Shelfwide Hypoxia Cruise 2017

Recently, I’ve been lucky enough to take part in Dr. Nancy Rabalais’ annual mapping of the hypoxic zone in the Gulf of Mexico. Dr. Rabalais has led this cruise for the past 31 years, and has graciously allowed me onboard the R/V Pelican for my first research cruise. This cruise set out July 31st and returned on August 1st.

The R/V Pelican in dock at LUMCON before departure.

My primary role was to collect surface water at each site that will be used by the Rabalais Lab for water nutrient and suspended sediment data. This consisted of throwing the infamous bucket overboard:

Water collection with the surface bucket.

While onboard, I also was able to collect some samples for the Thrash Lab. I sampled from stations nearshore on transects that extended outward from our Board of Regents coastal sites that we have been visiting for the past few years (check out Henson et al. 2016 for more info). I collected surface water via the CTD from sites of interest and used a peristaltic pump to size fraction the water through 2.7um and 0.2um filters. These filters will be used to study the community composition of sites offshore in relation to the three year data that we already have from our coastal sites.

IMG_2597 2
My filtering set-up in one of the labs onboard. The seas were mostly calm, so I was able to only lightly strap my materials.
LSU Research Assistant Tom (left) and LSU undergraduate Ethan (right) casting the CTD. Notice the lovely view at midnight.

The first day of the cruise was a bumpy ride, and I was a little seasick despite the motion sickness medicine. Gladly, the waves soon settled, and the rest of the cruise was smooth sailing! I was on the night shift (7pm-7am), which meant that we got to see all of the cool fauna! The floodlight that followed the CTD into the water was a beacon for sealife, and we saw jellyfish, eels, squid, dolphins, crabs, and fish off all kinds. The fauna actually became an indicator of the dissolved oxygen in the bottom waters. Often when we found crabs and eels swimming on the surface, the bottom waters had very low oxygen levels or were virtually anoxic. While we waited for the CTD to come back onboard, we sometimes netted some Sargassum to see what kind of critters were living there.

Cute fish that we pulled from the Sargassum (we threw it back).

One of my favorite parts about the trip was the spectacular views of the sky. At night on the shelf, the only lights come from oil rigs. Sometimes we were quite close to these rigs…

Oil rig next to our C6C sampling site. It was really neat to see one this close.
…while other times we were pretty far from their light pollution. When we found ourselves distanced from the rigs, the stars lit up the sky, and the Milky Way was visible from the bow of the ship. We often laid there gazing upwards and talking about our lives and how the open sky humbled our problems. I didn’t have a camera capable of imaging the night sky, but I did get some shots of the sunrises and sunsets that we witnessed:
Sunset from the bow of the boat.
Probably the most vivid sunset of the trip.
Sunrise from the work deck.
Overall, this was both a great sampling trip and an amazing life experience. I bonded with the science and boat crew, and learned so much from Dr. Rabalais, Dr. Turner, and Wendy. I am thankful for this opportunity, and eager to be at sea again.
The highly fashionable safety gear required on the work deck.
Check out for participants, daily logs, images, site maps, and results of this cruise (spoiler: the hypoxic zone this year is record breaking!), and follow me @vclanclos on twitter!

Breathless: Mike’s Journey to Find Elusive Bacteria in the Oxygen-less Ocean

By Paige Jarreau. LSU biological sciences graduate student Mike Henson recently conducted field research in the great big blue! Mike works in Dr. Cameron Thrash’s lab. We asked him to tell us more about his field experience at sea below. Enjoy!

Port is now behind us! The R/V Oceanus and crew is headed to sea. Credit: Mike Henson.

Waves stretch far into the horizon. The sun’s rays pierce the crystal clear blue water. The ocean here gives no hints about its oxygen-less waters beneath its depths. Yet, about 100 miles west of Manzanillo, Mexico in the Eastern Northern Tropical Pacific is one of largest anoxic bodies of water, or oxygen minimum zones (OMZ), in Earth’s oceans.

OMZs form when nutrient rich bottom waters from the Pacific Ocean are brought up to the surface, causing large blooms or growth explosions of photosynthetic algae. As the algae begin to die, other microscopic organisms (or backterioplankton) in the water consume oxygen to metabolize organic matter produced by the algal cells. Once you reach 100 meters below the surface, oxygen levels begin to decrease. At 300 meters, the oxygen has been completely consumed. Any organisms such as fish passing through these areas that are incapable of living without oxygen will die unless they can escape to the more oxygenated surface waters.

This may sound familiar to many Louisianans. However, unlike the hypoxia (a.k.a. the “dead zone”) that occurs seasonally in the Gulf of Mexico from nutrient pollution, this naturally occurring oxygen minimum zone is present year-round.

In the Thrash lab, we study the microbiology of northern Gulf of Mexico hypoxia. We are also collaborating with Chief Scientist Dr. Frank Stewart of the Georgia Institute of Technology, who has National Science Foundation funding to study the oxygen minimum zone in the Eastern Northern Tropical Pacific. Scientists from eight different countries, including USA, Canada, Mexico, Iceland, Denmark, Austria, Spain, and Germany, myself included, recently spent three weeks aboard the R/V Oceanus collecting water and sediment to elucidate the organisms and processes involved in forming this peculiar area of the ocean….

See the full interview with Mike and Paige Jarreau, including some epic photos, at The Pursuit LSU College of Science Blog HERE.

Thrash lab presentations at #ASMicrobe

Mike, Celeste, and Emily will all be presenting at the 2017 ASM Microbe conference in New Orleans this coming weekend. Here is the info to find them:

Saturday (6/3)
Poster Session: AES11 – Freshwater and Marine Microbiology I
Time: 12:15 PM – 2:15 PM

Cultivation and Ecology of Novel SAR11 Taxa from Coastal Louisiana Waters (#700), V. Celeste Lanclos

Metabolic and Physiological Flexibility in a Coastal Isolate from the OM252 Clade of Gammaproteobacteria (#712), Emily Nall

Sunday (6/4)
Symposium: 425 – Culturing the Unculturable in a Sequencing Age (Room 352)
Time: 2:30 PM – 5:00 PM

Fresh and Salty: Cultivating Bacteria from the Coast of Louisiana, Michael W. Henson

Storify on finishing bacterial genomes

Usually when you sequence bacterial genomes, the process of completely closing them (so-termed because most bacterial genomes are circular) whereby a single scaffold overlaps itself at the ends, requires a lot of effort. We’ve had very good luck with our Illumina sequencing and SPAdes assembly process, negating the need for things like primer walking, and we’re very close to finishing two very important genomes. Since this is unfamiliar territory for me (almost all genomes I’ve worked with thus far have been “draft” quality, usually with multiple scaffolds), I queried the Twitter micro community on the best methods for verifying a closed genome. This is from yesterday….