David F Gruber | CUNY - Baruch College (original) (raw)
Papers by David F Gruber
American Museum of Natural History Research Library, 2021
Biofluorescence has recently been reported to be phylogenetically widespread and phenotypically v... more Biofluorescence has recently been reported to be phylogenetically widespread and phenotypically variable across bony fishes, and is most common in tropical coral reef lineages. Here we provide the first documentation of prominent biofluorescence in Arctic fishes including two juvenile specimens of Liparis gibbus (variegated snailfish) collected from the coastal waters of Eastern Greenland, as well as an adult L. tunicatus (kelp snailfish) collected in the Bering Strait off of Little Diomede Island, AK. Observations of L. gibbus were made during nighttime dives within kelp forests in iceberg habitats in Southeastern Greenland in August 2019. The juvenile L. gibbus specimens exhibit both green (523-530 nm) and red (674-678 nm) biofluorescence on discrete anatomical areas, which provides a rare example of multiple fluorescent colors emitted from a single individual. Notably, the adult L. tunicatus emitted only red fluorescence in a bilaterally symmetrical pattern of discrete red dots and blotches. Potential weak green biofluorescence was also noted in a flatfish (Hippoglossoides platessoides) collected in Greenland, but in no other Arctic species. As the distribution and function of biofluorescence in marine fishes is further examined, this report adds context to its widespread geographical and environmental distributions, and shows that, although rare, biofluorescence does occur in Arctic fish lineages.
Deepstaria enigmatica (Semaeostomeae: Ulmaridae) is one of the largest and most mysterious invert... more Deepstaria enigmatica (Semaeostomeae: Ulmaridae) is one of the largest and most mysterious invertebrate predators of the deep sea. Humans have encountered this jellyfish on only a few occasions and many questions related to its biology, distribution, diet, environmental tolerances, and behavior remain unanswered. In the 45 years since its formal description, there have been few recorded observations of D. enigmatica, due to the challenging nature of encountering these delicate soft-bodied organisms. Members of Deepstaria, which comprises two described species, D. enigmatica and D. reticulum, reside in the meso-bathypelagic region of the world's oceans, at depths ranging from ~600 to 1750 m. Here we report observations of a large D. enigmatica (68.3 cm length × 55.7 cm diameter) using a custom color high-definition low-light imaging system mounted on a scientific remotely operated vehicle (ROV). Observations were made of a specimen capturing or "bagging" prey, and we report on the kinetics of the closing motion of its membranelike umbrella. In the same area, we also noted a Deepstaria "jelly-fall" carcass with a high density of crustaceans feeding on its tissue and surrounding the carcass. These observations provide direct evidence of singular Deepstaria carcasses acting as jelly falls, which only recently have been reported to be a significant food source in the deep sea.
PeerJ, 2018
Bioluminescent copepods are often the most abundant marine zooplankton and play critical roles in... more Bioluminescent copepods are often the most abundant marine zooplankton and play critical roles in oceanic food webs. Metridia copepods exhibit particularly bright bioluminescence, and the molecular basis of their light production has just recently begun to be explored. Here we add to this body of work by transcriptomically profiling Metridia lucens, a common species found in temperate, northern, and southern latitudes. In this previously molecularly-uncharacterized species, we find the typical luciferase paralog gene set found in Metridia. More surprisingly, we recover noteworthy putative luciferase sequences that had not been described from Metridia species, indicating that bioluminescence produced by these copepods may be more complex than previously known. This includes another copepod luciferase, as well as one from a shrimp. Furthermore, feeding experiments using mass spectrometry and 13C labelled L-tyrosine and L-phenylalanine firmly establish that M. lucens produces its own c...
Scientific Reports, 2020
Scleractinian “stony” corals are major habitat engineers, whose skeletons form the framework for ... more 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, (3) non-symbiotic, (4) solitary or small colonies and (5) bleaching-resistant. We then compared these traits to the traits of modern Scleractinian corals, using to IUCN Red List data, and report that corals with these same survival traits have relatively stable population...
PLOS ONE, 2019
Schooling fishes, like flocking birds and swarming insects, display remarkable behavioral coordin... more 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 (sCMOS) camera. Image analysis revealed nighttime schooling using synchronized bioluminescent flashing displays, and demonstrated that school motion synchrony exhibits correlation with relative swim speed. A computer model of flashlight fish schooling behavior shows that only a small percentage of individuals need to exhibit bioluminescence in order for school cohesion to be maintained. Flashlight fish schooling is unique among fishes, in that bioluminescence enables schooling in conditions of no ambient light. In addition, some members can still partake in the school while not actively exhibiting their bioluminescence. Image analysis of our field data and model demonstrate that if a small percentage of fish become motivated to change direction, the rest of the school follows. The use of bioluminescence by flashlight fish to enable schooling in shallow water adds an additional ecological application to bioluminescence and suggests that schooling behavior in mesopelagic bioluminescent fishes may be also mediated by luminescent displays.
Science Robotics, 2018
A robot end effector uses one rotary actuator to fold the net of a dodecahedron, completely surro... more A robot end effector uses one rotary actuator to fold the net of a dodecahedron, completely surrounding delicate mid-water organisms.
PloS one, 2018
Soft robotics is an emerging technology that has shown considerable promise in deep-sea marine bi... more 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 "fingernails", and re-fabrication of soft manipulators at sea. These were then used to successfully grasp fragile deep-sea animals, such as goniasterids and holothurians, which have historically been difficult to collect undamaged via rigid mechanical arms and suction samplers. As s...
Soft robotics, Jan 19, 2018
This article presents the development of modular soft robotic wrist joint mechanisms for delicate... more This article presents the development of modular soft robotic wrist joint mechanisms for delicate and precise manipulation in the harsh deep-sea environment. The wrist consists of a rotary module and bending module, which can be combined with other actuators as part of a complete manipulator system. These mechanisms are part of a suite of soft robotic actuators being developed for deep-sea manipulation via submersibles and remotely operated vehicles, and are designed to be powered hydraulically with seawater. The wrist joint mechanisms can also be activated with pneumatic pressure for terrestrial-based applications, such as automated assembly and robotic locomotion. Here we report the development and characterization of a suite of rotary and bending modules by varying fiber number and silicone hardness. Performance of the complete soft robotic wrist is demonstrated in normal atmospheric conditions using both pneumatic and hydraulic pressures for actuation and under high ambient hydr...
eLife, May 24, 2016
Transcriptome and genome data from twenty stony coral species and a selection of reference bilate... more Transcriptome and genome data from twenty stony coral species and a selection of reference bilaterians were studied to elucidate coral evolutionary history. We identified genes that encode the proteins responsible for the precipitation and aggregation of the aragonite skeleton on which the organisms live, and revealed a network of environmental sensors that coordinate responses of the host animals to temperature, light, and pH. Furthermore, we describe a variety of stress-related pathways, including apoptotic pathways that allow the host animals to detoxify reactive oxygen and nitrogen species that are generated by their intracellular photosynthetic symbionts, and determine the fate of corals under environmental stress. Some of these genes arose through horizontal gene transfer and comprise at least 0.2% of the animal gene inventory. Our analysis elucidates the evolutionary strategies that have allowed symbiotic corals to adapt and thrive for hundreds of millions of years.
Soft Robotics, 2016
This article presents the development of an underwater gripper that utilizes soft robotics techno... more This article presents the development of an underwater gripper that utilizes soft robotics technology to delicately manipulate and sample fragile species on the deep reef. Existing solutions for deep sea robotic manipulation have historically been driven by the oil industry, resulting in destructive interactions with undersea life. Soft material robotics relies on compliant materials that are inherently impedance matched to natural environments and to soft or fragile organisms. We demonstrate design principles for soft robot end effectors, bench-top characterization of their grasping performance, and conclude by describing in situ testing at mesophotic depths. The result is the first use of soft robotics in the deep sea for the nondestructive sampling of benthic fauna.
BMC Genomics
Marine Ecology Progress Series, 2014
Relating atmospheric CO 2 to δ 13 C of calcifying phytoplankton is often used as a proxy to recon... more Relating atmospheric CO 2 to δ 13 C of calcifying phytoplankton is often used as a proxy to reconstruct paleo-CO 2. Therefore, a firm undertanding of how living cells fractionate carbon under different environmental conditions (known as vital effects) is necessary when interpreting δ 13 C values. In this study, we measured the isotopic fractionation of carbon in organic matter (ε p) in the globally distributed, bloom-forming coccolithophorid Emiliania huxleyi grown in continuous culture under nutrient-replete conditions with growth rate limited by light or temperature. At a constant temperature of 18°C, growth followed a hyperbolic function of irradiance. At low irradiance levels, changes in ε p were highly correlated with growth rate. However, as growth became light-saturated, ε p declined with increasing light intensities. When temperature was increased from 7 to 18°C at a constant photon flux density, equilibrium partial pressure CO 2 concentrations ([pCO 2 ]) decreased from 17 to 13 µM, and ε p values declined from 25 to 19 ‰. As temperature was increased further to 26°C, [pCO 2 ] declined to 10 µM and ε p increased to 25 ‰. This non-linear pattern in isotopic fractionation is consistent with the induction of a carbon-concentrating mechanism at low [pCO 2 ] that replenishes the internal inorganic carbon pool with isotopically lighter carbon. In this study, we present an empirical model that predicts this non-linear behavior, and we validate this model with experimental data. These results suggest extreme variability in the isotopic fractionation of carbon in the bulk organic pool in E. huxleyi that precludes the reconstruction of pCO 2 from isotopic measurements without a priori knowledge of temperature.
Marine Biology, 2014
ABSTRACT During the 2010/2011 Exploration vessel Nautilus expedition to the Mediterranean Sea, sa... more ABSTRACT During the 2010/2011 Exploration vessel Nautilus expedition to the Mediterranean Sea, samples of Lamellibrachia (Siboglinidae, Annelida) were imaged in situ and collected from hydrothermal vent and methane “cold seeps.” An analysis of these Lamellibrachia and their endosymbiotic thioautotrophic gammaproteobacteria reveals two distinct endosymbiont phylotypes. Phylotype 1 was present in Lamellibrachia specimens from 947 m at the Eratosthenes seamount seep (a seep off Cyprus in the Eastern Mediterranean), and Phylotype 2 was found in siboglinids from 618 m at a hydrothermal vent within Palinuro volcanic complex in Tyrrhenian Sea. Both phylotypes coexist in siboglinids at 1,036 m from the Palmachim disturbance, a cold seep in the Eastern Mediterranean’s Levantine basin. Our results, combined with existing knowledge of siboglinid host and endosymbiotic bacteria biogeography, reveal that two major groups of endosymbionts coexist within lamellibranchids and escarpids. The phylogenetic clustering of these bacteria is primarily influenced by geographic location, rather than selection by the siboglinid host.
BMC Genomics, 2013
Background: Genomic and transcriptomic sequence data are essential tools for tackling ecological ... more 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 longer than 100 bp, with N50 values of 1,665 bp and 1,439 bp, respectively. Using the proteome of the sea anemone Nematostella vectensis as a reference, we were able to annotate almost 20% of each dataset using reciprocal homology searches. Homologous clustering of these annotated transcripts allowed us to divide them into 7,186 (Fav1) and 6,862 (Fav2) homologous transcript clusters (E-value ≤ 2e-30). Functional annotation categories were assigned to homologous clusters using the functional annotation of Nematostella vectensis. General annotation of the assembled transcripts was improved 1-3% using the Acropora digitifera proteome. In addition, we screened these transcript isoform clusters for fluorescent proteins (FPs) homologs and identified seven potential FP homologs in Fav1, and four in Fav2. These transcripts were validated as bona fide FP transcripts via robust fluorescence heterologous expression. Annotation of the assembled contigs revealed that 1.34% and 1.61% (in Fav1 and Fav2, respectively) of the total assembled contigs likely originated from the corals' algal symbiont, Symbiodinium spp. Conclusions: Here we present a study to identify the homologous transcript isoform clusters from the transcriptome of Favia corals using a far-related reference proteome. Furthermore, the symbiont-derived transcripts were isolated from the datasets and their contribution quantified. This is the first annotated transcriptome of the genus Favia, a major increase in genomics resources available in this important family of corals.
Coral bleaching occurs when environmental stress induces breakdown of the coral-algae symbiosis a... more Coral bleaching occurs when environmental stress induces breakdown of the coral-algae symbiosis and the host initiates algae expulsion. Two types of coral bleaching had been thoroughly discussed in the scientific literature; the first is primarily associated with mass coral bleaching events; the second is a seasonal loss of algae and/or pigments. Here, we describe a phenomenon that has been witnessed for repeated summers in the mesophotic zone (40–63 m) in the northern Red Sea: seasonal bleaching and recovery of several hermatypic coral species. In this study, we followed the recurring bleaching process of the common coral Stylophora pistillata. Bleaching occurred from April to September with a 66 % decline in chlorophyll a concentration, while recovery began in October. Using aquarium and transplantation experiments, we explored environmental factors such as temperature, photon flux density and heterotrophic food availability. Our experiments and observations did not yield one sing...
Over the past decade, fluorescent proteins (FPs) have become ubiquitous tools in biological resea... more Over the past decade, fluorescent proteins (FPs) have become ubiquitous tools in biological research. Yet, little is known about the natural function or evolution of this superfamily of proteins that originate from marine organisms. Using molecular phylogenetic analyses of 102 naturally occurring cyan fluorescent proteins, green fluorescent proteins, red fluorescent proteins, as well as the nonfluorescent (purple-blue) protein sequences (including new FPs from Lizard Island, Australia) derived from organisms with known geographic origin, we show that FPs consist of two distinct and novel regions that have evolved under opposite and sharply divergent evolutionary pressures. A central region is highly conserved, and although it contains the residues that form the chromophore, its evolution does not track with fluorescent color and evolves independently from the rest of the protein. By contrast, the regions enclosing this central region are under strong positive selection pressure to v...
ArXiv, 2021
The past decade has witnessed a groundbreaking rise of machine learning for human language analys... more The past decade has witnessed a groundbreaking rise of machine learning for human language analysis, with current methods capable of automatically accurately recovering various aspects of syntax and semantics — including sentence structure and grounded word meaning — from large data collections. Recent research showed the promise of such tools for analyzing acoustic communication in nonhuman species. We posit that machine learning will be the cornerstone of future collection, processing, and analysis of multimodal streams of data in animal communication studies, including bioacoustic, behavioral, biological, and environmental data. Cetaceans are unique non-human model species as they possess sophisticated acoustic communications, but utilize a very different encoding system that evolved in an aquatic rather than terrestrial medium. Sperm whales, in particular, with their highly-developed neuroanatomical features, cognitive abilities, social structures, and discrete click-based encod...
American Museum of Natural History Research Library, 2021
Biofluorescence has recently been reported to be phylogenetically widespread and phenotypically v... more Biofluorescence has recently been reported to be phylogenetically widespread and phenotypically variable across bony fishes, and is most common in tropical coral reef lineages. Here we provide the first documentation of prominent biofluorescence in Arctic fishes including two juvenile specimens of Liparis gibbus (variegated snailfish) collected from the coastal waters of Eastern Greenland, as well as an adult L. tunicatus (kelp snailfish) collected in the Bering Strait off of Little Diomede Island, AK. Observations of L. gibbus were made during nighttime dives within kelp forests in iceberg habitats in Southeastern Greenland in August 2019. The juvenile L. gibbus specimens exhibit both green (523-530 nm) and red (674-678 nm) biofluorescence on discrete anatomical areas, which provides a rare example of multiple fluorescent colors emitted from a single individual. Notably, the adult L. tunicatus emitted only red fluorescence in a bilaterally symmetrical pattern of discrete red dots and blotches. Potential weak green biofluorescence was also noted in a flatfish (Hippoglossoides platessoides) collected in Greenland, but in no other Arctic species. As the distribution and function of biofluorescence in marine fishes is further examined, this report adds context to its widespread geographical and environmental distributions, and shows that, although rare, biofluorescence does occur in Arctic fish lineages.
Deepstaria enigmatica (Semaeostomeae: Ulmaridae) is one of the largest and most mysterious invert... more Deepstaria enigmatica (Semaeostomeae: Ulmaridae) is one of the largest and most mysterious invertebrate predators of the deep sea. Humans have encountered this jellyfish on only a few occasions and many questions related to its biology, distribution, diet, environmental tolerances, and behavior remain unanswered. In the 45 years since its formal description, there have been few recorded observations of D. enigmatica, due to the challenging nature of encountering these delicate soft-bodied organisms. Members of Deepstaria, which comprises two described species, D. enigmatica and D. reticulum, reside in the meso-bathypelagic region of the world's oceans, at depths ranging from ~600 to 1750 m. Here we report observations of a large D. enigmatica (68.3 cm length × 55.7 cm diameter) using a custom color high-definition low-light imaging system mounted on a scientific remotely operated vehicle (ROV). Observations were made of a specimen capturing or "bagging" prey, and we report on the kinetics of the closing motion of its membranelike umbrella. In the same area, we also noted a Deepstaria "jelly-fall" carcass with a high density of crustaceans feeding on its tissue and surrounding the carcass. These observations provide direct evidence of singular Deepstaria carcasses acting as jelly falls, which only recently have been reported to be a significant food source in the deep sea.
PeerJ, 2018
Bioluminescent copepods are often the most abundant marine zooplankton and play critical roles in... more Bioluminescent copepods are often the most abundant marine zooplankton and play critical roles in oceanic food webs. Metridia copepods exhibit particularly bright bioluminescence, and the molecular basis of their light production has just recently begun to be explored. Here we add to this body of work by transcriptomically profiling Metridia lucens, a common species found in temperate, northern, and southern latitudes. In this previously molecularly-uncharacterized species, we find the typical luciferase paralog gene set found in Metridia. More surprisingly, we recover noteworthy putative luciferase sequences that had not been described from Metridia species, indicating that bioluminescence produced by these copepods may be more complex than previously known. This includes another copepod luciferase, as well as one from a shrimp. Furthermore, feeding experiments using mass spectrometry and 13C labelled L-tyrosine and L-phenylalanine firmly establish that M. lucens produces its own c...
Scientific Reports, 2020
Scleractinian “stony” corals are major habitat engineers, whose skeletons form the framework for ... more 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, (3) non-symbiotic, (4) solitary or small colonies and (5) bleaching-resistant. We then compared these traits to the traits of modern Scleractinian corals, using to IUCN Red List data, and report that corals with these same survival traits have relatively stable population...
PLOS ONE, 2019
Schooling fishes, like flocking birds and swarming insects, display remarkable behavioral coordin... more 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 (sCMOS) camera. Image analysis revealed nighttime schooling using synchronized bioluminescent flashing displays, and demonstrated that school motion synchrony exhibits correlation with relative swim speed. A computer model of flashlight fish schooling behavior shows that only a small percentage of individuals need to exhibit bioluminescence in order for school cohesion to be maintained. Flashlight fish schooling is unique among fishes, in that bioluminescence enables schooling in conditions of no ambient light. In addition, some members can still partake in the school while not actively exhibiting their bioluminescence. Image analysis of our field data and model demonstrate that if a small percentage of fish become motivated to change direction, the rest of the school follows. The use of bioluminescence by flashlight fish to enable schooling in shallow water adds an additional ecological application to bioluminescence and suggests that schooling behavior in mesopelagic bioluminescent fishes may be also mediated by luminescent displays.
Science Robotics, 2018
A robot end effector uses one rotary actuator to fold the net of a dodecahedron, completely surro... more A robot end effector uses one rotary actuator to fold the net of a dodecahedron, completely surrounding delicate mid-water organisms.
PloS one, 2018
Soft robotics is an emerging technology that has shown considerable promise in deep-sea marine bi... more 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 "fingernails", and re-fabrication of soft manipulators at sea. These were then used to successfully grasp fragile deep-sea animals, such as goniasterids and holothurians, which have historically been difficult to collect undamaged via rigid mechanical arms and suction samplers. As s...
Soft robotics, Jan 19, 2018
This article presents the development of modular soft robotic wrist joint mechanisms for delicate... more This article presents the development of modular soft robotic wrist joint mechanisms for delicate and precise manipulation in the harsh deep-sea environment. The wrist consists of a rotary module and bending module, which can be combined with other actuators as part of a complete manipulator system. These mechanisms are part of a suite of soft robotic actuators being developed for deep-sea manipulation via submersibles and remotely operated vehicles, and are designed to be powered hydraulically with seawater. The wrist joint mechanisms can also be activated with pneumatic pressure for terrestrial-based applications, such as automated assembly and robotic locomotion. Here we report the development and characterization of a suite of rotary and bending modules by varying fiber number and silicone hardness. Performance of the complete soft robotic wrist is demonstrated in normal atmospheric conditions using both pneumatic and hydraulic pressures for actuation and under high ambient hydr...
eLife, May 24, 2016
Transcriptome and genome data from twenty stony coral species and a selection of reference bilate... more Transcriptome and genome data from twenty stony coral species and a selection of reference bilaterians were studied to elucidate coral evolutionary history. We identified genes that encode the proteins responsible for the precipitation and aggregation of the aragonite skeleton on which the organisms live, and revealed a network of environmental sensors that coordinate responses of the host animals to temperature, light, and pH. Furthermore, we describe a variety of stress-related pathways, including apoptotic pathways that allow the host animals to detoxify reactive oxygen and nitrogen species that are generated by their intracellular photosynthetic symbionts, and determine the fate of corals under environmental stress. Some of these genes arose through horizontal gene transfer and comprise at least 0.2% of the animal gene inventory. Our analysis elucidates the evolutionary strategies that have allowed symbiotic corals to adapt and thrive for hundreds of millions of years.
Soft Robotics, 2016
This article presents the development of an underwater gripper that utilizes soft robotics techno... more This article presents the development of an underwater gripper that utilizes soft robotics technology to delicately manipulate and sample fragile species on the deep reef. Existing solutions for deep sea robotic manipulation have historically been driven by the oil industry, resulting in destructive interactions with undersea life. Soft material robotics relies on compliant materials that are inherently impedance matched to natural environments and to soft or fragile organisms. We demonstrate design principles for soft robot end effectors, bench-top characterization of their grasping performance, and conclude by describing in situ testing at mesophotic depths. The result is the first use of soft robotics in the deep sea for the nondestructive sampling of benthic fauna.
BMC Genomics
Marine Ecology Progress Series, 2014
Relating atmospheric CO 2 to δ 13 C of calcifying phytoplankton is often used as a proxy to recon... more Relating atmospheric CO 2 to δ 13 C of calcifying phytoplankton is often used as a proxy to reconstruct paleo-CO 2. Therefore, a firm undertanding of how living cells fractionate carbon under different environmental conditions (known as vital effects) is necessary when interpreting δ 13 C values. In this study, we measured the isotopic fractionation of carbon in organic matter (ε p) in the globally distributed, bloom-forming coccolithophorid Emiliania huxleyi grown in continuous culture under nutrient-replete conditions with growth rate limited by light or temperature. At a constant temperature of 18°C, growth followed a hyperbolic function of irradiance. At low irradiance levels, changes in ε p were highly correlated with growth rate. However, as growth became light-saturated, ε p declined with increasing light intensities. When temperature was increased from 7 to 18°C at a constant photon flux density, equilibrium partial pressure CO 2 concentrations ([pCO 2 ]) decreased from 17 to 13 µM, and ε p values declined from 25 to 19 ‰. As temperature was increased further to 26°C, [pCO 2 ] declined to 10 µM and ε p increased to 25 ‰. This non-linear pattern in isotopic fractionation is consistent with the induction of a carbon-concentrating mechanism at low [pCO 2 ] that replenishes the internal inorganic carbon pool with isotopically lighter carbon. In this study, we present an empirical model that predicts this non-linear behavior, and we validate this model with experimental data. These results suggest extreme variability in the isotopic fractionation of carbon in the bulk organic pool in E. huxleyi that precludes the reconstruction of pCO 2 from isotopic measurements without a priori knowledge of temperature.
Marine Biology, 2014
ABSTRACT During the 2010/2011 Exploration vessel Nautilus expedition to the Mediterranean Sea, sa... more ABSTRACT During the 2010/2011 Exploration vessel Nautilus expedition to the Mediterranean Sea, samples of Lamellibrachia (Siboglinidae, Annelida) were imaged in situ and collected from hydrothermal vent and methane “cold seeps.” An analysis of these Lamellibrachia and their endosymbiotic thioautotrophic gammaproteobacteria reveals two distinct endosymbiont phylotypes. Phylotype 1 was present in Lamellibrachia specimens from 947 m at the Eratosthenes seamount seep (a seep off Cyprus in the Eastern Mediterranean), and Phylotype 2 was found in siboglinids from 618 m at a hydrothermal vent within Palinuro volcanic complex in Tyrrhenian Sea. Both phylotypes coexist in siboglinids at 1,036 m from the Palmachim disturbance, a cold seep in the Eastern Mediterranean’s Levantine basin. Our results, combined with existing knowledge of siboglinid host and endosymbiotic bacteria biogeography, reveal that two major groups of endosymbionts coexist within lamellibranchids and escarpids. The phylogenetic clustering of these bacteria is primarily influenced by geographic location, rather than selection by the siboglinid host.
BMC Genomics, 2013
Background: Genomic and transcriptomic sequence data are essential tools for tackling ecological ... more 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 longer than 100 bp, with N50 values of 1,665 bp and 1,439 bp, respectively. Using the proteome of the sea anemone Nematostella vectensis as a reference, we were able to annotate almost 20% of each dataset using reciprocal homology searches. Homologous clustering of these annotated transcripts allowed us to divide them into 7,186 (Fav1) and 6,862 (Fav2) homologous transcript clusters (E-value ≤ 2e-30). Functional annotation categories were assigned to homologous clusters using the functional annotation of Nematostella vectensis. General annotation of the assembled transcripts was improved 1-3% using the Acropora digitifera proteome. In addition, we screened these transcript isoform clusters for fluorescent proteins (FPs) homologs and identified seven potential FP homologs in Fav1, and four in Fav2. These transcripts were validated as bona fide FP transcripts via robust fluorescence heterologous expression. Annotation of the assembled contigs revealed that 1.34% and 1.61% (in Fav1 and Fav2, respectively) of the total assembled contigs likely originated from the corals' algal symbiont, Symbiodinium spp. Conclusions: Here we present a study to identify the homologous transcript isoform clusters from the transcriptome of Favia corals using a far-related reference proteome. Furthermore, the symbiont-derived transcripts were isolated from the datasets and their contribution quantified. This is the first annotated transcriptome of the genus Favia, a major increase in genomics resources available in this important family of corals.
Coral bleaching occurs when environmental stress induces breakdown of the coral-algae symbiosis a... more Coral bleaching occurs when environmental stress induces breakdown of the coral-algae symbiosis and the host initiates algae expulsion. Two types of coral bleaching had been thoroughly discussed in the scientific literature; the first is primarily associated with mass coral bleaching events; the second is a seasonal loss of algae and/or pigments. Here, we describe a phenomenon that has been witnessed for repeated summers in the mesophotic zone (40–63 m) in the northern Red Sea: seasonal bleaching and recovery of several hermatypic coral species. In this study, we followed the recurring bleaching process of the common coral Stylophora pistillata. Bleaching occurred from April to September with a 66 % decline in chlorophyll a concentration, while recovery began in October. Using aquarium and transplantation experiments, we explored environmental factors such as temperature, photon flux density and heterotrophic food availability. Our experiments and observations did not yield one sing...
Over the past decade, fluorescent proteins (FPs) have become ubiquitous tools in biological resea... more Over the past decade, fluorescent proteins (FPs) have become ubiquitous tools in biological research. Yet, little is known about the natural function or evolution of this superfamily of proteins that originate from marine organisms. Using molecular phylogenetic analyses of 102 naturally occurring cyan fluorescent proteins, green fluorescent proteins, red fluorescent proteins, as well as the nonfluorescent (purple-blue) protein sequences (including new FPs from Lizard Island, Australia) derived from organisms with known geographic origin, we show that FPs consist of two distinct and novel regions that have evolved under opposite and sharply divergent evolutionary pressures. A central region is highly conserved, and although it contains the residues that form the chromophore, its evolution does not track with fluorescent color and evolves independently from the rest of the protein. By contrast, the regions enclosing this central region are under strong positive selection pressure to v...
ArXiv, 2021
The past decade has witnessed a groundbreaking rise of machine learning for human language analys... more The past decade has witnessed a groundbreaking rise of machine learning for human language analysis, with current methods capable of automatically accurately recovering various aspects of syntax and semantics — including sentence structure and grounded word meaning — from large data collections. Recent research showed the promise of such tools for analyzing acoustic communication in nonhuman species. We posit that machine learning will be the cornerstone of future collection, processing, and analysis of multimodal streams of data in animal communication studies, including bioacoustic, behavioral, biological, and environmental data. Cetaceans are unique non-human model species as they possess sophisticated acoustic communications, but utilize a very different encoding system that evolved in an aquatic rather than terrestrial medium. Sperm whales, in particular, with their highly-developed neuroanatomical features, cognitive abilities, social structures, and discrete click-based encod...