Jennifer Dean: Scientists and Surveys, May 16, 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 16th, 2018

Weather Data from the Bridge
Latitude: 32° 05.2647’ N
Longitude: 79°13.2777’ W
Sea Wave Height: 1-3 feet
Wind Speed:  9.2 knots
Wind Direction: 166.61°
Visibility: 7-8 nautical miles
Air Temperature: 21.7 °C
Sky:  Overcast, rainy and lightning

Science and Technology Log
Scientists- A Team of Diverse Skills:

Swiftia exerta
Swiftia exerta identified and photographed prior to collection by the ROV

After the ocean floor has been mapped with multibeam sonar, ROV (Remotely Operated Vehicle) dives are made to ground truth the maps and to describe the benthic habitat and fauna and flora.  In order to identify the taxonomy of what we see in the video and photos, we often need to sample the macrobiota.  Many species of sponges, gorgonians and black corals are very difficult to identify from photos alone, and some are even new species.  Taxonomist, specializing in deep-coral ecology, Professor John Reed, works in this field of science that involves an understanding of organisms by using a variety of features both on the macroscopic and microscopic level for identification.   The red arrow in the picture is pointing to one of the target species in these dives, the gorgonian coral, Swiftia exerta.  Gorgonian octocorals are often called by their common names of sea fans and sea whips.  They are characterized generally by being sessile (attached to the bottom), colonial (composed of hundreds of individual animals called polyps) and belonging to the phylum Cnidaria. For more information about corals see the link below.

ROV collects coral
Manipulator used to sample the Swiftia before depositing into a sampling bottle or drawer.

Once the coral is identified through visual inspection with the ROV’s high-definition video, Andrew David uses the robotic arm (called the “manipulator”) to get the sample into a collection bin. The ROV brings the sample to the surface to be processed by the scientists.  And yes — this picture with the red arrow pointing at a book below the monitor screen is for my students — they still use field guides!

Field guides help in confirming identification and to confirm key features on those species that may be spotted that are less common- or for science teachers who are trying to do a quick cram study.

Field Guide
Scientists still use field guides!


The calyces contain many calcareous sclerites that can interfere with the PCR reaction.  PCR selectively can amplify codes of DNA that then can be sequenced and its DNA compared in a nucleotide database program like BLAST (Basic Local Alignment Search Tool).  These samples will serve as an outgroup for phylogenetic analysis of Swiftia in the Gulf of Mexico. The captions of the pictures explain the actions of each of the scientific team members seen in the images and a listing below gives their names, titles, associated organization and a very brief description of a portion of their skill sets brought for this expedition at sea.

Stephanie Farrington, biological research specialist from Harbor Branch Oceanographic Institute at Florida Atlantic University. She not only has ability to identify the marine biota but also manages, analyzes and tracks the enormous amounts of data collected during the trip.

Elizabeth Gugliotti, graduate student at the University of Charleston.
She collects and processes the coral samples for future phylogenetic analysis. Her thesis advisor is Dr. Peter Etnoyer, a marine biologist and lead scientist for NOAA’s Deep Sea Coral Ecology Lab. In addition, on this adventure, she is my state room bunk mate.

Jason White, ROV technician, to be featured in the next blog.  University of North Carolina Wilmington Undersea Vehicles Program.  Piloting the ROV underwater to capture photo/video images and samples, bringing the ROV on and off the ship using a winch and pulleys.

Eric Glidden, ROV technician, University of North Carolina Wilmington Undersea Vehicles Program.  Piloting the ROV underwater to capture photo/video images and samples, bringing the ROV on and off the ship using a winch and pulleys.

Stacey Harter, research ecologist, NOAA National Marine Fishery Service, Panama City Laboratory.  See her featured in earlier blog under What’s My Story.

Andrew David, research fisheries biologist at Panama City Lab in Panama City, Florida.
He makes a running commentary on habitat and species recording with the live video footage, as well as operating the robotic arm to collect samples.

John Reed, Research Professor at Harbor Branch Oceanographic Institute, featured below.  He specializes in taxonomy of invertebrate and deep-sea coral ecology.  Featured below in What’s My Story.

LT Felicia Drummond, research scientist and NOAA corps member.  She assists in fish identification and brought the additional bonus skill set as a yoga instructor and volunteered to lead us in yoga on the Skybridge on breaks.

Personal Log

I am enjoying my crash course in fish and invertebrate identification.  LT Drummond in this image offered to identify species out loud for my benefit, filling the background noise of habitat readings and descriptions with shout-outs about Spotted Goatfish and Graysby.  My favorite, so far, has to be the Sharpnose Puffer.

Sharpnose Puffer
Sharpnose Puffer

Everyone on board Pisces is extremely helpful and friendly.  I can’t overstate this point enough, I continue to feel welcome and included in all aspects of the operations of this expedition.

Learning common names
LT Drummond teaching me the common names of a variety of fish species during live video stream during ROV dive

It is interesting to watch how many mini-lessons occur between the crew to help each other. From the database tutorial between a graduate student and the data manager to explanations by the ROV operator to the fisheries biologist on how to operate the joystick and other control buttons on the video equipment.

I could not have possibly anticipated moments like today, May 15th, when Prof. John Reed shared a video made about a deep dive in a manned submersible.  Witnessing the creatures of the deep from people who captured this footage themselves and are making novel discoveries in both the past and present continues to amaze me.

Morning view
Morning view from the porthole of my stateroom on Pisces

 I’m also surprised at the ease to which I am able to sleep on a bunkbed on the Pisces rocking in the Atlantic Ocean.  There is something calming at night about the motion or maybe it is my exhaustion after a full day of activity.  Whichever it might be, my basic needs have been met and exceeded for shelter, food and sleep.  I do miss my family and friends–and even my nonbiological kids (aka my students). I am thankful for my oldest daughter sending me emails that keep me in touch with the happenings at home.   There is so much to tell and words/photos don’t do justice to the experiences I am having.

Did You Know?
Certain species of Scamp or Mycteroperca phenax, have a coloration differential that distinguishes the dominant male in the group from lesser males and females.  And if the dominant male dies or is fished from the group, the most dominant female within 2 months can change sex and become the new leader for the school of females.  For the extra curious read about the research on this phenomenon, authored by R. Grant Gilmore and Robert S. Jones, Color Variation and Associated Behavior in the Epinepheline Groupers, Mycteroperca microlepis (Goode and Bean) and M. Phenax Jordan and Swain in the Bulletin of Marine Science  51(1): 83-103,1992.

Fact or Fiction?
A majority of corals reproduce by asexual reproduction and are considered r-strategist.
To learn more about their reproductive habits of sending out a larval form called a planula (after egg and sperm combine) visit NOAA’s link below.

What’s My Story? Professor John Reed
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?  Research Professor, Deep Sea Coral Program at Harbor Branch Oceanographic Institute

How long have you worked for Harbor Branch Oceanographic Institute and in this field?  42 years

What is your favorite and least favorite part of your job? Favorite part is going to sea and all parts of fieldwork, whether it is on land or sea.  His least favorite is the administrative paperwork and bureaucratic forms and processes that go along with the job.

When did you first become interested in this career and why?  He always knew he wanted to do something outside, and in middle school was interested in careers of such as a forest ranger or archaeologist.  In high school he started watching The Undersea World of Jacques Cousteau TV series and began following the travels of this family in the documentary type series as they visited underwater coral reefs and original marine habitat never explored and shared with the public before.  After that he was hooked.

What science classes or other opportunities would you recommend to high school students who are interested in preparing for this sort of career? He commented that students should take their basic STEM curriculum, but emphasized it is equally important to have a broad background of the arts, civics and humanities and studies outside the STEM focus.  In high school and undergraduate school students will need to develop their basic foundations of essential understandings of biology, chemistry, genetics, and mathematics including statistics, , and in his field to learn some basic anatomy/physiology of organisms.

What is one of the most interesting places you have visited?  He is by far a world traveler with 60 expeditions around the world, visiting 50 different countries and he considers himself extremely fortunate to have the opportunities to go down to 3000 feet deep in a submersible to see things that have never been seen before. He mentioned Papua New Guinea as one of his favorites, and that during one submersible dive off Granada, they accidentally dropped down into a volcano and then subsequently got blown out by the hot water plume.  In another exciting submersible dive in the Florida Keys, they were the first to dive into giant sink holes, 1000 ft deep and some ½ mile in diameter. On one of the sink hole dives, they got attacked by an eight foot swordfish which hit the plexiglass sphere in which they were sitting in the Johnson-Sea-Link submersible, which was rather unnerving. So in a pitch black environment, except for the lights provided by the sub he said it feels a bit like being in a fish bowl with a 380 degree field of view.

Do you have a typical day or skills and tasks you perform? A typical year involves 2-3 months at sea or in the field and then a return to the lab or office, where his work involves primarily computer work.  Following a typical 2 week cruise an additional 2-3 months is required to analyze the ROV photos and videos, to proof all the notes and data that has been recorded, and then write up the cruise report.  After that, then trying to publish manuscripts and write grants to do the fieldwork takes up the remainder of a typical year.  100% “soft” money is used to support this sort of research. “Soft” money means that they must get grants to support all aspects of the study, paying the principle investigator salary and his/her team, and 48% or more overhead is typically paid to the investigators home institution.

What are some other careers or divisions of study at the Harbor Branch Oceanographic Institute? The engineering division is developing AUVs (Automated Underwater Vehicles), and wave gliders, equipment used on submersibles, acoustics, and software the is used for tracking on the ROV.  Another division is their biomedical unit where chemists are looking at bioactive products from the sponges and other creatures found in the marine environment.  Their aquaculture program is developing a closed circulation system, trying to address the pollution created by some aquaculture programs.. And the division that Prof. Reed works for is the Deep Coral Biology Program that studies corals and fishes, and is  also studying  the genetics and bioinformatics of marine systems.

Why does your research matter?  He views his primary mission in the realm of basic science, discovering and researching new reefs and then trying to protect them.  His research and discoveries resulted in the first deep-water coral Marine Protected Area (MPA) in the world, the Oculina Coral Habitat Area of Particular Concern (HAPC) in 1984; and in 2010, a 16,000 sq. mile Deep-water Coral HAPC which extends from Florida to North Carolina. He is asking scientific questions such as, what kind of fish community do you see on a high relief vs. low relief bottom? How well are the MPAs working–are they providing spawning and breeding grounds, protecting from destructive fishing procedures?  How does the dive footage compare outside and inside the MPA area for human impacts?  In the long run he views his research helping the fishing community and providing protections for sustaining these habitats and food webs for future generations.




29 Replies to “Jennifer Dean: Scientists and Surveys, May 16, 2018”

  1. So what exactly is your role on the ship? How many people are on it? How do you know the range of visibility, like how can you specifically say “Oh I can see about this far.”? What exactly are you looking for in the coral, sponge,and gorgonian samples?

    1. good question- i have alot of freedom- i am basically involved in documenting and participating in whatever parts of operations of the mission I want- of course my particular interest is around science- but I have also been able to tour and ask questions of the engine room and the acoustic lab- and tomorrow I plan to interview the stewards and photograph the galley; 32; the visibility from the bridge- if you can see the horizon they say 10 nautical miles if I can’t see the horizon I ask the bridge officers to give me their approximation- i am hoping to spend more time on the bridge in the next few days- great question about visibility I will ask them. With waves they told me to just imagine being out in the water and how high do they look. These studies are exploratory- so they are trying to characterize what is here- and ultimately if there is something to protect to get it protected. Dives last night were quite sad- mainly just rubble of coral destroyed through destructive fishing practices. The sampling was done for the grad student for another study and scientist not on the ship. The main mission is basic science to document. I will share with you some of John’s scientific papers when I return to give you a senses of their purpose – and click on some the links in the future blogs.

  2. In the first sentence under the group of pictures you talk about “The calyces contain many calcareous sclerites that can interfere with the PCR reaction.” What is PCR reaction and what are the calyces, I didn’t really understand this part.

    1. Yes- Elizabeth changed that section- they are the hard calcium carbonate parts of the skeleton on a coral; PCR is polymerase chain reaction- which is just a way to amplify DNA., order to sequence DNA you first need more of it- so they will use the polyp tissue to extra the DNA from its cells and then amplify or copy it using what are called primers. if you take Biotech in your junior or senior year- or go to biotech camp this summer it is one of the processes used in biotech labs

  3. Are there any other benthic macrobiotic organisms which were noted by the team on the ROV? which of these organisms stood out to you as being interesting or unique?

  4. Throughout the day, are you going through the entire ship over and over again or do you stay in a certain section of the ship? And you talked about how there are a lot of mini lessons going on between you and your peers; have you been subject to any mini lessons? If so, what was it about? Have you given any mini lessons? I would love to know!

  5. How much training do you need to pilot the ROV and to accurately control the robotic arm on it? Are you planning on using the Robotic Arm or analyzing the samples?

    1. they said it is on the job training. Robotic arm control depends up which of those joint systems- if it is 5, 6 or 9. the more joints the easier to maneuver. biggest challenge is the current and visibility…and not touching bottom and stirring up huge amounts of sediment….and not getting caught under the ship or rock. we are done with the sampling. i am just watching the identification of the creatures now- looking at environment where light doesn’t penetrate. my last blog will have some of my favorite photos i got during all the dives.

  6. What do you do with the coral after you are done with processing it? Do you store it on the ship? I hope you have a fun time on the ship, but I can’t wait until you get back!

    1. They send it to a museum after it has been tested and inventoried. I believe at the Harbor Branch institute. ROV operator just suggested an awesome idea- if I have enough space on my hard drive- they will give me the ROV video footage – so I can take you guys on one of the dives and what we saw- and you all will be either fisheries specialist or invertebrates scientists…etc…and try to count and id what you see….todays dive we were at 250 meters….whole new creatures.

  7. Sounds like you are having tons of fun! How many species of coral have you researched on? What jobs do you have on the ship on the daily?

    1. the first night i stayed up till midnight to learn the multibeam sonar- but after that i have been on a fairly regular schedule of dives that begin at 7 am and being done with last dive around 7 pm…in between dives i tend to run up several flights of stairs to get the weather from the bridge, or interview a crew member. I have to get images transferred from my phone to PC (we can only have one device on the network- so I used my phone as my camera only), researching what I am learning, and writing take up all the time in between. I try to stop at 8 pm and read a little. It is a different kind of busy than when I am at school. I am helping on the deck with getting the ROV in and out of the water- learned to tie a crescent knot, pull fiber optic hose onto the deck and let it go…help release the ROV. Got a good arm work out yesterday because the hose had to go to 250 meters.

  8. Do they just take out a whole chunk of coral, or do they cut a piece off for them to observe? Do other fish change gender as well? What causes they gender change? Is it temperature or hormones?

  9. What other organisms have you seen and noted? Is controlling the ROV hard? We miss you too!!

    1. i will be featuring my favorites in the last blog; got a 15 minutes show at the front of the ship from dolphins…and got some cool videos that I will share in class. my favorites are the batfish and i really like all the strange sponges and sea anenomes- yesterday my favorite was the venus fly trap anenome

  10. What’s the most interesting organism that you have observed so far? Have there been any difficulties that you’ve had to overcome so far?

  11. What is the size of the coral speciments that you observe? Is there a specific method you use to extract the coral?

  12. Based on what you’ve observed, how rich do you think the species diversity is on the sea floor? I can see from most of the photos that there is quite a variety of species, but have you seen richer areas? What were they like/ what species there surprised you?

  13. The Sharpnose Puffer looks very interesting. I understand that you were able to identify various vertebrates and invertebrates. What did the species richness look like during the dives?

  14. What are other interesting organisms you have witnessed while at sea? Do you plan on doing a blog on them?

  15. When you got back you said that you saw a lot of fish while on the Pisces. Were there any fish that you would want to keep as pets either around the classroom or at home because of how they looked or a cool feature they had?

  16. How involved do you get to be in the science aspect of the trip? Do you get to look at samples much and help with the testing at all, or are you just observing and documenting?

  17. What has been the most difficult part of everyday life on the ship? Have you seen any organisms that don’t belong? (Invasive species that we didn’t really know about before)

  18. I may have just missed this part, but what exactly do you do on the ship? Are you underwater taking the pictures, and if so how much training did that take? Or are you staying on the ship and doing the investigating parts? Again, happy to hear this trip was a lot of fun!

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