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Microbialites, DNA and my trip to British Columbia

Posted on July 21st, 2011 by admin

Most days I do science in a bright, cluttered (yet clean), indoor laboratory. Right now, I am sitting on the shore of a pristine lake in British Columbia, waiting for samples of microbialites. Long days and late nights in lab is what you pay the piper for sample collections in beautiful, remote locations.

What I knew of British Columbia was what I saw during the Vancouver Olympics and a handful of nature shows. It was beautiful, with tall mountains, good skiing, and killer whales. What I didn’t know was how diverse and rugged the landscape would be. I flew into Vancouver and drove a rental car up to our field site along with my advisor, Dr. Jen Biddle. We passed through the city into tall snow-capped peaks covered in conifers. Beautiful, but about what I expected for BC. My expectations were quickly dashed. Lush forests spit waterfalls down into the Fraser River. Within an hour or two, the conifers gave way to more rock outcroppings, and eventually huge, sheer cliffs with rocks of all different colors. The vegetation changed to more bristly, desert flora. Winding streams worked their way through distant pastures, dotted with gnarled trees, horses, and cows; eventually all spilling into the Fraser, a constant throughout our drive. As we approached the town of Clinton, our base of operations for this expedition, the conifers returned, although this time in different arrangements. The dense coastal firs, spruces, and hemlocks gave way to more sparse cedars and ponderosa pine forests that populated steep, rocky canyons. Tucked away deep in the folds of these ancient canyons are two very unique and exciting lakes.

Pavilion Lake and Kelly Lake are home to a fantastic display of microbialites. A fun, quirky, inspired (from what I’m beginning to see) group of scientists with a variety of backgrounds have descended on these lakes to study these structures because they may hold answers to some of the most profound questions we can ask. What did some of the earliest life on this planet look like? How did it survive and evolve? The fossil records show that for a couple billion years of our planets history, life existed similarly to how it does on the microbialites of Pavilion and Kelly Lake. If these structures were such an important first step in Earth’s life history, might they also be something to look for when we eventually explore other planetary bodies in our solar system and beyond? As a microbiologist, with a strong interest in astrobiology, these questions floor me. To be here in this beautiful countryside searching for answers is what some refer to as “pinch me” moments.

My role here is to help understand the bacterial communities that live on the surface of the microbialites, and from what we can tell, drive their formation. I have spent the past few days taking part in planning and execution of submersible dives and sample collection. Once samples arrive at base camp, I extensively document what I see. Interesting features such as curious green and purple nodules that may be the site of carbonate formation on the surface of the microbialites are sub-sampled and examined under the microscope. Larger chunks of microbialite are carefully bagged and frozen for shipment back to the lab at the University of Delaware. There, I will extract DNA to study the microbial population of these structures on the genomic level to determine which members of this population are most important at different depths. This study highlights one of the unique attributes of Kelly Lake and Pavilion Lake. Microbialites are found in a handful of places around the globe yet these lakes are the only environment where they are found at such a variety of depths (thus differential access to light). It is our hope that these varying growth environments within the lake will be able to highlight distinct attributes of microbialites that made them so successful on early Earth and could possibly aid their formation on other planetary bodies.

Written by:  Joe Russell

One of our tough divers - water is not very warm.

Diving for Samples

Learning the Molecular Alphabet: DNA/RNA analysis at Pavilion Lake

Posted on June 29th, 2009 by Zena Cardman

I am an undergraduate at the University of North Carolina, and this year I’ll be collecting microbialite samples, to figure out how the microscopic species living on the microbialites vary throughout the lake. Currently I’m working in a lab in the Department of Marine Science at UNC with Andreas Teske and Jen Biddle, where I study the genetic diversity of microbes living around a deep-sea hydrothermal vent site near Guaymas, Mexico. Even though Pavilion Lake is a very different environment, I’ll be using many of the same techniques to study the microbial life in Pavilion Lake as I do to study the microbes living in mud almost 3,000 meters below the surface of the ocean.

My background is in molecular biology, so to study the diversity of the microbialites’ microbes, Jen and I will extract their DNA and RNA, and then determine the sequences of particular genes that they code for. If you need a quick crash course in molecular biology: DNA is a molecule made up of four different types of subunits (called A, T, G and C for short), which are repeated and reordered to form a long chain. The particular order of these subunits stores the genetic information for all life forms, much like different combinations of letters spell out different words. Genes that are “switched on” write the words that code for RNA, a molecule which in turn gets translated into proteins. By looking at the differences between these sequences, we can gain some insight into what types of organisms they are, and how closely related they are. It would be very cool if we find differences in the microbes associated with different types of microbialites!

The DNA and RNA of a biological sample degrade quickly, so you have to preserve it if you want to be able to study it back home in your lab. Often samples are frozen at –80 degrees, or in liquid Nitrogen, in order to preserve their genetic information for future analysis. But it can be difficult to freeze samples like this, and safely ship them back to your lab when you are out doing field research. Instead, I’ll be using a salty solution to preserve the RNA in the microbialite samples I take. Field work is a fun challenge, because you have to be so prepared ahead of time! Everyone with the Pavilion Lake Research Project has been working hard for months already to make sure we’re ready for anything at the lake.

While there is barely a week left I leave for Pavilion Lake, I’m currently attending a course on astrobiology in Spain. The students are all young (mostly in graduate school, or recent PhDs), and it’s wonderful to witness the beginnings of collaborations between young scientists. I think astrobiology is especially conducive to collaboration, because it’s so interdisciplinary, and field projects like PLRP are no exception.

I can’t wait to see everyone at Pavilion Lake!

~Zena

Zena behind a mammoth-sized stack of clone libraries

Zena behind a mammoth-sized stack of clone libraries