Resurrecting ancient microbes to understand evolution

The ever-growing popularity of the zombie apocalypse is testament to our fascination with the idea of resurrection, or the reanimation of the dead. Credit: Robert D. Brown Inc.

When you hear the word “resurrection”, what’s the first thing that comes to mind? Religious miracles? Zombie viruses? The end of the world?

Whatever your mental association, I’m willing to bet it’s not “an emerging scientific discipline.” Well, it just so happens a growing community of microbial ecologists are developing a new use for the traditionally mysticism-affiliated word. These scientists don’t just study modern microbes. Nor do they fashion themselves paleobiologists. No, these people actually straddle the boundary between life and death. They resurrect. And in doing so, they hope to gain insight into how evolution occurs: from single genes to entire communities.

I’ll admit Carl Zimmer beat me to this one , but the topic of resurrection ecology is too interesting and relevant for me to ignore. Zimmer’s article provides an excellent summary of many recent discoveries in the field- including the revival of a 1,500 year old Antarctic moss and the resurrection of a 30,000 year old virus frozen in Siberian permafrost. In previous posts, I’ve discussed both microbial resuscitation from ancient ice  as well as mechanisms some bacteria use to stay alive at subzero temperatures.

Today I’d like to dive a little deeper and really dissect what it is these resurrection ecologists are trying to do. Why resurrect an 8 million year old bacteria, or hatch 700 year old insect larvae? Other than the “cool” factor, is there any profound ecological or evolutionary insight to be gained from this research?

I’ll give you the punchline now: yes, there most certainly is. You see, resurrection of organisms from the past, a feat that was until quite recently considered impossible, offers scientists the opportunity to directly test hypotheses about why evolution occurs.

As an example, imagine a community of bacteria, happily swimming about in a shallow pool of water sitting on top of Siberian permafrost couple thousand years ago. One particularly cold winter, this water freezes and some of these bacteria get trapped in the ice. Perhaps it remains cold enough that the ice doesn’t melt again come spring. Over time, this ice, along with some hapless bacteria, get buried and compacted, frozen in space. But also frozen in time. While some of these guys may  have escaped cryosleep, continuing to grow, reproduce, and die, frozen bacteria don’t change. And because they remain static, evolution also freezes. No reproduction means no gene swapping, no adapting to new environmental pressures, no natural selection. Beyond their ice fortress, genetic cousins of the frozen bacteria are spreading their genes, mutating their DNA. Populations are growing, shrinking and migrating in response to their environment. They are evolving.

Fast forward to the present. Suppose you’re an ecologist studying the bacterial communities of a Siberian lake. You discover that a rare gene known as “cocA” is widespread. What sorts of selective pressures may have caused cocA to become so common? By collecting samples from the surrounding permafrost, you find traces of bacteria frozen in the ice. You extract and sequence their DNA, and determine, to your delight, these frozen organisms are a close genetic match to some of your lake bacteria. Similar, but different enough to infer that some evolution has occurred. Moreover, in all of your frozen samples, a different flavor of the cocA gene- let’s call it “colA” – is dominant.

Here’s where the resurrection part comes in. You’d really like to know how your bacterial communities shifted from colA-dominated to cocA-dominated. To do so, you try growing some of your frozen bacteria in the lab. You give them heat, carbon, and nutrients. Soon, you’ve got fossil bacteria happily multiplying on your lab bench. You have resurrected life.

 More importantly, you’ve got yourself a situation most paleontologists would kill for. You now have living replica of ancient organisms, and their  modern descendants. You set out to conduct a series of lab experiments in which you vary different environmental conditions- pH, nutrient concentrations, temperature- and monitor how your fossil bacteria change. Specifically, you track whether and how your gene of interest (colA) changes over time. What you are really doing is experimentally simulating evolution on an ancient organism. Ultimately, you might be able to determine what sorts of environmental changes must have occurred to lead to the modern, cocA-dominated descendants.

The concept of resurrection ecology is a powerful one. In no other subfield of biology can scientists directly study the ecology or evolution of an organism from a different time. Normally, scientists have to rely on fossils and other “proxies” to make inferences about past species, their ecology, and ultimately, the environment. Imagine what we might learn if we could resurrect a family of dinosaurs and tinker in the lab until we figured out what sorts of environmental conditions lead to the evolution of feathers.

Obviously this is a preposterous idea. Safety considerations aside (we all know how Jurassic Park turned out), dinosaurs reproduce too slowly to observe evolutionary change on useful timescales. Moreover their ranges are too large, and their species interactions too complex, to accurately simulate their habitats.

Microbes are a different story. They require only a petri dish to grow. They reproduce in minutes to hours. Changes in the genetic make-up of microbial communities can be observed within days or weeks. Antibiotic and pesticide resistance are powerful testimonial to the swift pace of microbial evolution.

Resurrection ecology thus represents a compelling new tool for understanding how genes, populations and communities evolve. But its significance may not be limited to the past. By informing population models with “biological archives”, scientists may be able to forecast adaption to future environmental changes. In other words, by helping scientists develop a deeper understanding of how evolution works, resurrection ecology may inform our expectations for the future, and allow us to prepare for it.

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A quick update: National Geographic’s cover story last week was on reviving extinct species! Check it out here.

Orsini, L., Schwenk, K., De Meester, L., Colbourne, J., Pfrender, M., & Weider, L. (2013). The evolutionary time machine: using dormant propagules to forecast how populations can adapt to changing environments Trends in Ecology & Evolution, 28 (5), 274-282 DOI: 10.1016/j.tree.2013.01.009

Frozen bacteria repair their DNA at -15ºC

Bacteria encased in ice can be resuscitated after thousands, perhaps even millions of years. How these hardy bugs manage to survive deep freeze is something of a mystery.  If nothing else, the low levels of radiation hitting Earth’s surface should cause any ice-bound bacterium’s DNA to break apart over time, eventually leading to irreparable damage. Some scientists think bacteria survive cryosleep by encasing their DNA in protective shells known as spores and entering a state of dormancy. Following spore formation, a bacterium can withstand harsh environmental conditions, including desiccation, strong acids, heat and UV radiation.

Spores don’t actually have eyes like they do in the popular video game, but they can resist drought, fire, ice, acid, and even antibiotics.

But other researchers think we aren’t giving enough credit to the ice dwellers. Recent studies have shown that some psycrhophiles– technical-speak for cold-loving bacteria – are able to maintain basic metabolic functions at subzero temperatures. Could psychrophiles trapped in ice be repairing their DNA faster than the UV radiation bombarding our planet pulls it apart? Microbiologist Markus Dieser at Lousiana State University was interested in finding out. In a study published  in the journal Applied and Environmental Microbiology, Dieser and colleagues show for the first time that one bacteria- Psychrobacter arcticus– can repair it’s DNA at temperatures as low as -15ºC, or 5ºF. Moreover, it can do so 100,000 times faster than damage occurs.

P. articus is an innocuous little bacteria that is famous for one thing: it really likes the cold. It can grow and metabolize at -10 ºC, making it one of the most psychrophilic organisms on Earth. To investigate P. articus’’s ability to repair DNA in deep freeze, Dieser and colleagues isolated viable P. articus cells from Siberian permafrost that has been frozen for 20 to 30 thousand years. In the lab, the researchers dosed their cell cultures with a large pulse of ionizing radiation- roughly equal to what P. articus might experience over 225 thousand years of field exposure. By using such an intense burst of radiation, the team hoped to induce many “double-strand breaks”, or breaks that cause small DNA fragments to separate off from P. articus’s main chromosome.They incubated the irradiated cultures at -15ºC and monitored their survival over the course of 505 days.

Rather astoundingly, the scientists found no significant difference between the survival rates of irradiated and non-irradiated bacteria over the year and a half long study. While this finding alone suggests P. articus can repair its DNA at subzero temperatures, Dieser and colleagues wanted direct evidence.  They used pulse-field electrophoresis, a technique which separates DNA fragments by size, to determine how may DNA double-strand breaks occurred after radiation exposure, and whether the DNA fragments reassembled themselves over time. Like Humpty Dumpty rebuilding himself, the scientists could literally watch P. articus reassemble its genome. On average, P. articus was able to patch thirteen double-strand DNA breaks over the course of the study-  quite close to the roughly sixteen breaks inducted by radiation.

DNA ligase repairing a DNA molecule that has suffered a double-strand break. Credit: Wikipedia

Not only can P. articus repair its DNA at subzero temperatures, it can do so really fast. Using annual radiation exposure data collected in the field, Dieser estimates that P. articus can repair double-strand breaks 100,000 times faster than they occur. The discovery has important implications for the survival of life in extreme environments, including cold extraterrestrial environments. For instance on the surface of Mars, where radiation levels are ~400 times greater than the Siberian permafrost, P. articus can still patch DNA breaks 280 times faster than they would accrue. As scientists continue exploring the “cold limit” to essential cellular functions such as DNA repair, they will continue to refine, and perhaps expand, our understanding of the fundamental boundaries for life.

Markus Dieser, John R. Battista, & Brent C. Christner (2013). DNA Double-Strand Break Repair at −15°C Applied and Environmental Microbiology DOI: 10.1128/AEM.02845-13

Cryogenics, gene popsicles and the oldest life on Earth

While the notion of “cryogenic freezing”, or putting a person into a state of frozen suspension, has been a common theme in science fiction for decades (think the Alien movies, Star Wars, Sleeper, Vanilla Sky) bacteria have probably been doing their own version of cryogenic sleep for billions of years.

Researchers studying ice cores from the Dry Valleys of Antarctica have found viable, frozen bacteria that are thousands to millions of years old. The ice in this region of the Dry Valleys ranges from modern to about ten million years old, making it some of the oldest known ice on earth. By analyzing the ice crystal structure and isotopic data, these researchers determined their ice samples had likely been permanently frozen (i.e., no thawing/refreezing), implying that the bacteria encased within the ice have been trapped since its formation.

Resuscitation

The scientists incubated meltwater from ice core samples at temperatures just above freezing for up to 300 days, adding supplemental nutrients to encourage bacterial growth. The samples they incubated represented a broad range of timescales, with ages ranging from 10,000 years to 8 million years. Astoundingly, bacterial growth was observed in all samples, though growth rates declined with sample age: bacteria that had been encased in ice for shorter periods of time grew much more rapidly than bacteria frozen for millions of years.

Caveats to cryogenic

The study concluded that even bacteria cannot maintain cryogenic preservation forever. In addition to slower growth rates for older bacteria, the study found an exponential decline in the size of the community DNA pool over time, suggesting the DNA is slowly degrading, even in a deep freeze. Very slowly. The estimated half-life for the reduction in DNA pool size (i.e., the amount of time it takes to reduce the amount of DNA in a sample by 50%) was 1.1 million years. (I think I just heard the microbial ecologists breathe a collective sigh of relief.) So, it may be perfectly reasonable to find frozen bacteria that are hundreds of thousands of years, even a couple million years old, that can still be resuscitated.

{An aside: why does DNA degrade, even in a deep freeze? The jury is still out, though one suspect in the present study is cosmic radiation (high-energy particles that bombard the Earth from space). Antarctica receives the highest levels of incoming cosmic radiation on the planet.}

Gene popsicles in a melting world

Bacteria encased in ice for thousands to millions of years are literally a gene bank. Collectively, the community DNA frozen in ice can be thought of as a “gene popsicle” that provides a snapshot into the past and another clue scientists can use to piece together ancient Earth environments. Moreover, it is well known that bacteria are capable of transferring genes amongst each other in a process known as lateral gene transfer. Could the periodic melting of ice sheets, due to shifts from glacial to interglacial periods, result in an influx of ancient genes into modern bacterial communities? Could genetic information perhaps be preserved for hundreds of millions, or even billions of years, through freezing, melting, and re-uptake of ancient genes by living bacteria?

And finally, the million dollar question: what are the implications for of melting gene popsicles on present-day Earth? As glaciers and ice sheets across the world continue to melt due to climate change, will hordes of ancient bacteria start to “wake up”? Could they plague the world with ancient diseases that no modern humans have resistance to? (Hmm…sounds like a good idea for a science fiction story 🙂 The answer to the former question is, probably yes, the latter, probably not. But time, and a lot more research on the microbial ecology of melting ice sheets is needed to answer these questions.

Journal reference: Proceedings of the National Academy of Sciences (DOI: 10.1073/pnas.0702196104)