2015 Summer Course on Microbial Oceanography

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”.

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2015 CMORE summer course students and some faculty

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.

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Hiking with the group before the course started.
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Enjoying a night on the beach with everyone after our first day of the course

The second week focused on Genomes and was taught mainly by Dr. Greig Steward, Dr. Craig Nelson, Dr. Ed DeLong, Dr. Alison Murray, Dr. Eric Allen, Dr. Bethany Jenkins, and Dr. Penny Chisholm. Topics including sequencing techniques, analysis of genomic data, Antarctica, Eukaryotes, microbial ecotypes, and much more. It was another awesome week that brought us to the end of our lecture portion and one step closer to getting on the RV Kilo Moana for a 7 day research cruise.

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Getting a tour of the sequencing facility at CMORE Hale
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The new Illumina technology for library prep using microfluidics
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The new NeoPrep machine from Illumina
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Why not have a robot to prep your samples for you

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.

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The Kilo Moana at port

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 🙂 .

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How you solidify a gel on a moving boat.
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Dr. Church doing his favorite thing…working the winch..though most of the time it was the students doing this.
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Waiting to recover a productivity array which we deployed every day
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Obligatory selfie
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One of the many amazing sunsets
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Bringing back the CTD
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A view from above
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Sorry but I love sunsets while on the water
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Trying on our Gumbi suites
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Heading out to sea
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Working on our C14 Primary Productivity samples
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Just catching a rainbow

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.

Sorry the movie had the music removed 😦

Storify on nucleic acid extraction methods

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:


Storify on microbial genome sequencing in 2014

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: