Higher throughput cultivation

Mike began the first official cultivation experiment using our epMotion robot today. I just couldn’t help myself and barged in to take video. What you’re seeing is LB distribution into 2 deep 96-well plates in a clean environment. We will be using a similar protocol to automate medium distribution, inoculation, and counting of our high-throughput cultivation experiments, thereby increasing the throughput and saving valuable human time.

Nicole Ratib Receives a Simons Postdoctoral Fellowship!

Nicole is currently finishing her Ph.D. with Steve Finkel at USC, where she studied, among other things, the genomic signatures of evolution in a long-term extended stationary phase experiment (1200 days!) in E. coli. She wanted to switch gears for her postdoc and work on marine microorganisms. Her proposal, “Quantifying dormancy rates and controlling factors in the globally abundant bacterioplankton SAR11”, has been funded as a Simons Foundation Postdoctoral Fellowship in Marine Microbial Ecology. Nicole will employ a variety of advanced techniques, including fluorescence-activated cell-sorting and nanoSIMS, to investigate dormancy in one of the most important marine microbial clades, near and dear to my heart, SAR11. We’re thrilled for Nicole to join the lab, starting in January, to begin this important work. Congratulations Nicole!

Recent papers

I’m happy to say that the first half of 2019 has been fairly productive from a publishing standpoint, with five papers out so far. Both Celeste and Jordan have first-author Genome Announcements in MRA:

Lanclos, V. Celeste, Michael W. Henson, Chase Doiron, and J. Cameron Thrash. 2019. Draft Genome Sequence of Strain LSUCC0057, a Member of the SAR92 Clade of Gammaproteobacteria. Microbiology Resource Announcements 8:e00599-19. doi:10.1128/MRA.00599-19

Coelho, Jordan T., Michael W. Henson, and J. Cameron Thrash. 2019. Draft Genome Sequence of Strain LSUCC0112, a Gulf of Mexico Representative of the Oligotrophic Marine Gammaproteobacteria. Microbiology Resource Announcements 8:e00521-19. doi:10.1128/MRA.00521-19

Our first curriculum paper for the microbiology-focused Course-based Undergraduate Research Experience (CURE sections) is available at JMBE:

Bakshi, Arundhati, Austen T. Webber, Lorelei E. Patrick, E. William Wischusen, and Cameron Thrash. 2019. The CURE for Cultivating Fastidious Microbes.Journal of Microbiology and Biology Education 20(1). doi:10.1128/jmbe.v20i1.1635.

And I published a short commentary proposing that we conduct risk assessment using expected value calculations when designing and evaluating studies aimed at cultivating new microorganisms from nature:

Thrash, J. Cameron. 2019. Culturing the uncultured: risk vs. reward.mSystems 4:e00130-90. doi:10.1128/mSystems.00130-19

Finally, a third Dead Zone paper with Olivia Mason’s lab (Lauren Campbell’s second first authorship paper on the topic), in collaboration with Nancy Rabalais, is out now as well:

Campbell, Lauren G., J. Cameron Thrash, Nancy N. Rabalais, and Olivia U. Mason. 2019. Extent of the annual Gulf of Mexico hypoxic zone influences microbial community structure. PLoS ONE 14(4): e0209055.

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.

 

Sampling at the Calcasieu Jetties

On Monday, January 15th, I got to join Celeste on a sampling trip to Calcasieu Jetties in Cameron, Louisiana. This was my first time going on a sampling trip since joining the Thrash Lab. While it was quite a cold morning, it was still a fun time. There were some beautiful views along the way of Louisiana’s marshes.

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View of the marshes

Once we got to the sampling site, Celeste had the joy of wading out into the cold water and collecting.  At least it was a beautiful morning with the sun shining down and bright blue skies.

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The sampling site

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Celeste striking a victory pose after collecting the water sample

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Celeste filtering the sample

The purpose of this trip was to obtain a water sample for the mCURE sections of introductory biology lab. Using this sample, the students will learn high throughput cultivation protocols used in the Thrash Lab. I’m happy to have been able to help with the fieldwork and hope that the students enjoy learning about what our lab does.