What happens to the samples after the cruise?

posted Nov 1, 2017, 5:29 AM by Beth Orcutt

By Kristin Yoshimura

 

During the cruise, we spent a lot of time collecting seawater from different depths in the ocean using the CTD Niskin Rosette. Some of the depths that we sampled: the surface ocean, the depth where a lot of photosynthesis occurs, the depth where there is very little oxygen, and deep in the ocean where there is no light. We filtered this water on board the ship to collect the microbes from these different depths. But what happens to these samples now that the cruise is over?

 

When I get back to my lab on shore, I will extract DNA from the microbes that I collected. DNA is the genetic material that codes for everything in the cell, from the structure of different parts of the cell to the cell’s function. This DNA will be sequenced to try to figure out what the microbes do in the environment by looking at their genes. Each microbe has a genetic fingerprint that helps us determine who they are, and the different genes can tell us what function they have in the environment, such as what types of carbon they eat or how they use different elements and nutrients like nitrogen or sulfur. When the DNA gets sequenced, it is transformed by a computer into short sequences like this: AGATCTCCGTCGATTAGC. We then use computer programs to stitch all of the pieces together, like a giant puzzle. Each complete picture represents the DNA from a different microbe, and there can be thousands and thousands of different microbes in a single sample.

 

Some of the questions that I am specifically trying to answer with the samples I collected are: Are the microbes that live inside of particles (floating pieces of dirt) different than those that do not? If so, do the microbes that live inside of particles have different genes than those that do not? And how do these change with depth in the ocean as light and oxygen concentrations change?

 

We know that microbes can be very sensitive to their environment and that each type of microbe has specific requirements that it needs to survive, so I expect that we will see distinct sets of microbes that live in the various depths and inside of particles. Different microbes will likely have different metabolisms, that is what they eat and what they produce in order to get energy to live, and therefore interact with the environment in different ways. We have studied the surface ocean extensively, but we still don’t have a good grasp on what happens in the deep ocean. These samples that we collected here will help us to have a better understanding of the identity and function of the microbes in the deep sea.

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