Boss Emmanuel S.

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Emmanuel S.

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  • Article
    Reply to a comment by Stephen M. Chiswell on: “Annual cycles of ecological disturbance and recovery underlying the subarctic Atlantic spring plankton bloom” by M. J. Behrenfeld et al. (2013)
    (John Wiley & Sons, 2013-12-12) Behrenfeld, Michael J. ; Doney, Scott C. ; Lima, Ivan D. ; Boss, Emmanuel S. ; Siegel, David A.
  • Article
    Satellite-detected fluorescence reveals global physiology of ocean phytoplankton
    (Copernicus Publications on behalf of the European Geosciences Union, 2009-05-08) Behrenfeld, Michael J. ; Westberry, Toby K. ; Boss, Emmanuel S. ; O'Malley, Robert T. ; Siegel, David A. ; Wiggert, Jerry D. ; Franz, Bryan A. ; McClain, Charles R. ; Feldman, G. C. ; Doney, Scott C. ; Moore, J. Keith ; Dall'Olmo, Giorgio ; Milligan, A. J. ; Lima, Ivan D. ; Mahowald, Natalie M.
    Phytoplankton photosynthesis links global ocean biology and climate-driven fluctuations in the physical environment. These interactions are largely expressed through changes in phytoplankton physiology, but physiological status has proven extremely challenging to characterize globally. Phytoplankton fluorescence does provide a rich source of physiological information long exploited in laboratory and field studies, and is now observed from space. Here we evaluate the physiological underpinnings of global variations in satellite-based phytoplankton chlorophyll fluorescence. The three dominant factors influencing fluorescence distributions are chlorophyll concentration, pigment packaging effects on light absorption, and light-dependent energy-quenching processes. After accounting for these three factors, resultant global distributions of quenching-corrected fluorescence quantum yields reveal a striking consistency with anticipated patterns of iron availability. High fluorescence quantum yields are typically found in low iron waters, while low quantum yields dominate regions where other environmental factors are most limiting to phytoplankton growth. Specific properties of photosynthetic membranes are discussed that provide a mechanistic view linking iron stress to satellite-detected fluorescence. Our results present satellite-based fluorescence as a valuable tool for evaluating nutrient stress predictions in ocean ecosystem models and give the first synoptic observational evidence that iron plays an important role in seasonal phytoplankton dynamics of the Indian Ocean. Satellite fluorescence may also provide a path for monitoring climate-phytoplankton physiology interactions and improving descriptions of phytoplankton light use efficiencies in ocean productivity models.
  • Article
    Simplified model of spectral absorption by non-algal particles and dissolved organic materials in aquatic environments
    (Optical Society of America, 2017-10-06) Cael, B. Barry ; Boss, Emmanuel S.
    Absorption by non-algal particles (NAP, ad) and colored dissolved organic matter (CDOM, ag) are frequently modeled by exponential functions of wavelength, either separately or as a sum. We present a new representation of NAP-plus-CDOM absorption adg based on the stretched exponential function adg(λ) = A exp{−[s(λ − λo)]β}, whose parameter β can be considered a measure of optical heterogeneity. A double exponential representation of adg can be fit extremely well by a stretched exponential for all plausible parameter combinations, despite having one fewer free parameter than a double exponential. Fitting two published compilations of in situ adg data – one at low spectral resolution (n = 5, λ = 412–555 nm) and one at high spectral resolution (n = 201, λ = 300–700 nm) – the stretched exponential outperforms the single exponential, double exponential, and a power law. We thereby conclude that the stretched exponential is the preferred model for adg absorption in circumstances when NAP and CDOM cannot be separated, such as in remote sensing inversions.
  • Article
    Methyl mercury dynamics in a tidal wetland quantified using in situ optical measurements
    (Association for the Sciences of Limnology and Oceanography, 2011-07) Bergamaschi, Brian A. ; Fleck, Jacob A. ; Downing, Bryan D. ; Boss, Emmanuel S. ; Pellerin, Brian A. ; Ganju, Neil K. ; Schoellhamer, David H. ; Byington, Amy A. ; Heim, Wesley A. ; Stephenson, Mark ; Fujii, Roger
    We assessed monomethylmercury (MeHg) dynamics in a tidal wetland over three seasons using a novel method that employs a combination of in situ optical measurements as concentration proxies. MeHg concentrations measured over a single spring tide were extended to a concentration time series using in situ optical measurements. Tidal fluxes were calculated using modeled concentrations and bi-directional velocities obtained acoustically. The magnitude of the flux was the result of complex interactions of tides, geomorphic features, particle sorption, and random episodic events such as wind storms and precipitation. Correlation of dissolved organic matter quality measurements with timing of MeHg release suggests that MeHg is produced in areas of fluctuating redox and not limited by buildup of sulfide. The wetland was a net source of MeHg to the estuary in all seasons, with particulate flux being much higher than dissolved flux, even though dissolved concentrations were commonly higher. Estimated total MeHg yields out of the wetland were approximately 2.5 µg m−2 yr−1—4–40 times previously published yields—representing a potential loading to the estuary of 80 g yr−1, equivalent to 3% of the river loading. Thus, export from tidal wetlands should be included in mass balance estimates for MeHg loading to estuaries. Also, adequate estimation of loads and the interactions between physical and biogeochemical processes in tidal wetlands might not be possible without long-term, high-frequency in situ measurements.
  • Article
    Expanding Tara oceans protocols for underway, ecosystemic sampling of the ocean-atmosphere interface during Tara Pacific expedition (2016-2018)
    (Frontiers Media, 2019-12-11) Gorsky, Gabriel ; Bourdin, Guillaume ; Lombard, Fabien ; Pedrotti, Maria Luiza ; Audrain, Samuel ; Bin, Nicolas ; Boss, Emmanuel S. ; Bowler, Chris ; Cassar, Nicolas ; Caudan, Loic ; Chabot, Genevieve ; Cohen, Natalie R. ; Cron, Daniel ; De Vargas, Colomban ; Dolan, John R. ; Douville, Eric ; Elineau, Amanda ; Flores, J. Michel ; Ghiglione, Jean-Francois ; Haëntjens, Nils ; Hertau, Martin ; John, Seth G. ; Kelly, Rachel L. ; Koren, Ilan ; Lin, Yajuan ; Marie, Dominique ; Moulin, Clémentine ; Moucherie, Yohann ; Pesant, Stephane ; Picheral, Marc ; Poulain, Julie ; Pujo-Pay, Mireille ; Reverdin, Gilles ; Romac, Sarah ; Sullivan, Mathew B. ; Trainic, Miri ; Tressol, Marc ; Troublé, Romain ; Vardi, Assaf ; Voolstra, Christian R. ; Wincker, Patrick ; Agostini, Sylvain ; Banaigs, Bernard ; Boissin, Emilie ; Forcioli, Didier ; Furla, Paola ; Galand, Pierre E. ; Gilson, Eric ; Reynaud, Stephanie ; Sunagawa, Shinichi ; Thomas, Olivier P. ; Vega Thurber, Rebecca ; Zoccola, Didier ; Planes, Serge ; Allemand, Denis ; Karsenti, Eric
    Interactions between the ocean and the atmosphere occur at the air-sea interface through the transfer of momentum, heat, gases and particulate matter, and through the impact of the upper-ocean biology on the composition and radiative properties of this boundary layer. The Tara Pacific expedition, launched in May 2016 aboard the schooner Tara, was a 29-month exploration with the dual goals to study the ecology of reef ecosystems along ecological gradients in the Pacific Ocean and to assess inter-island and open ocean surface plankton and neuston community structures. In addition, key atmospheric properties were measured to study links between the two boundary layer properties. A major challenge for the open ocean sampling was the lack of ship-time available for work at “stations”. The time constraint led us to develop new underway sampling approaches to optimize physical, chemical, optical, and genomic methods to capture the entire community structure of the surface layers, from viruses to metazoans in their oceanographic and atmospheric physicochemical context. An international scientific consortium was put together to analyze the samples, generate data, and develop datasets in coherence with the existing Tara Oceans database. Beyond adapting the extensive Tara Oceans sampling protocols for high-resolution underway sampling, the key novelties compared to Tara Oceans’ global assessment of plankton include the measurement of (i) surface plankton and neuston biogeography and functional diversity; (ii) bioactive trace metals distribution at the ocean surface and metal-dependent ecosystem structures; (iii) marine aerosols, including biological entities; (iv) geography, nature and colonization of microplastic; and (v) high-resolution underway assessment of net community production via equilibrator inlet mass spectrometry. We are committed to share the data collected during this expedition, making it an important resource important resource to address a variety of scientific questions.
  • Article
    On the future of Argo: A global, full-depth, multi-disciplinary array
    (Frontiers Media, 2019-08-02) Roemmich, Dean ; Alford, Matthew H. ; Claustre, Hervé ; Johnson, Kenneth S. ; King, Brian ; Moum, James N. ; Oke, Peter ; Owens, W. Brechner ; Pouliquen, Sylvie ; Purkey, Sarah G. ; Scanderbeg, Megan ; Suga, Koushirou ; Wijffels, Susan E. ; Zilberman, Nathalie ; Bakker, Dorothee ; Baringer, Molly O. ; Belbeoch, Mathieu ; Bittig, Henry C. ; Boss, Emmanuel S. ; Calil, Paulo H. R. ; Carse, Fiona ; Carval, Thierry ; Chai, Fei ; Conchubhair, Diarmuid Ó. ; d’Ortenzio, Fabrizio ; Dall'Olmo, Giorgio ; Desbruyeres, Damien ; Fennel, Katja ; Fer, Ilker ; Ferrari, Raffaele ; Forget, Gael ; Freeland, Howard ; Fujiki, Tetsuichi ; Gehlen, Marion ; Geenan, Blair ; Hallberg, Robert ; Hibiya, Toshiyuki ; Hosoda, Shigeki ; Jayne, Steven R. ; Jochum, Markus ; Johnson, Gregory C. ; Kang, KiRyong ; Kolodziejczyk, Nicolas ; Körtzinger, Arne ; Le Traon, Pierre-Yves ; Lenn, Yueng-Djern ; Maze, Guillaume ; Mork, Kjell Arne ; Morris, Tamaryn ; Nagai, Takeyoshi ; Nash, Jonathan D. ; Naveira Garabato, Alberto C. ; Olsen, Are ; Pattabhi Rama Rao, Eluri ; Prakash, Satya ; Riser, Stephen C. ; Schmechtig, Catherine ; Schmid, Claudia ; Shroyer, Emily L. ; Sterl, Andreas ; Sutton, Philip J. H. ; Talley, Lynne D. ; Tanhua, Toste ; Thierry, Virginie ; Thomalla, Sandy J. ; Toole, John M. ; Troisi, Ariel ; Trull, Thomas W. ; Turton, Jon ; Velez-Belchi, Pedro ; Walczowski, Waldemar ; Wang, Haili ; Wanninkhof, Rik ; Waterhouse, Amy F. ; Waterman, Stephanie N. ; Watson, Andrew J. ; Wilson, Cara ; Wong, Annie P. S. ; Xu, Jianping ; Yasuda, Ichiro
    The Argo Program has been implemented and sustained for almost two decades, as a global array of about 4000 profiling floats. Argo provides continuous observations of ocean temperature and salinity versus pressure, from the sea surface to 2000 dbar. The successful installation of the Argo array and its innovative data management system arose opportunistically from the combination of great scientific need and technological innovation. Through the data system, Argo provides fundamental physical observations with broad societally-valuable applications, built on the cost-efficient and robust technologies of autonomous profiling floats. Following recent advances in platform and sensor technologies, even greater opportunity exists now than 20 years ago to (i) improve Argo’s global coverage and value beyond the original design, (ii) extend Argo to span the full ocean depth, (iii) add biogeochemical sensors for improved understanding of oceanic cycles of carbon, nutrients, and ecosystems, and (iv) consider experimental sensors that might be included in the future, for example to document the spatial and temporal patterns of ocean mixing. For Core Argo and each of these enhancements, the past, present, and future progression along a path from experimental deployments to regional pilot arrays to global implementation is described. The objective is to create a fully global, top-to-bottom, dynamically complete, and multidisciplinary Argo Program that will integrate seamlessly with satellite and with other in situ elements of the Global Ocean Observing System (Legler et al., 2015). The integrated system will deliver operational reanalysis and forecasting capability, and assessment of the state and variability of the climate system with respect to physical, biogeochemical, and ecosystems parameters. It will enable basic research of unprecedented breadth and magnitude, and a wealth of ocean-education and outreach opportunities.
  • Article
    Autonomous, high-resolution observations of particle flux in the oligotrophic ocean
    (Copernicus Publications on behalf of the European Geosciences Union, 2013-08-16) Estapa, Margaret L. ; Buesseler, Ken O. ; Boss, Emmanuel S. ; Gerbi, Gregory P.
    Observational gaps limit our understanding of particle flux attenuation through the upper mesopelagic because available measurements (sediment traps and radiochemical tracers) have limited temporal resolution, are labor-intensive, and require ship support. Here, we conceptually evaluate an autonomous, optical proxy-based method for high-resolution observations of particle flux. We present four continuous records of particle flux collected with autonomous profiling floats in the western Sargasso Sea and the subtropical North Pacific, as well as one shorter record of depth-resolved particle flux near the Bermuda Atlantic Time-series Study (BATS) and Oceanic Flux Program (OFP) sites. These observations illustrate strong variability in particle flux over very short (~1-day) timescales, but at longer timescales they reflect patterns of variability previously recorded during sediment trap time series. While particle flux attenuation at BATS/OFP agreed with the canonical power-law model when observations were averaged over a month, flux attenuation was highly variable on timescales of 1–3 days. Particle fluxes at different depths were decoupled from one another and from particle concentrations and chlorophyll fluorescence in the immediately overlying surface water, consistent with horizontal advection of settling particles. We finally present an approach for calibrating this optical proxy in units of carbon flux, discuss in detail the related, inherent physical and optical assumptions, and look forward toward the requirements for the quantitative application of this method in highly time-resolved studies of particle export and flux attenuation.
  • Preprint
    Turbulence-plankton interactions : a new cartoon
    ( 2009-02-11) Jumars, Peter A. ; Trowbridge, John H. ; Boss, Emmanuel S. ; Karp-Boss, Lee
    Climate change will alter turbulence intensity, motivating greater attention to mechanisms of turbulence effects on organisms. Many analytic and analog models used to simulate and assess effects of turbulence on plankton rely on a one-dimensional simplification of the dissipative scales of turbulence, i.e., simple, steady, uniaxial shears, as produced in Couette vessels. There shear rates are constant and spatially uniform, and hence so is vorticity. Studies in such Couette flows have greatly informed, spotlighting stable orientations of nonspherical particles and predictable, periodic, rotational motions of steadily sheared particles in Jeffery orbits that steepen concentration gradients around nutrient-absorbing phytoplankton and other chemically (re)active particles. Over the last decade, however, turbulence research within fluid dynamics has focused on the structure of dissipative vortices in space and time and on spatially and temporally varying 2 vorticity fields in particular. Because steadily and spatially uniformly sheared flows are exceptional, so therefore are stable orientations for particles in turbulent flows. Vorticity gradients, finite net diffusion of vorticity and small radii of curvature of streamlines are ubiquitous features of turbulent vortices at dissipation scales that are explicitly excluded from simple, steady Couette flows. All of these flow components contribute instabilities that cause rotational motions of particles and so are important to simulate in future laboratory devices designed to assess effects of turbulence on nutrient uptake, particle coagulation and predatorprey encounter in the plankton. The Burgers vortex retains these signature features of turbulence and provides a simplified “cartoon” of vortex structure and dynamics that nevertheless obeys the Navier-Stokes equations. Moreover, this idealization closely resembles many dissipative vortices observed in both the laboratory and the field as well as in direct numerical simulations of turbulence. It is simple enough to allow both simulation in numerical models and fabrication of analog devices that selectively reproduce its features. Exercise of such numerical and analog models promises additional insights into mechanisms of turbulence effects on passive trajectories and local accumulations of both living and nonliving particles, into solute exchange with living and nonliving particles and into more subtle influences on sensory processes and swimming trajectories of plankton, including demersal organisms and settling larvae in turbulent bottom boundary layers. The literature on biological consequences of vortical turbulence has focused primarily on the smallest, Kolmogorov-scale vortices of length scale η. Theoretical dissipation spectra and direct numerical simulation, however, indicate that typical dissipative vortices with radii of 7η to 8η, peak azimuthal speeds of order 1 cm s-1 and lifetimes of order 10 s as a minimum (and much longer for moderate pelagic turbulence intensities) deserve new attention in studies of biological effects of turbulence.
  • Article
    Real-time quality control of optical backscattering data from Biogeochemical-Argo floats
    (European Commission, 2022-10-13) Dall'Olmo, Giorgio ; Bhaskar TVS, Udaya ; Bittig, Henry ; Boss, Emmanuel ; Brewster, Jodi ; Claustre, Hervé ; Donnelly, Matt ; Maurer, Tanya ; Nicholson, David ; Paba, Violetta ; Plant, Josh ; Poteau, Antoine ; Sauzède, Raphaëlle ; Schallenberg, Christina ; Schmechtig, Catherine ; Schmid, Claudia ; Xing, Xiaogang
    Background: Biogeochemical-Argo floats are collecting an unprecedented number of profiles of optical backscattering measurements in the global ocean. Backscattering (BBP) data are crucial to understanding ocean particle dynamics and the biological carbon pump. Yet, so far, no procedures have been agreed upon to quality control BBP data in real time. Methods: Here, we present a new suite of real-time quality-control tests and apply them to the current global BBP Argo dataset. The tests were developed by expert BBP users and Argo data managers and have been implemented on a snapshot of the entire Argo dataset. Results: The new tests are able to automatically flag most of the “bad” BBP profiles from the raw dataset. Conclusions: The proposed tests have been approved by the Biogeochemical-Argo Data Management Team and will be implemented by the Argo Data Assembly Centres to deliver real-time quality-controlled profiles of optical backscattering. Provided they reach a pressure of about 1000 dbar, these tests could also be applied to BBP profiles collected by other platforms.
  • Article
    Aerial imaging of fluorescent dye in the near shore
    (American Meteorological Society, 2014-06) Clark, David B. ; Lenain, Luc ; Feddersen, Falk ; Boss, Emmanuel S. ; Guza, R. T.
    Aerial images are used to quantify the concentration of fluorescent Rhodamine water tracing (WT) dye in turbid and optically deep water. Tracer releases near the shoreline of an ocean beach and near a tidal inlet were observed with a two-band multispectral camera and a pushbroom hyperspectral imager, respectively. The aerial observations are compared with near-surface in situ measurements. The ratio of upwelling radiance near the Rhodamine WT excitation and emission peaks varies linearly with the in situ dye concentrations for concentrations <20 ppb (r2 = 0.70 and r2 = 0.85–0.88 at the beach and inlet, respectively). The linear relationship allows for relative tracer concentration estimates without in situ calibration. The O(1 m) image pixels resolve complex flow structures on the inner shelf that transport and mix tracer.
  • Article
    Advantages and limitations to the use of optical measurements to study sediment properties
    (MDPI, 2018-12-19) Boss, Emmanuel S. ; Sherwood, Christopher R. ; Hill, Paul S. ; Milligan, Tim
    Measurements of optical properties have been used for decades to study particle distributions in the ocean. They are useful for estimating suspended mass concentration as well as particle-related properties such as size, composition, packing (particle porosity or density), and settling velocity. Measurements of optical properties are, however, biased, as certain particles, because of their size, composition, shape, or packing, contribute to a specific property more than others. Here, we study this issue both theoretically and practically, and we examine different optical properties collected simultaneously in a bottom boundary layer to highlight the utility of such measurements. We show that the biases we are likely to encounter using different optical properties can aid our studies of suspended sediment. In particular, we investigate inferences of settling velocity from vertical profiles of optical measurements, finding that the effects of aggregation dynamics can seldom be ignored.
  • Article
    Rate and apparent quantum yield of photodissolution of sedimentary organic matter
    (Association for the Sciences of Limnology and Oceanography, 2012-11) Estapa, Margaret L. ; Mayer, Lawrence M. ; Boss, Emmanuel S.
    We quantified rates of photochemical dissolution (photodissolution) of organic carbon in coastal Louisiana suspended sediments, conducting experiments under well-defined conditions of irradiance and temperature. Optical properties of the suspended sediments were characterized and used in a radiative transfer model to compute irradiances within turbid suspensions. Photodissolution rate increased with temperature (T), with activation energy of 32 ± 7 kJ mol−1, which implicates indirect (non-photochemical) steps in the net reaction. In most samples, dissolved organic carbon (DOC) concentration increased approximately linearly with time over the first 4 h of irradiation under broadband simulated sunlight, after higher rates in the initial hour of irradiation. Four-hour rates ranged from 2.3 µmol DOC m−3 s−1 to 3.2 µmol DOC m−3 s−1, but showed no relation to sample origin within the study area, organic carbon or reducible iron content, or mass-specific absorption coefficient. First-hour rates were higher—from 3.5 µmol DOC m−3 s−1 to 7.8 µmol DOC m−3 s−1—and correlated well with sediment reducible iron (itself often associated with organic matter). The spectral apparent quantum yield (AQY) for photodissolution was computed by fitting DOC photoproduction rates under different spectral irradiance distributions to corresponding rates of light absorption by particles. The photodissolution AQY magnitude is similar to most published dissolved-phase AQY spectra for dissolved inorganic carbon photoproduction, which suggests that in turbid coastal waters where particles dominate light absorption, DOC photoproduction from particles exceeds photooxidation of DOC.
  • Article
    Mercury dynamics in a San Francisco estuary tidal wetland : assessing dynamics using in situ measurements
    (Springer, 2012-04-03) Bergamaschi, Brian A. ; Fleck, Jacob A. ; Downing, Bryan D. ; Boss, Emmanuel S. ; Pellerin, Brian A. ; Ganju, Neil K. ; Schoellhamer, David H. ; Byington, Amy A. ; Heim, Wesley A. ; Stephenson, Mark ; Fujii, Roger
    We used high-resolution in situ measurements of turbidity and fluorescent dissolved organic matter (FDOM) to quantitatively estimate the tidally driven exchange of mercury (Hg) between the waters of the San Francisco estuary and Browns Island, a tidal wetland. Turbidity and FDOM—representative of particle-associated and filter-passing Hg, respectively—together predicted 94 % of the observed variability in measured total mercury concentration in unfiltered water samples (UTHg) collected during a single tidal cycle in spring, fall, and winter, 2005–2006. Continuous in situ turbidity and FDOM data spanning at least a full spring-neap period were used to generate UTHg concentration time series using this relationship, and then combined with water discharge measurements to calculate Hg fluxes in each season. Wetlands are generally considered to be sinks for sediment and associated mercury. However, during the three periods of monitoring, Browns Island wetland did not appreciably accumulate Hg. Instead, gradual tidally driven export of UTHg from the wetland offset the large episodic on-island fluxes associated with high wind events. Exports were highest during large spring tides, when ebbing waters relatively enriched in FDOM, dissolved organic carbon (DOC), and filter-passing mercury drained from the marsh into the open waters of the estuary. On-island flux of UTHg, which was largely particle-associated, was highest during strong winds coincident with flood tides. Our results demonstrate that processes driving UTHg fluxes in tidal wetlands encompass both the dissolved and particulate phases and multiple timescales, necessitating longer term monitoring to adequately quantify fluxes.
  • Article
    Globally 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, Ward
    In this paper we review the technologies available to make globally quantitative observations of particles in general—and plankton in particular—in the world oceans, and for sizes varying from sub-microns to centimeters. Some of these technologies have been available for years while others have only recently emerged. Use of these technologies is critical to improve understanding of the processes that control abundances, distributions and composition of plankton, provide data necessary to constrain and improve ecosystem and biogeochemical models, and forecast changes in marine ecosystems in light of climate change. In this paper we begin by providing the motivation for plankton observations, quantification and diversity qualification on a global scale. We then expand on the state-of-the-art, detailing a variety of relevant and (mostly) mature technologies and measurements, including bulk measurements of plankton, pigment composition, uses of genomic, optical and acoustical methods as well as analysis using particle counters, flow cytometers and quantitative imaging devices. We follow by highlighting the requirements necessary for a plankton observing system, the approach to achieve it and associated challenges. We conclude with ranked action-item recommendations for the next 10 years to move toward our vision of a holistic ocean-wide plankton observing system. Particularly, we suggest to begin with a demonstration project on a GO-SHIP line and/or a long-term observation site and expand from there, ensuring that issues associated with methods, observation tools, data analysis, quality assessment and curation are addressed early in the implementation. Global coordination is key for the success of this vision and will bring new insights on processes associated with nutrient regeneration, ocean production, fisheries and carbon sequestration.
  • Preprint
    Depleted dissolved organic carbon and distinct bacterial communities in the water column of a rapid-flushing coral reef ecosystem
    ( 2011-01-11) Nelson, Craig E. ; Alldredge, Alice L. ; McCliment, Elizabeth A. ; Amaral-Zettler, Linda A. ; Carlson, Craig A.
    Coral reefs are highly productive ecosystems bathed in unproductive, low-nutrient oceanic waters, where microbially-dominated food webs are supported largely by bacterioplankton recycling of dissolved compounds. Despite evidence that benthic reef organisms efficiently scavenge particulate organic matter and inorganic nutrients from advected oceanic waters, our understanding of the role of bacterioplankton and dissolved organic matter in the interaction between reefs and the surrounding ocean remains limited. Here we present the results of a four-year study conducted in a well-characterized coral reef ecosystem (Paopao Bay, Moorea, French Polynesia) where changes in bacterioplankton abundance and dissolved organic carbon (DOC) concentrations were quantified and bacterial community structure variation was examined along spatial gradients of the reef:ocean interface. Our results illustrate that the reef is consistently depleted in concentrations of both DOC and bacterioplankton relative to offshore waters (averaging 79 µmol L-1 DOC and 5.5 X 108 cells L-1 offshore and 68 µmol L-1 DOC and 3.1 X 108 cells L-1 over the reef, respectively) across a four year time period. In addition, using a suite of culture-independent measures of bacterial community structure, we found consistent differentiation of reef bacterioplankton communities from those offshore or in a nearby embayment across all taxonomic levels. Reef habitats were enriched in Gamma-, Delta-, and Beta-proteobacteria, Bacteriodetes, Actinobacteria and Firmicutes. Specific bacterial phylotypes, including members of the SAR11, SAR116, Flavobacteria, and Synechococcus clades, exhibited clear gradients in relative abundance among nearshore habitats. Our observations indicate that this reef system removes oceanic DOC and exerts selective pressures on bacterioplankton community structure on timescales approximating reef water residence times, observations which are notable both because fringing reefs do not exhibit long residence times (unlike those characteristic of atoll lagoons) and because oceanic DOC is generally recalcitrant to degradation by ambient microbial assemblages. Our findings thus have interesting implications for the role of oceanic DOM and bacterioplankton in the ecology and metabolism of reef ecosystems.
  • Article
    Role of iron and organic carbon in mass-specific light absorption by particulate matter from Louisiana coastal waters
    (Association for the Sciences of Limnology and Oceanography, 2012-01) Estapa, Margaret L. ; Boss, Emmanuel S. ; Mayer, Lawrence M. ; Roesler, Collin S.
    We investigated the influences of organic content and mineralogical composition on light absorption by mostly mineral suspended particles in aquatic and coastal marine systems. Mass-specific absorption spectra of suspended particles and surface sediments from coastal Louisiana and the lower Mississippi and Atchafalaya rivers were measured with a centered sample-mount integrating sphere and analyzed in conjunction with organic carbon (OC), hydrochloric acid– (HCl-) extractable iron, and dithionite-extractable iron contents. Compositions and absorption properties were comparable to published values for similar particles. Dithionite-extractable iron was strongly correlated with absorption at ultraviolet (UV) and blue wavelengths, while OC and HCl-extractable iron were weakly but positively correlated. Oxidative removal of OC from sediments caused small and variable changes in absorption, while dithionite extraction of iron oxides strongly reduced absorption. Shoulders in the absorption spectra corresponded to absorption bands of iron oxide minerals, and their intensities were well correlated to dithionite-extractable iron contents of the samples. These findings support a primary role for iron oxide and hydroxide minerals in the mass-specific absorption of mostly inorganic particles from the terrestrially influenced coast of Louisiana. Riverine particles had higher dithionite-extractable iron contents and iron oxide–specific absorption features than did marine particles, consistent with current knowledge regarding differential transport of particulate iron oxides and hydroxides through estuarine salinity gradients and reductive alteration of these oxide phases on the Louisiana shelf. The quantifiable dependence of UV absorption features on iron oxide content suggests that, under certain conditions, in situ hyperspectral absorption measurements could be designed to monitor water-column iron mineral transport and transformation.
  • Article
    The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean
    (Public Library of Science, 2019-09-23) Planes, Serge ; Allemand, Denis ; Agostini, Sylvain ; Banaigs, Bernard ; Boissin, Emilie ; Boss, Emmanuel S. ; Bourdin, Guillaume ; Bowler, Chris ; Douville, Eric ; Flores, J. Michel ; Forcioli, Didier ; Furla, Paola ; Galand, Pierre E. ; Ghiglione, Jean-Francois ; Gilson, Eric ; Lombard, Fabien ; Moulin, Clémentine ; Pesant, Stephane ; Poulain, Julie ; Reynaud, Stephanie ; Romac, Sarah ; Sullivan, Matthew B. ; Sunagawa, Shinichi ; Thomas, Olivier P. ; Troublé, Romain ; de Vargas, Colomban ; Vega Thurber, Rebecca ; Voolstra, Christian R. ; Wincker, Patrick ; Tara Pacific Consortium
    Coral reefs are the most diverse habitats in the marine realm. Their productivity, structural complexity, and biodiversity critically depend on ecosystem services provided by corals that are threatened because of climate change effects—in particular, ocean warming and acidification. The coral holobiont is composed of the coral animal host, endosymbiotic dinoflagellates, associated viruses, bacteria, and other microeukaryotes. In particular, the mandatory photosymbiosis with microalgae of the family Symbiodiniaceae and its consequences on the evolution, physiology, and stress resilience of the coral holobiont have yet to be fully elucidated. The functioning of the holobiont as a whole is largely unknown, although bacteria and viruses are presumed to play roles in metabolic interactions, immunity, and stress tolerance. In the context of climate change and anthropogenic threats on coral reef ecosystems, the Tara Pacific project aims to provide a baseline of the “-omics” complexity of the coral holobiont and its ecosystem across the Pacific Ocean and for various oceanographically distinct defined areas. Inspired by the previous Tara Oceans expeditions, the Tara Pacific expedition (2016–2018) has applied a pan-ecosystemic approach on coral reefs throughout the Pacific Ocean, drawing an east–west transect from Panama to Papua New Guinea and a south–north transect from Australia to Japan, sampling corals throughout 32 island systems with local replicates. Tara Pacific has developed and applied state-of-the-art technologies in very-high-throughput genetic sequencing and molecular analysis to reveal the entire microbial and chemical diversity as well as functional traits associated with coral holobionts, together with various measures on environmental forcing. This ambitious project aims at revealing a massive amount of novel biodiversity, shedding light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs and providing a reference of the biological state of modern coral reefs in the Anthropocene.
  • Article
    Plankton imagery data inform satellite-based estimates of diatom carbon
    (American Geophysical Union, 2022-06-18) Chase, Alison P. ; Boss, Emmanuel S. ; Haëntjens, Nils ; Culhane, Emmett ; Roesler, Collin S. ; Karp-Boss, Lee
    Estimating the biomass of phytoplankton communities via remote sensing is a key requirement for understanding global ocean ecosystems. Of particular interest is the carbon associated with diatoms given their unequivocal ecological and biogeochemical roles. Satellite-based algorithms often rely on accessory pigment proxies to define diatom biomass, despite a lack of validation against independent diatom biomass measurements. We used imaging-in-flow cytometry to quantify diatom carbon in the western North Atlantic, and compared results to those obtained from accessory pigment-based approximations. Based on this analysis, we offer a new empirical formula to estimate diatom carbon concentrations from chlorophyll a. Additionally, we developed a neural network model in which we integrated chlorophyll a and environmental information to estimate diatom carbon distributions in the western North Atlantic. The potential for improving satellite-based diatom carbon estimates by integrating environmental information into a model, compared to models that are based solely on chlorophyll a, is discussed.
  • Article
    Recommendations for plankton measurements on OceanSITES moorings with relevance to other observing sites
    (Frontiers Media, 2022-07-22) Boss, Emmanuel S. ; Waite, Anya M. ; Karstensen, Johannes ; Trull, Thomas W. ; Muller-Karger, Frank E. ; Sosik, Heidi M. ; Uitz, Julia ; Acinas, Silvia G. ; Fennel, Katja ; Berman-Frank, Ilana ; Thomalla, Sandy J. ; Yamazaki, Hidekatsu ; Batten, Sonia ; Gregori, Gerald ; Richardson, Anthony J. ; Wanninkhof, Rik
    Measuring plankton and associated variables as part of ocean time-series stations has the potential to revolutionize our understanding of ocean biology and ecology and their ties to ocean biogeochemistry. It will open temporal scales (e.g., resolving diel cycles) not typically sampled as a function of depth. In this review we motivate the addition of biological measurements to time-series sites by detailing science questions they could help address, reviewing existing technology that could be deployed, and providing examples of time-series sites already deploying some of those technologies. We consider here the opportunities that exist through global coordination within the OceanSITES network for long-term (climate) time series station in the open ocean. Especially with respect to data management, global solutions are needed as these are critical to maximize the utility of such data. We conclude by providing recommendations for an implementation plan.
  • Article
    Bio-GO-SHIP: the time is right to establish global repeat sections of ocean biology
    (Frontiers Media, 2022-01-10) Clayton, Sophie A. ; Alexander, Harriet ; Graff, Jason R. ; Poulton, Nicole J. ; Thompson, Luke R. ; Benway, Heather M. ; Boss, Emmanuel S. ; Martiny, Adam C.
    In this article, we present Bio-GO-SHIP, a new ocean observing program that will incorporate sustained and consistent global biological ocean observations into the Global Ocean Ship-based Hydrographic Investigations Program (GO-SHIP). The goal of Bio-GO-SHIP is to produce systematic and consistent biological observations during global ocean repeat hydrographic surveys, with a particular focus on the planktonic ecosystem. Ocean plankton are an essential component of the earth climate system, form the base of the oceanic food web and thereby play an important role in influencing food security and contributing to the Blue Economy. Despite its importance, ocean biology is largely under-sampled in time and space compared to physical and chemical properties. This lack of information hampers our ability to understand the role of plankton in regulating biogeochemical processes and fueling higher trophic levels, now and in future ocean conditions. Traditionally, many of the methods used to quantify biological and ecosystem essential ocean variables (EOVs), measures that provide valuable information on the ecosystem, have been expensive and labor- and time-intensive, limiting their large-scale deployment. In the last two decades, new technologies have been developed and matured, making it possible to greatly expand our biological ocean observing capacity. These technologies, including cell imaging, bio-optical sensors and 'omic tools, can be combined to provide overlapping measurements of key biological and ecosystem EOVs. New developments in data management and open sharing can facilitate meaningful synthesis and integration with concurrent physical and chemical data. Here we outline how Bio-GO-SHIP leverages these technological advances to greatly expand our knowledge and understanding of the constituents and function of the global ocean plankton ecosystem.