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The origin of life on Earth remains one of the greatest and most pervasive mysteries in science. We know the story in broad strokes: Around 4 billion years ago, simple chemical compounds gave rise to living cells, which later formed into organisms made of many cells of great diversity, and arranged in myriad ways.

How that happened remains elusive—and may always be unknown—but researchers who investigate the origins of life have unearthed tantalizing clues that suggest a terrifically messy interaction of geological, chemical and ecological factors tied together by a common microbiological thread. Fossils dating back 3.7 billion years reveal that every living thing, from fungi to foxes to centenarians, evolved from microbes. (More specifically, every living thing descends from the same single microbe).  

“If we want to better understand how that process unfolded and where it’s headed, we’ll need to answer fundamental questions about early microbial life,” said Michael Lynch, Ph.D., Director of the Center for Mechanisms of Evolution at Arizona State University. Those answers won’t just improve our scientific knowledge; they could also yield new insights for our future, such as how pathogens cause disease or even what life might look like elsewhere in the cosmos. Until recently, though, the earliest stages of evolution haven’t received much attention from the microbiology crowd.

“It’s peculiar,” said Lynch, “but most of the research on the origin of life is driven by chemists and physicists.” Despite the centrality of microbial life in the big picture of evolution, he said, very few evolutionary biologists work in the field.

But their numbers are growing, and so are efforts to address the gaps in knowledge. One recent project emerged from the American Academy of Microbiology (Academy), a think tank nestled within ASM, with financial support from the . About 2 years ago, the Academy enlisted Lynch to work with ºÚÁÏÕýÄÜÁ¿President-Elect Vaughn Cooper, Ph.D., a professor of microbiology and molecular genetics at the University of Pittsburgh School of Medicine, to put together a far-reaching, interdisciplinary project aimed at taking a microbial view on early evolution.  

The plan was to assemble experts from diverse fields including microbiology, geology, oceanography, mathematics and virology to talk about how life began and evolved. The idea was that even though researchers in these areas approach questions from different directions, making sense of how emergent biological processes unfolded on a changing planet will require a transdisciplinary collaboration. Their goals were multifaceted: they wanted to articulate what scientists have learned about early microbial life and identify gaps in their knowledge that could invite research opportunities, as well as integrate ASM’s evolutionary microbiology community into origin of life research. They also wanted to show researchers outside the field of evolutionary biology why the rules of evolution are just as applicable to the emergence of life as those from chemistry and physics.  

“We’re trying to bring together all these different fields to deal with … really difficult problems that can’t be handled by any one subdiscipline,” Lynch said during a at the ºÚÁÏÕýÄÜÁ¿Microbe meeting in June 2025. “What I’m seeing out of this is the emergence of this new field, what we call evolutionary cell biology.”  

This multidisciplinary effort, organized by the Academy and funded by the Moore Foundation, led to the June 2025 publication of Early Microbial Life: Our Past, Present, and Future, a 200+ page report highlighting the opportunities and challenges arising from efforts to articulate the microbial history of life on Earth. The findings, perspectives and advances described in the report, amassed during 3 scientific meetings known as colloquia, point toward rich research opportunities in the future.  

They also give the scientists a platform to make a case—not only for other researchers, but also for the general public—for the importance of making sense of evolution, said Academy Chair of Governors Vanessa Sperandio, Ph.D., professor and Chair of Medical Microbiology & Immunology at the University of Wisconsin-Madison. “We have to make it digestible to somebody who’s not necessarily an expert.” The report synthesizes the major transitions from single cells to more complex eukaryotes to multicellularity, outlining the history of all life, including ours. 

Examining Our Past 

By rounding up studies focused on understanding microbial origins, the authors note in the introduction to the report, researchers are “setting the stage to address our loftiest ambitions and, perhaps, to solve many of our biggest human challenges.” And, thanks to the advent of new technologies—imaging, microscopy, sequencing, artificial intelligence, deep-sea exploration—scientists now have an unprecedented set of sophisticated tools to address these fundamental, forward-looking challenges. 

LUCA: Our Common Ancestor  

The colloquia and resulting report follow the same ancient timeline, beginning with questions about the origin of cellular life and understanding how to study the emergence of prokaryotes like bacteria and archaea against the backdrop of the geochemical and planetary conditions that facilitated early evolution. Part of this focus means searching for the precursors to modern cells—and where they might have emerged—as well as clues that could reveal more about the last universal common ancestor, known as LUCA. “This is something that is ancestor to everything,” said Edmund Moody, Ph.D., an evolutionary biologist at the University of  Barcelona who was not involved in the new report, but whose work has focused on LUCA and, more recently, from LUCA forward. “Everything that is alive today is tied back into [LUCA].” 

People typically interrogate questions about the origin of life in 1 of 2 ways, said Tom Williams, Ph.D., a professor and computational biologist at the University of Bristol, during the panel discussion on the new report at ºÚÁÏÕýÄÜÁ¿Microbe 2025. One is a bottom-up approach, beginning with pre-biological ingredients found in the early Earth and studying how they might produce the building blocks of life. The other is top-down, which involves studying core features of organisms alive today. “We try to ask what those features mean about what early life could have been like,” he said.  

To push science forward, he said, requires a bit of both. “It’s really interfacing between the 2 where you actually get progress on the origin of life.”  

In a in Nature Ecology & Evolution, Williams and his colleagues, including Moody, reported on a new analysis of LUCA’s age, genome, metabolism and impact on early Earth. In short: LUCA wasn’t simple. “We think that LUCA was actually already a rather complex organism,” Williams said. It was likely a rod-shaped prokaryote that lived about 4 billion years ago, predating the oldest known fossils. It likely possessed cellular machinery similar to modern prokaryotes, and in its genome the researchers found evidence for an incomplete kind of CRISPR-Cas system—an early immune system that helped it fight off infections. “Even at 4 billion years ago, viruses may have already been attacking one of our earliest ancestors,” said Moody.   

LUCA may not even have been the only complex organism around at the time. Its complexity suggests it was part of a complicated community of diverse organisms that, for 1 reason or another, were left out of the next phase of evolution. LUCA “was maybe the lucky one,” Cooper said during a recent podcast episode of Meet the Microbiologist. “And you can’t help but wonder what those [other] organisms were.”  

Emergence of Eukaryotes  

The second major area addressed in a colloquium and highlighted by the report focused on the emergence of eukaryotic cells, which the report authors called “one of the most transformative events in the history of life on Earth.” Eukaryotic cells, unlike prokaryotes, contain organelles bound in membranes. They’re generally larger, messier and more complicated than prokaryotes, and even though they’re outnumbered by prokaryotes on Earth, eukaryotic cells evolved into a greater diversity of types.  

Recent research, driven by models and experiments, focuses not only on how eukaryotes emerged, but also how they diversified so quickly. “Eukaryogenesis represented a unique, major evolutionary transition that led to the evolution of complex cells,” said Purificación López-García, Ph.D., a microbiologist at the French National Centre for Scientific Research (CNRS) in Paris, who participated in the colloquium and helped author the report.  

In the last 2 decades, she said, scientists have accepted the idea that eukaryotes are symbiotic, likely the evolutionary product of a merger between bacteria and archaea. That would explain why eukaryotic cells contain genes and proteins involved in DNA replication—like archaea—but also use bioenergetic processes like those found in bacteria.  

But it also raises important questions around the details of the process, and around how the nucleus emerged. “This is an open question that many models don’t address,” she said. How about the mechanisms involved? Another open question. Researchers don’t know when mitochondria came into the picture, or how older bacterial genes worked their way into the eukaryotic genome. “Did they arrive by horizontal gene transfer from bacteria in the same environment?” These mysteries won’t be solved by microbiology alone: Solving them will require bringing in ideas from geochemistry and biochemistry to identify environmental and ecological pressures.  

Drivers of Multicellularity 

The third meeting, and a large part of the report, focused on mechanisms that give rise to multicellularity. Scientists in this area increasingly must grapple with the notion that multicellularity shows up in all domains of life, throughout planetary history. It’s evident in eukaryotic cells, of course, and in the past, the concept of “multicellularity”—and research that went with it—was primarily focused on complex eukaryotic organisms. But, according to microbiologist Julia Schwartzman, Ph.D., scientists have more recently expanded that definition. Schwartzman, from the University of Southern California, participated in the multicellularity colloquium and the panel discussion at the ºÚÁÏÕýÄÜÁ¿Microbe meeting in June 2025.  

Multicellularity, she said, can describe a group that comes together to cooperate and do something that is greater than the sum of its parts. Which means bacteria can exhibit multicellular behavior, even when it’s fleeting—as is the case when a biofilm forms and dissipates. In more recent studies, she said, researchers have even found evidence of multicellularity among archaea.  

“Taking a step back, how do we think about this as 1 framework, as opposed to staying… in different fields, grouped around individual domains?” she asked, explaining that instead of focusing on the mechanisms that drove multicellular organisms for 1 type of organism, researchers have begun looking for more general rules, broadly applicable across all forms of life.  

And those general rules may help them better determine the forces that have driven major diversification events in history. Schwartzman emphasized that there are likely many drivers, ranging from availability of oxygen to improving survival strategies for avoiding predators.  

An Experimental Future 

A common thread among the 3 main areas of research that are highlighted in this report is that the way life began and has evolved on Earth is 1 of many possible scenarios for ways it could have gone. “There were many, many alternative possibilities along the way for all the major transitions” in the history of microbial evolution, Cooper noted. He points to evidence that LUCA was likely surrounded by other complex organisms that died out for reasons unknown. Was LUCA just lucky? Or did something else prevent the other organisms from participating in the next phase of evolution? He referred to those lost microbes as “unfortunate neighbors.”  

Many of the findings highlighted in ASM’s report reiterate that chance may play an underappreciated role in natural selection and evolution. Cooper noted that Lynch’s research has helped scientists recognize this overlooked influence. “There’s just a lot of chance in the origin of life,” Cooper said. Luck may be even more important than adaptation. “And that’s both beautiful and kind of cumbersome.”  

The complexities and challenges raised by the report provide a roadmap showing where future work might lead—and how experiments might help answer central questions. Lynch said researchers are now building models and designing experiments to reconstruct the conditions of early life, hoping to test emerging ideas. Findings from the report could help synthetic biologists test various evolutionary alternatives—or even coax some of Cooper’s “unfortunate neighbors” into existence. Sperandio, in Wisconsin, also pointed out that understanding the beginning of life will help researchers avoid troublesome experiments. “You can figure out what you should or should not try,” she said.  

What’s become clear, said Jon Kaye, Ph.D., the Moore Foundation’s Program Director in Science Program, is that our understanding of the beginning of life will remain incomplete without bringing in insights of microbial evolution. “The report brings the biological lens to the forefront,” he said during ºÚÁÏÕýÄÜÁ¿Microbe 2025, “and demonstrates how integrating expertise across microbiology, geobiology and evolutionary biology holds potential to unlock discoveries that no single discipline can achieve alone today.”