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  • Oxygen  (10)
  • Dissolved organic carbon
  • Flow-through
  • John Wiley & Sons  (9)
  • American Chemical Society  (2)
  • American Society for Microbiology  (2)
  • American Chemical Society (ACS)
  • 1
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Geophysical Research Letters 42 (2015): 4032–4039, doi:10.1002/2015GL063065.
    Description: Using autonomous underwater gliders, we quantified diurnal periodicity in dissolved oxygen, chlorophyll, and temperature in the subtropical North Pacific near the Hawaii Ocean Time-series (HOT) Station ALOHA during summer 2012. Oxygen optodes provided sufficient stability and precision to quantify diel cycles of average amplitude of 0.6 µmol kg−1. A theoretical diel curve was fit to daily observations to infer an average mixed layer gross primary productivity (GPP) of 1.8 mmol O2 m−3 d−1. Cumulative net community production (NCP) over 110 days was 500 mmol O2 m−2 for the mixed layer, which averaged 57 m in depth. Both GPP and NCP estimates indicated a significant period of below-average productivity at Station ALOHA in 2012, an observation confirmed by 14C productivity incubations and O2/Ar ratios. Given our success in an oligotrophic gyre where biological signals are small, our diel GPP approach holds promise for remote characterization of productivity across the spectrum of marine environments.
    Description: The authors acknowledge support from the National Science Foundation (NSF) through an NSF Science and Technology Center, the Center for Microbial Oceanography Research and Education (C-MORE; NSF EF-0424599). D.N. also was supported by NSF (OCE-1129644) and an Independent Study Award from the Woods Hole Oceanographic Institution (WHOI). D.M.K. was also supported by the Gordon and Betty Moore Foundation. WHOI Summer Student Fellow Cole Stites-Clayton, Stanford University, contributed to early stages of Seaglider data analysis and was supported by an NSF REU grant to WHOI (OCE-1156952).
    Keywords: Primary productivity ; Glider ; Diel ; Oxygen ; Net community production ; Hawaii
    Repository Name: Woods Hole Open Access Server
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  • 2
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of Geophysical Research: Oceans 123 (2018): 6392-6407, doi:10.1029/2018JC014129.
    Description: Low levels of dissolved oxygen (DO) occur in many embayments throughout the world and have numerous detrimental effects on biota. Although measurement of in situ DO is straightforward with modern instrumentation, quantifying the volume of water in a given embayment that is hypoxic (hypoxic volume (HV)) is a more difficult task; however, this information is critical for determining whether management efforts to increase DO are having an overall impact. This paper uses output from a three‐dimensional numerical model to demonstrate that HV in Chesapeake Bay can be estimated well with as few as two vertical profiles. In addition, the cumulative hypoxic volume (HVC; the total amount of hypoxia in a given year) can be calculated with relatively low uncertainty (〈10%) if continuous DO data are available from two strategically positioned vertical profiles. This is because HV in the Chesapeake Bay is strongly constrained by the geometry of the embayment. A simple Geometric HV calculation method is presented and numerical model results are used to illustrate that for calculating HVC, the results using two daily‐averaged profiles are typically more accurate than those of the standard method that interpolates bimonthly cruise data. Bimonthly data produce less accurate estimates of HVC because high‐frequency changes in oxygen concentration, for example, due to regional‐weather‐ or storm‐induced changes in wind direction and magnitude, are not resolved. The advantages of supplementing cruise‐based sampling with continuous vertical profiles to estimate HVC should be applicable to other systems where hypoxic water is constrained to a specific area by bathymetry.
    Description: NOAA Grant Number: NA13NOS0120139
    Keywords: Chesapeake Bay ; Oxygen ; Dead zone ; Hypoxia ; Observing systems ; Estuary
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  • 3
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of Geophysical Research: Oceans 123 (2018): 7237-7263, doi:10.1029/2018JC013950.
    Description: Resuspension affects water quality in coastal environments by entraining seabed organic matter into the water column, which can increase remineralization, alter seabed fluxes, decrease water clarity, and affect oxygen and nutrient dynamics. Nearly all numerical models of water column biogeochemistry, however, simplify seabed and bottom boundary layer processes and neglect resuspension. Here we implemented HydroBioSed, a coupled hydrodynamic‐sediment transport‐biogeochemical model to examine the role of resuspension in regulating oxygen and nitrogen dynamics on timescales of a day to a month. The model was implemented for the northern Gulf of Mexico, where the extent of summertime hypoxia is sensitive to seabed and bottom boundary layer processes. Results indicated that particulate organic matter remineralization in the bottom water column increased by an order of magnitude during resuspension events. This increased sediment oxygen consumption and ammonium production, which were defined as the sum of seabed fluxes of oxygen and ammonium, plus oxygen consumption and ammonium production in the water column due to resuspended organic matter. The increases in remineralization impacted biogeochemical dynamics to a greater extent than resuspension‐induced seabed fluxes and oxidation of reduced chemical species. The effect of resuspension on bottom water biogeochemistry increased with particulate organic matter availability, which was modulated by sediment transport patterns. Overall, when averaged over the shelf and on timescales of a month in the numerical model, cycles of erosion and deposition accounted for about two thirds of sediment oxygen consumption and almost all of the sediment ammonium production.
    Description: DOC | National Oceanic and Atmospheric Administration (NOAA); U.S. National Oceanic and Atmospheric Administration's National Centers for Coastal Ocean Science Center for Sponsored Coastal Ocean Research Grant Numbers: NA09NOS4780231, NA09NOS4780229
    Keywords: Regional Ocean Modeling System (ROMS) ; Northern Gulf of Mexico continental shelf hypoxia ; Sediment transport and resuspension ; Particulate organic carbon (POC) ; Nitrogen ; Oxygen
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  • 4
    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2015. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 120 (2015): 608–633, doi:10.1002/2014JC010254.
    Description: The coastal waters of the northern portion of the California Current System experience a seasonal decline in oxygen concentrations and hypoxia over the summer upwelling season that results in negative impacts on habitat for many organisms. Using a regional model extending from 43°N to 50°N, with an oxygen component developed in this study, drivers of seasonal and regional oxygen variability are identified. The model includes two pools of detritus, which was an essential addition in order to achieve good agreement with the observations. The model was validated using an extensive array of hydrographic and moored observations. The model captures the observed seasonal decline as well as spatial trends in bottom oxygen. Spatially, three regions of high respiration are identified as locations where hypoxia develops each modeled year. Two of the regions are previously identified recirculation regions. The third region is off of the Washington coast. Sediment oxygen demand causes the region on the Washington coast to be susceptible to hypoxia and is correlated to the broad area of shallow shelf (〈60 m) in the region. Respiration and circulation-driven divergence contribute similar (60, 40%, respectively) amounts to the integrated oxygen budget on the Washington coast while respiration dominates the Oregon coast. Divergence, or circulation, contributes to the oxygen dynamics on the shelf in two ways: first, through the generation of retention features, and second, by determining variability.
    Description: This work was supported by a postdoctoral fellowship to Samantha Siedlecki from JISAO and the Program on Climate Change at the University of Washington, and grants from the Coastal Ocean Program of the National Oceanic and Atmospheric Administration (NOAA) (NA09NOS4780180) and the National Science Foundation (NSF) (OCE0942675) as part of the Pacific Northwest Toxins (PNWTOX) project.
    Description: 2015-08-05
    Keywords: Hypoxia ; Oxygen ; Respiration ; Upwelling
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  • 5
    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2017. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Global Biogeochemical Cycles 31 (2017): 1066–1088, doi:10.1002/2016GB005488.
    Description: In situ oxygen tracers (triple oxygen isotope and oxygen/argon ratios) were used to evaluate meridional trends in surface biological production and export efficiency across ~8000 km of the tropical and subtropical South Atlantic in March–May 2013. We used observations of picophytoplankton, nanophytoplankton, and microphytoplankton to evaluate community structure and diversity and assessed the relationships of these characteristics with production, export efficiency, and particulate organic carbon (POC) fluxes. Rates of productivity were relatively uniform along most of the transect with net community production (NCP) between 0 and 10 mmol O2 m−2 d−1, gross primary production (GPP) between 40 and 100 mmol O2 m−2 d−1, and NCP/GPP, a measure of export efficiency, ranging from 0.1 to 0.2 (0.05–0.1 in carbon units). However, notable exceptions to this basin-scale homogeneity included two locations with highly enhanced NCP and export efficiency compared to surrounding regions. Export of POC and particulate nitrogen, derived from sediment traps, correlated with GPP across the transect, over which the surface community was dominated numerically by picophytoplankton. NCP, however, did not correlate with POC flux; the mean difference between NCP and POC flux was similar to published estimates of dissolved organic carbon export from the surface ocean. The interrelated rates of production presented in this work contribute to the understanding, building on the framework of better-studied ocean basins, of how carbon is biologically transported between the atmosphere and the deep ocean.
    Description: National Science Foundation (NSF) Grant Number: OCE 1029676; Gordon and Betty Moore Foundation Grant Grant Number: 537.01; Woods Hole Oceanographic Institution (WHOI); WHOI Devonshire Postdoctoral Scholarship; National Defense Science and Engineering Graduate Fellowship; WHOI Ocean Life Institute; Woods Hole Oceanographic Institution (WHOI) Ocean and Climate Change Institute NSF Grant Numbers: OCE 1029676, OCE 1154320
    Description: 2018-01-11
    Keywords: Oxygen ; Net community production ; Gross primary production ; Carbon flux ; Triple oxygen isotopes ; Argon
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  • 6
    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2013. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Biogeosciences 118 (2013): 385–399, doi:10.1002/jgrg.20032.
    Description: The sea-air biological O2 flux assessed from measurements of surface O2 supersaturation in excess of Ar supersaturation (“O2 bioflux”) is increasingly being used to constrain net community production (NCP) in the upper ocean mixed layer. In making these calculations, one generally assumes that NCP is at steady state, mixed layer depth is constant, and there is no O2 exchange across the base of the mixed layer. The object of this paper is to evaluate the magnitude of errors introduced by violations of these assumptions. Therefore, we examine the differences between the sea-air biological O2 flux and NCP in the Southern Ocean mixed layer as calculated using two ocean biogeochemistry general circulation models. In this approach, NCP is considered a known entity in the prognostic model, whereas O2 bioflux is estimated using the model-predicted O2/Ar ratio to compute the mixed layer biological O2 saturation and the gas transfer velocity to calculate flux. We find that the simulated biological O2 flux gives an accurate picture of the regional-scale patterns and trends in model NCP. However, on local scales, violations of the assumptions behind the O2/Ar method lead to significant, non-uniform differences between model NCP and biological O2 flux. These errors arise from two main sources. First, venting of biological O2 to the atmosphere can be misaligned from NCP in both time and space. Second, vertical fluxes of oxygen across the base of the mixed layer complicate the relationship between NCP and the biological O2 flux. Our calculations show that low values of O2 bioflux correctly register that NCP is also low (〈10 mmol m−2 day−1), but fractional errors are large when rates are this low. Values between 10 and 40 mmol m−2 day−1 in areas with intermediate mixed layer depths of 30 to 50 m have the smallest absolute and relative errors. Areas with O2 bioflux higher than 30 mmol m−2 day−1 and mixed layers deeper than 40 m tend to underestimate NCP by up to 20 mmol m−2 day−1. Excluding time periods when mixed layer biological O2 is undersaturated, O2 bioflux underestimates time-averaged NCP by 5%–15%. If these time periods are included, O2 bioflux underestimates mixed layer NCP by 20%–35% in the Southern Ocean. The higher error estimate is relevant if one wants to estimate seasonal NCP since a significant amount of biological production takes place when mixed layer biological O2 is undersaturated.
    Description: This work was supported in part by funding from the National Aeronautic and Space Administration (NASA NNX08AF12G) and National Science Foundation (NSF OPP-0823101).
    Keywords: Biological production ; Southern Ocean ; O2/Ar ; Modeling ; Oxygen ; GCM
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  • 7
    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2018. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Biogeosciences 123 (2018): 2711-2726, doi:10.1029/2018JG004441.
    Description: Accurate determination of air‐water gas exchange fluxes is critically important for calculating ecosystem metabolism rates from dissolved oxygen in shallow aquatic environments. We present a unique data set of the noble gases neon, argon, krypton, and xenon in a salt marsh pond to demonstrate how the dissolved noble gases can be used to quantify gas transfer processes and evaluate gas exchange parameterizations in shallow, near‐shore environments. These noble gases are sensitive to a variety of physical processes, including bubbling. We thus additionally use this data set to demonstrate how dissolved noble gases can be used to assess the contribution of bubbling from the sediments (ebullition) to gas fluxes. We find that while literature gas exchange parameterizations do well in modeling more soluble gases, ebullition must be accounted for in order to correctly calculate fluxes of the lighter noble gases. In particular, for neon and argon, the ebullition flux is larger than the differences in the diffusive gas exchange flux estimated by four different wind speed‐based parameterizations for gas exchange. We present an application of noble gas derived ebullition rates to improve estimates of oxygen metabolic fluxes in this shallow pond environment. Up to 21% of daily net oxygen production by photosynthesis may be lost from the pond via ebullition during some periods of biologically and physically produced supersaturation. Ebullition could be an important flux of oxygen and other gases that is measurable with noble gases in other shallow aquatic environments.
    Description: NSF. Grant Numbers 1233678, 1238212, DEB 1354494; Woods Hole Oceanographic Institution (WHOI); National Defense Science and Engineering Graduate Fellowship; Northeast Climate Science Center Grant Number: DOI G12AC00001
    Description: 2019-03-07
    Keywords: Bubbles ; Ecosystem metabolism ; Noble gases ; Ebullition ; Oxygen ; Salt marsh pond
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  • 8
    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Inomura, K., Deutsch, C., Wilson, S. T., Masuda, T., Lawrenz, E., Lenka, B., Sobotka, R., Gauglitz, J. M., Saito, M. A., Prášil, O., & Follows, M. J. Quantifying oxygen management and temperature and light dependencies of nitrogen fixation by Crocosphaera watsonii. Msphere, 4(6), (2019): e00531-19, doi: 10.1128/msphere.00531-19.
    Description: Crocosphaera is a major dinitrogen (N2)-fixing microorganism, providing bioavailable nitrogen (N) to marine ecosystems. The N2-fixing enzyme nitrogenase is deactivated by oxygen (O2), which is abundant in marine environments. Using a cellular scale model of Crocosphaera sp. and laboratory data, we quantify the role of three O2 management strategies by Crocosphaera sp.: size adjustment, reduced O2 diffusivity, and respiratory protection. Our model predicts that Crocosphaera cells increase their size under high O2. Using transmission electron microscopy, we show that starch granules and thylakoid membranes are located near the cytoplasmic membranes, forming a barrier for O2. The model indicates a critical role for respiration in protecting the rate of N2 fixation. Moreover, the rise in respiration rates and the decline in ambient O2 with temperature strengthen this mechanism in warmer water, providing a physiological rationale for the observed niche of Crocosphaera at temperatures exceeding 20°C. Our new measurements of the sensitivity to light intensity show that the rate of N2 fixation reaches saturation at a lower light intensity (∼100 μmol m−2 s−1) than photosynthesis and that both are similarly inhibited by light intensities of 〉500 μmol m−2 s−1. This suggests an explanation for the maximum population of Crocosphaera occurring slightly below the ocean surface.
    Description: We thank Stephanie Dutkiewicz and Sallie W. Chisholm for useful discussion, Martin Lukeš for technical assistance for the N2 fixation measurement, and the members of Writing and Communication Center at MIT for their advice on writing. This research was supported by the Japan Student Service Organization (JASSO) (grant L11171020001 to K.I.), the Gordon and Betty Moore Foundation (grant GBMF 3775 to C.D. and grant GBMF 3778 to M.J.F.), the U.S. National Science Foundation (grant OCE-1756524 to S.T.W., grant OCE-1558702 to M.J.F., and grant OCE-PRF 1421196 to J.M.G), the Simons Foundation (Simons Postdoctoral Fellowship in Marine Microbial Ecology award 544338 to K.I., Simons Collaboration on Ocean Processes and Ecology award 329108 to M.J.F., Simons Collaboration on Computational BIOgeochemical Modeling of Marine EcosystemS [CBIOMES] award 549931 to M.J.F.), the Czech Science Foundation (GAČR) (grant 16-15467S to O.P.), and the National Sustainability Programme (NPU) (grant LO1416 Algatech plus to O.P.).
    Keywords: Crocosphaera ; Carbon ; Cell flux model ; Daily cycle ; Iron ; Light ; Nitrogen ; Nitrogen fixation ; Oxygen ; Photosynthesis ; Temperature
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  • 9
    Publication Date: 2022-10-21
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Colson, B. C., & Michel, A. P. M. Flow-through quantification of microplastics using impedance spectroscopy. ACS Sensors, 6(1), (2021): 238–244, doi:10.1021/acssensors.0c02223.
    Description: Understanding the sources, impacts, and fate of microplastics in the environment is critical for assessing the potential risks of these anthropogenic particles. However, our ability to quantify and identify microplastics in aquatic ecosystems is limited by the lack of rapid techniques that do not require visual sorting or preprocessing. Here, we demonstrate the use of impedance spectroscopy for high-throughput flow-through microplastic quantification, with the goal of rapid measurement of microplastic concentration and size. Impedance spectroscopy characterizes the electrical properties of individual particles directly in the flow of water, allowing for simultaneous sizing and material identification. To demonstrate the technique, spike and recovery experiments were conducted in tap water with 212–1000 μm polyethylene beads in six size ranges and a variety of similarly sized biological materials. Microplastics were reliably detected, sized, and differentiated from biological materials via their electrical properties at an average flow rate of 103 ± 8 mL/min. The recovery rate was ≥90% for microplastics in the 300–1000 μm size range, and the false positive rate for the misidentification of the biological material as plastic was 1%. Impedance spectroscopy allowed for the identification of microplastics directly in water without visual sorting or filtration, demonstrating its use for flow-through sensing.
    Description: The authors thank the Richard Saltonstall Charitable Foundation and the National Academies Keck Futures Initiative (NAKFI DBS13) for their funding support.
    Keywords: Microplastics ; Plastics ; Impedance spectroscopy ; Dielectric properties ; Instrumentation ; Particle detection ; Flow-through ; Environmental sensing
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  • 10
    Publication Date: 2023-02-25
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Miranda, K., Weigel, B., Fogarty, E., Veseli, I., Giblin, A., Eren, A., & Pfister, C. The diversity and functional capacity of microbes associated with coastal macrophytes. MSystems, 7(5),(2022): e0059222, https://doi.org/10.1128/msystems.00592-22.
    Description: Coastal marine macrophytes exhibit some of the highest rates of primary productivity in the world. They have been found to host a diverse set of microbes, many of which may impact the biology of their hosts through metabolisms that are unique to microbial taxa. Here, we characterized the metabolic functions of macrophyte-associated microbial communities using metagenomes collected from 2 species of kelp (Laminaria setchellii and Nereocystis luetkeana) and 3 marine angiosperms (Phyllospadix scouleri, P. serrulatus, and Zostera marina), including the rhizomes of two surfgrass species (Phyllospadix spp.), the seagrass Zostera marina, and the sediments surrounding P. scouleri and Z. marina. Using metagenomic sequencing, we describe 63 metagenome-assembled genomes (MAGs) that potentially benefit from being associated with macrophytes and may contribute to macrophyte fitness through their metabolic activity. Host-associated metagenomes contained genes for the use of dissolved organic matter from hosts and vitamin (B1, B2, B7, B12) biosynthesis in addition to a range of nitrogen and sulfur metabolisms that recycle dissolved inorganic nutrients into forms more available to the host. The rhizosphere of surfgrass and seagrass contained genes for anaerobic microbial metabolisms, including nifH genes associated with nitrogen fixation, despite residing in a well-mixed and oxygenated environment. The range of oxygen environments engineered by macrophytes likely explains the diversity of both oxidizing and reducing microbial metabolisms and contributes to the functional capabilities of microbes and their influences on carbon and nitrogen cycling in nearshore ecosystems.
    Description: We thank The University of Chicago’s Microbiome Center for pilot award funding, Washington Department of Natural Resources, grants 93099282 and 93100399 (CAP), and NSF-DEB grant (no. 1556874) awarded to J.T. Wootton. We appreciate the work of C. Sauceda in the isotope analysis, as well as A. Wootton, A. Wood, and K. Foreman in the field sampling. S. Owens and S. Greenwald at Argonne National Lab provided expertise in sequencing. K.M. was supported by an EE Fellowship from The University of Chicago.
    Keywords: Host-microbiome relationships ; Kelp ; Macrophytes ; Marine microbiology ; Oxygen ; Seagrass ; Surfgrass
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