Night-Time Net Tows

Red indicates the reach of each frequency, for 18, 38 and 70 kHz this is
the seafloor. Higher frequencies don’t penetrate as far so show a “false bottom”
much shallower. The trace indicated by the black arrow is another false bottom.

There is a migration of “prey” species like small fish and zooplankton to shallower waters after dark, which are then followed by larger, predatory species. It’s a phenomenon that can be seen using the echo sounder onboard R/V Sally Ride called a Fish Finder that sends out pings at five different frequencies. The plots of sound return data (shown here) are used to infer the density of animal populations of various sizes. From left to right, the frequency increases: 18, 38, 70, 120 and 200 kHz. This screenshot was taken just as it was getting dark, so the blue scatters in each plot are noticeably moving shallower, indicating the migration of animals towards the surface.

In order to “ground-truth” the data, net tows are performed and samples collected. The density of animals found at a certain depth of water when the net was towed for a known amount of time is matched up to the plots from the echo sounder. When it’s time to sort and identify the samples, people tend to congregate in the wet lab to see the trays of fish, invertebrates, jellies, and various other interesting, colorful, and often strange critters that were found. Hover over photos in the gallery below for more information about each animal, all collected in net tows on this trip! 

Thanks to Dr. Jack Butler, a postdoc in the Širović lab at SIO for most of the pictures, and to Eadoh Reshef of the Baumann-Pickering lab for species identifications.

SIO Acoustic Ecology Lab

Simone and Jenny recover a hydrophone,
which will be cleaned off, tested, and redeployed.

Sometimes when R/V Sally Ride leaves port in San Diego there’s a long transit to the first station and the science party gets some downtime (the crew is always working). Not so on this trip – within 3 hours the fantail was crawling with scientists ready to deploy a mooring in the San Diego Trough. Within 24 hours, two moorings had been deployed and another recovered. Each string of instruments is anchored to the seafloor with an old train wheel. Just above that is a release mechanism that communicates with a deck box that looks like a briefcase but opens into a display and keypad like something out of a spy movie. A signal is sent out using a transducer lowered over the side of the ship, and everything above the anchor is detached. Within a matter of minutes, the gear is all at the surface and can be brought onboard using the ship’s A-frame. 

Dr. Simone Baumann-Pickering is Chief Scientist onboard R/V Sally Ride this week. She, along with Dr. Ana Širović and students and technicians from their labs, use sound traveling through the ocean to study animal populations off the coast of Southern California. They use devices that collect data from both passive and active acoustic recordings to learn about everything from krill to whales. Passive acoustics uses hydrophones strapped onto lines throughout the water column that record sound, whether that’s dolphin whistles or ship traffic. Active acoustic studies use instruments that send out a ping of noise and records the time and angle of return. In this case, 70 and 200 kHz signals are sent out, which provides data on the density of prey species such as krill and small fish. Both kinds of instruments can be attached to the same line of rope that is anchored to the bottom of the ocean, held upright with the use of floats.

The HARP is recovered using the ship’s A-frame.

In addition to the moorings that were deployed, a HARP (high-frequency acoustic recording package) was released from its anchor and recovered. It was originally deployed a year ago, but the batteries only last about 10 months. The data was downloaded, and all-new equipment was loaded up and deployed at the same site. The HARP includes only one hydrophone that floats a few meters above the seafloor. Dr. Širović’s lab will use this data to track ambient noise from nearby shipping lanes over time. 

Nets will are used to collect biological samples in order to check the inferences made using sound recordings. More on that in a separate post.

Seafloor Images from ROV Trident

SIO technicians took ROV Trident to the seafloor multiple times during the week-long cruise on R/V Sally Ride. Above are some images of animals on the seafloor. For scale, the red lasers are set 15cm (6 inches) apart. There were no biology groups onboard so animals weren’t the focus, but it’s always fun to see them in their natural environment. The ROV is controlled from a modified container van on the back deck, but a connection was also run to the big screen in the lab. Crew members and scientists alike often crowded around the screen to follow along. Check back for more pictures as we continue to dive!

Animal IDs thank to Scripps graduate student Natalya Gallo.

Overnight Ops: CTD Yo-Yos

Chart of the work area along the contours of the La Jolla Canyon. Deep station marked with a
triangle on the left, intermediate with cursor in center, and ship icon on shallow station.

There’s a lot of different groups of Scripps scientists onboard R/V Sally Ride this week, all vying to get their science objectives done. One of the groups has been here before. Back in December, grad student Maddie Hamann was chief scientist of a three day cruise recovering moorings and doing CTD surveys to study internal tides around the La Jolla Canyon. Click here to check out the blog post with more details. 

Graduate students Susheel and Maddie monitor the CTD casts
from the main lab.

Maddie and other members of Dr. Matthew Alford’s lab are back and have run two nights worth of CTD yo-yos, 12.5 hour operations where the CTD and other sensors on the frame are lowered to within a few meters of the seafloor, then brought back to a few meters below the surface, over and over again. The first night was a deep station, about 20 nautical miles offshore in 1,000 meters of water. Twenty-two round trips were made with the CTD. The second night was an intermediate station, this time 10nm out, with 29 roundtrips in 700 meters of water. 

The multibeam sonars were left running while on station and the CTD rosette itself showed up on the water column view. On the screenshot below, picture the ship at the top of the triangle, with the grayscale underneath mapping the intensity of the return signal from pings sent out. The red line approximates the seafloor. The cone directly under the ship is the most clear, with the wedges to either side being slightly skewed due to the angle. And right in the middle of the screen is the CTD package, glowing like a UFO. 

Screenshot of the multibeam water column view. x-axis is meters to port and starboard of the ship’s keel; y-axis is depth in meters.
The CTD package shows up as a bright spot at around 680 meters depth, right in the middle of the screen.
The CTD is deployed over the starboard side of R/V Sally Ride.

There’s not much to do but watch the data plot for 12.5 hours each night, so the unexpected ability to track the CTD’s progress on the multibeam screen added a bit of intrigue to an otherwise dull experience. Both the scientists watching screens in the lab and the crew running the winch work in shifts, so that no one gets sleepy or bored. The Alford lab has gained two nights worth of data collected from the CTD and ADCP on the rosette frame, along with multibeam maps, which they will use to understand how the shape of La Jolla Canyon affects internal waves bringing nutrient-rich water into the cove. 

Overnight Ops: Mapping a Fault

A map of offshore faults in the Southern California Bight.
Figure from the Bulletin of the Seismological Society of America.

For three nights on this research cruise aboard R/V Sally Ride, John DeSanto, a graduate student in Dr. David Sandwell’s lab at Scripps, used the ship’s multibeam to map the seafloor. His target was an area of the San Diego Trough fault, which runs offshore from the Mexican border to Catalina Island. The multibeam, as you may remember from a previous post, sends out acoustic pings and uses the response time and angle to create a detailed map of the seafloor. John provided waypoints to the bridge, used by the mate on watch to drive the ship at a speed of 5 knots in transects over the area around the fault. 

John at his station in the main lab.

The below picture is a screenshot from one of the multibeam systems, which John and the computer tech Daniel monitored during the survey each night. The first night had some rough weather, which can lead to rough data. The software is integrated with a motion reference unit onboard to compensate for the pitch and roll of the ship. And though the hull of Sally Ride was specifically designed to minimize bubbles forming around the transducers mounted to it, the latest storm, with 20 knot winds and waves up to 12 feet, still left gaps in the data. Night two was much calmer, and the ship began the transects after recovering the ROV. This time, just as we approached the crosshairs of the grid, of where the fault line is most prominent, a slow-moving tanker moved into our path. Lining up for the Santa Barbara Channel, one of the busiest shipping lanes on the planet, it had the right of way. So R/V Sally Ride deviated from its path, crossing west of the intended area (red arrow below). The final night of the survey, however, was uninterrupted, and provided great detail of the fault as it slashes through a seamount.

Multibeam data overlapped from the three nights of surveys. The red area is a seamount bisected by the fault (black arrow). Ship track lines are in yellow, including the diversion made to avoid ship traffic (red arrow). Artifacts of “bad” data (purple arrows) can be removed in processing. Depth scale is 650 meters (in red) to 1100 meters (in blue) below sea level.

Multi-beam data from SIO ships, and others in the academic fleet, are part of the public domain. Google Earth incorporates these detailed maps into their database. Try zooming in on certain sections of the ocean, and you’ll see swaths where the data is noticeably better than others. Those are cruise tracks where multibeam data was recorded, which provides resolution on the scale of ~100 meters while the rest of the ocean has been mapped using satellite altimetry (also a result of the Sandwell lab at Scripps), which has more like 500 meter resolution. It’s a fun exercise for those of us who work at sea to zoom in on detailed tracks we know we were part of. SIO Games put together a ship track visualization so you can see where Scripps ships have explored over the past 60+ years, check it out here and try matching it up with the detailed areas on Google Earth. R/V Sally Ride runs her multibeam systems almost all the time, so we’re adding to the dataset even when it’s not the main science focus onboard. Something on the order of 10% of the world’s oceans have been mapped in this fine detail, so there’s a lot left to cover. 

This Google Earth screenshot, with areas of higher resolution populated in part by SIO data, matches up to a research cruise (right) on the R/V Roger Revelle in the Southern Pacific Ocean. Ship track by SIO Games site

ROV Trident

For the next week, Scripps’ remotely-operated vehicle (ROV) will be aboard Sally Ride. Named Trident after UC San Diego’s mascot, it’s rated to a depth of 2,000 meters. Technicians from SIO plan to deploy the ROV each day using a small crane bolted to the port side of the ship. The control center is in a converted shipping container also bolted to the back deck of Sally Ride. From there, with the help of computer software and multiple cameras, techs use joysticks to control the ROV’s movements. Trident carries multiple oceanographic sensors including a CTD (conductivity, temperature, depth).

Check back here and on social media for more pictures and updates!

Multi-Corer Trials

As part of this science verification cruise, groups from Scripps, WHOI, Oregon State, Sacramento State, URI, CSU Bakersfield, and the USGS are testing out various coring devices using R/V Sally Ride. This requires a very specific setup on the fantail, with two small cranes bolted down for fine-tune positioning of the heavy coring equipment. Also on deck are two container vans, one housing a mobile laboratory for analysis while the other is basically an oversized toolbox. 

The main column of the multi-corer includes
weights (top), the tripping mechanism (disc at middle),
and a frame for the eight numbered sample tubes.

The cylinder that collects gravity and piston cores is staged along the aft portion of the starboard rail, with the ship’s crane used to move it to the fantail for launching. This requires moving the A-frame forward out of the way, an ability unique to newer research vessels. Once the sequence was established, a total of twelve piston and gravity cores were successfully deployed

The multi-corer deployment is logistically more straightforward, but there are still many factors that can cause it to return empty-handed. The center column is connected to the trawl wire, which is run through a block connected to the A-frame. When the package lands on the seafloor, the wire goes slack, lowering the weights which in turn push the open core tubes into the sediment. When the wire is hauled back in, the line goes taut again, which triggers the caps on top of the tubes to shut, creating suction and securing the samples. For good measure, a cover snaps into place across the bottom as soon as the tubes are above the seafloor. 

 There’s netting around the frame to keep the wire from getting wrapped around any instrumentation when it’s slack while on the seafloor. The wood at the bottom of the frame keeps the feet from settling into the sediment too far, which could make it harder to recover and risks the samples penetrating past the surface of the seafloor. 

Portrait of a hopeful scientist. USGS researcher Jason waits
to see if the tubes captured samples.

The first deployment of the multi-corer from R/V Sally Ride did not bring back any samples. Neither did the second, or the third. In between each, adjustments were made. Springs on sample tubes, weights on the frame, speed of the wire going down, payout of wire once on the seafloor, time spent sitting on the seafloor before hauling back, which person was giving directions over the radio – there’s a lot of factors. And there’s also environmental conditions, such as how choppy the sea surface is, how much the ship heaves, or whether there’s sub-surface currents.

On the fourth try, two of the eight tubes had samples in them. More adjustments. And then, on the fifth recovery, success! All eight sample tubes had both sediment and water in them, which tells the scientists that these are indeed seafloor surface samples, along with the water just above. The sixth deployment was also a success, garnering eight more samples from a different site. 

The sample tubes are carefully removed from the frame and split amongst various groups onboard. Some researchers will study the sediment, others the water. Groups from Sac State and the USGS remove most of the water, and preserve the sediment for analysis and archiving. The data will be matched up with piston and trigger core data taken at the same site to build a continuous record of seafloor sedimentation. Dr. Dennis Graham from the University of Rhode Island gets two of the samples, and will study the hydrographic properties. His tubes have a series of holes pre-drilled into them, plugged by electrical tape during the cast, which he then uses to syringe samples through. Nutrient, alkalinity, and other analyses will be run back in the lab. 

Portrait of a happy scientist. Multi-corer samples are removed from the frame (left), extruded and preserved onboard (middle) by the Sac State and USGS groups, with filtered water samples taken for analysis at URI (right).

The purpose of the science verification cruises on Sally Ride is to ensure that the ship is ready for full science operations. This has been a successful trip, involving scientists at the top of their fields working together to put the ship through its paces, and get samples to take home as a bonus.

Logging Core Samples

Gus, Amy, and Liane cut the core sample into smaller sections (left), which are then processed by Emily (right) in the MST (multi-sensor track) van.

The core samples taken so far onboard R/V Sally Ride have utilized either a 20 or 30 foot long cylinder with PVC pipe inside. Ideally, the entirety of the pipe is filled, but the amount of sediment actually recovered can vary. For example, if a layer underneath the surface of the seafloor is harder clay, the pipe may get stopped short. Once back onboard, the samples are stored in the PVC pipe, and cut into smaller sections in order to be processed by the core logger. Inside a converted container van with a painting of the OSU beaver on it, a non-destructive suite of tests are run with various instrumentation. SIO grad student Emily, from Dr. Neal Driscoll’s lab, oversees the measurements.

Data plots generated by the core logger. The piston core (blue)
and trigger core (red) were taken on the same deployment.

P-wave velocity data is used to determine grain size, gamma density measures water content and porosity, and magnetic susceptibility helps to match up different samples taken in the same area. This includes traces from the deeper piston core (labelled JPC in the chart), mid-level trigger core (TC), and surface multi-cores (not yet part of the data set).
In this example, the magnetic susceptibility trace (far right) can be used to determine that the piston core (blue trace) slightly overshot its target, sinking below the surface. The zig-zag at around 120 centimeters matches one in the trigger core (red) at closer to 150cm.

The trigger core (left) is rigged to hit the
seafloor first, releasing the piston core (right).
Photo from OSU CEOAS.

Having the piston core and trigger core overlap helps determine that the piston core sample likely starts at closer to 20cm than 0cm, and the trace should be shifted down. 

Back on shore, the samples will be split amongst the multiple institutions onboard. At SIO and the USGS, they will be cut in half length-wise so that one half can be analyzed while the rest is archived for future use. Until then, they are stored in a walk-in climate-controlled room just off the main lab. We’re collecting as many cores as possible during the week, while also learning the procedures that optimize time and sample quality – all part of the plan on this science verification cruise. 

Photos from the Multi-Corer

One of the many instruments onboard the multi-corer frame is a 24-megapixel camera that take flash photographs every 10 seconds. The camera belongs to the NSF-funded MISO (Multidisciplinary Instrumentation in Support of Oceanography) facility at WHOI, and is designed to visually document the area of the seafloor where core samples are taken. An added bonus of taking pictures during the descent and ascent through the water column is that sometimes it captures critters. The slideshow above contains photographs taken by this camera during the first test of the 8-place multi-corer, shown below. 

The multi-corer is launched over the stern. The two strobe
lights for the camera are visible on the lower rung.

The photo of the seafloor will be used to supplement information determined from the core samples themselves. As you can see, the first shot gives a nice view of the type of sediment on the surface of the seafloor. In the second shot, it’s been disturbed by the movement of the multi-corer. Subsequent shots (not included) are mostly dark and murky, as the sediment is kicked up by the landing of the package. A few minutes later, once the multi-corer begins to rise and is rinsed off, the pictures clear up again.

In this instance, no viable core samples were recovered. There are many factors that could have caused cores to either not be taken properly, or to fall out on the ascent. That’s why R/V Sally Ride is conducting these science verification cruises, to work out the kinks. Weights have been added, problem triggers were adjusted, and measurements have been double-checked. The multi-corer will be reset and sent back out, until we get it right! Stay tuned for further updates.

Thanks to Dr. Amanda Netburn (NOAA), Natalya Gallo (SIO), and Dr. Pete Davison (SIO) for identifying the critters we caught on camera. Click on each to see a bigger photo.

– Seafloor, Scyphozoan jellyfish and longspine thornyhead 
– Seafloor, being disturbed by the multi-corer movement, with the same thornyhead 
– Hydromedusa (we collected one of this species on the Jason cruise- was surprisingly tiny and transparent)
– Sergestid shrimp
– Siphonophore
– Abandoned larvacean house (tadpole-like larvaceans filter-feed through a large mucous net that is referred to as a “house”- these clog easily, and are abandoned by the animal multiple times a day)
– Schyphozoan jellyfish (this order contains what most people think of when they think of a jellyfish) 
– fish (ID pending)
– Mysid shrimp
–  Narcomedusa (lower left) and Siphonophore (upper right)

Choosing a Coring Site

Coring operations are taking place mostly during daylight hours, with the ship running overnight survey transits. An echo sounder mounted to the bottom of the ship sends a 3.5kHz ping and records the return, producing sub-bottom profiles. These images typically show the types of sediments 20-50 meters below the ocean floor, and can capture up to 100 meters under certain conditions. The ping is a loud chirping noise easily heard from the lower levels of the ship, and the time between pings decreases in shallow water, when the reflected noise returns quicker.

Sub-bottom profile produced by the ship’s echo sounder.

The plot above shows the profile produced by that ping data. The seafloor is represented by the top layer, and any lines or shading below shows sediment layers underneath. On the far left, the line is darker, indicating that the seafloor is sandy, so the signal reflects back strongly. Further along, as it fades and stratifies, the seafloor is muddy. Some of the signal reflects back, and some travels farther into the sediment and reflects back from other layers. In the middle, a hill rises up, bringing the seafloor shallower. Then it drops off into a channel. As the signal flattens out on the far right, the ship is slowing down and then stopping on station, giving a flat line as we hold position.

OSU Research Professor Mitch and USGS scientist
Jason use maps and data plots to pinpoint
locations for sampling.

On this cruise, we’re collecting core samples in channels and along fault lines, but also in areas just outside of those features, in order to compare and contrast the sediment layers. The data from overnight surveys is reviewed each morning, and a determination is made about where to position the ship in order to collect sediment samples. 

I’ve been sailing on research vessels for years and never really knew what this readout showed or how it was useful. It reminded me of ink wash paintings, with just the hint of trees and pagodas on the hilltops. Or, if I was hungry, it looked like a layered dessert. Thanks to this science verification cruise and conversations with Chief Scientist Mitch Lyle and others, it’s clear how valuable this grey-scale map of the seafloor is for coring operations by sediment scientists.

Chinese ink wash painting by Zhu Yamei and Oreo dessert by