SCIENCE sciencemag.org 16 AUGUST 2019 • VOL 365 ISSUE 6454 631PHOTO:
THE ASAHI SHIMBUN
/GETTY IMAGES
A
fter 12 years of dogged effort, a team
in Japan has grown an organism from
seafloor mud that it says could explain
how simple microbes evolved into
eukaryotes—organisms with complex,
nucleated cells, including animals,
plants, and ourselves. The microbe sports
unusual branched appendages, leading the
group to suggest that an ancestral version
long ago used similar tentacles to corral and
envelop the symbiotic bacteria that gave rise
to mitochondria, the energy-producing or-
ganelles characteristic of eukaryotic cells.
“This is the work that many people in
the field have been waiting for,” says Thijs
Ettema, an evolutionary microbiologist at
Wageningen University in the Netherlands.
The finding has not yet been published in a
peer-reviewed journal, but on Twitter, other
scientists have described a preprint on the
work as the “paper of the year” and the
“moon landing for microbial ecology.”
The tree of life has three major branches:
eukaryotes, plus bacteria and archaea, which
both lack nuclei, mitochondria, and internal
membranes. Biologists have long debated the
origins of those branches, with some pro-
posing that they sprang from a single com-
mon ancestor and others saying eukaryotes
branched off archaea, making those microbes
our direct ancestors.
That “two domain idea” was bolsteredmud. The researchers confirmed last week in
their preprint, posted on bioRxiv, that some
of the microbe’s genes look like those found
in eukaryotes. It’s as if the microbe “were
primed to become eukaryotes,” Ettema says.
Electron microscope images revealed an-
other suggestive feature: multiple branched
appendages. The team hypothesizes that
early in the history of life, the protrusions
of an ancient member of the same archaeon
family encircled the bacterial ancestor of mi-
tochondria—an organism that could convert
oxygen to energy. The researchers propose
that as the concentration of oxygen increased
on early Earth, the oxygen-using partners
gave a Prometheoarchaeum-like host an ad-
vantage, and eukaryotic life took off.
“This is exactly what we predicted,” Baum
says. In 2014, he and a colleague published
this idea, called the “inside out” theory. Previ-
ously, most researchers had assumed that the
mitochondria were pulled into their archaeal
hosts—the “outside in” theory, with the cell’s
internal membrane-bound compartments
evolving from cell membrane folded inward.
Baum proposed instead that appendages on
the original host cell encased the protomito-
chondria, then merged to form the body of
the early eukaryotic cell. Prometheoarchae-
um’s tentacles support the idea, he says.
Ettema cautions that the archaeal ancestor
to eukaryotic cells may not have looked and
acted just like Prometheoarchaeum. More-
over, DNA studies indicate that other archaea
are more closely related to eukaryotes than
this one. He expects, however, that the team’s
work will help him and others grow related
archaea: “I’m sure it will not take 12 years to
get the next Asgard into culture.”
As impressive as the work is, the cultur-
ing of this Asgard—or others—doesn’t an-
swer whether there are two kingdoms or
three, says Patrick Forterre, a microbiologist
at the Pasteur Institute in Paris. Based on
his group’s extensive DNA studies of the mi-
crobes, Forterre argues that Asgard archaea
are not close kin to eukaryotes. He maintains
that its eukaryotelike genes were borrowed
from the real eukaryotic ancestors, which
evolved from a common ancestor to both ar-
chaea and eukaryotes. “They don’t look like
[an] ‘intermediate’ cell between prokaryote
and eukaryote but 100% as a classical (but
very small) archaeon,” he wrote in an email.
But even if Asgard archaea don’t prove
to be the ancestor of eukaryotes, the new
work “reveals all kinds of exciting biology,”
says Willem van Schaik, a microbiologist at
the University of Birmingham in the United
Kingdom. “It feels like this will go into micro-
bial textbooks immediately.” jTentacled microbe hints at how
simple cells became complex
A “gargantuan” effort grew archaea from deep-sea mud
BIOLOGYA Japanese submersible brought up a seabed sample
from which a microbe was grown.By Elizabeth Pennisi when Ettema and colleagues sieved frag-
ments of DNA from seafloor mud that re-
vealed a new class of microbes with some
ge netic features resembling eukaryotes: the
so-called Asgard archaea. But to explore that
possible link, researchers needed to isolate
and grow them—a tall order, as the archaea
live in oxygen-deprived environments deep
in the seabed and grow very slowly.
Hiroyuki Imachi and Ken Takai, micro-
biologists at the Japan Agency for Marine-
Earth Science and Technology in Yokosuka,
and their colleagues persisted. For 2000 days,
they kept mud from a core sample extracted
from a depth of 2500 meters off the coast of
Japan in bioreactors fed continuously with
methane, a gas common in deep-sea mud.
The team then incubated samples of the mud
in glass tubes supplied with a wide variety of
nutrients and other substances. A year later,
they detected microbes in one of the tubes.
DNA analyses indicated the tube held an
Asgard archaeon. It took about 20 days for
its numbers to double—bacteria commonly
double in less than an hour—but eventu-
ally, the team grew enough of the organism
to study it. “It was really a gargantuan task,”
says David Baum, an evolutionary biologist at
the University of Wisconsin in Madison.
The Japanese researchers, who declined
to comment while a journal reviews their
manuscript, named the microbe Prometheo-
archaeum syntrophicum, after the Greek ti-
tan Prometheus, who created humans out of