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  • 1
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    Sub-tropical seagrass ecosystem metabolism measured by eddy covariance (2015)
    Inter-Research
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    Publication Date: 2022-05-25
    Description: Author Posting. © Inter-Research, 2015. This article is posted here by permission of Inter-Research for personal use, not for redistribution. The definitive version was published in Marine Ecology Progress Series 529 (2015): 75-90, doi:10.3354/meps11314.
    Description: The metabolism of seagrass ecosystems was examined at 4 sites in south Florida, USA, using the eddy covariance technique under in situ conditions. Three sites were located across a phosphorus-driven productivity gradient to examine the combined effects of dynamic variables (irradiance, flow velocity) and state variables (sediment phosphorus and organic content, seagrass biomass) on ecosystem metabolism and trophic status. Gross primary production and respiration rates varied significantly across Florida Bay in the summer of 2012 with the lowest rates (64 and –53 mmol O2 m–2 d–1, respectively) in low-phosphorus sediments in the northeast and the highest (287 and –212 mmol O2 m–2 d–1, respectively) in the southwest where sediment phosphorus, organic matter, and seagrass biomass are higher. Seagrass ecosystems offshore of the Florida Keys had similar large daily production and respiration rates (397 and –17 mmol O2 m–2 d–1, respectively) and were influenced by flow through the permeable offshore sediments. Across all sites, net ecosystem metabolism rates indicated that the seagrass ecosystems were autotrophic in the summertime. Substantial day-to-day variability in metabolic rates was found due to variations in irradiance and flow velocity. At all sites the relationship between photosynthesis and irradiance was linear and did not show any sign of saturation over the entire irradiance range (up to 1400 µmol photons m–2 s–1). This was likely due to the efficient use of light by the large photosynthetic surface area of the seagrass canopy, an effect which can only be examined by in situ measurements that integrate across all autotrophs in the seagrass ecosystem.
    Description: This study received financial support from the Jones Environmental and Barley Scholars Program at the University of Virginia and the National Science Foundation (Chemical Oceanography grant OCE- 0536431).
    Keywords: Seagrass ; Eddy covariance ; Metabolism ; Carbon cycling
    Repository Name: Woods Hole Open Access Server
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  • 2
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    Seagrass metabolism across a productivity gradient using the eddy covariance, Eulerian control volume, and biomass addition techniques (2015)
    John Wiley & Sons
    Details
    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): 3624–3639, doi:10.1002/2014JC010352.
    Description: The net ecosystem metabolism of the seagrass Thalassia testudinum was studied across a nutrient and productivity gradient in Florida Bay, Florida, using the Eulerian control volume, eddy covariance, and biomass addition techniques. In situ oxygen fluxes were determined by a triangular Eulerian control volume with sides 250 m long and by eddy covariance instrumentation at its center. The biomass addition technique evaluated the aboveground seagrass productivity through the net biomass added. The spatial and temporal resolutions, accuracies, and applicability of each method were compared. The eddy covariance technique better resolved the short-term flux rates and the productivity gradient across the bay, which was consistent with the long-term measurements from the biomass addition technique. The net primary production rates from the biomass addition technique, which were expected to show greater autotrophy due to the exclusion of sediment metabolism and belowground production, were 71, 53, and 30 mmol carbon m−2 d−1 at 3 sites across the bay. The net ecosystem metabolism was 35, 25, and 11 mmol oxygen m−2 d−1 from the eddy covariance technique and 10, −103, and 14 mmol oxygen m−2 d−1 from the Eulerian control volume across the same sites, respectively. The low-flow conditions in the shallow bays allowed for periodic stratification and long residence times within the Eulerian control volume that likely reduced its precision. Overall, the eddy covariance technique had the highest temporal resolution while producing accurate long-term flux rates that surpassed the capabilities of the biomass addition and Eulerian control volume techniques in these shallow coastal bays.
    Description: This research was conducted under Everglades National Park permit # EVER-2011-SCI-0057. This study received financial support from the Jones Environmental and Barley Scholars Program at the University of Virginia and the National Science Foundation (Chemical Oceanography grant OCE-0536431).
    Description: 2015-11-22
    Keywords: Eddy covariance ; Eulerian ; Metabolism ; Seagrass ; Eddy correlation
    Repository Name: Woods Hole Open Access Server
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  • 3
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    Eddy correlation measurements of oxygen fluxes in permeable sediments exposed to varying current flow and light (2014)
    Association for the Sciences of Limnology and Oceanography
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    Publication Date: 2022-05-26
    Description: Author Posting. © Association for the Sciences of Limnology and Oceanography, 2013. This article is posted here by permission of Association for the Sciences of Limnology and Oceanography for personal use, not for redistribution. The definitive version was published in Limnology and Oceanography 58 (2013): 1329–1343, doi:10.4319/lo.2013.58.4.1329.
    Description: Based on noninvasive eddy correlation measurements at a marine and a freshwater site, this study documents the control that current flow and light have on sediment–water oxygen fluxes in permeable sediments. The marine sediment was exposed to tidal-driven current and light, and the oxygen flux varied from night to day between −29 and 78 mmol m−2 d−1. A fitting model, assuming a linear increase in oxygen respiration with current flow, and a photosynthesis–irradiance curve for light-controlled production reproduced measured fluxes well (R2 = 0.992) and revealed a 4-fold increase in oxygen uptake when current velocity increased from ∼ 0 to 20 cm s−1. Application of the model to a week-long measured record of current velocity and light showed that net ecosystem metabolism varied substantially among days, between −27 and 31 mmol m−2 d−1, due to variations in light and current flow. This variation is likely typical of many shallow-water systems and highlights the need for long-term flux integrations to determine system metabolism accurately. At the freshwater river site, the sediment–water oxygen flux ranged from −360 to 137 mmol m−2 d−1. A direct comparison during nighttime with concurrent benthic chamber incubations revealed a 4.1 times larger eddy flux than that obtained with chambers. The current velocity during this comparison was 31 cm s−1, and the large discrepancy was likely caused by poor imitation by the chambers of the natural pore-water flushing at this high current velocity. These results emphasize the need for more noninvasive oxygen flux measurements in permeable sediments to accurately assess their role in local and global carbon budgets.
    Description: Support for this study was provided by the following National Science Foundation grants: OCE-0420575, OCE- 0536431, and OCE-1061364.
    Repository Name: Woods Hole Open Access Server
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  • 4
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    Ebullition of oxygen from seagrasses under supersaturated conditions (2019)
    Wiley
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Long, M. H., Sutherland, K., Wankel, S. D., Burdige, D. J., & Zimmerman, R. C. Ebullition of oxygen from seagrasses under supersaturated conditions. Limnology and Oceanography, (2019), doi:10.1002/lno.11299.
    Description: Gas ebullition from aquatic systems to the atmosphere represents a potentially important fraction of primary production that goes unquantified by measurements of dissolved gas concentrations. Although gas ebullition from photosynthetic surfaces has often been observed, it is rarely quantified. The resulting underestimation of photosynthetic activity may significantly bias the determination of ecosystem trophic status and estimated rates of biogeochemical cycling from in situ measures of dissolved oxygen. Here, we quantified gas ebullition rates in Zostera marina meadows in Virginia, U.S.A. using simple funnel traps and analyzed the oxygen concentration and isotopic composition of the captured gas. Maximum hourly rates of oxygen ebullition (3.0 mmol oxygen m−2 h−1) were observed during the coincidence of high irradiance and low tides, particularly in the afternoon when oxygen and temperature maxima occurred. The daily ebullition fluxes (up to 11 mmol oxygen m−2 d−1) were roughly equivalent to net primary production rates determined from dissolved oxygen measurements indicating that bubble ebullition can represent a major component of primary production that is not commonly included in ecosystem‐scale estimates. Oxygen content comprised 20–40% of the captured bubble gas volume and correlated negatively with its δ18O values, consistent with a predominance of mixing between the higher δ18O of atmospheric oxygen in equilibrium with seawater and the lower δ18O of oxygen derived from photosynthesis. Thus, future studies interested in the metabolism of highly productive, shallow water ecosystems, and particularly those measuring in situ oxygen flux, should not ignore the bubble formation and ebullition processes described here.
    Description: Two anonymous reviewers provided thoughtful contributions that improved this manuscript. We thank Miraflor Santos, Victoria Hill, David Ruble, Jeremy Bleakney, and Brian Collister for assistance in the field and the staff of the Anheuser‐Busch Coastal Research Center for logistical support. This work was supported by NSF OCE grants 1633951 (to MHL) and 1635403 (to RCZ and DJB), NASA Fellowship NESSF NNX15AR62H (to KS), and a fellowship from the Hansewissenschaftskolleg (Institute for Advanced Studies; to SDW).
    Repository Name: Woods Hole Open Access Server
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  • 5
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    Closing the oxygen mass balance in shallow coastal ecosystems (2020)
    Wiley
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Long, M. H., Rheuban, J. E., McCorkle, D. C., Burdige, D. J., & Zimmerman, R. C. Closing the oxygen mass balance in shallow coastal ecosystems. Limnology and Oceanography, 64(6), (2019): 2694-2708, doi: 10.1002/lno.11248.
    Description: The oxygen concentration in marine ecosystems is influenced by production and consumption in the water column and fluxes across both the atmosphere–water and benthic–water boundaries. Each of these fluxes has the potential to be significant in shallow ecosystems due to high fluxes and low water volumes. This study evaluated the contributions of these three fluxes to the oxygen budget in two contrasting ecosystems, a Zostera marina (eelgrass) meadow in Virginia, U.S.A., and a coral reef in Bermuda. Benthic oxygen fluxes were evaluated by eddy covariance. Water column oxygen production and consumption were measured using an automated water incubation system. Atmosphere–water oxygen fluxes were estimated by parameterizations based on wind speed or turbulent kinetic energy dissipation rates. We observed significant contributions of both benthic fluxes and water column processes to the oxygen mass balance, despite the often‐assumed dominance of the benthic communities. Water column rates accounted for 45% and 58% of the total oxygen rate, and benthic fluxes accounted for 23% and 39% of the total oxygen rate in the shallow (~ 1.5 m) eelgrass meadow and deeper (~ 7.5 m) reef site, respectively. Atmosphere–water fluxes were a minor component at the deeper reef site (3%) but a major component at the shallow eelgrass meadow (32%), driven by diel changes in the sign and strength of atmosphere–water gradient. When summed, the measured benthic, atmosphere–water, and water column rates predicted, with 85–90% confidence, the observed time rate of change of oxygen in the water column and provided an accurate, high temporal resolution closure of the oxygen mass balance.
    Description: This work was substantially improved by comments from two anonymous reviewers. We thank Victoria Hill, David Ruble, Jeremy Bleakney, and Brian Collister for assistance in the field and the staff of the Bermuda Institute of Ocean Sciences and the Anheuser‐Busch Coastal Research Center for logistical support. This work was supported by NSF OCE grants 1657727 (to M.H.L. and D.C.M.), 1635403 (to R.C.Z. and D.J.B.), and 1633951 (to M.H.L.).
    Repository Name: Woods Hole Open Access Server
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  • 6
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    Selective preservation of coccolith calcite in Ontong-Java Plateau sediments (2020)
    American Geophysical Union
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    Publication Date: 2022-05-26
    Description: Author Posting. © American Geophysical Union, 2019. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Paleoceanography and Paleoclimatology, 34, (2019): 2141-2157, doi: 10.1029/2019PA003731.
    Description: Dissolution of calcite in deep ocean sediments, which is required to balance global marine CaCO3 production and burial fluxes, is still a poorly understood process. In order to assess the mechanisms of dissolution in sediments, we analyzed four multicore tops taken along a depth transect on the Ontong‐Java Plateau. These cores were taken directly on the equator, and span water column calcite saturation states from ∼0.93 to ∼0.74, allowing us to assess the effect of dissolution on carbonate sediment composition. The top 2 cm of each multicore was sectioned and sieved to separate coccolith from foraminiferal calcite, and the %CaCO3, δ13C, Δ14C, and Mg/Ca were evaluated. The mass ratio of coccoliths to foraminifera increases by a factor of 3 as a function of water depth, reflecting the preferential dissolution of foraminifera. Carbon isotope (δ13C and Δ14C) data suggest that most dissolution takes place at the sediment‐water interface and primarily affects foraminifera. Mg/Ca analyses indicate that the Mg content of the entire foraminiferal assemblage decreases as a function of dissolution. In contrast, coccolith dissolution takes place within the sediments, rather than at the interface. Together these two processes cause coccoliths to be up to 1,000 radiocarbon years younger than foraminifera from the same depth horizon. Despite this within‐sediment coccolith dissolution flux, sediments below the calcite saturation horizon remain enriched in coccolith calcite. Combined with global seafloor hypsometry and calcium carbonate content, this enrichment suggests that globally, coccoliths may outweigh foraminifera in deep ocean sediments by a factor of 1.8.
    Description: A. V. S. thanks the NOSAMS facility and the WHOI/NOSAMS postdoc scholar program, James Funds, and the Bessette family for funding and support. A. Q. acknowledges Williams College research and travel funds. We thank the Stanley W. Watson Director's Discretionary Fund for the Picarro‐Automate analyzer. We thank Ellen Roosen at the WHOI core repository for help with sample identification and sectioning. Thanks to Gretchen Swarr and the WHOI plasma mass spectrometry facility. Finally, we thank Bill Martin and Wally Broecker for enlightening discussions on dissolution and radiocarbon dating of deep ocean sediments. All data are included as supporting information files and are archived with NOAA's World Data Service for Paleoceanography (WDS Paleo; https://www.ncdc.noaa.gov/paleo/study/28150).
    Description: 2020-05-15
    Repository Name: Woods Hole Open Access Server
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  • 7
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    Automated classification of three-dimensional reconstructions of coral reefs using convolutional neural networks (2020)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hopkinson, B. M., King, A. C., Owen, D. P., Johnson-Roberson, M., Long, M. H., & Bhandarkar, S. M. Automated classification of three-dimensional reconstructions of coral reefs using convolutional neural networks. PLoS One, 15(3), (2020): e0230671, doi: 10.1371/journal.pone.0230671.
    Description: Coral reefs are biologically diverse and structurally complex ecosystems, which have been severally affected by human actions. Consequently, there is a need for rapid ecological assessment of coral reefs, but current approaches require time consuming manual analysis, either during a dive survey or on images collected during a survey. Reef structural complexity is essential for ecological function but is challenging to measure and often relegated to simple metrics such as rugosity. Recent advances in computer vision and machine learning offer the potential to alleviate some of these limitations. We developed an approach to automatically classify 3D reconstructions of reef sections and assessed the accuracy of this approach. 3D reconstructions of reef sections were generated using commercial Structure-from-Motion software with images extracted from video surveys. To generate a 3D classified map, locations on the 3D reconstruction were mapped back into the original images to extract multiple views of the location. Several approaches were tested to merge information from multiple views of a point into a single classification, all of which used convolutional neural networks to classify or extract features from the images, but differ in the strategy employed for merging information. Approaches to merging information entailed voting, probability averaging, and a learned neural-network layer. All approaches performed similarly achieving overall classification accuracies of ~96% and 〉90% accuracy on most classes. With this high classification accuracy, these approaches are suitable for many ecological applications.
    Description: This study was funded by grants from the Alfred P. Sloan Foundation (BMH, BR2014-049; https://sloan.org), and the National Science Foundation (MHL, OCE-1657727; https://www.nsf.gov). The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.
    Repository Name: Woods Hole Open Access Server
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  • 8
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    Editorial: Canopies in aquatic ecosystems: integrating form, function, and biophysical processes (2020)
    Frontiers Media
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    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 Samson, J. E., Ghisalberti, M., Adams, M. P., Reidenbach, M. A., Long, M. H., Shavit, U., & Pasour, V. B. Editorial: Canopies in aquatic ecosystems: integrating form, function, and biophysical processes. Frontiers in Marine Science, 6, (2019): 697, doi: 10.3389/fmars.2019.00697.
    Description: This Research Topic presents new research investigating the coupling between physical (fluid dynamics, mass transport, and light availability) and biological (nutrient cycling, particle transport, ecosystem structure, and biodiversity) processes in aquatic canopies. The starting point for this topic was the observation that our notion of “canopy” in the aquatic sciences, in contrast to that of our terrestrially-focused colleagues, remains underdeveloped. Forest canopy studies have been considered a new field of science (Nadkarni et al., 2011) and the concept of forest canopy research is clearly documented in the literature (Barker and Pinard, 2001; Nadkarni, 2001; Lowman, 2009); we have not found similar mentions of the canopy concept in aquatic studies. Over the past decade, however, there has been an increase in the number of studies on underwater canopies, as well as a shift toward more multidisciplinary studies that consider more than just the physical impacts of the canopy's presence (Ackerman, 2007; Nepf et al., 2007; O'Brien et al., 2014).
    Description: MA acknowledges funding support from Australian Research Council (ARC) Linkage Grant LP160100496 and the National Environmental Science Programme (NESP) Tropical Water Quality Hub. Funding to MR provided by the National Science Foundation (DEB-1237733 and DEB-1832221) and by a NSF CAREER grant (OCE-1151314). ML was supported by NSF OCE grant 1633951.
    Keywords: Fluid dynamics ; Ecosystem engineering ; Coral ; Algae ; Canopy ; Mass transport ; Light availability ; Nutrient cycling
    Repository Name: Woods Hole Open Access Server
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  • 9
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    Evaluating benthic flux measurements from a gradient flux system (2022)
    Association for the Sciences of Limnology and Oceanography
    Details
    Publication Date: 2022-06-17
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Coogan, J., Rheuban, J., & Long, M. Evaluating benthic flux measurements from a gradient flux system. Limnology and Oceanography: Methods, 20, (2022): 222-232, https://doi.org/10.1002/lom3.10482.
    Description: Multiple methods exist to measure the benthic flux of dissolved oxygen (DO), but many are limited by short deployments and provide only a snapshot of the processes occurring at the sediment–water interface. The gradient flux (GF) method measures near bed gradients of DO and estimates the eddy diffusivity from existing turbulence closure methods to solve for the benthic flux. This study compares measurements at a seagrass, reef, and sand environment with measurements from two other methods, eddy covariance and benthic chambers, to highlight the strengths, weaknesses, and uncertainty of measurements being made. The results show three major areas of primary importance when using the GF method: (1) a sufficient DO gradient is critical to use this method and is limited by the DO sensor precision and gradient variability; (2) it is important to use similar methods when comparing across sites or time, as many of the methods showed good agreement but were often biased larger or smaller based on the method; and (3) in complex bottom types, estimates of the length scale and placement of the DO sensors can lead to large sources of error. Careful consideration of these potential errors is needed when using the GF method, but when properly addressed, this method showed high agreement with the other methods and may prove a useful tool for measuring long-term benthic fluxes of DO or other chemical sensors or constituents of interest that are incompatible with other methods.
    Description: This work was supported by NSF OCE grants 1657727 and 2023069.
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  • 10
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    Extreme low oxygen and decreased pH conditions naturally occur within developing squid egg capsules (2016)
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2016. This is the author's version of the work. It is posted here by permission of Inter-Research for personal use, not for redistribution. The definitive version was published in Marine Ecology Progress Series 550 (2016): 111-119, doi:10.3354/meps11737.
    Description: Young animals found future cohorts and populations but are often particularly susceptible to environmental changes. This raises concerns that future conditions, influenced by anthropogenic changes such as ocean acidification and increasing oxygen minimum zones, will greatly affect ecosystems by impacting developing larvae. Understanding the potential impacts requires addressing present tolerances and the current conditions in which animals develop. Here, we examined the changes in oxygen and pH adjacent to and within normally-developing squid egg capsules, providing the first observations that the egg capsules, housing hundreds of embryos, had extremely low internal pH (7.34) and oxygen concentrations (1.9 μmol L-1). While early-stage egg capsules had pH and oxygen levels significantly lower than the surrounding seawater, late-stage capsules dropped dramatically to levels considered metabolically stressful even for adults. The structure of squid egg capsules resulted in a closely packed unit of respiring embryos, which likely contributed to the oxygen-poor and CO2-rich local environment. These conditions rivaled the extremes found in the squids’ natural environment, suggesting they may already be near their metabolic limit and that these conditions may induce a hatching cue. While squid may be adapted to these conditions, further climate change could place young, keystone squid outside of their physiological limits.
    Description: This work was supported by a NSF Ocean Acidification grant (#1220034; TAM) and the WHOI Ocean Climate Change Institute (Ocean Acidification Initiative; MHL).
    Description: 2017-05-25
    Keywords: Cephalopod ; Climate change ; Hypoxia ; Boundary layer ; Eggs ; Larva
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
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