Wednesday, April 17, 2013

Staring at the Sea… Through Sound

              During our cruise we have been working in shifts around the clock to sample the biological, physical, and chemical properties of the off shore Gulf of Mexico from the surface to thousands of meters depth. The efforts required for the collection of these samples utilizing an array of oceanographic equipment are great. However, the acoustical instruments we are using require very little effort in their deployment, and continuously sample 24 hours a day, even when weather conditions are too rough for deck operations.

              In water, sound travels faster than it does though air by a factor of five and dissipates less energy than in air. Given these properties, acoustic instruments provide an excellent means for remotely sensing the underwater environment in large volumes over great distances at a high spatial resolution. For our cruise we are using active acoustics. These instruments operate by sending sound impulses, or pings, and waiting for the pulse to hit an object. When it does, the sound is scattered in multiple directions creating an echo to which the instrument’s receiver listens for. Knowing the time between a ping and an echo to return, we can determine how far away an object is with high precision.

              Acoustics typically ping sound at one or several frequencies. Low frequencies travel long distances while high frequencies travel a shorter distance as the sound is attenuated more quickly. For our application we are using a Sentinel Work Horse Acoustic Doppler Current Profiler (ADCP) with a 1200 Hz frequency, and an ASL Environmental Sciences Acoustic Water Column Profiler (AWCP) with dual frequencies, 446 Hz and 720 Hz. Organisms in the sea scatter sound differently across a spectrum of sound frequencies. By using multiple frequencies simultaneously, it is easier to determine specifically what organisms are responsible for a proportion of the total backscatter measured in an acoustical survey.

              There are two problems in resolving acoustic data. First is the “inverse problem” which is the issue of using target strength (TS), which is the sound scatter strength of an object, to calculate the number of individual objects (N) that are present from the measured scatter volume (Sv­). The second is the “forward problem”, which is the application of ground-truthing data (data from nets and optical samplers) to acoustical data to see what was actually present in the water during an acoustic survey. Data on physical parameters of the water column are equally important to determine the effect they have on sound in water.

              It is easy to see that there is no single tool that is perfect for sampling plankton. Optics and nets help verify the cause of sound scatter in the water column, while acoustics give information relative to the large scale abundances and distributions of organisms collected by optical and net sampling instruments. Despite so many difficulties inherent with acoustic instruments, the inversion of acoustic data for accurate biological estimations is regularly accomplished. Acoustics are fast becoming standard tools for surveying fish stocks, and are regularly used to map the ocean floor with incredible precision.

-Fredrick D. Marin

The Acoustic Doppler Current Profiler, 1200 Hz (top) and the Acoustic Water Column Profiler, 446 Hz & 720 Hz (bottom) mounted to a pole which is turned to point down in the water while conducting acoustic surveys. 

A plot of acoustic data collected over multiple days. The red undulation is the deep-scattering layer (DSL), which is the massive daily vertical migration of small fishes and zooplankton into the upper water column at night and back down to the deep during the day.

Tuesday, April 16, 2013

Drifting Sediment Traps

              Sediment traps are devices that scientists place in the water at different depths to collect particles falling towards the seafloor. In simplest form, they represent tubes or funnels open at the top with a collecting jar at the bottom. They usually have a baffle at the top to keep out very large objects that might clog the containers.  Scientists studying the flux of particles in the upper 500 meter of the ocean deploy these traps clamped at specific depths to a fixed cable attached to a surface drifting buoy. Analyzing the samples help scientists understand how fast and how much nutrients (C,N,P) and oil derived  carcinogens like PAHs sink from surface to deep ocean. This allow us to understand the residence time of contaminants like PAHs in the upper ocean, the amount of food reaching the benthic community at the seafloor, as well as the amount of CO2 sequestered to deep ocean via the ocean biological pump.

-Kanchan Maiti, Ph.D.

The sediment traps hang suspended from a buoy seen here being recovered after 72 hours of drifting.

Sediment traps on deck ready for sampling.  Each trap closes after a set time interval to help determine the rate of particle flux from the water column.

Monday, April 15, 2013

Shipboard Experiments

              Before sunrise every morning, water is collected in niskin bottles affixed to the CTD Rosette at two depths, the surface (approximately 10 m) and the deep chlorophyll-a maximum. Immediately following collection, two simultaneous experiments are set-up.

Collecting water from Niskin bottles

              First, 300 mL BOD bottles are filled with water to measure O2 concentrations using standard Winkler reagents. O2 concentrations measure two important microbial processes, respiration (consumption of O2) and primary production (production of O2). These processes are measured using two treatments: dark bottles (bottles covered with foil) and light bottles (no foil). In the light treatment bottles both respiration and primary production will occur. In the dark bottles primary production will not occur because it is a light dependent process. Thus, the dark treatment bottles are used to determine the respiration rates. Primary production rates are determined as the difference between the light and dark bottles.

              Secondly, an experiment is set up to measure microzooplankton grazing rates. Two liter Nalgene bottles are filled with dilutions of 20, 45, and 100% whole seawater to create a gradient of zooplankton grazer abundance. The change in phytoplankton abundance is determined by measuring initial and final concentrations of chlorophyll-a as well as direct counts in a FlowCam (an imaging microscope).

               The BOD and grazing bottles are incubated in a flow through seawater tank to simulate in situ temperature. As shown in the picture, one half the incubator containing bottles from the deep chl-a maximum is covered with a layer of neutral density film to simulate in situ light conditions. After 12 hours, around sunset, the bottles are removed from the incubator and final conditions are measured.

- Ashley Riggs/Danielle Edwards

Shipboard Incubator

In Situ Ichthyoplankton Imaging System (ISIIS)

              The off-shore waters of the Gulf of Mexico are characteristically oligotrophic meaning that the water column is well stratified within the upper 50-200 meters preventing the warmer surface water from mixing with the nutrient richer deep cold water (see Figure 1). At low latitudes there is plenty of sunlight so nutrients in the surface waters are quickly taken up by primary producers, phytoplankton, which are then consumed by secondary producers, zooplankton. Once these organisms are consumed or die, they then sink to the deeper waters taking the nutrients they carry with them resulting in surface waters that have depleted nutrients, or are oligotrophic. In these oligotrophic waters, plankton are inherently in low concentrations meaning larger sample volumes are needed to accurately estimate the abundances and distribution of plankton communities, especially rare taxa. Typically optical systems are not ideal for estimating the abundance of rare taxonomic groups. This is part of the reason the LSU zooplankton team brought its new In Situ Ichthyoplankton Imaging System (ISIIS) out to the Gulf of Mexico for the second year in a row.

              The state-of-the-art In Situ Ichthyoplankton Imaging System (ISIIS) is a unique optical system designed specifically to sample zooplankton of relatively low concentrations, specifically fish larvae or Ichthyoplankton (see Figure 2). Instead of using a conventional camera that would record images at a set frame rate, the ISIIS uses a line-scan camera. The line-scan camera collects a continuous image, meaning that the image collected can be viewed as one long picture without any separation. Rather than taking a picture the usual way with a strobe and a camera, the ISIIS uses shadow-graph imaging, a technique which utilizes a low power Light Emitting Diode (LED) light source and special optics resulting in plankton and particles being silhouetted against a white background (see Figure 3). The unique optics also allow for a large depth of field. The focal range of the ISIIS is the full distance between the camera and light source. The system is also telecentric, meaning objects imaged close or far from the camera appear the same size. At a speed of 5 knots, the ISIIS samples 9720 liters of water per minute and images objects in the size range of 1mm to 130 mm (see Figure 4).

              The ISIIS system is an underwater vehicle with a depressor V-fin to keep the instrument stable and oriented as it moves through the water. Using a fiber optic hydro-wire, the instrument is powered from the ship allowing for continuous deployment in the water that is not limited by battery life time. The instrument also sends back real time video, flight, and hydrographic data.

-Fredrick D. Marin

For more information about ISIIS visit:

Figure 1: A well stratified water column showing the chlorophyll peak in green and water density in red.

Figure 1: The In Situ Ichthyoplankton Imaging System (ISIIS) 

Figure 2: Example images of zooplankton collected by the ISIIS. 

Figure 3: A video of the original prototype ISIIS being deployed off Cape Cod. Note: the camera used in this early system is not a line scan camera as the images appearing on the screen are individual frames.

Sunday, April 14, 2013

Who ordered a Dark and Stormy?

              Around 2:30 am today we recovered the ZOOVIS-Deep after a successful deployment and were prepared to send the Digital-autonomous Video Plankton Recorder (DAVPR) over the side of the ship for a 1000m vertical profile when suddenly the winds increased to 25 knots sustained. The seas quickly built from 2-3 foot waves to 6-8 foot swells. For safety, we cancelled our DAVPR tow and decided to wait for the storm to pass. The seas calmed a bit and the decision was made to continue with our routine 5am CTD cast. At the last minute with tag lines in hand and just moments from dropping the CTD rosette into the water, the captain observed a small but powerful storm headed our way on the horizon. We cancelled the operation as gusts of 60 knot winds moved through the area. The seas climbed to 12-15 foot swells. After the squall passed we faced sustained 25-30 knot winds and episodic rain throughout the morning and early afternoon. Presently the science team and crew are taking a snow day and ride out the storm safely tucked away in the galley catching up on data entry and kicking back. We found out that somebody on the ship had never seen Star Wars so we are attempting to play the whole trilogy for them. A video will be uploaded at a later date after we return to land and have enough bandwidth.

-Fredrick D. Marin

Gone Fishin'

              It is day 10 into our yearly fishing trip aboard the R/V Walton Smith, and so far we have made an excellent haul collecting more than 8 dozen zooplankton samples (see banner for example specimens)! Though “fishin’” does not sound super scientific, it is actually a key component to our research in Dr. Malinda Sutor’s Lab at Louisiana State University. Collecting physical samples may be “old school” compared to our modern in-situ imaging systems, however it still remains the most thorough way to sample zooplankton.

              A physical sample can theoretically last forever and may be analyzed in various ways such as by expert classification, with lab based imaging systems, and even with more destructive methods such as carbon content analysis. Along with this benefit, a net system can sample much larger volumes of water than current in-situ systems ensuring rare taxa are accurately documented. On the flip side, in-situ imaging systems ensure that fragile organisms, which are damaged by nets, are documented as they capture zooplankton undisturbed in their natural orientation. Imaging systems also have much higher spatial resolutions allowing us to hone in on changes between very narrow depth ranges. Since both systems obviously have different benefits our cruises involve a combination of both in order to collect the best data possible.

              So, for our fishing part of the operation, we have exclusively used the 1m² MOCNESS net system developed in the mid 1980’s by Dr. Peter Wiebe of Woods Hole Oceanographic Institute in Woods Hole, MA. This net system is simple to deploy and allows us to sample zooplankton in meaningful ways. Our particular system consists of an array of nine 1m² nets which each sample discrete depth ranges while simultaneously logging relevant data with a CTD sensor (Conductivity, Temperature, Depth). At a tow speed of 2 knots, we are able to sample ~60000 liters a minute! Back at the lab, samples collected will be imaged with a Hydroptic Zooscan then analyzed using special software: Zooprocess and Plankton Identifier. The resulting data should give us species abundance, community composition, size distributions, and biomass estimates.

Visit our SEAMAP project website for more information about land based image analysis, and example Zooscan images.

-Eric Muhlbach 

Below we deploy, recover, and sample the R/V Walton Smith's MOCNESS

Setting out the nets

Deploying MOCNESS with the A-frame

Out to catch some zooplankton!

Rinsing nets to ensure all zooplankton is collected.

Collecting our catch on the aft deck.

Sieved sample ready for preservation.

Preserving a sample for transport back to the lab! 

Saturday, April 13, 2013

Dissolved Oxygen

              The Winkler titration method is being used on this cruise to measure dissolved oxygen in seawater. Samples are meticulously drawn from the sample bottles (Niskins) and properly treated with reagents on deck. The samples are then analyzed using a titration apparatus set up in the lab in order to calibrate the dissolved oxygen sensor. Dissolved oxygen is also being measured for the light/dark experiment that takes place every day during the daylight hours.

For information on Eric Quiroz and Gerg, visit:

-Eric Quiroz

Erix Quiroz using a dissolved oxygen sensor


Thursday, April 11, 2013

The Digitally-autonomous Video Plankton Recorder (DAVPR)

              Plankton in aquatic environments are not homogenously distributed; instead distributions of plankton tend to be patchy over a range of spatial and temporal scales. Characterizing a plankton community by applying only traditional sampling methods would provide little resolution about the true distributions of plankton comprising that community through space and time. Sampling plankton abundances and distributions in discrete volumes at rapid intervals in conjunction with environmental variables can provide valuable insight to the hydrographic mechanisms driving patchiness in plankton distributions.

              The Digitally-autonomous Video Plankton Recorder (DAVPR) is an underwater video microscope system designed to rapidly quantify distributions of planktonic taxa and particulate matter in the water column over the range of millimeters to hundreds of kilometers. The DAVPR can image plankton and particulate matter in the size range of fifty microns to a few centimeters. As a non-invasive optical sampler, the DAVPR allows for rapid high resolution measure on the distributional patterns of plankton and particulate matter without destroying the natural morphology and orientation of plankton and particles in the water column. Integrating a variety of environmental sensors, the DAVPR can simultaneously log physical data and images of plankton and particles allowing observations to be made regarding the dependency of plankton distributions on hydrography 1.

              For our application during our cruise the DAVPR is towed behind the vessel on hydro-cable at a speed of ~2.0 knots or just by drifting with the currents and is lowered from the surface to a maximum depth of 1100 meters (see Figure 1). A depressor v-fin keeps the instrument stable and properly oriented as the DAVPR glides through the water column. The unit is powered autonomously by a battery pack which can be quickly accessed and changed between water column profiles. Additionally, to limit avoidance by plankton the DAVPR is colored black, is hydrodynamic, and has no external moving parts to keep the instruments motion through the water stable and quiet (see Figure 2).

              The DAVPR operates by using a camera and a ring-strobe that are each individually mounted inside one of the DAVPR’s two forward projecting pressure housings. The ring-strobe provides 360 degree dark field illumination to the focal point of the camera which is an undisturbed volume of water centered between the camera and the strobe. The DAVPR can be set to any of 4 magnification settings. The setting we are using for this cruise is the second highest magnification the DAVPR offers, and provides a 14mm x 14mm field of view which combined with focal depth provides a 2.4 milliliter imaged volume per each image. The imaged volume is sampled at rate of 15 frames per second meaning 2.2 liters of water is sampled each minute. Hydrographic data on density, salinity, temperature, depth (CTD), and fluorescence are logged at a rate of 16 Hz. All the data collected by the camera and CTD is recorded to a removable hard-disk for analysis post DAVPR deployment (see Figure 3).

              Vignettes of plankton and particles are cropped from each 14mm x 14mm image frame and time stamped individually in millisecond time of day (see Figure 4). This time stamp is matched to the recorded physical data so that each image has a known position in space and time. Sorting a subset of these vignette images into the desired particle and taxonomic categories, we can train the computer to automatically identify tens to hundreds of thousand, and even millions of plankton images. This automatic classification of plankton images collected by the DAVPR is accomplished by using the software “Visual Plankton”.

              To summarize the advantages of the DAVPR for sampling plankton, the instrument provides (1) High-resolution data on the distributions of particles and plankton taxa, as well (2) providing a rapid measurement of these distributions. The DAVPR has (3) the ability to automatically identify plankton taxa, and to (4) record high-resolution hydrographic data (example: CTD, fluorescence, optical backscatter, light). Lastly, the DAVPR has (5) the unique ability to sample unobtrusively, as well as provide (6) information from which behavioral observations of plankton in-situ can be infered. Limitations of the DAVPR at present are that the instrument is not capable of identifying plankton to the species level, and rare taxa (<50/m3) are under sampled.

To learn more about the Video Plankton Recorder visit:

-Fredrick D. Marin

1 Davis, C. S., S. M. Gallager, M. S. Berman, L. R. Haury, and J. R. Strickler, (1992) The Video Plankton Recorder (VPR): Design and initial results. Arch. Hydrobiol, Beih, Ergebn, Limno, Vol. 36, p 67-81.

Figure 1: The distribution of marine detritus showing a typical DAVPR vertical profile from 0 - 600 meters depth (x-axis is “Julian Day”, and y-axis is “depth in meters”).

Figure 2: The Digitally-autonomous Plankton Recorder (DAVPR) returning from a 1000 meter cast in the Gulf of Mexico off-shore waters.
Figure 3: The DAVPR with labeling of the instrument’s features.

Figure 4: Images collected by the DAVPR: (A) Pteropod, (B) Copepod, (C) Euphausiid (Krill), (D) Copepod (with visible lipid sac), (E) Acantharia,(F) Collozoum, (G) Appendicularia, (H) Marine snow (organic particulate matter), (I) Radiolaria, (J) Medusa, (K) unknown, (L) Trichodesmium sp..

GRI Cruise Plan

              This cruise is the second of two annual surveys funded by a GRI (Gulf Research Initiative) grant, in order to assess the biological responses of microbes and plankton (phytoplankton, zooplankton, & ichthyoplankton) to the Deepwater Horizon oil spill. These organisms are the base of the food web and also play a major role in carbon and organic matter transport to the seafloor. Understanding the response of marine communities at this level is critical to interpreting the response of larger organisms, such as fish, in higher trophic levels.

CTD Rosette being deployed

              The oil and dispersants that were released into the open ocean during the spill were a huge source of organic carbon in a typically low-nutrient environment. Another aim of our project is to determine whether or not this input of carbon will alter natural carbon cycling and particle fluxes in the ecosystem around the spill site. We are also interested in the potential export and removal pathways of PAH (polycylic aromatic hydrocarbon) compounds released from the oil to the seafloor.

Krista Longnecker sampling for bacterial production 

Fred Marin sampling Niskin Bottles

              During this cruise we will utilize several traditional biological and sediment sampling methods, state-of-the-art imaging equipment, and high-resolution physical data to characterize the water column structure as well as the distribution and abundance of microbes and plankton in the Northern Gulf of Mexico. We will deploy the MOCNESS (Multiple Opening Closing Net Enclosure System), ZOOVIS-Deep (Zooplankton Visualization Identification System), DAVPR (Digital Autonomous Video Plankton Recorder), and ISIIS (In-Situ Ichthyoplankton Imaging System) to assess the distribution and abundance of plankton. We will also conduct experiments in the field to measure the rates of bacterial production, primary production, respiration and grazing. We will deploy a floating sediment trap to get a direct estimate of particulate organic carbon (POC), employ a water pump system to estimate PAH inventory in the suspended particles, and core samples will be collected to measure PAH accumulation in bottom sediments.

-Kate Lingoni

The MOCNESS being deployed

Wednesday, April 10, 2013

Touring the R/V F. G. Walton Smith

              Today we will be taking you on a tour of the R/V F. G. Walton Smith which is a research vessel owned and operated by the University of Miami.

R/V F.G. Walton Smith

              We’ll first start on the Aft Deck. This is where oceanographic equipment is stored and deployed. All of this equipment will take turns being deployed off of the stern of the boat throughout the cruise.

Oceanographic equipment on the aft deck

Deploying a drifter off of the stern of the ship

              As we leave the aft deck, we enter the main compartment of the ship. The first room is the Wet Lab. This is where we process chlorophyll samples, sieve and preserve zooplankton samples, and preserve phytoplankton samples.

The Wet Lab

              Next we enter the Dry Lab. This is where nutrient samples are processed. This room is also where oceanographers will monitor equipment that is being towed behind the ship.

The Dry Lab

              As we exit the Dry Lab, we enter the Mess. This is where the crew eats their meals. The Mess also doubles as the living room. It’s common to find crew members spending their free time reading, hanging out, or watching TV in the Mess.

The Mess

              Beyond the Mess is the Galley. Here is Lynn, the ship’s cook, she prepares three meals a day for twenty-two people. That’s sixty-six meals a day!

The Galley

              Above the Galley is the Bridge. This is where the captain navigates the ship.

The Bridge

              Finally we’ll take a peek at the crew’s quarters. This is where we’ll be living for two weeks.

-Tom Aepelbacher

My Bunk

Tuesday, April 9, 2013

We're On A Boat

We are almost halfway through our cruise on the F.G. Walton Smith, the University of Miami’s Research Vessel, with about a week and a half remaining. Along with the 14 Scientists in our group, the Walton Smith is also the temporary home of 8 crew, including the Captain, three Mates, one engineer, one marine tech, one intern, and one cook.

R/V Walton Smith

One of the many liferings

               The Walton Smith is a 96-foot long catamaran; this is important because the separate propellers allow us to deploy nets and imaging equipment off of the stern into undisturbed waters, and it also provides a smoother ride. There are separate Wet and Dry Lab areas, and two cranes, several winches, and a hydraulically operated A-frame that enable us to move equipment around on the deck and deploy equipment over the side or the stern.

-Kate Lingoni

R/V Walton Smith's A-frame

One of the two cranes

Monday, April 8, 2013


Researchers at Texas A&M University are using environmentally friendly driftcards as a means of studying currents.  During the April cruise onboard the R/V Walton Smith, approximately 200 cards will be tossed into the Gulf of Mexico at random locations.  The latitude, longitude, and GMT date and time are recorded every time a stack of 10 cards is deployed.  The cards will drift freely until they are picked up on land or at sea.  The instructions on the card ask for anyone who finds them to either call or email as much information as possible pertaining to the location that the card(s) was/were found.  Each card, which is about the size of a 3x5 index card, has a designated number to identify the origin of where it was released.

For more information on the driftcard program, visit:

-Erik Quiroz

A closeup of a driftcard

Erik Quiroz throwing driftcards into the Gulf of Mexico

Saturday, April 6, 2013

Runaway Barge Footage

            It only took 12 hours, but the video has finally uploaded! This is the view from the R/V Walton Smith’s mess hall.
            The barge broke away from the dock during the wind gusts and was pushed towards a Chiquita Banana cargo ship.  At the end of the video, you can see the barge start to scrape the side of the cargo ship. It eventually came to rest on a rock pile at the interior of the port. The Chiquita Banana cargo ship did not appear to take much damage, although the crew did have to patch up a hole with a steel sheet. No bananas were harmed during the filming of this video.

-Nick Fayland

Runaway Barge

Well, it’s time for the first blog post! Sorry for the delay, we have been quite busy.
Wednesday, we drove all of the scientific instruments and necessary equipment to our dock location in Gulfport, Mississippi. The weather was not great, but everyone made it there without any major problems.  After we pulled up to the dock, we began unloading the lighter items from the U-Hauls onto our vessel, the R/V Walton Smith. During the process of unloading, the wind and rain began to intensify rather quickly. Eventually, we decided to take a break and wait out the inclement weather.
After hunkering down on the vessel, the weather only seemed to get worse. Suddenly, the boat started to hit and grind against the dock. As I looked out the porthole, I could see that the dock lines anchoring the boat were beginning to strain and snap. The captain quickly began to maneuver the boat away from the dock, and eventually the final dock line snapped. Once broken free, we continued to wait out the storm in the harbor. As we floated, someone noticed that a nearby barge had broken free. It appeared to be heading towards a cargo ship that was also in the harbor. We were able to get some footage of this. However, uploading videos with our limited bandwidth is painfully slow. So, I will try to add the video as soon as I can upload it to YouTube.
The storm eventually subsided and we were able to securely re-dock. I surveyed some of the damage, and was able to capture a shot of the dock that we were grinding against. Luckily, there was minimal damage to the boat, and we were able to finish unloading everything onto it.

           Thursday, we finished setting up the vessel and have finally set sail. As we progress through the research cruise, we will try to update whenever our workload (and limited internet) permits. So keep checking back for updates!

-Nick Fayland