Marine Biology Commons^™

A Putative Chordate Luciferase From A Cosmopolitan Tunicate Indicates Convergent Bioluminescence Evolution Across Phyla, Michael Tessler, Jean P. Gaffney, Anderson G. Oliveira, Andrew Guarnaccia, Krista C. Dobi, Nehaben A. Gujarati, Moira Galbraith, Jeremy D. Mirza, John S. Sparks, Vincent A. Pieribone, Robert J. Wood, David F. Gruber

Publications and Research

Pyrosomes are tunicates in the phylum Chordata, which also contains vertebrates. Their gigantic blooms play important ecological and biogeochemical roles in oceans. Pyrosoma, meaning “firebody”, derives from their brilliant bioluminescence. The biochemistry of this light production is unknown, but has been hypothesized to be bacterial in origin. We found that mixing coelenterazine—a eukaryote-specific luciferin—with Pyrosoma atlanticum homogenate produced light. To identify the bioluminescent machinery, we sequenced P. atlanticum transcriptomes and found a sequence match to a cnidarian luciferase (RLuc). We expressed this novel luciferase (PyroLuc) and, combined with coelenterazine, it produced light. A similar gene was recently predicted from a …

Morphological And Molecular Characterizationof A New Species Of Black Coral From Elvers Bank, North-Western Gulf Of Mexico (Cnidaria:Anthozoa: Hexacorallia: Antipatharia:Aphanipathidae: Distichopathes), Dennis M. Opresko, Samantha L. Goldman, Raven Johnson, Katherine Parra, Marissa Nuttall, G.P. Schmahl, Mercer R. Brugler

Publications and Research

The continental shelf edge of the NW Gulf of Mexico supports dozens of reefs and banks, including the West and East Flower Garden Banks (FGB) and Stetson Bank that comprise the Flower Garden Banks National Marine Sanctuary (FGBNMS). Discovered by fishermen in the early 1900s, the FGBs are named after the colourful corals, sponges and algae that dominate the region. The reefs and banks are the surface expression of underlying salt domes and provide important habitat for mesophotic coral ecosystems (MCE) and deep coral communities to 300 m depth. Since 2001, FGBNMS research teams have utilized remotely operated vehicles (e.g. …

Evolutionary Traits That Enable Scleractinian Corals To Survive Mass Extinction Events, Gal Dishon, Michal Grossowicz, Michael Krom, Gilad Guy, David F. Gruber, Dan Tchernov

Publications and Research

Scleractinian “stony” corals are major habitat engineers, whose skeletons form the framework for the highly diverse, yet increasingly threatened, coral reef ecosystem. Fossil coral skeletons also present a rich record that enables paleontological analysis of coral origins, tracing them back to the Triassic (~241 Myr). While numerous invertebrate lineages were eradicated at the last major mass extinction boundary, the Cretaceous-Tertiary/K-T (66 Myr), a number of Scleractinian corals survived. We review this history and assess traits correlated with K-T mass extinction survival. Disaster-related “survival” traits that emerged from our analysis are: (1) deep water residing (>100 m); (2) cosmopolitan distributions, …

Deep Machine Learning Techniques For The Detection And Classification Of Sperm Whale Bioacoustics, Peter C. Bermant, Michael M. Bronstein, Robert J. Wood, Shane Gero, David F. Gruber

Publications and Research

We implemented Machine Learning (ML) techniques to advance the study of sperm whale (Physeter macrocephalus) bioacoustics. This entailed employing Convolutional Neural Networks (CNNs) to construct an echolocation click detector designed to classify spectrograms generated from sperm whale acoustic data according to the presence or absence of a click. The click detector achieved 99.5% accuracy in classifying 650 spectrograms. The successful application of CNNs to clicks reveals the potential of future studies to train CNN-based architectures to extract finer-scale details from cetacean spectrograms. Long short-term memory and gated recurrent unit recurrent neural networks were trained to perform classification tasks, including (1) …

Bioluminescent Flashes Drive Nighttime Schooling Behavior And Synchronized Swimming Dynamics In Flashlight Fish, David F. Gruber, Brennan T. Phillips, Rory O'Brien, Vivek Boominathan, Ashok Veeraraghavan, Ganesh Vasan, Peter O'Brien, Vincent A. Pieribone, John S. Sparks

Publications and Research

Schooling fishes, like flocking birds and swarming insects, display remarkable behavioral coordination. While over 25% of fish species exhibit schooling behavior, nighttime schooling has rarely been observed or reported. This is due to vision being the primary modality for schooling, which is corroborated by the fact that most fish schools disperse at critically low light levels. Here we report on a large aggregation of the bioluminescent flashlight fish Anomalops katoptron that exhibited nighttime schooling behavior during multiple moon phases, including the new moon. Data were recorded with a suite of low-light imaging devices, including a high-speed, high-resolution scientific complementary metal-oxide-semiconductor …

Phytoene Accumulation In The Novel Microalga Chlorococcum Sp. Using The Pigment Synthesis Inhibitor Fluridone, Kelly Laje, Mark Seger, Barry Dungan, Peter Cooke, Juergen Polle, F. Omar Holguin

Publications and Research

Carotenoids are lipophilic pigments found in plants and algae, as well as some bacteria, archaea, and fungi that serve two functions—(1) as light harvesting molecules—primary carotenoids, and (2) as antioxidants, acting against reactive oxygen species–secondary carotenoids. Because of their strong antioxidant properties, they are also valuable for the development of anti-aging and photo-protective cosmetic applications. Of particular interest is the carotenoid phytoene, for its colorless and UV absorption characteristics. In this study, we targeted a reduction of phytoene desaturase (PDS) activity with the pigment-inhibiting herbicide 1-methyl-3-phenyl-5-[3- (trifluoromethyl)phenyl]pyridin-4-one (fluridone), which leads to the over-accumulation of phytoene in the recently characterized microalgal …

A Dexterous, Glove-Based Teleoperable Low-Power Soft Robotic Arm For Delicate Deep-Sea Biological Exploration, Brennan T. Phillips, Kaitlyn P. Becker, Shunichi Kurumaya, Kevin C. Galloway, Griffin Whittredge, Daniel M. Vogt, Clark B. Teeple, Michelle H. Rosen, Vincent A. Pieribone, David F. Gruber, Robert J. Wood

Publications and Research

Modern marine biologists seeking to study or interact with deep-sea organisms are confronted with few options beyond industrial robotic arms, claws, and suction samplers. This limits biological interactions to a subset of “rugged” and mostly immotile fauna. As the deep sea is one of the most biologically diverse and least studied ecosystems on the planet, there is much room for innovation in facilitating delicate interactions with a multitude of organisms. The biodiversity and physiology of shallow marine systems, such as coral reefs, are common study targets due to the easier nature of access; SCUBA diving allows for in situ delicate …

The Transcriptome Of The Bermuda Fireworm Odontosyllis Enopla (Annelida: Syllidae): A Unique Luciferase Gene Family And Putative Epitoky-Related Genes, Mercer R. Brugler, M. Teresa Aguado, Michael Tessler, Mark Siddall

Publications and Research

The Bermuda fireworm Odontosyllis enopla exhibits an extremely tight circalunar circadian behavior that results in an impressive bioluminescent mating swarm, thought to be due to a conventional luciferase-mediated oxidation of a light-emitting luciferin. In addition, the four eyes become hypertrophied and heavily pigmented, and the nephridial system is modified to store and release gametes and associated secretions. In an effort to elucidate transcripts related to bioluminescence, circadian or circalunar periodicity, as well as epitoky-related changes of the eyes and nephridial system, we examined the transcriptomic profile of three female O. enopladuring a bioluminescent swarm in Ferry Reach, Bermuda. …

Shipboard Design And Fabrication Of Custom 3d-Printed Soft Robotic Manipulators For The Investigation Of Delicate Deep-Sea Organisms, Daniel M. Vogt, Kaitlyn P. Becker, Brennan T. Phillips, Moritz A. Graule, Randi D. Rotjan, Timothy M. Shank, Erik E. Cordes, Robert J. Wood, David F. Gruber

Publications and Research

Soft robotics is an emerging technology that has shown considerable promise in deep-sea marine biological applications. It is particularly useful in facilitating delicate interactions with fragile marine organisms. This study describes the shipboard design, 3D printing and integration of custom soft robotic manipulators for investigating and interacting with deep-sea organisms. Soft robotics manipulators were tested down to 2224m via a Remotely-Operated Vehicle (ROV) in the Phoenix Islands Protected Area (PIPA) and facilitated the study of a diverse suite of soft-bodied and fragile marine life. Instantaneous feedback from the ROV pilots and biologists allowed for rapid re-design, such as adding ªfingernailsº, …

Wsq: At Sea Editors' Note, Cynthia Chris, Matt Brim

Publications and Research

This Editor's Note introduces the WSQ issue "At Sea" co-edited by Terri Gordon-Zolov and Amy Sodaro and Shefali Chandra, which explores the sea as a gendered and radicalized site of violence.

Caged Oysters Still Get Scared: Predator Presence And Density Influence Growth In Oysters, But Only At Very Close Ranges, Stephen Gosnell J., Kali Spurgin, Erica A. Levine

Publications and Research

Two common forms of variation that may influence consumptive and non-consumptive effects differently are how the biomass of predators is allocated among individual predators (e.g., several small vs few large predators) and how predators are spaced throughout a community. We analyzed how varying the presence, biomass (density, size, and total biomass), and distance to crown conchs (Melongena corona) impacted growth in eastern oysters (Crassostrea virginica) grown in field conditions. The presence of predators decreased growth (new shell added and mass) and increased shell thickness in a 58-day experiment. Although these effects were more pronounced as predator …

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 …

Novel Adaptive Photosynthetic Characteristics Of Mesophotic Symbiotic Microalgae Within The Reef-Building Coral, Stylophora Pistillata, Shai Einbinder, David F. Gruber, Eitan Salomon, Oded Liran, Nir Keren, Dan Tchernov

Publications and Research

Photosynthetic coral reef structures extend from the shallow sundrenched waters to the dimly lit, “twilight” mesophotic depths. For their resident endosymbiotic dinoflagellates, primarily from the genus Symbiodinium spp., this represents a photic environment that varies ~15-fold in intensity and also differs in spectral composition. We examined photosynthesis in the scleractinian coral Stylophora pistillata in shallow (3 m) and mesophotic settings (65 m) in the northern Red Sea. Symbiodinium spp. in corals originating from the mesophotic environment consistently performed below their photosynthetic compensation point and also exhibited distinct light harvesting antenna organization. In addition, the non-photochemical quenching activity of Symbiodinium spp. …

Natural Cultch Type Influences Habitat Preference And Predation, But Not Survival, In Reef-Associated Species, Erica A. Levine, Stephen Gosnell J., Emily M. Goetz, Christopher R. Malinowski

Publications and Research

A shared origin with fresh and dredged cultch and availability via mining have made fossil cultch a commonly used reef restoration substrate. However, important differences in shape and size between whole-shell cultch and fossil cultch may impact the complexity of reefs constructed from these materials. To determine if these differences may impact the development of restored reefs, we quantified the interstitial space each cultch type provides and constructed reef mesocosms to measure (1) the immediate effects of exposure to each cultch type on mortality of blue crab (Callinectes sapidus) and pink shrimp (Farfantepenaeus duorarum); (2) the …

Population Genomics Reveals Seahorses (Hippocampus Erectus) Of The Western Mid-Atlantic Coast To Be Residents Rather Than Vagrants, J. T. Boehm, John Waldman, John D. Robinson, Michael J. Hickerson

Publications and Research

Understanding population structure and areas of demographic persistence and transients is critical for effective species management. However, direct observational evidence to address the geographic scale and delineation of ephemeral or persistent populations for many marine fishes is limited. The Lined seahorse (Hippocampus erectus) can be commonly found in three western Atlantic zoogeographic provinces, though inhabitants of the temperate northern Virginia Province are often considered tropical vagrants that only arrive during warm seasons from the southern provinces and perish as temperatures decline. Although genetics can locate regions of historical population persistence and isolation, previous evidence of Virginia Province persistence is only …

Romero’S Curiosity Rooted In Undersea World, Aldemaro Romero Jr.

Publications and Research

No abstract provided.

Octopus Tetricus (Mollusca: Cephalopoda) As An Ecosystem Engineer, David Scheel, Peter Godfrey-Smith, Matthew Lawrence

Publications and Research

The Sydney octopus (Octopus tetricus) occurs in unusual numbers on a shell bed of its prey remains that have accumulated as an extended midden where additional octopuses excavate dens. Here, O tetricus are ecosystem engineers, organisms that modulate availability of resources to other species and to their own species by causing physical state changes in materials. A community of invertebrate grazers and scavengers has developed on the shell bed. Fishes are attracted to the shell bed in numbers significantly greater than in nearby habitats. Large predators, including wobbegong sharks, were attracted to and fed on concentrations of fish, inhibiting the …

Environmental History Of Marine Mammal Exploitation In Trinidad And Tobago, W.I. And Its Ecological Impact, Aldemaro Romero Jr., Ruth Baker, Joel E. Creswell, Anuradha Singh, Annabelle Mckie, Michael Manna

Publications and Research

No abstract provided.

Transcriptome Deep-Sequencing And Clustering Of Expressed Isoforms From Favia Corals, Shaadi F. Pooyaei Mehr, Rob Desalle, Hung-Teh Kao, Apurva Narechania, Zhou Han, Dan Tchernov, Vincent A. Pieribone, David F. Gruber

Publications and Research

Background: Genomic and transcriptomic sequence data are essential tools for tackling ecological problems. Using an approach that combines next-generation sequencing, de novo transcriptome assembly, gene annotation and synthetic gene construction, we identify and cluster the protein families from Favia corals from the northern Red Sea.

Results: We obtained 80 million 75 bp paired-end cDNA reads from two Favia adult samples collected at 65 m (Fav1, Fav2) on the Illumina GA platform, and generated two de novo assemblies using ABySS and CAP3. After removing redundancy and filtering out low quality reads, our transcriptome datasets contained 58,268 (Fav1) and 62,469 (Fav2) contigs …

Edges And Overlaps In Northwest Atlantic Phylogeography, Safra Altman, John D. Robinson, James M. Pringle, James E. Byers, John P. Wares

Publications and Research

As marine environments change, the greatest ecological shifts—including resource usage and species interactions—are likely to take place in or near regions of biogeographic and phylogeographic transition. However, our understanding of where these transitional regions exist depends on the defining criteria. Here we evaluate phylogeographic transitions using a bootstrapping procedure that allows us to focus on either the strongest genetic transitions between a pair of contiguous populations, versus evaluation of transitions inclusive of the entire overlap between two intraspecific genetic lineages. We compiled data for the Atlantic coast of the United States, and evaluate taxa with short- and long-dispersing larval phases …

Brunkow Studies Health Of Midwest Freshwaters, Aldemaro Romero Jr.

Publications and Research

No abstract provided.

Preface In New Approaches To The Study Of Marine Mammals, Aldemaro Romero Jr.

Publications and Research

No abstract provided.

When Whales Became Mammals: The Scientific Journey Of Cetaceans From Fish To Mammals In The History Of Science, Aldemaro Romero Jr.

Publications and Research

No abstract provided.

Medusoid Cnidarians From The Montral-Alcover Lagerstätten (Triassic), Northeastern Spain, Aldemaro Romero Jr., Raymond R. Rogers, Lisa A. Gershwin

Publications and Research

No abstract provided.

Deplete Locally, Impact Globally: Environmental History Of Shore-Whaling In Barbados, W.I, Aldemaro Romero Jr., Joel E. Creswell

Publications and Research

No abstract provided.

Typhlichthys Subterraneus, Aldemaro Romero Jr.

Publications and Research

No abstract provided.

Marine Mammals Laboratory Manual, Aldemaro Romero Jr., Kristen Irwin

Publications and Research

No abstract provided.

Arkansas State University Students Examine Calif. Seal, Aldemaro Romero Jr.

Publications and Research

No abstract provided.

Ozark Cavefish Aka Amblyopsis Rosae, Aldemaro Romero Jr.

Publications and Research

No abstract provided.

Blind Cave Fish Found In Northern Ar. Lake, Aldemaro Romero Jr., Michel Conner

Publications and Research

No abstract provided.