Saturday, January 12, 2019

Salt, Space, Acid, Heat

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On Sat, Jan 12, 2019, 11:00 Off Topic < wrote:
Survival tips from Earth's toughest creatures

As humans continue to ruin the planet, we're only making our own environment more hostile. It's time to look for survival tips from the toughest creatures on Earth: the microbes we call extremophiles.

Words by Cara Giaimo. Illustrated by Nicolle Rager Fuller.

Read it on Topic.

Four billion years ago, a tiny microbe lived deep in one of the Earth's oceans, near a hydrothermal vent. It fed on hydrogen, floated among smelly sulfides and corrosive heavy metals, bathed in plumes of near-boiling seawater, and handled the pressure of thousands of feet of water bearing down upon it. It was a badass. Or, if you prefer, an extremophile—literally a "lover of extremes," able to survive in conditions that would kill other living things. Scientists think this single-celled creature may have been the last universal common ancestor, or LUCA—the creature that branched out into today's entire tree of life.

If their theory is true, we've strayed far from our roots. Humans function optimally within a very small temperature window. We do not do well without oxygen, or in environments filled with arsenic or hydrogen sulfide, or encrusted in salt. These days, many of us can barely survive without cell service or wifi.

But LUCA's more direct descendants are everywhere. After a decade of study, an international research group just announced that about 70 percent of the Earth's population of bacteria and archaea—the two types of single-celled organisms that themselves constitute most of the world's species—live beneath the planet's surface, many "under the greatest extremes of pressure, temperature, and low energy and nutrient availability." Put together, these microbes, all extremophiles, weigh about 300 times as much as all the humans in the world—even though most are smaller than one of our red blood cells. And this is only a subset: name a habitat, and at least one microbe has almost certainly figured out how to thrive there. Scientists have found extremophiles everywhere from the hot springs of Yellowstone National Park to the permafrost of Siberia.

Despite their prevalence, for most of human history, this entire category of creatures escaped our notice. Although we cared about particular specimens, the blanket term "extremophile" was coined fewer than 50 years ago, "gather[ing] together organisms … that previously had little to do with one another," as the anthropologist Stefan Helmreich writes in his 2009 book Alien Ocean, which follows experts as they study deep-sea microbes.

Now that scientists can consider these organisms, and their possible uses, as a group, "the lowly microbe has … become invested with such speculative promise," says Helmreich. Although humans aren't quite so good at handling extremes, our current era is full of them—the climate is changing rapidly, environments are becoming unlivably polluted, and we're losing species left and right. We're trying to fix what we've broken, we're wondering how to preserve what we hold dear, and we're thinking about moving to Mars.

As a number of experts, from chemists to astrobiologists to poets, do their best to think past our current ecological crisis, past our current planet, or even past our own existence, extremophiles provide both inspiration and support. Here are some of the ones paving the way.


Unafraid of the Dark: Green Sulfur Bacteria

Green sulfur bacteria 1 lives near deep-sea hydrothermal vents and performs photosynthesis using the glow from the vents rather than the sun.

Chloroflexus bacteria are thermophiles—microbes that love extreme heat. Communities of them float in the hot springs around the El Tatio geyser field in northwest Chile together with other thermophiles, in the form of brightly colored mats. Some of them have skills besides the ability to tolerate high temperatures: they can grow in the dark, or without oxygen. And although the waters of El Tatio happen to have the greatest naturally-occurring concentration of toxic arsenic (known as arsenic III) in the world, some Chloroflexus strains are unbothered. They break the arsenic III down into a less toxic type, getting energy from the extra electrons.

Chile is full of unique landscapes that are home to unique inhabitants. "You have the Atacama desert—the driest desert in the world. You have the Andes mountains, very close to the sea. And you have the very cold south," says Michael Seeger, the director of the Molecular Microbiology and Environmental Biotechnology Laboratory at the Federico Santa María Technical University in Valparaíso. "We have been isolating microbes in all of these environments." Halophiles—salt lovers—live in saline crusts in the Atacama. Psychrophiles, which thrive in cold environments, fill the icy lakes of Patagonia.

When "extremophiles, in addition to being adapted to different, very stressful conditions, can do other things—like degrade hydrocarbons or synthesize bioplastics," exciting possibilities arise, says Seeger. Plus, "if you have strains from all these sites, then you can see for which [situation] you can use which type." In other words, match each of these extremophiles with the right mission, and what looked like a rogues' gallery of microbes suddenly becomes a toolbox.


The Heat Freaks: Thermophiles

Thermus aquaticus can survive temps up to 176 degrees Fahrenheit and was the first extremophile to be officially discovered, in 1969, in a hot spring in Yellowstone National Park.

Take those Chloroflexus around El Tatio. Plenty of drinking water sources have unhealthy amounts of arsenic, endangering the health of communities around the world. As Seeger's lab pointed out in a catalogue of Chile's extremophiles and their potential uses, published this past October, it's possible to imagine a scenario in which the Chloroflexus strains that can break down arsenic are taken from their ancestral geyser and put to work improving a contaminated environment. It would be able to do this work under a number of conditions, including extreme heat or complete darkness.

This strategy, called bioaugmentation, is currently in use by businesses like the UK's Advetec, a waste management company that uses extremophiles originally gathered from undersea vents on tanks of organic waste. Organisms like these "are attracting the attention of speculative capital investment," Helmreich says, a sector that "is very much about trying to imagine new kinds of resources in a resource-depleting world."

An added bonus: through this kind of lens, some of humanity's most shameful landscape legacies—our sludge-filled mines, our oil-slicked oceans—become training grounds for microscopic cleanup crews. ("Very polluted sites … are also extreme environments," says Seeger.) Currently, Seeger's group is working with specimens they took from dirt next to a petroleum refinery in the Valparaíso region, trying to see if they will clean up oil-infused soil in a lab setting. If it goes well, they'll transfer the top contenders to a polluted area in the middle of the city of Valparaíso. After that, they hope to tackle Quintero harbor—which is known locally as "the victim zone," due to the effects of industrial waste on the people who live there—as well as a degraded site in Tierra del Fuego.

Seeger sees parallels between the species he studies and his own. "Humans also have to deal with adaptations to conditions that are not so easy," he explains. Many of these conditions, such as pollution, are of our own making. But extremophiles could help us turn some of them around.


The Cosmonaut: OU-20

OU-20 can withstand exposure to cosmic rays, UV, extremely high and low temperatures, and desiccation. Starting in 2008, it survived on the outside of the International Space Station for nearly 553 days.

Sphingomonas dessicabilis is a xerophile—a creature that doesn't mind having very little water. It's a soil bacterium, and is normally found in the desert crusts of the Colorado Plateau. Next year, it will travel to the International Space Station, in the company of several other species, to see how it handles life in low gravity. In the meantime, it just finished a rigorous lab trial, during which it was exposed to a modern imitation of the salty brines of ancient Mars.

Because extremophiles have already conquered the frontiers of Earth, researchers have made them the guinea pigs of astrobiology—the study of how life might survive in and around other planets. "Life in general seems to have limits," says Adam Stevens, a researcher with the UK Centre for Astrobiology at the University of Edinburgh, Scotland. "What we try to do is explore the edges of those limits."

When Stevens wants to figure out whether life is possible in a particular extraterrestrial environment, he chooses a microbe that might do well there and puts it through its paces. "You pick a condition—say, pressure—and you look at the place that you want to try and simulate," he explains. "So that could be the surface of Mars, where you want to go down in pressure. Or it could be the bottom of an icy moon ocean, where it's very high-pressure." Since S. dessicabilis does well in water-free environments, Stevens decided to see if it could handle a cycle of extreme dryness, followed by immersion in the kind of brine that Mars may have once had.

There are a few different reasons to do all of this. One of them—"the most time-relevant one," Stevens says—is to work to protect other planets from Earth's most dogged inhabitants. The UN's outer-space treaty includes a provision mandating that members "conduct exploration of [celestial bodies] so as to avoid their harmful contamination." To that end, space programs like NASA maintain immaculately clean rooms, equipped with air filters and subject to frequent scrubdowns.

But as a team of scientists discovered last year, some species of bacteria—mostly members of the family Acinetobacter—have learned to survive in this man-made extreme environment by eating the cleaning agents. (Close relatives of S. dessicabilis have also been discovered in spacecraft clean rooms, Stevens says.) If we know that certain species might not only survive but thrive on Mars, we will want to be extra careful to make sure they never get there.

Astrobiologists are also using research into extremophiles to aid them in the discovery of space life that may already exist. Christos Georgiou, a professor of biochemistry at the University of Patras, Greece, is on the hunt for "biomarkers of extraterrestrial life"—chemical structures that, if gathered by a probe or found in a meteor, would prove beyond a doubt that the truth is out there. "Extraterrestrial life in our solar system, extinct [or] extant, would be more likely to exist as microorganisms developing under extreme environmental conditions," Georgiou wrote in a paper published this past fall.

It follows, he continued, that it would share certain bodily aspects—amino acids, for instance—with earthly extremophiles. Meaning that if there is life on Mars (or somewhere else), David Bowie was probably right, and it's a god-awful small affair.

It also isn't probably anything like S. dessicabilis, which, it turns out, isn't doing so well within imitation-Mars. "As soon as we had this cycle of wetting and drying—which is what we would expect on the surface of Mars—everything died straight away," Stevens reports. But other specimens have fared better. Currently, lichens, are the most promising extremophilic spacefarers: certain types have successfully weathered 16 completely unprotected days in space. The secret to their success is teamwork. As Georgiou says, a lichen is "actually two microorganisms in a symbiotic association," a fungus, and then either a cyanobacterium or an algae. The fungal cells provide structure and defense, keeping the algal cells safe until they're in a situation where they can photosynthesize. In this way, both species "can protect each other much better than by being alone."


The World's Toughest: Polyextremophiles

Deinococcus radiodurans can survive extreme cold, desiccation, vacuums, and extreme radiation, without mutating.

Deinococcus radiodurans is a polyextremophile—a creature that can handle not just one difficult situation, but many. (Some have called it "Conan the Bacterium.") It has been found everywhere from the Dry Valleys of Antarctica to the filtered air of a hospital in Ontario, and it is more resistant to radiation than almost any other living thing. It can handle being dried out, oxidized, or bombarded with UV rays, all without losing its genetic integrity. It was discovered in 1956, at Oregon State University, when scientists irradiated a can of meat and were surprised to find that it spoiled anyway.

Its true pedigree is much more mysterious, though. "It's an old organism—it's from a very ancient time in the history of the planet," says the Canadian experimental poet Christian Bök. "We don't even know its natural habitat. We don't really understand how it accumulated all of these immunities, because there is no environment on the planet that is so extreme in its hostilities that would drive its evolution into this peculiar niche." (Stevens, the astrobiologist, posits that D. radiodurans likely adapted to super-dry conditions, and that the radioactive immunity was a bonus.)

Bök, currently a lecturer at Charles Darwin University in Darwin, Australia, likes to challenge himself. (His best-known work, Eunoia, from 2001, contains only one vowel per chapter.) For the past 16 years, he has been working with D. radiodurans on a project he calls The Xenotext. The idea, he explains, is "to write a book that lasts forever," by embedding encoded text into the genome of this bacterium that stands a better chance than most at surviving various flavors of apocalypse.


Best Served Cold: Psychrophiles

Planococcus halocryophilus, which lives in Canadian permafrost, can grow at 5 degrees Fahrenheit and keep its metabolism going at -13.

"I was thinking about the potential existential threats that await us in this century," Bök says. "We don't have any means of preserving our cultural heritage against planetary disaster, like nuclear warfare or astrophysical barrage." If humans were to go extinct, by the time a few million years went by, our major footprint would consist of plastic traces, radionucleotides, and extra methane—all geology, no culture. Most of the interesting and good things we've put into the world "would be ground into an almost undetectable layer of dust," Bök explains.

Bök was directly inspired by the work of Pacific Northwest National Laboratory information technologist Pak Chung Wong. In 2003, Wong turned the words of the song "It's a Small World" into a code organized around genetic bases, strung them together into an artificial DNA strand, capped the strand with a special "sentinel" sequence that prevented the bacterium from realizing it was being invaded, and injected it into D. radiodurans. Because this vessel is so resistant to mutation, "even after a hundred bacterial generations we were able to retrieve the exact message," Wong told New Scientist at the time, adding that "bacteria may be an inexpensive and stable long-term means of data storage."

While Bök is using similar techniques in his work, the idea motivating The Xenotext is slightly more complex. Instead of just giving it some coded words to carry, "I'm trying to get the organism to read the poem," Bök says. To achieve this, he has written two verses, each of which corresponds exactly with the other on a letter-by-letter basis. (Where the letter a appears in the first poem, for example, the letter t appears in the second; the word any becomes the, and so on.) Like Wong, he turns the first poem into a code based on sets of nucleotides, makes it into an artificial DNA strand, and inserts it into the bacterium. When the bacterium "reads" the first poem by peeling the strand apart, it "writes" the second poem in the form of messenger RNA.


The Salt Lovers: Halophiles

Halococcus salifodinae was first found in an Austrian salt mine in 1994.

The two poems, which have not yet been published, are thematically complementary as well. The first, called "Orpheus," boasts about creating life. The second, "Eurydice," playfully pushes back against the hubris involved in that endeavor. For instance, one stanza of "Orpheus" reads, "my myth / now is the word," while the mirror stanza in "Eurydice" reads, "we wean / him of any milk." (If you'd like, you can check the mutual correspondence of the letters—for example, notice how each m becomes a w.)

These poems "are the only two that I was able to confabulate from the biochemical constraints that I imposed," Bök says. It took him four years just to write them: "To get something that says something intelligible and beautiful was nearly impossible." He also built in another layer of meaning. The first line of "Eurydice" is "the faery is rosy / of glow," and the protein Bök chose to encode in the poem causes a red fluorescence. "When it starts writing those lines, the organism blushes—it begins to glow red in the dark," says Bök. "It actually does what it says it will do."

There's just one problem: D. radiodurans isn't biting. Bök has successfully implanted the poem into E. coli, but so far, his desired collaborator—the one that might shepherd his work through the apocalypse—has yet to fully accept it. "I can't just tamper with [the bacterium] and expect it to work," he says. "I have to appease it … I give it an offer, I give it a sample gene sequence, and I wait around to see if it's worthy or not."

"If it's not," he continues, "then I have to change my behavior." After all, if you want to survive, adaptation is key.


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