The lab has moved to USC and we’re slowly getting up and running. Ken Nealson has graciously provided us with temporary space in his laboratory. We’ve figured out how to order things, located most of the light switches, gone through our safety trainings, and even have wet lab operations going again. Mike and Alex went on the SPOT cruise last week (look for an upcoming blog post on that) and began our first high-throughput cultivation experiment with surface and DCM water. Those are incubating as I write, and the new isolates will inaugurate our USC Culture Collection (US3C for convenience). Jordan, Mike, and Celeste have also been sequencing genomes with our Oxford Nanopore MinION for the last couple weeks, generating a deluge of new As, Ts, Cs, and Gs. We’re watching as the lab space comes together, which is an exciting process.
It’s also an El Niño season, so southern California has been a bit wetter than usual. However, snow in the San Gabriel mountains makes a magnificent backdrop for Los Angeles. And El Niño is roughly translated by some in SoCal to mean “great surf.” I was at UCSD during the 1997-1998 El Niño season, and I remember watching Black’s at triple overhead from the safety of the cliffs. I also remember getting bounced off the bottom after taking a big set on the head at Boomer’s in La Jolla…but that’s a story for a different time.
For now, I’ll just leave you with a sunrise photo from the USC quad a few weeks ago.
Emily Nall, an undergraduate researcher in our lab for 4 1/2 years, graduated from LSU yesterday Summa Cum Laude. She also received the University Medal and was one of only two students to receive the College Honors distinction for completing all of her honors coursework as well as successfully writing and defending an Honors Thesis. She had quite a bit of hardware! We’re so proud of you Emily. Thanks for all you’ve done for the lab and we wish you the best in the future.
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 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!
Although many have already heard the news, I think it’s time to make an official announcement and fill in a few details. After five and a half very good years here at LSU, the lab is moving to the University of Southern California. Starting in January 2019, we’ll be joining the Marine and Environmental Biology section of the Department of Biological Sciences, in the Dornsife College of Letters, Arts and Sciences. In addition to a strong emphasis on marine microbiology and biogeochemistry, MEB has close connections with the Geobiology faculty in the Department of Earth Sciences and the Center for Dark Energy Biosphere Investigations (C-DEBI). As part of this transdisciplinary group, we will continue to investigate microbial functions and ecology in aquatic systems, and advance our emphasis on combining cultivation with ‘omics methodologies. Our high-througput culturing protocol will get some upgrades, and we’ll be adding Pacific Ocean prokaryotes to our culture collection. I’m personally very grateful to the support we’ve received here at LSU over the years, and I know I will remember our time in Baton Rouge fondly. We are also very excited to become part of the USC family and join the close collaborative atmosphere among the related micro, geo, chem, and physics faculty.
The lab is active this summer. I spoke at ASM’s Microbe2018 in Atlanta and just returned from presenting a poster at the Marine Microbes GRC in beautiful Barga, Italy. Mike is heading to ISME17 in Leipzig, Germany to present his work later this month. Mike, Celeste, and I have also been traipsing all over southern Louisiana in support of our NSF-funded project to unravel lineage-specific evolutionary adaptations to alternative salinity regimes in coastal SAR11 bacterioplankton. Every month we cover over 800 miles to get to our four coastal sites.
We also welcome Jordan Coelho to the lab as our newest Ph.D. student! Jordan just finished a second bachelors degree, this time in microbiology, from Oregon State University and worked in the lab of Kim Halsey. Later this month we’ll be joined by Alex Hyer, another Ph.D. student coming from the University of Utah. He worked in the lab of William Brazelton and is currently doing a summer internship with NASA! We’re excited to have you both with us, Jordan and Alex.