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.