2019 Annual Report
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Photo by Steve Haddock

Bioluminescence: Behavior, biochemistry, and genomics

One of the dominant traits of life in the deep sea is the ability to produce light, called bioluminescence. Thanks to MBARI’s decades of remotely operated vehicle (ROV) observations, scientists have been able to map the vertical distributions of organisms and then cross-reference those with a database of bioluminescent capabilities. The resulting data show more than three-quarters of the animals seen drifting in the water column can create their own light!

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This figure shows the abundance of non-luminous and luminous organisms seen on midwater ROV dives. There are about three times as many bioluminescent species seen, and that ratio is nearly constant from the surface to 4,000 meters (13,123 feet) depth.

The surprising prevalence of bioluminescence has raised an array of challenging questions for scientists. What function does bioluminescence serve across the diversity of all organisms with light-producing mechanisms? What unique chemicals do organisms use to make light? What are the genetic pathways involved in bioluminescence capabilities?

Recent technological advances have allowed MBARI Scientist Steven Haddock and his Zooplankton Biodiversity Group to make breakthroughs in understanding the behavior, biochemistry, and genomics of bioluminescence.

Bioluminescent behaviors

A sea cucumber radiates a frenzy of bioluminescent light captured by a special low-light camera mounted on an ROV.

Observing the natural behaviors of deep-sea animals is extremely challenging. We rely on chance encounters with our ROVs, blazing spotlights that can scare creatures away, and cameras that, while impressive, are nowhere near as sensitive as the human eye. Even if we could patrol with the lights off, our submersible-mounted cameras could not pick up the glows and flashes that occur around us. However, recent advances in technology have led to the development of cameras that can film in full-color, ultra-high-definition (4K) resolution, and with sufficient sensitivity to record natural bioluminescence. MBARI engineers and ROV pilots mounted such a camera on an ROV, resulting in video footage of behaviors never recorded before in the wild. As the team gathers more of this unique footage, they will begin to develop a catalog of behaviors, such as luring prey, emitting distracting sparkles to elude predators, and even communication between members of the same species.

Biochemical breakthroughs

Examples of biochemical revelations include finding luminescence in organisms that weren’t previously known to be bioluminescent (for example, chaetognaths or doliolids) and discovering new chemical reactions that animals use to emit light. While many unrelated animals use the same chemical to produce blue light (most commonly, a compound called coelenterazine), the worm Tomopteris uses a previously unknown chemical to make its unique yellow light. Using an ROV to collect the animals, Haddock’s team can purify relatively large quantities of the worms’ luminous fluids. Using sophisticated instruments, they can then identify the structure of the fluid's underlying compounds. In Tomopteris, a chemical called aloe-emodin was found to provide bright yellow fluorescence and was almost certainly involved in the emission. Researchers are still working on isolating all the components needed to make yellow light. Such discoveries broaden the set of tools that researchers can use for biomedical research because the same chemicals that make light in natural cells can also be used for laboratory experiments.

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Although most animals in the sea make blue bioluminescent light, the worm Tomopteris is one of the few that makes yellow light. The chemical that gives it this yellow color was discovered by MBARI researchers. Photo by Steve Haddock.

Genetic insights

Underlying an organism’s ability to produce light are the genes used to manufacture all the required components. Researchers can study these genes most effectively by sequencing the genomes or transcriptomes of bioluminescent animals from the deep sea. A transcriptome is the snapshot of genes being expressed at any given time. These methods provide a complete view of an animal’s capabilities using only a small amount of tissue from a single specimen. This opens the possibility of doing in-depth, comparative studies of rare deep-sea creatures.

Vampy And Fluorescent Tentacle

The genes, proteins, and chemicals that animals use to make light have not all been discovered or characterized. The vampire squid uses the same light-emitting chemical as some jellyfish to make the bioluminescent spots on its arms (right), but the protein it uses to trigger light emission is still under investigation. Vampire squid are generally less than 30 centimeters (12 inches) long.

Haddock’s group is using genomics to learn about the bioluminescence genes of the vampire squid; the photoproteins of deep-sea radiolarians; the genetic origins of the most common light-emitting compound, coelenterazine; and the multiple evolutionary origins of bioluminescence in cnidarians (jellyfish), chaetognaths (arrow worms), and other invertebrates.

As beautiful as they may be, deep-sea videos using bright lights give a very different perspective than do low-light videos of bioluminescence and fluorescence. The natural views provide a much better idea of how the inhabitants of the deep sea actually perceive their environment and their neighbors. As our ability to “see through their eyes” improves, we will garner even more insights about how life functions in the very cold, very dark, but also very diverse, deep ocean.

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The sea pen, Umbellula, uses fluorescent proteins to shift the color of its bioluminescent light from blue to green. Here we can see the animal under normal white light and then under blue illumination which selectively excites its fluorescent proteins. Photo by Steve Haddock.

A rich history of collaboration informs management of the Monterey Bay National Marine Sanctuary

Discoveries during fundamental exploration and scientific research prove valuable for meeting federal mandates, conservation efforts, and public interests.