Ohman
Mark D.
Ohman
Mark D.
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ArticleMachine learning techniques to characterize functional traits of plankton from image data(Association for the Sciences of Limnology and Oceanography, 2022-06-30) Orenstein, Eric C. ; Ayata, Sakina Dorothée ; Maps, Frédéric ; Becker, Érica C. ; Benedetti, Fabio ; Biard, Tristan ; de Garidel-Thoron, Thibault ; Ellen, Jeffrey S. ; Ferrario, Filippo ; Giering, Sarah L. C. ; Guy-Haim, Tamar ; Hoebeke, Laura ; Iversen, Morten H. ; Kiørboe, Thomas ; Lalonde, Jean-François ; Lana, Arancha ; Laviale, Martin ; Lombard, Fabien ; Lorimer, Tom ; Martini, Séverine ; Meyer, Albin ; Möller, Klas O. ; Niehoff, Barbara ; Ohman, Mark D. ; Pradalier, Cédric ; Romagnan, Jean-Baptiste ; Schröder, Simon-Martin ; Sonnet, Virginie ; Sosik, Heidi M. ; Stemmann, Lars ; Stock, Michiel ; Terbiyik-Kurt, Tuba ; Valcárcel-Pérez, Nerea ; Vilgrain, Laure ; Wacquet, Guillaume ; Waite, Anya M. ; Irisson, Jean-OlivierPlankton imaging systems supported by automated classification and analysis have improved ecologists' ability to observe aquatic ecosystems. Today, we are on the cusp of reliably tracking plankton populations with a suite of lab-based and in situ tools, collecting imaging data at unprecedentedly fine spatial and temporal scales. But these data have potential well beyond examining the abundances of different taxa; the individual images themselves contain a wealth of information on functional traits. Here, we outline traits that could be measured from image data, suggest machine learning and computer vision approaches to extract functional trait information from the images, and discuss promising avenues for novel studies. The approaches we discuss are data agnostic and are broadly applicable to imagery of other aquatic or terrestrial organisms.
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DatasetJeDI: Jellyfish Database Initiative(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2015-03-09) Condon, Robert H. ; Lucas, Cathy H. ; Duarte, Carlos M. ; Pitt, Kylie A. ; Haddock, Steven H. D. ; Madin, Laurence P. ; Brodeur, Richard D. ; Sutherland, Kelly R. ; Mianzan, Hermes W. ; Purcell, Jennifer E. ; Decker, Mary Beth ; Uye, Shin-Ichi ; Malej, Alenka ; Bogeberg, Molly ; Everett, John T. ; Gibbons, Mark ; Gonzalez, H. ; Hay, S. ; Hensche, N. ; Hobson, R. J. ; Kingsford, Michael J. ; Kremer, P. ; Lehtiniemi, Maiju ; Ohman, Mark ; Rissik, D. ; Sheard, K. ; Suthers, Iain ; Coleman, N. ; Costello, John H. ; Gershwin, L. A. ; Graham, William M. ; Robinson, Kelly L. ; Richardson, T. M. ; Giesecke, R. ; Gorsky, Gabriel ; Greve, Wulf ; Halsband-Lenk, C. ; Hays, Graeme ; Hobson, V. ; Klein, David ; Lebrato, Mario ; Loveridge, Jan ; Martens, P. ; Milos, C. ; Perry, G. ; Stemmann, Lars ; Sullivan, Barbara ; Walker, T. ; Schildhauer, Mark ; Regetz, J.The Jellyfish Database Initiative (JeDI) is a scientifically-coordinated global database dedicated to gelatinous zooplankton (members of the Cnidaria, Ctenophora and Thaliacea) and associated environmental data. The database holds 476,000 quantitative, categorical, presence-absence and presence only records of gelatinous zooplankton spanning the past four centuries (1790-2011) assembled from a variety of published and unpublished sources. Gelatinous zooplankton data are reported to species level, where identified, but taxonomic information on phylum, family and order are reported for all records. Other auxiliary metadata, such as physical, environmental and biometric information relating to the gelatinous zooplankton metadata, are included with each respective entry. JeDI has been developed and designed as an open access research tool for the scientific community to quantitatively define the global baseline of gelatinous zooplankton populations and to describe long-term and large-scale trends in gelatinous zooplankton populations and blooms. It has also been constructed as a future repository of datasets, thus allowing retrospective analyses of the baseline and trends in global gelatinous zooplankton populations to be conducted in the future.
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ArticleGlobally consistent quantitative observations of planktonic ecosystems(Frontiers Media, 2019-04-25) Lombard, Fabien ; Boss, Emmanuel S. ; Waite, Anya M. ; Vogt, Meike ; Uitz, Julia ; Stemmann, Lars ; Sosik, Heidi M. ; Schulz, Jan ; Romagnan, Jean-Baptiste ; Picheral, Marc ; Pearlman, Jay ; Ohman, Mark D. ; Niehoff, Barbara ; Möller, Klas O. ; Miloslavich, Patricia ; Lara-Lpez, Ana ; Kudela, Raphael M. ; Lopes, Rubens M. ; Kiko, Rainer ; Karp-Boss, Lee ; Jaffe, Jules S. ; Iversen, Morten H. ; Irisson, Jean-Olivier ; Fennel, Katja ; Hauss, Helena ; Guidi, Lionel ; Gorsky, Gabriel ; Giering, Sarah L. C. ; Gaube, Peter ; Gallager, Scott M. ; Dubelaar, George ; Cowen, Robert K. ; Carlotti, François ; Briseño-Avena, Christian ; Berline, Leo ; Benoit-Bird, Kelly J. ; Bax, Nicholas ; Batten, Sonia ; Ayata, Sakina Dorothée ; Artigas, Luis Felipe ; Appeltans, WardIn 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.
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ArticleClimate impacts on zooplankton population dynamics in coastal marine ecosystems(The Oceanography Society, 2013-12) Batchelder, Harold P. ; Daly, Kendra L. ; Davis, Cabell S. ; Ji, Rubao ; Ohman, Mark D. ; Peterson, William T. ; Runge, Jeffrey A.The 20-year US GLOBEC (Global Ocean Ecosystem Dynamics) program examined zooplankton populations and their predators in four coastal marine ecosystems. Program scientists learned that environmental controls on zooplankton vital rates, especially the timing and magnitude of reproduction, growth, life-cycle progression, and mortality, determine species population dynamics, seasonal and spatial distributions, and abundances. Improved knowledge of spatial-temporal abundance and distribution of individual zooplankton taxa coupled with new information linking higher trophic level predators (salmon, cod, haddock, penguins, seals) to their prey yielded mechanistic descriptions of how climate variation impacts regionally important marine resources. Coupled ecological models driven by improved regional-scale climate scenario models developed during GLOBEC enable forecasts of plausible future conditions in coastal ecosystems, and will aid and inform decision makers and communities as they assess, respond, and adapt to the effects of environmental change. Multi-region synthesis revealed that conditions in winter, before upwelling, or seasonal stratification, or ice melt (depending on region) had significant and important effects that primed the systems for greater zooplankton population abundance and productivity the following spring-summer, with effects that propagated to higher trophic levels.
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ArticleTime lags: insights from the U.S. Long Term Ecological Research Network(Ecological Society of America, 2021-05-17) Rastetter, Edward B. ; Ohman, Mark D. ; Elliott, Katherine J. ; Rehage, Jennifer S. ; Rivera-Monroy, Victor H. ; Boucek, Ross E. ; Castaneda-Moya, Edward ; Danielson, Tess M. ; Gough, Laura ; Groffman, Peter M. ; Jackson, C. Rhett ; Ford Miniat, ChelcyEcosystems across the United States are changing in complex ways that are difficult to predict. Coordinated long-term research and analysis are required to assess how these changes will affect a diverse array of ecosystem services. This paper is part of a series that is a product of a synthesis effort of the U.S. National Science Foundation’s Long Term Ecological Research (LTER) network. This effort revealed that each LTER site had at least one compelling scientific case study about “what their site would look like” in 50 or 100 yr. As the site results were prepared, themes emerged, and the case studies were grouped into separate papers along five themes: state change, connectivity, resilience, time lags, and cascading effects and compiled into this special issue. This paper addresses the time lags theme with five examples from diverse biomes including tundra (Arctic), coastal upwelling (California Current Ecosystem), montane forests (Coweeta), and Everglades freshwater and coastal wetlands (Florida Coastal Everglades) LTER sites. Its objective is to demonstrate the importance of different types of time lags, in different kinds of ecosystems, as drivers of ecosystem structure and function and how these can effectively be addressed with long-term studies. The concept that slow, interactive, compounded changes can have dramatic effects on ecosystem structure, function, services, and future scenarios is apparent in many systems, but they are difficult to quantify and predict. The case studies presented here illustrate the expanding scope of thinking about time lags within the LTER network and beyond. Specifically, they examine what variables are best indicators of lagged changes in arctic tundra, how progressive ocean warming can have profound effects on zooplankton and phytoplankton in waters off the California coast, how a series of species changes over many decades can affect Eastern deciduous forests, and how infrequent, extreme cold spells and storms can have enduring effects on fish populations and wetland vegetation along the Southeast coast and the Gulf of Mexico. The case studies highlight the need for a diverse set of LTER (and other research networks) sites to sort out the multiple components of time lag effects in ecosystems.
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ArticleRelative exposure to microplastics and prey for a pelagic forage fish(IOP Publishing, 2022-06-07) Chavarry, Julia M. ; Law, Kara L. ; Barton, Andrew D. ; Bowlin, Noelle M. ; Ohman, Mark D. ; Choy, C. AnelaIn the global ocean, more than 380 species are known to ingest microplastics (plastic particles less than 5 mm in size), including mid-trophic forage fishes central to pelagic food webs. Trophic pathways that bioaccumulate microplastics in marine food webs remain unclear. We assess the potential for the trophic transfer of microplastics through forage fishes, which are prey for diverse predators including commercial and protected species. Here, we quantify Northern Anchovy (Engraulis mordax) exposure to microplastics relative to their natural zooplankton prey, across their vertical habitat. Microplastic and zooplankton samples were collected from the California Current Ecosystem in 2006 and 2007. We estimated the abundance of microplastics beyond the sampled size range but within anchovy feeding size ranges using global microplastic size distributions. Depth-integrated microplastics (0–30 m depth) were estimated using a depth decay model, accounting for the effects of wind-driven vertical mixing on buoyant microplastics. In this coastal upwelling biome, the median relative exposure for an anchovy that consumed prey 0.287–5 mm in size was 1 microplastic particle for every 3399 zooplankton individuals. Microplastic exposure varied, peaking within offshore habitats, during the winter, and during the day. Maximum exposure to microplastic particles relative to zooplankton prey was higher for juvenile (1:23) than adult (1:33) anchovy due to growth-associated differences in anchovy feeding. Overall, microplastic particles constituted fewer than 5% of prey-sized items available to anchovy. Microplastic exposure is likely to increase for forage fishes in the global ocean alongside declines in primary productivity, and with increased water column stratification and microplastic pollution.