ALBERT

Description: Particle size distribution data was collected during multiple cruises globally with several regularly intercalibrated Underwater Vision Profilers, Version 5 (UVP5; Picheral et al 2010). During the respective cruises, the UVP5 was mounted on the CTD-Rosette or as a standalone instrument and deployed in vertical mode. The UVP5 takes pictures of an illuminated watervolume of about 1 Liter every few milliseconds. Imaged items are counted, their size measured and abundance and biovolume of the particles is calculated. For different size bins, this information is summarized in the columns "Particle concentration" and "Particle biovolume". For further details please refer to Kiko et al. (in prep.) "A global marine particle size distribution dataset obtained with the Underwater Vision Profiler 5".

Description: In this paper we review the technologies available to make globally quantitative observations of particles in general—and plankton in particular—in the world oceans, and for sizes varying from sub-microns to centimeters. Some of these technologies have been available for years while others have only recently emerged. Use of these technologies is critical to improve understanding of the processes that control abundances, distributions and composition of plankton, provide data necessary to constrain and improve ecosystem and biogeochemical models, and forecast changes in marine ecosystems in light of climate change. In this paper we begin by providing the motivation for plankton observations, quantification and diversity qualification on a global scale. We then expand on the state-of-the-art, detailing a variety of relevant and (mostly) mature technologies and measurements, including bulk measurements of plankton, pigment composition, uses of genomic, optical and acoustical methods as well as analysis using particle counters, flow cytometers and quantitative imaging devices. We follow by highlighting the requirements necessary for a plankton observing system, the approach to achieve it and associated challenges. We conclude with ranked action-item recommendations for the next 10 years to move toward our vision of a holistic ocean-wide plankton observing system. Particularly, we suggest to begin with a demonstration project on a GO-SHIP line and/or a long-term observation site and expand from there, ensuring that issues associated with methods, observation tools, data analysis, quality assessment and curation are addressed early in the implementation. Global coordination is key for the success of this vision and will bring new insights on processes associated with nutrient regeneration, ocean production, fisheries and carbon sequestration.

Description: Author Posting. © John Wiley & Sons, 2009. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Marine Ecology 30 (2009): 133-150, doi:10.1111/j.1439-0485.2009.00288.x.

Description: Climate change will alter turbulence intensity, motivating greater attention to mechanisms of turbulence effects on organisms. Many analytic and analog models used to simulate and assess effects of turbulence on plankton rely on a one-dimensional simplification of the dissipative scales of turbulence, i.e., simple, steady, uniaxial shears, as produced in Couette vessels. There shear rates are constant and spatially uniform, and hence so is vorticity. Studies in such Couette flows have greatly informed, spotlighting stable orientations of nonspherical particles and predictable, periodic, rotational motions of steadily sheared particles in Jeffery orbits that steepen concentration gradients around nutrient-absorbing phytoplankton and other chemically (re)active particles. Over the last decade, however, turbulence research within fluid dynamics has focused on the structure of dissipative vortices in space and time and on spatially and temporally varying 2 vorticity fields in particular. Because steadily and spatially uniformly sheared flows are exceptional, so therefore are stable orientations for particles in turbulent flows. Vorticity gradients, finite net diffusion of vorticity and small radii of curvature of streamlines are ubiquitous features of turbulent vortices at dissipation scales that are explicitly excluded from simple, steady Couette flows. All of these flow components contribute instabilities that cause rotational motions of particles and so are important to simulate in future laboratory devices designed to assess effects of turbulence on nutrient uptake, particle coagulation and predatorprey encounter in the plankton. The Burgers vortex retains these signature features of turbulence and provides a simplified “cartoon” of vortex structure and dynamics that nevertheless obeys the Navier-Stokes equations. Moreover, this idealization closely resembles many dissipative vortices observed in both the laboratory and the field as well as in direct numerical simulations of turbulence. It is simple enough to allow both simulation in numerical models and fabrication of analog devices that selectively reproduce its features. Exercise of such numerical and analog models promises additional insights into mechanisms of turbulence effects on passive trajectories and local accumulations of both living and nonliving particles, into solute exchange with living and nonliving particles and into more subtle influences on sensory processes and swimming trajectories of plankton, including demersal organisms and settling larvae in turbulent bottom boundary layers. The literature on biological consequences of vortical turbulence has focused primarily on the smallest, Kolmogorov-scale vortices of length scale η. Theoretical dissipation spectra and direct numerical simulation, however, indicate that typical dissipative vortices with radii of 7η to 8η, peak azimuthal speeds of order 1 cm s-1 and lifetimes of order 10 s as a minimum (and much longer for moderate pelagic turbulence intensities) deserve new attention in studies of biological effects of turbulence.

Description: This research was supported by collaborative U.S. National Science Foundation grant (OCE- 0724744) to Jumars and Karp-Boss.

Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Chase, A. P., Boss, E. S., Haentjens, N., Culhane, E., Roesler, C., & Karp-Boss, L. Plankton imagery data inform satellite-based estimates of diatom carbon. Geophysical Research Letters, 49(13), (2022): e2022GL098076, https://doi.org/10.1029/2022GL098076.

Description: Estimating the biomass of phytoplankton communities via remote sensing is a key requirement for understanding global ocean ecosystems. Of particular interest is the carbon associated with diatoms given their unequivocal ecological and biogeochemical roles. Satellite-based algorithms often rely on accessory pigment proxies to define diatom biomass, despite a lack of validation against independent diatom biomass measurements. We used imaging-in-flow cytometry to quantify diatom carbon in the western North Atlantic, and compared results to those obtained from accessory pigment-based approximations. Based on this analysis, we offer a new empirical formula to estimate diatom carbon concentrations from chlorophyll a. Additionally, we developed a neural network model in which we integrated chlorophyll a and environmental information to estimate diatom carbon distributions in the western North Atlantic. The potential for improving satellite-based diatom carbon estimates by integrating environmental information into a model, compared to models that are based solely on chlorophyll a, is discussed.

Description: Funding for this work was provided by NASA grants #NNX15AE67G and #80NSSC20M0202. A. Chase is supported by a Washington Research Foundation Postdoctoral Fellowship.

Description: This technical manual guides the user through the process of creating a data table for the submission of taxonomic and morphological information for plankton and other particles from images to a repository. Guidance is provided to produce documentation that should accompany the submission of plankton and other particle data to a repository, describes data collection and processing techniques, and outlines the creation of a data file. Field names include scientificName that represents the lowest level taxonomic classification (e.g., genus if not certain of species, family if not certain of genus) and scientificNameID, the unique identifier from a reference database such as the World Register of Marine Species or AlgaeBase. The data table described here includes the field names associatedMedia, scientificName/ scientificNameID for both automated and manual identification, biovolume, area_cross_section, length_representation and width_representation. Additional steps that instruct the user on how to format their data for a submission to the Ocean Biodiversity Information System (OBIS) are also included. Examples of documentation and data files are provided for the user to follow. The documentation requirements and data table format are approved by both NASA’s SeaWiFS Bio-optical Archive and Storage System (SeaBASS) and the National Science Foundation’s Biological and Chemical Oceanography Data Management Office (BCO-DMO).

Description: This report was an outcome of a working group supported by the Ocean Carbon and Biogeochemistry (OCB) project office, which is funded by the US National Science Foundation (OCE1558412) and the National Aeronautics and Space Administration (NNX17AB17G). AN, SB, and CP conceived and drafted the document. IC, IST, JF and HS contributed to the main body of the document as well as the example files. All members of the working group contributed to the content of the document, including the conceptualization of the data table and metadata format. We would also like thank the external reviewers Cecile Rousseaux (NASA GSFC), Susanne Menden-Deuer (URI) Frank Muller-Karger (USF), and Abigail Benson (USGS) for their valuable feedback.

Description: EXport Processes in the Ocean from Remote Sensing (EXPORTS) is a large-scale NASA-led and NSF co-funded field campaign that will provide critical information for quantifying the export and fate of upper ocean net primary production (NPP) using satellite information and state of the art technology.

Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lombard, F., Boss, E., Waite, A. M., Vogt, M., Uitz, J., Stemmann, L., Sosik, H. M., Schulz, J., Romagnan, J., Picheral, M., Pearlman, J., Ohman, M. D., Niehoff, B., Moeller, K. M., Miloslavich, P., Lara-Lpez, A., Kudela, R., Lopes, R. M., Kiko, R., Karp-Boss, L., Jaffe, J. S., Iversen, M. H., Frisson, J., Fennel, K., Hauss, H., Guidi, L., Gorsky, G., Giering, S. L. C., Gaube, P., Gallager, S., Dubelaar, G., Cowen, R. K., Carlotti, F., Briseno-Avena, C., Berline, L., Benoit-Bird, K., Bax, N., Batten, S., Ayata, S. D., Artigas, L. F., & Appeltans, W. Globally consistent quantitative observations of planktonic ecosystems. Frontiers in Marine Science, 6, (2019):196, doi:10.3389/fmars.2019.00196.

Description: In this paper we review the technologies available to make globally quantitative observations of particles in general—and plankton in particular—in the world oceans, and for sizes varying from sub-microns to centimeters. Some of these technologies have been available for years while others have only recently emerged. Use of these technologies is critical to improve understanding of the processes that control abundances, distributions and composition of plankton, provide data necessary to constrain and improve ecosystem and biogeochemical models, and forecast changes in marine ecosystems in light of climate change. In this paper we begin by providing the motivation for plankton observations, quantification and diversity qualification on a global scale. We then expand on the state-of-the-art, detailing a variety of relevant and (mostly) mature technologies and measurements, including bulk measurements of plankton, pigment composition, uses of genomic, optical and acoustical methods as well as analysis using particle counters, flow cytometers and quantitative imaging devices. We follow by highlighting the requirements necessary for a plankton observing system, the approach to achieve it and associated challenges. We conclude with ranked action-item recommendations for the next 10 years to move toward our vision of a holistic ocean-wide plankton observing system. Particularly, we suggest to begin with a demonstration project on a GO-SHIP line and/or a long-term observation site and expand from there, ensuring that issues associated with methods, observation tools, data analysis, quality assessment and curation are addressed early in the implementation. Global coordination is key for the success of this vision and will bring new insights on processes associated with nutrient regeneration, ocean production, fisheries and carbon sequestration.

Description: Much of this manuscript flows from discussions of the authors with the members of SCOR working groups 150 (TOMCAT) and 154 (P-OBS) as well as discussions with the greater community in various GOOS workshops. We also thank Mike Sieracki, Cabell Davis, Daniele Iudicone, Eric Karsenti, Sebastien Colin, Colomban de Vargas, Ulf Riebesell, Fabrice Not, David Checkley, George Jackson, Cédric Guigand, Ed Urban, Frank Muller-Karger, Sanae Chiba and Daniel Dunn, who contributed to the initial abstracts to OceanObs'19. FL is supported by the Institut Universitaire de France. EB is supported by the NASA biology and biogeochemistry program. RKi and HH were supported by the German Science Foundation through the Collaborative Research Center 754 ‘Climate-Biogeochemistry Interactions in the Tropical Ocean’. SDA acknowledges the CNRS for her sabbatical year as visiting researcher at ISYEB on the use of genomics and next generation sequencing for plankton studies. HS acknowledges support from the Simons Foundation, the U.S. National Science Foundation, and the U.S. National Oceanic and Atmospheric Administration through the Cooperative Institute for the North Atlantic Region. FL and EB contribution was also inspired by their years of work within the Tara Expeditions initiative.