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Thrash Lab research at Ocean Sciences 2020

We’re at the Ocean Sciences Meeting next week! Both Celeste and Jordan are presenting posters showing their research on some very important groups of marine microorganisms, directly benefitting from new isolates in each clade:

New isolates and genomes allow for a comprehensive characterization of SAR11 subclade IIIa
Presenter: V. Celeste Lanclos
Poster #: MM14A-0284
Abstract ID: 652607
Time: 02/17/2020 16:00-18:00

Pangenomics and ecophysiology of SAR116 bacterioplankton
Presenter: Jordan T. Coelho
Poster #: MM14A-0285
Abstract ID: 646870
Time: 02/17/2020 16:00-18:00

See you there!

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Welcome to the lab Nicole!

Nicole Ratib has officially joined the lab as a Simons Postdoctoral Fellow in Marine Microbial Ecology. We introduced her a little in a previous post, but some more interesting things about Nicole- she’s a So-Cal native and grew up in my home town! She also loves to fish and makes a damn fine poke. Nicole is diving head-first into growing SAR11 and all the fun that entails. She will also be throwing a lot of technology at this project, including FACS, nanoSIMS, and more, so stay tuned for updates. We’re excited to have you join the team Nicole and looking forward to your discoveries!

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Mike moves on to a postdoc in the Coleman Lab

Mike is leaving us to join Maureen Coleman’s lab at the University of Chicago beginning in 2020. We’re thrilled that he has cultivated (pun intended) such an excellent opportunity and look forward to seeing the great work that comes from his time in the Coleman Lab. Mike leaves behind an impressive legacy: over 400 axenic cultures from a diverse set of coastal bacterioplankton groups, including LD12 and other SAR11 subclades; a well-trained cadre of students who can all thank him for helping them achieve their level of proficiency; numerous upgraded techniques and protocols; and of course several excellent manuscripts. Mike had three first-author publications before he graduated, one this year, and will likely have two more from his dissertation research (stay tuned for more as good stuff is on the way, and see the Publications page for details). The isolates he generated are also the basis for several upcoming papers from other students in the lab like Celeste and Jordan. We are all in your debt Mike, and no one more than me. Your hard work and dedication during your time in the lab was massively instrumental to our success thus far, and the results of your efforts here will carry forward for many years. Thank you from all of us, and best of luck in your new position.

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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.

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Welcome Chuankai to the lab!

Extending a warm welcome to Chuankai Cheng, our newest Ph.D. student, who has just started as an MBBO student this semester. Chuankai did a Masters with Bernhard Palsson at USCD, and has published a stimulating paper modeling overflow metabolism in E. coli from that work. He also has participated in developing an algorithm to cluster Hi-C data. Most recently he worked in Terry Hwa‘s lab, and is now part of our team. We’re thrilled to have you Chuankai and looking forward to some great science!

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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!

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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.