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DEOS PhD Defense: Elizabeth Emily Ells

“Quantifying Nitrogen Removal via Natural and Engineered Remediation Strategies for Southeastern Massachusetts Estuaries”

By: Elizabeth Emily Ells

Advisors
Dr. Micheline Labrie (UMass Dartmouth)

Dr. Miles Sundermeyer (UMass Dartmouth)

Committee Members
Dr. Mark Altabet (UMass Dartmouth), Dr. David Schlezinger (UMass Dartmouth), and Dr. Craig Taylor (WHOI)

Tuesday July 15, 2025
11:00 AM
SMAST West 204
706 S. Rodney French Blvd, New Bedford
and via Zoom

Abstract:

Anthropogenic nitrogen (N) enrichment has degraded water quality and ecosystem function in southeastern Massachusetts (MA) estuaries and globally. In coastal communities like Cape Cod, nitrate from septic systems enters groundwater and discharges into estuaries, serving as a primary source of N pollution. This has prompted municipalities to explore innovative, cost-effective strategies to reduce N loading and restore impaired estuaries. This dissertation focused on in-transit and in-estuarine approaches for N reduction that rely on microbial conversion of nitrate to dinitrogen gas. Specifically, this dissertation evaluated: oyster-associated denitrification, macrophyte-associated denitrification, and surface-water permeable reactive barriers (PRBs).

Chapter One quantified denitrification associated with Eastern oysters (Crassostrea virginica) using aquaculture oysters collected from three temperate estuaries. Significant denitrification rates were measured in association with both live oysters and empty shells. In Lonnie’s Pond (Orleans, MA), these rates contributed an estimated 12 kg N2-N annually to the N removal budget based on a standardized deployment of 225 kg dry tissue weight. N removal via oyster-associated denitrification was comparable to oyster-enhanced sediment denitrification and made up almost half of the N removed through harvest. Thus, oyster-associated denitrification represents a potentially significant pathway that should be included in future N removal budgets.

Chapter Two evaluated macrophyte-associated denitrification through a case study of Mill Pond (Falmouth, MA), a temperate freshwater pond characterized by dense macrophyte growth and seasonal anoxia. The pond naturally attenuates N, reducing loading to the downstream Green Pond estuary. Previous research indicated that 50% of incoming N was attenuated within Mill Pond; however, known freshwater attenuation pathways (e.g. sediment burial and denitrification, and plant assimilation) failed to fully account for observed N losses. This study showed that macrophyte-associated denitrification accounted for an attenuation of 818 ± 80 kg N annually, resolving 67% of the previously unexplained N attenuation. This research suggests that macrophyte-associated denitrification is a dominant N removal process within this eutrophic freshwater pond, contributing to a 14% reduction in the potential watershed load entering Green Pond.

Chapter Three examined surface-water PRBs as an innovative N reduction approach for agricultural freshwater flow-through systems. These carbon-based treatment barriers were evaluated in laboratory column and flume experiments and deployed in the channels of two cranberry bogs in southeastern MA. Results from column and flume experiments and field deployments were synthesized in a conceptual model to evaluate the underlying factors (e.g., PRB design parameters, and biological and physical timescales) which combined to produce the observed measurements. Results indicated that surface-water PRB success depends on the co-occurrence of labile carbon, sustained anoxic conditions and sufficient flushing to support measurable nitrate reduction.

Collectively, this dissertation quantified N removal using three natural and engineered N reduction strategies currently being applied or considered in southeastern MA. Chapter One added empirical data necessary to determine the potential efficacy of oyster-associated denitrification and for integrating it into an existing oyster N attenuation budget. Chapter Two refined the N budgets in a eutrophic freshwater pond, and established macrophyte-associated denitrification as an important N removal pathway. Chapter Three developed and evaluated a retrofitted approach to the traditional PRB to treat agricultural waters prior to their discharge into coastal ecosystems; however, effectiveness in the field was limited by hydraulic interactions with the PRB. Together this work offers municipalities new low-cost and innovative tools to manage their N loads to reach compliance with total maximum daily loads prior to discharge in coastal estuaries, particularly when combined with other attenuation methods.

https://umassd.zoom.us/j/92396171223

Meeting ID: 923 9617 1223

Passcode: 482554

Boating Safety Class

SMAST has partnered with the Mass Environmental Police to offer a 2-day Boating safety class on Monday, June 9th  and Wednesday, June 11th.  The class will be offered in SMAST East 101-102. The Class size is limited, so if you are interested, please email Mike Marino (mmarino@umassd.edu) to reserve your spot. If this date/time does not work for you but you are interested in a future training, please let him know.

 

 

 

DFO Defense: Alison Frey

Department of Fisheries Oceanography

“The Spawning Dynamics and Biology of Cod in Southern New England Offshore Wind Energy Areas”

By:

Alison Frey

Advisor

Steven X. Cadrin (UMass Dartmouth)

Committee Members

Kevin Stokesbury (UMass Dartmouth), Lauran Brewster (UMass Dartmouth), and Greg DeCelles (Ørsted)

Thursday June 5, 2025

1:00 PM

SMAST East 101-103

836 S. Rodney French Blvd, New Bedford

and via Zoom

Abstract:

Atlantic cod (Gadus morhua) supported a robust fishery through most of the 20th century, but due to overfishing and environmental change, stocks collapsed in the 1990s, and populations remain below target biomass levels. Successful spawning and recruitment are critical for stock rebuilding, but spawning is a sensitive period within the lifecycle of cod and is vulnerable to anthropogenic activities. The most southern cod stock off Southern New England is currently assessed to be overfished with overfishing occurring. Offshore wind energy development is occurring on a known spawning ground, Cox Ledge, which is designated as Essential Fish Habitat and a Habitat Area of Particular Concern, and may have impacts on cod reproduction. To characterize impacts of offshore wind development on spawning of Southern New England cod, data on habitat use and spawning dynamics were collected via acoustic telemetry to compare pre-construction and post-construction residency to the spawning ground (chapter 1). Environmental drivers of cod presence on Cox Ledge will be assessed with generalized linear models (chapter 2), and biological sampling will be used to estimate size at maturity to inform the data-moderate Southern New England stock assessment (chapter 3). This proposed work will aid in effective assessment and management of fisheries and offshore wind interactions with vulnerable living marine resources.

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Topic: Ali Frey Thesis Defense

Time: Jun 5, 2025 12:00 Eastern Time (US and Canada)

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https://umassd.zoom.us/j/94363529761

 

Meeting ID: 943 6352 9761

Passcode: 595695

 

DFO Defense: Angelia Miller

Department of Fisheries Oceanography

“Impacts to stock abundance indices due to offshore wind development-driven changes to fishery-independent survey effort”

By:

Angelia Miller

Advisor

Dr. Gavin Fay (University of Massachusetts Dartmouth)

Committee Members

Dr. Steven X. Cadrin (University of Massachusetts Dartmouth), and Dr. Catherine Foley (NOAA NEFSC)

Tuesday May 20th, 2025

1:30 PM

SMAST East 101-103

836 S. Rodney French Blvd, New Bedford

and via Zoom

Abstract:

Offshore wind energy development is occurring throughout the Northeast Large Marine Ecosystem and will interact with many marine use sectors, including fisheries. Wind areas overlap spatially with the footprint of the National Marine Fisheries Service (NMFS) Northeast Fisheries Science Center (NEFSC) multispecies bottom trawl survey, which has been conducted since the 1960s, and whose data are relied upon for the assessment and management of many fisheries stocks in the Northeast U.S. This fishery-independent survey is confronted by potential preclusion of trawl sampling efforts due to the spatial conflict arising from offshore wind energy development. My thesis aims to quantify the impacts of preclusion to monitoring and operations and understand changes to species distributions and abundances within wind areas, which could jointly affect downstream data products, such as stock abundance indices, and fisheries management advice. The first phase of my study serves as a proxy for expected losses for comparison to my species distribution modeling and suggests that, when accounting for reduced trawl samples, annual estimates of relative abundance are lower than those calculated when including all samples. Additionally, when compared to a random, null model of effort reduction, preclusion of wind areas resulted in lower abundance estimates. Applying summer flounder (Paralichthys dentatus) and Atlantic mackerel (Scomber scombrus) as two case study species, I fit a spatiotemporal generalized linear mixed effects model (GLMM), generate simulated survey data, and calculate indices of abundance and population trends to compare survey outcomes with and without trawl samples inside proposed wind development areas in the second phase of my study. I employed the species distribution operating model to examine changes in fish density under assumed changes in species productivity, and to survey catch rates, as a function of offshore wind development. I found that the loss of samples inside wind areas has a substantial impact on estimates of abundance indices and population trends. This study contributes directly to implementation of the Federal Survey Mitigation Strategy for the Northeast U.S. Region (Action 3.2.2) as a part of the Survey Simulation Evaluation and Experimentation Project, which aims to assess potential impacts to the bottom trawl survey operations and data products and identify mitigation strategies to maintain data integrity. Furthermore, this study contributes to the current knowledge surrounding the impacts that offshore wind energy development can have on fishery-independent surveys, which globally is scarce.

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https://umassd.zoom.us/j/92249874120

Meeting ID: 922 4987 4120

Passcode: 747985

DFO Defense: Nicholas M. Calabrese

Department of Fisheries Oceanography

“LOOK BUT DON’T TOUCH: MINIMALLY INVASIVE TRAWL SURVEY TECHNOLOGY”

By:

Nicholas M. Calabrese

Advisor

Kevin Stokesbury (UMass Dartmouth)

Committee Members

Steven X. Cadrin (UMass Dartmouth), Pingguo He (UMass Dartmouth), Michael J.W. Stokesbury (Acadia University), and Anna Mercer (NOAA Federal)

Wednesday May 28th, 2025

1:00 PM

SMAST East 101-103

836 S. Rodney French Blvd, New Bedford

and via Zoom

Abstract:

The School for Marine Science and Technology (SMAST) video trawl survey employs cameras mounted in the open codend of a trawl to identify and numerate groundfish. This minimally invasive survey technology has been used for semi-annual surveys of Atlantic Cod (Gadus morhua) in the Western Gulf of Maine since 2020. Accurate estimates of absolute abundance from the video trawl survey required estimates of catchability, efficiency, and fish length. This project aimed to address these requirements through three experiments and evaluate sampling methodology in a fourth experiment. First, a passive integrated transponder (PIT) tag detection system was developed, tested, and installed in the codend of the net. The custom-designed PIT tag detection system achieved an efficiency of 79%, with detection rates influenced by tag orientation and group size. Then, a mark-recapture experiment to estimate the efficiency and catchability of Atlantic cod was conducted using this system. A Petersen mark-recapture model, based on 1,094 tagged fish and six recaptures, accounting for both discard mortality and reader efficiency, yielded a doorspread efficiency of 12% and a catchability coefficient of 0.0024 per hour of towing. Next, the accuracy of length measurements derived from an off-the-shelf stereoscopic camera mounted within the trawl was assessed. This camera produced inaccurate length measurements, however, these findings helped inform the design of a custom imaging system. Finally, optical data from the survey were used to evaluate the effects of sampling design, tow duration, and sampling intensity on the variance of population estimates through a novel analytical approach. Stratified random sampling produced more precise biomass estimates than simple random sampling. In addition, CPUE mean, and variance increased with shorter tow durations. A 30-minute tow duration minimized within-tow variability and yielded the most precise abundance estimates, although this analysis lacked factors such as fish size and logistical constraints. Collectively, this research advances fisheries-independent survey methodology by addressing key limitations of new approaches.

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https://umassd.zoom.us/j/92695694559

Meeting ID: 926 9569 4559

Passcode: 106409

 

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For additional information, please contact Callie Rumbut at c.rumbut@umassd.edu

DFO Seminar 4/30: Alex Hansell

Department of Fisheries Oceanography

“Collapse, recovery and collapse of an important fishery”

Alex Hansell

Research Fishery Biologist, NEFSC

Wednesday, April 30, 2025

3:00 – 4:00 pm

SMAST E 101-102 and via Zoom

Abstract:

Georges Bank is a shallow plateau off the coast of New England that has supported productive fisheries for centuries. One of these fisheries targeted yellowtail flounder (Limanda ferruginea), which at its peak caught over 30,000 mt a year. However, over the last 100 years the stock has fluctuated, with periods of high abundance (1970s and 2000s) and low stock size (1990s and 2020s). A previous review published twenty years ago documented the collapse of the stock in the 1990s and subsequent recovery in the 2000s, hypothesizing the major reason for recovery was bilateral science and successfully coordinated management intervention. Unfortunately, by the time that review was published, the stock had started to decrease again and collapsed in the 2010s. Here, we update empirical indicators of spatial distribution and growth for Georges Bank yellowtail as well as apply a state-space stock assessment model that includes process error and environmental effects on annual recruitment. Results suggest that the stock has spatially contracted on the Bank, fish are smaller with less variation in size, and recruitment has decreased in recent years due to low stock size and increasing water temperature. These results give insight into an iconic New England groundfish stock, as well as, provide a unique opportunity to study the fluctuations of a stock through multiple periods of recovery and collapse.

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https://umassd.zoom.us/j/93758230260

Meeting ID: 937 5823 0260

Passcode: 426839

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For additional information, please contact Callie Rumbut at c.rumbut@umassd.edu

DEOS Seminar 4/30: John Mohan

Department of Estuarine and Ocean Sciences

“Advancements in fisheries conservation using technology and chemistry “

John Mohan

Fisheries Scientist

Wednesday, April 30, 2025

12:30 – 1:30 pm

SMAST E 101-102 and via Zoom

Abstract:

Effective fisheries conservation remains challenging due to overfishing and complex population structure of highly migratory species. Sharks and tunas migrate across international management regions and are captured, either accidentally as bycatch, or intentionally in commercial or recreational fisheries. Developing technology that can decrease shark bycatch and refining chemical tracer methods to elucidate population structure of fished stocks, will enhance fisheries conservation. Here, case studies will highlight the testing of shark bycatch technology and the application of natural chemical tags in migratory fish to support sustainable management and fisheries conservation.

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https://umassd.zoom.us/j/97440069270

Meeting ID: 974 4006 9270

Passcode: 428029

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For additional information, please contact Callie Rumbut at c.rumbut@umassd.edu

DFO Thesis Defense Announcement: Sean Boisvert

Department of Fisheries Oceanography

“A Numerical Investigation of Size-Selectivity in a Modified Scallop Dredge”

By:

Sean Boisvert

Advisor

Geoffrey Cowles (University of Massachusetts Dartmouth)

Committee Members

Pingguo He (University of Massachusetts Dartmouth), and Douglas Zemeckis (Rutgers University)

Thursday May 8th, 2025

2:00 PM

SMAST East 101-103

836 S. Rodney French Blvd, New Bedford

and via Zoom

Abstract:

The US Atlantic sea scallop (Placopecten magellanicus) fishery, one of the most economically significant in the country, faces challenges related to unintentional capture of undersized scallops and other non-target species. Minimizing retention of bycatch and small scallops can result in economic gain and healthier populations. To address these issues, a modified scallop dredge was developed by Atlantic Cape Fisheries, LLC and features a modified cutting bar with a foreface angle that can be adjusted to a range of angles relative to the seabed to improve the size-selective sorting process. This study complements field research conducted using paired trawls of the modified dredge and standard turtle deflector dredge (TDD) by investigating the underlying hydrodynamic effects of different cutting bar angles and tow speeds on scallop escapement. A coupled computational fluid dynamics (CFD) and particle tracking model approach is used to analyze these effects. The unsteady viscous flowfield is computed with the FUN3D CFD flow solver using an unstructured body-fitted mesh to resolve the boundary layer on the dredge frame. The resulting time-dependent velocity field is used to drive simulations of the trajectories of scallops using a dynamical particle tracking scheme implemented in MATLAB. This model quantifies escape probabilities and other metrics such as shedding frequency, vertical particle velocities, average time to reach the twine top, average height achieved, and average particle trajectories. Simulations were conducted for multiple cutting bar angles, tow speeds, and scallop sizes to assess the modified dredge’s effectiveness compared to the standard TDD. We examined scallop trajectories across 26 size bins (30-160 mm shell height) for nine cutting bar angles (15°-75°) and the standard TDD at a nominal tow speed of 2.5 ms-1 (~5 knots), with additional experiments at 2 ms-1 (~4 knots) and 3 ms-1 (~6 knots) for three angles (30°, 45°, 60°). In total, 468 numerical experiments tracked 15 million particles, requiring approximately 50 hours of computational walltime. Results show that shedding frequency decreased as cutting bar angle increased. The 15° and 30° angle cutting bar angle yielded the highest escape probabilities, particularly for smaller scallops, exceeding the TDD by up to 40%. Higher angles (60°-75°) produced intermittent high vertical velocities but led to lower escape probabilities, attributed to less frequent eddy formation. Scallops released near the cutting bar (0.1 m above seabed, 0.4 m downstream) had the highest escape probabilities. Tow speed had a positive effect on escape probability, especially for the TDD configuration. This study bridges the gap between field trials and the fundamental understanding of scallop sorting mechanisms in the dredge’s wake. The findings of this research have important implications for the design and testing of modified fishing gear. The use of CFD modeling, as evidenced in this study, presents a valid, cost-effective alternative to traditional at-sea gear testing, allowing for extensive design exploration and optimization in a controlled and computationally efficient manner.

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https://umassd.zoom.us/j/94519380509

Meeting ID: 945 1938 0509

Passcode: 913059

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For additional information, please contact Callie Rumbut at c.rumbut@umassd.edu

DFO Seminar 4/16: Janne Haugen

Department of Fisheries Oceanography

“What does successful ecosystem-based management look like and how do we know when we are successful?”

Janne Haugen

Postdoc with IBSS Corp in support of NEFSC

Wednesday, April 16, 2025

3:00 – 4:00 pm

SMAST E 101-102 and via Zoom

Abstract:

Understanding what successful ecosystem-based management (EBM) looks like is essential for evaluating whether management objectives are being met. Linking performance measures to these objectives is therefore crucial for assessing progress. Although EBM holds promise for improving social, economic, and ecological outcomes, its implementation has been challenging, and its effectiveness unclear. One key difficulty lies in developing performance measures that are systematic, integrated, and adaptable to the diverse contexts and ocean-use sectors within an ecosystem – without becoming overly complex or difficult to implement. A semi-quantitative assessment framework that integrates transdisciplinary performance measures for ocean-use sectors, marine ecosystem status, management and tradeoffs, and human dimensions can help assess the effectiveness of EBM strategies. The framework measures performance across categories and synthesizes how well EBM is performing by tracking a multitude of indicators in each category. Case studies, utilization, and impacts of the framework will be discussed as well as how performance measures move management forward.

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https://umassd.zoom.us/j/93758230260?pwd=OHJ5UDloQkZZaCtXcTlBNlR6Qm0rQT09

Meeting ID: 937 5823 0260

Passcode: 426839

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For additional information, please contact Callie Rumbut at c.rumbut@umassd.edu

DEOS Seminar 4/16: Beckett Colson

Department of Estuarine and Ocean Sciences

“From Methane to Microplastics: Developing Next Generation In Situ Instrumentation “

Beckett Colson

Research Engineer, Woods Hole Oceanographic Institution

Wednesday, April 16, 2025

12:30 – 1:30 pm

SMAST E 101-102 and via Zoom

Abstract:

Marine and freshwater processes have global impacts but are challenging to observe due to the range of spatial scales, environmental conditions, and temporal variability. In the Chemical Sensors Laboratory (CSL) at the Woods Hole Oceanographic Institution, we develop in situ instrumentation to reveal these processes by making continuous measurements directly in the environment. These instruments can deliver unprecedented spatiotemporal resolution. This seminar will focus on two instruments we have recently developed: (1) SAGE for measuring deep-sea methane and carbon dioxide, and (2) Scout for quantifying microplastics in waterways. SAGE uses laser spectroscopy with a membrane inlet to quantify dissolved methane and pCO2, and a hollow-core fiber absorption cell to minimize dead volume and achieve a time response of only four minutes. SAGE has been deployed in a variety of deep-sea environments, from hydrothermal vents to cold seeps and mud volcanoes. Scout uses electrical impedance to detect, size, and count microplastics in a continuous water flow. It uses the unique electrical characteristics of microplastics to distinguish them from naturally occurring particulates. Scout has been used locally for surface water measurements, and we are developing a next generation suitable for use on autonomous and underwater platforms. With continued improvements to these instruments, we aim to unlock more avenues for scientific inquiry and collaboration.

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https://umassd.zoom.us/j/97440069270?pwd=L2Z1bDZESTFCKzJYZWduYVhWenYvZz09

Meeting ID: 974 4006 9270

Passcode: 428029

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For additional information, please contact Callie Rumbut at c.rumbut@umassd.edu

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