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What are DHABs?

Deep Hypersaline Anoxic Basins, or DHABs, are some of the most extreme environments on Earth—and yet, life thrives there. DHABs are also very new to science. Learn more about DHABs »

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from “mikro,” meaning small, and “skopein,” meaning to behold or look at

SID’s first splash

November 28, 2011 (posted November 29, 2011)
by Cherie Winner

Whenever scientists have ventured into unknown territory, whether in outer space, microscopic realms, or the bottom of the sea, they have needed new tools and techniques to reveal what’s there.

On Sunday and Monday of this week, a brand new instrument named the SID-ISMS (Submersible Incubation Device-In Situ Microbial Sampler) made its maiden voyage to the bottom of the sea, where it sought evidence of life in an ultra-salty, no-oxygen environment called a Deep Hypersaline Anoxic Basin (DHAB). [ Learn more in Deeper Discovery ]

The SID-ISMS was lowered on a cable from the research vessel Atlantis to Urania Basin, a DHAB in the eastern Mediterranean Sea. Its mission was to collect protists—eukaryotic microbes—and to process them in several different ways so different experiments could be done with them when they were brought back to the surface.

About 10 years ago, bacteria were discovered living in several Mediterranean DHABs—an exciting finding, because the basins are among the most extreme environments on Earth. In 2009 scientists discovered the first indications of protists living in the DHABs.

But DHAB protists are hard to study. They are so well adapted to their unusual habitat that many of them die or simply break up if they are brought to the surface in an ordinary sampling bottle. So a few years ago WHOI biologists Craig Taylor and Ginny Edgcomb, the chief scientist on this cruise, started thinking about how to answer the questions they had about the protists that live in DHABs. They needed an instrument that would collect organisms and preserve them right in their native habitat, or “in situ.”

That’s exactly what the SID-ISMS does. Taylor and Edgcomb, who designed and built the SID-ISMS with engineers at McLane Engineering in Falmouth, Mass., call this instrument a “robotic micro-laboratory.” It uses a pump to pull water through 48 sample tubes that can be equipped in different ways to accomplish different research goals.

On its first dive, most of the tubes were fitted with filter units that trapped microbes on a thin filter as the water passed through it. A preservative solution called “RNALater” was then added to the filters to preserve the RNA in the cells. RNA can tell scientists a lot about what kinds of cells were there and what they were doing, but it degrades very quickly once the cells die unless it is preserved. Other tubes were fitted with a RAS bag, a silver metallized bag in which cells can be preserved in formaldehyde so their anatomy can be studied later.

The SID-ISMS looked beautiful on the deck as it was being readied to be deployed in the ocean, but the scientists were nervous. They had never tested it in deep water. Its construction had run behind schedule, and they just had time for quick tests in the lab in Woods Hole before crating it up and sending it to Greece for the cruise. To go from just-made to the bottom of the sea, with no tests in between to work out any “bugs,” was more than a little scary.

But on Sunday, with R/V Atlantis holding position over the DHAB called the Urania Basin, the SID-ISMS made its very first dive. Taylor snapped photographs as it splashed into the deep blue water. Ocean swells pushed it up and it dropped back down, its fragile-looking tubes gleaming in the sun. Then it sank out of sight.

The cable continued to play out for the next hour and a half, and then, down in the ship’s computer lab, the signal from SID’s turbidity sensor jumped. It had entered the halocline, the transition zone between normally salty seawater and the ultra-salty DHAB. Taylor and Edgcomb slowed its descent so the instrument inched its way gently into the halocline. Then they set the brake. The SID-ISMS stayed right there for the next 16 hours, taking in water and pumping it to the various sample tubes. It responded perfectly to commands transmitted from Taylor and others on the team aboard the ship.

The SID-ISMS worked through the night, attended only by pairs of scientists keeping their eyes on its activities. At noon Monday it finished its last procedure, and the winch started pulling it up. Atlantis technicians brought it safely on board and secured it to the deck. Then came a flurry of activity, as hands moved in from every direction to remove the sample tubes, which were taken to the lab. The instrument’s filters and bags were removed and new ones installed. Within two hours, the SID-ISMS was completely re-assembled and ready to go again. The second launch went as smoothly as the first, and again, the instrument worked through the night.

After the second launch, the scientists began analyzing what the SID-ISMS had brought them from its first dive. By dinnertime, they had some not-so-good news. WHOI postdoc Bill Orsi found that in about half of the chambers, much of the RNALater that was added went through the filters rather than staying on top of them, where the cells were. It wasn’t supposed to do that; it hadn’t done that in tests on land.

“But you never can tell what’s going to happen at 3,500 meters,” he said. He had already figured out a way to keep more of the preservative in contact with the cells. He’ll try the new procedure on Dive 3, which is scheduled to begin today. For Dive 2, the scientists solved the problem by loading an injector to inject  extra RNALater onto each filter.

Then, about an hour after dinner, postdoc Maria Pachiadaki from Technische Universität Kaiserslautern came into the lab with exciting news. She had removed the preserved samples from her RAS bags and treated them with DAPI, a blue fluorescent dye that binds to DNA. Through a fluorescence microscope she could see many, many cells, both bacteria and protists. The SID-ISMS had brought intact cells back from the deep. Maria now has the information she needs to prepare her experiment on protists that graze on bacteria, which will run during the instrument’s third dive.

All in all, it was a great first day on the job for the SID-ISMS.

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