Mike successfully defends his Dissertation

Last Friday, on the last day of November, 2018, Mike Henson successfully defended his dissertation, entitled High-Throughput Cultivation of Bacterioplankton from the Gulf of Mexico and Genomics of the First Cultured LD12 Representative. It was a sunny, beautiful morning and Mike had a great turnout. His dissertation contains three data chapters, two of which have already been published (Henson et al. mSphere 2016; Henson et al. ISME J 2018), and a third that is nearing submission. These chapters describe improvements we made to the dilution-based cultivation protocol pioneered by Don Button and colleagues and enhanced to a high-throughput format by Steve Giovannoni and many of his former students and post-docs (including yours truly). It also quantifies the relative efficacy of our cultivation work by strain, explores why cultivation effectiveness might differ across taxa, and highlights the added cultivar diversity contributed by Mike’s efforts over the years. The dissertation also includes an in-depth exploration of the genomics of the first cultivated LD12 representative, which Mike has previously posted about below. Mike also has another first-author publication on the microbiome of the Mississippi River (Henson et al. L&O 2018) that is not included in the dissertation. So in short, Mike has three first authored publications after 4.5 years of graduate school, and has two in the pipe, combined with many other co-authorships. Mike was also able to secure two different grants during his time here at LSU. He will be coming with the lab to USC for a one year postdoc to finish his projects and help get us rolling there. We’re very happy we don’t have to say goodbye to Mike yet!

Emily successfully defends her Honors Thesis

Emily Nall (far left in the photo), who has been an undergraduate researcher in the lab for her entire time at LSU, defended her Honors Thesis yesterday entitled Physiological and Genomic Characterization of a Novel Isolate from the OM252 Clade of Gammaproteobacteria. Emily has been working steadily on this project for a couple years. She has used comparative genomics to reconstruct the metabolism of strain LSUCC0096, tested a number of physiological parameters, some of which were predicted from the genome, and has examined the organism’s distribution throughout our coastal data as well as the Tara Oceans data. The next step will be getting the final pieces of this project together for publication. It’s important to note that Emily also funded part of this project herself through a Louisiana Sea Grant Undergraduate Research Opportunities Program (UROP) Fellowship. We’re very proud of you Emily and wish you all the best after graduation!

Our LD12 cultivation manuscript has been published

Our paper on the cultivation and genomics of the freshwater SAR11 strain LSUCC0530 has been published online in the ISME Journal (Here). The SAR11 LD12 lineage evolved to colonize freshwater ecosystems, and, like its marine cousins, occurs as one of the most abundant freshwater bacterioplankton worldwide. Strain LSUCC0530 represents the first cultivated representative of the LD12 clade and presented the Thrash lab with an unprecedented opportunity to provide new insights into the important evolutionary processes behind marine-freshwater transitions. Specifically, we demonstrated the capacity of strain LSUCC0530 to grow in salinities up to 5, provided evidence for LD12 ecotype differentiation based on temperature, and developed a hypothesis on how the loss of key genetic functions enabled the SAR11 clade to transition into fresh water. This work is only the beginning of our exploration into the SAR11 LD12 clade and its marine-freshwater transition, so be on the look out for more data soon!

If you have any questions or want to know more about LSUCC0530, please feel free to contact us! We are more than willing to answer any questions you may have.

Henson, Michael W.,  V. Celeste Lanclos, Brant C. Faircloth, and J. Cameron Thrash. (2018) Cultivation and genomics of the first freshwater SAR11 (LD12) isolate. The ISME Journal. AOP.

 

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

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 😦

Storify on nucleic acid extraction methods

Let’s face it. There are a lot of different ways to skin a microbe, and get the DNA and RNA out for whatever purposes you might deem necessary or useful. If you ask one or two people you’ll get one or two answers. What if you ask more than a thousand? Here is some insightful crowd-sourced feedback from Twitter on favorite and least-favorite methods of nucleic acid extraction, and we’ve done our best to include references with real comparative data, protocols, and applications:

-jct