Oceanography Commons^™

Mapping The Water Quality Of Jamaica Bay, New York (1996-2024): Principal Component Analysis And K-Means Clustering, Sneha Srivastava

Dissertations, Theses, and Capstone Projects

Jamaica Bay, located along the southeastern coast of New York City, acts as a biodiverse estuary of wetlands, meadows, and salt marsh islands. The purpose of this study is to analyze the water quality conditions of the region over time, comparing locations around the bay to identify hyperlocal features that influence larger trends in the hydrological system. Ten variables were used as water quality indicators, including total Kjeldahl nitrogen, salinity, pH, Secchi disk depth, and total phosphorus, among others, across five stations in the bay, between 1994 and 2024. After data cleaning and standardization methods were applied, principal component analysis …

Productive Armature, Gabriel Ofem Peter

Masters Theses

What if water was all you had, what if your only source of survival was a body of water? I shudder to think that some people get to be put in this situation in the world we live in. As I understand the importance of water to survival, it is obvious that water can be the only lifeline of survival for a community. This is the experience for residents of Makoko, Lagos. Their survival depends on the Lagos Lagoon, a large body of water flowing in from the Atlantic Ocean. This research looks beyond the surface of what this community …

Changes In Land, Ocean, Atmospheric Parameters Associated With The 2025 Myanmar (Mw 7.7) Earthquake, Feng Jing, Akshansa Chauhan, Ashwani Raju, Ramesh P. Singh

Mathematics, Physics, and Computer Science Faculty Articles and Research

Multiple parameters associated with the land, atmosphere, and ocean were analyzed to study short-term and immediate pre-earthquake changes associated with the 28 March 2025 Myanmar earthquake (Mw 7.7). Anomalous clear-sky outgoing longwave radiation (ClrOLR) and trace gases (CH₄, CO, and O₃) were detected within two months prior to the mainshock. Vertical changes at different pressure levels suggest a possible underground source. High-temporal-resolution observations of the infrared brightness temperature and surface air pressure revealed short-lived fluctuations shortly before the earthquake, which may reflect localized stress adjustments and surface latent heat flux release during the final stage of earthquake preparation. In the …

Is The Chesapeake Bay Browning?, Samantha Williamson, Jessie Turner

Knowledge and Creativity Expo

Brownification is when water bodies turn brown over time. It occurs due to high amounts of color-dissolved organic matter (CDOM). CDOM is organic material, such as decaying leaves and organisms, that leaches into the water column like tea. It absorbs ultraviolet and blue light more than red light, causing the water to appear brown. After comparing surveys from 1987 and 2018, scientists discovered the Adirondack lakes underwent brownification as they recovered from acid rain. However, while increased CDOM can signify an ecosystem’s recovery, it can also hinder seagrass growth. Although scientists have studied this phenomenon in lakes, estuaries have not …

Biogeochemical Controls On Phosphorus Transport And Legacy Storage Across A Coastal Watershed, Lee Potter

LSU Doctoral Dissertations

Excess phosphorus (P) loading is a key driver of eutrophication and harmful algal blooms (HABs) in aquatic systems worldwide. This relationship is of increasing concern in coastal Louisiana, where climate variability, altered hydrology, and land-use change converge, resulting in increased hydrologic and nutrient loading into coastal systems. This dissertation examines controls on P cycling in the Lake Pontchartrain Basin through a multi-scale framework linking estuarine processes, watershed loading, climate and weather patterns, and sediment dynamics. The dissertation begins with an overview of the study region, P dynamics, and changes in hydrology and nutrient loading patterns. Chapter 2 presents a spatial …

A Probabilistic Deep Learning Framework For Retrieving Chlorophyll-A From Hyperspectral Imagery: Integrating Channel Attention And Mixture Density Networks, Wenzhao Li, Surendra Maharjan, Rejoice Thomas, Junde Chen, Hesham Morgan, Michael J. Garay, Olga V. Kalashnikova, Shahryar Fazli, Charles Ichoku, Hesham El-Askary

Mathematics, Physics, and Computer Science Faculty Articles and Research

Accurate monitoring of Chlorophyll-a (Chla) is critical for assessing aquatic ecosystem health, yet ecological complexity often leads to ambiguous spectral signatures in satellite data. Traditional deterministic models assume a one-to-one mapping between spectra and pigments, often failing to capture these high-dimensional analytical challenges. In this study, we propose a novel deep learning architecture, the Channel Attention-Mixture Density Network (CA-MDN), to retrieve Chla from the National Aeronautics and Space Administration (NASA) Earth Surface Mineral Dust Source Investigation (EMIT) hyperspectral mission. The CA-MDN integrates an attention mechanism to dynamically select ecologically relevant spectral bands and employs a probabilistic output layer to quantify …

Chesapeake Bay Water Clarity: Challenges And Successes, Jessica S. Turner, Carl T. Friedrichs, David B. Parrish, Kelsey A. Fall

OES Faculty Publications

The Chesapeake Bay is a large estuarine system spanning multiple jurisdictions and serves as a model for estuarine health worldwide. Historically, nutrient loading degraded water quality, prompting the need for regulation. Water clarity, one component of water quality, is vital for benthic communities and serves as a key indicator of overall ecosystem health. Here, physical resuspension and salinity gradients, nutrient and sediment inputs, production of organic detritus by phytoplankton, and benthic communities all interact to drive clarity patterns, with high spatial variability. Trends over the last 50 years show improvement, though with a temporary increase in organic detritus in response …

Contribution Of Non-Linear Internal Waves To Marine Net Primary Production Has Been Underestimated, Xiaoju Pan, Tung-Yuan Ho, George T. F. Wong, Jen-Hua Tai, Shoude Guan, Fuh-Kuo Shiah

OES Faculty Publications

Field observations in the northern South China Sea (NSCS) indicate that elevated concentrations of chlorophyll a (Chl_a) associated with non-linear internal waves (NIWs) were more pronounced in the subsurface than at the sea-surface. At a given surface Chl_a, the vertically integrated Chl_a in an NIW-active area was 45% higher than that in an area where the NIW activities were minimal. As a result, net primary production (PP_eu) estimated from surface Chl_a from remote sensing by using the current Chl_a-based PP_eu model (e.g. VGPM) would have underestimated the true value by the same amount. If this correction is …

Lessons For Transformative Ocean Science From The Integrated Marine Biosphere Research (Imber) Project, Deborah Santos Prado, Ella-Kari Muhl, Mia Strand, Derek Armitage, Nina Bednaršek, Stephanie Brodie, Christopher Cvitanovic, John Claydon, Sam Dupont, Karen Evans, Alistar Hobday, Eileen Hofmann, Raleigh Hood, Laura Kaikkonen, Dongyan Liu, Jessica Melbourne-Thomas, Franz Mueter, Eugene Murphy, Prateep Kumar Nayak, Alice Newton, Heidi Pethybridge, Carol Robinson, Samiya Selim, Rowan Trebilco, Micaela Trimble, Fang Zuo

CCPO Publications

This paper synthesizes the key contributions and lessons learned from Integrated Marine Biosphere Research (IMBeR), a large-scale global research project aimed at fostering ocean sustainability under global change for the benefit of society. The UN Decade of Ocean Science for Sustainable Development has catalyzed a renewed focus on the importance of transforming ocean science. IMBeR’s global activity over the past decade has focused on promoting transformative science by generating, mobilizing, and communicating the knowledge needed to support ocean governance. Key contributions from IMBeR participants include quantifying and comparing historic and present structure and functioning of linked ocean and human systems, …

A Preliminary Investigation Of Research Collaboration Through Scientific Paper Co-Authorship In The Gulf Of Mexico, Juliet Vallejo, Evelyn Roozee, Dongkyu Kim, Andrew M. Song, Christopher A. Gabler, Jasper R. De Vries, Antonia Sohns, Gordon M. Hickey, Owen Temby

School of Earth, Environmental, & Marine Sciences Faculty Publications

It is well known that publications with collaborators from external institutions increase citations. This effect scales with spatial distance. There are also many barriers to long-distance collaborations, including linguistic differences, funding constraints, and the incremental costs of remote collaboration. This paper uses the Gulf of Mexico as a case study to examine long-distance research collaboration because it consists of three countries with diverse development levels and two prominent diplomatic languages, within a singular regional ecosystem of tremendous natural and economic value. This paper uses bibliometric network analysis to examine scientific research article co-authorship in the Gulf of Mexico from 2000 …

Multi-Satellite Image Matching And Deep Learning Segmentation For Detection Of Daytime Sea Fog Using Gk2a Ami And Gk2b Goci-Ii, Jonggu Kang, Hiroyuki Miyazaki, Seung Hee Kim, Menas Kafatos, Daesun Kim, Jinsoo Kim, Yangwon Lee

Institute for ECHO Articles and Research

Traditionally, sea fog detection technologies have relied primarily on in situ observations. However, point-based observations suffer from limitations in extensive monitoring in marine environments due to the scarcity of observation stations and the limited nature of measurement data. Satellites effectively address these issues by covering vast areas and operating across multiple spectral channels, enabling precise detection and monitoring of sea fog. Despite the increasing adoption of deep learning in this field, achieving further improvements in accuracy and reliability necessitates the simultaneous use of multiple satellite datasets rather than relying on a single source. Therefore, this study aims to achieve higher …

Understanding Enso Through Mathematical Models, Maria I. Sanchez Muniz

Open Educational Resources

This assignment introduces students to conceptual models of the El Niño–Southern Oscillation (ENSO) and guides them through a structured investigation of their physical and mathematical foundations. Students analyze the recharge–oscillator and delayed–oscillator frameworks, explore how differential equations capture ocean–atmosphere interactions, and evaluate parameter-driven changes in oscillatory behavior. A key component of the work is the guided use of generative AI as a research tool: students employ AI models to locate peer-reviewed literature, interrogate model extensions, and refine their understanding of complex mechanisms, while synthesizing all final explanations in their own words. By blending classical climate modeling with modern AI-supported inquiry, …

Coupled Machine Learning Models: Combining Observations And Numerical Analysis In A Physics-Regularized Approach, Austin B. Schmidt

LSU New Orleans Theses and Dissertations

This dissertation investigates surrogate modeling for fixed-location environmental forecasting using novel data-combination techniques. The work surveys the landscape of observational measurements and numerically generated data, identifying similar research and gaps in current methodologies. The ratio-coupled training framework is introduced to combine two data sources per predicted feature through a tunable parameter that weights training signal strength. An optimization scheme is developed to simultaneously tune surrogate weights and the coupled signal ratio, allowing relative influence between signals to act as an explicit regularizer. Three case studies demonstrate the methodology and approach in a variety of contexts. The first study is based …

Benthic Infaunal Responses To Shoreline Restoration, Jessica Lauren Cline

Theses and Dissertations

In the age of increasing urban coastal sprawl, natural shorelines are being replaced by hard armoring structures, which result in the loss of valuable ecosystem services. Hybrid living shorelines, areas that include limited and less intensive armoring strategies paired with the integration of plants and other natural materials, present an opportunity to marry the need for more aggressive stabilization with the continued preservation of ecosystem functions and biological communities. This project uses benthic infauna to evaluate the success of a living shoreline installation in Palm Bay, Florida. The deployment features experimental treatments of breakwaters and red mangroves to explore how …

Locations Of Outfalls In The Indian River Lagoon And Lake Worth Lagoon, Florida, Kelly M. Kibler, Melinda J. Donnelly, Vincent Encomio, Madison Giuntoli, Manisha Thenuwara, Brice Bennett, Laura Andrade Barron, Mariam Sonbol, Wynter Raine Seppala, Namritha Ramakrishnan, Jennifer Jordan Báez, Beth Orlando, Irene Arpayoglou, Melissa Meisenburg

Indian River Lagoon Shorelines

The spatial dataset: UCF_Outfalls_IRL_LWL.shp was created under grants from the Indian River Lagoon National Estuaries Program and Florida Sea Grant. These projects cumulatively led to creation of a living shoreline restoration prioritization model and hydrodynamic habitat suitability models for 1,550 km (963 miles) of estuarine shorelines in Indian River Lagoon (IRL) and Lake Worth Lagoon (LWL).

The dataset presented here includes the location of outfalls identified throughout the study region and general characteristics of the shoreline where they were identified.

Seagrass Persistence In The Indian River Lagoon And Lake Worth Lagoon, Florida, Kelly Kibler, Melinda Donnelly, Vincent Encomio, Madison Giuntoli, Manisha Thenuwara, Brice Bennett, Laura Andrade Barron, Mariam Sonbol, Wynter Raine Seppala, Namritha Ramakrishnan, Jennifer Jordan Báez, Beth Orlando, Irene Arpayoglou, Melissa Meisenburg

Indian River Lagoon Shorelines

The spatial dataset: UCF_seagrasspersistence_IRL_LWL.shp was created with support from the Indian River Lagoon National Estuaries Program and Florida Sea Grant. These projects cumulatively led to creation of a living shoreline restoration prioritization model and hydrodynamic habitat suitability models for 1,550 km (963 miles) of estuarine shorelines in Indian River Lagoon (IRL) and Lake Worth Lagoon (LWL). The dataset presented herein represents persistence of seagrass throughout waters of the IRL and LWL.

Living Shoreline Prioritization And Hydrodynamic Habitat Suitability Models For Restoration In The Indian River Lagoon And Lake Worth Lagoon, Florida, Kelly M. Kibler, Melinda J. Donnelly, Vincent Encomio, Madison Giuntoli, Manisha Thenuwara, Brice Bennett, Laura Andrade Barron, Mariam Sonbol, Wynter Raine Seppala, Namritha Ramakrishnan, Jennifer Jordan Báez, Beth Orlando, Irene Arpayoglou, Melissa Meisenburg

Indian River Lagoon Shorelines

The spatial dataset: UCF_shorelinemodel_IRL_LWL.shp, was created with support from the Indian River Lagoon National Estuaries Program and Florida Sea Grant. These projects cumulatively led to creation of a living shoreline restoration prioritization model and hydrodynamic habitat suitability models for 1,550 km (963 miles) of estuarine shorelines in Indian River Lagoon and Lake Worth Lagoon.

The dataset presented herein includes:

1. shoreline data from >15,000 transects collected in the field,
2. shoreline wave climate data created through hydrodynamic modeling and frequency analysis of historic data,
3. categorization of potential risk for shoreline boat wake impact,
4. persistence of seagrass within 210 m of the shoreline, …

Technology Transfer In The Implementation Of The Biodiversity Beyond National Jurisdiction Agreement, Christine Nzambi Mulatya

World Maritime University Dissertations

No abstract provided.

Ocean And Coastal Acidification Monitoring Priorities For The Northeast Us And Eastern Canada, Christopher Hunt, Austin Pugh, Jake Kritzer, Samantha Siedlecki, Kumiko Azetsu-Scott, Parker Gassett, Diane Lavoie, Adam Pimenta, Amy Trice, Elizabeth Turner

Faculty Publications

The Interagency Working Group on Ocean Acidification Monitoring Prioritization Plan 2024 calls for Coastal Acidification Networks to identify the ocean and coastal acidification (OCA) monitoring needs most important for their regions. The Northeast Coastal Acidification Network (NECAN) organized a webinar series to study regional needs, which culminated with a workshop in November 2023. This workshop led to the identification of six priority new Monitoring Needs in addition to the maintenance of current monitoring efforts:

• Improve spatial and temporal scale of monitoring co-located OCA variables and biological measurements to better resolve variability of acidification dynamics in concert with biological processes …

Assessment Of Estuarine Respiration And Benthic Nutrient Fluxes In Mississippi Sound, Nur Pasha Sufian

Master's Theses

This study quantified seasonal and spatial variability of both water column and benthic respiration rates as well as benthic nutrient fluxes along the Mississippi Sound. Respiration was measured in recirculating incubation chambers using Firesting optical DO sensors (PyroScience GmbH), and changes in nutrient concentrations were assessed. Mean water column respiration rates ranged from 0.35 and 2.76 µM O₂ hr⁻¹, with the lowest rates in the winter and the highest in the summer while detectable nutrient concentrations (ammonium, (NH₄⁺), and soluble reactive phosphate (PO₄³⁻)) showed only slight decreases (< 1 µM) over all seasons. Sediment incubation chambers consistently had much greater oxygen declines than the water incubations and showed seasonal trends with the highest mean respiration rates measured in the summer and the lowest mean in the winter, with a range from 107.4 to 1514.9 µmol O₂ m⁻² hr⁻¹ (2.6 to 36.3 mmol O₂ m⁻² d⁻¹). Sediment incubations consistently showed increases in NH₄⁺ concentrations in the overlying water, resulting in calculated NH₄⁺ benthic flux rates of 0.73 to 379.01 µM N m⁻² hr⁻¹ with the lowest rates in the winter and highest rates in the summer. Although PO₄³⁻ concentrations were often below detection in cooler seasons, PO₄³⁻ flux also peaked during the summer (< 28.8 µmol P m⁻² hr⁻¹). In this study, temperature was a key regulator for estuarine respiration and benthic nutrient flux rates, and these rates were positively correlated with porewater nutrient concentrations and sedimentary organic matter. These findings illustrate that benthic respiration can contribute to water column hypoxia and that sediments serve as a source of nutrients to the water column. Overall, these findings provide us with valuable insight about the seasonal coupling of oxygen demand and nutrient flux in the Mississippi Sound and provide valuable baseline data for future biogeochemical modelling of hypoxia, eutrophication, and productivity.

The Influence Of Monsoon Variability On The Circulation Of The Near-Surface Indian Ocean And The Depth-Integrated Chlorophyll, Marufa Ishaque

OES Theses and Dissertations

The Indian Ocean experiences a strong semiannual reversal of monsoon winds, which determines the weather and climate of Asia, including freshwater fluxes between the atmosphere, land, and ocean. Studies and model projections suggest that the timing and intensity of the seasonal monsoon have already started to change, with more dramatic changes likely in the future. However, the impact of these changes on the Indian Ocean circulation system, including the inter-basin salt/freshwater transport between the Bay of Bengal and the Arabian Sea, remains unclear. To better understand how monsoon variability affects Indian Ocean circulation patterns, a Regional Ocean Modeling System simulation …

How’S It Growing? Tools For Observing Snow And Sea Ice In A Changing Arctic Ocean, Ian Alexander Raphael

Dartmouth College Ph.D Dissertations

September Arctic sea ice extent has diminished by roughly 50% in the 45 years since satellite observations began. The Arctic Ocean may experience ice-free summers within the next decade, with implications for habitat, resource extraction, geopolitics, and local and global climate change. To predict how Arctic sea ice will change in the future, we need to understand its behavior in the present. In situ sea ice mass balance measurements (snow accumulation, ice growth, snow and ice surface melt, and bottom melt) are essential for studying the processes driving rapid changes in the ice pack, and for validating remote sensing measurements …

Land Instability Compounds The Risk Of Sea Level Rise In Alexandria, Egypt, Rejoice Thomas, Sara Zouriq, Shahryar Fazli, Amr Fawzy, Nikolay Grisel Todorov, Surendra Maharjan, Wenzhao Li, Erik Linstead, Daniele Struppa, Hesham El-Askary

Mathematics, Physics, and Computer Science Faculty Articles and Research

The coastal region of Alexandria Governorate in Egypt holds significant strategic importance for trade while being susceptible to extreme weather events. It confronts a dual challenge of the rising sea levels and, as found in this study, land instability. While much attention has been rightly directed towards sea level rise (SLR), the stability of the land warrants equal consideration. Here, a comprehensive analysis of land stability is conducted in Alexandria by measuring Line of Sight (LOS) displacements and assessing their topographical, hydrological, and coastal impacts. Persistent Scatterer Interferometry technique is used to measure the LOS displacements in association with land …

The Petm: A Window Into Earth's Future Climate, Jacalyn M. Wittmer Malinowski

Climate Change and the Individual, 2025-26

The Paleocene-Eocene Thermal Maximum (PETM) is not just an event that occurred in Earth’s distant past (~55 million years ago) but is a crucial lesson for today’s meteoric climate change. The PETM offers a historical parallel of rapid flux of greenhouse gases into the atmosphere that caused global warming, ocean acidification, dramatic changes in weather, and extinctions. This global warming event was the result of 20,000 years of “rapid” warming (in geological terms) however, we are experiencing rates of warming that are 5-10x higher than PETM levels. We are not experiencing rapid warming today, in comparison to the past, we …

08 - Blue Carbon Sequestration And Sediment Storage In Seagrass Meadows Of South Bay, Luke C. Clements, Adriana Amrhein, Richard P. Hale

Undergraduate Research Symposium

Blue carbon is stored in coastal and marine ecosystems like seagrass meadows and salt marshes, which helps combat climate change by preventing greenhouse gas emissions. This study examines the role of seagrass in carbon storage by comparing sediment cores from a mud channel and a seagrass meadow in South Bay.

We collected a 100 cm core from the mud channel and a 55 cm core from the seagrass area, taking samples every 10 cm to analyze grain size and organic carbon content. Using a wet sieving method, we separated sand from mud and measured organic carbon through loss on ignition. …

Transcriptional Profiles Reveal Physiological Mechanisms For Compensation During A Simulated Marine Heatwave In Yellowtail Kingfish (Seriola Lalandi), Sharon E. Hook, Ryan J. Farr, Jenny Su, Alistair J. Hobday, Catherine Wingate, Lindsey Woolley, Luke Pilmer

Fisheries Research Articles

Background

Changing ocean temperatures are already causing declines in populations of marine organisms. Predicting the capacity of organisms to adjust to the pressures posed by climate change is a topic of much current research effort, particularly for species we farm or harvest. To explore one measure of phenotypic plasticity, the physiological compensations in response to heat stress as might be experienced in a marine heatwave, we exposed Yellowtail Kingfish (Seriola lalandi) to sublethal heat stress, and used the transcriptome in gill and muscle, benchmarked against heat shock proteins and oxidative stress indicators, to characterise the acute heat stress …

Exploring Single Cell Microbial Protein As A Sustainable Fishmeal Alternative In Yellowtail Kingfish (Seriola Lalandi) Diets: Impacts On Health And Gut Microbiome, Luke Pilmer, Lindsey Woolley, Alan Lymbery, Chinh Dam, Abigail Elizur, Md Javed Foysal, Gavin Partridge

Fisheries Research Articles

Background

With the global expansion of aquaculture and the increasing demand for fish meal, identifying appropriate and sustainable alternative protein sources for aquafeeds has become essential. Single-cell protein (SCP), derived from methanotrophic bacteria, presents a promising alternative by converting methane into protein, potentially addressing both the need for alternative protein sources and reducing industrial greenhouse gas emissions. This study aimed to evaluate the effects of different levels of SCP inclusion (0%, 25%, 50%, and 75% fish meal replacement) on the health, gene expression, and gut microbiome of yellowtail kingfish (YTK, Seriola lalandi) following a 35-day growth trial.

Results

The …

My Octopus Teacher (2020) Directed By Pippa Ehrlich And James Reed, Peter Shea

Picture Books

My Octopus Teacher combines a carefully structured love story with astonishing information about undersea life, documenting a year of encounters between a photographer and an octopus. It is important as a non-standard love story and as a reflection on the possibility of deep connection with non-human creatures.

A Collaborative Assessment Of Coastal Ocean Acidification Monitoring In Maine & Standard Operating Procedures And Best Practices For The Collection Of Continuous Ph Data In Coastal Marine Environments, Christopher W. Hunt, Curtis Bohlen, Mike Doan, Jeremy Miller

Faculty Publications

The ‘Sensor Squad’ of the Maine Ocean Climate Collaborative is the product of a 2023 Maine Coastal and Marine Climate Action Fund grant to conduct “A two-year pilot project designed to address and overcome technological barriers to ocean acidification data collection, develop protocols to elevate quality assurance and ensure comparable data, and meet regularly to discuss project results and data compilation”. The Squad consists of representatives from Friends of Casco Bay (FOCB), Wells National Estuarine Research Reserve (WNERR), and the University of New Hampshire (UNH). This report is a summary of their efforts to assess affordable, repeatable means of continuously …

Successful Eastern Oyster (Crassostrea Virginica) Recruitment On Intertidal Artificial Substrates In Virginia, Usa, Rochelle D. Seitz, Kathleen E. Knick, Emily Suchonic, Amanda Pysher

OES Faculty Publications

Declines of eastern oyster (Crassostrea virginica) populations and scarcity of natural oyster shell necessitate quantifying the effectiveness of artificial oyster reef substrates over varying environmental conditions. Oyster castles are often used in intertidal areas with moderate wave energy; however, new concrete, natural-looking substrates, GROW Reef Tiles, are now available. Eastern oyster recruitment and size on oyster castles (OC) and GROW Reef Tiles (GT), with 27% higher surface area on OC, were assessed three times over 25 months in locations with varying salinity. Four sites in the Chesapeake Bay region were examined: Cherrystone Inlet, Mockhorn Bay, Elizabeth River, and …