Long Matthew H.

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Matthew H.

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  • Article
    Sub-tropical seagrass ecosystem metabolism measured by eddy covariance
    (Inter-Research, 2015-06-08) Long, Matthew H. ; Berg, Peter ; McGlathery, Karen J. ; Zieman, Joseph C.
    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.
  • Article
    The challenges of detecting and attributing ocean acidification impacts on marine ecosystems
    (Oxford University Press, 2020-08-09) Doo, Steve ; Kealoha, Andrea K. ; Andersson, Andreas ; Cohen, Anne L. ; Hicks, Tacey L. ; Johnson, Zackary I. ; Long, Matthew H. ; McElhany, Paul ; Mollica, Nathaniel R. ; Shamberger, Kathryn E. F. ; Silbiger, Nyssa J. ; Takeshita, Yuichiro ; Busch, D. Shallin
    A substantial body of research now exists demonstrating sensitivities of marine organisms to ocean acidification (OA) in laboratory settings. However, corresponding in situ observations of marine species or ecosystem changes that can be unequivocally attributed to anthropogenic OA are limited. Challenges remain in detecting and attributing OA effects in nature, in part because multiple environmental changes are co-occurring with OA, all of which have the potential to influence marine ecosystem responses. Furthermore, the change in ocean pH since the industrial revolution is small relative to the natural variability within many systems, making it difficult to detect, and in some cases, has yet to cross physiological thresholds. The small number of studies that clearly document OA impacts in nature cannot be interpreted as a lack of larger-scale attributable impacts at the present time or in the future but highlights the need for innovative research approaches and analyses. We summarize the general findings in four relatively well-studied marine groups (seagrasses, pteropods, oysters, and coral reefs) and integrate overarching themes to highlight the challenges involved in detecting and attributing the effects of OA in natural environments. We then discuss four potential strategies to better evaluate and attribute OA impacts on species and ecosystems. First, we highlight the need for work quantifying the anthropogenic input of CO2 in coastal and open-ocean waters to understand how this increase in CO2 interacts with other physical and chemical factors to drive organismal conditions. Second, understanding OA-induced changes in population-level demography, potentially increased sensitivities in certain life stages, and how these effects scale to ecosystem-level processes (e.g. community metabolism) will improve our ability to attribute impacts to OA among co-varying parameters. Third, there is a great need to understand the potential modulation of OA impacts through the interplay of ecology and evolution (eco–evo dynamics). Lastly, further research efforts designed to detect, quantify, and project the effects of OA on marine organisms and ecosystems utilizing a comparative approach with long-term data sets will also provide critical information for informing the management of marine ecosystems.
  • Dataset
    Quantifying pelagic primary production and respiration via automated in-situ incubation system
    (Woods Hole Oceanographic Institution, 2022-10-20) Chen, Solomon ; Long, Matthew H.
    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.
  • Article
    Detection and quantification of a release of carbon dioxide gas at the seafloor using pH eddy covariance and measurements of plume advection
    (Elsevier, 2021-10-22) Koopmans, Dirk ; Meyer, Volker ; Schaap, Allison ; Dewar, Marius ; Färber, Paul ; Long, Matthew H. ; Gros, Jonas ; Connelly, Douglas P. ; Holtappels, Moritz
    We detected a controlled release of CO2 (g) with pH eddy covariance. We quantified CO2 emission using measurements of water velocity and pH in the plume of aqueous CO2 generated by the bubble streams, and using model predictions of vertical CO2 dissolution and its dispersion downstream. CO2 (g) was injected 3 m below the floor of the North Sea at rates of 5.7–143 kg d − 1. Instruments were 2.6 m from the center of the bubble streams. In the absence of injected CO2, pH eddy covariance quantified the proton flux due to naturally-occurring benthic organic matter mineralization (equivalent to a dissolved inorganic carbon flux of 7.6 ± 3.3 mmol m − 2 d − 1, s.e., n = 33). At the lowest injection rate, the proton flux due to CO2 dissolution was 20-fold greater than this. To accurately quantify emission, the kinetics of the carbonate system had to be accounted for. At the peak injection rate, 73 ± 13% (s.d.) of the injected CO2 was emitted, but when kinetics were neglected, the calculated CO2 emission was one-fifth of this. Our results demonstrate that geochemical techniques can detect and quantify very small seafloor sources of CO2 and attribute them to natural or abiotic origins.
  • Article
    Editorial: Canopies in aquatic ecosystems: integrating form, function, and biophysical processes
    (Frontiers Media, 2019-11-15) Samson, Julia E. ; Ghisalberti, Marco ; Adams, Matthew Philip ; Reidenbach, Matthew A. ; Long, Matthew H. ; Shavit, Uri ; Pasour, Virginia B.
    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).
  • Article
    Seagrass metabolism across a productivity gradient using the eddy covariance, Eulerian control volume, and biomass addition techniques
    (John Wiley & Sons, 2015-05-22) Long, Matthew H. ; Berg, Peter ; Falter, James L.
    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.
  • Preprint
    Extreme low oxygen and decreased pH conditions naturally occur within developing squid egg capsules
    ( 2016-04) Long, Matthew H. ; Mooney, T. Aran ; Zakroff, Casey
    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.
  • Article
    Ebullition of oxygen from seagrasses under supersaturated conditions
    (Wiley, 2019-08-08) Long, Matthew H. ; Sutherland, Kevin M. ; Wankel, Scott D. ; Burdige, David J. ; Zimmerman, Richard C.
    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.
  • Article
    Automated classification of three-dimensional reconstructions of coral reefs using convolutional neural networks
    (Public Library of Science, 2020-03-24) Hopkinson, Brian M. ; King, Andrew C. ; Owen, Daniel P. ; Johnson-Roberson, Matthew ; Long, Matthew H. ; Bhandarkar, Suchendra M.
    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.
  • Article
    Closing the oxygen mass balance in shallow coastal ecosystems
    (Wiley, 2019-07-10) Long, Matthew H. ; Rheuban, Jennie E. ; McCorkle, Daniel C. ; Burdige, David J. ; Zimmerman, Richard C.
    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.
  • Article
    Selective preservation of coccolith calcite in Ontong-Java Plateau sediments
    (American Geophysical Union, 2019-11-15) Subhas, Adam V. ; McCorkle, Daniel C. ; Quizon, Alex ; McNichol, Ann P. ; Long, Matthew H.
    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.
  • Article
    Aquatic biogeochemical eddy covariance fluxes in the presence of waves
    (American Geophysical Union, 2021-01-19) Long, Matthew H.
    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.
  • Article
    Deoxygenation, acidification and warming in Waquoit Bay, USA, and a shift to pelagic dominance
    (Springer, 2023-02-18) Long, Matthew H. ; Mora, Jordan W.
    Coastal nutrient pollution, or eutrophication, is commonly linked to anthropogenic influences in terrestrial watersheds, where land-use changes often degrade water quality over time. Due to gradual changes, the management and monitoring of estuarine systems often lag environmental degradation. One example can be found at the Waquoit Bay National Estuarine Research Reserve, where we developed an analysis framework to standardize and analyze long-term trends in water quality and submerged vegetation data from monitoring programs that began in the 1990s. These programs started after the nearly complete loss of historically extensive Zostera marina(eelgrass) meadows throughout the estuary. Recently, eelgrass only persisted in small, undeveloped sub-embayments of the estuary, with conservative declines of over 97% in areal coverage. Over the past 2 decades, the average deoxygenation, acidification, and warming were −24.7 µmol O2 kg −1(−11%), 0.006 µmol H+ kg −1 (+ 34%), and 1.0 °C (+ 4%), respectively. Along with the loss of eelgrass, there was also a decline in macroalgal biomass over 3 decades, resulting in a system dominated by pelagic metabolism, indicated by a 71% increase in water column chlorophyll a concentrations since 2009. This recent increase in phytoplankton biomass, which is highly mobile and transported throughout the estuary by tides, has resulted in recent degradation of isolated embayments despite their lower nutrient loads. This shift toward pelagic dominance in Waquoit Bay may indicate that other eutrophic and warming estuaries may also shift toward pelagic dominance in the future, as the Northeastern US is one of the fastest warming regions across the world.
  • Article
    Toward a new era of coral reef monitoring
    (American Chemical Society, 2023-03-17) Apprill, Amy ; Girdhar, Yogesh ; Mooney, T. Aran ; Hansel, Colleen M. ; Long, Matthew H. ; Liu, Yaqin ; Zhang, W. Gordon ; Kapit, Jason ; Hughen, Konrad ; Coogan, Jeff ; Greene, Austin
    Coral reefs host some of the highest concentrations of biodiversity and economic value in the oceans, yet these ecosystems are under threat due to climate change and other human impacts. Reef monitoring is routinely used to help prioritize reefs for conservation and evaluate the success of intervention efforts. Reef status and health are most frequently characterized using diver-based surveys, but the inherent limitations of these methods mean there is a growing need for advanced, standardized, and automated reef techniques that capture the complex nature of the ecosystem. Here we draw on experiences from our own interdisciplinary research programs to describe advances in in situ diver-based and autonomous reef monitoring. We present our vision for integrating interdisciplinary measurements for select “case-study” reefs worldwide and for learning patterns within the biological, physical, and chemical reef components and their interactions. Ultimately, these efforts could support the development of a scalable and standardized suite of sensors that capture and relay key data to assist in categorizing reef health. This framework has the potential to provide stakeholders with the information necessary to assess reef health during an unprecedented time of reef change as well as restoration and intervention activities.
  • Article
    Eddy correlation measurements of oxygen fluxes in permeable sediments exposed to varying current flow and light
    (Association for the Sciences of Limnology and Oceanography, 2013-07) Berg, Peter ; Long, Matthew H. ; Huettel, Markus ; Rheuban, Jennie E. ; McGlathery, Karen J. ; Howarth, Robert W. ; Foreman, Kenneth H. ; Giblin, Anne E. ; Marino, Roxanne
    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.
  • Article
    Evaluating benthic flux measurements from a gradient flux system
    (Association for the Sciences of Limnology and Oceanography, 2022-03-04) Coogan, Jeffrey ; Rheuban, Jennie E. ; Long, Matthew H.
    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.