2015 Summer Course on Microbial Oceanography

Okay, first off, sorry for all these late posts. This summer has been pretty crazy for all of the Thrash lab! We have been busy with sampling, trips, etc…safe to say, we have generated plenty of data this summer.

This summer I was able to take part in the 2015 CMORE Summer Course on Microbial Oceanography. The course is roughly a five week long intensive learning environment hosted by the Center for Microbial Oceanography: Research and Education at The University of Hawaii Moana in Honolulu, Hawaii.  In total, 16 students from around the world (Germany, Austria, Israel, Spain to name a few) were invited through an application process to attend the course titled ” Microbial Oceanography: Genomes to Biomes”.

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2015 CMORE summer course students and some faculty

After some awesome introductions the first day by Dr. Dave Karl, Dr. Matt Church, and Dr. Ed DeLong, we started our first week of lectures from our main speakers Dr. Angelicque White, Dr. Mick Follows, and Dr. Dan Repeta. The topics covered nutrient cycling to modeling and focused more on describing the ocean as a habitat. For me, it was my first time really tackling this type of information and it was a lot of information to take in. But lucky for me, we had some of the best teachers there to help us through it all.

Even though the group came from a diverse background, we all felt a strong bond with each other.

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Hiking with the group before the course started.
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Enjoying a night on the beach with everyone after our first day of the course

The second week focused on Genomes and was taught mainly by Dr. Greig Steward, Dr. Craig Nelson, Dr. Ed DeLong, Dr. Alison Murray, Dr. Eric Allen, Dr. Bethany Jenkins, and Dr. Penny Chisholm. Topics including sequencing techniques, analysis of genomic data, Antarctica, Eukaryotes, microbial ecotypes, and much more. It was another awesome week that brought us to the end of our lecture portion and one step closer to getting on the RV Kilo Moana for a 7 day research cruise.

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Getting a tour of the sequencing facility at CMORE Hale
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The new Illumina technology for library prep using microfluidics
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The new NeoPrep machine from Illumina
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Why not have a robot to prep your samples for you

The RV Kilo Moana was an amazing ship and quite big. Especially if this was your first time being on a research cruise or a research vessel. I guess, I was a bit spoiled.

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The Kilo Moana at port

The cruise was one of the things I was most excited about. And to be honest, it was amazing. The CMORE crew did an amazing job prepping the ship and materials for us to use. During the cruise, we had five groups that rotated through five “stations”. The “stations” were flow cytometry (counts and sorting), molecular (DNA extractions, PCR, Sequencing Prep), physical oceanography (CTD prep, casting, retrieval ,etc), productivity (PP and BP), and nutrient analysis (Chlorophyll, ATP, Nutrients). Each day gave us a new station to work at and the ability to learn new techniques. To be short, for those familiar with the Hawaiian Ocean Time Series (HOTS), this is the type of data we collected. The data we collected and analyzed as well as protocols can be found on the CMORE website.  The cruise was hard work and I found myself learning something new every time we did a station. We even learned what happens when an array gets too close to the boat 🙂 .

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How you solidify a gel on a moving boat.
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Dr. Church doing his favorite thing…working the winch..though most of the time it was the students doing this.
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Waiting to recover a productivity array which we deployed every day
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Obligatory selfie
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One of the many amazing sunsets
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Bringing back the CTD
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A view from above
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Sorry but I love sunsets while on the water
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Trying on our Gumbi suites
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Heading out to sea
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Working on our C14 Primary Productivity samples
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Just catching a rainbow

It is hard to put into words how much I learned on this trip, how many new friends and colleagues I gained, and the amount I grew as a scientist. I cannot thank all the individuals that put this on, participated in, and helped out with this course enough.

Enjoy a little closing video I made for the group and everyone after we presented our data at a seminar for all SOEST and CMORE.

Sorry the movie had the music removed 😦

Failed dive attempt at C6C

Last week we sailed on the R/V Acadiana to C6C to de-winterize the SONDE attachments only to be stymied by a jack-up rig and increasingly bad sea state. We sailed for three hours, and when we arrived, the water was calm enough to dive, so we suited up. With the first team of divers literally standing on the transom to jump in, a jack-up rig radioed for us to wait so they could post up near our dive site. We waited for two hours on station (incidentally, we could have completed everything we needed to do in that time), with 10-15 kt wind on the water for the duration, and when the first team finally splashed, the sea state was trash. Dive Safety Officer Lora Pride called it all off. These things happen. But there were some good photos, and a video of the scene out there at C6C before we got stopped, so I thought I’d post them. We’ll be out again soon.

The R/V Acadiana poised for action at dawn
The LUMCON docks at 0 dark 30.
Heading out, with an old friend coming in – the R/V Pelican returning to LUMCON
Breakfast on the ship- a major perk of the Acadiana!

Here you’ll see some video of one of the many service helicopters that land on the rig and some of us getting ready on the back of the Acadiana. The sea state is relatively calm at this point, so it would have been perfect timing to dive.


Back at the dock, our dive flags still flying. We’ll get ’em next time


FRONTS: a 24 Hour Microbial Survey

A few weeks back, Dec. 18-19, Dr. Thrash and I took part in sampling the tidal exchange at Barataria Pass in Grand Isle, Louisiana in collaboration with Dr. Chunyan Li (http://www.oceandynamics.lsu.edu/) from the LSU Department of Oceanography and Coastal Sciences. The sampling involved a 24 hour survey across Barataria Pass collecting physical ocean, microbial community, and chemical data.

The day started early with us leaving Baton Rouge at zero dark thirty so that we could be in Grand Isle and ready to sample by 0900. Beyond running out of coffee mid trip, the drive down was smooth and filled with great views of the land slowly disappearing to be replaced by more and more water. Once on Grand Isle, we made base camp at the cozy Sand Dollar Motel and the accompanying marina.

This type of sampling was a first for me. The sampling scheme had a crew, composed of Dr. Li, Dr. Thrash, Mr. Eddie Weeks, and myself, sampling every 4 hours. The sampling consisted of collecting water for microbial community and chemical analysis, and realtime data from a YSI and CTD at three different points. Then two laps across the Barataria Pass were performed to collect the physical data using an acoustic Doppler current profiler (ADCP) attached to the front of our boat.

View from the docks in at the Grand Isle marina
The sampling gear getting ready to be loaded onto the boat.

The sampling would take about an hour from start to finish. The water was collected using a peristaltic pump that was onboard the boat and the water was transferred to shore where the filtering took another bit of time. We used the same protocol we have detailed before and you can watch here: https://thethrashlab.com/2014/10/08/thrash-lab-sampling-at-calcasieu-lake-jetties/

Mr. Weeks, Dr. Thrash discussing science during an ADCP run.

We were lucky because for the most part the water remained calm, and the rain held off for most of the day and night. The weather was a bit chilly for the Louisianans, but I didn’t mind it too much. On many of our passes, we were lucky enough to be accompanied by dolphins, who seemed to very interested in the ADCP that was on the front of our boat.

The ADCP on front of the boat that seemed to really excite the dolphins.

They would swim along with us as we sampled and recorded our data, and even sometimes interrupted the signal by swimming underneath.  However, they made for awesome pictures and entrainment. Not many microbiologists get to say they sampled with dolphins.

A dolphin swimming in front of the boat as we sampled with the ADCP

As most of you readers know, the Thrash lab really enjoys finding new ways to showcase the science we are doing; this blog being one of them. While sampling for this project, we were lucky enough to have the talents of Mr. Eddie Weeks, who also works as a drone pilot for a variety of purposes. You can check out some of his videos here http://vimeo.com/user473306.  Mr. Weeks, along with driving our boat and helping sample, brought along a drone to help video some of our work. We were able to use our GoPro to video some of our setup process in between sampling. In the future, we hope to use a more detailed setup but for now this is pretty awesome if you ask us!

The drone
Getting ready to fly the drone.

Though the sampling was long, we made it through the whole 24 hour period successfully and got some great images and data to go along with it. We would like to thank coffee for its kind contributions of keeping us awake during this trip including the 0400 time point.

The crew at 4am. We probably needed more coffee.

Cheers to all and hope everyone had a safe and fun holiday break.

Signing off,


Platform dive number 3 at Pelto-6.

Last Saturday (12/5/14) we trucked out to Pelto-6, an unmanned platform near C6C, for more training dives and practice with underwater sample collection for me. While it was raining in Baton Rouge, we had a beautiful warm day in the Gulf. Water temps were ~69˚F, max bottom depth was 46 ft. There were some Portuguese man of war on the surface, but they were drifting away from the platform and posed a minimal danger. On our third dive of the day, I shot this GoPro footage (Hero 3). It’s a little shaky, sometimes pointed in the wrong direction, and I need to move my head more slowly. But it’s useful and you can see a massive school of catfish that were hanging out in the middle of the rig, along with some other interesting creatures.


Shelfwide cruise roundup, for now

Nancy Rabalais’s team has been able to process some of the data and issued a press release on this year’s bottom water hypoxia. As I mentioned in the last post, the zone of hypoxia was actually two zones, which you can see below. The total estimated square mileage of bottom water at or below 2 mg/L dissolved oxygen was 5,052 square miles/14,785 square kilometers, which is almost three times larger than the goal proposed by the Mississippi River Gulf of Mexico Watershed Nutrient Task Force in 2001 and 2008.

Bottom water dissolved oxygen measured on the 2014 shelfwide cruise. Source: Nancy N. Rabalais, LUMCON, and R. Eugene Turner, LSU
Bottom water dissolved oxygen measured on the 2014 shelfwide cruise. Source: Nancy N. Rabalais, LUMCON, and R. Eugene Turner, LSU
Surface water chlorophyll a measured on the 2014 shelfwide cruise. Source: Nancy N. Rabalais, LUMCON and R. Eugene Turner, LSU
Surface water chlorophyll a measured on the 2014 shelfwide cruise. Source: Nancy N. Rabalais, LUMCON and R. Eugene Turner, LSU

I can provide some additional thoughts with pretty HD video to boot. The eastern stations, as seen in the chlorophyll map, were predominantly green water, with considerable phyotoplankton mass present in the water column. We could observe significant green-colored biomass both on the GF/D pre-filters and the 0.22 µm Sterivex filters. This is also what you see if you are actually in the water, and the video from the green-water CTD cast at station B6 confirms what was seen with the CTD instrumentation and the filters. Convenient, eh? There is dense, murky greenness at the surface. Deeper, the visibility improves as we get below the highest biomass concentration, but towards the bottom, where hypoxia was observed, we again see increased turbidity, but of a different sort. It’s much whiter than that at the surface. On the return trip, considerable marine snow can be seen (along with a jelly or two and other marine invertebrates).


The western stations, as you might imagine by looking at the surface chlorophyll data, were blue water, with very little phyotplankton mass compared to the eastern stations. The cast at station K3 shows beautiful blue water with high visibility (diver’s paradise), but as you descend, you again pick up the whitish turbidity at the bottom layer where hypoxia was observed.

Sterivex filters from this section were light pink, a phenomenon we observed last year as well. The 16S rRNA and metagenomic data will, among other things, help us uncover a bit more about the variant prokaryotic taxa seen in these contrasting zones of hypoxia.


2014 Shelfwide cruising update 4

Well, that’s all folks. We’re headed home. We only found isolated pockets of hypoxia found a smaller coastal patch of hypoxia west of the F line. We searched western transects all the way to the P line, which is off the map I posted below in the first update. All in all, Lauren and I collected over 100 samples. It’s going to be an exciting dataset, for sure. I’ll update the blog with higher quality images when I get back, and look for some cool CTD cast videos, brought to you by Mike Henson’s GoPro.



2014 Shelfwide cruising update 3

We’ve finished the H transect and are motoring westward to I. As of now, we have observed no hypoxia west of the F line. However Nancy and Gene have described situations in the past where the hypoxia is discontinuous. We will know soon enough. The last couple days have been very calm, with almost glassy seas. It hasn’t been terribly hot either, so all in all, it’s a pretty ideal situation for sampling. Lauren and I have filtered 3-12 liters from the surface and the oxygen minimum at over 35 sites so far. This will be combined with lots of additional metadata being collected via the CTD and other researchers on board.