Mission: Microbial Stowaways: Exploring Shipwreck Microbiomes in the deep Gulf of Mexico
Geographic Area: Gulf of Mexico
Date: July 1, 2019
Interview with Scientist Melanie Damour
Melanie Damour is the Co-Principal Investigator and Co-Chief Scientist on the expedition. She is responsible for directing all archaeological aspects of the investigation. We talked about her path to her career, and her advice for young people who might want to pursue ocean science.
Melanie Damour, Marine Archaeologist
When I asked her what sea creature she would choose to be, she immediately answered “A mermaid. Mermaids have the agility of fish, but they are smart.” Melanie may not be a mermaid, but she is agile as a fish and smart.
Melanie knew from early childhood what she wanted to be when she grew up. Her father was a fire and rescue diver, and Melanie sometimes got to see him at work. She was fascinated by scuba diving. With her father’s support, she learned to scuba dive when she was only eight years old. The second event that shaped her career was a visit to the USS Constitution in Boston Harbor. This historic sailing ship is open to the public and played an important role in the war for independence from Britain. When Melanie visited this ship, she was awed by the ship and its history, and decided that somehow she was going to marry her two favorite things – diving and maritime history – for her career.
She got her scuba diving certification when she was 14 years old, and studied history in high school. She went to Florida State University to study anthropology. She took classes in archaeology, cultural and physical anthropology, and linguistics, all the disciplines within Anthropology. She was offered a teaching assistantship which allowed her to get into a graduate program and study submerged paleoindian sites in Florida. The offer was too good to refuse, so she began her graduate work at Florida State right away. Now she works for the federal Bureau of Ocean Energy Management (BOEM) as a marine archaeologist.
Melanie reflected on what makes a good scientist. Her first response was that good scientists are always asking questions; being curious is what leads to new understandings. It’s also important to be open-minded. Scientists can’t expect things to turn out a certain way as this would blind them to what is actually happening. A scientist has to be persistent in the face of problems and always be looking for different ways and better ways to attack a problem. The ability to work well in a team is key. Each member of a good team contributes to the end goal. Taking into account different perspectives leads to a more accurate and complete picture.
Melanie has worked on projects in the Gulf of Mexico, the Atlantic and the Pacific. Her personal research interests led her to Guatemala, where she worked in Lake Petén Itzá on a submerged Mayan port site. She went to Panama to map a Spanish merchant ship that sank off the coast in 1681. This is her favorite shipwreck so far. It is well preserved by the river sediments that poured into the Gulf there. The ship contains hundreds of wooden boxes full of supplies that Spain had sent to the colonies. The boxes contain nails and scissors, and some yet to be opened my contain books that are still preserved. After this expedition, Melanie is heading to Mexico to dive with her husband on a site that may turn out to be her new favorite. They will be looking for the wreck of one of the ships belonging to Hernán Cortés, the Spanish explorer. In 1519, Cortés sank his own ships to prevent his crew from leaving and returning to Cuba. This set the course for the conquest of the Aztecs. Last summer, Melanie and her husband found an anchor and wood that dated to the early 1500s. The wood was determined to be from Spain. This puts the anchor in the right time frame to be one of Cortés’ sunken ships.
Melanie pointed out that it isn’t easy to get a job as a marine archaeologist because it is a small field and there are not many permanent jobs. But she also encourages anyone who wants to pursue this as a career to be persistent and not give up. “It’s not always a straight line from A to B,” she says; in fact, you may discover that when your plan isn’t working out, you actually prefer the new track your life takes – that Plan B option that you may not have known existed when you began your career.
“The greatest threat to our oceans today is humans,” Melanie said. “Our lack of consideration for the consequences of our actions is the greatest threat we face.”
Marine archaeology is one of many subdisciplines in ocean sciences, and the future of our oceans depends on many scientists working together to reverse the trajectory of degradation we are on.
Game Plan and Trawling Line: Four trawls on the San Miguel Line in the Channel Islands.
Time Recap: 5:00 PM: Wake up and then Squat Challenge. 5:30 PM: Dinner. 8:30 PM: Report to fish lab. Learn how to count to ten in French. Kristin sang France’s National Anthem (she learned in 7th grade). 10 PM: First Haul. 3AM: Kaila used her face flip app to turn us into the opposite sex and it was the most hilarious thing ever. 4AM: Latte made by Kaila. A lot of laughing. 6:20 AM: Finish fish lab clean up. 6:21 AM: Still heavily caffeinated so Team Red Hats headed up to the flying dock to watch the sunrise. The sea was very smooth and glassy as we approached Conception Point. We saw several dolphins and a humpback whale. 7:00 AM: To the Galley for a breakfast of blueberry pancakes. 7:45 AM: Lights out.
Part 1: How to distinguish between myctophid species in our catches
In this survey, we are conducting trawls at 30 meters, which is technically the epipelagic zone, so why do we catch deep sea creatures? Many deep sea creatures, such as myctophids, participate in a daily vertical migration where they swim up into the upper layer of the ocean at night, likely following the migration of zooplankton on which they feed. Myctophids are also known as lantern fish or lampfish and they feature photophore organs which bioluminesce. Around 250 species of mcytophids have been described. Graduate student Ily Iglesias is saving a lot of the myctophidae we catch on this cruise for her dissertation work.
Tonight most of the catches were small in volume (filling about 10% of a blue bucket), but had good species density. The catches consisted mostly of salps, anchovies and several species of myctophids. It is important to learn how to properly distinguish between the various myctophids in our catches. This is a daunting task for the novice fish sorter, such as myself, since these fish are small (1 to 2 inches long) and appear very similar to each other. It is worth noting that most of the myctophids lose their skin (scales) during the trawling operation. This exposes the underlying pink muscle tissue, however, their photophores remain intact. Fish collected in a bongo net deployment typically have better preserved scales.
Northern lampfish, Stenobrachius leucopsarus, have 3 photophores in a slanted line under the lateral line while the similar looking Mexican lampfish, Triphoturus mexicanus, have more streamlined bodies and have 3 photophores on the lateral line. Many of the Northern lumpfish had a heart parasite which is evident in the photo below. California lanternfish, Symbiophorus californiensis, are typically larger fish and have a distinguished lateral line. California headlight fish, Diaphus theta, have two photophores “headlights” on the front on their face. Blue lanternfish, Tartetonbeania crenularis, are easy to distinguish from the others because they have wider bodies and blue/silver scales.
Northern lampfish, Stenobrachius leucopsarus, have three photophores in a row (circled).
Mexican lampfish, Triphoturus mexicanus, are more narrow than Northern lampfish and have three photophores right on the lateral line.
California lanternfish, Symbiophorus californiensis, have a distinguished lateral line.
California headlight fish, Diaphus theta, are easy to distinguish because of the two large photophores on the face.
Blue lanternfish, Tartetonbeania crenularis, collected in a bongo net with intact scales. Photo courtesy of Lauren Valentino.
Photoorgans lining ventral surface of Blue lanternfish, Tartetonbeania crenularis.
Part 2: Rockfish: why are we catching so few?
Last night there were 4 rockfish in the last haul, and the fish sorting team got excited because we have not seen very many. The title of this survey is officially “Juvenile Rockfish Recruitment and Ecosystem Assessment Survey,” however, sampling for pelagic juvenile rockfish is only one of the project’s objectives. Other objectives include sampling for other epi-pelagic micronekton species, studying prevailing ocean conditions and examining prominent hydrographic features, mapping the distribution and abundance of krill (Euphausiacea), and observing seabird and marine mammal distribution and abundance.
Rockfish, perch, or redfish are common names for the Sebastes genus of fish (with more than 100 species) which are abundant off of the California coast, and are a very important genus for the commercial fishing industry. Rockfish are benthic fish that live among rocks, and can be found in kelp forests or in the bathypelagic zone. One of the goals of this survey is to inform the fishing industry on the status of the population of rockfish so that reasonable catch limits can be set.
This year is proving to be a poor year for the rockfish pre-recruitment index, lower than the previous several years, says Chief Scientist, Keith Sakuma. He explains that one year of a weak young of year (YOY) rockfish class is not enough to have an impact on the fishing industry, but if the index was low for say, 10 years in a row, then this could potentially affect the exploitable population. He explains that since rockfish can live to be 100 years old or greater, they have many seasons to reproduce. Rockfish prefer cold water habitats. Keith’s research has demonstrated that most poor pre-recruitment index years are correlated to El Nino events which cause an increase in water temperatures and a reduction in cold water upwelling. This year’s slump in terms of rockfish numbers is not correlated to a strong El Nino event.
Two young Cabazon Rockfish, Scorpaenichthys marmoratus.
Part 3: Environmental DNA (eDNA) Sampling on the Reuben Lasker
Last night Flora Cordoleani and I helped Dr. Kelly Goodwin collect water from the Conductivity, Temperature and Depth (CTD) bottles for the purpose of collecting environmental DNA (eDNA). Kelly’s assistant, Lauren Valentino, is primarily on the day shift (see photo of Lauren with the CTD apparatus below). Isolation of eDNA from seawater is a newer technique used to determine which species swam through a particular location based on the DNA they left behind, through shedding of cells. This technique does not require that the organism be harvested to know that it had been present, and could be of value in detection of the presence of endangered species, for example.
For this CTD deployment, three bottles are filled at depths of 5 and 100 meters, and at the chlorophyll max somewhere between 5 – 20 meters. The water from each depth is run through a filter (pore size of 2 microns) in the eDNA lab on the ship (see photo below). The vacuum filtration procedure is a time-consuming process, as samples must be processed in triplicate, and in which aseptic technique is paramount so that human DNA does not contaminate the water. Once the DNA is trapped on the filters, they are stored at -20C. The DNA will be purified from the filters back in the San Diego NOAA lab using a Qiagen kit. Species-specific regions of DNA known as bar-code regions will be amplified by Polymerase chain reaction (PCR) using 3 primers sets for analysis of DNA from bacteria, plankton, and fish. Illumina techology will be used to obtain DNA sequences, which are compared to DNA libraries for species determination.
The results from the eDNA study will give us a list of species that were present at each trawling station up to 48 hours prior to CTD deployment and fishing using the Cobb Trawl. We will be able to compare this list with the list of species that were physically caught in nets. Nighttime CTDs are deployed at the same station as bongo nets. Daytime CTD trawls occur at the same stations as night fishing.
Lauren Valentino with the Conductivity, Temperature and Depth (CTD) Rosette on the Reuben Lasker.
Kelly Goodwin filtering water in the eDNA lab on the Reuben Lasker.
Part 4: Career Spotlight: NOAA Commissioned Officer Corps, Scientist Interview: Keith Hanson, NOAA Lab Operation Officer B.S. Marine Biology, University of Miami (UM) Hometown: Rye, New York
NOAA Lab Operation Officer Keith Hanson with a large catch of anchovies.
NOAA Lab Operation Officer Keith Hanson sorting the catch.
Keith Hanson joins this survey to assist with research and is a knowledgeable and experienced member of the science team. Keith has taught me a lot about the fish we are collecting and was the first to show me around the ship.
Keith earned a Bachelor’s degree in Marine Biology from the University of Miami (UM) where he was vice president of the scuba club. His favorite part of being a student at UM was being located so close to ocean and the many trips he took to Biscayne Beach and The Everglades. While at UM, Keith worked as a Naturalist at the Biscayne Nature Center and with the Marine Operations Department at The Rosenstiel School of Marine and Atmospheric Science (RSMAS), where he managed boats and vehicles.
After graduating from UM, Keith started the NOAA Corps Basic Officer Training Class (BOTC) at the U.S. Coast Guard Academy in New London, Connecticut. His first assignment as a Junior Officer was on the NOAA Ship Nancy Foster in Charleston, SC which has a multi-mission platform with fish habitat and population studies, seafloor mapping surveys, oceanographic studies, and maritime heritage survey. Keith enjoys the traveling opportunities afforded in this line of work. On the Nancy Foster, he got to travel to Cuba, the Caribbean, and Mexico. After 2.5 years of service, Keith advanced to OP Officer.
Keith is currently on his land assignment in Santa Cruz NOAA working as the Vessel Operations Coordinator and he manages a fleet of small boats from kayaks to a 28 foot barge. Most vessels are used for river salmon work and groundfish research. His favorite vessel is the Egret offshore fishing boat which is used for rockfish hook and line sampling.
When asked what advice he has for undergraduate students wanting to purse degrees and careers in marine biology, he suggests getting involved in a research lab early on to gain a competitive edge.
Mission: Northern Gulf of Alaska (NGA) Long-Term Ecological Research (LTER)
Geographic Area of Cruise: Northern Gulf of Alaska
Date: 30 June 2019
Weather Data from the Bridge
Latitude: 60.32 N Longitude: 147.48 W Wind Speed: 3.2 knots Wind Direction: 24 degrees Air Temperature: 72 °F Sky: Hazy (smoke)
Science and Technology Log
We arrived in Seward mid-day on Thursday, June 27th to find it hazy from fires burning north of us; the normally picturesque mountain ranges framing the bay were nearly obscured, and the weather forecast predicts that the haze will be with us at sea for a while as well. Most of the two days prior to departure were busy with loading, sorting, unpacking and setting up of equipment.
All equipment and supplies are placed on pallets to load on board
There are multiple experiments and different types of studies that will be taking place during the course of this cruise, and each set of researchers has a specific area for their equipment. I am on the particle flux team with Stephanie O’Daly (she specifically requested to have “the teacher” so that she’d have extra hands to help her), and have been helping her as much as I can to set up. Steffi has been very patient and is good about explaining the equipment and their function as we go through everything. Particle flux is about the types of particles found in the water and where they’re formed and where they’re going. In addition, she’ll be looking at carbon matter: what form it takes and what its origin is, because that will tell her about the movement of specific types of plankton through the water column. We spent a part of Friday setting up a very expensive camera (the UVP or Underwater Visual Profiler) that will take pictures of particles in the water down to 500 microns (1/2 a millimeter), will isolate the particles in the picture, sort the images and download them to her computer as well.
Steffi’s friend Jess was very helpful and instructive about setting up certain pieces of equipment. I found that my seamanship skills luckily were useful in splicing lines for Steffi’s tows as well as tying her equipment down to her work bench so that we won’t lose it as the ship moves.
Spliced lines
Steffi’s work space
As everyone worked to prepare their stations, the ship moved to the refueling dock to make final preparations for departure, which was about 8:30 on Saturday morning.
Day one at sea was a warm up for many teams. Per the usual, the first station’s testing went slowly as participants learned the procedures. We deployed the CTD (conductivity, temperature and depth) at the second station. A CTD is a metal framework that carries various instruments and sampling bottles called Niskin bottles. In the video, you can see them arranged around the structure. The one we sent on June 28 had 24 plastic bottles that were “fired” at specific depths to capture water samples. These samples are shared by a number of teams to test for things like dissolved oxygen gas, and nutrients such as nitrate, nitrites, phosphate and silicate, and dissolved inorganic carbon.
The CTD is lowered over the side of the ship long enough to fill sample bottles and then is brought back on board. (This still photo is a placeholder for the video.)
One of my tasks today was to help her collect samples from specific bottles by attaching a tube to the bottle, using water from the sample to cleanse it and them fill it. Another team deployed a special CTD that was built completely of iron-free materials in order to run unbiased tests for iron in the water.
By late Saturday night, we will be in Prince William Sound, and will most likely spend a day there, before continuing on to Copper River. Usually LTER cruises are more focused on monitoring the state of the ecosystem, but in this case, the cruise will also focus on the processes of the Copper River plume, rates and interactions. This particular plume brings iron and fresh water into the Northern Gulf of Alaska ecosystem, where it is dispersed by weather and current. After spending some time studying the plume, the cruise will continue on to the Middleton Line to examine how both fresh water and iron are spread along the shelf and throughout the food web.
Personal Log
As the science team gathered yesterday, it
became evident that the team is predominantly female. According to lead scientist Seth Danielson,
this is a big change from roughly 20 years ago, and has become more of the norm
in recent times. We also have five
undergraduates with us who have never been out on a cruise, which is
unusual. They are all very excited for
the trip and to begin their own research by assisting team leaders. I’ve met most of the team and am slowly
getting all the names down.
I have to admit that I’m feeling out of my
element, much like a fish in a very different aquarium. I’m used to going to sea, yes, but on a
vessel from another time and place.
There is much that is familiar about gear, lines, weather, etc., but
there are also great differences. The
ship’s crew is a separate group from the science crew, although most are friendly
and helpful. Obviously, this is a much
larger and more high tech vessel with many more moving parts. Being on the working deck requires a hard
hat, protective boots, and flotation gear.
There are viewing decks that are less restricted.
I am excited to be at sea again, but a little
bit nervous about meeting expectations and being as helpful as I can without
getting in the way. It’s a little strange
to be primarily indoors, however, as I’m used to being out in the open! I’m
enjoying the moments where I can be on deck, although with the haze in the air,
I’m missing all the scenery!
Did you know?
Because space is limited onboard, many of the
researchers are collecting samples for others who couldn’t be here as well as
collecting for themselves and doing their own experiments.
Something to think about:
How do we get more boys interested in marine
sciences?
Questions of the day (from the Main Lab):
Do whales smell the smoke outside?
Answer: Toothed whales do not have a sense of
smell, and baleen whales have a poor sense of smell at best.
Mission: Microbial Stowaways: Exploring Shipwreck Microbiomes in the deep Gulf of Mexico
Geographic Area: Gulf of Mexico
Date: June 30, 2019
Science Log
When the ROV returns to the ship, the scientists jump into action. The sediment cores are brought into the lab for sampling.
Core samples are loaded on the ROV in crates and with luck they all come back the same way.
Dr. Justyna Hampel, an aquatic biogeochemist and postdoctoral research assistant at the University of Southern Mississippi, is researching how microorganisms colonize on and around deep sea shipwrecks. She is taking sediment samples for DNA testing, and identifying nutrients in sediment pore water, the water trapped inside the sediment. Her study will help us learn about the relationship between microbes and shipwreck biomes. It took many hands to process the core sediments for her research.
As assistant to graduate student Rachel Mugge, I felt a bit like a nurse in an operating room. Every sample was taken carefully to ensure it was not contaminated.
Here’s how it went: Carefully remove the plug from the bottom of the core sample tube. Slide the core onto the extruder quickly so as not to lose any sediment. (An extruder is a wheel on a threaded bolt. It is precisely calibrated to measure 2 cm increments as you turn the wheel 4 2/3 times. )
Remove the lid and use a siphon hose to remove the sea water on the surface. Rachel does this by placing one end of the hose in the core tube and the other end in her mouth and sucking gently to get the flow of water going. Once it is moving she lets the water drain into a basin. Try this at home! You can get water to flow up and over an obstacle with this technique.
It takes finesse to get the siphon working.
Next Rachel turns the extruder wheel until the mud is exposed at the top of the tube. She describes the mud to lab manager Anirban Ray, who writes it down next to the sample number. (“S 54, brown, unconsolidated, black streaks, tube worm burrows.”) I snap the paper wrapping off a wooden tongue depressor and hand it to her. She uses it to dig a sample out of the center of a sediment core. I hand her an open vial and she fills it. I cap it. Next she puts some sediment into a petri dish and Anirban seals and labels it. Then I hand her an open sterile whirl-pak for a final blob of sediment. I whirl this little baggy and twist tie it closed. Vials and whirl-paks go in the deep freezer. We do these three steps 40 times for 120 samples. The challenge I find in this kind of repetitive task is how quick and efficient can I be while still being careful and precise? Let me tell you. Pretty fast and efficient.
Putting a sediment sample into a vial. The core is on the extruder, which pushes the sediment upward when you turn the wheel.
At the same time this was going on, Justyna was extracting pore water (water that comes from inside the sediment) to analyze it for nutrients.
Justyna attaches syringes to the peepers to extract the pore water from the sediment.
Personal Log
While we worked, I had a porthole at my station to keep an eye on the ocean as we cruised out to our third and final shipwreck. Dolphins raced with our ship this evening. Silvery flying fish skittered over the water reminding me of hummingbirds, the way their fins were a blur of movement. The color of the ocean now can best be described in terms of watercolors. Ultramarine. That says it all.
