Marine Biology Commons^™

Novel Microbiological Medium Developed For The Isolation Of Bacteria Associated With Estuarine Anemones, Parker K. Lund, Catalina Cuellar-Gempeler

IdeaFest: Interdisciplinary Journal of Creative Works and Research from Cal Poly Humboldt

Out of the nearly one trillion species of microbiota estimated to inhabit Earth only ten thousand have been cultured in the laboratory. Culturing continues to play a vital role in determining the physiology and ecologic function of individual bacteria in microbial communities and for microbes associated with host organisms one of the major challenges is developing microbiological media that mimics the bacteria’s natural environment enough to promote growth. Here, we target bacteria associated with the estuary anemones Diadumene lineata and Metridium senile by developing a novel medium that uses anemone tissue as the sole source of nutrients. We further measured …

Impacts Of Algal Morphology And Water Flow On Macroalgal Microplastic Capture, Cheyenne M. Adams

Honors College Theses

Microplastic pollution is a major area of concern in marine environments, especially as microplastics enter the food web. This study used pipe cleaners and two lichen species as algal mimics, and Chaetomorpha sp. and Chondrus crispus as model algal species to test the effects of morphology and biomass on microbead and foam capture. This study also utilized two different water flow methods: vortices and waves. Results suggest that water flow, as well as biomass and morphology, play a role in microplastic capture in macroalgae. For all mimics and algal species, except Cladonia lichens, turfs with increased biomass and length showed …

A Genomic Investigation Of Divergence Between Tuna Species, Pavel V. Dimens

Dissertations

Effective management and conservation of marine pelagic fishes is heavily dependent on a robust understanding of their population structure, their evolutionary history, and the delineation of appropriate management units. The Yellowfin tuna (Thunnus albacares) and the Blackfin tuna (Thunnus atlanticus) are two exploited epipelagic marine species with overlapping ranges in the tropical and sub-tropical Atlantic Ocean. This work analyzed genome-wide genetic variation of both species in the Atlantic basin to investigate the occurrence of population subdivision and adaptive variation. A de novo assembly of the Blackfin tuna genome was generated using Illumina paired-end sequencing data and …

Using Deep Learning And Uav Imagery To Detect Elkhorn Coral In St. Croix’S East End Marine Park, Samuel Wyatt

Master's Theses

Elkhorn coral, or Acropora palmata, is an important reef building species that promotes species abundance and other ecological services to the communities in the US Virgin Islands. We captured high resolution imagery of a reef in St. Croix’s East End Marine Park using a Wingtra One UAV. We then used deep learning techniques to detect individual coral colonies. We compared two deep learning models, FasterRCNN and MaskRCNN, and found that the models achieved accuracy shores up to 0.78. These scores improved when examining only larger corals in shallow waters. The model was able to both detect Elkhorn coral and …

Crassostrea Gigas Invasion In Southern California: Macrofaunal Diversity And Local Community Impacts Of Ecosystem Engineers On Estuarine Habitats, Noah Jansen-Yee

Theses

Many marine ecosystems are facing the growing threat of biological invasions. These invasions can have a variety of different impacts on ecosystems and their inhabitants. The Pacific oyster, Crassostrea gigas, is currently in the relatively early stages of invasion in San Diego estuaries. Crassostrea gigas is a large, filter-feeding bivalve that forms dense oyster beds on hard substrate. These oysters are known to outcompete native counterparts and drastically alter habitats where they are present. Crassostrea gigas is an ecosystem engineer that, through shell creation and formation of a dense oyster matrix, impacts ecosystems in a variety of direct and indirect …

Final Report Floating Upwelling System Harvest Road Oceans, Robert Michael, Scott Bennett

Fisheries occasional publications

A Floating Upwelling System or FLUPSY is a mechanical system for the culture of seed stock during the nursery stage of commercial bivalve production.

Impact Of Seawall Type On Mollusc Size And Diversity In South Water Caye Belize: A Case Study, Morgan O. Orand, Ginger R. Fisher

Ursidae: The Undergraduate Research Journal at the University of Northern Colorado

The size and diversity of molluscs on and in front of artificial and natural sea walls in the tropical rocky intertidal of South Water Caye, Belize were investigated with the intent of determining the suitability of artificial surfaces to replace natural seawalls. Four seawalls, three artificial and one natural, were observed over a period of eight days. Mollusc size did not change based on distance from the wall for any of the walls. However, there were some significant differences in the species and number of molluscs in front of each wall as well as on the walls themselves. Measures of …

Effects Of Invasional Meltdown On Community Structure In Marine Ecosystems In The Damariscotta Estuary Of Maine, Kate Lazzeri

Student Research Poster Presentations 2021

Basibiont organisms form the foundation of marine ecosystems by providing additional space for new species to settle on as epibionts. Invasive epibionts may take advantage of this new basibiont presence, which leads to many harmful effects on native organisms such as competition for both resources and food. In some cases, invasive species facilitate recruitment of other invasive organisms, a phenomenon referred to as invasional meltdown, but it is not known if invasion of new basibionts increases invasive epibiont occurrence. The purpose of this study is to answer the following research questions: 1) does the invasion status of the basibiont alter …

Conserving Critical Seagrass Habitat For Dugong. Dugong Seagrass Associations Summary Data., Kathryn M. Mcmahon, Paul Lavery, Nicole Said, Chris Cleguer, Amanda Hodgson

Research Datasets

This is the summary dataset of the dugong seagrass associations data containing dugong counts, benthic habitat cover, seagrass nutrient content, water temperature, water current speed, water depth and water transparency from three locations in the Pilbara over 3 time periods in 2018-2019.

Conserving Critical Seagrass Habitat For Dugong. Seagrass Network Monitoring Data Summary, Kathryn M. Mcmahon, Paul Lavery, Nicole Said

Research Datasets

This is the summary dataset of the seagrass monitoring data containing benthic habitat, seagrass meadow characteristics, seed density and environmental variables from three locations in the Pilbara over 3-4 time periods in 2018-2019.

Predictors Of Marine Genetic Structure In The Indo-Australian Archipelago [Dataset], Kathryn M. Mcmahon, Udhi Eko Hernawan

Research Datasets

This is the dataset extracted from 101 publications on 99 marine species from eight taxonomic groups in the Indo Australian Archipelago. Data extracted includes measures of genetic structure and the potential predictors.

Anthropogenic Change On The Distribution Of Marine Megafauna And Their Prey, Baylie Fadool

Honors Theses

Anthropogenic change is impacting the distribution and survival of marine megafauna and their prey. Humans are changing every aspect of the marine environment, with effects reaching as large as changing the composition of marine environments to directly overexploiting species through the fishing industry. The role that marine megafauna play in balancing ecosystems, including as top apex predators, leads to detrimental results in the absences and population declines of these species. Migrations and declines due to threats on marine apex predator species will alter their environments by causing mesopredator release and changes in community structure, which is often associated with reduced …

An International Laboratory Comparison Of Dissolved Organic Matter Composition By High Resolution Mass Spectrometry: Are We Getting The Same Answer?, Jeffrey A. Hawkes, Juliana D'Andrilli, Jeffrey N. Agar, Mark P. Barrow, Stephanie M. Berg, Núria Catalán, Hongmei Chen, Rosalie K. Chu, Richard B. Cole, Thorsten Dittmar, Rémy Gavard, Gerd Gleixner, Patrick G. Hatcher, Chen He, Nancy J. Hess, Ryan H.S. Hutchins, Amna Ijaz, Hugh E. Jones, William Kew, Maryam Khaksari, Diana Catalina Palacio Lozano, Jitao Lv, Lynn R. Mazzoleni, Beatriz E. Noriega-Ortega, Helena Osterholz, Nikola Radoman, Christina K. Remucal, Nicholas D. Schmitt, Simeon K. Schum, Quan Shi, Carsten Simon, Gabriel Singer, Rachel L. Sleighter, Aron Stubbins, Mary J. Thomas, Nikola Tolic, Shuzhen Zhang, Phoebe Zito, David C. Podgorski

Chemistry & Biochemistry Faculty Publications

High-resolution mass spectrometry (HRMS) has become a vital tool for dissolved organic matter (DOM) characterization. The upward trend in HRMS analysis of DOM presents challenges in data comparison and interpretation among laboratories operating instruments with differing performance and user operating conditions. It is therefore essential that the community establishes metric ranges and compositional trends for data comparison with reference samples so that data can be robustly compared among research groups. To this end, four identically prepared DOM samples were each measured by 16 laboratories, using 17 commercially purchased instruments, using positive-ion and negative-ion mode electrospray ionization (ESI) HRMS analyses. The …

The Chumash Heritage National Marine Sanctuary: An Exploration Of Changing The Discourse On Conservation, Arielle Ben-Hur

Pitzer Senior Theses

In 2015, the Northern Chumash Tribal Council submitted a National Marine Sanctuary Nomination to establish the Chumash Heritage National Marine Sanctuary– a means by which to ensure the protection of one of the most culturally and biologically diverse coastlines in the world. On October 5, 2015, John Armor of the National Oceanic and Atmospheric Administration (NOAA) responded to the nomination, adding it to the inventory of areas NOAA may consider in the future for national marine sanctuary designation.

In my thesis, I explore how the nomination of the Chumash Heritage National Marine Sanctuary acts as a platform from which Traditional …

Red Abalone Hemocyanin As An Alternative Hapten-Carrier For Vaccine Production, Isaiah N. Mansour

Honors College

Vaccines protect millions of human lives per year from otherwise fatal illnesses. Vaccination promotes immunity by simulating infection with a non-pathogenic representative of the disease, an antigen, to prepare and train an immune response. Vaccine-safe antigens are often too small to elicit an immune response. These non-immunogenic molecules are referred to as haptens and are introduced to the immune system by hapten-carriers, large immune-stimulating proteins. Keyhole Limpet Hemocyanin (KLH), a respiratory protein of the giant keyhole limpet (Megathura crenulata), is the industry standard hapten-carrier. KLH is a potent yet safe immune-stimulant relied upon in research, available human medications, and emerging …

Extending Observations Further: Using Historic Biogeochemical Data To Understand Trends In Puget Sound, Ben Larson, Stephanie Jaeger, Wendy Eash-Loucks, Kimberle Stark, Bruce Nairn

Salish Sea Ecosystem Conference

Fluctuations in Puget Sound water quality reflect a combination of natural variability and anthropogenic influence. Predictions of how future changes will unfold requires an understanding of the complex interplay between these factors. Recent and ongoing measurement of water quality parameters allow a thorough assessment of variability over short time scales, but understanding changes over longer (e.g., decadal) timescales is critical for forecasting future changes. Examining long term trends requires the use of historical data, however, measurements that pre-date modern monitoring programs can be scarce, and the detection limits are often higher than newer analytical techniques. Here, we will consider several …

Coral Reef Fishes Exhibit Beneficial Phenotypes Inside Marine Protected Areas, Robert Y. Fidler, Jessica Fidler, Kristen W. Rynerson, Danielle F. Matthews, Ralph G. Turingan

Ocean Engineering and Marine Sciences Faculty Publications

Human fishing effort is size-selective, preferentially removing the largest individuals from harvested stocks. Intensive, size-specific fishing mortality induces directional shifts in phenotypic frequencies towards the predominance of smaller and earlier-maturing individuals, which are among the primary causes of declining fish biomass. Fish that reproduce at smaller size and younger age produce fewer, smaller, and less viable larvae, severely reducing the reproductive capacity of harvested populations. Marine protected areas (MPAs) are extensively utilized in coral reefs for fisheries management, and are thought to mitigate the impacts of size-selective fishing mortality and supplement fished stocks through larval export. However, empirical evidence of …

Composition Of Dissolved Organic Matter In Pore Waters Of Anoxic Marine Sediments Analyzed By 1h Nuclear Magnetic Resonance Spectroscopy, Christina A. Fox, Hussain A. Abdulla, David J. Burdige, James P. Lewicki, Tomoko Komada

OES Faculty Publications

Marine sediments are globally significant sources of dissolved organic matter (DOM) to the oceans, but the biogeochemical role of pore-water DOM in the benthic and marine carbon cycles remains unclear due to a lack of understanding about the molecular composition of DOM. To help fill this knowledge gap, we used 1H nuclear magnetic resonance (NMR) spectroscopy to examine depth variability in the composition of pore-water DOM in anoxic sediments of Santa Barbara Basin, California Borderland. Proton detected spectra were acquired on whole samples without pre-concentration to avoid preclusion of any DOM components from the analytical window. Broad unresolved resonance (operationally …

Ms Environmental Biology Capstone Project, Alyssa Herrin

Regis University Student Publications (comprehensive collection)

The study of visitor use in museums, zoos, and aquariums is an important aspect of understanding visitor engagement and evaluating the function of the institution. Here, visitor demographics such as age, group size, and number of children were assessed to see their influence on time spent and number of stops visitors made while visiting the Denver Botanic Gardens in Denver, Colorado. This study evaluated differences in time spent and number of stops made among different gardens by observing visitors and mapping their paths and activities through each zone. The results show that older visitors and larger groups spent more time …

Pros And Cons Of Marine Zoological Parks According To Marine Conservationists, Kayla L. Patama

HCNSO Student Capstones

Throughout history zoos and aquariums have satisfied a number of different, albeit to some, conflicting roles (Ballantyne, Packer, Hughes, & Dierking, 2007). In recent years, zoos and aquariums have shifted their focus on taking a proactive role in wildlife conservation and promoting conservation learning among their visitors. The present capstone addresses the justifications that marine conservationists see in marine zoological parks and how they believe parks can become more relevant and valuable in the future. A 65 question survey (Appendix I) was distributed to marine science professionals online through personal contact between June and September 2017 questioning participant’s personal opinions …

Reconciling The Challenge Of Aphanic Species Within Marine Conservation, Kerri L. Bolow

HCNSO Student Capstones

Aphanic species are those within a taxonomic complex that may not be readily distinguishable from other sympatric species. The existence of these species is becoming apparent at an increasing rate through the use of technological tools like molecular genetic analyses. A lack of clarity on the definitions of terms used to describe similar species, how these species are identified, and how prevalent they are can confound identification, description, and management of these organisms. This review collects and defines the terms used to describe these hidden species and suggests the use of the term aphanic for situations where additional information (and …

Art And Science: A Case Study Of Their Interconnectedness In The Marine Natural Sciences, Julia Mackin-Mclaughlin

Honors College

Science and art are interrelated in the form of scientific illustration: the act of observing a subject and translating the gained knowledge into a visual form. Humans have found inspiration from the natural world since our beginnings, but the practice of accurately portraying it arose with the growing interest in natural science in the 15th century. This paper explores three questions: what is scientific illustration, what is its role in scientific research, and how has it changed through history? Modern scientific illustration thrives as an effective method to teach the general public environmental issues. I present a case study using …

The Potential Impact Of Climate Change On Blue Whale Migration In The Eastern Pacific, Amanda Shuman

Honors College

Climate change is one of the most pressing problems the world is facing today. Due to human emissions, the amount of greenhouse gasses in the atmosphere is escalating at a concerning rate. This increase is causing ocean temperatures to rise, pH levels to lower, and altering the habitats of countless species. Balaenoptera musculus, or the blue whale, is a highly migratory species that relies on the stability of its’ habitats for foraging and calving grounds. They rely on the upwelling of nutrients and consistent conditions that allow for substantial prey populations to accumulate. With the effects of climate change altering …

Marine Phosphorus Biogeochemistry Ecological Insights From Analytical Chemistry, Douglas W. Bell

Theses and Dissertations

The supply of phosphorus (P) directly impacts the growth and speciation of marine microbes (i.e., phytoplankton, bacteria, Archaea). In turn, microbial communities shape the magnitude and rate of marine biogeochemical cycles, ultimately affecting global climate and food production. This dynamic reflects the continuum of temporal and spatial scales at which the marine P cycle operates. However, linking multiple scales of cycling remains a consistent challenge. The primary objective of my dissertation was to gain insight into marine P biogeochemistry, by means of analytical chemistry, at the molecular and environmental scales of cycling. The first component of my research was to …

Multiscale Habitat Suitability Modeling For Canary Rockfish (Sebastes Pinniger) Along The Northern California Coast, Portia N. Saucedo

Cal Poly Humboldt theses and projects

Detailed spatially-explicit data of the potential habitat of commercially important rockfish species are a critical component for the purposes of marine conservation, evaluation, and planning. Predictive habitat modeling techniques are widely used to identify suitable habitat in un-surveyed regions. This study elucidates the predicted distribution of canary rockfish (Sebastes pinniger) along the largely un-surveyed northern California coast using data from visual underwater surveys and predictive terrain complexity covariates. I used Maximum Entropy (MaxEnt) modelling software to identify regions of suitable habitat for S. pinniger greater than nine cm in total length at two spatial scales. The results of …

Sweating The Small Stuff: Linking Plankton To Climate Change, Brian Kim '18 Makes Conncetions, Stephen Collins

Colby Magazine

It takes an expansive mind to connect microscopic marine copepods (certain crustacean plankton) unwittingly chomping on floating microplastics with a bigger picture: the planet’s carbon pump and global climate change. But that’s what Brian Kim ’18 decided to investigate during Jan Plan, working with Bigelow Lab Senior Research Scientist David Fields.

Host-Parasite Relationships Between The Copepod Naobranchia Lizae And Its Host (Striped Mullet, Mugil Cephalus): A Description Of Morphological Development, Sara R. Teemer

DePaul Discoveries

The parasitic copepod, Naobranchia lizae, is often found within the gill arches of the striped mullet, Mugil cephalus, in the Charleston Harbor Estuarine System of South Carolina. The parasite is relatively common, but little is known about its early stages of development. In order to describe the developmental stages and pattern of morphological development, 221 female N. lizae that were collected between February 2002 and May 2003 were used. Using variation in morphological characters (maxilla, trunk), these parasites were assigned to developmental stages (juvenile, subadult, adult). A small number of the males (three ‘dwarf’ males) were also found …

Ocean Acidification And Predator-Prey Relations: Correlating Disruption Of Predator Avoidance With Chemosensory Deficits, Alexandra Fw Sidun, William G. Wright

Student Scholar Symposium Abstracts and Posters

One of the most destructive effects of global climate change is the increased carbon sequestering and consequential acidification of our world’s oceans. The impacts of ocean acidification on marine organisms are still relatively unknown, especially effects on behavioral ecology. Avoiding predation has emerged from recent behavioral ecology literature as a critical feature in the life history of a wide array of animal species; experiments on marine fishes suggest acidic water compromises their predator-avoidance abilities. Recent assays in our lab suggest predator-induced behavior is reduced by weakly acidic water. These experiments do not address the potential factor of generalized malaise caused …

Isolation And Identification Of Bacterial Endosymbionts In The Brooding Brittle Star Amphipholis Squamata, Abbey Rose Tedford

Honors Theses and Capstones

Symbiotic associations with subcuticular bacteria (SCB) have been identified and studied in numerous echinoderms, including the SCB of the brooding brittle star, Amphipholis squamata. These SCB, however, have not been studied using current next generation sequencing technologies. Previous studies on the SCB of A. squamata placed these bacteria in the genus Vibrio (γ-Proteobacteria), but subsequent studies suggested that the SCB are primarily composed of α-Proteobacteria. The present study examines the taxonomic composition of SCB associated with A. squamata from the Northwest Atlantic. DNA was extracted using a CTAB protocol and 16S rRNA sequences were amplified …

Surveying Coral Reef Fishes : A Manual For Data Collection, Processing, And Interpretation Of Fish Survey Information For The Tropical Northwest Atlantic, Emily Schmitt Lavin, Deena Feeley, Kathleen Sullivan-Sealey

Emily F Schmitt Lavin

In order to utilize the untapped resources of volunteers, REEF and TNC, in active partnership, established the REEF Fish Survey Project. The Project involves the training and mobilization of a large corps of volunteers and is currently the only program with the technical and organizational ability to gather marine biodiversity data in a systematic and reliable manner. Objectives of the project are: 1.) to provide training and education opportunities for SCUBA divers and snorkelers to learn to identify and appreciate marine life 2.) to make data and summary reports readily accessible to the marine science, resource management, and conservation communities …