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.
Okay, first off, sorry for all these late posts. This summer has been pretty crazy for all of the Thrash lab! We have been busy with sampling, trips, etc…safe to say, we have generated plenty of data this summer.
This summer I was able to take part in the 2015 CMORE Summer Course on Microbial Oceanography. The course is roughly a five week long intensive learning environment hosted by the Center for Microbial Oceanography: Research and Education at The University of Hawaii Moana in Honolulu, Hawaii. In total, 16 students from around the world (Germany, Austria, Israel, Spain to name a few) were invited through an application process to attend the course titled ” Microbial Oceanography: Genomes to Biomes”.
After some awesome introductions the first day by Dr. Dave Karl, Dr. Matt Church, and Dr. Ed DeLong, we started our first week of lectures from our main speakers Dr. Angelicque White, Dr. Mick Follows, and Dr. Dan Repeta. The topics covered nutrient cycling to modeling and focused more on describing the ocean as a habitat. For me, it was my first time really tackling this type of information and it was a lot of information to take in. But lucky for me, we had some of the best teachers there to help us through it all.
Even though the group came from a diverse background, we all felt a strong bond with each other.
The RV Kilo Moana was an amazing ship and quite big. Especially if this was your first time being on a research cruise or a research vessel. I guess, I was a bit spoiled.
The cruise was one of the things I was most excited about. And to be honest, it was amazing. The CMORE crew did an amazing job prepping the ship and materials for us to use. During the cruise, we had five groups that rotated through five “stations”. The “stations” were flow cytometry (counts and sorting), molecular (DNA extractions, PCR, Sequencing Prep), physical oceanography (CTD prep, casting, retrieval ,etc), productivity (PP and BP), and nutrient analysis (Chlorophyll, ATP, Nutrients). Each day gave us a new station to work at and the ability to learn new techniques. To be short, for those familiar with the Hawaiian Ocean Time Series (HOTS), this is the type of data we collected. The data we collected and analyzed as well as protocols can be found on the CMORE website. The cruise was hard work and I found myself learning something new every time we did a station. We even learned what happens when an array gets too close to the boat 🙂 .
It is hard to put into words how much I learned on this trip, how many new friends and colleagues I gained, and the amount I grew as a scientist. I cannot thank all the individuals that put this on, participated in, and helped out with this course enough.
Enjoy a little closing video I made for the group and everyone after we presented our data at a seminar for all SOEST and CMORE.
Let’s face it. There are a lot of different ways to skin a microbe, and get the DNA and RNA out for whatever purposes you might deem necessary or useful. If you ask one or two people you’ll get one or two answers. What if you ask more than a thousand? Here is some insightful crowd-sourced feedback from Twitter on favorite and least-favorite methods of nucleic acid extraction, and we’ve done our best to include references with real comparative data, protocols, and applications:
Technology is improving by leaps and bounds. With the current trends of massive, ultra-high-sequencing-coverage-combined-with-state-of-the-art-computational-binning-algorithms supported metagenomic assemblies and lasertweezer/microfluidics-enhanced, flow-cytometry based, MDA-powered single-cell genomics churning out incredible insights into the world of uncultivated microbes, it’s important to return, every once in a while, to the humble pursuit of good old-fashioned genome sequencing of simple, pure culture microbes. Here is a storify on just this from a recent Twitter exchange: