USC Dana and David Dornsife College of Letters, Arts & Sciences > Blog

October 29, 2014

Small Microbes. Big Computers.

Filed under: Wrigley Institute — Jessica Dutton @ 8:06 am

USC Wrigley Institute

By: Rohan Sachdeva

rohan_4x3 me sampling

Hi – I’m Rohan and I adore marine bacteria. Bacteria in the ocean? Now I know that sounds strange. And that’s the first thing I thought too.

Then I was told that there are roughly five million bacteria in a teaspoon of seawater, and ten times as many viruses. There are also millions of different types or species of bacteria in the world’s oceans. If you were to lay all of the bacteria and viruses end to end, they would span farther than the nearest 60 galaxies – give or take a couple of galaxies. On top of that, there are vastly many more microbes on Earth than there are stars in the sky.

Actually if you look in the microscope at a seawater sample you’d see something very similar to the night’s sky (only a lot more dense).

Screen Shot 2014-10-28 at 3.06.12 PM

Night’s sky or seawater sample? Microscope view of fluorescently labeled bacteria (rectangle) and viruses (oval) in a teaspoon of seawater

After hearing all of this, I thought to myself “Well Rohan, I guess I’m never going in the ocean again.” But turns out that >99.9% of these bacteria are totally harmless and don’t cause any diseases. Makes sense since we swim in the ocean every day and rarely ever get sick. Actually, marine microbes are absolutely essential to life and run many of the major chemical cycles on the planet. For example, about half of the oxygen on the planet comes from marine microbes known as phytoplankton that perform photosynthesis just like plants. So every other breath you take comes from a microbe in the ocean!

What other processes are performed by marine microbes? That’s the big problem – we don’t know exactly. That’s because the vast majority of environmental microbes simply can not be isolated and grown in the lab. It’s such a major problem that environmental microbiologists have dramatically dubbed it “The Great Plate Count Anomaly”, referring to that fact that we can see a huge amount of microorganisms in the microscope, but can’t grow them on Petri plates.

So how do we figure out what’s going on with these microbes if we can’t directly study them in the lab? That’s where I come in.

filtering microbes

On a research boat filtering seawater to collect microbes

First, I collect the microbes in the field by filtering seawater through water filters that are typically meant to remove bacteria from water. Instead of tossing the filter, the DNA is extracted from the cells by popping them open using a little detergent and some vigorous shaking with glass beads. Next, the exact code of their DNA is determined using a technique called sequencing. From the microbial DNA sequence, we can determine genes involved in all different types of processes – namely those important to chemical cycles important to life on the planet. We know which genes are important in chemical cycling based on those microbes that we can grow in the lab for experiments. So the DNA sequences from oceanic microbes that can’t be grown in the lab are compared to those that can be grown in the lab.

Comparing these sequences requires a good amount of computing. And since there are A LOT of microbes and types of microbes in the ocean, we need A LOT of sequence information to get a good grasp on what they’re doing. Multiply that by the huge number of microbes and microbial types in the ocean and you need a massive amount of computing power. To do that, I run a large computer cluster similar to companies that handle huge amounts of data like Google, Microsoft, and Apple. This computer cluster is made up of hundreds of smaller computers equivalent to your home computer – each can only match one sequence at a time, but together they can process a huge amount of microbial data.

computer : executor

One member of the computer cluster, affectionately named “Executor” after Darth Vader’s flagship

So far, I have sequences from around the globe including the Indian Ocean, North Atlantic, and even off the coast of Southern California. Right now I’m processing the data and identifying new microbial species and the chemical processes that they’re running. In the meantime, if you’re interested in learning more about microbes and sequencing in the ocean you can check out this TED talk and the Ocean Sampling Day.

 Rohan is a former WIES Summer Fellow, and a doctoral candidate in the laboratory of Dr. John Heidelberg in the Marine Environmental Biology program at USC. (Twitter: @archaeaologist)

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September 30, 2014

Preserving rock images from Catalina’s past

Filed under: Graduate,Wrigley Institute — Jessica Dutton @ 8:11 am

USC Wrigley Institute

By: Tom McClintock

Cultures around the world have been creating images in caves and other rock surfaces for at least 34,000 years. Whether their purpose was aesthetic or functional, these images represent some of the earliest known, and in some cases the best preserved, artistic expressions of prehistoric people.

Many indigenous cultures have rich traditions of creating rock images, especially in California. To contemporary indigenous people, the sites that feature these images continue to be regarded as sacred. But these images are increasingly threatened by development, over-visitation and natural deterioration. How can these sites be cared for?

This question is at the heart of my research on Catalina Island, where I will be conducting original documentation and condition assessment for a number of rock image sites.

Picture 1

The first step has been, necessarily, to consult with the Tongva community – the original inhabitants of the island – to determine their vision for the future of these sacred sites. This was a component of this summer’s Pimu Catalina Island Archaeological Project (PCIAP) field school course, hosted at the WMSC, whose focus was teaching the fundamentals of indigenous archaeology. Through the course, I was able to both establish a connection with the Tongva community and to instruct students from diverse educational backgrounds in the fundamentals of “condition assessment” of rock image sites and documentation photography.

Technology has played an important role in this summer’s research. We used Decorellation Stretch, a program that allows the user to manipulate digital photographs based on minute differences in Red/Green/Blue values for each pixel. From these enhanced images, entirely new surfaces have been identified for further study, leading to a better understanding of the site’s original appearance to the Tongva.

Slide1

Image on rock face – photograph of image before/after digital manipulation

After a successful and productive season with PCIAP’s field school, a complete condition assessment has been performed for a number of rock image sites. This includes assessing not only the tangible elements of the image panels (such as the quality of the rock substrate and the condition of the images’ pigment), but also the intangible (such as the integrity of the landscape and the sites’ accessibility), which are of equal importance to the preservation of the sites’ significance. Gauging these qualities, along with performing photographic documentation, represent the first portion of my research.

Picture 2

This summer’s work will be followed by continued consultation with the Tongva community, as well as the Catalina Island Conservancy (who own the land) and the island community, to explore what measures can be taken to best protect these sacred sites.

Tom is a graduate student in the UCLA/Getty Master’s Program in the “Conservation of Archaeological and Ethnographic Materials”. He attended the Wrigley Marine Science Center this summer as part of the Pimu Catalina Island Archaeological Field School.

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