Marine Biology Commons^™

Revolutionizing Coral Research: The Power Of Holo-Omics, Mohammad M. Binsarhan

Journal of King Abdulaziz University: Marine Science

This mini-review highlights the emerging field of holo-omics and its application in unraveling the complex dynamics of the coral holobiont. Corals exist as meta-organisms, closely interacting with a diverse microbiota including bacteria, archaea, microeukaryotes, viruses, and algal symbionts. Understanding these intricate relationships is critical for assessing coral health, stress responses, and resilience to environmental change. We explore the application of meta-omics approaches such as metabarcoding, metagenomics, meta-transcriptomics, metabolomics, and proteomics in profiling coral-associated microbial communities and their functions. The review sheds light on the methodological advantages and limitations of each approach, as well as some of the technical challenges involved …

Geographic Variation In Proteomic Responses To Ocean Acidification In A Cold-Water Coral (Balanophyllia Elegans), Keana A. Richmond

Cal Poly Humboldt theses and projects

In the face of a rapidly changing climate, assessing organismal responses to future stressors in the context of current, natural exposure to stress could provide key insights to understanding marine ecosystem resilience. I used Balanophyllia elegans, a cold-water, solitary, azooxanthellate coral as a model to better understand how varying oceanographic conditions across its geographic range have shaped its ability to tolerate and potentially adapt to current and future ocean acidification conditions. I collected B. elegans individuals from four sites across 2,500km of their range and subjected them to two pH treatments to investigate site-specific protein expression in response to …

Corals, Creation, And Conservation: Evaluating Human-Marine Relations Through Coral Reef Biology And Artistic Practice, Emma Gray Garman

Scripps Senior Theses

This thesis investigates the relationship between humans and marine ecosystems through two complementary lenses: scientific research and artistic practice. The biology chapter proposes a five-year coral reef monitoring study across four Queensland, Australia islands — two heavily visited and inhabited (Fitzroy and Green Islands) and two minimally visited and uninhabited (High and Woody Islands) — to assess whether human activity correlates with bleaching severity over time. Grounded in preliminary survey data from Green Island in 2024, which revealed approximately 54% of coral bleached or dead, the study hypothesizes that reefs adjacent to inhabited islands will exhibit greater bleaching severity, consistent …

High Coral Thermal Tolerance At A Potentially Climate-Resistant Reef, Kate M. Quigley, C. Siqueira, Kira Brereton, Andrew H. Baird

Research outputs 2022 to 2026

Ecosystems globally are under increasing pressure from warming caused by climate change. However, some locations appear resistant to impacts. Although rare, these locations might be able to better resist damage from thermal stress. In marine environments, coral bleaching is widely viewed as one of the most pervasive stress responses threatening reef health, structure, and function. Yet we still have a poor understanding of the drivers of spatial and temporal variation in the scale and severity of coral bleaching. Here, we characterize a prolonged, intense, and widespread marine heatwave event and uncover a conspicuous lack of bleaching at the southernmost coral …

The Relationship Between Reef Fish And Coverage Of Coral And Turf Algae In Coral Reef Ecosystems Of Biak Island, Papua, Ludi Parwadani Aji, Risandi Dwirama Putra, Muhammad Abrar, Rikoh Manogar Siringoringo, Giyanto Giyanto

Makara Journal of Science

In this study, we examine the influence of benthic coverage on fish diversity in coral reef ecosystems. Benthic and reef fish community surveys were conducted at 14 sites using underwater photographic transect and underwater visual census methods, respectively. Coral cover (26.1%) was found to be lower than turf algae cover (42.1%). A total of 56 fish species, comprised of 14 carnivores, 21 corallivores, and 21 herbivores, were recorded. The most widely distributed carnivore and herbivore species were Lethrinus harak and Ctenochaetus striatus, respectively. Two species of butterflyfish, Chaetodon citrinellus and Chaetodon trifasciatus, were the most widely distributed species …

The Coral Porites Lutea As A Regional And Local Proxy For Sea Surface Temperature In Hong Kong, And The Effects Of Typhoons On Proxy Accuracy, Brenna E. Bell

CMC Senior Theses

Proxies related to the climate have been used as a method to observe long-term changes occurring underwater that span long before we had the capability to measure environmental characteristics. Porites corals have been used as sea surface temperature (SST) proxies due to annual cyclicity in their growth process and mineral composition. As the climate differs globally, it is important to ensure that proxies are accurate regardless of location to measure changes in climate. This study examines Porites lutea corals as an SST proxy in the region of Hong Kong. Potential local differences in SST proxy calibrations within the surrounding waters …

Assessment And Prioritization Of Contaminants Of Concern Along Florida's Coral Reef, Ellen Regina E. Skelton

All HCAS Student Capstones, Theses, and Dissertations

Florida’s Coral Reef (FCR) is the third largest barrier reef in the world and faces significant stress from localized land, water, and air-based sources of pollution. Numerous chemical contaminants have been found in waters surrounding reefs and within corals, including pesticides, hydrocarbons, personal care products, pharmaceuticals, and trace metals. However, for most current and emergent environmental contaminants, little to no consistent information exists regarding environmental concentrations or toxicological effects on corals. Assessment of the levels of contaminants in coral reef environments is needed to conduct risk assessments to guide management, restoration, and recovery strategies, and the coral reef resource management …

Corals In Crisis: A Transcriptomic Investigation Of Stony Coral Tissue Loss Disease, Kelsey M. Beavers

Biology Dissertations - Archive

Coral reefs face existential threats due to climate change and human activities. The combined effects of ocean warming, overfishing, pollution, and habitat destruction have fundamentally altered the functionality of coral reefs and are driving a drastic increase in the prevalence and severity of coral disease outbreaks. Stony coral tissue loss disease (SCTLD) has emerged one of the most devastating disturbances to Caribbean reef ecosystems on record. Despite notable progress, the cellular mechanisms driving SCTLD pathogenesis remain poorly understood. To address this issue, my dissertation investigates the gene expression, histopathology, immune protein activity, and symbiont community dynamics involved in SCTLD progression …

Toxicity And Effectiveness Of A New Two-Part Underwater Adhesive For Coral Restoration, Matthew Rojano

All HCAS Student Capstones, Theses, and Dissertations

As coral cover decreases around the world due to disease, bleaching events, and anthropogenic effects, coral restoration projects become increasingly important. A crucial part of many coral restoration projects is the attachment of corals to substrates in nurseries or reef substrates during outplanting. The effective anchoring of transplants is a critical phase in coral restoration and the adhesive used for attachment is crucial. Commonly used adhesives have several drawbacks: there are long mixing times, low substrate adhesion, and lengthy hardening times. To address these issues and provide an effective alternative for coral restoration activities, a new two-part Mixed Adhesive was …

Ecological Risk Assessment For The Marine Aquarium Fish Resource, Kimberley Smith, Amelia Bissell, Carly Bruce

Fisheries Research Reports

In November 2021, the Department of Primary Industries and Regional Development convened an Ecological Risk Assessment (ERA) of the Western Australian fisheries that access the Marine Aquarium Fish Resource. ERAs are conducted by the Department as part of its Ecosystem-Based Fisheries Management framework. Outputs of this ERA will inform future versions of the Harvest Strategy for the Resource. Additionally, this ERA is a requirement of the Wildlife Trade Operation approval for the Marine Aquarium Fish Managed Fishery (MAFMF).

Ecological impacts of the MAFMF, which is the only commercial fishery that targets the Resource, and other extractive sectors that access the …

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 …

Unified Methods In Collecting, Preserving, And Archiving Coral Bleaching And Restoration Specimens To Increase Sample Utility And Interdisciplinary Collaboration, Rebecca Vega Thurber, Emily R. Schmeltzer, Andréa G. Grottoli, Robert Van Woesik, Robert J. Toonen, Mark Warner, Kerri L. Dobson, Rowan H. Mclachlan, Katie Barott, Daniel J. Barshis, Justin Baumann, Leila Chapron, David J. Combosch, Adrienne M.S. Correa, Thomas M. Decarlo, Mary Hagedorn, Laetitia Hédouin, Kenneth Hoadley, Thomas Felis, Christine Ferrier-Pagès, Carly Kenkel, Ilsa B. Kuffner, Jennifer Matthews, Mónica Medina, Christopher Meyer, Corinna Oster, James Price, Hollie M. Putnam, Yvonne Sawall

Biological Sciences Faculty Publications

Coral reefs are declining worldwide primarily because of bleaching and subsequent mortality resulting from thermal stress. Currently, extensive efforts to engage in more holistic research and restoration endeavors have considerably expanded the techniques applied to examine coral samples. Despite such advances, coral bleaching and restoration studies are often conducted within a specific disciplinary focus, where specimens are collected, preserved, and archived in ways that are not always conducive to further downstream analyses by specialists in other disciplines. This approach may prevent the full utilization of unexpended specimens, leading to siloed research, duplicative efforts, unnecessary loss of additional corals to research …

Optimization Of Grow-Out Of Bouldering Coral Microfragments: Land Vs. Offshore Nursery, Ashlee A. Steinberg

All HCAS Student Capstones, Theses, and Dissertations

Corals along the Florida Reef Tract and the wider Caribbean have been declining for decades. Low densities of adult colonies hinder the ability of corals to replenish themselves through sexual reproduction, thus reef managers are focusing on restoration actions that increase coral biomass. Microfragmentation is a way to quickly increase the biomass of bouldering corals by cutting the coral into small pieces which forces the coral to allocate its resources away from reproduction and back into growth, increasing its growth rate. This study assessed the optimal location for grow-out (land vs. offshore nursery) and its synergy with size of fragment …

The Roles Of Host Species, Geographic Scale And Environmental Stressors In Shaping The Composition Of Coral Microbiomes, Alicia Marie Riegel Parker

LSU Doctoral Dissertations

Reef-building corals are long-lived and may take many centuries to adapt, making them especially susceptible to climate change. However, corals host microbial symbionts that can change quickly, potentially speeding acclimation. My dissertation aimed to determine the degree of coevolution and flexibility between corals and their microbiomes among hosts, across space, and in response to stress.

Microbial communities are usually surveyed by sequencing the 16S rRNA gene, however the PCR primers used also amplify coral DNA, thereby limiting prokaryotic read coverage. To mitigate this contamination, I designed a peptide nucleic acid clamp that increased the recovery of bacterial reads by 2-11x …

Reproductive Effort Of Montastraea Cavernosa Across Depth In The Context Of Both Climate Change Refugia And Emergent Disease, Jeanne Bloomberg

LSU Master's Theses

As coral populations on shallow reefs decline globally, mesophotic coral ecosystems (MCE) have been suggested as potential coral refugia in the face of climate changes, leading to the development of a comprehensive deep reef refugia hypothesis. The current study assesses the climate and disease refuge potential of MCEs in the U.S. Virgin Islands (USVI) for the gonochoric, broadcast-spawning species Montastraea cavernosa. Polyp, population, and total habitat fecundities were estimated across the species’ depth range, and changes to population oocyte production over time due to recent ecosystem disturbances were considered. The number of gonads producing oocytes in each polyp and oocyte …

How Corals Avoid Mating Between Different Species, Amanda Kempton

Scientific Communication News

No abstract provided.

Desperate Coral Larvae? Behavioral Responses To Settlement Cues In Aging Agaricia Agaricites Larvae, Helena Sasha Fulmore

HCNSO Student Theses and Dissertations

The global stressors of ocean warming and acidification, as well as local stressors such as eutrophication, overfishing, and coastal construction, have all contributed to the severe decline in coral populations worldwide. Recovery of coral reefs depends partly on recruitment, which relies on the response of larvae to settlement cues indicative of habitat quality; however, it remains unclear whether recruitment in disturbed areas will be compromised. Specifically, as reefs become more disturbed and dominated by macroalgae, it is important to understand larval behavior in response to changes in habitat quality. In this study, we first assessed the settlement success of newly …

Optimizing Lighting Regimes For Rearing Orbicella Faveolata And Acropora Cervicornis Recruits, Paul D. Kreh

HCNSO Student Theses and Dissertations

Coral reef decline worldwide has led to the need for coral reef restoration. The use of sexual reproduction in restoration efforts is required to increase genetic diversity; however, the procedures for rearing newly-settled coral recruits ex situ still need to be optimized. Recruits initially require low light irradiance, but it is unclear when higher irradiances are required to enhance growth and survival. Here we determined the optimal light regime for Orbicella faveolata and Acropora cervicornis recruits. Newly settled recruits were reared under treatments with varied rates of increasing irradiance (after reaching 5 weeks of age), and their survival, growth, and …

Outplanted Acropora Cervicornis Enhances The Fish Assemblages Of Southeast Florida, Ellen Dignon Goldenberg

HCNSO Student Theses and Dissertations

Acropora cervicornis, commonly known as the staghorn coral has historically been a major contributor to reef structural complexity, providing habitat for many functionally important fish species throughout Florida and the Caribbean. Unfortunately, due to disease, bleaching, and local anthropogenic stressors, A. cervicornis populations have suffered drastic declines that have negatively impacted associated reef fish populations. In order to promote recovery, A. cervicornis fragments can be cultivated in nurseries and outplanted back onto reefs. This practice can effectively increase A. cervicornis abundance, but the long-term effects on local fish assemblages, and specifically functionally important grazing fishes, has not been assessed. …

Effects Of Deposited Sediment And Turbidity On Survival And Growth Of Orbicella Faveolata Recruits, Morgan Stephenson

HCNSO Student Theses and Dissertations

Corals are frequently exposed to elevated turbidity and deposited sediment caused from coastal construction, dredging, and/or beach renourishment. This study addresses the effects of turbidity and deposited sediment on the survival and growth of newly settled and 6-week-old Orbicella faveolata recruits and disentangles the effects of turbidity and deposited sediment. We conducted two experiments in which newly settled coral recruits were reared in one of ten different turbidity and deposited sediment treatments for five weeks (0 NTU/ 0 mg cm^-2, 3.4 NTU/ 0 mg cm^-2, 8.2 NTU/ 0 mg cm^-2, 16 NTU/ 0 mg …

Environmental And Anthropogenic Factors Affecting Coral Health, Kristin Jones

2019 Symposium

Plastic pollution is a large and growing problem in our ever producing world. Not only does it litter our cities, but it is cluttering up the natural world as well, the largest being our oceans. Plastic is dumped into the seas where it floats and slowly breaks down into microplastics that are then ingested by marine animals. I will conduct an experiment to test the effects of micro plastics on coral health by subjecting palythoa corals to different plastic levels in a controlled environment. I hypothesize that corals will ingest micro plastics and will suffer health consequences, leading to a …

Indirect Effects Of Ocean Warming And Acidification On The Realized Recruitment Of Agaricia Agaricites, Allan Anderson

HCNSO Student Theses and Dissertations

Over the past few decades, coral cover has declined worldwide due to overfishing, disease, and storms, and these effects have been exacerbated by ocean warming and acidification. Corals are extremely susceptible to these changes because they are already living close to their thermal and aragonite saturation thresholds. Ocean warming and acidification (OAW) may also impact coral survival and growth by impacting their settlement cues. Coral larvae use crustose coralline algae (CCA) and their associated biofilms as cues for settlement, i.e., habitat selection. Settlement cues can also be negatively affected by increased water temperature and acidity. It was hypothesized that the …

Optimization Of Light Irradiance During The Early Life Of Sexually-Produced Porites Astreoides And Agaricia Agaricites Recruits, Nicholas J. Mcmahon

HCNSO Student Theses and Dissertations

Current solutions of coral restoration rely mainly on fragmentation. Though a reliable technique, this asexual form of reproduction does not benefit the genetic diversity of the coral reef. With many global and local stressors threatening corals’ existence, the resiliency of corals to future ocean conditions depends highly on sexual reproduction to produce new genotypes. New technology allows coral spawning/larval release, larval settlement and rearing to be carried out in an aquarium system. Many of the techniques necessary to maintain coral recruits are well-established, however the effects of light intensity remain to be studied for these early life stages. Newly …

Spatiotemporal Change In The Benthic Community Of Southeast Florida, Nicholas P. Jones

HCNSO Student Theses and Dissertations

High-latitude reefs have been postulated as refugia, centers for resilience or the first areas to undergo re-organization under climate change. The Southeast Florida Reef Tract (SEFRT) is a high-latitude reef system (>25 °N) running parallel to the highly urbanized coastline of southeast Florida. With a benthic community comprised of a mixture of coral reef associated assemblages, the SEFRT is towards the northern limit of stony coral cover due to temperature constraints. This study analyzed spatial variations in benthic cover, spatiotemporal changes in the benthic community and the impact of spatial and temporal fluctuations in temperature on benthic cover on …

Effects Of Ocean Warming, Sedimentation, And Parental Genotype On The Post-Settlement Survival And Growth Of Acropora Cervicornis Recruits, Jena Robbins

HCNSO Student Theses and Dissertations

Ocean warming and increased sedimentation from coastal activities are major threats to coral persistence. This study assessed the effects of increased temperature and sedimentation on the survival and growth of Acropora cervicornisrecruits. The potential for adults from different regions and genotypes to confer their offspring with higher or lower tolerance to heat and/or sediment was also determined. Gametes were collected and brought to the laboratory for cross fertilization of different genotypes within the regions collected. Larval rearing and settlement were then performed in the laboratory. Newly settled recruits were reared at 29 and 31°C (current summer temperature for August …

Patterns In Caribbean Coral Spawning, Anna C. Jordan

HCNSO Student Theses and Dissertations

Most corals worldwide are broadcast spawners that rely on synchronous gamete release for successful fertilization. Spawning synchrony may also decrease the probability of heterospecific fertilization that may produce maladaptive hybrids. Despite the importance of reproductive timing, researchers have only recently begun to collect spawning data across coral species in the Caribbean, but these data remain to be analyzed. This study investigates interannual, seasonal, and environmental patterns that may influence Caribbean scleractinian spawning times. The number of spawning observations varies widely among location and species. Most spawning observations were collected in Florida, Curaçao, and Flower Garden Banks National Marine Sanctuary. Acropora …

A Phylogeographic Analysis Of Black Coral (Antipatharia) On Artificial And Natural Reefs In The Northwestern Gulf Of Mexico, Heather Otte

Theses and Dissertations

NOAA's Islands in the Stream concept (IitS) of designating networks of marine protected areas as refugia in the Gulf of Mexico depends on genetic connectivity. Isolated habitats like those proposed by the IitS occur naturally off the Texas coast where hard-bottom structures protrude from mudflats, offering a small-scale study of the IitS feasibility. Two sequences, mitochondrial 16S ribosomal RNA and nuclear internal transcribed spacer, were used to build haplotype networks of Antipatharians (Anthozoa: Hexacorallia), corals with planktonic larvae that can act as a proxy for connectivity of other organisms. Two species showed no significant genetic differentiation or pattern of genetic …

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 …

"The Effects Of Ocean Warming And Sedimentation On The Survival And Growth Of Acropora Cervicornis" And "Differential Prevalence Of Chimerism During Embryogenesis In Corals", Hayley De Marchis

HCNSO Student Theses and Dissertations

Part I:

Coral reefs are essential to coastal economies, protecting coastlines from storms, and harboring high biodiversity. However, reefs are declining due to local anthropogenic stressors and ocean warming. Sedimentation, a local stressor, aggravates the impacts of warming on corals and hinders their survival and growth. Therefore, it is important to investigate whether sedimentation and temperature have a synergistic effect on vulnerable coral species, especially during earlier stages of development. To quantify these effects, survival and growth of newly settled Acropora cervicornis corals were measured at two temperatures (29 and 31°C, representing current and predicted for 2050 Summer temperatures) and …

Coral Vs. Macroalgae: Relative Susceptibility To Sedimentation And Ocean Warming, Ashton J. Galarno

HCNSO Student Theses and Dissertations

Sedimentation and ocean warming are two major anthropogenic stressors that directly affect coral recruitment and recovery. Many coral-dominated reefs have undergone phase shifts becoming macroalgae-dominated because of the coral population’s inability to tolerate these increasing stressors. Predicting these phase shifts requires a determination of the relative susceptibility of coral and macroalgae to these stressors. The objective of this study was to quantitatively assess the synergistic effects of sedimentation and elevated temperature on the survival and growth of Montastraea cavernosa newly settled coral juveniles, and fragments of the macroalgae, Dictyota ciliolata. A crossed experimental design tested the two temperatures and …