Hi, my name is Luke Thompson and

I'm a marine microbiologist.

This means I study bacteria and
viruses in the ocean.
Today, I'm going to tell you
a little bit about the work I and
other marine microbiologist do.
We use many of the same
tools of genomics and
transcriptomics, that you've heard
about in the last couple of lectures.
Here you can see some photos from
a research cruise I went on,
in the Mediterranean and Red Sea.
In the upper right,
is me standing next to a device we
use to collect water from the ocean.
It's called a CTD.
On the left you can see two of my
colleagues bringing the CTD full of water,
back onto the ship's deck.
It's very heavy so they use a crane.
On the lower right,
are some other colleagues sampling
sediment from the ocean floor.
That metal device is called a box corer.
There are all sorts of microorganisms,
in sea water and sediment.
We can study them by sequencing,
their DNA and RNA.
Here you can see a 3D map of the Red Sea.
It's colored by temperature,
with the warmest water in red and
the coolest water in blue.
On a 2011 cruise, I sampled 50 stations
throughout the Red Sea, taking water and
microbes, from the surface
down to 500 meters.
Our CTD, measured physical parameters
like temperature, salinity and oxygen.
When we got back on land,
we measured certain chemicals,
like nitrate, phosphate, and silicate.
Which are nutrients for
the micro-organisms.
The hardest and most expensive part,
was isolating and
sequencing DNA from all those samples.
From the millions of DNA sequences,
we were able to calculate, which genes and
pathways, are present in
the microbes from the Red Sea.
The diagram on the right, shows how we
take samples from different environments,
filter out their microbes,
extract the DNA, and sequence it.
From all these data, we are now
learning how marine microbes and
their genes, are organized in relation to
their physical and chemical environment.

These kinds of tools have been applied to

marine environments closer to home too.
We all remember the deep water
horizon oil spill in 2011,
when 5 million barrels of oil were
spilled into the Gulf of Mexico.
We humans, put a lot of effort
into cleaning up the spill,
but so
did the microbes living in the Gulf.
Marine microbiologists
when down to the Gulf,
to see how microbes were
responding to the oil spill.
They found that a group
of uncultured bacteria,
was blooming in response to the oil.
They sequenced the DNA and
RNA from these microbes.
As you learned in the last few lectures,
the study of DNA is called genomics.
And the study of RNA is a transcriptomics.
These tools, help us understand who is in
an environment, and what they're doing.
Using these tools, the researchers
determined that the blooming microbes,
were using genes that allowed them
to move to the oil and degrade it.
The diagram on the right,
shows the different genetic functions of
these bacteria, that were
activated in response to the oil.
It turns out,
the microbes use the oil as food.
Thanks to genomics and related methods,
we now have a better understanding,
of how the ocean responds to both
natural and human-caused events.