By growing an unusual tentacled microbe in the lab, microbiologists may have taken a big step toward resolving the earliest branches on the tree of life and unraveling one of its great mysteries: how the complex cells that make up the human body—and all plants, animals, and many single-celled organisms—first came to be. Such microbes, called Asgard archaea, have previously been cultured—once—but the advance reported today in Nature marks the first time they’ve been grown in high enough concentrations to study their innards in detail.
The resulting electron microscopy images reveal complex internal structures suggestive of those in our own cells, adding support to the still controversial idea that ancient Asgard-like microbes may have been the key ancestor of complex cells. The microbe, from 15-centimeter-deep mud in a canal in an estuary in Slovenia, possesses a complex cytoskeleton made of the protein actin, suggesting this structure arose in archaea before becoming an integral part of plant and animal cells. Those findings add to recent work showing Asgard archaea possess genes once thought to exist only in more complex organisms—another indication they may be an important evolutionary precursor.
“This paper is beautiful,” says Buzz Baum, an evolutionary cell biologist at the Medical Research Council’s Laboratory of Molecular Biology. “The images are stunning.” Baum suspects many researchers will want to study the newly cultured microbes.
Considered a third domain of life by most scientists, archaea are distinct from bacteria and eukaryotes, the evolutionary branch that includes humans. Still, archaea and bacteria bear some key similarities—typically neither has core eukaryotic features such as mitochondria, cells’ internal powerhouses, or DNA encased inside a nucleus, for example. Although many researchers think early eukaryotic cells arose after an archaeon engulfed a bacterium that became the mitochondria, they have struggled to figure out how other features of eukaryotes, such as their many internal membranes and organelles, evolved. “Until recently, life’s journey towards complexity was a blur” says Masaru Nobu, a microbiologist at the National Institute of Advanced Industrial Science and Technology.
Telltale genes
The idea that Asgard-like archaea might be the ancestors of eukaryotes came about in 2015 when Thijs Ettema, an environmental microbiologist at Wageningen University, discovered eukaryoticlike genes in strange archaea from sediment samples collected by Christa Schleper, now an environmental microbiologist at the University of Vienna, and her student, Steffen Jørgensen. By 2017, Ettema had found similar genes in several more groups of archaea, which collectively make up the Asgards.
At the time, however, Ettema had only roughly assembled genomes cobbled together from environmental DNA (eDNA), which typically includes genetic material from many organisms in a soil or water sample—and skeptics argued he couldn’t be sure the eukaryoticlike genes really belonged to archaea. But in 2019, Nobu’s team cultured the first Asgard microbe, isolated from ocean mud off Japan, and reported that its genome also had eukaryotic genes.
Additional evidence came earlier this year when Victoria Orphan, a geobiologist at the California Institute of Technology and her colleagues isolated enough of two other Asgard species—from rock collected from a hydrothermal vent in the Gulf of California—to sequence their complete genomes. The genes in those genomes bolstered the case that these genes really did arise in archaea. Moreover, the genomes harbored mobile pieces of DNA that contained bacterial genes involved in metabolism, suggesting these elements played a role in transferring genes among life’s major branches, Orphan and her colleagues reported on 13 January in Nature Microbiology.
By comparing the proteins encoded by Asgard archaea and eukaryotes, researchers including Ettema, Baum, and Mohan Balasubramanian, a cellular microbiologist at the University of Warwick, recently connected the two domains in another way. They focused on the interacting protein complexes eukaryotic cells use to bend, cut up, and stitch together their membranes to link internal compartments. To that point, only two of those protein complexes had been found in archaea. But Asgard genomes contain instructions for making four of them, the team reported on 13 June in Nature Communications.
After predicting the proteins’ structures, the group synthesized some of the molecules in the lab and showed they work similarly to the eukaryotic versions. To the scientists, that suggests this membrane-manipulating machinery predates the evolution of eukaryotes.
A new Asgard
To nail down such questions, scientists need Asgard cells to work with, but it took 12 years of trial and error to culture the first Asgard, and the second one described today wasn’t much easier. “I didn’t know how difficult it would be,” says Schleper, who led the 7-year project.
With their long tentacles, the Asgard cells are fragile, so it was challenging to concentrate them by transferring them from one growth flask to another or to study them by staining them before putting them under a microscope. Finally, Schleper’s postdoc Thiago Rodrigues-Oliveira devised a way to grow them in high enough concentrations to create samples for cryo–electron tomography (cryo-ET), a technique wherein fast-frozen specimens are tilted and viewed at many angles by an electron microscope to develop a composite image. But the team’s imaging studies were complicated by the fact that the samples it cultured also contained two other microbes. A 2020 discovery helped them home in on the Asgard in the end.
Two years ago, geomicrobiologist Jennifer Glass at the Georgia Institute of Technology noticed something unusual about the ribosomes, the cellular structures that translate genetic information into proteins, in Asgards from deep sea sediments. The genes for a key part of these structures were much longer, and so the resulting ribosomes were much bigger than those in other prokaryotes and even in many eukaryotes. So Schleper’s collaborators, Martin Pilhofer and Florian Wollweber at ETH Zürich were able to pick out Asgard cells by looking for big ribosomes. Even so, it took Wollweber 36 hours to identify just 17 of the microbes in the cryo-ET images.
The new Asgard, which is different enough genetically from the one isolated by Nobu’s team and the ones studied by Orphan to be put into a separate genus with the tentative name Lokiarchaeum ossiferum, has tentacles as well, but there are thickenings and small bubbles poking out along the tentacles. Its cell wall, too, is complex, with tiny lollipop structures sticking out, as if to sample the environment. “Overall, the cellular structures of [these cells] look like they come from another planet,” Ettema says.
Its genome is larger and has more eukaryotic genes than the other cultured Asgard, and its DNA includes four genes for the protein actin, a key component of a eukaryotic cell’s internal skeleton, Schleper’s team reports. That skeleton extends throughout the cell and into the tentacles, and it varies from cell to cell, suggesting it’s capable of being rearranged. “We show that the ‘eukaryotic’ cytoskeleton—which is crucial for eukaryotes—was an invention within archaea, meaning it evolved before the emergence of the first eukaryotic cells,” Schleper explains.
“This study further strengthens that our ancestor is archaea,” agrees Nobu’s collaborator, Hiroyuki Imachi, a microbiologist at the Japan Agency for Marine-Earth Science and Technology.
Some scientists now believe the most likely scenario for the emergence of eukaryotes, some 2 billion years after bacteria and archaea arose, is that an Asgard-like microbe enveloped an oxygen-using bacterium, turning it into an extra energy producer for its host. The archaea may have also acquired other bacteria to make the combined cell that comprise eukaryotes.
But not everyone agrees. Some evolutionary biologists, including Patrick Forterre of the Pasteur Institute, have argued the family trees built based on comparing certain genes from Asgard and eukaryotes don’t support Asgard archaea playing such a predominant role in the birth of eukaryotes. And last year, Sven Gould, an evolutionary cell biologist at Heinrich Heine University Düsseldorf calculated that Asgard archaea contributed very little to the first eukaryotes, as little as 0.3% of the protein families believed to exist in the common ancestor of the eukaryotes.
Gould agrees with the widespread view that a merger between archaea and bacteria gave rise to the first eukaryotes, but thinks the archaeal partner was nothing like the newly cultured microbes. Instead, he says, the genetic evidence points to a much simpler host. In a 10 November paper in eLife, Gould and colleagues propose it was the presence of bacterium inside these cells causing new stresses on the Archaea’s cellular processes that spurred the evolution of eukaryotic features such as the nucleus, and the network of membranes and internal compartments called the Golgi apparatus, and even the evolution of sex.
Ettema, too, thinks the full story has yet to unfold. He notes that based on eDNA sampling by his group and others, the two cultured Asgards represent just a small subset of the group’s diversity. He points out that recent work indicates eukaryotes branched off a specific branch of Asgard archaea. Also, the last common ancestor of Asgard archaea and eukaryotes most likely was very different from the two Asgard archaea characterized so far. So, he and others are trying to culture and characterize other Asgards.
Microbiologists and evolutionary biologists eagerly await results for those efforts. “It will be exciting to see what other Asgard-like archaea are discovered and what they look like,” Baum says.
Source: Science Mag