Bringing a Lab to seafloor - New device probes deep-sea microbial life

by Lonny Lippsett on 28 Dec 2014 If you can’t bring the ocean into the laboratory, you have no choice but to take the lab into the sea.

Marine biologists have always sought to conduct experiments to peer into the inner workings of marine ecosystems. Their holy grail is to reveal the numerous biochemical reactions performed by multitudes of marine microbes. These unseen reactions—converting inorganic chemicals into energy and biomass—jumpstart the food chain and make the whole ecosystem go.

But it’s impossible to recreate the ocean’s dynamic conditions in the laboratory. And the ocean is a tough place to bring in delicate scientific instruments and get them to survive, let along work.

That hasn’t deterred Craig Taylor, a biologist at Woods Hole Oceanographic Institution (WHOI). More than two decades ago, he began working with WHOI engineer Ken Doherty to develop an instrument they called SID—the Submersible Incubation Device. Essentially, it draws seawater and microbes into incubation chambers and measures the biochemical business going on under natural conditions.

At first, Taylor used SID to measure how photosynthetic plankton near the sea surface convert carbon dioxide into organic carbon. When it worked, other scientists wanted to up the ante, requesting modifications that would allow SID to operate under harsher conditions in other parts of the ocean. SID begat Deep-SID, and the recent MS-SID, which worked under higher pressures and preserved microbial samples in situ, allowing scientists to probe organisms living at deeper, darker depths.

In today’s version of the SID, filters collect the microbes and preserve their RNA, which is used to both identify them and to determine their functions. Stable isotopes of elements—carbon or nitrogen, for example—are injected into the incubation chambers, where they are either converted or incorporated into chemical compounds produced by the microbes. The isotopes act as labels that scientists can track to measure the types and rates of the reactions taking place in the chambers. All together, the SID provides a picture of what microbes are using which chemicals in which reactions, and how these reactions change in response to changing environmental conditions.

Heat in the deep
WHOI microbiologist Stefan Sievert learned all about SID when he came to WHOI in 2000 as a postdoctoral scholar working with Taylor. Naturally, he and Taylor wondered whether they could develop another variation of SID to work under the even more extreme conditions of deep-sea hydrothermal vents. These vents, in volcanic regions of the seafloor, spew hot fluids like geysers. The fluids are filled with chemicals that microbes convert into food that sustains lush communities of deep-sea organisms. But very little is known about the biochemical reactions used by vent microbes at the heart of this chemosynthetic-based food web.

'The best way to observe the activity that truly exists is to conduct experiments in situ,' Sievert said. He, Taylor, and Jeremy Rich of Brown University proposed and were awarded a grant by the National Science Foundation to develop a SID that could operate at vents.

WHOI engineers Fred Thwaites, Ed Hobart, Steven Faluotico and Micheil Boesel were enlisted to work on mechanical designs for the new SID’s chambers and electronics hardware and software. Having built a SID that worked under high pressure, the next engineering hurdle was to build an incubator that could keep vent fluid samples bathwater-hot at the frigid bottom of the ocean.

'You’re surrounded by endless cold water,' Taylor said. 'That inhibited people from trying, I think. People joked, ‘You’re going to have to have a nuclear power plant nearby to heat the chamber.’ '

Power supplies are always an obstacle at the seafloor. Scientists have to bring their own power down, usually in the form of batteries with limited capacity. 'My knee-jerk reaction was, ‘It’s impossible,’ ' Taylor said. But the solution turned out to be not so difficult.

The team insulated the SID’s twin incubation chambers with 4-inch-thick polypropylene, which appreciably slowed down heat loss to the environment, resulting in low enough power consumption to enable incubations at the temperatures of the emanating vent fluids or at elevated temperatures—to probe for life living in the deeper parts of the subseafloor. 'It didn’t matter if the chambers were surrounded by stagnant seawater or in a current,' Taylor said. 'It consumed 10 to 12 watts of power for each of the two chambers to maintain sample temperatures at 28°C [82°F].' So the team could add enough batteries without exceeding weight constraints.

The twin incubation chambers allow scientists to simultaneously use different isotopic tracers during a given deployment or to conduct simultaneous experiments at different temperatures, Taylor said.

Next, the team created an umbilicus with a nozzle that sucks in vent fluids. The umbilicus is insulated with viscous silicone oil to prevent heat loss as the fluid travels into the chambers. The Vent-SID was born.

A visit to Crab Spa
The entire Vent-SID measures 3.5 by 2.5 by 8 feet tall. It was designed to be deployed by wire from a ship, as close to a vent site as possible. From there, pilots operating a submersible such as Alvin or a remotely operated vehicle such as Jason could pick up and re-position Vent-SID as necessary, stick the nozzle into the flowing vent fluids, and trigger the instrument to start by using the manipulator arms. At least, theoretically, Taylor said in an interview in late October 'Individual parts have been tested to withstand pressure, but the combination of everything hasn’t been tested under pressure. Really nothing can substitute for putting it at the seafloor.'

In November 2014, Vent-SID was slated to travel aboard the research vessel Atlantis for its first sea trials. The instrument made its seafloor debut at a vent site about 600 miles south of Manzanillo, Mexico, on the East Pacific Rise, a volcanic mid-ocean ridge system. It collected and preserved samples on its filters, but something interrupted the incubation experiments. Vent-SID was brought back aboard Atlantis, where Taylor and colleagues worked out software glitches, installed new batteries, and conducted several Vent-SID tests near the surface. With time running out on the voyage, the team deployed Vent-SID on Nov. 18 for a final try. It was deployed by Alvin atop a tall pillar of basalt at a vent site called Crab Spa, a site that Sievert and colleagues have been using as a model system to study chemosynthetic processes at deep-sea vents.

For 24 hours, the scientists waited aboard Atlantis, unable to know what was happening nearly a mile and a half below. Then Alvin released weights at the bottom of the Vent-SID, and floats atop the device brought it back to the surface. When it was hauled onboard, they were thrilled to learn that the device had worked.

'It did what it was supposed to do,' Sievert said. 'We now have a new tool that we can take to other sites with different settings to measure and understand the biogeochemical underpinnings of deep-sea vents or other ecosystems that we had no way to study before. This represents a major step forward in the way we study these ecosystems. It allows us to get more realistic estimates of the overall productivity (the rate of biomass created) occurring in them, and to assess the ecosystems’ roles in cycling carbon, nitrogen, and other chemicals throughout the ocean.'