Marine Biology Commons^™

Microbiome And Bacterioplankton Rrna Gene Sequence Data Collected From Gulf Of Mexico Seawater Samples, Cruises Dp03 And Dp04 From April - August 2016, Cole Easson, Lindsey Freed

DEEPEND Datasets

Seawater was collected and filtered for microbiome and bacterioplankton sequencing and analyses at various depths during planned DEEPEND cruise expeditions to the GOM in 2016. Filters were stored and then processed for total environmental genomic DNA according to standard methods (see earthmicrobiome.org). 16S rRNA amplicon libraries covering the V4 hypervariable regions were generated with universal PCR primers and then sequenced on an Illumina MiSeq DNA sequencing platform. Raw paired-end sequences were joined and quality filtered in the bioinformatics program, QIIME. Vertical baseline characterizations will track alpha and beta diversity at different depths ranging from 0 – 1500 m, assess seasonal …

Marine Bioactives From Saccharina Latissima, Orlaith O'Connell

Masters

Due to rapid global urbanization and therefore increased adoption of a 'Westernized' lifestyle, including decreased physical activity and increased consumption of highly processed and refined foods with a high sugar, fat and salt content, prevalence of gastrointestinal disorders are on the rise. Inflammatory bowel disease (IBD) in particular is closely associated with this type of lifestyle. IBD is a term used to describe chronic inflammatory conditions which affects all or parts of the gastrointestinal tract. It includes conditions such as Crohn's Disease, which affects all the gastrointestinal tract and Ulcerative Colitis which mainly affects the colan. Due to the role …

Anaerobic Oxidation Of Ethane, Propane, And Butane By Marine Microbes: A Mini Review, Rajesh Singh, Michael S. Guzman, Arpita Bose

Biology Faculty Research

The deep ocean and its sediments are a continuous source of non-methane short-chain alkanes (SCAs) including ethane, propane, and butane. Their high global warming potential, and contribution to local carbon and sulfur budgets has drawn significant scientific attention. Importantly, microbes can use gaseous alkanes and oxidize them to CO₂, thus acting as effective biofilters. A relative decrease of these gases with a concomitant ¹³C enrichment of propane and n-butane in interstitial waters vs. the source suggests microbial anaerobic oxidation. The reported uncoupling of sulfate-reduction (SR) from anaerobic methane oxidation supports their microbial consumption. To date, strain …

Microbial Community Richness Distinguishes Shark Species Microbiomes In South Florida, Rachael Cassandra Karns

HCNSO Student Theses and Dissertations

The microbiome (microbial community) of individuals is crucial when characterizing and understanding processes that are required for organism function and survival. Microbial organisms, which make up an individual’s microbiome, can be linked to disease or function of the host organism. In humans, individuals differ substantially in their microbiome compositions in various areas of the body. The cause of much of the composition diversity is yet unexplained, however, it is speculated that habitat, diet, and early exposure to microbes could be altering the microbiomes of individuals (Human Microbiome Project Consortium, 2012b, 2012a). To date, only one study has reported on microbiome …

Bacterial Communities Associated With Healthy And Diseased Acropora Cervicornis (Staghorn Coral) Using High-Throughput Sequencing, Charles Walton

HCNSO Student Theses and Dissertations

Coral diseases were first noted in the 1960s and 1970s and have had major impacts globally on coral reef community structures. In the Caribbean, a major outbreak of white band disease has been considered responsible for the drastic decline of Caribbean Acroporids since the 1970s. In addition to white band disease, another more recently described condition known as rapid tissue loss (RTL) has had major impacts on Acropora cervicornis populations, specifically offshore Broward County Southeast Florida. While these diseases have contributed to the population decline, determining their etiologies has been elusive.

Coral diseases have been characterized by shifts in their …

The Role Of Dietary Highly Unsaturated N-3 Fatty Acids In Northern Quahogs, Mercenaria Mercenaria, Through Decreasing Temperature, Sixto E. Portilla

Dissertations, Theses, and Capstone Projects

The series of investigations described in this thesis were designed to assess the effect of diet on mortality through decreasing temperature in two genetic varieties of M. mercenaria important to the natural environment and the aquaculture industry: “wild” from natural stocks and “notata” selected for fast growth. Data from these novel investigations demonstrate a temperature specific sensitivity to each dietary component designating 20:5n-3 as homeoviscously favorable in the upper thermal range above 12°C, and 22:6n-3 as favorable in the lower. Statistical analyses of variance demonstrate distinct cumulative mortalities among the 5 dietary treatments (P < 0.05) for each genetic variety at each thermal range, upper (>12°C) and lower (2 = 0.9326 …

Molecular Assisted Identification Reveals Hidden Red Algae Diversity From The Burica Peninsula, Pacific Panama, David Wilson Freshwater, Jennifer N. Idol, Seth L. Parham, Cindy Fernández-García, Noemi León, Paul W. Gabrielson, Brian Wysor

Arts & Sciences Faculty Publications

The marine flora of Panama harbors a rich diversity of green, red and brown algae, and despite chronic understudy, it is reported as the second most diverse marine flora along the Pacific Central American coast, with 174 macroalgal species. Extensive new collections and molecular assisted identification (MAI) by an international team of researchers has revealed an even greater diversity for this country. Here, the intertidal and shallow subtidal marine flora of the remote Burica Peninsula is introduced. This area is characterized by an uplifted extensive intertidal flat composed of firm, sedimentary benthos known as mudrock, on which abundant algal communities …

Microbiome And Bacterioplankton Rrna Gene Sequence Data Collected From Gulf Of Mexico Seawater Samples, Cruises Dp01 And Dp02 From May 2015 - August 2015, Cole Easson, Jose V. Lopez

DEEPEND Datasets

Seawater was collected and filtered for microbiome and bacterioplankton sequencing and analyses at various depths during two planned DEEPEND cruise expeditions to the GOM. Filters were stored and then processed for total environmental genomic DNA according to standard methods (see earthmicrobiome.org). 16S rRNA amplicon libraries covering the V4 hypervariable region was generated with universal PCR primers and then sequenced on an Illumina MiSeq DNA sequencing platform. Bioinformatics analyses in QIIME and R was used to quality filter and assess microbial community diversity and taxonomic composition. These baseline characterizations track alpha and beta diversity at different depths ranging from 0 – …

Bioethics In The Work Of Ernest Everett Just: + Missing - Some 400 Pages, Theodore Walker

Perkins Faculty Research and Special Events

Biology + ethics = bioethics. Here we see that Howard University biologist Ernest Everett Just (born 1883, died 1941) connected biology to ethics.

According to Just, various forms of specific biology (including especially cell biology) plus “general biology” are necessary for explaining adequately the origin of ethical behaviors. Social ethical behaviors, especially mutual aid and cooperative interactions with others and the environment, are essential to evolutionary advances among living creatures, ranging from humans to cells. Accordingly, theory of ethics (moral theory) should have roots in biology.

Also, Just wrote an unpublished book-length manuscript—“some 400 typed pages” (Just 1940)—on seeking the …

Season, But Not Symbiont State, Drives Microbiome Structure In The Temperate Coral Astrangia Poculata., Koty H. Sharp, Zoe A. Pratte, Allison H. Kerwin

Arts & Sciences Faculty Publications

BACKGROUND: Understanding the associations among corals, their photosynthetic zooxanthella symbionts (Symbiodinium), and coral-associated prokaryotic microbiomes is critical for predicting the fidelity and strength of coral symbioses in the face of growing environmental threats. Most coral-microbiome associations are beneficial, yet the mechanisms that determine the composition of the coral microbiome remain largely unknown. Here, we characterized microbiome diversity in the temperate, facultatively symbiotic coral Astrangia poculata at four seasonal time points near the northernmost limit of the species range. The facultative nature of this system allowed us to test seasonal influence and symbiotic state (Symbiodinium density in the coral) on microbiome …

Review Of The Cultivation Program Within The National Alliance For Advanced Biofuels And Bioproducts, Peter J. Lammers, Michael Huesemann, Wiebke Boeing, Daniel B. Anderson, Robert G. Arnold, Xuemei Bai, Manish Bhole, Yalini Brhanavan, Louis Brown, Jola Brown, Judith K. Brown, Stephen Chisholm, C. Meghan Downes, Scott Fulbright, Yufeng Ge, Jonathan E. Holladay, Balachandran Ketheesan, Avinash Khopkar, Ambica Koushik, Paul Laur, Babetta L. Marrone, John B. Mott, Nagamany Nirmalakhandan, Kimberly L. Ogden, Ronald L. Parsons, Juergen Polle, Randy D. Ryan, Tzachi Samocha, Richard T. Sayre, Mark Seger, Thinesh Selvaratnam, Ruixiu Sui, Alex Thomasson, Adrian Unc, Wayne Van Vorrhies, Peter Waller, Yao Yao, José A. Olivares

Publications and Research

The cultivation efforts within the National Alliance for Advanced Biofuels and Bioproducts (NAABB)were developed to provide four major goals for the consortium, which included biomass production for downstream experimentation, development of new assessment tools for cultivation, development of new cultivation reactor technologies, and development of methods for robust cultivation. The NAABB consortium test beds produced over 1500 kg of biomass for downstream processing. The biomass production included a number of model production strains, but also took into production some of the more promising strains found through the prospecting efforts of the consortium. Cultivation efforts at large scale are intensive and …

Comparative Genomics, Transcriptomics, And Physiology Distinguish Symbiotic From Free-Living Chlorella Strains, Cristian F. Quispe, Olivia Sonderman, Maya Khasin, Wayne R. Riekhof, James L. Van Etten, Kenneth Nickerson

Kenneth Nickerson Papers

Most animal–microbe symbiotic interactions must be advantageous to the host and provide nutritional benefits to the endosymbiont. When the host provides nutrients, it can gain the capacity to control the interaction, promote self-growth, and increase its fitness. Chlorella-like green algae engage in symbiotic relationships with certain protozoans, a partnership that significantly impacts the physiology of both organisms. Consequently, it is often challenging to grow axenic Chlorella cultures after isolation from the host because they are nutrient fastidious and often susceptible to virus infection. We hypothesize that the establishment of a symbiotic relationship resulted in natural selection for nutritional and metabolic …

Population Dynamics And Community Composition Of Ammonia Oxidizers In Salt Marshes After The Deepwater Horizon Oil Spill, Anne E. Bernhard, Roberta Sheffer, Anne E. Giblin, John M. Marton, Brian J. Roberts

Biology Faculty Publications

The recent oil spill in the Gulf of Mexico had significant effects on microbial communities in the Gulf, but impacts on nitrifying communities in adjacent salt marshes have not been investigated. We studied persistent effects of oil on ammonia-oxidizing archaeal (AOA) and bacterial (AOB) communities and their relationship to nitrification rates and soil properties in Louisiana marshes impacted by the Deepwater Horizon oil spill. Soils were collected at oiled and unoiled sites from Louisiana coastal marshes in July 2012, 2 years after the spill, and analyzed for community differences based on ammonia monooxygenase genes (amoA). Terminal Restriction Fragment …

Characterization Of The Marine Sponge Amphimedon Compressa Microbiome Across A Spatial Gradient, Renee Michelle Potens

HCNSO Student Theses and Dissertations

Diverse and ecologically important microbial communities (microbiomes) are symbiotic within marine sponges. In this study, the microbiome of Amphimedon compressa from three sample locations (Broward and Dade Counties, Southeast Florida, USA and the Southern Caribbean, Bocas del Toro, Panama) is characterized using 16S rRNA Illumina sequencing. The predominant taxa are Proteobacteria and Cyanobacteria, as expected for Low Microbial Abundance sponges, accounting for over 53% of the total microbiome community. The numbers of Operational Taxonomic Units (OTUs) decrease from Broward County (2,900) to Dade County (2,300) and then Bocas del Toro (1,200). The correlates to a decreasing north-south gradient of …

Bacteriophages That Can Lyse Antibiotic Resistant Bacteria, Michael Monaco

Honors Theses

A Klebsiella pneumoniae bacteriophage was isolated from waste water and purified over multiple rounds of plaque removals and serial titrations. This bacteriophage was imaged in a transmission electron microscope and then tested with selected antibiotics for effectiveness in reducing optical density of K. pneumoniae colonies. The phage was shown to have an increased effectiveness in reducing the optical density when used together with an antibiotic that the bacteria was susceptible to.

"Patterns In The Abundance Of Benthic Algae In Streams", Courtney Wright

Honors Theses

Benthic, microscopic algae are the main drivers of primary productivity in streams. The relationship between the abundance and productivity of benthic algae in streams and lakes and the availability of limiting nutrients, especially soluble reactive phosphorus (SRP), has been extensively studied (reviewed in Allan and Castillo 2007, Larned 2010). However, nearly all of this research has been conducted on the periphyton assemblage found on hard substrates (e.g., stones, wood), while very little work has addressed the factors affecting the abundance of epipelic algae (i.e., the algae associated with depositional (soft) sediments such as sands and silts). One of the few …

Experimental Demonstration Of An Allee Effect In Microbial Populations, Rajreni B. Kaul, Andrew M. Kramer, Fred C. Dobbs, John M. Drake

OES Faculty Publications

Microbial populations can be dispersal limited. However, microorganisms that successfully disperse into physiologically ideal environments are not guaranteed to establish. This observation contradicts the Baas-Becking tenet: ‘Everything is everywhere, but the environment selects’. Allee effects, which manifest in the relationship between initial population density and probability of establishment, could explain this observation. Here, we experimentally demonstrate that small populations of Vibrio fischeri are subject to an intrinsic demographic Allee effect. Populations subjected to predationby the bacterivore Cafeteria roenbergensis display both intrinsic and extrinsic demographic Allee effects. The estimated critical threshold required to escape positive densitydependence is around 5, 20 or …

Isolation And Characterization Of Microbial Community Associated With Diadumene Lineata, The Orange-Striped Sea Anemone, Tiffany Lin, Andrew Weir

Student and Faculty Research Days

The orange-striped sea anemone, Diadumene lineata, is a marine invertebrate that can be found in the Northern Hemisphere. Distribution of Diadumene lineata ranges from Japan to the Gulf of Argentina. This invasive anemone originated from the Pacific Coast of Asia and serves as a host for a diverse microbial community including a photosynthetic alga. The epiphytic bacteria adhere to the outer surface as well as to the gastrovascular cavity of the host. The microbial community associated with Diadumene lineata is relatively unknown. This study attempted to isolate and identify bacteria commonly associated with this invasive marine invertebrate. Diadumene lineata was …

The Contribution Of Marine Aggregate-Associated Bacteria To The Accumulation Of Pathogenic Bacteria In Oysters: An Agent-Based Model, Andrew M. Kramer, J. Evan Ward, Fred C. Dobbs, Melissa L. Pierce

OES Faculty Publications

Bivalves process large volumes of water, leading to their accumulation of bacteria, including potential human pathogens (e.g., vibrios). These bacteria are captured at low efficiencies when freely suspended in the water column, but they also attach to marine aggregates, which are captured with near 100% efficiency. For this reason, and because they are often enriched with heterotrophic bacteria, marine aggregates have been hypothesized to function as important transporters of bacteria into bivalves. The relative contribution of aggregates and unattached bacteria to the accumulation of these cells, however, is unknown. We developed an agent-based model to simulate accumulation of vibrio-type bacteria …

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 …

Attached Algae As An Indicator Of Water Quality: A Study Of The Viability Of Genomic Taxonomic Methods, Allison R. Wood

Honors Theses and Capstones

This research involved evaluating algae as an indicator of water quality in New Hampshire's rivers, with a focus on the Great Bay Estuary. The project had three main goals. First, determining whether or not algae would work as an indicator of water quality in the great bay ecosystem, an environment where tidal currents are strong and water composition is mixed. The second goal was to compare traditional microscopic methods of taxonomy with emerging genomic methods, increasing the economic viability of attached algae monitoring. The third project goal, still underway, is to evaluate massive amounts of genomic data from the Great …

Stressed Induced Changes In Karenia Brevis Ribosomal Rna, David Scott Jayroe

Master's Theses

Karenia brevis is a toxic marine dinoflagellate that causes harmful algal blooms (HABs), also known as red tides, in the Gulf of Mexico. These blooms are responsible for massive fish kills, shellfish bed contaminations, adverse human health effects, and vast economic loss. For these reasons, extensive research has gone into understanding the mechanisms and dynamics of bloom behavior by studying K. brevis in the field and in the lab. In order to understand higher order bloom behavior and dynamics it is imperative to understand K. brevis at the cellular level. In growing K. brevis in vitro under a variety of …

Long-Term Impacts Of Disturbance On Nitrogen-Cycling Bacteria In A New England Salt Marsh, Anne E. Bernhard, Courtney Dwyer, Adrian Idrizi, Geoffrey Bender, Rachel Zwick

Biology Faculty Publications

Recent studies on the impacts of disturbance on microbial communities indicate communities show differential responses to disturbance, yet our understanding of how different microbial communities may respond to and recover from disturbance is still rudimentary. We investigated impacts of tidal restriction followed by tidal restoration on abundance and diversity of denitrifying bacteria, ammonia-oxidizing bacteria (AOB), and ammonia-oxidizing archaea (AOA) in New England salt marshes by analyzing nirS and bacterial and archaeal amoA genes, respectively. TRFLP analysis of nirS and betaproteobacterial amoA genes revealed significant differences between restored and undisturbed marshes, with the greatest differences detected in …

Iron Deficiency Increases Growth And Nitrogen-Fixation Rates Of Phosphorus-Deficient Marine Cyanobacteria, Nathan S. Garcia, Feixue Fu, Peter N. Sedwick, David A. Hutchins

OES Faculty Publications

Marine dinitrogen (N²)-fixing cyanobacteria have large impacts on global biogeochemistry as they fix carbon dioxide (CO₂) and fertilize oligotrophic ocean waters with new nitrogen. Iron (Fe) and phosphorus (P) are the two most important limiting nutrients for marine biological N₂ fixation, and their availabilities vary between major ocean basins and regions. A long-standing question concerns the ability of two globally dominant N₂-fixing cyanobacteria, unicellular Crocosphaera and filamentous Trichodesmium, to maintain relatively high N₂-fixation rates in these regimes where both Fe and P are typically scarce. We show that under P-deficient …

Characterization Of Vibrio Vulnificus Strains Using Phenotypic And Genotypic Assays, James Conrad

Masters Theses, 2010-2019

In this study 143 V. vulnificus isolates of clinical and environmental origin, were examined for growth on differential media, identified to species and tested for antibiotic resistance. A multiplex PCR was created and optimized, and phylogenetic analysis was conducted. The first objective was to compare phenotypic methods to identify V. vulnificus. Colony colors of confirmed V. vulnificus isolates on selective media (Vibrio vulnificus agar, thiosulfate citrate bilesalts sucrose agar, CHROMAgar Vibrio (CAV), and colistin polymyxin B cellobiose agar), mostly matched those characteristic of V. vulnificus. To test the ability of these media to select for V. vulnificus, new presumptive V. …

A Functional Approach To Resolving The Biogeocomplexity Of Two Extreme Environments, Haydn Rubelmann Iii

USF Tampa Graduate Theses and Dissertations

The biodiversity of two distinct marine environments was observed to describe the biogeocomplexity of these extreme ecological systems. A shallow-water hydrothermal vent in Papua New Guinea served as a study of a thermophilic ecosystem influenced by arsenic rich vent fluids while a 60 m deep offshore primarily anoxic karst sink served as a study of an anaerobic sulfur-influenced habitat. Both environments support unique biological communities that are influenced by the physical and chemical pressures imposed on them by the harsh conditions of these systems. In Tutum Bay, Ambitle Isle, Papua New Guinea, a transect was created from a shallow hydrothermal …

Two Distinct Microbial Communities Revealed In The Sponge Cinachyrella, Marie L. Cuvelier, Emily Blake, Rebecca Mulheron, Peter J. Mccarthy, Patricia Blackwelder, Rebecca Vega-Thurber, Jose V. Lopez

Marine & Environmental Sciences Faculty Articles

Marine sponges are vital components of benthic and coral reef ecosystems, providing shelter and nutrition for many organisms. In addition, sponges act as an essential carbon and nutrient link between the pelagic and benthic environment by filtering large quantities of seawater. Many sponge species harbor a diverse microbial community (including Archaea, Bacteria and Eukaryotes), which can constitute up to 50% of the sponge biomass. Sponges of the genus Cinachyrella are common in Caribbean and Floridian reefs and their archaeal and bacterial microbiomes were explored here using 16S rRNA gene tag pyrosequencing. Cinachyrella specimens and seawater samples were collected from the …

Predation Thresholds In Marine Microbial Communities Applied To Environments With Low Prey Abundances, Bonnie Bailey

OES Theses and Dissertations

Prokaryotes (Bacteria and Archaea) comprise the largest component of biomass in the world's oceans. Their abundances are controlled by resource availability, viral infections and protist grazing. Many pico- and nano-eukaryotic predators grow almost as quickly as their prey, and greatly increase in numbers as soon as their prey do, leading in tum to depletion in prokaryotes. It is still unclear however, as to what extent microbial predators are able to feed in low prey environments, most prominently in the largest biome on Earth, the deep sea (below l 000 m depth). It has been hypothesized that in low prey environments, …

Phytoplankton And Nutrient Dynamics In A Tidally Dominated Eutrophic Estuary: Daily Variability And Controls On Bloom Formation, Ryan E. Morse, Margaret R. Mulholland, Todd A. Egerton, Harold G. Marshall

OES Faculty Publications

To better understand nutrient dynamics and factors that promote the initiation of algal blooms, the Lafayette River, a tidal subestuary of Chesapeake Bay that experiences seasonal algal blooms, was sampled daily for a period of 54 d in the fall of 2005. Three phytoplankton blooms (chl a concentrations exceeding twice the average of monthly measurements from 2000 to 2009) occurred during this period: a mixed bloom of Akashiwo sanguinea and Gymnodinium sp., a monospecific Skeletonema costatum bloom, and a monospecific Gymnodinium sp. bloom. Over the sampling period, nutrient concentrations increased following precipitation events and were elevated between bloom periods but …

Emergence Of Algal Blooms: The Effects Of Short-Term Variability In Water Quality On Phytoplankton Abundance, Diversity, And Community Composition In A Tidal Estuary, Todd A. Egerton, Ryan E. Morse, Harold G. Marshall, Margaret R. Mulholland

OES Faculty Publications

Algal blooms are dynamic phenomena, often attributed to environmental parameters that vary on short timescales (e.g., hours to days). Phytoplankton monitoring programs are largely designed to examine long-term trends and interannual variability. In order to better understand and evaluate the relationships between water quality variables and the genesis of algal blooms, daily samples were collected over a 34 day period in the eutrophic Lafayette River, a tidal tributary within Chesapeake Bay's estuarine complex, during spring 2006. During this period two distinct algal blooms occurred; the first was a cryptomonad bloom and this was followed by a bloom of the mixotrophic …