Discovering Fossilized Microbes in Antarctic Ice Cores With Manuel Martinez Garcia

Manuel Martinez Garcia, Ph.D., a professor of microbiology in the Physiology, Genetics and Microbiology Department at the University of Alicante in Spain, paints a picture of what microbial life looked like thousands of years ago by analyzing microbial genomic signatures within ice cores collected from the Antarctic ice shelves in the 1990s. 

Links for the Episode 

• New avenues for potentially seeking microbial responses to climate change beneath Antarctic ice shelves – mSphere paper. 
• Viruses under the Antarctic Ice Shelf are active and potentially involved in global nutrient cycles – Nature communications article. 
• Manuel Martinez Garcia’s Lab website. 
• How stable is the West Antarctic Ice Shelf? – Press Release from Alfred Wegener Institute.
• Take the MTM listener survey!
• Watch this episode: https://youtu.be/CHCMO74_gIY

Ashley’s Biggest Takeaways

• There is a unique habitat beneath Antarctic ice shelves, where microbes live without light and rely on unusual energy sources. 
• Ice cores from these Antarctic ice shelves can preserve fossilized genomic records of microbial life from long ago. 
• Comparing past and present samples can help us understand how microbial life is responding to environmental stressors, like temperature changes and acidification, over time.
• It can also provide key insights to changes in biodiversity.

Featured Quotes: 

Motivation for the Research

Ice shelves are like massive floating ice that are in Antarctica, mainly. They can be as big as, for example, France, the country. So, they are super big—they are enormous. And they can be as thick as, let's say, 1000 meters. So, this is a massive [piece of] ice that we have in our planet.  

And beneath that massive ice, we can have a very peculiar and a special habitat in which microbes live without light. They have to manage, to thrive and reproduce, without using a standard energy like we have on the surface of the sea or in the forest, where we have light that is driving and providing the energy for the ecosystem. But in this case, these ecosystems are totally different. 

[The ice shelves] are deep and interconnected. Basically, there are different oceanic currents, for example, there is one Circumpolar Current that surrounds Antarctica, and there are also other currents that basically go from the bottom to the surface, moving, you know, all the water masses. 

The interesting part of this story is that every single second in our lives, this sea that is beneath the platform, the ice shelf, is frozen over and over, and then we have different layers of antiquity that preserve the microbes that are living in the ocean. So, for example, let's say, 1000 years ago, the sea water was frozen, and then we can find a layer beneath the Antarctica ice shelf, where these microbes are preserved and frozen. Basically, it's like a record—a library of microbes, fossil records of microbes—from the past ocean, from 1000 years ago until present, more or less. 

And then we can go to these records, to these layers of frozen sea water, and pick these samples to somehow recover the genetic material of the microbes that were preserved and frozen 1000 years ago or 500 years ago, in the way that we can somehow reconstruct or build the genetic story of the microbes from the past, for example, pre-industrial revolution to present. 

We need to think that microbes sustain the rest of the food web. So, they sustain of the rest of life in the ocean. They provide carbon for the rest of organisms, the fishes, whales [and other] big animals that we have in our oceans. And if the microbes are responding in a way that is not satisfactory, or in the way that we think can maintain the food web, this is kind of scary. And this is what we are trying to do: we are trying to go back to the past and see how the microbes are changing [genetically]. 

Sample Collection

We didn't collect the samples. [They were collected] back in the 90s, so, 40 years ago, by a German group led by the Alfred Wegener Institute, which is probably one of the most famous polar institutes in the world. They, basically, led an expedition, I think it was in 92, and they decided to go to this ice shelf in Antarctica, in the Filchner–Ronne Ice Shelf to collect these ice cores.  

And then the surprise was when they were progressing in the drilling, they realized that on the top part of the ice core was fresh water, meteoric snow that was compacted forming the ice. But they realized that below that part, there was a sea water that was frozen. And then they thought that these samples were very interesting, because they somehow store material from the past, and they shipped these samples to Alfred Werner Institute in Bremerhaven in Germany.  

And half of the samples were stored for 40 years until I decided to contact the Institute and to propose this research. And I basically contacted the director of the Institute, and also the group of Frank Wilhelm, to propose the idea. And basically, I said, ‘Hey, I think what you have in your research is a valuable material that that can provide interesting answers for climate change and microbiology.’ And they say, ‘Well, that's interesting. And we never thought about that.’ And then we started a collaboration to dig into these questions. 

Shipping the Ice Cores

We had a meeting after one of the first pandemic lockdowns, when they allow [me] to travel. I went to Bremerhaven to have a personal meeting with the team. And we decided to ship some samples to Spain.  

They arrived frozen and very well packaged and preserved in an isolated container. But it was really surprising to see that that they were delivered in the same compartment with a dry ham. That was a that was a funny story! 

Sample Preparation

When we received the samples, the first thing was to basically decontaminate the surface of the [ice]. Because when you unpackage, you have an ice core, pieces like a half meter. And then, we have to think that this ice core has been manipulated by different groups, different people. And you have to decontaminate the surface of the ice core in order to just have the center of the ice core for the for the investigation. 

And basically, we adapted a protocol in order to make sure that we didn’t have cross contamination from the rest of the from the surface. 

So, what we did was we melted the center of the core—well, in fact, different parts of the core with different ages, from 1000 years old to 200 years old—and we melted in a very dedicated laminar flow hood that we have in a clean room. And then, we extracted the DNA from that piece. And in our case, the amount of DNA was so little that we had to amplify with some molecular techniques in order to have [enough] copies of this genetic material to do sequencing. 

Sample Analysis

I will say that we are in the middle of the project. We had, like, 2 years ongoing for the project. 

The most surprising was 2 things. One, in the sea water, beneath the Antarctic, we discovered a very autoctonos (indigenous) viral community that was quite different from the rest of the world, I will say, from the rest of the ocean. So, I think this viral community is quite adapted to infect the microbes that are living in this peculiar environment beneath the Antarctica ice shelf. 

And these viruses were carrying some genes that we think are very important for microbes. We call these genes auxiliary metabolic genes. And these genes are very important because somehow the viruses provide these pieces of information, of DNA material, to microbes that are driving important ecological roles, like, for example, carbon fixation. 

It's very important, because carbon fixation is probably the primary step in all ecosystems—to provide food for the rest of the organisms. And if this is altering, or we are altering it with different factors—like temperature increase, like melting of the ice—its going to change these patterns and the rate of carbon fixation. This is going to produce a deep impact for the rest of organisms. 

We are still investigating, but we think that it's interesting to think that microbes that live in our ocean now are responding to stressing factors like increasing temperature and also acidification by different ways. In fact, it is unclear—it is a very hot topic and a very hot question—because we don't know for sure what the fate of these microbes in our oceans is going to be. For example, people think that we are going to lose biodiversity. There are some hypotheses that say that heterotrophy is going to be more predominant in the sea water. But it's unclear, because we don't really have fossil records that can compare the past to the present, and this is what we can provide, or at least potentially provide. We can say, ‘Hey, we can go before the industrial revolution, before the CO2 increase, and try to compare series of different samples until the present in order to see if, for example, heterotrophy, or microbes that are heterotrophs, are more predominant in modern samples compared to unseen samples.