The John B. Pierce Laboratory


Colors of the covert world of the deep

By Madhuvanthi Kannan

Inhabiting the darkest realms of ocean waters near the Gulf of Mexico, animals such as the catshark use body fluorescence as a privy code to find and be found by their peers…and even perhaps, evade potential predators. Their skin proteins absorb the stray rays of sunlight to emit a brilliant green color. While other animals can be oblivious of its presence, only the catshark, with a yellow filter in its eye, can perceive the neon hue on its mates.

Scientists including Dr. Vincent Pieribone dive into oceanic depths to feast on the spectacular color of numerous fluorescent creatures. The play of light is not just a treat to their eyes, but holds promise to their everlasting endeavor of unraveling the mysteries of the human brain. By tagging cells and tissues with fluorescent proteins, they are on the brink of gaining unprecedented access to the inner workings of life.

New Views of Deep-Sea Bioluminescence: Low-Light Camera Reveals Life on a Hydrothermal Chimney

By Ashik Siddique

A video of bioluminescence in a hydrothermal chimney, collected by low-light camera on the ROV Hercules:

A team of scientists including Dr. Vincent Pieribone and Dr. Ganesh Vasan of the John B. Pierce Laboratory have discovered the first evidence of bioluminescence on a “black smoker” hydrothermal vent at the bottom of the ocean, using an unprecedented new method for capturing deep-sea imagery. Their findings were published last month in Deep Sea Research Part I: Oceanographic Research Papers, as well as in an article in Oceanography.

Bioluminescence – the emission of light by living organisms, often as a means of communication – is very common in the ocean, from shallow to deep seas. But images of this phenomenon are rare in these organisms’ natural habitat, largely because of the lack of widely available camera technology for capturing imagery in dimly lit deep-sea conditions.

“The problem of course is that bioluminescence is in very dim light, and your target is moving,” said Pieribone. “The human eye can see it beautifully, it’s pretty well adapted to the dark. But when you go diving in person, you see all this beautiful stuff glowing but you can’t record it with a camera.”

As a result, most studies published on marine bioluminescence have been based on organisms that can be readily observed in labs, with much still unknown about its role in their natural environment.

To tackle this problem, the team tested the novel underwater use of a scientific complementary-metal-oxide-semiconductor (sCMOS) microscopy camera system, which was designed and assembled by Dr. Pieribone and John Buckley, Tom D’Alessandro, and Andrew Wilkins of the Pierce Laboratory’s technical support team, with all software for the camera’s computers coded by Vasan.

With high resolution and high speed capabilities, this low-light camera surpasses the technical limits of other types of cameras that have been used in previous efforts to observe deep-sea bioluminescence.

“Even this camera is not as sensitive as the human eye,” said Pieribone. “But we’ve put it underwater and gotten some pretty good images with it of bioluminescence. It’s the first time anything like this has been built and brought down in the ocean, and this camera has been very useful, it’s worked every time.”

Figure 1. Internal view of the underwater sCMOS camera system, 75 cm long, 20 cm diameter, with an approximate weight of 18 kg.

New Views of Deep-Sea Bioluminescence

Over the course of several diving expeditions from 2013 to 2015, a team of oceanographers led by Brennan Phillips of the University of Rhode Island deployed the low-light camera in three oceanic regions (the Solomon Islands in the Western Tropical Pacific, the Galapagos Islands in the Eastern Equatorial Pacific, and the New England shelf break in the Northwestern Atlantic), to depths up to 2500 meters.

During each dive, bioluminescent responses of marine organisms were induced using stimulation from strobe lights, and recorded by the camera at high frame rates and in high resolution. All recordings were made at night to eliminate the possibility of ambient light from the surface.

The results, over 200 15-30 second high-speed recordings made at depths ranging from 30 to 2500 meters, revealed a remarkable range of responses.

During a manned submersible dive with a particularly high bioluminescent response, members of the expedition briefly witnessed a bright display of light from all directions, much like the Milky Way observed in a clear night sky.

At various depths, layers of major zooplankton groups could be recognized by the shape and pattern of bioluminescence, illustrating the system’s potential to quantify light-stimulated bioluminescence as a function of zooplankton population density and vertical migration patterns.

Free-swimming animals like siphonophores, comb jellies, and fish were tracked by their light response patterns in otherwise complete blackness, suggesting the system’s potential for exploring how bioluminescence operates in multicellular organisms.

The quality of imagery recorded by the low-light scientific camera offers a new view into the kinematics of bioluminescence, potentially setting a new standard for observing and quantifying how marine animals produce light.

Interestingly, bioluminescent responses stimulated by strobe lights were almost nonexistent on the seafloor. Since bioluminescence is so prevalent among deep-sea mid-water species, but not on the seafloor, the team believes that, at least among animals large enough to be visible on camera, the number of bioluminescent sources may be a proxy of total living biomass at various depths. If so, the lack of observable bioluminescence suggests that there may not be as many creatures on the seafloor.

Bright Spots on the Seafloor

A notable finding, published in Oceanography, was the first evidence of bioluminescence on a “black smoker” hydrothermal chimney, one of many vents at the bottom of the ocean that produce superheated water through cracks in the Earth’s crust.

During an expedition on the EV Nautilus in the Galapagos Islands region on July 1, 2015, the team used the Hercules remotely operated vehicle (ROV) to closely observe the Iguanas hydrothermal field, which had only been discovered in 2006.

“There are very few vehicles that have access and can actually can go down to those kind of things because they’re so dangerous,” said Pieribone. “These are just plumes of essentially super-boiling, high-pressure water, and it’s amazing that life can survive in these very extreme conditions.”

On a previous expedition to the Solomon Islands, sponsored by National Geographic, the team discovered the existence of sharks living in an underwater volcano.

At a depth of 1,643 meters in the Iguanas field, with the low-light camera pointing directly downward toward the seafloor, the ROV hovered one meter over the vent orifice of one of the larger active chimneys, about 11 meters high, for 20 minutes.  All ROV system lights were turned off, except for the strobe lights used to stimulate bioluminescent responses.

No bioluminescence was observed to be stimulated by strobe lights. However, two recordings made without strobes revealed a weak, moving luminescent source around the vent orifice (see video). Footage obtained before these recordings showed that the area around the chimney was sparsely populated, with scattered Bythograeid crabs, squat lobsters, and numerous Alvinocarid shrimp. Based on these observations and the movement of the light source, it was likely a mobile organism and could have been a free-swimming shrimp.

“If you see an object that’s glowing and you’re trying to focus the camera, it’s really hard,” said Pieribone. “So the fact that Brennan [Phillips] could get all those together at the same moment, get the camera, get the lights off, get one of these black smokers, and get everything to work, is pretty remarkable, and luck I guess fell into it.”

The new observations suggest that, in the absence of sunlight from the surface, shrimp living around deep-sea vents may use primitive photosensitive organs to detect bioluminescence, not just to detect thermal radiation in order to locate or avoid heat sources, as others have previously hypothesized.

Animals that live on or near these vents are “extremophiles,” which can only survive in water near boiling temperature. Pieribone hopes that further study of their bizarre biochemistry may reveal unique compounds that can be used to develop new research techniques in neurophysiology. One of the ongoing projects in his lab is the identification of fluorescent proteins that can be used to develop genetically-encoded probes in neurons.

“These animals have all sorts of proteins and enzymes that have been evolved to handle the temperature and not boil, and not denature,” he said. “So how does that happen? Can we utilize that in the laboratory, in the kind of stuff that I do? It offers the idea that there are organisms, like whatever that was in the picture, it’s hard to know what it is, but at least we know that organisms there are capable of glowing.”

“It was kind of an interesting thing to discover. There wasn’t as much bioluminescence as one might have thought, but we only have one picture, so we don’t really know. This will at least allow us to go down again and study them a little bit more.”


The other authors of the articles are Brennan Phillips and Christopher Roman of the University of Rhode Island, David Gruber of the City University of New York at Baruch College, and John Sparks of the American Museum of Natural History.

Contact information: Dr. Vincent Pieribone, The John B. Pierce Laboratory, New Haven, CT.  Email:

Catsharks have an eye for fluorescence and they use it to perceive their kin


By Madhuvanthi Kannan

Scientists including Dr. Vincent Pieribone have shown that catsharks – spotty, reticent fishes of deep ocean waters – have extraordinary vision that helps them distinguish their mates from other species. The research performed in collaboration with the City University of New York and the American Museum of Natural History, among others, has just been published in Nature’s Scientific Reports.

At depths of 300 to 500 meters in the ocean, where catsharks thrive, only blue light from the sun makes its way through. All other colors of the spectrum are dispersed away by the immense volume of the ocean. When blue light strikes their bodies, the molecules on the shark skin absorb it, and in return, emit light of lower energy, lending a green hue to their facade. This biophysical phenomenon is what we call bio-fluorescence.

The team of scientists, who are in fact expert divers, unveiled in 2014 for the first time that marine fishes inhabiting the ocean waters of the Caribbean and the Western Pacific exhibit fluorescence. The finding came in as a surprise since, until then, fluorescence had only been observed in the aquatic inmates of shallower reefs. The recent study is a follow-up of the 2014 report. Here, the scientists probe deeper into whether and how catsharks perceive the fluorescence on their peers.

To do this, they isolated the pigment in the shark’s eyes and examined its light-absorbing properties. Just as the human eye is equipped with pigments that can detect the red, green and blue colors of the spectrum, the shark eye is also fitted but with pigments that can only perceive blue and green. For the sharks, this comes in handy because their skin is composed of complementary pigments that emit the exact same colors when blue light from the sun bounces off of their bodies. This means that, in the secret world of the deep, the sharks cloak themselves in an outfit only perceivable to their own kin. Even the human eye is insensitive to the fluorescence. Divers need blue illumination from an external light source and yellow barrier filters to be able to see the shark’s greenish hue.

What’s more, the team also established that catshark fluorescence elevates the contrast at the patches on their skin so much that they “stand out like a sore thumb” among themselves. The dark patches are areas of intense blue fluorescence while the paler tone on the rest of the body glows green in front of their eyes.

The other authors in the study are David Gruber, Ellis Loew, Dimitri Deheyn, Derya Akkaynak, Jean Gaffney, Leo Smith, Matthew DAVIS, Jennifer Stern and John Sparks.

Contact information: Dr. Vincent Pieribone, The John B. Pierce Laboratory, New Haven, CT.  E-mail: