The Creature That Gave Up Parasitism for … Wait, What?

It’s a mystery wrapped in a riddle wrapped in a kidney.

Nephromyces cells under a microscope.
Mary Beth Saffo, Ph.D / PNAS

In the late 19th century, when scientists first discovered the single-celled creature called Nephromyces, they thought it was a parasitic fungus. They were wrong. Instead, it’s … well … how to even describe it? It’s a reformed parasite. It’s a creature of extremes, surviving in a world of acids and dining on, of all things, kidney stones. And perhaps strangest of all, it’s an organism that cannot survive as an individual. A single ant will do badly away from its colony; a single Nephromyces wouldn’t even get that far.

Nephromyces can be found all along the eastern coast of the U.S., living inside the bodies of translucent, blobby animals called sea squirts. Some sea squirts look like beautiful glass vases; those that house Nephromyces, known as sea grapes, look more like cysts that have grown bunny ears.

Inside each sea grape is a large organ called a renal sac, so named because scientists originally thought it was a kidney. But as the biologist Mary Beth Saffo once told The New York Times, “If it was a kidney, it was a pretty odd one.” For a start, it has no opening. It accumulates the chemicals you’d expect in a kidney—uric and oxalic acids, crystallized into what are essentially kidney stones—but instead of excreting these as a normal kidney would, it stores them for the sea grape’s entire life. As a result, the sac is extremely acidic. Despite that, it’s teeming with life. Cut into one, and “cells just pour out,” Saffo told me.

Scientists first noticed these cells in the 1870s. They came in a variety of shapes—blobs and threads, barrels and baskets. Researchers deduced that these were all different life stages of the same organism, which was named Nephromyces after the Greek for “kidney fungus.” But as Saffo showed in 2010, after sequencing its DNA, Nephromyces isn’t a fungus at all. It’s part of a group of nefarious single-celled organisms called the “apicomplexans,” whose members cause diseases such as malaria and toxoplasmosis. There are about 6,000 species of apicomplexans, and they’re almost all parasites.

Almost all. If Nephromyces is a parasite, it’s a pretty odd one. It doesn’t seem to harm its sea-grape host in any way. And though sea grapes aren’t born with Nephromyces, they always acquire these cells from the surrounding seawater. Every adult sea grape that’s ever been examined harbors hordes of Nephromyces in its renal sac—a 100 percent infection rate that actual parasites almost never achieve, because their hosts tend to fight back. The sea grape doesn’t, which suggests that Nephromyces’s presence is benign, if not beneficial. It just sits there in the renal sac, minding its own business, eating kidney stones. It’s a black sheep in a family of vampires—a creature that has abandoned its relatives’ penchant for exploitation. Such transitions are incredibly rare. Parasites usually become so dependent on their hosts that they lose genes, traits, and body parts that they need for a free-living life. That’s why many organisms take up parasitism but very few ever give it up. How did Nephromyces manage?

One possibility: It has help. In 1990, Saffo showed that Nephromyces is chronically infected with bacteria—microbes that live inside it, just as it lives inside the sea grape. Many creatures are home to internal bacteria, which might provide them with nutrients that are missing from their diet, or help them to digest food they otherwise could not. Perhaps, then, the bacteria in Nephromyces perform similar services. Do they help it to digest the kidney stones around it? Do they provide it with nutrients that its parasitic ancestors lost the ability to make?

Like others before him, Chris Lane, from the University of Rhode Island, assumed that sea grapes contain just one species of Nephromyces, which contains just one species of bacteria, perhaps a pretty odd one. But when he looked closer, he found that they’re pretty odd ones. By sequencing the DNA inside the renal sacs, his students found evidence of a much larger community—many kinds of bacteria, and dozens of Nephromyces species.

The team showed that the bacteria in the community belong to three major groups, which Lane thinks of as “flavors.” Each species of Nephromyces contains one and only one of these flavors (perhaps because there simply isn’t space for more). The bacteria are crucial; they help Nephromyces produce essential vitamins and amino acids that it otherwise couldn’t get. But here’s the catch: No single flavor of bacteria can provide all of the nutrients that Nephromyces requires. It needs all three flavors together—but no species can ever have more than one. For that reason, no Nephromyces species can thrive on its own. They must exist as a community—a multispecies swarm that survives by trading the nutrients that their respective bacteria provide. Lane describes it as a “hippie commune.” In the wild, he showed, sea grapes tend to harbor somewhere between three and eight Nephromyces species.

Is this what it takes for a parasite to give up parasitism? Because, to be honest, “it’s a bit of a mess,” Lane told me. Remember that each sea grape picks up Nephromyces from the surrounding seawater. And Nephromyces does well only if different species with the right bacterial flavors somehow manage to co-infect a single sea grape. “This is just a dumb situation,” Lane said. “It seems like it shouldn’t exist, but here we are.”

“The first time you see something like this, you say to yourself: Go home, evolution, you’re drunk,” John McCutcheon, an evolutionary biologist at Arizona State University, told me. “But evolution doesn’t go out looking for simple solutions to things: It cobbles together solutions from what’s there.” The results can be bafflingly complicated. McCutcheon and his colleagues have studied an insect with bacteria living inside its cells and bacteria living inside those—bugs in bugs in bugs. They found an entire dynasty of bacteria that are splitting into new species inside the bodies of cicadas. “Now we all know to look for crazy combinations,” he said.

With Nephromyces, many mysteries still remain. Are the blobs, barrels, and other shapes actually different life stages, as scientists once thought, or different species, as Lane now suspects? How do the different Nephromyces species ensure that enough of them get inside the same sea grape? How did the different species even evolve? (Many organisms diversify into a variety of species when each gets to exploit a different corner of the environment—but where are the niches in a sea grape’s renal sac?) Are there Nephromyces species that cheat—that contain no bacteria of their own and instead mooch off the nutrients produced by the rest of the commune? (“We think so,” Lane told me.) Also, how does the sea grape benefit from the community inside its body, if at all? Lab-raised sea grapes that lack Nephromyces “do just fine,” Lane said. And though many animals depend on internal microbes for nutrients, sea grapes “live in almost laughably nutrient-rich ocean waters,” Saffo told me.

“We’re not even close to getting to the bottom of this,” she said. “The details get filled in and get even more confusing.”