Jennifer Dean: Sampling the Sea Floor, May 15, 2018

NOAA Teacher at Sea

Jennifer Dean

Aboard NOAA Ship Pisces

May 12 – May 24, 2018

Mission: Conduct ROV and multibeam sonar surveys inside and outside six marine protected areas (MPAs) and the Oculina Experimental Closed Area (OECA) to assess the efficacy of this management tool to protect species of the snapper grouper complex and Oculina coral

Geographic Area of Cruise: Continental shelf edge of the South Atlantic Bight between Port Canaveral, FL and Cape Hatteras, NC 

Date: May 15, 2018

Weather from the Bridge
Latitude: 32° 23.3070’ N
Longitude: 79°02.4555’ W
Sea Wave Height: 2-3 feet
Wind Speed:  10.7 knots
Wind Direction: 131.42°
Visibility:  10 nautical miles
Air Temperature: 25.1°C
Sky:  Scattered Cloud Cover

Science and Technology Log

Multibeam Bathymetry
Lieutenant Jamie Hart (seen on the bridge in the picture below) explained how sonar pings allow software to paint a picture of the ocean floor.

Communication between the bridge, the technicians and the scientists are continuous to keep the mission coordinated and progressing.

With GPS that determines the latitude and longitude, the sonar determines the last piece of information to gain a three-dimensional view.  Adjustments have to be made below deck by Mr. Todd Walsh, Hydrographic senior technician (see previous post for additional information). The echo of return waves are detected downstream and calibrated to adjust for time, salinity, depth and a host of other factors to create the images used by the scientist to choose a path for sampling.

Images like the ones above are being used to determine locations for the ROV (Remotely Operated Vehicle) dives and to aid in navigation during the collection of samples and observations when running transects for inventory of the fish, coral and habitat.

Robotic Arms and Taking Samples of Coral and Sponges

Screen displays in front of the ROV operator, Eric Glidden, includes information on the sea floor gathered from the multibeam sonar technology. Other screens include information coming in from a still camera, cameras that are set to view the sampling bottles and drawers, as well as high definition images of the live ocean floor feed ahead of the ROV and images from cameras directly on the robotic arm.  The blue image in the picture is Pisces, another smaller red image not visible on this photo is the location of the ROV. The ROV operator ensures that there are no collisions, even if there is a loss of power or other malfunction, the ROV floats to the surface for recovery.

Two modes of sampling with ROV attachments visible in this image; on the left a suction hose and on the right is the robotic claw, used both to maneuver the hose and to grab samples for removal from the ocean floor by twisting and rotating the claw device. Using this arm reminds me a bit of those arcade area claws where one attempts to grab that coveted stuffed animal prize to have it ultimately not clasp or drop the treasure.  Unlike these games, the ROV operator and the claw expertly grasp and deposit coral and sponges with a 5 function arm system.

For a fun engineering activity that models these robotic systems visit this activity

After samples are recovered topside they are brought inside the wet lab for processing, barcoding, photographing and for those samples needing genetic analysis, placed in vials and test tubes filled with ethanol for longer term storage and preservation of the coral’s tissues.

John K. Reed (Biologist/Taxonomist) discusses the sampling of a recovered sponge with Felicia Drummond (LT NOAA Corps).  Dr. Reed explains to me the octagonal polyps to look for when identifying this particular type of coral.

Caribbean Spiny lobster
Caribbean Spiny lobster, Panulirus argus. One of the many biotic factors observed on this ROV dive.

Other highlights this day were observations of two sandbar sharks and a stout moray eel, spotted on May 14th dive, and May 13th respectively.

Personal Log

May 13th, day 2 on the ship, I had one of the most surreal experiences of my life. I found myself playing corn hole off the back of a ship in the Atlantic ocean with Navy officers, deckhands, stewards, engineers and scientists at sunset. For those of you that may not have heard of such a game, it involves throwing 4 bean bags at a hole.  Landing on the board seen in the pictures without sliding off, is a point.  Getting the bean bag into the hole is 3 points.  First team to 12 wins.  I enjoyed the additional challenge of being on a swaying ship, keeping one’s balance and making the toss, all at the same time.

This was a fun and an amazing day with a fire hose dose of information coming at me.  There are so many interesting directions of study pulling for my attention.  I am curious about the formation of the ocean floor that gives the appearance of ancient Mayan formations.  The evolution of these block-like limestone formations created from water erosion and the laying down of sediment layers makes for beautiful habitat for a diversity of creatures seen during the dives.  Yet the biotic factors are equally fascinating to study with their adaptations of form, corals with polyps that have 6 tentacles, belonging to a subclass of Hexacoralia to 8 tentacles, from another subclass Octacoralia.  What advantages and disadvantages do these differences in form provide to these creatures in their marine environment?  Some of these hard corals we are observing and collecting evolved back in the Miocene.  To learn more about coral and for ideas and activities for teaching about coral evolution visit this site:

Last, but not least, I was on this adventure during Mother’s Day, so I not only want to thank my own mother for helping to get my daughters to school and looking after pets and plants during my absence, but for being a constant and committed pillar of support for me growing up and now into my adult life.  I wouldn’t be living the dream without her guidance and not to mention those brutal critiques of my writing over the decades.  Thanks to my mom and all the others mom’s out there reading this blog!  Happy Belated Mother’s Day.

Did You Know?
Scientists make observations about not only a sponges’ appearance but also its texture and smell.  Some are very stinky giving off odors similar to that of a rotten egg and vomit while others can emit a spicy aroma!

Fact or Fiction?
Excretions from certain sponges are demonstrating pancreatic cancer fighting properties.  Additional information can be found at this link for the extra curious:

What’s My Story?  Stacey Harter
The following section of the blog is dedicated to explaining the story of one crew member on Pisces.

What is your specific title and job description on this mission?  Chief Scientist and Fisheries Ecologist

Stacey Harter
Stacey Harter, Chief Scientist and Fisheries Ecologist, posing after emergency training

How long have you worked for NOAA?  16 years

What path did you take to get to your current position?  Undergraduate at Florida State University with a degree in Biology;  As an undergraduate, she did an internship at the Panama City lab and fell in love with the research side of marine science. She got her Master’s degree in marine science at the University of South Alabama and at the end of her Master’s she took a position as a contractor for 5 years before becoming a staff member with NOAA as a federal employee.

What is your favorite and least favorite part of your job? She enjoys going to the South Atlantic Fishery Management Council meetings and giving them information on what they have learned about the MPAs and then seeing that data being used to make management decisions.
Reading all the ROV data is quite time consuming and can become monotonous at times.

When did you first become interested in this career and why? Even though Stacey grew up in landlocked New York, her passion for marine science started early on with visits to Sea World and watching the Discovery channel as a kid. In high school she realized that she could take this interest in the marine world and make a career out of it.

What science classes or other opportunities would you recommend to high school students who are interested in preparing for this sort of career?  She recommends as much math and science as one can take.  She highly recommends students participate in internships.  She has witnessed many times over the years that these internship opportunities later turn into long-term employment. In addition she recommends students volunteer in research labs and try to experience as many aspects of the different parts of the career as possible.

What is one of the most interesting places you have visited for work?Around 2009 she went down in a manned submersible and explored the unique deep ocean communities at 2500 feet. She was blown away by the incredible different and original biota found in this environment.

Do you have a typical day? Or tasks and skills that you perform routinely in this job? Her typical day involves identifying fish species on video footage collected during and after dives. Another task she regularly performs is using software programs like Access and Excel for data analysis. She shared that about every couple of years she communicates their research by attending both scientific meetings and delivering information to the South Atlantic Fisheries Management Council.

Has technology impacted the way you do your job from when you first started to the present? Definitely.  When she first started, pad and paper were used for recording dive information and species observed which was later entered after a dive into Excel.  Now everything is done digitally and directly into computer software as the dive occurs.  In addition to the approach to data collection, media storage has changed with how video footage is stored into hard drives rather than on mini-DV tapes.

What is one misconception or scientific claim you hear about how the ocean and atmosphere works and/or NOAA’s mission that you wished the general public had a greater awareness of? She doesn’t spend all of her time on boats doing field work. While field work is a fun, it is actually a very small portion of the job. She actually spends about 90% of her time at a desk in front of her computer analyzing data and writing reports.



39 Replies to “Jennifer Dean: Sampling the Sea Floor, May 15, 2018”

  1. What is the ROV like to control, does it respond quickly or is there a lag time from when you control it to when it responds? Do you have to have training to be able to operate it?

    1. Check the “What’s My Story” on the blog called “Databases and Downward Dog” – that will have all your ROV questions answered after I talk to the ROV technicians

  2. How heavy is the ROV? How tough is it? How expensive is it? If it somehow broke, what would you have to do? Try and repair it on the ship with spare parts?

    1. So some of these I’ve added in for the interview with Jason and Eric; Repair is being done whenever needed- a camera had to be fixed at the beginning of the trip and I have footage I will post later of the zodiac being used to run into shore and get the part needed for it. And that’s what the engineers are here for- there is always something getting fixed- and technicians as well- nothing every works smoothly all the time in science. Some items have spare parts- other larger ones do not. That is true for multiple things on the ship.

    1. I counted 3 I think…but I am interviewing the ROV guys this afternoon- I will ask during that time and put it into the next blog 🙂 Easy is a relative term and it really seems to depend on the conditions 1/2 knot vs. 2 knot current makes the difference in a dive aborted or a dive that is easily maneuverable.

  3. When you were talking about how scientists identify sponges, you say they smell the sponges. My question: is there any sponge that is poisonous to humans/ result in negative effects if smelt, and how would they know before they already smell it? How do they make sure this process is safe?

    1. Wafting a good policy. Dr. John Reed recommends sniffing not snorting- and we are getting good amusement from your question- thank you! He used to do skin tests on himself- back in the days where people had less safety regulations. Mainly ingestion is the issue with toxic sponges.

  4. I was wondering how many people are working to get the coral tissue analyzed, and I was also wondering what you were helping in during the process. Lastly, did you win the cornhole game??

    1. In my first question i meant to ask, in the whole process of obtaining the coral and analyzing it, how many people does it take?

      1. Depends at what stage you are talking about “obtaining” the coral- because actually obtaining the coral takes ROV operator, deck hands to get ROV in and out of water, XO or officers up navigating ship so we don’t get the tether attaching ROV caught, then the team of scientists in the lab watching the feed identifying- and the scientists actually running the manipulator (robotic arm)- if you mean back up top- Elizabeth did all the pulling apart of the tissue- we were just supporting her with wrapping tubes in parafilm and providing barcoded labels for larger samples in test tubes and smaller ones in microfuge tubes. BAck at her lab onshore- running PCR could be done by one scientist on the tissue.

    2. I didn’t but I did get the bean bag in the hole once and one the board many times- and it was close! especially considering i had never played before and I am pretty sure the other team has played this many times- the steward and an engineer were our competition- my partner was Dr. John Reed.

  5. Is what you are seeing on the east coast similar to what you would find on the west coast? Also, what has been your biggest “aha” so far?

    1. these are deep-sea coral communities- so it seems very different; i have seen very little starfish or anemone- but they seem surprised as well at the lack of the anenomes; also no flounder….lots of what they call TomTate and Amber Jacks- none of which I see when diving in the sound. The marine debris looks different as well- there is this constant snow coming down. Lionfish are at every site- which thankfully I have never seen on dives in the Puget Sound. My biggest “aha”- i think -there have been many almost every day- but today it was about the fact that there are a handful of coral that can live without their zooxanthella- and I’ve always taught and thought once they expel their symbiotic partner they were done for….and that little is known 1-how they are surviving and 2-how these algae come back in and rejoin with their coral partner….that there is so much still to figure out

  6. Is there any direct correlation about the scent of the sponge to its properties/ edibility? Although only a small array of species can consume the sponges, such as anglertfish, sea slugs, hawkbill turtle, etc, are there any other natural defenses (other than the spicules) which are signified by the smell?

  7. How does the water erosion cause the block-like limestone formations to evolve into the Mayan-like formations that you observed?

  8. Seems like your having a very fun time there! I never knew such an important scientific investigation would give someone, “one of the most surreal experiences of my life”. I’m sure you have seen some cool organisms through the ROV operator, but what has been the coolest, craziest thing you’ve seen so far?

  9. Have you ever controlled the robotic claw that’s used to maneuver the hose and to grab samples or do you need special training in order to do so? Also, is there a specific time or place that you go scuba diving?

  10. Are the sponges a type of coral? What information do you collect after taking in some samples? I am glad you are having fun playing with everyone on the ship!

    1. sponges are phylum Porifera and Coral are Phylum Cnidaria- my last blog discusses the differences; we didn’t sample any sponges- this is really a baseline data- basic science to see what is here type of study.

  11. Wow, that would be amazing to pilot the ROV through the water. What is it like to control the ROV, it is easy to move around or is it difficult to position it. Also how many cameras are on the ROV?

    1. read the section at the bottom from Jason white’s interview- the ROV operator

  12. Is the ROV easy to maneuver/ have you ever used it and how long does it take to analyze and take data on the coral?

    1. depends on arm system. this is a cheaper system- the more joints – represented by 5, 6 or 9 arm systems- the easier to use. main issue is currents and visibility. takes about 1 year for Stacey to analyze the fish data from a trip like this

  13. Have you ever controlled the robotic arm and if so is it easy to maneuver? Also, how long does it take to analyze and take data on the coral?

    1. I have not- it is kind of very expensive and I am sure a liability for me to be in control of it. taking data- the dives last about 1 to 2 hours each and we are doing about 3 a day. To analyze the data will take at least a year.

  14. When smelling the sponges, do they use their hand to smell it or do they just go for it? How much of the sponge do they need to remove to get the results they need?

    1. wafting is the best policy; they actually took the sponge for the museum- i don’t know if they are doing dna tests or not on that one- but they would only need small samples – gram amounts for PCR/DNA analysis

  15. It’s good to see that while on the boat, it’s not all work and no play, as you played cornhole. I’m really fascinated that things like GIS that we learned in class are being applied to the real world. Another thing that I thought was cool was the robotic arm. Just a question, how big were the samples that were collected by the robotic arm?

  16. What is the most interesting sea life you have seen so far? How hard is it to find specimens to test?

  17. How do you smell the sponges? Also how bad do they smell and who gets chosen to smell it? (I’m guessing the smell isn’t pleasant and no one chooses to voluntarily smell it).

  18. You said that you have a GPS system that can tell you where you are and sonar that gives you a 3d view. Is the crew trained in star navigation or another method do you know where you are in case the GPS goes out?

  19. It seems like there is a lot happening on the ship all the time, and a lot of jobs to be done. About how many people are on the ship with you?

  20. Wow, that sounds like quite the day. One thin I couldn’t help but notice is the sunset in that picture. Are the sunsets and the night skies especially beautiful because there isn’t much light pollution out there?

  21. Does the method of retrieving samples from the ocean floor significantly disrupt the environment?

  22. I’m glad to see you got to enjoy an interesting new game on the deck! How easy is it to collect the samples from the ocean floor and to control the ROV?

  23. Were you worried about damaging too much of the coral, or messing with the natural habitat, or was it not that much area you took samples from? Also, very happy to hear you’re enjoying the trip and having some fun on the boat.

  24. Just wondering, how is the ROV stabilized? I imagine thermohaline circulation and things like upwellings that would move the ROV while trying to get samples. My done has both downward facing cameras and GPS/GLONASS. Does the ROV?

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