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!

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

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.

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.

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.