate change. Manual methods for analysis are time-consuming and have limitations on the ecological studies of these organisms. Real-time, fast and accurate in situ zooplankton detection and classification remains a challenge. Currently, research focuses on automating zooplankton image classification using handcrafted computer vision techniques and neural network based approaches [1,2]. Most recent approaches adopt deep learning techniques for identification and classification [3,4]. In this paper, we propose the use of Fast Region-based Convolutional Neural Network (Faster R-CNN) for fast and accurate in situ detection and classification of zooplankton groups in underwater images. Faster R-CNN is a region-based object detection framework which combines region proposal and classification in a unified network [5]. Indeed, end-to-end learning reduces overall training time and increases the accuracy of the network. Faster R-CNN has shown state-of-the-art performance on benchmarks such as ImageNet and VOC [6,7]. We perform the experiments over ZooScan, Kaggle, WHOI-Plankton datasets [8,9,10]. We evaluate the performance of our proposed approach of in situ zooplankton identification and classification in terms of detection speed and mean Average Precision (mAP). In addition, we compare the performance of the proposed method with popular detectors such as Single Shot Multibox Detector (SSD) and You Only Look Once (YOLOv3) to demonstrate its efficacy at processing noisy underwater images [11,12]. Results of our evaluation recommend the use of Faster R-CNN for real-time zooplankton image analysis. The ultimate goal of this work is to automate the current manual process exerted in the lab while improving the accuracy and processing speed of an otherwise time-consuming task for marine biologists.

Multi-frequency acoustic backscatter measurement can be used to observe spatial profiles of suspended sediment. The use of multiple frequencies helps to resolve mean particle size by exploiting the frequency-dependent relationship between scattering intensity and particle size. The AQUAscat acoustic backscatter profiler uses this principle to estimate mean particle size and concentration profiles with spatial resolution between 2.5 mm and 40 mm. The instrument is usually configured to acquire profiles of backscatter amplitude. However, an infrequently used setting on the standard instrument provides direct access to the quadrature sampled backscatter data stream, from which amplitude is normally calculated. By using the in-phase and quadrature sample data, the backscatter phase can also be calculated. The rate of phase change between profiles can then be related to the along-beam velocity of the scatterers. For a vertical beam, in the absence of vertical water motion, this is the settling velocity. This paper evaluates datasets and data processing approaches for estimating particle settling velocity. The experimental data is acquired with various types of laboratory generated suspensions, including glass spheres, sands, and flocculating mud. Besides extracting settling velocity data, the processing aim is to enhance the quality of acoustic backscatter data analysis.

In 2012, Aquatec launched an equipment award scheme for postgraduate students and early career scientists. Successful recipients with limited budgets gain free access to high quality subsea instrumentation for a laboratory or ‘eld campaign of up to three months, plus a travel grant to allow them to present their work at a conference. So far there have been 11 successful awardees who have applied from or deployed instruments in 13 countries spanning ’ve continents, in *umes, lakes, rivers, and coastal seas. In this paper, we present an overview of the most successful award projects. We also evaluate the impact of the scheme on the award recipients’ chosen project work and how it in*uenced their future career. The evaluation draws on analysis of the recipient study reports and the use of questionnaires and interviews. The scheme has also suffered the occasional setback. We attempt to identify some of the potential pitfalls of such a program, and highlight the key factors that lead not only to the best student experience, but also a positive outcome for the awarding company

The Amazon River discharges more than 200,000 m3 s-1 into the Western Tropical Atlantic Ocean from May to June. The low salinity surface plume extends more than 1800 km from the mouth and covers an area greater than 1 million square kilometers. We hypothesize that the plume exhibits distinct microbial community assemblages driven by plume age, nutrient supply, and light availability. We collected samples for nutrients and flow-cytometry measurements to investigate the spatial variability of the cyanobacteria Prochlorococcus spp. and Synechococcus spp., picoeukaryotes, and heterotrophic bacteria. Overall the surface salinity of the water we sampled ranged from 15.5 ppt at the southernmost station to 36.3 ppt in the open ocean station. The surface nitrate and soluble reactive phosphorus concentrations ranged from below detection limit to 3.3 µM and 2 µM, respectively. Generally, in the freshest surface plume waters (15-28 ppt) we found the highest abundances of Synechococcus spp., picoeukaryotes, and hetrotrophic bacteria with little or no Prochlorococcus spp. In the transition of surface salinities from 28 ppt to 32 ppt, a population of Prochlorococcus spp. began to form below the surface plume while Synechococcus spp. abundances at the surface remained unchanged and picoeukaryotes, and heterotrophic bacteria abundances decreased. As the surface salinity climbed over 32 ppt, the Prochlorococcus spp. abundance was uniformly high throughout the euphotic zone. On the other hand, as surface salinities increased over 32 ppt Synechococcus spp. abundances at the surface gradually decreased, while picoeukaryote and hetrotrophic bacterial abundances remained constant. We will discuss changes in the microbial community composition as a function of nutrient and light availability, as well as plume age in the Amazon Plume-Ocean continuum in both surface and deep chlorophyll maximum assemblages.

We report the design and results from a series of recent cruises using a fast vertical profiling autonomous underwater vehicle called Clio. Clio has been designed specifically to complement conventional wire-based sampling techniques—to improve ship-time utilization by operating simultaneously and independently of conventional techniques, and thereby to cost-effectively improve the understanding of marine microorganism ecosystem dynamics on a global scale. Life processes and ocean chemistry are linked: ocean chemistry places constraints on marine metabolic processes, and life processes alter the speciation, chemical associations, and water-column residence time of seawater constituents. Advances in sequencing technology and in situ preservation have made it possible to study the genomics (DNA), transcriptomics (RNA), proteomics (proteins and enzymes), metabolomics (lipids and other metabolites), and metallomics (metals), associated with marine microorganisms; however, at present these techniques require sample collection. For this purpose, Clio’s primary payload consists of two Suspended-Particle Rosette (SUPR) multi-samplers capable of returning up to 20 sets of filtered samples and filtrate per dive, and filtering up to 280 L of water per sample. Clio hosts additional profiling sensors consisting presently of a Seabird Electronics CTD, WET Labs combined chlorophyll and backscatter fluorimeter, and C-Star transmissometer. Since sea trials in 2017 Clio has participated in 5 cruises including most recently a section cruise between Bermuda and Woods Hole in June of 2019. On that cruise Clio executed a total of 9 nightly dives 12-16 hours in length and filtered a total of 20,878 L of seawater. The vehicle holds depth to a precision of better than 5 cm, is rated to 6000 m (4100 m maximum depth to date) and transits the water column at 45 m/min. Clio has demonstrated consistent reliable performance in its intended role; however, opportunities exist to further exploit its capabilities. Clio’s last two dives included autonomous data-driven selection of sample depths to better capture the deep chlorophyll maximum. Clio’s large payload capacity (10s W, 10s kg) could host novel samplers as well as in situ sample processors and other profiling instruments.