Category Archives: Uncategorized

Marine Biological Laboratory

I was fortunate enough to be able to visit the Marine Biological Laboratory (MBL) in Woods Hole, Massachusetts today. MBL is nestled in among the village campus of Woods Hole Oceanographic Institution (WHOI), NOAA, the aquarium, and more. The village of Woods Hole sits right on the bay at the southern end of Cape Cod. The buildings in Woods Hole are quite old or seem to be converted homes. It is a charming place.

I went to MBL today to collect some things from an old lab there. Out the window, I had an awesome view of the R/V Neil Armstrong, one of WHOI’s vessels.28058420_10215433495820616_6389295462023942644_n

I also visited the MBL/WHOI library and found some very old volumes of scientific journals.

The library contained volumes of The Lancet all the way back to the very first one, published in 1823! It was very cool. There were also vintage photos of ladies in long dresses sampling at the water’s edge, letters like the one from MBL’s first president to whomever occupied the buildings during WWII pleading for them to preserve the equipment for the Japanese students after the war. There was a Nobel Prize awarded to Thomas Hunt Morgan in 1933 “for discoveries elucidating the role that the chromosome plays in heredity”.27867852_10215434008673437_3003570610163716391_n

Across the parking lot were buildings for marine animal study, an old school house was across Eel pond, and there were lots of little boats up on the pier of the pond just waiting for summer.

What a fun little adventure.

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Loihi Seamount

This August I will be taking part in a research cruise to Loihi seamount. Loihi is an active underwater volcano just off the coast of the Big Island of Hawaii. The seamount is being formed by the same hotspot that created the Hawaiian Islands, and someday may breach the surface of the ocean to create a new island in the chain.

Image result for loihi seamount

Loihi vent sites are characterized by the presence of thick iron mats filled with iron-oxidizing Zetaproteobacteria and little to no macrofauna. As hydrothermal fluid vents from the basaltic basement and mixes with cold, oxygen-rich seawater, the iron (Fe) in the fluids is easily oxidized. Bacteria take advantage of this energy imbalance and proliferate along the seafloor near venting fluids. Clara Chan at the University of Delaware has made some interesing discoveries about these organisms.

Loihi Seamount structures built by iron-oxidizing microbes.
Photo Credit: Clara Chan, University of Delaware

This summer when I visit Loihi, I will sample the venting fluids and perform a set of analyses to describe the metabolic potential and activities of microbes in the fluids. The goal is to describe the microbial community in these fluids to better understand how they are influenced by the geochemistry of the system. Most microbial studies to date have focused on the inhabitants of the Fe mats, and we aim to understand what is happening beneath the surface of the rock.

More information is to come in future posts, and the cruise will be accessible online, so I will post that information when it is available.

Links to learn more about Loihi Seamount:

Hawaii Center for Volcanology

The Iron Eaters of Loihi Seamount

Carbon sequestration in subsurface rock

Carbon sequestration by injection of supercritical carbon dioxide (CO2) into rocks is a viable option to combat global warming and the rise in CO2 in the atmosphere. Supercritical CO2 behaves as a fluid under high pressure and can be injected into the subsurface using wells drilled deep into the Earth.  The carbon dioxide used for injection would ideally be waste from a manufacturing plant that can be captured and put back into the Earth instead of released into the atmosphere as CO2.  When supercritical CO2 is injected into rock layers, it can form new rocks called carbonates that will trap the CO2 underground.  This is important because the global rise in CO2 levels is contributing to ocean acidification, sea level rise, loss of habitat for arctic and antarctic life, loss of coral reefs, and global warming.
I am currently working on a side project that will determine how the biosphere will be affected by the injection of supercritical CO2.  We have core material from the well and a fellow student ground up the rock from inside the core and extracted all the DNA so we can build a phylogenetic, or family, tree to see what organisms are there before the injection.  We will also have a look at the community of microorganisms present after a simulated injection of supercritical CO2 and determined how it has changed.  This information is critical to the success of these types of endeavors for a number of reasons, one being because we do not want to increase organisms that make methane from the CO2.  Methane is even more potent as a greenhouse gas than CO2.

Today I am finishing up the procedure to get the DNA ready for sequencing.  We are using Illumina sequencing which will give us millions of sequences to work with.  Once we have the sequences, we can compare them to known organisms and determine how related they are using algorithms.  We can also determine the percent composition of each organism and diversity of the community by determining how abundant each organism is in the community and how many organisms there are.  Well, it’s about time for me to go finish up and send the samples off for sequencing!  Wish me luck.

Amy