Storify on finishing bacterial genomes

Usually when you sequence bacterial genomes, the process of completely closing them (so-termed because most bacterial genomes are circular) whereby a single scaffold overlaps itself at the ends, requires a lot of effort. We’ve had very good luck with our Illumina sequencing and SPAdes assembly process, negating the need for things like primer walking, and we’re very close to finishing two very important genomes. Since this is unfamiliar territory for me (almost all genomes I’ve worked with thus far have been “draft” quality, usually with multiple scaffolds), I queried the Twitter micro community on the best methods for verifying a closed genome. This is from yesterday….

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.

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 Lake Borgne

Last week David and I got up early enough to duck a series of storms coming through the region for some sunny sampling on Lake Borgne. This also saw the maiden voyage of a new Thrash Lab capital acquisition, the R/V Schipperke. We put in at Campo’s Marina, toodled out to a site past the old fort (these are commonplace in this region), and took measurements and water collections. The water was almost fresh, with a salinity ~5. David used these to inoculate the latest high throughput cultivation experiment since Mike Henson is currently at the C-MORE summer course. Here are some photos.

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On the way through the cut
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David taking YSI readings

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Jessica and David win prestigious microbiology awards

On Tuesday night, Jessica and David were both awarded for their undergraduate research contributions in microbiology. Jessica took home the Marion D. Socolofsky Award, given to a senior in microbiology (with an overall grade point average of at least 3.5 and/or an ACT score of at least 25) “who has shown significant improvement in academic development since the freshman year” and who is “engaged in a research project with one of the Department of Microbiology faculty members.” David received a Robert L. Amborski Award, given to “outstanding” graduating seniors with excellence in “scholarship, perseverance, individual attainments, and a sense of social awareness.” Congratulations to both of you!

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