Aloha again from the Atlantic Ocean! The cruise is wrapping up, we’re getting near the end! The Rappé lab representatives have finished up our last dive. We managed to collect more crustal fluid from the deep sea CORKs we’ve been sampling. As was the case every time we sent our equipment down to ~4,500 meters, we were anxious to see our bags filled and on deck, definitely wanted to end the expedition on a high note.
For our last dive, Jason was back on the ship at just about 11 PM, a solid crew of the women scientists on board helped us dismantle the necessary gear and get all of the crustal fluid into the walk-in fridge. I had my fingers crossed when we grabbed our gear to head out and collect the samples, and was pleased as punch that everything was good to go. It was a bitter sweet moment taking off all the cables and cutting the zip ties holding our gear on the frame, our collection was successful but it was our last time heading out to grab the samples and gear.
After all the effort to collect the crustal fluid, it’s been interesting to learn about what experiments different research groups had ready to set up. There are representatives from multiple labs with various interests and I’ve gotten the chance to discuss their projects with some of the scientists here on the ship. Over the next few posts I’ll briefly outline some of the cool projects that were set up right here on the RV Atlantis, and what their goals are.
Elizabeth Trembath-Reichert from Julie Huber’s laboratory at Wood Hole Oceanographic Institution, with help from Ben Tully currently at USC and Megan Mullis at Texas A&M, had a suite of experiments designed to better understand the microbial community living under the sea floor. The main theme of their experiments was trying to understand differences among autotrophic (can make their own organic carbon) and heterotrophic (rely on readily available organic carbon) microbes inhabiting crustal fluid. While it’s not clear what percentage they account for, basaltic aquifers are the largest among all those on Earth. Understanding what microbial processes dominate in these systems is crucial to figuring out global carbon budgets.
The main questions the Huber contingent wanted to address: who is there and what are they doing? One way to determine these answers is through metagenomics, which involves filtering the crustal fluid and then sequencing everything stuck on the membrane. However, this approach won’t highlight what microbes are actively doing in the basaltic fluids. To identify the genes used by the active community, Elizabeth and co. will also sequence the transcriptome (the actively transcribed genes being used when the microbes were collected). She used both the manifold we sent down on Jason to fill bags with CORK fluid to filter 15 liters of fluid through membranes in situ and she also filtered water we brought up in the laboratory to see if the way the samples are processed make a difference in the community or activity we see.
Another nifty approach Elizabeth is employing is using stable isotopes to trace metabolic activity. There are a few different ways that she is going to look at her samples. First, she took samples for nanoscale secondary ion mass spectrometry (NanoSIMS) stable isotope probing (SIP) to determine which taxonomic groups are active. To prepare the fluid samples they were incubated with targeted metabolic tracers, which includes different carbon sources such as acetate, bicarbonate, methylamine, and even diatoms that had been previously grown with labeled bicarbonate and nitrate. Samples were then incubated either at room temperature or refrigerated for different periods of time during which the actively growing microbes would incorporate the stable isotopes into their cells (you are what you eat!). The microbes can then be visualized as maps of single cells and the isotopes they contain using the NanoSIMS.
In addition to the NanoSIMS-SIP method, they will also be using RNA SIP, to link specific processes (the what) to the community characterized (the who). RNA SIP involves incubating 1 liter volumes of samples with labeled bicarbonate. This method will allow Elizabeth to identify which genes are actively being transcribed. As with the previous method, samples were incubated for different periods of time, filtered, and coated before visualization.
There are plenty other cool experiments that were undertaken on the ship. While we’re wrapping up the cruise soon, I’ll be posting some short summaries of what various labs have been focusing on. In addition to having a great experience out here on the ship, we’ve been lucky to see some fantastic sunsets and dramatic lightning storms, with nothing but deep blue sea for miles in every direction. Although I’m looking forward to being on land again, the views have been breathtaking and will be missed when back to standing on solid ground.
Contributed by Kelle Freel, a postdoc at the Hawaii Institute of Marine Biology, University of Hawaiʻi at Mānoa.