Aquatic biogeochemical eddy covariance fluxes in the presence of waves

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Long, M. H. Aquatic biogeochemical eddy covariance fluxes in the presence of waves. Journal of Geophysical Research: Oceans, 126(2), (2021): e2020JC016637, https://doi.org/10.1029/2020JC016637.The eddy covariance (EC) technique is a powerful tool for measuring atmospheric exchange rates that was recently adapted by biogeochemists to measure aquatic oxygen fluxes. A review of aquatic biogeochemical EC literature revealed that the majority of studies were conducted in shallow waters where waves were likely present, and that waves biased sensor and turbulence measurements. This review identified that larger measurement heights shifted turbulence to lower frequencies, producing a spectral gap between turbulence and wave frequencies. However, some studies sampled too close to the boundary to allow for a spectral turbulence‐wave gap, and a change in how EC measurements are conducted and analyzed is needed to remove wave‐bias. EC fluxes have only been derived from the time‐averaged product of vertical velocity and oxygen, often resulting in wave‐bias. Presented is a new analysis framework for removing wave‐bias by accumulation of cross‐power spectral densities below wave frequencies. This analysis framework also includes new measurement guidelines based on wave period, currents, and measurement heights. This framework is applied to sand, seagrass, and reef environments where traditional EC analysis resulted in wave‐bias of 7.0% ± 9.2% error in biogeochemical (oxygen and H+) fluxes, while more variable and higher error was evident in momentum fluxes (10.5% ± 21.0% error). It is anticipated that this framework will lead to significant changes in how EC measurements are conducted and evaluated, and help overcome the major limitations caused by wave‐sensitive and slow‐response sensors, potentially expanding new chemical tracer applications and more widespread use of the EC technique.This work was supported by the Independent Research & Development Program at WHOI grant 25307and NSF OCE grants 1657727 and 1633951

Mapping the invisible hand: a body model of a phantom limb

After amputation, individuals often have vivid experiences of their absent limb (i.e., a phantom limb). Therefore, one’s conscious image of one’s body cannot depend on peripheral input only (Ramachandran & Hirstein, 1998). However, the origin of phantom sensations is hotly debated. Reports of vivid phantoms in the case of congenital absence of the limb show that memory of former body state is not necessary (Brugger et al., 2000). According to one view, phantoms may reflect innate organization of sensorimotor cortices (Melzack, 1990). Alternatively, phantoms could reflect generalization from viewing other people’s bodies (Brugger et al., 2000), a sensorimotor example of the classic theory that understanding oneself follows from understanding the “generalized other” (Mead, 1934, p. 154). Because phantom limbs cannot be stimulated, sensory testing cannot directly compare visual and somatosensory influences on representations of phantom limbs. Consequently, empirical investigation of phantoms is limited

Quantifying pelagic primary production and respiration via automated in-situ incubation system

We developed and validated a novel automated water incubator that measures in-situ rates of photosynthesis and respiration. This dataset includes raw data, Monte-Carlo simulation method, and processed results from field deployments in Summer, 2021. Deployment of the incubator was conducted near Ucantena Island, Massachusetts, USA. The dataset includes timeseries of automated incubation experiments, reporting dissolved oxygen concentration (DO), temperature, and photosynthetically active radiation (PAR). There are four deployments spanning from late august to early October, 2021. Each deployment lasted approximately 72 hours. Hourly DO fluxes from photosynthesis/respiration are calculated and reported for each deployment respectively. Data of derivative analysis are also included for various validation on the automated incubator and data analysis techniques.National Science Foundation OTIC 184109

Automated classification of three-dimensional reconstructions of coral reefs using convolutional neural networks

© 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.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.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

A Serological Study of Tularemia in Domestic Animals and the Potential Threat to Humans

Author Institution: Division of Laboratory Animal Medicine, Medical College of OhioSerological evidence was obtained that demonstrated previous infection with Pasteurella tularensis in 2 of 9 sheep raised in Monroe County, MI. Although no ectoparasites were found on the sheep in April and May when the testing was done, it was assumed that they were infected by ticks. Titers for Brucella were much less than those for P. tularensis and were not considered meaningful. Eight New Zealand white rabbits from nearby Risingsun, OH were serologically negative for tularemia and brucellosis. These animals had been confined in a commercial rabbitry and were free of ectoparasites. One of 8 dogs from Fulton County, OH, had a positive titer for P. tularensis, but not Brucella. No ectoparasites were observed on the dogs, but they had been recently dipped. The possibility that man as well as other animals might become infected with Pasteurella tularensis in the Toledo, OH area exists

Extreme low oxygen and decreased pH conditions naturally occur within developing squid egg capsules

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.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.This work was supported by a NSF Ocean Acidification grant (#1220034; TAM) and the WHOI Ocean Climate Change Institute (Ocean Acidification Initiative; MHL).2017-05-2

Seagrass metabolism across a productivity gradient using the eddy covariance, Eulerian control volume, and biomass addition techniques

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.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.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).2015-11-2

Evaluating benthic flux measurements from a gradient flux system

© 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.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.This work was supported by NSF OCE grants 1657727 and 2023069

Examining hope as a transdiagnostic mechanism of change across anxiety disorders and CBT treatment protocols.

Hope is a trait that represents the capacity to identify strategies or pathways to achieve goals and the motivation or agency to effectively pursue those pathways. Hope has been demonstrated to be a robust source of resilience to anxiety and stress and there is limited evidence that, as has been suggested for decades, hope may function as a core process or transdiagnostic mechanism of change in psychotherapy. The current study examined the role of hope in predicting recovery in a clinical trial in which 223 individuals with 1 of 4 anxiety disorders were randomized to transdiagnostic cognitive behavior therapy (CBT), disorder-specific CBT, or a waitlist controlled condition. Effect size results indicated moderate to large intraindividual increases in hope, that changes in hope were consistent across the five CBT treatment protocols, that changes in hope were significantly greater in CBT relative to waitlist, and that changes in hope began early in treatment. Results of growth curve analyses indicated that CBT was a robust predictor of trajectories of change in hope compared to waitlist, and that changes in hope predicted changes in both self-reported and clinician-rated anxiety. Finally, a statistically significant indirect effect was found indicating that the effects of treatment on changes in anxiety were mediated by treatment effects on hope. Together, these results suggest that hope may be a promising transdiagnostic mechanism of change that is relevant across anxiety disorders and treatment protocols.R01 MH090053 - NIMH NIH HHSAccepted manuscrip

Ebullition of Oxygen From Seagrasses Under Supersaturated Conditions

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