We are, fundamentally, a fusion. As I wrote in my essay for Science on the origin of eukaryotes, there's now a wealth of evidence that our cells evolved from the combination of two different microbes. The mitochondria that generate fuel for our cells started out as free-living bacteria. Today, they still retain traces of their origin in the bacterial DNA they carry, as well as their bacterial structure, including the membrane within a membrane that envelops them.

Scientists I spoke with as I worked on the essay agreed that this merging was a profound event in the history of life. No living eukaryote, whether animal, plant, fungus, or protozoan, has completely lost its mitochondria since that symbiotic milestone some 2 billion years ago. It wasn't the only time that two species merged, however. Plants, for example, descend from algae that engulfed a species of photosynthesizing bacteria. Many protozoans have swallowed up photosynthetic partners as well.

Yet in all these cases, eukaryotes did the swallowing. It's striking that scientists have such a hard time finding an example of a noneukaryote (a prokaryote such as Escherichia coli and other bacteria) hosting a prokaryote symbiont. Some scientists have gone so far as to argue that swallowing up a partner requires lots of intricate molecular systems that can create a pocket in the surface of a cell and can draw that pocket inside the cell as a bubble. Eukaryotes have this sort of cellular skeleton, and prokaryotes, it seems, don't. If that's true, then our ancestors swallowed up mitochondria only after they evolved the molecules necessary for the swallowing.

But today, there's a provocative new alternative to consider. Maybe a lot of today's prokaryotes are also the result of an ancient merger. The idea comes from James Lake of the University of California, Los Angeles, a veteran researcher on the early history of life. In my essay, I describe how Lake first proposed in the early 1980s that the host cell that gave rise to eukaryotes belonged to a lineage of prokaryotes he dubbed eocytes. Now, a quarter of a century later, new studies on genomes are strongly supporting his eocyte hypothesis. In today's issue of Nature, Lake questions whether we may be too quick to assume that only eukaryotes are the result of fusion. He observes that aphids depend on a species of bacterium called Buchnera to digest their food, and Buchnera in turn contains other bacteria on which its own survival depends. These two bacteria are still distinct enough from each other that we can tell them apart. But what if two bacteria joined together billions of years ago and their identities blurred together? How would we tell them apart?

To look for possible signs of ancient fusion, Lake compared proteins in over 3000 different prokaryote genomes. He concluded that a major group of bacteria known as Gram-negative bacteria is actually the result of a fusion of two different kinds of bacteria, known as Actinobacteria and Clostridia. These bacteria, which include the ancestors of mitochondria, are unusual in many ways, but the most obvious one is their membranes. Whereas other bacteria are surrounded by a single membrane, Gram-negative bacteria are surrounded by two. It's possible, Lake argues, that the double-membrane structure of these bacteria is a vestige of one kind of bacteria living inside another.

How exactly they made that merger is one of many questions Lake's hypothesis raises. Buchnera's microbial residents may offer some clues. There are also predatory bacteria that push their way into other bacteria in order to feed on them from the inside; in some cases, these predators spare their victims and just live harmless inside them. Lake also points out that microbes don't actually have to take up residence with each other to mix their genomes.

When scientists dredge up muck from the ocean floor, for example, they often find different species of microbes living together in tight clumps. They have to live close to other species to survive because each species takes care of chemical reactions that their partners can't carry out on their own. That intimacy makes it easier for individual genes to move from host to host, as viruses infect different microbes or as microbes die and other microbes slurp up their genes.

It will be interesting to see if Lake's new hypothesis fares as well as his eocyte hypothesis is doing. If he's right, this symbiosis had an impact on the history of life on par with the origin of eukaryotes. Gram-negative bacteria were the first photosynthesizers, for example, and were then swallowed up by the ancestors of plants. And the same lineage also gave rise to the bacteria that became our own mitochondria. Our cells, in other words, are not just microbes within microbes; they are microbes within microbes within microbes: a true Russian doll of evolution.

—Carl Zimmer

Toadstools, people, plants, and amoebae have strikingly similar cells. All these organisms keep their DNA coiled up in a nucleus. Their genes are interspersed with chunks of DNA that cells have to edit out to make proteins. Those proteins are shuttled through a maze of membranes before they can float out into the cell. And these cells all manufacture fuel in compartments called mitochondria.

All species with this arrangement are known as eukaryotes. The word is Greek for “true kernel,” referring to the nucleus. All other living things that lack a nucleus and mitochondria are known as prokaryotes. “It’s the deepest divide in the living world,” says William Martin of the University of Düsseldorf in Germany.

In this month’s Origins essay, Carl Zimmer looks at the evolution of the eukaryotic cell, one of the most important transitions in the history of life. Indeed, when you look at the natural world, most of what you see are these “true kernel” organisms.

Much of what we have learned about eukaryotes comes from studying their cell biology and their genomes. Through these efforts, researchers have made tremendous advances in the past 20 years in understanding that eukaryotes represent the merging of primitive microbes from both the archaeal and the bacterial worlds.

In addition to the essay, Zimmer talks about eukaryotes in a podcast.

—Elizabeth Pennisi

Image: Katharine Sutliff

We're halfway through the Origins series of essays in honor of Charles Darwin's 200th birthday, and I'd wager that the other writers who have contributed to it will agree that it's a guaranteed recipe for glorious failure. The origin of life in 2000 words? That's just enough room to give a taste of the wide range of research going on these days but hardly enough to set up a proper banquet. The same goes for my latest essay, on the origin of sex. There, I focused on the intriguing question of why eukaryotes (animals, plants, fungi, and protozoans) have so much sex when it seems to come at a high cost compared with just cloning yourself. But there's an equally intriguing question that I didn't have room to address: Do bacteria have sex, too?

If you define sex as the way we reproduce, then the answer is no. Bacteria (left) aren't born as males and females, and they don't make sperm and eggs. And if you define sex as meiosis—the shuffling of two genomes to produce a new one—-again, the answer is no. But if you define sex as the combining of DNA from two individuals, they've definitely got it.

Viruses can move DNA from one bacterial host to another. Many bacteria carry little extra ringlets of DNA called plasmids that can cause bacteria to join together so that copies of the plasmids can be transferred. Sometimes the plasmids even drag along some of the DNA from the main chromosome. Some species of bacteria will even secrete DNA into their surroundings and slurp up naked DNA they encounter.

This foreign genetic material can be smoothly integrated into a bacterium's own genome. In some cases (known as homologous recombination), the microbe takes up a different version of a gene it already has. It swaps the new version for the old one. In other cases (nonhomologous recombination), it acquires a gene it never had before.

Like eukaryotic sex, bacterial sex has some evolutionary disadvantages. It takes energy to secrete DNA into the environment, for example, and it also takes energy to pump it in and incorporate it into a genome. The energy bacteria put into having sex could be used to grow faster and make more offspring. So, once again, the question arises: Why sex?

In a review in this month's issue of Trends in Microbiology, Michiel Vos of the Netherlands Institute of Ecology takes a look at the potential answers. A lot of them echo the answers that have been offered for the evolution of our own brand of sex. Sex can speed up the evolution of adaptations, for example, by combining beneficial mutations from different bacteria. Sex can bring about entirely new adaptations (such as antibiotic resistance) with the importing of entirely new genes. Sex can add more variation to a population of bacteria, allowing them to adapt to an ever-changing environment, instead of getting stuck in an evolutionary dead end. Sex may help some bacteria do a better job of making us sick by generating new variants that our immune system may not recognize very well.

It's possible, however, that these long-term benefits of sex do not account for their origin through the short-term, generation-by-generation process of evolution. In fact, sex may actually be more of a side effect—what Stephen Jay Gould and Richard Lewontin termed a spandrel. Taking in loose DNA can have an immediate benefit to bacteria that has nothing to do with sex: It's good eating. Some strains of bacteria can live on DNA alone. The fact that sometimes some of the genes they devour end up inserted into their genome does not necessarily mean that the bacteria have evolved a full-blown sexual system. The proteins that swap in new versions of genes during homologous recombination spend most of their time repairing damaged DNA. They may plug new genes in purely by accident.

It's also possible that the adaptation for sex resides not in the bacteria but in their parasites. Plasmids and viruses may evolve increasingly sophisticated ways to move their own DNA from host to host. If they bring genes that benefit their new bacterial host, they benefit as well.

Vos's paper makes the evolution of sex in eukaryotes all the more remarkable. Sex in eukaryotes is a far more complex process, and it's at the core of our biology. Whereas bacteria occasionally swap a gene, eukaryotes blend their genomes every time they reproduce. Biochemist Nick Lane, author of the new book Life Ascending, argues that eukaryotes became different because of a landmark event in their evolution: A microbe took up residence in the eukaryote cell, becoming mitochondria, which we depend on to generate energy. Now the eukaryotic genome was under constant invasion from foreign DNA, coming from close quarters. Worst of all, this foreign DNA included viruslike segments that could make copies of themselves, swamping our own genes. True sex—complete with meiosis—became our best defense. If Lane is right, then it's bacteria we have to thank for not having sex like bacteria.

—Carl Zimmer

Credit: Anlace, English Wikipedia Project