May 20, 2006
Robotic DNA lab helps scientists study microscopic marine life on Earth and other planets
After developing a robotic undersea DNA lab, what do you do for an encore? You might be tempted to improve it, or to build copies for other scientists to use. Perhaps you would design a version that could work in deep water, so you could collect data on bacteria at undersea hydrothermal vents. If you were really thinking big, you might consider modifying your DNA lab so that it could be sent into outer space, to look for life on other planets. MBARI molecular biologist Chris Scholin is working with a team of scientists and engineers to pursue all of these goals, and more, over the next three years. On March 16, the team achieved a major milestone, deploying a new, improved version of their robotic DNA lab for the first time in Monterey Bay.
Scholin’s robotic laboratory is called the Environmental Sample Processor, otherwise known as the ESP. As its name implies, the ESP can automatically collect water samples and then process these samples in a variety of ways, depending on how it is configured and programmed.
Because it is modular and programmable, the ESP could theoretically be used to perform a wide variety of different types of chemical and biological analyses. To date, however, it has been used primarily to analyze the genetic material of marine microorganisms. This allows scientists on shore to find out whether certain types of microorganisms are present at a particular place and time. In work on both the Pacific and Atlantic coasts of the United States, the ESP has been used to detect marine bacteria, marine algae (including those that cause toxic “red tides”), and the microscopic young of mussels and barnacles.
How the ESP works
Samples within the ESP are stored and processed using small metal or plastic disks known as “pucks” (see photo below). In the middle of each puck is a special membrane that is used to filter, process, or archive a water sample. A single sample may be passed through as many as three different pucks.
The ESP, in its current configuration, contains two robotic stages that handle water samples in assembly-line fashion. The first stage collects water samples and filters these samples to retain only organisms of a specific size. In some cases, the organisms on the filter may be exposed to preservatives and archived for later analysis on shore. More often, the organisms are filtered and then exposed to chemicals that break down their cell walls and release their genetic material into solution. At this point, the sample is passed on to ESP’s second stage.
Within the second stage of the ESP, a sample is passed over a puck that contains an array of tiny printed dots. Instead of being printed with ink, these dots are printed using special mixtures of chemicals and fragments of genetic material known as DNA “probes.” As shown in the figure below, different types of DNA probes are located in different parts of the array. After a sample has been processed, some or all of these DNA probes begin to glow, depending on what types of organisms are present in the sample. Thus, the locations of the glowing dots on the filter indicate the types of microorganisms that have been detected.
After processing a sample, the ESP takes a close-up photograph of the glowing dots in the DNA probe array. This photograph is then relayed to shore using a radio transmitter at the sea surface. This allows Scholin and other scientists to find out what types of microorganisms are drifting around in Monterey Bay, without ever leaving their offices.
The next generation: refining and cloning the ESP
The first-generation ESP proved that such a complex robotic device could be made to work in the demanding environment of the open ocean. In 2002, Scholin and his team received funds from the National Science Foundation and the National Oceanographic Partnership Program (NOPP) to build a new, improved version. After several years of work and many engineering challenges, the team came up with a device that is smaller, simpler, more durable, less power-hungry, and more user-friendly. On March 16, 2006, they deployed this second-generation ESP for its first field test in Monterey Bay.
Not surprisingly, many other scientists have wanted to used the ESP for their own research projects. After the second-generation ESP has proven itself in the field, Scholin’s team will be building four copies of the device. These instruments will be loaned to scientists at MBARI and other oceanographic research institutions.
Some scientists want to use the ESP to study and help predict harmful algal blooms. Other scientists hope to learn about the larval forms of commercial shellfish, which often drift at sea for weeks or months before settling onto their final homes on sediment or rock. Still other scientists hope to discover ecological relationships among the thousands of different microbes that live in each teaspoon of seawater.
Making the ESP into a “plug-and-play” system
“Mass producing” this complex robotic lab might seem like a daunting task, but Scholin isn’t stopping there. He recently received funding from the Moore Foundation to take the ESP to the next level. This involves making the ESP into a “plug-and-play” sample-processing laboratory, which would allow other scientists to add their own analytical modules. For example, one proposed module would include a DNA microarray, which can detect thousands of gene sequences within a single sample, instead of the few dozen gene sequences that can be detected using in the current device.
Working with John Zehr at the University of California at Santa Cruz, Scholin hopes to develop additional ESP modules that adapt cutting-edge analytical methods from the biotechnology or biomedical industries to study marine microorganisms. These instruments could lead to breakthroughs in our understanding of biogeochemical processes in the ocean, many of which are controlled by complex communities of microbes.
Ultimately, Scholin would like to create a version of the ESP with built-in “intelligence” that can make decisions to route samples through a variety of different analytical modules depending on the content of the sample, just as a human molecular biologist would do in the laboratory.
Processing samples in the deep sea
Having seen how the ESP can detect and identify marine microorganisms in surface waters, marine biologists are eager to find out what it can do in the little-explored realms of the deep sea. With funding from the Keck Foundation, Scholin and his coworkers have spent several years designing a system that can work in waters as deep as 1,000 meters (about two thirds of a mile). They found that adapting the ESP to work deep beneath the ocean surface involved more than just mounting the instrument in a thick pressure housing. The biggest challenge was finding a way to collect water samples under the immense pressure of the deep sea, and then decompressing these samples so that they could be processed at normal atmospheric pressure inside the ESP’s robotic laboratory.
Engineers and scientists in Scholin’s lab are currently in the final stages of designing a water-sample decompression system that can work at 1,000 meters depth. During 2006, they plan to add this decompression system to one of the second generation ESP clones. The resulting “Deep ESP” would then be placed on the sea bottom and hooked up to a cable carrying power and data from shore as part of the MARS unmanned undersea observatory currently being constructed in Monterey Bay. Other MBARI researchers are hoping to use MBARI’s remotely operated vehicles to carry the Deep ESP to study communities of microorganisms around cold seeps or whale falls in Monterey Bay.
Detecting life on other planets
The ESP has shown so much promise in detecting life in the oceans that NASA is interested in finding out if it can be used to look for life in outer space. Searching for extraterrestrial life is one of NASA’s main research goals for the 21st century. In order to move toward this goal, NASA created the ASTEP program to investigate new instruments that can automatically detect and monitor biological activity in extreme environments on Earth, from the Atacama desert to the deep sea.
Deep-sea hydrothermal vents certainly qualify as one of Earth’s most extreme environments. In such areas, superheated (over 350 degrees centigrade), corrosive, mineral-laden fluids mix with near-freezing seawater at pressures hundreds of times higher than on the Earth’s surface. Yet life not only survives, but thrives in these environments. Similar conditions may also exist on other bodies within our solar system. For example, the surface of Europa (one of Jupiter’s satellites), appears to be entirely submerged beneath an ice-covered sea. Some scientists have speculated that life could have evolved around active volcanoes or hydrothermal vents on the floor of this sea.
Scholin recently received a $3 million grant from NASA to develop a version of the Deep ESP and install it at a hydrothermal vent on the Juan de Fuca ridge off the coast of Washington State. The ESP will monitor microbes in chemical-rich fluids flowing out of the seafloor. Scholin and others are particularly interested in finding out how populations of these microbes change over time. During the ESP deployment, other instruments near the vents would monitor earthquake activity and rates of fluid flow through seafloor rocks and sediments. The overall goal would be to better understand the relationships between the biological and geological processes at this site. The ESP might also help determine if and how these sea-bottom microorganisms spread from one vent to another through surrounding ocean waters.
Scholin will be cooperating in this grant with researchers from the California Institute of Technology (Caltech), Jet Propulsion Laboratory (JPL), and the Lawrence Livermore National Laboratories (LLNL). The Caltech scientists will help develop genetic probes specific to cold seeps. JPL engineers will consider how elements of the ESP might be useful in looking for life on other planets. For example, the ESP could be combined with a module that would allow it to collect air, dust or ice samples and mix these into a liquid that could be analyzed by the ESP.
Researchers at LLNL will be developing additional modules that could be added to the ESP to expand its capacities. For example, one proposed module would allow the ESP to detect not just a few individual genes but various combinations of hundreds of genes. This would allow scientists to study and perhaps identify organisms that perform specific biological processes, such as obtaining nutrition from methane or other chemicals seeping out of the seafloor.
The ESP has shown great promise as a tool for learning about life in Earth’s oceans. If mass produced, the ESP could also prove useful in industrial settings and even monitoring microbes in sewage treatment plants. As Scholin’s latest grant from NASA proves, when it comes to the ESP’s research applications, the sky is the limit.
For additional information or images relating to this article, please contact: Kim Fulton-Bennett