Editor's Note: Journalist and crew member Kathryn Eident and scientist Jeremy Jacquot are traveling on board the RV Atlantis on a monthlong voyage to sample and study nitrogen fixation in the eastern tropical Pacific Ocean, among other research projects. This is the second blog post detailing this ongoing voyage of discovery for Scientific American.com.

RV ATLANTIS MAIN DECK—The winch makes a whirring sound as it slowly winds the quarter-inch galvanized wire out of the water, through the block and onto the drum. Rigged over the side of the ship, the sturdy wire extends deep below the water's surface where it is attached to a round metal frame holding plastic bottles and various sensors.

Two scientists, outfitted in hard hats and life preservers, stand ready to steer the rosette carefully onboard. As the rosette nears the surface, they each lash guidelines to huge eyehooks and cleats on the steel deck. Nearby, Shipboard Science Support Technician (SSSG) Dave Sims reaches for his walkie-talkie: "Bridge-deck. We're almost at the surface."

It's Sims's job to make sure each piece of scientific equipment is launched and recovered safely at sea. Today's recovery is going smoothly; the mate standing watch on the bridge has been notified, scientists in the lab are on standby to take samples, and the winch operator has a steady hand on the controls.

Finally the rosette begins to appear under the sparkling water's deep blue surface. Sims uses hand signals to "talk" with the winch operator and tell the scientists when to pull a line tight or when to leave it slack. Soon the winch boom retracts and the rosette comes in for a safe landing on board the R/V Atlantis.

Once fastened securely in place, more scientists appear, ready with buckets and carboys to decant the liters of water gathered in this latest "CTD" (Conductivity, Temperature and Depth) cast. The rosette has visited various depths over the past few hours, sampling water at as many as 24 points in the water column and taking measurements ranging from the water's salinity and temperature to the amount of chlorophyll present. While in the ocean, the bottles and sensors on the rosette are remotely operated via a cable running from rosette to a shipboard computer.

As one scientist put it, a CTD cast is like getting a "road map" of a piece of ocean, and it's one of the more commonly used tools scientists use at sea.

The 274-foot Atlantis was designed to accommodate a variety of instruments aimed at gathering samples and data from the water's surface to the sea floor below. Cranes and winches make quick work of deploying nets over the side to gather whatever organisms may be present. The crane can also be used to launch moorings and deploy buoys, then recover them sometimes years later. An A-frame can handle even bigger loads like the submarine Alvin.

For scientists interested in mapping, a device called the "Seabeam" constructs a picture of the contours of the seafloor. This tool is installed into the hull of the ship and emits sound waves that bounce off solid matter—like mountains and volcanoes—thus developing a map of the seafloor.

Scientists can also make use of equipment like the Tow Cam, another remotely operated tool with the ability to take photographs underwater. Weighing nearly a ton and about the size of a refrigerator on its side, the Tow Cam can take photos of the ocean bottom and even gather rock and sediment samples while being towed at slow speeds behind the ship.

And when it's simply too deep for the Tow Cam to gather samples, scientists can also use various coring implements. For instance, the box corer is a metal box that can be inserted vertically into the ocean bottom, gathering rock and sediment as it is pushed down. Successful cores can display a cross section of the ocean bottom, and some of the deeper cores have brought back sections of rock thousands of years old.

Atlantis is also equipped with a suite of weather instruments measuring air temperature, wind speed, barometric pressure and more. These instruments are used by crew and scientists alike to, among other things, ensure the cruise track isn't headed straight for a storm!

These are just some of the tools scientists use when conducting research in the field. Often, scientists design and construct their own uniquely specialized gear, bringing a host of new challenges and discoveries. In a future post, we'll look at some of the ingenious contraptions scientists have created to ensure they get the data they want.

Image: Dave Sims, a shipboard science support technician, directs a CTD deployment on the main deck of RV Atlantis.