Sampling the Mississippi River Delta

Mike and I went on a sampling trip Tuesday (1/12/16) to the Mississippi Delta (“The Birdfoot”) near Buras, LA. This was my first sampling trip ever with the Thrash lab, and I must say that it was a great experience! We headed out loaded up with our equipment and coffee, and ended up with a fantastic view of  the sunrise at the edge of Lake Pontchartrain. Sadly, the picture does not come close to the beauty of  our actual view.

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Sunrise at the edge of Lake Pontchartrain

At the site, Mike waded out into the water to collect the sample while I got to hang back and enjoy the scenery. It was a great day to be outdoors with cool air and the sun shining.

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Our view from the dock

 

Some pelicans that didn't seem to mind us
Some pelicans that didn’t seem to mind us

 

Mike taking YSI readings
Mike taking YSI readings

 

Mike filtering a water sample
Mike filtering a water sample

Overall, I really enjoyed my sampling adventure with Mike. This trip was a part of our 3 year study of the coastline to characterize the microbial population of the Louisiana coast in conjunction with adding microbes to our Louisiana State culture collection (LSUCC) from the Gulf of Mexico. I’m hopeful that we will isolate some novel organisms from this and future trips. Not all undergraduates are lucky enough to be a part of a lab that allows us to be out in the field for data collection, so I’m grateful to Dr. Thrash and Mike for the opportunity!

 

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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 😦

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.

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View from the docks in at the Grand Isle marina
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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/

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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.

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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.

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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!

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The drone
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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.

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

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

Signing off,

Mike

Our Trip to the Atchafalaya River Delta for sampling

Well it was that time again, time to go acquire another water sample as part of the LSU Culture Collection and surveying of the microbial communities of Southern Louisiana coastline grant. For this site, because we had a prospective student with us, we decided to pick somewhere to see the beauty of Southern Louisiana. Though I find myself spoiled having lived near Pictured Rocks National Lakeshore and Sleeping Bear Dunes in Michigan, there is nothing like driving along a road with over hanging Oak tree branches that are covered in Spanish Moss with the sun just peaking through. So we picked a site near the Atchafalaya River mouth, the site was Burns Point Recreational Park in Franklin, La.

The “adventures” have become less dramatic as we have become more acquainted with how to properly get our act together, but this time instead of a change in site like the last time, it was just cold. Okay… for most of you not from the South, it wasn’t that cold. It was roughly 32-40F when we were driving and sampling and for someone from the North after the last winter this weather is getting close to shorts weather.

Burn's Recreational Park, Franklin, LA
Burn’s Recreational Park, Franklin, LA
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The cool transition zone between the Bay and the swamp area. This was to the right of where we sampled.

With the help of some friendly Duck Hunters of Louisiana, we were able to have a sample taken just off the launch site away from the shoreline and boat channel.

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Looking out towards Marshall Island and where our sample was taken.

Once we had our water sample, we followed our previously demonstrated protocol (see https://thethrashlab.com/2014/10/08/thrash-lab-sampling-at-calcasieu-lake-jetties/) of filtering 100mL of water through a 2.7um prefilter followed by a 0.2um sterivex filter. We also collect water for nutrients and cell culturing. To compliment the nutrient data and to provide ever more information, we also took our handy YSI reader with us to get real time data from the site.

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Don’t say that as a Graduate student you don’t get to live dangerously, because I will have you know that those rocks were slippery when I took the YSI readings!

Once all the data was collected and filtration done, it was back to the lab to prep the sample and inoculate dilution plates for cultures.
So cheers to another round of successful sampling and here is to hoping we “Catch ’em all”.
–Michael Henson

Thrash Lab Sampling at Calcasieu Lake Jetties

About a month ago, David Pitre (Thrash Lab undergraduate) and I went on our first excursion to collect Gulf of Mexico water samples as part of the LSU Culture Collection and surveying of the microbial communities of Southern Louisiana coastline grant. The Gulf of Mexico offers a vast realm of sampling sites for a microbiologist. Many sites around the Southern Louisiana coastline have never been characterized and are waiting for scientist like us to reveal their secrets and potential new uncharacterized microbes. One might say the Thrash lab motto may be “Gotta catch ‘em all”.

Like most great scientific expeditions, it started off with a change in sites. Though Louisiana does not suffer from a lack of water and coastline, roads leading to that coastline tend to disappear and end abruptly. So, with no road and a swath of bugs finding their way towards us, we decided it was appropriate to change our site from Freshwater Bayou (Kaplan, La) to the Calcasieu Lake Jetties (Cameron, La). An hour and a half drive east, and we arrived at the Calcasieu Jetties to an awesome view of the Gulf of Mexico and even some sandy beach!

Though the trip was for work, as a Northern kid, I always get excited seeing the beach and ocean.

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Calcasieu Lake Jetties (Cameron, La)

But we had some water to collect, so we got the filtering things ready, got my waders on, and I headed out about a quarter of a mile into the Gulf to collect our first sample.

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Heading out to sample
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The journeying out to collect our samples
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Yeah, I am out there

Once the samples were collected, they were brought back to our informal lab (the trunk of my car) and processed. Samples were collected for high thoughput culturing, cell counts, nutrients, and community sequencing (planktonic and particle associated). Samples were placed into our coolers and brought back to the lab for final processing.

Overall, it was a great trip and a great sampling site. Louisiana offers a beautiful coastline with ample sampling opportunities! Now I am back to continue to monitor isolates that we captured from the Calcasieu Lake Jetties sample. Here is to some exciting new cultures…Cheers!

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–Michael Henson

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.

-jct

First run on the Barataria Transect

Yesterday I joined Jim Lee and Charlie Milan to help them execute sampling for the monthly Barataria Transect, one of Eugene Turner’s projects. His lab has been doing this transect, monthly, since 1994 to monitor water chemistry and some of the biology that occurs across this contiguous estuarine system. Over the years, various other sampling has been done, including work on the Macondo oil spill and toxic algal blooms. They brought me along so I could collect samples at the beginning of the transect in support of our microbial community survey of the Southern Louisiana coastline and our high-throughput culturing activities. I also brought my camera.

Grand Isle at sunset, facing southeast. Some oil platforms are visible in the distance.
Grand Isle at sunset, facing southeast. Some oil platforms are visible in the distance.
The quaint Grand Isle Suites where we stayed overnight. Our LSU van and 19' whaler are visible in front.
The quaint Grand Isle Suites where we stayed overnight. Our LSU van and 19′ whaler are visible in front.
Calibrating the YSI
Calibrating the YSI
The Sand Dollar Motel, where we launched
The Sand Dollar Motel, where we launched
An early sampling station
An early sampling station
Early segments of the transect are mostly water with faraway marsh
Early segments of the transect are mostly water with faraway marsh
Oil production in the northwest corner of Lake Salvador
Oil production in the northwest corner of Lake Salvador
Coolers and action-packers make the sampling go 'round
Coolers and action-packers make the sampling go ’round
A charming camp near one of our sampling sites.
A charming camp near one of our sampling sites.

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Jim doing turbidity measurements, old school
Jim doing turbidity measurements, old school

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HWY 90, also known as station 30.
HWY 90, also known as station 30.
Old HWY 90
Old HWY 90
Some of the local architecture
Some of the local architecture
Me and Jim
Me and Jim
A lonely cypress in Lac des Allemandes
A lonely cypress in Lac des Allemandes
The entrance to Bayou Chevreuil
The entrance to Bayou Chevreuil
Beautiful Bayou Chevreuil
Beautiful Bayou Chevreuil
Bayou Chevreuil
Bayou Chevreuil

-jct