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….
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.
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.
It is with great excitement that I get to post that our manuscript on cultivating members of the microbial majority using an artificial seawater medium is finally out! This manuscript represents the hard work of not just myself, but Dr. Thrash, our undergraduates (past and present), and Austen Webber. Over the last two years, I have traveled to sites along the Gulf of Mexico collecting water for cultivation experiments (> 2000 miles traveled, > 4500 well inoculated). From the sites along the coasts of Louisiana, we have cultivated organisms from the Gulf of Mexico representing many important marine clades: SAR11, SAR116, OM43, OM252, Roseobacter, and many more. While isolating these organisms is important, it is also important to isolate organisms that represent abundant taxa within your source water. We compared OTUs from community sequencing of the source water to our isolate sequences to demonstrate that our method frequently captured some of the most abundant organisms in the system.
This work also represents the first instance where many of these clades were isolated from the Gulf of Mexico, and importantly, on an artificial seawater medium. While high throughput, dilution-to-extinction culturing using natural seawater has been highly successful, we hope that this new approach using artificial seawater media will help more researchers cultivate important microorganisms without the hassle of collecting large volumes of natural seawater and needing a boat.
If you have any questions, please feel free to contact us! We are more than willing to answer any questions you may have. You can check out our list of organisms isolated so far HERE!
On March 23rd, research on the microbial variation across a 5500 km transect of Antarctic surface sediment that Dr. Thrash and I had worked on with Dr. Deric Learman from Central Michigan University was finally published in Frontiers in Microbiology under the special topic: Microbiology of the rapidly changing polar environments. Since then, the article has had >1200 views from around the globe and was one of the top ten articles in Frontiers in Microbiology for the month of March. The research began when I was a Masters student in Dr. Learman’s lab. When I came here to LSU, Dr. Thrash was added to the project. This research would of never happened without the help of Dr. Andrew Mahon (CMU), Dr. Scott Santos (Auburn), Dr. Kenneth Halanych (Auburn), and Dr. Pamala Brannock (Auburn). Each one helped collect our sediment samples while they were out to sea doing their own research. I’d also like to thank Dr. Ben Temperton (University of Exeter) who helped with our analyzes. We are excited to finally have it published!
Here is a quick blurb on it:
Western Antarctica, one of the fastest warming locations on Earth, is a unique environment that harbors under explored levels of biodiversity. Our work focuses on the seemingly “invisible” inhabitants of the ocean floor that boarder the western and peninsula portion of the Antarctic continent. While microorganisms are the smallest forms of life on Earth, they are abundant (typically more than 10 million cells per gram of sediment) and influence the cycling of important nutrient such as carbon and nitrogen. They also represent the foundation of the food chain that supports larger and more complex forms of life. To study this environment, ocean sediment samples from the continental shelf of western Antarctica were collected over a 5,500 km transect from the Ross Sea to the Weddell Sea. By using 16S and 18S rRNA amplicon sequencing, this work has shown these sediments to be incredibly diverse and were distinguished by their correlations to organic matter and stable isotope fractions (TN, δ13C, etc.). Our work further demonstrates the versatility of marine microbial life and its ability to persist at near zero temperatures as well as greatly increases the available information for this region.
Emily 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.
Celeste 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.