Marine Biology Commons^™

Development And Validation Of Rapid Edna Detection Method For Yellow Mud Turtle, Kinosternon Flavescens: A Field Study In South Texas, Usa, Sakib Tahmid Rishan, Richard Kline, Md Saydur Rahman

School of Earth, Environmental, & Marine Sciences Faculty Publications

The conservation of freshwater turtle species depends on precise and effective monitoring techniques. Environmental DNA (eDNA) analysis is a potential method for identifying cryptic and elusive turtle species in aquatic ecosystems. eDNA analysis can help to identify key regions for conservation efforts and monitor changes in population levels over time. This study aims to evaluate the effectiveness of a rapid eDNA detection method for the yellow mud turtle (Kinosternon flavescens, an indicator species that is endangered in some states in the USA), which inhabits local oxbow lakes (e.g., resacas) in Cameron County, South Texas. A species-specific nested PCR …

Ghost Fishing Due To Derelict Crab Traps In Louisiana’S Barataria Basin, Emma C. Villemarette

LSU Master's Theses

Ghost fishing, the unintentional entrapment of sea life by derelict fishing gear, is an ecologic and socioeconomic concern in Louisiana's crabbing industry (blue crab, Callinectes sapidus). These ghost fishing traps cause unknown and unaccounted for mortality in blue crab and bycatch species. I aimed to track changes to derelict crab trap catch and trap deterioration over seasons and between habitats. I set and monitored 33 simulated derelict crab traps over 367 soak days in three varying habitats along Barataria Bay, Louisiana. Traps were checked once every two weeks and an additional daily check for five days per season. Blue …

Monitoring And Assessment Of Population, Reproductive, And Health Effects In Colonial Waterbirds Breeding At Contaminated Great Lakes Sites In Michigan, Keith A. Grasman, Mandy Annis, Carly Eakin, Jeremy Moore, Lisa L. Williams

University Faculty Publications and Creative Works

Immunological, reproductive, and population endpoints were assessed in fish-eating birds during 2010–2019 in the Saginaw River and Bay and River Raisin Areas of Concern (AOCs) and Grand Traverse Bay, which are ecosystems historically contaminated with polychlorinated biphenyls, dibenzo-p-dioxins, and dibenzofurans. Reference sites were in the lower St. Marys River (herring gulls and Caspian terns), eastern Lake Superior (terns), and eastern Lake Huron (black-crowned night herons). Relative risk ratios for embryonic nonviability (from both infertility and mortality) in gull embryos were 2–3-fold higher than the reference site in both AOCs and Grand Traverse Bay. Twelve of 13 deformed embryos and chicks …

Examining The Probiotic Potential Of Pseudoalteromonas Rubra Situated In The Scholarly And Public Spheres, Sam Ruemmler

Honors Senior Capstones and Theses

Climate change is affecting our oceans negatively in many ways, such as rising temperatures and increased disease outbreaks. While there are many diseases that are affecting marine organisms, bacteria of the genus Vibrio are present globally and are known to favor warmer waters, which means increasing temperatures will cause an uptick in infections. One species, V. coralliilyticus, has been identified as a pathogen responsible for coral disease and death as well as mortality in rainbow trout, brine shrimp, and Pacific oyster larvae. A possible solution to the rising prevalence of disease is the use of probiotics. One such probiotic candidate …

Study On Motion Prediction Analysis Of Large Vessels Entering Kaohsiung Port Second Harbor, Li-Heng Cheng, Hsing-Yu Wang

Journal of Marine Science and Technology–Taiwan

Pilotage is a primary service offered by ports, ensuring the safe passage of entering and exiting vessels. This study applied motion prediction analysis to large vessels navigating the constrained waterways of Kaohsiung Port’s second harbor. To address the needs of pilots and port operators, a simplified planar motion equation was developed that incorporated speed over ground and rate of turn (ROT) as primary variables. The model relied on inputs of limited navigational data, enabling pilots to predict changes in heading and position over time and determine the conditions for safe harbor entry. Vessel paths and turning angles were analyzed to …

Appendix To Campbell, D. C. & C. Lydeard. Three Decades Of Mussel Mitochondria. Malacologia, V. 68, David Campbell

Department of Natural Sciences Faculty Publications

This table lists all cytochrome oxidase 1 sequences available for Unionida as of June, 2025, with corrections and updates to nomenclature and publication information. A second workbook lists all currently recognized species, identifying which ones have associated molecular data.

Marine Heatwave Response Plan For Western Australia’S Wild Capture Fisheries And Aquaculture, Department Of Primary Industries And Regional Development, Western Australia

Fisheries Management Papers

The purpose of the Western Australian wild capture fisheries and aquaculture marine heatwave response plan (the Plan) is to document the Department’s approach for identifying and responding to the hazard of a marine heatwave on wild catch fisheries (commercial, recreational, charter and customary) and aquaculture resources within the geographic boundaries of WA. It provides risk reduction strategies and establishes best-practice processes for each stage of the hazard management and response continuum, ensuring that DPIRD is able to adequately prepare for, respond to, and recover from marine heatwave events. This Plan operates in conjunction with WA’s existing aquatic resource management framework, …

Macroinvertebrate Community Dynamics In A Recovering, Hypersaline Estuary, Catherine M. Eckert, Claudia A. Tamez, Erin E. Easton, David W. Hicks

Gulf and Caribbean Research

The Bahia Grande is a 6,500—acre tidal basin located at the southernmost tip of Texas. Tidal flow into this coastal estuary was cut off in the 1930s, causing the basin to dry up for ~70 y. A pilot channel connecting the Bahia Grande to tidal waters was constructed in 2005, allowing flooding of the basin to occur. Throughout the period reported herein (2005–2019), the system remained characterized by persistent spatial and temporal episodes of extreme hypersalinity (>70)—a critical factor influencing estuarine community composition and driving key ecological processes. With additional rehabilitation actions forthcoming, characterization of the estuary is essential …

Lack Of Consistent Diurnal Trends In Acoustic Metrics From Restored Coral Reefs, Jeremy Velázquez-Alvarado, Valentina Pérez-García, Javier S. Tellechea, Joni T. Backstrom, Alex Mercado-Molina

Gulf and Caribbean Research

Once vibrant ecosystems, coral reefs are degrading at unprecedented rates due to natural and human—induced disturbances, necessitating immediate restoration and conservation efforts. Evaluating the success of these projects often involves assessing changes in reef biodiversity. Bioacoustics has emerged as a promising, non—invasive method for such evaluations, though its efficacy remains debated. This study aimed to determine whether the diurnal soundscapes of restored coral reefs are consistent across different time frames (months) and spatial scales (reefs), which is crucial for developing reliable monitoring tools for reef health. To achieve this, 2 commonly used acoustic indices, the Acoustic Complexity Index (ACI) and …

Resource Assessment Report No. 1: Mid-West Scallop Resource 2024 Assessment, Jason How, Arani Chandrapavan, Rachel Marks

Resource Assessment Reports

The Mid-West Scallop Resource (Resource) is only accessed by the Abrolhos Islands Mid-West Trawl Managed Fishery (AIMWTMF). The AIMWTMF is the second largest scallop fishery in Western Australia. Access is limited to the 10 licences granted to access the Resource, which are managed through a range of, gear controls, catch rates and seasonal closures. They access saucer scallops, Ylistrum balloti (formerly Amusium balloti) using otter trawls fished over predominantly sand. The fishery was certified by the Marine Stewardship Council in 2021, with the fishery entering re-certification in 2026.

In 2024, 95.7 t meat weight (478.5 t whole weight) of saucer …

Investigating The Refugial River Mouth Hypothesis: Assessing The Effects Of Low Salinity Conditions On The Microscopic Life Stages Of Nereocystis Luetkeana, Duncan Jackson

Cal Poly Humboldt theses and projects

Populations of Nereocystis luetkeana (bull kelp) have experienced localized extinction events in northern California since 2014 due to multiple stressor events, including the area’s most severe marine heatwave (MHW) to-date. Previous surveys in the region observed that bull kelp recovered and persisted at river mouths following the 2014-2015 MHW, suggesting that river mouths may serve as refugia – the refugial river mouth hypothesis. My study aimed to assess this hypothesis and the long-term stability of these refugia by studying how freshwater influences communities at these sites and bull kelp recruitment. Field surveys of salinity fluctuation and kelp and sea urchin …

A Review Of Contact Dependent Interactions Among Encrusting Bryozoans, Sheena Emily Stephens-Norton

Cal Poly Humboldt theses and projects

This review of published literature is focused on bryozoan interactions and discusses overgrowths, “stalemates,” erect bi-laminate growths and fusions. Overgrowths, where one colony grows zooids atop another, have received the most attention in the scientific literature. Stalemates, where two colonies cease growth at the region of contact, have received relatively little research investigating the possible reasons for its occurrence. Erect, bi-laminate growth, following inter- and/or intraspecific contact between colonies, has also received little research, but could reflect mutualistic behavior of encrusting species to increase feeding and reproduction. Fusion of self-self-contacts appears common, yet non-self-fusions to form natural chimeras may also …

Benthic Community Structure Changes In Northern California Following A Marine Heatwave, Franklin D. Moitoza

Cal Poly Humboldt theses and projects

In 2014, an unprecedented ecosystem shift impacted the rocky reef communities of northern coastal California following a rapid succession of severe disturbance events. Rocky reef communities shifted from kelp forests to large scale urchin barrens due to the demise of the sunflower sea star (Pycnopodia helianthoides), an unprecedented marine heatwave event (MHW) and increased purple sea urchin densities. This “perfect storm” caused a decrease in benthic species richness and led to a change in community structure due to intense sea urchin grazing. Here I examine the richness of the benthic community across four survey sites over an 8-year time …

Associational Seaweed Defense Reduces Sea Urchin Grazing On Bull Kelp: Potential Use In Restoration, Brayden Tate Wiley

Cal Poly Humboldt theses and projects

Kelp forests are declining globally under warming seas, altered predator–prey dynamics, and intensified herbivory, with sea urchins often driving shifts from canopy-dominated forests to persistent urchin barrens. Management commonly relies on labor-intensive urchin removals, with variable success, underscoring the need for complementary, ecosystem-based tools that directly reduce urchin grazing pressure. Focusing on far northern California kelp forests, we combined subtidal surveys, field experiments, and laboratory feeding assays to assess whether the understory alga Desmarestia cf. herbacea can provide associational defense for bull kelp (Nereocystis luetkeana) by physically deterring purple sea urchin (Strongylocentrotus purpuratus) grazing and offering low …

Developing New Methods For Quantifying Karenia Brevis In Florida Waters, Antonia N. Ferguson

Honors Undergraduate Theses

Harmful Algal Blooms (HABs), known as red tides, have long impacted Florida’s coastal ecosystems. Caused by the toxic dinoflagellate Karenia brevis, these blooms are named based on the characteristic red discoloration of coastal waters. Negative impacts of K. brevis range from fish kills, neurotoxic shellfish poisoning, and respiratory irritation in humans. Traditionally, K. brevis monitoring has been conducted weekly by Florida Fish and Wildlife Conservation Commission’s Fish and Wildlife Research Institute (FWC-FWRI) using light microscopy for cell identification and enumeration of collected water samples. However, this method is time-consuming, costly, and relies on deep taxonomic expertise for proper cell …

The Effect Of Temperature And Salinity On Margalefidinium Polykrikoides Group Iii Va, Usa Strain Growth, Eduardo Pérez-Vega, Margaret R. Mulholland, Katherine E. Crider, Kimberly E. Powell, P. Dreux Chappell, Alexander Bochdansky

OES Faculty Publications

Margalefidinium polykrikoides is a cosmopolitan dinoflagellate that blooms in coastal waters. Despite genomic evidence that it belongs to Group III and so closely related to isolates from Puerto Rico, Malaysia, North America, and Central America, M. polykrikoides blooms in the Chesapeake Bay at warmer temperatures and lower salinities than in coastal ecosystems occupied by its closest relatives. In this study, the effect of temperature and salinity on the growth rate and total cell yield of an M. polykrikoides VA culture isolate were examined and compared with environmental observations made during M. polykrikoides blooms in the Chesapeake Bay. M. polykrikoides group …

Organic Carbon Decay Mediated By A Mesopelagic Microbial Community: The Relevance Of Carbon Pools And Broad Biochemical Composition, Noah J. Craft, Alexander B. Bochdansky

OES Faculty Publications

The mesopelagic zone is a site of strong microbially driven particle attenuation with depth and thus plays a crucial role in controlling the transfer efficiency of the ocean's biological pump. However, little quantitative information exists on the dependency of decay processes on the source material. Here we followed the decay of ¹⁴C-labeled dead particulate organic carbon (POC) and dissolved organic carbon (DOC) from three different phytoplankton species, and two incubations of live diatoms, in mesopelagic water over 3 months. Commonly used first-order kinetics failed to adequately describe the decay of organic material as rate constants varied from day to day. …

Pygoscelis Penguins Prefer Different Oceanographic And Terrestrial Habitats During The Austral Summer, Katherine L. Gallagher, Rachel Herman, Katherine Walton, Michael S. Dinniman, Heather J. Lynch

OES Faculty Publications

Pygoscelis penguins interact with both terrestrial and marine environments, especially during the austral summer when they raise their chicks. Accessible ice-free ground spaces serve as locations for penguins to build colonies and successfully raise chicks while the surrounding marine environment serves as the foraging grounds for adult birds. Penguins must be able to navigate through the waters around their colonies to forage for Antarctic krill (Euphausia superba), their primary prey during the austral summer. Krill, whose distributions are driven partially by the surrounding physics and partially by their behaviors, must also be plentiful in the waters near the …

Characterization Of Microbial Biofilms On Marine Plastics: Community Development And Density Implications For Vertical Transport Dynamics, Gregory M. Joern, Rut Pedrosa-Pàmies, Xiangtao Jiang, Zhanfei Liu, Alexander B. Bochdansky

OES Faculty Publications

Marine plastic pollution poses a significant and escalating threat to ocean ecosystems, with microbial colonization on plastics playing a critical role in determining their environmental fate. Despite the recognized importance of microbial biofilms, their composition, dynamics, and functional contributions on buoyant plastics remain poorly understood. In this study, we leveraged a novel integrative approach by simultaneously employing 16S, 18S, and ITS sequencing alongside microscopy, lipidomics, pigment analysis, adenosine triphosphate and biogenic silica quantification. This comprehensive methodology allowed for a thorough characterization of microbial growth and community dynamics on plastic debris in a mid-latitude, tidal sub-estuary. Our analyses consistently identified diatoms, …

Florida Statewide Coastal Restoration Guide, Melinda J. Donnelly, Matthew Martin, Christen Fleming, Kelly Kibler, Linda Walters, Patrick Shearer, Lauren Jennison, Erika Lin, George Zaragoza

Faculty Scholarship and Creative Works

The Statewide Coastal Restoration Guide (SCRG) is a comprehensive planning resource developed through a collaboration between Florida Department of Environmental Protection (FDEP), University of Central Florida (UCF), and Resource Environmental Solutions (RES) to strengthen and unify shoreline restoration efforts across Florida. With over 4,500 miles of estuarine shoreline, Florida’s coasts are vital to the state’s ecological health, economic prosperity, and community resilience. However, they face increasing threats from sea level rise, stronger storms, erosion, habitat degradation, and development. The SCRG responds to these challenges by providing science-based, non-regulatory guidance for implementing resilient, nature-based restoration strategies that protect both ecosystems and …

The Future Of Shipping At The Biodiversity-Climate Nexus : Round Table Report, Mary S. Wisz, Fabio Berzaghi, Mikaela Gomez, Maud C. Quinzin, Renis Auma Ojwala, Emily Nuckolls

Reports

This report presents the outcomes of a cross-disciplinary Round Table hosted by the World Maritime University (WMU) from May 13-15, 2024, in Malmö, Sweden. The event brought together 51 experts from academia, industry, NGOs, and international organizations, including the IMO, to explore shipping’s role at the biodiversity-climate nexus. The Round Table had a particular focus on the impacts of shipping that are currently unregulated or under-regulated, and opportunities to address biodiversity loss and pollution as the sector decarbonizes. The report highlights the need to apply comprehensive, ecosystem-based approaches to effectively manage shipping's impacts, including cumulative impacts, on the environment, people, …

Swansea Waterways Plan, Kimberly Starbuck, Kristin Uiterwyk, Shannon Hogan, Allison Novelly

Urban Harbors Institute Publications

UHI worked with the Town of Swansea to engage members of the public in waterways planning activities. The plan covered a wide range of topics including public access, water quality, natural resources, commercial and recreational uses, and climate change.

Husbandry Of Jellyfish And Ctenophores: Why Gelatinous Forms Thrive In Their Natural Habitat And Yet Often Struggle To Survive In Aquaria, Regina Garza Ramirez

Undergraduate Theses and Capstone Projects

Recent observations in the behaviors of several gelatinous forms in the wild have demonstrated that human impacts to their environment have likely accelerated growth of their populations tremendously. Interestingly enough, population growth of jellyfish and ctenophores in aquariums and artificial habitats is less often observed under controlled conditions, while they often bloom in rapidly changing environments of nature. Seeking the knowledge of aquarists and researchers that have worked directly with gelatinous animals through interviews, and documenting the experiences of each individual, allowed acquisition of data that can be used to compare the reproductive success of these animals in captivity and …

Quantifying The Vulnerability Of Smooth Dogfish And Winter Skate To Electromagnetic Fields From Offshore Wind Transmission Cables In The Mid-Atlantic Shelf, Rachel A. Sechrist

Theses, Dissertations and Culminating Projects

The development of offshore wind structures in the northeastern U.S. will contribute to renewable energy goals, but will overlap with many marine species as well as economically important fisheries. High voltage transmission cables from offshore wind farms emit electromagnetic fields (EMFs) that elasmobranchs may detect using sensory organs known as ampullae of Lorenzini. However, sensitivity to EMFs varies by species due to differences in the number and arrangement of pores, the length of subdermal canals within the ampullae of Lorenzini sensory network, and the habitats they reside and regions they forage. For species who reside or forage in benthic regions, …

Zinc Or Swim: Investigating Zinc Pollution From Restoration Materials, Megan R. Jensik

Honors Undergraduate Theses

Zinc is an essential nutrient, but can be toxic at high concentrations, negatively affecting various biological functions. Gabions are galvanized metals coated in zinc that are used for many human purposes, including coastal restoration efforts attempting to avoid using plastic materials. However, gabions can degrade in marine environments, potentially leaching metal into the water and soil. There is a knowledge gap regarding the occurrence and impacts of zinc pollution in the areas where these gabions are deployed, including the Indian River Lagoon (IRL). To address this, sediment samples were collected from the IRL and analyzed for their physical and chemical …

Noaa Oceanic And Atmospheric Research Ocean Carbon Observing Science Plan Fy25 To Fy35, United States National Oceanographic And Atmospheric Administration

National Oceanographic and Atmospheric Administration: Technical Reports and Related Materials

United States National Oceanographic and Atmospheric Administration oceanic and atmospheric research ocean carbon observing science plan for fiscal years 2025 through 2035.

Investigating The Role And Expression Of Aquaporin 10 Paralogs In Spiny Dogfish (Squalus Acanthias), Esosa Omoregie

College of Graduate Studies: Theses & Dissertations

Aquaporins (AQPs) are integral membrane proteins that facilitate the selective transport of water and small solutes across cell membranes, playing essential roles in maintaining osmotic balance in vertebrates. Among them, aquaglyceroporins such as AQP10 are capable of transporting water, glycerol, and urea, contributing to osmoregulatory and metabolic processes. This study investigated the expression, localization, and potential physiological roles of two AQP10 paralogs, AQP10C1 and AQP10C2, in the spiny dogfish (Squalus acanthias), a marine elasmobranch that maintains osmotic equilibrium through urea retention and ion regulation. Using RT-PCR, quantitative PCR, Western blotting and immunohistochemistry the study identified tissue-specific expression patterns of …

The Role Of Heterotrophy In The Response Of Oculina Arbuscula To Ocean Acidification, Alejandra E. Daniel

College of Graduate Studies: Theses & Dissertations

On both tropical and temperate reefs, the calcium carbonate skeletons produced by scleractinian corals provide habitat that supports a high biodiversity of fishes and invertebrates. Ocean acidification (OA), driven by excess anthropogenic CO₂ uptake, causes declines in seawater pH and carbonate ion concentration and can compromise coral calcification by causing increased energetic demands. Deciphering how corals meet this increased energetic demand is critical to predicting their future persistence. Oculina arbuscula is a facultatively symbiotic temperate coral common on subtropical reefs of the South Atlantic Bight. This coral has demonstrated calcification resilience to reduced pH conditions in both symbiotic and …

The Effects Of A River Closure On A Snook (Centropomus Spp.) Nursery Community In The Rio Grande River, Texas, Ethan Getz, Perry Trial, Catherine Eckert, Joel Anderson

Gulf and Caribbean Research

Snook (Centropomus spp.) support important fisheries in the Gulf of Mexico and populations are increasing in Texas. However, a primary snook nursery, the Rio Grande River, remains one of the most imperiled rivers in North America. In 2001—2002, low flows led to the formation of a sandbar and the complete blockage of the Rio Grande, eliminating exchange with coastal waters. Here, data collected by the Texas Parks and Wildlife Department were used to determine how the Rio Grande closure affected juvenile and subadult snook and the estuarine community. Seine and trawl samples were collected prior to (1992—1997) and during …

ผลกระทบของไมโครพลาสติกต่อปะการังดอกกะหล่ำ Pocillopora Damicornis (Linnaeus, 1758) ในแต่ละช่วงอายุ, กลวัชร จันทร์หอม

Chulalongkorn University Theses and Dissertations (Chula ETD)

ไมโครพลาสติก (Microplastics) คือ พลาสติกที่มีขนาดเล็กกว่า 5 มิลลิเมตร เป็นปัญหาสำคัญที่ส่งผลต่อสิ่งแวดล้อมและสิ่งมีชีวิตต่าง ๆ ไมโครพลาสติกเกิดการสะสมได้ในบริเวณแนวชายฝั่ง ส่งผลกระทบต่อระบบนิเวศที่สำคัญในบริเวณ คือ ระบบนิเวศปะการัง งานวิจัยนี้ได้ทำการทดลองผลของไมโครพลาสติกต่อปะการังดอกกะหล่ำ Pocillopora damicornis (Linnaeus, 1758) ซึ่งปะการังที่พบได้ทั่วไปตามแนวปะการังและเป็นปะการังที่มีส่วนสำคัญในการสร้างแนวปะการัง ทำการศึกษาผลกระทบของไมโครพลาสติก PVC (polyvinyl chloride) ขนาด 100-250 และ 251-400 ไมโครเมตร ที่ความเข้มข้น 5 ระดับ ได้แก่ 0 (ชุดควบคุม), 0.0005, 0.001, 0.005 และ 0.01 กรัมต่อลิตร ที่มีต่อตัวอ่อนของปะการัง ทั้งนี้ เมื่อสิ้นสุดการทดลอง (96 ชั่วโมง) พบว่า ปะการังในชุดการทดลองไมโครพลาสติกขนาด 251-400 ไมโครเมตรที่ระดับความเข้มข้น 0. กรัม/ลิตร มีอัตรารอดต่ำที่สุด (85±5 เปอร์เซ็นต์) และมีความแตกต่างอย่างมีนัยสำคัญเมื่อเทียบกับชุดควบคุม ในส่วนอัตราการลงเกาะพบว่า แต่ละชุดทดลองมีอัตราการลงเกาะของตัวเกาะใกล้เคียงกันและไม่ต่ำกว่า 67 เปอร์เซ็นต์ และไม่พบความแตกต่างทางสถิติในแต่ละชุดทดลอง สำหรับผลของไมโครพลาสติกต่อปะการังโตเต็มวัย เมื่อสิ้นสุดการทดลอง (96 ชั่วโมง) พบว่า ไมโครพลาสติกไม่ส่งผลกระทบอย่างมีนัยสำคัญต่ออัตรารอดของปะการัง (ชิ้นส่วนของกิ่งปะการัง) แต่เมื่อนำชิ้นส่วนปะการังมาย่อย พบไมโครพลาสติกชนิดที่นำมาทดลองสะสมภายในเนื้อเยื่อปะการังเท่านั้น โดยพบไมโครพลาสติกขนาด 100-250 ไมโครเมตร สะสมในชุดทดลองที่ความเข้มข้น 0.005 และ 0.01 กรัม/ลิตร โดยปริมาณของไมโครพลาสติกที่พบเท่ากับ 0.06±0.12 และ 0.80±0.34 ชิ้นต่อ 100 โพลิป ตามลำดับ