Aquaculture and Fisheries Commons^™

Assessment Of Goose-Beaked Whale Responsesto Mid-Frequency Active Sonar Usinga Hierarchical Hidden Markov Model, Stacy L. De Ruiter, Erin A. Falcone, Shannon N. Coates, Brenda K. Rone, David A. Sweeney, Karin A. Dolan, Susan M. Jarvis, Russel D. Andrews, Stephanie L. Watwood, Gregory S. Schorr

University Faculty Publications and Creative Works

Background

Acoustic disturbance is increasingly recognized as an ecological concern, particularly at sea. In light of marine mammal stranding events associated with use of naval mid-frequency active sonar (MFAS), which often involve goose-beaked whales (Ziphius cavirostris), research has sought to detect and characterize Ziphius behavioral responses to MFAS.

Methods

We deployed Sound and Motion Recording and Telemetry (SMRT) tags on 13 Ziphius in the Southern California Bight. The study area includes the United States Navy’s Southern California Anti-submarine Warfare Range (SOAR), and deployments overlapped temporally with training exercises including MFAS use. We used hierarchical hidden Markov models (HHMMs), which provided …

Assessing The Effect Of A Human-Made Reservoir On The Mussel Community In Caney Creek, Trakker Estes

ATU Scholars Symposium

Freshwater mussels are one of the most threatened taxonomic groups globally, with less than 32% of North American taxa considered secure. In Arkansas, over half of the state’s 85 species are endangered, threatened, or of special concern. Small impoundments may contribute to these declines through reduced hydrological connectivity and the resulting decline of fish community movement. This study examines the effects of Tri-County Lake, a small impoundment of Caney Creek in southern Arkansas, on mussel abundance and diversity. In total, eight sites were surveyed upstream, within, and downstream of the impoundment across various habitat types. A timed-search approach utilizing scuba …

Greenhouse Gas Report For Western Australian Wild-Catch Fisheries And Aquaculture 2004-2025, Christophe D'Abbadie, Johnny Machon, Dipesh Maharjan, Mark Goninon, Pia Dobson, Jason How, Rodney Duffy Dr., Ainslie Denham, Shaye Carman, Trina Anderson

Climate Science Published Reports

This report provides a comprehensive analysis of greenhouse gas (GHG) emissions from Western Australian wild-catch fisheries and aquaculture for the fiscal years (FY) 2004/05 to 2024/25. These industries represent important components of the Western Australian primary production sector, with distinct emissions profiles and trends.

Key Findings:

Emissions from wild-catch fisheries have declined significantly over time, from approximately 0.341 million tonnes of carbon dioxide equivalent (Mt CO₂e) in FY 2004/05 to 0.136 Mt CO₂e in FY 2024/25, a reduction of approximately 60%.

Emissions from aquaculture in FY 2024/25 were approximately 0.350 Mt CO₂e, reflecting substantial industry growth from near-negligible levels in …

Indigenizing Aquaculture: In Pursuit Of An Integrated Multi-Trophic Aquaculture System For Enhanced Self-Sufficiency In Akaroa Harbour, Aotearoa New Zealand, Cali R. Trainor

Capstone Collection

This study assessed the feasibility of integrating two pre-existing aquaculture activities in Akaroa Harbour, Aotearoa New Zealand into an integrated multi-trophic aquaculture (IMTA) system. The cultivation of giant kelp (Macrocystis pyrifera) presents an opportunity to improve the sustainability of Chinook salmon (Oncorhynchus tshawytscha) farming by introducing alternative food sources for salmon, which can be used to produce fish feed locally, enhancing the self-sufficiency of the community and boosting the holistic efficiency of the system. Macroinvertebrates residing in giant kelp wrack were collected, identified, and quantified to determine if any of the Macrocystis-associated specimens could serve as …

A Comparison Of Diving Behavior Of Goose-Beaked And Dense-Beaked Whales From Tagging Studies In Multiple Ocean Basins, Jay Barlow, Robin W. Baird, Janelle Badger, Gregory S. Schorr, Erin A. Falcone, Shannon N. Coates, Peter L. Tyack, Andrew J. Read, Leigh S. Hickmott, John W. Durban, Diane Claridge, Natacha Aguilar De Soto, Daniel Miranda Gonzalez, Fleur Visser, Machiel G. Oudejans, Stacy L. De Ruiter, David A. Sweeney, Brenda K. Rone, Stephanie L. Watwood

University Faculty Publications and Creative Works

Studies of cetacean diving behavior in multiple locations in different ocean basins allow for an assessment of variability within and among populations. We examine foraging dive behaviors of goose-beaked whales (Ziphius cavirostris) and dense-beaked whales (Mesoplodon densirostris) using data from 132 tagged whales in seven locations in the Pacific and Atlantic Oceans and the Mediterranean Sea. Acoustic recording tags are used to identify foraging dives by the presence of echolocation. For other tag types, foraging dives are identified based on maximum dive depth. Five parameters are used to characterize foraging dives: maximum dive depth, foraging dive duration, dive cycle duration, …

Drift Dynamics Of Early Life-Stage Invasive Carps, Saurav Karki

Department of Civil and Environmental Engineering: Dissertations, Theses, and Student Research

Asian carp species pose significant ecological threats to North American freshwater systems due to their invasive nature and prolific reproduction. Their semi buoyant eggs develop while drifting downstream with the river current. Understanding early life-stage transport is therefore critical for predicting recruitment potential and guiding management efforts. Existing fluvial egg drift models, including those relying on 1-D hydraulics and fully 3-D CFD-based models, are either inadequate for complex braided rivers or too computationally demanding for large-scale application. The Platte River in Nebraska, characterized by wide, shallow, multi-threaded channels, is dominated by two-dimensional flow conditions, making a depth-averaged 2-D modeling approach …

Capfish Project Report : Summer Academy For The Pacific Islands, Kathleen Auld, Francis Neat, Raphaël Baumler

Reports

The CAPFISH Project was created in response to an identified need for capacity-building to address illegal, unreported and unregulated (IUU) fishing and related matters - a complex problem affecting aquatic ecosystems, coastal communities, fishers and fish workers, and economic and national security. Over the last four years, the CAPFISH Project has provided training and educational materials on IUU fishing to developing country administrations around the world, most recently with a two-week regional Summer Academy for the Pacific Islands. This Academy ran for two weeks and included delegates from fisheries, labour, safety, maritime, foreign affairs, and enforcement administrations in the Pacific …

Assessment Of Sampling Gears For Bigheaded Carp In Mid-Order Prairie Rivers In Nebraska, Brett M. Anderson

School of Natural Resources: Dissertations, Theses, and Student Research

Silver Carp Hypophthalmichthys molitrix and Bighead Carp H. nobilis (collectively bigheaded carp) have invaded tributaries to the Missouri River and Platte River in Nebraska, USA. Information pertaining to efficient sampling protocols for assessing bigheaded carp populations as well as benefiting removal efforts is needed. Herding is a method used to increase the capture efficiency and detection probability of adult bigheaded carp by simultaneously using active and passive sampling gears. During June-July 2023, four herding techniques were assessed regarding their ability to elicit directional movement past an enclosure gate. The combination of sound and electrofishing resulted in the highest mean …

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 …

Marine Heatwave Conditions In Western Australia Marine Waters - 20 February 2025, Department Of Primary Industries And Regional Development, Western Australia

Marine Heatwave Notification Reports

Marine heatwave (MHW) conditions across all Bioregions of Western Australia have eased over the last two weeks. MHW status no longer applies to the majority of the North Coast and West Coast Bioregions. MHW conditions in the Gascoyne and South Coast Bioregion have eased to Category 1 - Moderate.

Western Australia’S Marine Heatwave Update - 16 February 2025, Department Of Primary Industries And Regional Development, Western Australia

Marine Heatwave Notification Reports

No abstract provided.

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 …

Cellular Responses Of Astrangia Poculata (Ellis And Solander, 1786) And Its Symbiont To Experimental Heat Stress, Tyler E. Harman, Daniel Barshis, Briana Hauff Salas, Kevin B. Strychar

Biological Sciences Faculty Publications

Climate change has had devastating effects on tropical coral reefs; however, much less is known regarding how heat stress affects temperate coral. This research focuses on Astrangia poculata (Ellis and Solander, 1786) collected from Narragansett Bay, RI, during the summer and winter seasons and understanding the effect of experimental thermal extremes (i.e., 26 °C) on seasonally different populations. Photosynthetic efficiency (Fv/Fm), symbiont density (via an inverse relationship with pixel intensity), and oxidative stress via reactive oxygen species (ROS) concentrations were measured on symbiotic and aposymbiotic A. poculata. Higher Fv/Fm rates were observed in summer- vs. winter-collected corals (p ≤ …

Low Salinities Impair Heat Tolerance And Alter Reproductive Traits With No Implications For Survival In A Marine Annelid From Coastal Habitats, Gabrielle Newton, Gloria Massamba-N'Siala

Biological Sciences Faculty Publications

Climate change is expected to intensify salinity and temperature fluctuations in estuarine and coastal habitats. However, the impact of salinity variation on ectotherms’ thermal tolerance remains underexplored, limiting our understanding of the interplay between these stressors. This study investigated salinity-dependent changes in life history traits (survival, growth rate, fecundity, and egg size) over a 33-day exposure to a salinity gradient (12, 17, 22, 27, 32, 35, 40, 45, 50) in the marine annelid Ophryotrocha labronica. Individuals that survived the salinity treatments were assessed for their upper and lower thermal tolerance limits. Female individuals, the target of the study, exhibited …

Identifying Intangible And Biocultural Heritage Elements Toward Environmental Understanding: Engaging Stakeholders Through Art, Martha B. Lerski

Publications and Research

Grounded in a case study in Barbuda in the Caribbean, this research examines sustainability from the perspective of what arts and heritage can contribute to community engagement and local and broader understandings about the environment. This article documents a growing body of literature recognizing the role of arts and culture, including local knowledge and traditional ecological knowledge (TEK), in climate change endeavors. Art and TEK present expansive world views. Contextual information situates research done on the island of Barbuda pre- and post-Hurricane Irma. Visual arts workshops engaged community members in mixed methods research. Results documented cultural elements, particularly intangible and …

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.

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 …

A Multispecies, Multisite Assessment Of Coral Thermal Tolerances In American Samoa, Using Acute Heat Stress Assays, Ponchanok Weeriyanun, Nicolas R. Evensen, Katherine E. Parker, Veronica Z. Radice, Daniel J. Barshis

Biological Sciences Faculty Publications

Reef-building corals are being impacted by increasing seawater temperatures, with marine heatwaves leading to mass bleaching events and extensive mortality. However, corals can display variation in thermal tolerance, both within and among species. In this study, we sampled four coral species (Acropora hyacinthus, Montipora grisea, Pocillopora verrucosa, and Porites lobata) from two sites on Tutuila, American Samoa, with contrasting environmental regimes but similar Maximum Monthly Means (MMM). Coral fragments were subjected to short-term acute heat stress experiments using the Coral Bleaching Automated Stress System (CBASS). PAM Fluorometry was used to measure the symbiont’s effective quantum yield (Fv/Fm) following heat stress …

An Economic And Production Analysis Of Seaweed Farms In California And The Pacific Northwest, Brian Donovan

Cal Poly Humboldt theses and projects

Since the early 2010s, the seaweed aquaculture industry has steadily expanded in the United States, with states like Alaska, Maine, Hawaii, and Connecticut leading the way in the development of this emerging sector. However, information gaps remain concerning certain aspects of the domestic seaweed aquaculture industry. The purpose of this study was to examine the status of the seaweed aquaculture industry along the West Coast of the United States; specifically in the states of California, Oregon, and Washington. Seaweed farmers in these states were invited to voluntarily complete surveys asking important production, economic, and commercial questions regarding their operations. Data …

Comparing Metabolism And Hypoxia Tolerance Of Native And Non-Native Florida Freshwater Fishes In Climate Change Scenarios, Benjamin A. Share

All HCAS Student Capstones, Theses, and Dissertations

As climate change brings rising water temperatures and lower dissolved oxygen (DO) concentrations to freshwater bodies, it has become increasingly important to understand how this will affect ecosystems with established non-native or invasive species. Fishes of the family Cichlidae are the most pervasive non-native fishes in the Everglades and may increase their range further north under a changing climate. To better understand potential invasibility and competition with native fishes, the metabolism and hypoxia tolerance of non-native Blue Tilapia Oreochromis aureus was compared to native Bluegill Lepomis macrochirus when acclimated across a range of seasonal and projected temperatures. Intermittent-flow respirometry was …

Informing Management Of American Shad (Alosa Sapidissima) In The Carolinas: Evaluating Novel Fish Passage Approaches And Acoustic Tracking Methods, Margaret Gaither

All Theses

Acoustic telemetry is a valuable tool for fisheries scientists to study the movements and migratory behaviors of aquatic organisms. A critical assumption of this method is that tagged fish exhibit similar behaviors and survival rates as their untagged counterparts. To investigate this, we conducted a 12-week laboratory study on adult American Shad (Alosa sapidissima) using gastroesophageal insertion of acoustic transmitters. We implanted 80 fish with dummy transmitters and monitored tag retention and survival. Our analysis, employing a mixed effects Cox’s proportional hazards model, revealed no significant differences in survival between tagged and control fish, regardless of sex. Additionally, …

Investigating Nekton Response To Changing Salinities In The Mississippi Sound: An Experimental And Statistical Approach, Adam Murray

Master's Theses

The Mississippi Sound provides nursery habitats for many coastal species and is recognized for its commercial fisheries. Previous freshening events linked to the Bonnet Carré Spillway, a Mississippi River flood diversion structure, proved catastrophic for oyster populations in the Mississippi Sound, but effects on mobile fish and shellfish species are not well-defined. The planned Mid-Breton Sediment Diversion (MBSD), an initiative to combat wetland loss, is also forecasted to lower salinities in the region, increasing the need to better understand responses of commercially and ecologically important species to freshening events. The objective of this study was to characterize effects of salinity …

Density-Dependence Inside A Marine Protected Area Increases Natural Mortality And Stunts The Growth Of A Spiny Lobster, Emma-Jade Tuffley, Simon De Lestang

Fisheries Research Articles

Sustainable fisheries management often requires the modelling of stocks under unfished conditions, when the influence of population densities on animal growth and mortality can be substantial. This can be especially true for species such as spiny rock lobster, which are very habitat specific. Using western rock lobster (Panulirus cygnus) tag-recapture data from adjacent and similar fished and unfished areas, the key life history parameters of natural mortality and growth were examined and compared under different population density scenarios. In an area representative of virgin biomass levels, lobsters exhibited reduced growth rates and a substantially higher rate of natural mortality …

“It’S A No Brainer”: Ensuring Just Transitions In Iceland’S Fishing Industry, Olivia Bowers

Independent Study Project (ISP) Collection

Iceland’s government intends to achieve carbon neutrality by 2040, aiming to target various economic sectors and industries for increased renewable-energy usage. One of its most important plans revolves renewable-energy usage in the fishing industry, which accounts for almost 12% of the country’s GHG emissions. This study aims to understand the perspectives of different stakeholders concerning renewable energy in the fishing industry, using these opinions and existing literature to provide recommendations for a just, equitable, and achievable energy transition. Additionally, this study particularly focuses on the opinions of actors in Vestmannaeyjar, an island community of 4,300 with an especially vibrant, significant, …

Multimodel Approach To A Support Stock Assessment Of Standardized Catch And Effort Data: A Case Study Of Blue Shark (Prionace Glauca) In The Indian Ocean By The Taiwanese Large-Scale Longline Fishery, Chun-Yi Hung, Hoang Huy Huynh, Xing-Han Wu, Wen-Pei Tsai

Journal of Marine Science and Technology–Taiwan

In the context of stock assessment and fishery conservation, determining catch per unit effort (CPUE) accurately and reliably is essential. This study estimated trends in the relative abundance of blue sharks (Prionace glauca) in the Indian Ocean from 2005 to 2022. Blue sharks constitute a resilient bycatch species in pelagic tuna and swordfish longline fisheries. We employed a multimodel approach that included delta-lognormal, zero-inflated negative binomial, and vector autoregressive spatiotemporal (VAST) models to standardize catch rates recorded by observers in the Taiwanese large-scale longline fishery. Our analysis concentrated on the CPUE of blue sharks, including standardizing the number of fish …

Complex Dynamics Of Coral Gene Expression Responses To Low Ph Across Species, Veronica Z. Radice, Ana Martinez, Adina Paytan, Donald C. Potts, Daniel J. Barshis

Biological Sciences Faculty Publications

Coral capacity to tolerate low pH affects coral community composition and, ultimately, reef ecosystem function. Low pH submarine discharges (‘Ojo’; Yucatán, México) represent a natural laboratory to study plasticity and acclimatization to low pH in relation to ocean acidification. A previous >2‐year coral transplant experiment to ambient and low pH common garden sites revealed differential survivorship across species and sites, providing a framework to compare mechanistic responses to differential pH exposures. Here, we examined gene expression responses of transplants of three species of reef‐building corals (Porites astreoides, Porites porites and Siderastrea siderea) and their algal endosymbiont communities …

Western Boundary Current-Subtropical Continental Shelf Interactions, William B. Savidge, Dana K. Savidge, Frederico Brandini, Adam T. Greer, Eileen E. Hofmann, Moninya Roughan, Iison De Silvera, Iain M. Suthers

CCPO Publications

Western boundary currents (WBCs) adjacent to subtropical continental shelves (STCSs; between ~25° and 35° latitude; Figure 1) transport heat, nutrients, and biota poleward along the western margins of major ocean basins, interacting with the continental margins and influencing their physics and biology. Eddies and meanders along the shelf edge upwell deep, nutrient-laden water that can be advected onto the adjacent shelves with a corresponding export of particle-rich shelf water (e.g., Lee et al., 1991; Kimura et al., 1997; Campos et al., 2000; Roughan and Middleton, 2002, 2004; Lutjeharms, 2006; Savidge and Savidge, 2014). Despite their similarities, the various STCS regions …

Abalones At Risk: A Global Red List Assessment Of Haliotis In A Changing Climate, Howard Peters, Gina M. Ralph, Laura Rogers-Bennett

Biological Sciences Faculty Publications

There is increasing awareness that marine invertebrates such as abalones are at risk from the combined stressors of fishing and climate change. Abalones are an important marine fishery resource and of cultural importance to Indigenous and non-Indigenous people. A highly priced marine delicacy, they are inherently vulnerable: individuals are slow-growing and long-lived and successful reproduction requires dense assemblages. However, their global conservation status is poorly understood. Using IUCN Red List methodology, we assessed the extinction risk to all 54 species of abalone (genus Haliotis). Of the 21 fished commercially for human consumption either now and/or in the past, 15 …

The Impacts Of Anthropogenic Activity And Climate Change On The Formation Of Harmful Algal Blooms (Habs) And Its Ecological Consequence, Zhangxi Hu, Aifeng Li, Zhun Li, Margaret R. Mulholland

OES Faculty Publications

No abstract provided.

Diel Vertical Migration Rates Of The Dinoflagellate Species Margalefidinium Polykrikoides In A Lower Chesapeake Bay Tributary, S. Clayton, Jacqueline B. Chrabot, Michael Echevarria, Leah Gibala-Smith, Kathryn Mogatas, Peter Bernhardt, Margaret R. Mulholland

OES Faculty Publications

Margalefidinium polykrikoides is a mixotrophic dinoflagellate harmful algal bloom (HAB) species that blooms annually in the lower Chesapeake Bay. M. polykrikoides undertakes a diel vertical migration (DVM) which may give it a competitive advantage over purely phototrophic organisms who cannot access deeper nutrient pools and allow it to form large toxic blooms. Laboratory-based estimates of M. polykrikoides’ DVM rates suggest that it is one of the fastest known dinoflagellate swimmers and understanding this behavior is likely important for modeling and predicting M. polykrikoides blooms. However, to date, no field-derived estimates of M. polykrikoides’ DVM rates have been made in the …