The Microbes of the Mississippi River – A Rowing Adventure for Science

For the past four months a crew of four rowers and four shore crew members with OAR Northwest, a not-for-profit adventure education organization, have been on a journey of a lifetime on the Mississippi River. After over 100 days of rowing, the crew has traveled from the headwaters of the River in Minnesota to the Gulf of Mexico. They arrived in Baton Rouge on November 16, 2016 and spent a few days visiting LSU and talking to students about their journey.

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After months on the Mississippi River, OAR Northwest rowers Audra and Calli arrived in Baton Rouge. Researchers at LSU met the rowers near the new bridge to retrieve water samples the rowers had collected for analysis of microbe DNA. Photo by Dawn Jenkins.

Just as the state of Louisiana has a special connection with the “Mighty” Mississippi River, the OAR Northwest rowing crew has a special connection with LSU. This is the second OAR Northwest Mississippi River adventure during which rowers have collected water samples for Dr. Cameron Thrash, an assistant professor in the LSU Biological Sciences department. Cameron’s research focuses on relationships between microorganisms and biogeochemical cycles, particularly in marine systems. Thanks to a relationship with the OAR Northwest team that started when founder Jordan Hanssen met Cameron’s family in Washington, and which has developed into an ongoing citizen science project, the Thrash lab is now building a complete microbial “map” of the Mississippi river…

See more from Paige Jarreau and me about this amazing project at The Pursuit LSU College of Science Blog HERE.

Cultivating members of the microbial majority

It is with great excitement that I get to post that our manuscript on cultivating members of the microbial majority using an artificial seawater medium is finally out! This manuscript represents the hard work of not just myself, but Dr. Thrash, our undergraduates (past and present), and Austen Webber. Over the last two years, I have traveled to sites along the Gulf of Mexico collecting water for cultivation experiments (> 2000 miles traveled, > 4500 well inoculated). From the sites along the coasts of Louisiana, we have cultivated organisms from the Gulf of Mexico representing many important marine clades: SAR11, SAR116, OM43, OM252, Roseobacter, and many more. While isolating these organisms is important, it is also important to isolate organisms that represent abundant taxa within your source water. We compared OTUs from community sequencing of the source water  to our  isolate sequences to demonstrate that our method frequently captured some of the most abundant organisms in the system.

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This work also represents the first instance where many of these clades were isolated from the Gulf of Mexico, and importantly, on an artificial seawater medium. While high throughput, dilution-to-extinction culturing using natural seawater has been highly successful, we hope that this new approach using artificial seawater media will help more researchers cultivate important microorganisms without the hassle of collecting large volumes of natural seawater and needing a boat.

If you have any questions, please feel free to contact us! We are more than willing to answer any questions you may have. You can check out our list of organisms isolated so far HERE!

Henson, Michael W., David M. Pitre, Jessica Lee Weckhorst, V. Celeste Lanclos, Austen T. Webber, and J. Cameron Thrash. (2016). Artificial seawater media facilitates cultivating members of the microbial majority from the Gulf of Mexico. mSphere 1(2). doi: 10.1128/mSphere.00028-16. (Undergraduate authors) Supplementary Information.

Some associated press became available on May 1st. Check out Becoming Acculturated, by Jeffrey M. Perkel.

Antarctica research published

On March 23rd, research on the microbial variation across a 5500 km transect of Antarctic surface sediment that Dr. Thrash and I had worked on with Dr. Deric Learman from Central Michigan University was finally published in Frontiers in Microbiology under the special topic: Microbiology of the rapidly changing polar environments. Since then, the article has had >1200 views from around the globe and was one of the top ten articles in Frontiers in Microbiology for the month of March. The research began when I was a Masters student in Dr. Learman’s lab. When I came here to LSU, Dr. Thrash was added to the project. This research would of never happened without the help of Dr. Andrew Mahon (CMU), Dr. Scott Santos (Auburn), Dr. Kenneth Halanych (Auburn), and Dr. Pamala Brannock (Auburn). Each one helped collect our sediment samples while they were out to sea doing their own research. I’d also like to thank Dr. Ben Temperton (University of Exeter) who helped with our analyzes.  We are excited to finally have it published!

Here is a quick blurb on it:

Western Antarctica, one of the fastest warming locations on Earth, is a unique environment that harbors under explored levels of biodiversity. Our work focuses on the seemingly “invisible” inhabitants of the ocean floor that boarder the western and peninsula portion of the Antarctic continent.   While microorganisms are the smallest forms of life on Earth, they are abundant (typically more than 10 million cells per gram of sediment) and influence the cycling of important nutrient such as carbon and nitrogen. They also represent the foundation of the food chain that supports larger and more complex forms of life. To study this environment, ocean sediment samples from the continental shelf of western Antarctica were collected over a 5,500 km transect from the Ross Sea to the Weddell Sea. By using 16S and 18S rRNA amplicon sequencing, this work has shown these sediments to be incredibly diverse and were distinguished by their correlations to organic matter and stable isotope fractions (TN, δ13C, etc.). Our work further demonstrates the versatility of marine microbial life and its ability to persist at near zero temperatures as well as greatly increases the available information for this region.

Learman, Deric R., Michael W. Henson, J. Cameron Thrash, Ben Temperton, Pamela M. Brannock, Scott R. Santos, Andrew R. Mahon, and Kenneth M. Halanych. (2016)
 Biogeochemical and microbial variation across 5500 km of Antarctic surface sediment implicates organic matter as a driver of benthic community structureFrontiers in Microbiology7:284. doi: 10.3389/fmicb.2016.00284

Emily and Celeste present at LSU Discover Day

IMG_7074Emily presented her LA Sea Grant-funded work to characterize one of our coastal isolates from the OM252 clade, LSUCC0096. She showed this organism has remarkable salinity tolerance, and can grow under chemolithoautotrophic conditions, a feature that was predicted from genome analysis.

 

 

 

 

IMG_7071Celeste presented results of her experiment to enrich for microorganisms that could utilize fulvic acids as their sole carbon source. She compared her work to that of former lab member Jessica Weckhorst who performed a similar experiment with humic acids. These are both extremely important fractions of the marine DOC pool.

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!

 

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