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  • 1
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    Closing the oxygen mass balance in shallow coastal ecosystems (2020)
    Wiley
    Details
    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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  • 2
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    Selective preservation of coccolith calcite in Ontong-Java Plateau sediments (2020)
    American Geophysical Union
    Details
    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
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  • 3
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    Automated classification of three-dimensional reconstructions of coral reefs using convolutional neural networks (2020)
    Public Library of Science
    Details
    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.
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  • 4
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    pH, temperature, salinity, and oxygen data from SeapHOx sensors deployed at three sites in the Florida Keys in June 2018 (2020)
    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Details
    Publication Date: 2022-05-26
    Description: Dataset: Florida Keys SeapHOx
    Description: An eddy covariance system, known as ECHOES, was deployed at three sites offshore of Key Largo, Florida during June 2018. The ECHOES systems logged the three-dimensional velocity, depth, O2 optode, pH sensor, and triaxial Inertial Measurement Unit. A separate frame at each site contained a photosynthetically active radiation (PAR) sensor and a Seabird SeapHOx, measuring salinity, temperature, depth, O2, and pH. This dataset contains pH, temperature, salinity, and oxygen data recorded by the SeapHOx sensor. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/821091
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1657727
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  • 5
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    Current velocity, wave velocity, and O2, H+, and momentum flux from the ECHOES system deployed at three sites in the Florida Keys in June 2018 (2020)
    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Details
    Publication Date: 2022-05-26
    Description: Dataset: Florida Keys velocity and flux
    Description: An eddy covariance system, known as ECHOES, was deployed at three sites offshore of Key Largo, Florida during June 2018. The ECHOES systems logged the three-dimensional velocity, depth, O2 optode, pH sensor, and triaxial Inertial Measurement Unit. A separate frame at each site contained a photosynthetically active radiation (PAR) sensor and a Seabird SeapHOx, measuring salinity, temperature, depth, O2, and pH. This dataset contains current velocities, wave velocities, and O2, H+, and momentum flux. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/820984
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1657727
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  • 6
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    Absolute proteomic quantification reveals design principles of sperm flagellar chemosensation (2020)
    EMBO Press
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Troetschel, C., Hamzeh, H., Alvarez, L., Pascal, R., Lavryk, F., Boenigk, W., Koerschen, H. G., Mueller, A., Poetsch, A., Rennhack, A., Gui, L., Nicastro, D., Struenker, T., Seifert, R., & Kaupp, U. B. Absolute proteomic quantification reveals design principles of sperm flagellar chemosensation. Embo Journal, 39(4), (2020): e102723, doi:10.15252/embj.2019102723.
    Description: Cilia serve as cellular antennae that translate sensory information into physiological responses. In the sperm flagellum, a single chemoattractant molecule can trigger a Ca2+ rise that controls motility. The mechanisms underlying such ultra‐sensitivity are ill‐defined. Here, we determine by mass spectrometry the copy number of nineteen chemosensory signaling proteins in sperm flagella from the sea urchin Arbacia punctulata. Proteins are up to 1,000‐fold more abundant than the free cellular messengers cAMP, cGMP, H+, and Ca2+. Opto‐chemical techniques show that high protein concentrations kinetically compartmentalize the flagellum: Within milliseconds, cGMP is relayed from the receptor guanylate cyclase to a cGMP‐gated channel that serves as a perfect chemo‐electrical transducer. cGMP is rapidly hydrolyzed, possibly via “substrate channeling” from the channel to the phosphodiesterase PDE5. The channel/PDE5 tandem encodes cGMP turnover rates rather than concentrations. The rate‐detection mechanism allows continuous stimulus sampling over a wide dynamic range. The textbook notion of signal amplification—few enzyme molecules process many messenger molecules—does not hold for sperm flagella. Instead, high protein concentrations ascertain messenger detection. Similar mechanisms may occur in other small compartments like primary cilia or dendritic spines.
    Description: We thank Heike Krause for preparing the manuscript. Financial support by the Deutsche Forschungsgemeinschaft (DFG) via the priority program SPP 1726 “Microswimmers” and the Cluster of Excellence 1023 “ImmunoSensation” is gratefully acknowledged. We thank D. Stoddard for management of the UTSW cryo‐electron microscope facility, which is funded in part by a Cancer Prevention and Research Institute of Texas (CPRIT) Core Facility Award (RP170644). This study was supported by HHS|National Institutes of Health (NIH) grant R01 GM083122 and by CPRIT grant RR140082 to D. Nicastro.
    Keywords: Cilium ; Electron tomography ; Fertilization ; Quantitative mass spectrometry ; Signaling
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  • 7
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    Editorial: Canopies in aquatic ecosystems: integrating form, function, and biophysical processes (2020)
    Frontiers Media
    Details
    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
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  • 8
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    A preindustrial sea-level rise hotspot along the Atlantic Coast of North America (2020)
    American Geophysical Union
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gehrels, W. R., Dangendorf, S., Barlow, N. L. M., Saher, M. H., Long, A. J., Woodworth, P. L., Piecuch, C. G., & Berk, K. A preindustrial sea-level rise hotspot along the Atlantic Coast of North America. Geophysical Research Letters, 47(4), (2020): e2019GL085814, doi:10.1029/2019GL085814.
    Description: The Atlantic coast of North America north of Cape Hatteras has been proposed as a “hotspot” of late 20th century sea‐level rise. Here we test, using salt‐marsh proxy sea‐level records, if this coast experienced enhanced sea‐level rise over earlier multidecadal‐centennial periods. While we find in agreement with previous studies that 20th century rates of sea‐level change were higher compared to rates during preceding centuries, rates of 18th century sea‐level rise were only slightly lower, suggesting that the “hotspot” is a reoccurring feature for at least three centuries. Proxy sea‐level records from North America (Iceland) are negatively (positively) correlated with centennial changes in the North Atlantic Oscillation. They are consistent with sea‐level “fingerprints” of Arctic ice melt, and we therefore hypothesize that sea‐level fluctuations are related to changes in Arctic land‐ice mass. Predictions of future sea‐level rise should take into account these long‐term fluctuating rates of natural sea‐level change.
    Description: This work is funded by the Natural Environment Research Council (grant NE/G003440/1). All radiocarbon dating was supported by the Natural Environment Research Council Radiocarbon Facility (allocations 1490.0810, 1566.0511, 1604.0112). Mark Wood assisted with fieldwork. Rob Scaife analyzed pollen data for core SN‐3.3. Sönke Dangendorf and Kevin Berk acknowledge the University of Siegen for their support within the PEPSEA project. Christopher Piecuch was supported by National Science Foundation awards OCE‐1558966 and OCE‐1834739. We thank project members Miguel Ángel Morales Maqueda, Chris Hughes, Vassil Roussenov and Ric Williams for valuable discussions. We are grateful to the International Space Science Institute (ISSI; Bern, Switzerland) for support of the International Team “Towards a unified Sea Level Record”. Data used in this paper are freely available online (https://www.doi.org/10/dgvq).
    Keywords: Sea level ; Late Holocene ; Common Era ; Climate ; Ocean
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  • 9
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    Spectral analyses of high-frequency data during two hour-long periods from the ECHOES system deployed at three sites in the Florida Keys in June 2018 (2020)
    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Details
    Publication Date: 2022-05-26
    Description: Dataset: Florida Keys Spectral Analyses
    Description: Spectral analyses (power spectra and cross power spectral density (CPSD)) of high-frequency data (turbulence; momentum, oxygen and hydrogen ion fluxes) from two hour-long periods during a high-energy wave period (Hr 38) and a low-energy wave period (Hr 116). For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/821294
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1657727
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  • 10
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    Photosynthetically active radiation (PAR) from Odyssey PAR sensors deployed at three sites in the Florida Keys in June 2018 (2020)
    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Details
    Publication Date: 2022-05-26
    Description: Dataset: Florida Keys PAR
    Description: An eddy covariance system, known as ECHOES, was deployed at three sites offshore of Key Largo, Florida during June 2018. The ECHOES systems logged the three-dimensional velocity, depth, O2 optode, pH sensor, and triaxial Inertial Measurement Unit. A separate frame at each site contained a photosynthetically active radiation (PAR) sensor and a Seabird SeapHOx, measuring salinity, temperature, depth, O2, and pH. This dataset contains the PAR data. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/821036
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1657727
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