It was Charles Darwin who first guessed at the mysterious creature that gave rise to all life as we know it.
"Probably all the organic beings which have ever lived on this Earth have descended from some primordial form, into which life was first breathed," he wrote in "On the Origin of Species" in 1859.
But that primordial form lived and died 4 billion years ago. Its traits — where it lived, what it ate, how it survived the brutal conditions on early Earth — are obscured by time and a scant fossil record. So researchers have tried to learn about the Last Universal Common Ancestor, or LUCA, by looking at its legacy: every creature alive on Earth today.
In a study published Monday in the journal Nature Microbiology, scientists at Heinrich Heine University in Düsseldorf, Germany, examined 6.1 million protein-coding genes found in simple, single-celled creatures today. They created phylogenetic (or evolutionary family) trees for each gene and evaluated them to determine whether they were present in both bacteria and archaea — the two oldest domains of life. That process helped them identify 355 genes that were probably present in LUCA, which in turn helped illuminate what this ancient ancestor was: a simple organism that lived off the gases spewing out of deep sea fissures in the Earth's crust.
Not only was LUCA our most recent ancestor, said co-author Bill Martin, a microbiologist who lead the team. It was probably our first — a find that supports theories that life began around hydrothermal vents.
"We are seeing something for which there was previously no evidence," Martin said. "Just by asking the right questions of genome data, we were able to obtain some very interesting answers that also mesh well with what we know from geochemistry."
The genetic reconstruction suggests that LUCA was an autotrophic ("self-nourishing") organism that lived in a hot, oxygen-less environment; on a scale from "D.C. metro in August" to "stinky, boiling hot spring," it would have been at the latter end. LUCA had an enzyme that allowed it to exist at extremely high temperatures and was dependent on metallic elements, like iron. It was also equipped for a set of reactions called the Wood-Ljungdahl pathway, by which some single-celled organisms use carbon dioxide and hydrogen (rather than oxygen) to acquire energy. The hydrogen for the reaction must have come from geologic sources, they say, indicating that LUCA lived around the cracks in Earth's crust where that kind of chemistry takes place.
Similar organisms still exist today. Martin and his colleagues write that LUCA is most closely related to a class of bacteria called Clostridia and archaeons known as Methanogens. The former group includes the bacteria that produces botulism; the latter includes organisms that produce methane inside human guts (causing flatulence) and dwell inside hot springs or deep in the solid "rock" of the crust.
Though they come from different domains in the tree of life, both groups use LUCA's unusual metabolic pathway of turning carbon dioxide and hydrogen into energy. And phylogenetic analysis suggests they "branch deeply in trees of LUCA’s genes," the scientists say.
LUCA would have been well-suited to the conditions on Earth at the time. Constant bombardment by comets and asteroids would have made the planet almost unbearably hot; even the oceans may have been periodically vaporized. Oxygen would have been hard to come by, since the first photosynthetic organisms hadn't evolved yet.
Until about 40 years ago, we didn't know that life could exist in that environment. It was assumed that living things needed light and oxygen to survive.
But in 1977 scientists found strange creatures thriving around hydrothermal vents, and years of research since has revealed organisms hidden in dark caves, buried in Antarctic ice, borne aloft in clouds, and bubbling inside hot springs. These discoveries demonstrated that life is far more pervasive than we thought, and could have lived at a time when we considered Earth inhospitable. Martin and his colleagues say that hydrothermal vents provide the right ingredients for simple, chemically powered life to arise.
"I think that there’s a very direct link between geochemical processes, LUCA ... and the first lineages of microorganisms that arose," Martin said.
The authors acknowledge a hitch in their results: Microbes are infamous for horizontal gene transfer, a process by which cells can acquire snippets of DNA from other organisms. It's not clear whether the shared genes the team identified were all passed down vertically from LUCA, or distributed by other means.
But Martin said that his team was extremely stringent about what genetic material they examined. Rather than simply looking for common bits of code, they focused on ones that were present in at least two species of bacteria and two archaea — it's unlikely that horizontal transfer could account for a gene that was so widespread.
The findings "have significantly advanced our understanding of what LUCA did for a living," writes University of Manchester biologist James McInerney.
But they don't tell us everything we need to know about the origins of life. Although LUCA was our oldest ancestor and certainly a very early life form, it was not necessarily the first living thing. McInerney points out that LUCA's heat-loving, autotrophic traits may have meant it was simply the only organism to survive an evolutionary bottleneck, and thus the only one to pass on its genes. To be the parent of all living things, LUCA didn't need to be the first organism on Earth — just the luckiest.
Other scientists were even more skeptical of the claim that life originated with a deep sea dwelling organism like LUCA. University of Cambridge chemist John Sutherland, who has done experiments reproducing the chemistry that may have given rise to early organisms, believes that living things required ultraviolet light to set the right reactions in motion. He told the New York Times it seems more likely that life got started in land-based pools, then took refuge in the deep ocean during the bombardment of Earth 3.8 billion to 4 billion years ago.
But Martin said that LUCA's reconstructed genome doesn't include any of the genetic coding for energy synthesis fueled by light. It only has the Wood-Ljungdahl pathway, which is fueled completely by chemical energy.
As for McInerney's suggestion that other organisms may have preceded LUCA and died out, "yes it's possible," Martin said, "but I’m not sure how we would go about investigating any kind of question like that." Without fossil evidence and no genetic legacy, life before LUCA — if it ever existed — will always be a black box.
"The goal of evolutionary biology is to understand the history of the organisms that we know," Martin said. "When we’re done with that we can worry about the ones we can imagine."