1
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Tapics T, Sosik HM, Huot Y. A discrete, stochastic model of colonial phytoplankton population size structure: Development and application to in situ imaging-in-flow cytometer observations of Dinobryon. J Phycol 2023; 59:1005-1024. [PMID: 37497766 DOI: 10.1111/jpy.13357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 04/03/2023] [Accepted: 05/20/2023] [Indexed: 07/28/2023]
Abstract
The scientific community lacks models for the dynamic changes in population size structure that occur in colonial phytoplankton. This is surprising, as size is a key trait affecting many aspects of phytoplankton ecology, and colonial forms are very common. We aim to fill this gap with a new discrete, stochastic model of dynamic changes in phytoplankton colonies' population size structure. We use the colonial phytoplankton Dinobryon as a proof-of-concept organism. The model includes four stochastic functions-division, stomatocyst production, colony breakage, and colony loss-to determine Dinobryon population size structure and populations counts. Although the functions presented here are tailored to Dinobryon, the model is readily adaptable to represent other colonial taxa. We demonstrate how fitting our model to in situ observations of colony population size structure can provide a powerful approach to explore colony size dynamics. Here, we have (1) collected high-frequency in situ observations of Dinobryon in Lac (Lake) Montjoie (Quebec, Canada) in 2013 with a moored Imaging FlowCytobot (IFCB) and (2) fit the model to those observations with a genetic algorithm solver that extracts parameter estimates for each of the four stochastic functions. As an example of the power of this model-data integration, we also highlight ecological insights into Dinobryon colony size and stomatocyst production. The Dinobryon population was enriched in larger, flagellate-rich colonies near bloom initiation and shifted to smaller and emptier colonies toward bloom decline.
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Affiliation(s)
- Tara Tapics
- Département de géomatique appliquée, Faculté des lettres et sciences humaines, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Heidi M Sosik
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Yannick Huot
- Département de géomatique appliquée, Faculté des lettres et sciences humaines, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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2
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Zheng B, Lucas AJ, Franks PJS, Schlosser TL, Anderson CR, Send U, Davis K, Barton AD, Sosik HM. Dinoflagellate vertical migration fuels an intense red tide. Proc Natl Acad Sci U S A 2023; 120:e2304590120. [PMID: 37639597 PMCID: PMC10483641 DOI: 10.1073/pnas.2304590120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/20/2023] [Indexed: 08/31/2023] Open
Abstract
Harmful algal blooms (HABs) are increasing globally, causing economic, human health, and ecosystem harm. In spite of the frequent occurrence of HABs, the mechanisms responsible for their exceptionally high biomass remain imperfectly understood. A 50-y-old hypothesis posits that some dense blooms derive from dinoflagellate motility: organisms swim upward during the day to photosynthesize and downward at night to access deep nutrients. This allows dinoflagellates to outgrow their nonmotile competitors. We tested this hypothesis with in situ data from an autonomous, ocean-wave-powered vertical profiling system. We showed that the dinoflagellate Lingulodinium polyedra's vertical migration led to depletion of deep nitrate during a 2020 red tide HAB event. Downward migration began at dusk, with the maximum migration depth determined by local nitrate concentrations. Losses of nitrate at depth were balanced by proportional increases in phytoplankton chlorophyll concentrations and suspended particle load, conclusively linking vertical migration to the access and assimilation of deep nitrate in the ocean environment. Vertical migration during the red tide created anomalous biogeochemical conditions compared to 70 y of climatological data, demonstrating the capacity of these events to temporarily reshape the coastal ocean's ecosystem and biogeochemistry. Advances in the understanding of the physiological, behavioral, and metabolic dynamics of HAB-forming organisms from cutting-edge observational techniques will improve our ability to forecast HABs and mitigate their consequences in the future.
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Affiliation(s)
- Bofu Zheng
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA92093
| | - Andrew J. Lucas
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA92093
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA92093
| | - Peter J. S. Franks
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA92093
| | - Tamara L. Schlosser
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA92093
| | - Clarissa R. Anderson
- Southern California Coastal Ocean Observing System, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA92093
| | - Uwe Send
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA92093
| | - Kristen Davis
- Department of Earth System Science, University of California, Irvine, CA92697
- Department of Civil and Environmental Engineering, University of California, Irvine, CA92697
| | - Andrew D. Barton
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA92093
- Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, CA92093
| | - Heidi M. Sosik
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA02543
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3
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Catlett D, Peacock EE, Crockford ET, Futrelle J, Batchelder S, Stevens BLF, Gast RJ, Zhang WG, Sosik HM. Temperature dependence of parasitoid infection and abundance of a diatom revealed by automated imaging and classification. Proc Natl Acad Sci U S A 2023; 120:e2303356120. [PMID: 37399413 PMCID: PMC10334780 DOI: 10.1073/pnas.2303356120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/19/2023] [Indexed: 07/05/2023] Open
Abstract
Diatoms are a group of phytoplankton that contribute disproportionately to global primary production. Traditional paradigms that suggest diatoms are consumed primarily by larger zooplankton are challenged by sporadic parasitic "epidemics" within diatom populations. However, our understanding of diatom parasitism is limited by difficulties in quantifying these interactions. Here, we observe the dynamics of Cryothecomonas aestivalis (a protist) infection of an important diatom on the Northeast U.S. Shelf (NES), Guinardia delicatula, with a combination of automated imaging-in-flow cytometry and a convolutional neural network image classifier. Application of the classifier to >1 billion images from a nearshore time series and >20 survey cruises across the broader NES reveals the spatiotemporal gradients and temperature dependence of G. delicatula abundance and infection dynamics. Suppression of parasitoid infection at temperatures <4 °C drives annual cycles in both G. delicatula infection and abundance, with an annual maximum in infection observed in the fall-winter preceding an annual maximum in host abundance in the winter-spring. This annual cycle likely varies spatially across the NES in response to variable annual cycles in water temperature. We show that infection remains suppressed for ~2 mo following cold periods, possibly due to temperature-induced local extinctions of the C. aestivalis strain(s) that infect G. delicatula. These findings have implications for predicting impacts of a warming NES surface ocean on G. delicatula abundance and infection dynamics and demonstrate the potential of automated plankton imaging and classification to quantify phytoplankton parasitism in nature across unprecedented spatiotemporal scales.
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Affiliation(s)
- Dylan Catlett
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA02543
| | - Emily E. Peacock
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA02543
| | - E. Taylor Crockford
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA02543
| | - Joe Futrelle
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA02543
| | - Sidney Batchelder
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA02543
| | | | - Rebecca J. Gast
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA02543
| | - Weifeng G. Zhang
- Department of Applied Ocean Physics and Engineering, Woods Hole Oceanographic Institution, Woods Hole, MA02543
| | - Heidi M. Sosik
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA02543
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4
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Archibald KM, Sosik HM, Moeller HV, Neubert MG. Predator switching strength controls stability in diamond-shaped food web models. J Theor Biol 2023; 570:111536. [PMID: 37201720 DOI: 10.1016/j.jtbi.2023.111536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/27/2023] [Accepted: 05/11/2023] [Indexed: 05/20/2023]
Abstract
In food web models that include more than one prey type for a single predator, it is common for the predator's functional response to include some form of switching-preferential consumption of more abundant prey types. Predator switching promotes coexistence among competing prey types and increases diversity in the prey community. Here, we show how the dynamics of a diamond-shaped food web model of a marine plankton community are sensitive to a parameter that sets the strength of predator switching. Stronger switching destabilizes the model's coexistence equilibrium and leads to the appearance of limit cycles. Stronger switching also increases the evenness of the asymptotic prey community and promotes synchrony in the dynamics of disparate prey types. Given the dependence of model behavior on the strength of predator switching, it is important that modelers carefully consider the parameterization of functional responses that include switching.
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Affiliation(s)
- Kevin M Archibald
- University of California Santa Barbara, Santa Barbara, CA, USA; Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
| | - Heidi M Sosik
- Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Holly V Moeller
- University of California Santa Barbara, Santa Barbara, CA, USA
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5
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Ducklow H, Cimino M, Dunton KH, Fraser WR, Hopcroft RR, Ji R, Miller AJ, Ohman MD, Sosik HM. Marine Pelagic Ecosystem Responses to Climate Variability and Change. Bioscience 2022. [DOI: 10.1093/biosci/biac050] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
abstract
The marine coastal region makes up just 10% of the total area of the global ocean but contributes nearly 20% of its total primary production and over 80% of fisheries landings. Unicellular phytoplankton dominate primary production. Climate variability has had impacts on various marine ecosystems, but most sites are just approaching the age at which ecological responses to longer term, unidirectional climate trends might be distinguished. All five marine pelagic sites in the US Long Term Ecological Research (LTER) network are experiencing warming trends in surface air temperature. The marine physical system is responding at all sites with increasing mixed layer temperatures and decreasing depth and with declining sea ice cover at the two polar sites. Their ecological responses are more varied. Some sites show multiple population or ecosystem changes, whereas, at others, changes have not been detected, either because more time is needed or because they are not being measured.
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Affiliation(s)
- Hugh Ducklow
- Columbia University , New York, New York, United States
| | - Megan Cimino
- University of California Santa Cruz , Santa Cruz, California, United States
| | - Kenneth H Dunton
- University of Texas, Port Aransas , Port Aransas, Texas, United States
| | - William R Fraser
- Polar Oceans Research Group, part of the Holtzman Wildlife Foundation , Farmington Mills, Michigan, United States
| | | | - Rubao Ji
- Woods Hole Oceanographic Institution , Woods Hole, Massachusetts, United States
| | - Arthur J Miller
- Scripps Institution of Oceanography , La Jolla, California, United States
| | - Mark D Ohman
- Scripps Institution of Oceanography , La Jolla, California, United States
| | - Heidi M Sosik
- Woods Hole Oceanographic Institution , Woods Hole, Massachusetts, United States
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6
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Orenstein EC, Ayata S, Maps F, Becker ÉC, Benedetti F, Biard T, de Garidel‐Thoron T, Ellen JS, Ferrario F, Giering SLC, Guy‐Haim T, Hoebeke L, Iversen MH, Kiørboe T, Lalonde J, Lana A, Laviale M, Lombard F, Lorimer T, Martini S, Meyer A, Möller KO, Niehoff B, Ohman MD, Pradalier C, Romagnan J, Schröder S, Sonnet V, Sosik HM, Stemmann LS, Stock M, Terbiyik‐Kurt T, Valcárcel‐Pérez N, Vilgrain L, Wacquet G, Waite AM, Irisson J. Machine learning techniques to characterize functional traits of plankton from image data. Limnol Oceanogr 2022; 67:1647-1669. [PMID: 36247386 PMCID: PMC9543351 DOI: 10.1002/lno.12101] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 04/21/2022] [Accepted: 04/27/2022] [Indexed: 06/16/2023]
Abstract
Plankton 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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Affiliation(s)
- Eric C. Orenstein
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de VillefrancheVillefranche‐sur‐MerFrance
| | - Sakina‐Dorothée Ayata
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de VillefrancheVillefranche‐sur‐MerFrance
- Sorbonne Université, Laboratoire d'Océanographie et du Climat, Institut Pierre Simon Laplace (LOCEAN‐IPSL, SU/CNRS/IRD/MNHN)ParisFrance
| | - Frédéric Maps
- Département de BiologieUniversité LavalQuébecCanada
- Takuvik Joint International Laboratory Université Laval‐CNRS (UMI 3376), Québec‐Océan, Université LavalQuébecCanada
| | - Érica C. Becker
- Universidade Federal de Santa Catarina (UFSC)FlorianópolisSanta CatarinaBrazil
| | - Fabio Benedetti
- ETH ZürichInstitute of Biogeochemistry and Pollutant DynamicsZürichSwitzerland
| | - Tristan Biard
- Laboratoire d'Océanologie et de GéosciencesUniversité du Littoral Côte d'Opale, Université de Lille, CNRS, UMR 8187WimereuxFrance
| | | | - Jeffrey S. Ellen
- Scripps Institution of Oceanography, University of California San DiegoLa JollaCalifornia
| | - Filippo Ferrario
- Département de BiologieUniversité LavalQuébecCanada
- Takuvik Joint International Laboratory Université Laval‐CNRS (UMI 3376), Québec‐Océan, Université LavalQuébecCanada
- Department of Fisheries and OceansMaurice Lamontagne InstituteMont‐JoliQuébecCanada
| | | | - Tamar Guy‐Haim
- National Institute of Oceanography, Israel Oceanographic and Limnological ResearchHaifaIsrael
| | - Laura Hoebeke
- KERMIT, Department of Data Analysis and Mathematical ModellingGhent UniversityGhentBelgium
| | | | - Thomas Kiørboe
- Centre for Ocean Life, DTU‐AquaTechnical University of DenmarkKongens LyngbyDenmark
| | | | - Arancha Lana
- Institut Mediterrani d'Estudis Avançats (IMEDEA, UIB‐CSIC)Balearic IslandsSpain
| | | | - Fabien Lombard
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de VillefrancheVillefranche‐sur‐MerFrance
| | | | - Séverine Martini
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UMMarseilleFrance
| | - Albin Meyer
- Université de Lorraine, CNRS, LIECMetzFrance
| | - Klas Ove Möller
- Helmholtz‐Zentrum HereonInstitute of Carbon CycleGeesthachtGermany
| | - Barbara Niehoff
- Alfred Wegener Institute for Polar and Marine ResearchBremerhavenGermany
| | - Mark D. Ohman
- Scripps Institution of Oceanography, University of California San DiegoLa JollaCalifornia
| | | | - Jean‐Baptiste Romagnan
- IFREMER, Centre Atlantique, Laboratoire Ecologie et Modèles pour l'Halieutique (EMH)Unité HALGO, UMR DECODNantesFrance
| | | | - Virginie Sonnet
- Graduate School of OceanographyUniversity of Rhode IslandNarragansettRhode Island
| | - Heidi M. Sosik
- Woods Hole Oceanographic InstitutionWoods HoleMassachusetts
| | - Lars S. Stemmann
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de VillefrancheVillefranche‐sur‐MerFrance
| | - Michiel Stock
- KERMIT, Department of Data Analysis and Mathematical ModellingGhent UniversityGhentBelgium
| | - Tuba Terbiyik‐Kurt
- Department of Basic SciencesCukurova University, Faculty of FisheriesAdanaTurkey
| | | | - Laure Vilgrain
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de VillefrancheVillefranche‐sur‐MerFrance
| | | | - Anya M. Waite
- Ocean Frontier Institute, Dalhousie UniversityHalifaxNova ScotiaCanada
| | - Jean‐Olivier Irisson
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de VillefrancheVillefranche‐sur‐MerFrance
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7
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Hunter-Cevera KR, Hamilton BR, Neubert MG, Sosik HM. Seasonal environmental variability drives microdiversity within a coastal Synechococcus population. Environ Microbiol 2021; 23:4689-4705. [PMID: 34245073 PMCID: PMC8456951 DOI: 10.1111/1462-2920.15666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 04/27/2021] [Accepted: 07/07/2021] [Indexed: 11/29/2022]
Abstract
Marine microbes often show a high degree of physiological or ecological diversity below the species level. This microdiversity raises questions about the processes that drive diversification and permit coexistence of diverse yet closely related marine microbes, especially given the theoretical efficiency of competitive exclusion. Here, we provide insight with an 8‐year time series of diversity within Synechococcus, a widespread and important marine picophytoplankter. The population of Synechococcus on the Northeast U.S. Shelf is comprised of six main types, each of which displays a distinct and consistent seasonal pattern. With compositional data analysis, we show that these patterns can be reproduced with a simple model that couples differential responses to temperature and light with the seasonal cycle of the physical environment. These observations support the hypothesis that temporal variability in environmental factors can maintain microdiversity in marine microbial populations. We also identify how seasonal diversity patterns directly determine overarching Synechococcus population abundance features.
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Affiliation(s)
- Kristen R Hunter-Cevera
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA.,Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Bryan R Hamilton
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Michael G Neubert
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Heidi M Sosik
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
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8
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Fowler BL, Neubert MG, Hunter-Cevera KR, Olson RJ, Shalapyonok A, Solow AR, Sosik HM. Dynamics and functional diversity of the smallest phytoplankton on the Northeast US Shelf. Proc Natl Acad Sci U S A 2020; 117:12215-12221. [PMID: 32414929 PMCID: PMC7275697 DOI: 10.1073/pnas.1918439117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Picophytoplankton are the most abundant primary producers in the ocean. Knowledge of their community dynamics is key to understanding their role in marine food webs and global biogeochemical cycles. To this end, we analyzed a 16-y time series of observations of a phytoplankton community at a nearshore site on the Northeast US Shelf. We used a size-structured population model to estimate in situ division rates for the picoeukaryote assemblage and compared the dynamics with those of the picocyanobacteria Synechococcus at the same location. We found that the picoeukaryotes divide at roughly twice the rate of the more abundant Synechococcus and are subject to greater loss rates (likely from viral lysis and zooplankton grazing). We describe the dynamics of these groups across short and long timescales and conclude that, despite their taxonomic differences, their populations respond similarly to changes in the biotic and abiotic environment. Both groups appear to be temperature limited in the spring and light limited in the fall and to experience greater mortality during the day than at night. Compared with Synechococcus, the picoeukaryotes are subject to greater top-down control and contribute more to the region's primary productivity than their standing stocks suggest.
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Affiliation(s)
- Bethany L Fowler
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543;
| | - Michael G Neubert
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543
- Marine Policy Center, Woods Hole Oceanographic Institution, Woods Hole, MA 02543
| | | | - Robert J Olson
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543
| | - Alexi Shalapyonok
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543
| | - Andrew R Solow
- Marine Policy Center, Woods Hole Oceanographic Institution, Woods Hole, MA 02543
| | - Heidi M Sosik
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543;
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9
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Hunter‐Cevera KR, Neubert MG, Olson RJ, Shalapyonok A, Solow AR, Sosik HM. Seasons of Syn. Limnol Oceanogr 2020; 65:1085-1102. [PMID: 32612307 PMCID: PMC7319482 DOI: 10.1002/lno.11374] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 09/17/2019] [Accepted: 09/30/2019] [Indexed: 06/11/2023]
Abstract
Synechococcus is a widespread and important marine primary producer. Time series provide critical information for identifying and understanding the factors that determine abundance patterns. Here, we present the results of analysis of a 16-yr hourly time series of Synechococcus at the Martha's Vineyard Coastal Observatory, obtained with an automated, in situ flow cytometer. We focus on understanding seasonal abundance patterns by examining relationships between cell division rate, loss rate, cellular properties (e.g., cell volume, phycoerythrin fluorescence), and environmental variables (e.g., temperature, light). We find that the drivers of cell division vary with season; cells are temperature-limited in winter and spring, but light-limited in the fall. Losses to the population also vary with season. Our results lead to testable hypotheses about Synechococcus ecophysiology and a working framework for understanding the seasonal controls of Synechococcus cell abundance in a temperate coastal system.
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Affiliation(s)
- Kristen R. Hunter‐Cevera
- Josephine Bay Paul CenterMarine Biological LaboratoryWoods HoleMassachusetts
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusetts
| | - Michael G. Neubert
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusetts
| | - Robert J. Olson
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusetts
| | - Alexi Shalapyonok
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusetts
| | - Andrew R. Solow
- Marine Policy CenterWoods Hole Oceanographic InstitutionWoods HoleMassachusetts
| | - Heidi M. Sosik
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusetts
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10
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Sathyendranath S, Brewin RJW, Brockmann C, Brotas V, Calton B, Chuprin A, Cipollini P, Couto AB, Dingle J, Doerffer R, Donlon C, Dowell M, Farman A, Grant M, Groom S, Horseman A, Jackson T, Krasemann H, Lavender S, Martinez-Vicente V, Mazeran C, Mélin F, Moore TS, Müller D, Regner P, Roy S, Steele CJ, Steinmetz F, Swinton J, Taberner M, Thompson A, Valente A, Zühlke M, Brando VE, Feng H, Feldman G, Franz BA, Frouin R, Gould RW, Hooker SB, Kahru M, Kratzer S, Mitchell BG, Muller-Karger FE, Sosik HM, Voss KJ, Werdell J, Platt T. An Ocean-Colour Time Series for Use in Climate Studies: The Experience of the Ocean-Colour Climate Change Initiative (OC-CCI). Sensors (Basel) 2019; 19:E4285. [PMID: 31623312 PMCID: PMC6806290 DOI: 10.3390/s19194285] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 09/15/2019] [Accepted: 09/17/2019] [Indexed: 11/17/2022]
Abstract
Ocean colour is recognised as an Essential Climate Variable (ECV) by the Global Climate Observing System (GCOS); and spectrally-resolved water-leaving radiances (or remote-sensing reflectances) in the visible domain, and chlorophyll-a concentration are identified as required ECV products. Time series of the products at the global scale and at high spatial resolution, derived from ocean-colour data, are key to studying the dynamics of phytoplankton at seasonal and inter-annual scales; their role in marine biogeochemistry; the global carbon cycle; the modulation of how phytoplankton distribute solar-induced heat in the upper layers of the ocean; and the response of the marine ecosystem to climate variability and change. However, generating a long time series of these products from ocean-colour data is not a trivial task: algorithms that are best suited for climate studies have to be selected from a number that are available for atmospheric correction of the satellite signal and for retrieval of chlorophyll-a concentration; since satellites have a finite life span, data from multiple sensors have to be merged to create a single time series, and any uncorrected inter-sensor biases could introduce artefacts in the series, e.g., different sensors monitor radiances at different wavebands such that producing a consistent time series of reflectances is not straightforward. Another requirement is that the products have to be validated against in situ observations. Furthermore, the uncertainties in the products have to be quantified, ideally on a pixel-by-pixel basis, to facilitate applications and interpretations that are consistent with the quality of the data. This paper outlines an approach that was adopted for generating an ocean-colour time series for climate studies, using data from the MERIS (MEdium spectral Resolution Imaging Spectrometer) sensor of the European Space Agency; the SeaWiFS (Sea-viewing Wide-Field-of-view Sensor) and MODIS-Aqua (Moderate-resolution Imaging Spectroradiometer-Aqua) sensors from the National Aeronautics and Space Administration (USA); and VIIRS (Visible and Infrared Imaging Radiometer Suite) from the National Oceanic and Atmospheric Administration (USA). The time series now covers the period from late 1997 to end of 2018. To ensure that the products meet, as well as possible, the requirements of the user community, marine-ecosystem modellers, and remote-sensing scientists were consulted at the outset on their immediate and longer-term requirements as well as on their expectations of ocean-colour data for use in climate research. Taking the user requirements into account, a series of objective criteria were established, against which available algorithms for processing ocean-colour data were evaluated and ranked. The algorithms that performed best with respect to the climate user requirements were selected to process data from the satellite sensors. Remote-sensing reflectance data from MODIS-Aqua, MERIS, and VIIRS were band-shifted to match the wavebands of SeaWiFS. Overlapping data were used to correct for mean biases between sensors at every pixel. The remote-sensing reflectance data derived from the sensors were merged, and the selected in-water algorithm was applied to the merged data to generate maps of chlorophyll concentration, inherent optical properties at SeaWiFS wavelengths, and the diffuse attenuation coefficient at 490 nm. The merged products were validated against in situ observations. The uncertainties established on the basis of comparisons with in situ data were combined with an optical classification of the remote-sensing reflectance data using a fuzzy-logic approach, and were used to generate uncertainties (root mean square difference and bias) for each product at each pixel.
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Affiliation(s)
- Shubha Sathyendranath
- National Centre for Earth Observation, Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK.
| | - Robert J W Brewin
- National Centre for Earth Observation, Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK.
| | - Carsten Brockmann
- Brockmann Consult, Max-Planck-Straße 2, D-21502 Geesthacht, Germany.
| | - Vanda Brotas
- Marine Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal.
| | - Ben Calton
- PML Applications Ltd, Prospect Place, Plymouth PL1 3DH, UK.
| | - Andrei Chuprin
- Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK.
| | - Paolo Cipollini
- Telespazio Vega UK for ESA Climate Office, European Space Agency/ECSAT, Harwell Campus OX11 0FD, UK.
| | - André B Couto
- Marine Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal.
| | - James Dingle
- Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK.
| | - Roland Doerffer
- Helmholtz-Zentrum Geesthacht, Zentrum für Material- und Küstenforschung GmbH, Max-Planck-Straße 1, D-21502 Geesthacht, Germany.
| | - Craig Donlon
- European Space Agency/ESTEC, Keplerlaan 1, 2201 AZ Noordwijk, The Netherlands.
| | - Mark Dowell
- European Commission, Joint Research Centre (JRC), Via Enrico Fermi, 2749, I-21027 Ispra, Italy.
| | - Alex Farman
- Telespazio VEGA UK Ltd., 350 Capability Green, Luton, Bedfordshire LU1 3LU, UK.
| | - Mike Grant
- Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK.
| | - Steve Groom
- Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK.
| | - Andrew Horseman
- Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK.
| | - Thomas Jackson
- Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK.
| | - Hajo Krasemann
- Helmholtz-Zentrum Geesthacht, Zentrum für Material- und Küstenforschung GmbH, Max-Planck-Straße 1, D-21502 Geesthacht, Germany.
| | - Samantha Lavender
- Telespazio VEGA UK Ltd., 350 Capability Green, Luton, Bedfordshire LU1 3LU, UK.
| | | | | | - Frédéric Mélin
- European Commission, Joint Research Centre (JRC), Via Enrico Fermi, 2749, I-21027 Ispra, Italy.
| | - Timothy S Moore
- Ocean Process Analysis Laboratory, Morse Hall, University of New Hampshire, Durham, NH 03824, USA.
| | - Dagmar Müller
- Brockmann Consult, Max-Planck-Straße 2, D-21502 Geesthacht, Germany.
- Helmholtz-Zentrum Geesthacht, Zentrum für Material- und Küstenforschung GmbH, Max-Planck-Straße 1, D-21502 Geesthacht, Germany.
| | - Peter Regner
- European Space Agency, ESRIN, Via Galileo Galilei, Casella Postale 64, 00044 Frascati (Roma), Italy.
| | - Shovonlal Roy
- Department of Geography and Environmental Sciences, University of Reading, Whiteknights, Reading RG6 6DW, UK.
| | - Chris J Steele
- Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK.
| | | | - John Swinton
- Telespazio VEGA UK Ltd., 350 Capability Green, Luton, Bedfordshire LU1 3LU, UK.
| | - Malcolm Taberner
- Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK.
| | - Adam Thompson
- Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK.
| | - André Valente
- Marine Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal.
| | - Marco Zühlke
- Brockmann Consult, Max-Planck-Straße 2, D-21502 Geesthacht, Germany.
| | | | - Hui Feng
- Ocean Process Analysis Laboratory, Morse Hall, University of New Hampshire, Durham, NH 03824, USA.
| | - Gene Feldman
- NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA.
| | - Bryan A Franz
- NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA.
| | - Robert Frouin
- Scripps Institution of Oceanography Mail Code 0218, University of California San Diego, La Jolla, CA 92039-0218, USA.
| | - Richard W Gould
- Naval Research Laboratory, Bldg. 1009, Code 7331, Stennis Space Center, MS 39529, USA.
| | | | - Mati Kahru
- Scripps Institution of Oceanography Mail Code 0218, University of California San Diego, La Jolla, CA 92039-0218, USA.
| | - Susanne Kratzer
- Department of Ecology, Environment and Plant Sciences, University of Stockholm, 106 91 Stockholm, Sweden.
| | - B Greg Mitchell
- Scripps Institution of Oceanography Mail Code 0218, University of California San Diego, La Jolla, CA 92039-0218, USA.
| | - Frank E Muller-Karger
- Institute for Marine Remote Sensing, College of Marine Science, University of South Florida, 140 7th Ave. South St, Petersburg, FL 33701, USA.
| | - Heidi M Sosik
- Biology Department, MS 32, Woods Hole Oceanographic Institution, Woods Hole, MA 02543-1049, USA.
| | - Kenneth J Voss
- Department of Physics, University of Miami, James L. Knight Physics Building, 1320 Campo Sano Dr., Coral Gables, FL 33124, USA.
| | - Jeremy Werdell
- NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA.
| | - Trevor Platt
- Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK.
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11
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Kalb DM, Olson RJ, Sosik HM, Woods TA, Graves SW. Resonance control of acoustic focusing systems through an environmental reference table and impedance spectroscopy. PLoS One 2018; 13:e0207532. [PMID: 30427942 PMCID: PMC6235394 DOI: 10.1371/journal.pone.0207532] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/01/2018] [Indexed: 11/19/2022] Open
Abstract
Acoustic standing waves can precisely focus flowing particles or cells into tightly positioned streams for interrogation or downstream separations. The efficiency of an acoustic standing wave device is dependent upon operating at a resonance frequency. Small changes in a system's temperature and sample salinity can shift the device's resonance condition, leading to poor focusing. Practical implementation of an acoustic standing wave system requires an automated resonance control system to adjust the standing wave frequency in response to environmental changes. Here we have developed a rigorous approach for quantifying the optimal acoustic focusing frequency at any given environmental condition. We have demonstrated our approach across a wide range of temperature and salinity conditions to provide a robust characterization of how the optimal acoustic focusing resonance frequency shifts across these conditions. To generalize these results, two microfluidic bulk acoustic standing wave systems (a steel capillary and an etched silicon wafer) were examined. Models of these temperature and salinity effects suggest that it is the speed of sound within the liquid sample that dominates the resonance frequency shift. Using these results, a simple reference table can be generated to predict the optimal resonance condition as a function of temperature and salinity. Additionally, we show that there is a local impedance minimum associated with the optimal system resonance. The integration of the environmental results for coarse frequency tuning followed by a local impedance characterization for fine frequency adjustments, yields a highly accurate method of resonance control. Such an approach works across a wide range of environmental conditions, is easy to automate, and could have a significant impact across a wide range of microfluidic acoustic standing wave systems.
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Affiliation(s)
- Daniel M. Kalb
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico, United States
- * E-mail: (SWG); (DMK)
| | - Robert J. Olson
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Heidi M. Sosik
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Travis A. Woods
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico, United States
- University of New Mexico Center for Molecular Discovery, 1 University of New Mexico, Albuquerque, NM, United States
| | - Steven W. Graves
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico, United States
- * E-mail: (SWG); (DMK)
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12
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Muller‐Karger FE, Hestir E, Ade C, Turpie K, Roberts DA, Siegel D, Miller RJ, Humm D, Izenberg N, Keller M, Morgan F, Frouin R, Dekker AG, Gardner R, Goodman J, Schaeffer B, Franz BA, Pahlevan N, Mannino AG, Concha JA, Ackleson SG, Cavanaugh KC, Romanou A, Tzortziou M, Boss ES, Pavlick R, Freeman A, Rousseaux CS, Dunne J, Long MC, Klein E, McKinley GA, Goes J, Letelier R, Kavanaugh M, Roffer M, Bracher A, Arrigo KR, Dierssen H, Zhang X, Davis FW, Best B, Guralnick R, Moisan J, Sosik HM, Kudela R, Mouw CB, Barnard AH, Palacios S, Roesler C, Drakou EG, Appeltans W, Jetz W. Satellite sensor requirements for monitoring essential biodiversity variables of coastal ecosystems. Ecol Appl 2018; 28:749-760. [PMID: 29509310 PMCID: PMC5947264 DOI: 10.1002/eap.1682] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 10/30/2017] [Accepted: 12/08/2017] [Indexed: 05/27/2023]
Abstract
The biodiversity and high productivity of coastal terrestrial and aquatic habitats are the foundation for important benefits to human societies around the world. These globally distributed habitats need frequent and broad systematic assessments, but field surveys only cover a small fraction of these areas. Satellite-based sensors can repeatedly record the visible and near-infrared reflectance spectra that contain the absorption, scattering, and fluorescence signatures of functional phytoplankton groups, colored dissolved matter, and particulate matter near the surface ocean, and of biologically structured habitats (floating and emergent vegetation, benthic habitats like coral, seagrass, and algae). These measures can be incorporated into Essential Biodiversity Variables (EBVs), including the distribution, abundance, and traits of groups of species populations, and used to evaluate habitat fragmentation. However, current and planned satellites are not designed to observe the EBVs that change rapidly with extreme tides, salinity, temperatures, storms, pollution, or physical habitat destruction over scales relevant to human activity. Making these observations requires a new generation of satellite sensors able to sample with these combined characteristics: (1) spatial resolution on the order of 30 to 100-m pixels or smaller; (2) spectral resolution on the order of 5 nm in the visible and 10 nm in the short-wave infrared spectrum (or at least two or more bands at 1,030, 1,240, 1,630, 2,125, and/or 2,260 nm) for atmospheric correction and aquatic and vegetation assessments; (3) radiometric quality with signal to noise ratios (SNR) above 800 (relative to signal levels typical of the open ocean), 14-bit digitization, absolute radiometric calibration <2%, relative calibration of 0.2%, polarization sensitivity <1%, high radiometric stability and linearity, and operations designed to minimize sunglint; and (4) temporal resolution of hours to days. We refer to these combined specifications as H4 imaging. Enabling H4 imaging is vital for the conservation and management of global biodiversity and ecosystem services, including food provisioning and water security. An agile satellite in a 3-d repeat low-Earth orbit could sample 30-km swath images of several hundred coastal habitats daily. Nine H4 satellites would provide weekly coverage of global coastal zones. Such satellite constellations are now feasible and are used in various applications.
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13
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Hunter-Cevera KR, Neubert MG, Olson RJ, Solow AR, Shalapyonok A, Sosik HM. Physiological and ecological drivers of early spring blooms of a coastal phytoplankter. Science 2017; 354:326-329. [PMID: 27846565 DOI: 10.1126/science.aaf8536] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 09/09/2016] [Indexed: 11/02/2022]
Abstract
Climate affects the timing and magnitude of phytoplankton blooms that fuel marine food webs and influence global biogeochemical cycles. Changes in bloom timing have been detected in some cases, but the underlying mechanisms remain elusive, contributing to uncertainty in long-term predictions of climate change impacts. Here we describe a 13-year hourly time series from the New England shelf of data on the coastal phytoplankter Synechococcus, during which the timing of its spring bloom varied by 4 weeks. We show that multiyear trends are due to temperature-induced changes in cell division rate, with earlier blooms driven by warmer spring water temperatures. Synechococcus loss rates shift in tandem with division rates, suggesting a balance between growth and loss that has persisted despite phenological shifts and environmental change.
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Affiliation(s)
| | - Michael G Neubert
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Robert J Olson
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Andrew R Solow
- Marine Policy Center, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Alexi Shalapyonok
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Heidi M Sosik
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
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14
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Hunter-Cevera KR, Post AF, Peacock EE, Sosik HM. Diversity of Synechococcus at the Martha's Vineyard Coastal Observatory: Insights from Culture Isolations, Clone Libraries, and Flow Cytometry. Microb Ecol 2016; 71:276-289. [PMID: 26233669 PMCID: PMC4728178 DOI: 10.1007/s00248-015-0644-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Accepted: 06/25/2015] [Indexed: 06/04/2023]
Abstract
The cyanobacterium Synechococcus is a ubiquitous, important phytoplankter across the world's oceans. A high degree of genetic diversity exists within the marine group, which likely contributes to its global success. Over 20 clades with different distribution patterns have been identified. However, we do not fully understand the environmental factors that control clade distributions. These factors are likely to change seasonally, especially in dynamic coastal systems. To investigate how coastal Synechococcus assemblages change temporally, we assessed the diversity of Synechococcus at the Martha's Vineyard Coastal Observatory (MVCO) over three annual cycles with culture-dependent and independent approaches. We further investigated the abundance of both phycoerythrin (PE)-containing and phycocyanin (PC)-only Synechococcus with a flow cytometric setup that distinguishes PC-only Synechococcus from picoeukaryotes. We found that the Synechococcus assemblage at MVCO is diverse (13 different clades identified), but dominated by clade I representatives. Many clades were only isolated during late summer and fall, suggesting more favorable conditions for isolation at this time. PC-only strains from four different clades were isolated, but these cells were only detected by flow cytometry in a few samples over the time series, suggesting they are rare at this site. Within clade I, we identified four distinct subclades. The relative abundances of each subclade varied over the seasonal cycle, and the high Synechococcus cell concentration at MVCO may be maintained by the diversity found within this clade. This study highlights the need to understand how temporal aspects of the environment affect Synechococcus community structure and cell abundance.
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Affiliation(s)
| | - Anton F Post
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, 02882, USA
| | - Emily E Peacock
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Heidi M Sosik
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
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15
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Brosnahan ML, Velo-Suárez L, Ralston DK, Fox SE, Sehein TR, Shalapyonok A, Sosik HM, Olson RJ, Anderson DM. Rapid growth and concerted sexual transitions by a bloom of the harmful dinoflagellate Alexandrium fundyense (Dinophyceae). Limnol Oceanogr 2015; 60:2059-2078. [PMID: 27667858 PMCID: PMC5014212 DOI: 10.1002/lno.10155] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 06/19/2015] [Accepted: 07/20/2015] [Indexed: 05/04/2023]
Abstract
Transitions between life cycle stages by the harmful dinoflagellate Alexandrium fundyense are critical for the initiation and termination of its blooms. To quantify these transitions in a single population, an Imaging FlowCytobot (IFCB), was deployed in Salt Pond (Eastham, Massachusetts), a small, tidally flushed kettle pond that hosts near annual, localized A. fundyense blooms. Machine-based image classifiers differentiating A. fundyense life cycle stages were developed and results were compared to manually corrected IFCB samples, manual microscopy-based estimates of A. fundyense abundance, previously published data describing prevalence of the parasite Amoebophrya, and a continuous culture of A. fundyense infected with Amoebophrya. In Salt Pond, a development phase of sustained vegetative division lasted approximately 3 weeks and was followed by a rapid and near complete conversion to small, gamete cells. The gametic period (∼3 d) coincided with a spike in the frequency of fusing gametes (up to 5% of A. fundyense images) and was followed by a zygotic phase (∼4 d) during which cell sizes returned to their normal range but cell division and diel vertical migration ceased. Cell division during bloom development was strongly phased, enabling estimation of daily rates of division, which were more than twice those predicted from batch cultures grown at similar temperatures in replete medium. Data from the Salt Pond deployment provide the first continuous record of an A. fundyense population through its complete bloom cycle and demonstrate growth and sexual induction rates much higher than are typically observed in culture.
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Affiliation(s)
- Michael L Brosnahan
- Biology Department Woods Hole Oceanographic Institution Woods Hole Massachusetts
| | - Lourdes Velo-Suárez
- Department Dynamiques de l'Environment Côtier Institut Français de Recherche pour L'Exploitation de la MER Plouzané France
| | - David K Ralston
- Applied Ocean Physics and Engineering Department Woods Hole Oceanographic Institution Woods Hole Massachusetts
| | - Sophia E Fox
- Cape Cod National Seashore, National Park Service Wellfleet Massachusetts
| | - Taylor R Sehein
- Biology Department Woods Hole Oceanographic Institution Woods Hole Massachusetts
| | - Alexi Shalapyonok
- Biology Department Woods Hole Oceanographic Institution Woods Hole Massachusetts
| | - Heidi M Sosik
- Biology Department Woods Hole Oceanographic Institution Woods Hole Massachusetts
| | - Robert J Olson
- Biology Department Woods Hole Oceanographic Institution Woods Hole Massachusetts
| | - Donald M Anderson
- Biology Department Woods Hole Oceanographic Institution Woods Hole Massachusetts
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16
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Zhang X, Huot Y, Bricaud A, Sosik HM. Inversion of spectral absorption coefficients to infer phytoplankton size classes, chlorophyll concentration, and detrital matter. Appl Opt 2015; 54:5805-5816. [PMID: 26193033 DOI: 10.1364/ao.54.005805] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Measured spectral absorption coefficients were inverted to infer phytoplankton concentration in three size classes (picoplankton, nanoplankton, and microplankton), chlorophyll concentration [Chl], and both magnitude and spectral shape of absorption by colored detrital matter (CDM). Our algorithm allowed us to solve for the nonlinear factor of CDM absorption slope separately from the other linear factors, thus fully utilizing the additive characteristic inherent in absorption coefficients. We validated the inversion with three datasets: two spatially distributed global datasets, the Laboratoire d'Océanographie de Villefranche dataset and the NASA bio-Optical Marine Algorithm Dataset, and a time series coastal dataset, the Martha's Vineyard Coastal Observatory dataset. Comparison with high performance liquid chromatography analyses showed that the phytoplankton size classes can be retrieved with correlation coefficients (r)>0.7, root mean square errors of 0.2, and median relative errors of 20% in oceanic waters and with similar performance in coastal waters. Much improved agreement was found for the entire phytoplankton population, with r>0.90 for [Chl] and absorption coefficients (aph) for all three datasets. The inferred aCDM(400) and CDM spectral slope agree within ±4% of measurements in both oceanic and coastal waters. The results indicate that the chlorophyll-a specific absorption spectra used as an inversion kernel represent well the global mean states for each of the three phytoplankton size classes. The method can be applied to either bulk or particulate absorption data and is spectrally flexible.
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17
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Keeling PJ, Burki F, Wilcox HM, Allam B, Allen EE, Amaral-Zettler LA, Armbrust EV, Archibald JM, Bharti AK, Bell CJ, Beszteri B, Bidle KD, Cameron CT, Campbell L, Caron DA, Cattolico RA, Collier JL, Coyne K, Davy SK, Deschamps P, Dyhrman ST, Edvardsen B, Gates RD, Gobler CJ, Greenwood SJ, Guida SM, Jacobi JL, Jakobsen KS, James ER, Jenkins B, John U, Johnson MD, Juhl AR, Kamp A, Katz LA, Kiene R, Kudryavtsev A, Leander BS, Lin S, Lovejoy C, Lynn D, Marchetti A, McManus G, Nedelcu AM, Menden-Deuer S, Miceli C, Mock T, Montresor M, Moran MA, Murray S, Nadathur G, Nagai S, Ngam PB, Palenik B, Pawlowski J, Petroni G, Piganeau G, Posewitz MC, Rengefors K, Romano G, Rumpho ME, Rynearson T, Schilling KB, Schroeder DC, Simpson AGB, Slamovits CH, Smith DR, Smith GJ, Smith SR, Sosik HM, Stief P, Theriot E, Twary SN, Umale PE, Vaulot D, Wawrik B, Wheeler GL, Wilson WH, Xu Y, Zingone A, Worden AZ. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol 2014; 12:e1001889. [PMID: 24959919 PMCID: PMC4068987 DOI: 10.1371/journal.pbio.1001889] [Citation(s) in RCA: 615] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans.
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Affiliation(s)
- Patrick J. Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Canadian Institute for Advanced Research, Integrated Microbial Biodiversity program, Canada
- * E-mail: (PJK); (AZW)
| | - Fabien Burki
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Heather M. Wilcox
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
| | - Bassem Allam
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, United States of America
| | - Eric E. Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States of America
| | - Linda A. Amaral-Zettler
- The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
- Department of Geological Sciences, Brown University, Providence, Rhode Island, United States of America
| | - E. Virginia Armbrust
- School of Oceanography, University of Washington, Seattle, Washington, United States of America
| | - John M. Archibald
- Canadian Institute for Advanced Research, Integrated Microbial Biodiversity program, Canada
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Arvind K. Bharti
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Callum J. Bell
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Bank Beszteri
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Kay D. Bidle
- Institute of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Connor T. Cameron
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Lisa Campbell
- Department of Oceanography, Department of Biology, Texas A&M University, College Station, Texas, United States of America
| | - David A. Caron
- Department of Biology, University of Southern California, Los Angeles, California, United States of America
| | - Rose Ann Cattolico
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Jackie L. Collier
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, United States of America
| | - Kathryn Coyne
- University of Delaware, School of Marine Science and Policy, College of Earth, Ocean, and Environment, Lewes, Delaware, United States of America
| | - Simon K. Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Phillipe Deschamps
- Unité d'Ecologie, Systematique et Evolution, CNRS UMR8079, Université Paris-Sud, Orsay, France
| | - Sonya T. Dyhrman
- Department of Earth and Environmental Sciences and the Lamont-Doherty Earth Observatory, Columbia University, New York, New York, United States of America
| | | | - Ruth D. Gates
- Hawaii Institute of Marine Biology, University of Hawaii, Hawaii, United States of America
| | - Christopher J. Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, United States of America
| | - Spencer J. Greenwood
- Department of Biomedical Sciences and AVC Lobster Science Centre, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Stephanie M. Guida
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Jennifer L. Jacobi
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | | | - Erick R. James
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bethany Jenkins
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, United States of America
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, United States of America
| | - Uwe John
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Matthew D. Johnson
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America
| | - Andrew R. Juhl
- Department of Earth and Environmental Sciences and the Lamont-Doherty Earth Observatory, Columbia University, New York, New York, United States of America
| | - Anja Kamp
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Jacobs University Bremen, Molecular Life Science Research Center, Bremen, Germany
| | - Laura A. Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
| | - Ronald Kiene
- University of South Alabama, Dauphin Island Sea Lab, Mobile, Alabama, United States of America
| | - Alexander Kudryavtsev
- Department of Invertebrate Zoology, Saint-Petersburg State University, Saint-Petersburg, Russia
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Brian S. Leander
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America
| | - Connie Lovejoy
- Département de Biologie, Université Laval, Québec, Canada
| | - Denis Lynn
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Adrian Marchetti
- Department of Marine Sciences, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - George McManus
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America
| | - Aurora M. Nedelcu
- University of New Brunswick, Department of Biology, Fredericton, New Brusnswick, Canada
| | - Susanne Menden-Deuer
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, United States of America
| | - Cristina Miceli
- School of Biosciences and Biotechnology, University of Camerino, Camerino, Italy
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | | | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, Georgia, United States of America
| | - Shauna Murray
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology, Sydney, Australia
| | - Govind Nadathur
- Department of Marine Sciences, University of Puerto Rico, Mayaguez, Puerto Rico, United States of America
| | - Satoshi Nagai
- National Research Institute of Fisheries Science, Kanagawa, Japan
| | - Peter B. Ngam
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Brian Palenik
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States of America
| | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | | | - Gwenael Piganeau
- CNRS, UMR 7232, BIOM, Observatoire Océanologique, Banyuls-sur-Mer, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7232, BIOM, Banyuls-sur-Mer, France
| | - Matthew C. Posewitz
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, Colorado, United States of America
| | | | | | - Mary E. Rumpho
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Tatiana Rynearson
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, United States of America
| | - Kelly B. Schilling
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Declan C. Schroeder
- The Marine Biological Association of the United Kingdom, Plymouth, United Kingdom
| | - Alastair G. B. Simpson
- Canadian Institute for Advanced Research, Integrated Microbial Biodiversity program, Canada
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Claudio H. Slamovits
- Canadian Institute for Advanced Research, Integrated Microbial Biodiversity program, Canada
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - G. Jason Smith
- Moss Landing Marine Laboratories, Moss Landing, California, United States of America
| | - Sarah R. Smith
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States of America
| | - Heidi M. Sosik
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America
| | - Peter Stief
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Edward Theriot
- Section of Integrative Biology, University of Texas, Austin, Texas, United States of America
| | - Scott N. Twary
- Los Alamos National Laboratory, Biosciences, Los Alamos, New Mexico, United States of America
| | - Pooja E. Umale
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Daniel Vaulot
- UMR714, CNRS and UPMC (Paris-06), Station Biologique, Roscoff, France
| | - Boris Wawrik
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Glen L. Wheeler
- The Marine Biological Association of the United Kingdom, Plymouth, United Kingdom
- Plymouth Marine Laboratory, Plymouth, United Kingdom
| | - William H. Wilson
- NCMA, Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, United States of America
| | - Yan Xu
- Princeton University, Princeton, New Jersey, United States of America
| | | | - Alexandra Z. Worden
- Canadian Institute for Advanced Research, Integrated Microbial Biodiversity program, Canada
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
- * E-mail: (PJK); (AZW)
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Brosnahan ML, Farzan S, Keafer BA, Sosik HM, Olson RJ, Anderson DM. Complexities of bloom dynamics in the toxic dinoflagellate Alexandrium fundyense revealed through DNA measurements by imaging flow cytometry coupled with species-specific rRNA probes. Deep Sea Res 2 Top Stud Oceanogr 2014; 103:185-198. [PMID: 24891769 PMCID: PMC4039218 DOI: 10.1016/j.dsr2.2013.05.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Measurements of the DNA content of different protist populations can shed light on a variety of processes, including cell division, sex, prey ingestion, and parasite invasion. Here, we modified an Imaging FlowCytobot (IFCB), a custom-built flow cytometer that records images of microplankton, to measure the DNA content of large dinoflagellates and other high-DNA content species. The IFCB was also configured to measure fluorescence from Cy3-labeled rRNA probes, aiding the identification of Alexandrium fundyense (syn. A. tamarense Group I), a photosynthetic dinoflagellate that causes paralytic shellfish poisoning (PSP). The modified IFCB was used to analyze samples from the development, peak and termination phases of an inshore A. fundyense bloom (Salt Pond, Eastham, MA USA), and from a rare A. fundyense 'red tide' that occurred in the western Gulf of Maine, offshore of Portsmouth, NH (USA). Diploid or G2 phase ('2C') A. fundyense cells were frequently enriched at the near-surface, suggesting an important role for aggregation at the air-sea interface during sexual events. Also, our analysis showed that large proportions of A. fundyense cells in both the Salt Pond and red tide blooms were planozygotes during bloom decline, highlighting the importance of sexual fusion to bloom termination. At Salt Pond, bloom decline also coincided with a dramatic rise in infections by the parasite genus Amoebophrya. The samples that were most heavily infected contained many large cells with higher DNA-associated fluorescence than 2C vegetative cells, but these cells' nuclei were also frequently consumed by Amoebophrya trophonts. Neither large cell size nor increased DNA-associated fluorescence could be replicated by infecting an A. fundyense culture of vegetative cells. Therefore we attribute these characteristics of the large Salt Pond cells to planozygote maturation rather than Amoebophrya infection, though an interaction between infection and planozygote maturation may also have contributed. The modified IFCB is a valuable tool for exploring the conditions that promote sexual transitions by dinoflagellate blooms but care is needed when interpreting results from samples in which parasitism is prevalent.
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Affiliation(s)
- Michael L. Brosnahan
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543
- (Corresponding Author) Tel: 508 289-3633
| | - Shahla Farzan
- Department of Entomology, University of California-Davis, Davis, CA 95616
| | - Bruce A. Keafer
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543
| | - Heidi M. Sosik
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543
| | - Robert J. Olson
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543
| | - Donald M. Anderson
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543
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19
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Campbell L, Henrichs DW, Olson RJ, Sosik HM. Continuous automated imaging-in-flow cytometry for detection and early warning of Karenia brevis blooms in the Gulf of Mexico. Environ Sci Pollut Res Int 2013; 20:6896-6902. [PMID: 23307076 DOI: 10.1007/s11356-012-1437-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2012] [Accepted: 12/13/2012] [Indexed: 06/01/2023]
Abstract
Monitoring programs for harmful algal blooms (HABs) typically rely on time-consuming manual methods for identification and enumeration of phytoplankton, which make it difficult to obtain results with sufficient temporal resolution for early warning. Continuous automated imaging-in-flow by the Imaging FlowCytobot (IFCB) deployed at Port Aransas, TX has provided early warnings of six HAB events. Here we describe the progress in automating this early warning system for blooms of Karenia brevis. In 2009, manual inspection of IFCB images in mid-August 2009 provided early warning for a Karenia bloom that developed in mid-September. Images from 2009 were used to develop an automated classifier that was employed in 2011. Successful implementation of automated file downloading, processing and image classification allowed results to be available within 4 h after collection and to be sent to state agency representatives by email for early warning of HABs. No human illness (neurotoxic shellfish poisoning) has resulted from these events. In contrast to the common assumption that Karenia blooms are near monospecific, post-bloom analysis of the time series revealed that Karenia cells comprised at most 60-75 % of the total microplankton.
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Affiliation(s)
- Lisa Campbell
- Department Oceanography, Texas A&M University, College Station, TX, 77843, USA,
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20
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Pearl MR, Swanstrom JA, Bruckman LS, Richardson TL, Shaw TJ, Sosik HM, Myrick ML. Taxonomic classification of phytoplankton with multivariate optical computing, part III: demonstration. Appl Spectrosc 2013; 67:640-647. [PMID: 23735249 DOI: 10.1366/12-06785] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We describe the automatic analysis of fluorescence tracks of phytoplankton recorded with a fluorescence imaging photometer. The optical components and construction of the photometer were described in Part I and Part II of this series in this issue. An algorithm first isolates tracks corresponding to a single phytoplankter transit in the nominal focal plane of a flow cell. Then, the fluorescence streaks in the track that correspond to individual optical elements on the filter wheel are identified. The fluorescence intensity of each streak is integrated and used to calculate ratios. This approach was tested using 853 fluorescence measurements of the coccolithophore Emiliania huxleyi and the diatom Thalassiosira pseudonana. Average intensity ratios for the two classes closely follow those predicted in Part I of this series, with a distribution of ratios in each class that is consistent with the signal-to-noise ratio calculations in Part II for single cells. No overlap of the two class ratios was observed, yielding perfect classification.
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Affiliation(s)
- Megan R Pearl
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
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21
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Duffy JE, Amaral-Zettler LA, Fautin DG, Paulay G, Rynearson TA, Sosik HM, Stachowicz JJ. Envisioning a Marine Biodiversity Observation Network. Bioscience 2013. [DOI: 10.1525/bio.2013.63.5.8] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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22
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Arrigo KR, Perovich DK, Pickart RS, Brown ZW, van Dijken GL, Lowry KE, Mills MM, Palmer MA, Balch WM, Bahr F, Bates NR, Benitez-Nelson C, Bowler B, Brownlee E, Ehn JK, Frey KE, Garley R, Laney SR, Lubelczyk L, Mathis J, Matsuoka A, Mitchell BG, Moore GWK, Ortega-Retuerta E, Pal S, Polashenski CM, Reynolds RA, Schieber B, Sosik HM, Stephens M, Swift JH. Massive phytoplankton blooms under Arctic sea ice. Science 2012; 336:1408. [PMID: 22678359 DOI: 10.1126/science.1215065] [Citation(s) in RCA: 517] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Phytoplankton blooms over Arctic Ocean continental shelves are thought to be restricted to waters free of sea ice. Here, we document a massive phytoplankton bloom beneath fully consolidated pack ice far from the ice edge in the Chukchi Sea, where light transmission has increased in recent decades because of thinning ice cover and proliferation of melt ponds. The bloom was characterized by high diatom biomass and rates of growth and primary production. Evidence suggests that under-ice phytoplankton blooms may be more widespread over nutrient-rich Arctic continental shelves and that satellite-based estimates of annual primary production in these waters may be underestimated by up to 10-fold.
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Affiliation(s)
- Kevin R Arrigo
- Department of Environmental Earth System Science, Stanford University, Stanford, CA 94305, USA.
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Henrichs DW, Sosik HM, Olson RJ, Campbell L. PHYLOGENETIC ANALYSIS OF BRACHIDINIUM CAPITATUM (DINOPHYCEAE) FROM THE GULF OF MEXICO INDICATES MEMBERSHIP IN THE KARENIACEAE(1). J Phycol 2011; 47:366-374. [PMID: 27021868 DOI: 10.1111/j.1529-8817.2011.00960.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Brachidinium capitatum F. J. R. Taylor, typically considered a rare oceanic dinoflagellate, and one which has not been cultured, was observed at elevated abundances (up to 65 cells · mL(-1) ) at a coastal station in the western Gulf of Mexico in the fall of 2007. Continuous data from the Imaging FlowCytobot (IFCB) provided cell images that documented the bloom during 3 weeks in early November. Guided by IFCB observations, field collection permitted phylogenetic analysis and evaluation of the relationship between Brachidinium and Karenia. Sequences from SSU, LSU, internal transcribed spacer (ITS), and cox1 regions for B. capitatum were compared with five other species of Karenia; all B. capitatum sequences were unique but supported its placement within the Kareniaceae. From a total of 71,487 images, data on the timing and frequency of dividing cells was also obtained for B. capitatum, allowing the rate of division for B. capitatum to be estimated. The maximum daily growth rate estimate was 0.22 d(-1) . Images showed a range in morphological variability, with the position of the four major processes highly variable. The combination of morphological features similar to the genus Karenia and a phylogenetic analysis placing B. capitatum in the Karenia clade leads us to propose moving the genus Brachidinium into the Kareniaceae. However, the lack of agreement among individual gene phylogenies suggests that the inclusion of different genes and more members of the genus Karenia are necessary before a final determination regarding the validity of the genus Brachidinium can be made.
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Affiliation(s)
- Darren W Henrichs
- Department of Biology, Texas A&M University, College Station, Texas 77843, USADepartment of Biology, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, USADepartment of Oceanography and Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Heidi M Sosik
- Department of Biology, Texas A&M University, College Station, Texas 77843, USADepartment of Biology, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, USADepartment of Oceanography and Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Robert J Olson
- Department of Biology, Texas A&M University, College Station, Texas 77843, USADepartment of Biology, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, USADepartment of Oceanography and Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Lisa Campbell
- Department of Biology, Texas A&M University, College Station, Texas 77843, USADepartment of Biology, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, USADepartment of Oceanography and Department of Biology, Texas A&M University, College Station, Texas 77843, USA
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Green RE, Sosik HM. Analysis of apparent optical properties and ocean color models using measurements of seawater constituents in New England continental shelf surface waters. ACTA ACUST UNITED AC 2004. [DOI: 10.1029/2003jc001977] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rebecca E. Green
- Biology Department; Woods Hole Oceanographic Institution; Woods Hole Massachusetts USA
| | - Heidi M. Sosik
- Biology Department; Woods Hole Oceanographic Institution; Woods Hole Massachusetts USA
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Green RE, Sosik HM, Olson RJ, DuRand MD. Flow cytometric determination of size and complex refractive index for marine particles: comparison with independent and bulk estimates. Appl Opt 2003; 42:526-541. [PMID: 12570275 DOI: 10.1364/ao.42.000526] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We advance a method to determine the diameter D and the complex refractive index (n + n'i) of marine particles from flow cytometric measurements of forward scattering, side scattering, and chlorophyll fluorescence combined with Mie theory. To understand better the application of Mie theory with its assumptions to flow cytometry (FCM) measurements of phytoplankton cells, we evaluate our flow cytometric-Mie (FCM-Mie) method by comparing results from a variety of phytoplankton cultures with independent estimates of cell D and with estimates of n and n' from the inversion of bulk measurements. Cell D initially estimated from the FCM-Mie method is lower than independent estimates, and n and n' are generally higher than bulk estimates. These differences reflect lower forward scattering and higher side scattering for single-cell measurements than predicted by Mie theory. The application of empirical scattering corrections improves FCM-Mie estimates of cell size, n, and n'; notably size is determined accurately for cells grown in both high- and low-light conditions, and n' is correlated with intracellular chlorophyll concentration. A comparison of results for phytoplankton and mineral particles suggests that differences in n between these particle types can be determined from FCM measurements. In application to natural mixtures of particles, eukaryotic pico/nanophytoplankton and Synechococcus have minimum mean values of n' in surface waters, and nonphytoplankton particles have higher values of n than phytoplankton at all depths.
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Affiliation(s)
- Rebecca E Green
- Woods Hole Oceanographic Institution, Department of Biology, Woods Hole, Massachusetts 02543, USA
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Sosik HM, Green RE, Pegau WS, Roesler CS. Temporal and vertical variability in optical properties of New England shelf waters during late summer and spring. ACTA ACUST UNITED AC 2001. [DOI: 10.1029/2000jc900147] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
BACKGROUND Active fluorescence techniques are becoming commonly used to monitor the state of the photosynthetic apparatus in natural populations of phytoplankton, but at present these are bulk water measurements that average all the fluorescent material in each sample. Here we describe two instruments that combine individual-cell "pump-during-probe" (PDP) measurements of chlorophyll (Chl) fluorescence induction, on the time scale of 30 to 100 micros, with flow cytometric or visual characterization of each cell. METHODS In the PDP flow cytometer, we measure Chl fluorescence yield as a function of time during a 150 micros excitation flash provided by an argon ion laser; each particle is subsequently classified as in a conventional flow cytometer. In the PDP microfluorometer, individual cells in a sample chamber are visually identified, and fluorescence excitation is provided by a blue light-emitting diode that can be configured to provide a saturating flash and also a subsequent series of short flashlets. This sequence allows both saturation and relaxation kinetics to be monitored. RESULTS Phytoplankton from natural samples and on-deck iron-enrichment incubation experiments in the Southern Ocean were examined with each PDP instrument, providing estimates of the potential quantum yield of photochemistry and the functional absorption cross section for photosystem 2, for either individuals (for cells larger than a few micrometers) or populations (for smaller cells). CONCLUSIONS Results from initial field applications indicate that single-cell PDP measurements can be a powerful tool for investigating the nutritional state of phytoplankton cells and the regulation of phytoplankton growth in the sea.
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Affiliation(s)
- R J Olson
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, USA.
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