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Another day at sea – one of our last for this cruise.

My name is Laura Timm and I am a PhD student at Florida International University. This is my fourth DEEPEND cruise and the data we collect from it will contribute to the last chapter of my dissertation.

I work on crustacean genetics. Specifically, I use the DNA of a few shrimp species to describe diversity and characterize how (or if) it is moving within the Gulf. These two things, diversity and gene flow, provide a lot of insight into the health and resilience of these target species. Most of my work with DEEPEND has focused on three shrimp: Acanthephyra purpurea is a bright red color and produces a bioluminescent spew to scare off predators.



Systellaspis debilis is also red (though younger ones can look orange), but with tiny light-producing organs called photophores polka-dotting its body.



Sergia robusta can be dark red or even purple and has photophores around its mouth and tail.


To me, all three are uniquely beautiful.

My research focuses on questions related to genetic diversity, which is a good metric for species health. Where is the most diversity found? Has this changed since 2011? How is diversity distributed? Is some genetic diversity unique to certain places? Answers to these questions provide unprecedented insight into how the Gulf copes with disturbances.

Now, a little perspective.

We trawl with a MOC10 net. It is very large. Every person on the ship could go stand in the frame of the net. However, when compared to the size of the ocean, it is tiny – it has been described as the equivalent of investigating terrestrial diversity using just a butterfly net. Yet, we still catch thousands of shrimp. Of these thousands of shrimp, a few hundred are targeted (A. purpurea, S. debilis, S. robusta). Of these hundreds, 96 are sequenced (this is due to the sequencing process; I can only sequence 96 at a time). The genomes of these species have not been sequenced, so I target a few thousand base pairs of DNA. A few thousand base pairs out of billions of base pairs. About 100 shrimp out of hundreds, hundreds out of thousands, thousands out of every shrimp in the Gulf. This tiny amount of data (which, in the history of science, is unprecedentedly large) can tell us so much about the animals living in the Gulf and how they came to be there and whether they are likely to survive whatever comes next.

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Written by Tess Rivenbark



My name is Tess Rivenbark and I am representing the Optical Oceanography Lab at the University of South Florida College of Marine Science. Most of the scientists here focus on biology, but my job is to collect data that ties this biology to the physical processes happening in the ocean, looking at different types of particles in the water. 

With the CTD, I collect water samples and then filter them to measure chlorophyll and colored dissolved organic materials. Here is a picture of the CTD as it is being deployed from the ship. We send it down to 1500 meters collecting water samples along the way at various depths and measuring the physical properties of water such as temperature, salinity, and dissolved oxygen.
Another instrument I use, a spectral backscattering sensor, is known to the other scientists as the "fish disco" because it emits multi-colored lights. It measures how these lights bounce, or scatter, off of particles in the water. 
My last instrument, a handheld spectral radiometer, measures the sunlight that reflects off the water. This is the same thing that many satellites orbiting the earth, like the Aqua MODIS, are measuring. We use the data we collect out here on the water to help understand what the satellite measurements tell us about the particles in the water. The two photos below show this instrument in use at sea and below that is a satellite image showing the concentration of chlorophyll with our proposed cruise track and sample stations plotted on top.
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For centuries, sailors and scientists have observed birds landing on ships. A ship out at sea is like a moving island in the ocean. Various birds may seek refuge on ships, especially when storms occur, or are attracted to the lights of the ship at night. It makes sense that many of these birds are sea birds, but a number of land birds may make migrations across ocean areas or get blown out to sea by storms along the coast. Given the several storms during our cruise, it is no surprise we have had a number of birds land on or fly close to our ship, while it was 100-150 miles off the coast of Louisiana, Mississippi, and Alabama. So, here is a short rundown of the birds we have seen recently…


Purple Gallinule – spent a couple days resting on one of the deck cranes until it took off.


Louisiana Waterthrush – this wood warbler took refuge in a corner of the deck for a while before flying away.


Northern Oriole – just showed up on the ship superstructure, rested for an hour, and took off.


Cattle Egrets – we have had several stay around the ship, with a flock of 14 circling the ship one morning.


Bobolink – a few individuals flew around the boat this morning and one perched on the anchor chains and other structures on the bow.


Barn Swallows – One morning just before another squall, there was a flock of approximately 100 circling the ship from 5-6 AM. A flock of about 8 flew by the ship yesterday after several days of clear weather. This morning 3 were perched on some fixtures.


We also had a very large flock of a small birds that might have been American Goldfinches, but it was too dark at 4-5 AM to see them clearly.




Coastal birds we have also seen far out at sea include…


Osprey – one landed on a container on the forward deck, sat for a few minutes, and then left when it was disturbed by a crew member.


Brown Pelicans – three juveniles paddled along with the ship and flew short stretches to catch up again.


Caspian Tern and Royal Terns – one Caspian and two Royals sought a perch on a part of the stern of the ship during a rain storm.


Laughing Gulls – 3 juveniles and 1 adult stayed around the boat for a day during and immediately after a storm.


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 Studying the animals in the deep sea within their natural habitat is very difficult. It often requires sophisticated instruments or equipment and scientists have to be careful to make sure that they don’t disturb the animals they are studying. During the DEEPEND cruises, we use sound to study how animals move through the ocean and the daily movement patterns as they go up and down from the surface at night to the deep sea during the day.  Using sonars, we can create a picture of where the animals are by measuring how much sound they reflect. While this gives scientists a broad picture of where the animals are, it does not provide enough detail to look at the individuals within the layers.

During this cruise, we have been using a new tool to study fish and invertebrates down in the depths of the ocean. We have attached an autonomous sonar (WBAT- WideBand Autonomous Transceiver) on to the MOCNESS (see photo above) to look at the animals that are near the net. This new sonar provides much higher resolution data at small scales, kind of like an underwater magnifying glass.  With this new instrument we can look at the individuals that are being collected by the MOCNESS and then compare this back to what we see on the ship’s sonar. So far we have noticed that the animals do not seem to avoid the net as we expected they would.


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This is my first research cruise in over ten years, and I am quite excited by the great opportunity.  I once went out to sea fairly routinely when I worked at Harbor Branch Oceanographic Institution (HBOI), but the goals were much different then. This time for DEEPEND, we focus on the pelagic mid water column organisms in the Gulf of Mexico, which remains a fairly new habitat for me to explore.
My role for DEEPEND on this DP05 cruise is to ensure proper collection of new bacterioplankton samples from Gulf of Mexico seawater at various depths.  I am basically following the same procedures as past cruises for consistency.
The main instrument for collecting water is the CTD (conductivity, temperature, and depth) which is loaded with a rosette (circular arrangement) of twelve Niskin bottles that can each hold 12 L. These traditional aquatic water collectors close at precise depths which I can control from the ship. R/V Point Sur crew member, Marshall Karmanec, helped get me accustomed to running and deploying the CTD on this cruise. With the controls, I can designate where and when bottles are opened at specific depths. Once the bottles are filled and back on deck, I am able to drain 4-5 L of seawater and bring them into the lab.  I share a filtering station corner of the ship’s lab with FWC/USF technician Tess Rivenbark.  While most of the other DEEPEND scientists are identifying charismatic deepwater megafauna, I filter marine microbiomes onto special sterile 0.45 micron filters. “Sterile” is the operative word here, since the lab is not the optimal place for traditional “microbiology” methods. Essentially I am preserving the communities on the filter by careful handling, freezing and recording, so they can all be brought back intact to my molecular lab at the NSU Oceanographic Center for DNA extractions and sequencing that will eventually illuminate the distribution and dynamics bacterioplankton in much greater detail.
b2ap3_thumbnail_sunset.jpgThe CTD also measures where the very important oxygen minimum and chlorophyll maximum zones occur vertically within the water column.  These zones represent important parameters for oceanographic work since they can delimit where food chains begin or end, where maximum photosynthesis (the production of oxygen from cyanobacteria) happens, and we also have found distinct microbial communities (also known as “microbiomes”) associated with each zone. With DEEPEND postdoctoral scientist Cole Easson, we have been characterizing these microbiomes from past cruises, and our current results point to significant depth stratification of microbiomes in DEEPEND Year 1 data, which among other interesting findings will be submitted in a forthcoming manuscript.  This year 3 sampling adds to the temporal dimension of the project and is also very exciting.

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On every cruise, it’s tradition to send decorated Styrofoam cups down on one of the instruments to shrink them.  Styrofoam is mostly air, so when cups made of Styrofoam are sent to the depths, as the pressure increases with depth, the air inside the cups is compressed, and the cups shrink accordingly.  Once they shrink, they stay that way, as Styrofoam isn’t particularly flexible – it doesn’t expand again when it comes to the surface.  This year, we received a set of beautifully decorated cups from Theresa McCaffrey’s Advanced Art Classes at Tualatin High School.  Ruth Musgraves, who developed and runs our Creep into the DEEPEND summer camps ( has a daughter in one of these art classes, and they heard about the shrinking cups through her.  They send out a box of cups, and the artwork is quite amazing, as you can see in the photos below.   The best part is that they made some cups for us as well.

I’m really thrilled about that, because I’m pretty much still at the stick figure level when it comes to my artistic endeavors.


There is a pretty careful protocol that we must follow to package the cups, so that the cups shrink without collapsing inside of each other as they shrink at different rates.  If two cups shrink together, one inside of the other, they’re almost impossible to get apart without breaking one.  They must be loaded in mesh bags with open ends facing each other, with each row separated by tie wraps so they don’t float together and collapse together. 

We can load 14 cups per bag, and two bags per CTD rosette.   The CTD rosette is deployed to collect water samples at various depths, monitoring conductivity (C – as a measurement of salinity) and temperature (T) as a function of depth (D).  We have to be careful that the bags do not interfere with any of the sensors or closing mechanisms on the bottles, so we never load more than two  bags per deployment.

We had just finished shrinking all the cups, and the CTD was down, cupless this time, when a squall came through, and 10 foot swells came along with it.  The CTD had to be brought to the surface immediately, and it was quite a dangerous recovery trying to keep the CTD from swinging like a pendulum with safety lines.  As you can see, the cups are just attached by tie wraps, and in those seas, the bag might have snapped off or cups damaged when the protective frame around the rosette was pulled next to the ship to prevent swinging.   We lucked out on that one!   

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Written by: Matt Woodstock – DEEPEND graduate student, Nova Southeastern University

Hello, my name is Matt Woodstock and I am a graduate student at Nova Southeastern University working with the DEEPEND Consortium. This is my first time on a research cruise and I wanted to share a bit of my experience so far. Our ship, the R/V Point Sur, is equipped with all the supplies we need to do our science.

Pictured here (Left to Right): Gray Lawson (Technician), Joe Lopez, Travis Richards, Laura Timm, Tracey Sutton, Jon Moore, and Rosanna Boyle

 My job aboard the ship is to help Travis Richards (PhD student at Texas A&M Galveston) pull tissue samples for genetic sequencing. An average day for us begins early in the morning, hauling nets in from the tow the night before. We sort through each sample, dividing the fishes, crustaceans, squids, and jellyfishes.

Pictured here (Left to Right): Tammy Frank, Tracey Sutton, Mike Vecchione

After being identified by our experts, the animals are measured, weighed, and organized so they can be sent to different labs that study each species. We are currently freezing animals for stable isotope analysis, polycyclic aromatic hydrocarbon (PAH) analysis, and parasite analysis (my thesis study).

 A Red Velvet Whalefish, Barbourisia rufa, caught between 600-1000 m that was sampled for stable isotope and genetic sequencing

Three Helmet Jellyfish, Periphylla periphylla, caught in an oblique tow (0-1500 m) is a deep-sea bioluminescent jellyfish

Other animals are persevered and sent to several different labs for later studies. We do this twice a day (day and night) and observe differences in the distribution of animals on a diurnal cycle. Occasionally we will take a break from our sample processing to see anything cool happening on the deck. This morning, we saw the sunrise.


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Hello everyone!

Well, our first day of sampling was a success! We managed to deploy the MOCNESS twice at Station B081 (check out our home page to follow the ship!). While retrieving the night trawl we saw a lot of bioluminescence in the water which turned out to be pyrosomes, Pyrosoma atlantica, seen in the picture below. Each pyrosome is a colony of animals called tunicates which related to sea squirts. They form a tube which can pump water to allow them to vertically migrate. The longest species of pyrosome can get up to 20 m in length! We also saw some flyingfish which were being chased and eaten by dolphins!


Today we continued on to B082 and completed two additional successful trawls. Below are some images from the team processing the catch.


Here several of us are emptying the codends and sorting the catch.


Once we've sorted the catch, our team of taxonomic experts identify each organism to species. From front to back we have Dr. Tracey Sutton, Nova Southeastern University who specializes in fish identification, Dr. Jon Moore, Florida Atlantic University who also specializes in fish identification, Dr. Tammy Frank, Nova Southeastern University who specialized in shrimp identification, and last but not least, Mike Vecchione, NOAA's National Systematics Lab specializes in squid identification.


Here, Laura Timm, PhD student at Florida International University takes the species identified by Dr. Frank and samples them to run genetic analyses back in her lab after the cruise.


Travis Richards (foreground) is a PhD student at Texas A&M Galveston whose research involves stable isotope analysis, however, on this cruise he is taking tissue samples for the fish genetics team with the help of NSU graduate student, Matthew Woodstock (middle). I'm at the end of the line in this picture measuring fish lengths.


Our DEEPEND mascot, Squirt, hangs out with us in the lab making sure we're doing our job! You'll see more of him this week on instagram - @deepend_gom

The acoustics team have detected some very large animals under the ship. They will be blogging all about their new gear and what they are "seeing" with sound later this week!

Thank you for following our blog and stay tuned for more!


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