Recent Microbial Discoveries: Rethinking Our Perception of Life on Earth

Gumdrop with an earring.

That’s what pops to mind when I look at Sebastian Hess’ photos of a kind of plump, violent, single-celled creature he collected from a pond rich in sphagnum moss in southern Germany. The shape-shifting amoebozoan cell, prowling for algal cells to attack, curls its long strand of a flagellum into an earringlike loop. Holding the loop steady, the cell somehow glides. Yet the loop doesn’t flick, lash or wave. “They look basically like tiny flying saucers,” Hess says.

He first collected the creatures, with no species name and a baffling form of locomotion, in 2010 and wondered for years how the locomotion worked. Hess has been seeking and tending such single-celled wonders since he was a teenager with a windowsill microzoo. As a grown-up, now at Technical University of Darmstadt in Germany, he specializes in the microscopic group his zoo featured: the protists.

This big, varied group of single cells are among the closest microbial cousins to multicellular life, and they wrap their genetic material inside a cell nucleus just as animals, plants and fungi do. Schoolroom trees of life for much of the 20th century and sometimes afterward often relegated the protist kingdom to some lower branch beneath the glorious crown of mostly multicellular kingdoms. Biologists think a little differently now, and bigger than mere kingdoms.

Today’s more modern schemes feature at least two vast hoops of microbial creatures, called the domains of Bacteria and Archaea (SN: 7/29/15). A third hoop, the Eukaryota, sweeps together the protists and the formerly proud treetop kingdoms: the animals, plants and fungi. Another sweep may be imminent, as the whole domain of eukaryotes, including the protists and the people who classify them, appear to be a branch of Archaea.

As for the flying saucers, Hess and colleagues worked off and on for almost 10 years to understand how such a cell moves so strangely. It’s a form of locomotion never found before in a living being, Hess says. This toroidal, or “doughnut,” swimming inspired Hess and colleagues in 2019 to put the newfound species in its own new genus — Idionectes, roughly meaning “peculiar swimmer.”

More in a bit on how to swim like a doughnut, but the species, Idionectes vortex, makes a fine example of how high-tech biology plus old-fashioned boots-in-mud exploration are creating a rush of discovery for a charismatic group of tiny lives on Earth. These single-celled organisms are far from boring little dots. Plus, they’re adding some unexpected twigs and branches to the evolutionary tree of life.

To pick just a few examples of 2023’s new protists, a species named in June has the one-celled equivalent of a rotating head. In this roughly globe-shaped cell discovered in a South American termite’s gut, the top spins steadily around without ripping or self-strangling. Discoverers picked a demon-themed name, Daimonympha friedkini, inspired by the spinning head of the demonically possessed child in director William Friedkin’s 1973 film The Exorcist.

Some other new species belong to the odd-looking but ecologically important coccolithophores. This branch as a whole may do as much as 10 percent of the oceans’ photosynthesis, turning sunlight into stuff other creatures eat. Each coccolithophore cell covers itself in what look like tiny hubcaps. Among the distinctive features of the newly named Calciopappus curvus is a pair of thumblike stubs on some of those hubcaps.

Researchers in China named a notably small species in the Euplotes genus, E. mazeii. Euplotes cells grow several sets of skinny projections called cirri that look like stick-drawing legs. Even with no brain or nervous system, the various kinds of Euplotes can move their legs with enough coordination to walk on an underwater surface. Engineers seeking inspiration for microscale robots have been analyzing such gaits.

Even long-known protists have allure as a form of micro­wildlife. Like big cats and polar bears, many of these charismatic microfauna deserve their own nature documentaries. Hess has helped film one of his longtime favorite protists, a kind of Lacrymaria. This mildly pretty teardrop-shaped cell chases prey by shooting out a cartoonishly long swan neck that can stretch more than seven times the organism’s original body length. The neck, with a headlike bump at the end, swerves this way and that lithe as a snake, until a sudden pounce finally snags dinner.

“Stunning” is Hess’ word for protists. “They really behave like entire organisms. But they are just cells.”

Or consider five new species of tiny, voracious cells nicknamed nibblerids. Only about 3 micrometers across in their sickle-shaped hungry form, these protists bite (sort of) their typically larger victims by closing down on them with a special body groove armored with hardened toothlike bits called denticles.

The nibblerids and their closest known relatives, called nebulids, represent such a distinct and ancient lineage that they deserve their own big branch on the eukaryote family tree, evolutionary biologist Patrick Keeling of the University of British Columbia in Vancouver and colleagues reported last year. Keeling speaks passionately about the importance of predators as more than nature-watching fun. “If you took all the lions and cheetahs and killed them all,” he says, “the whole ecosystem would go wacky.” That’s likely the case with protists, too.

Today’s protists are sorted into supergroups, which are branches bigger than the classic eukaryote kingdoms and give a broad and deep view of evolution. The Amorphea supergroup, for example, spans all animals and fungi plus some one-celled relatives including many amoebas. The new supergroup named for the nibblerids and nebulids, Provora, alludes to “devouring voracious protists,” Keeling and his colleagues wrote.

Idionectes too, for all its serene UFO-like travel, is a fierce predator. When it finds algae to feed on, the gliding spaceship becomes an attack amoeba. It dissolves a hole through the algal cell wall but doesn’t feed tiger-style, flesh-ripping from outside the kill. Instead, Idionectes slides through the hole in the wall, decanting itself into the doomed prey cell. Then this hunter devours its prey from the inside.

Watching protists could be terrifying, if they were bigger. Or if humans were smaller.

“We spend so much time trying to imagine alien worlds,” says Keeling. “There’s one right under our noses, more weird than anything we can think of.”

He’s not being theatrical. Consider the way specks of protist bodies experience water, for example. It’s radically different from the way giant lumbering humans and other macroscopic swimmers do. Lone cells are so tiny, the properties of plain water push them down evolutionary paths barely recognizable to us.

Dive into a swimming pool and, “if you’re not kicking, you still go forwards for quite a while until you stop, right?” Keeling says. A single cell, though, is so small that even the viscosity of water means the tiny swimmer barely glides at all (SN: 6/19/09). If it stops swimming, it just … stops. “It’s more like you’re in corn syrup,” Keeling says.

Besides slowing locomotion to a creep, the Syrup World no longer allows for certain swimming strokes. A scallop normally jets around by opening its shell slowly and closing it fast. But if magically miniaturized, the scallop would be stuck in place, flapping, physicists have predicted. It would make progress by shutting its shell but unmake that progress opening it again.

On the upside, though, motions that are useless for full-size people or scallops could propel a tiny swimmer. In 1952, physicist Geoffrey Ingram Taylor theorized that a microbial swimmer shaped like a doughnut could move itself with a sort of inward rotation. (The idea gets credited to a charming talk in 1976 by U.S. Nobel laureate and physicist Edward Mills Purcell, but Taylor came before Purcell.)

That rotation is basically how the loop Idionectes cell turned out to swim, Hess and colleagues announced nearly 70 years after Taylor’s suggestion. The cell’s long, stringy flagellum curls into the scrawniest, skinniest thing ever likely to be described as a doughnut. It’s far more hole than dough, but it still approximates Taylor’s notion.

In a diagram developed by Taylor, the sides of a doughnut rise through the hole, over the rim and wrap around the other side for another slide into the middle. At first, Hess could tell that his gumdrop cell clearly spun, but looking at the flagellum’s skimpy doughnut-shape with plain microscopy, “you cannot see any movement,” he says. But when he and colleagues made underwater blizzards of latex microparticles in syrupy fluid (a technique that gave the researchers a breakthrough eight years into their efforts), Hess saw telltale particle movements showing the flagellum was rotating.

The protist Idionectes vortex was discovered in 2010, but only recently did scientists show that it moves via toroidal swimming. Its flagellum loops like a doughnut. The flagellum and the dome-shaped part both rotate (purple arrows).

Vittorio Boscaro, in Keeling’s lab at the University of British Columbia, has another rotation mystery. “We have no idea why they’re doing this,” he says. We’re on a video call, and he’s sharing his screen to show the new protist species with a rotating head, D. friedkini. In the ghostly grays of light microscopy video, a chunky cell swims as its top, like a large knobby polar ice cap, steadily rotates. It’s mesmerizing.

The 2023 paper announcing the discovery of D. friedkini calls rotating wheel structures “famously rare” in biology. Bacteria can freely spin their flagella without twisting themselves into pieces, but cells with more built-in structures rarely manage.

Still, this wasn’t the first spin-top among complex cells. Analyzing genetic material, researchers worked out a probable family tree of near and far relatives. Oddly, this beast doesn’t seem that closely related to another species with a rotating head informally called rubberneckia, which researchers have sporadically written about since 1974. To study protists is to live in weirdness.

That the new species came from a termite gut was no big deal, Boscaro gently tells me, because protistologists have been gutting termites in search of new species of rotating protists (rubberneckia and D. friedkini both belong to a group called Parabasalia) for more than a century.

Protists are everywhere. Kiran More, then an undergraduate at Dalhousie University in Halifax, Canada, picked up a bunch when he added a little bit of species prospecting to a family trip in 2016.

As summer waned before More’s senior year, his family went driving through the eastern countryside of Nova Scotia. They stopped at a village on Cape Breton Island to admire a replica of the beloved 1920s schooner pictured on the Canadian dime, and More scooped up some shore sand. It took only a matter of minutes; he had packed a set of sampling tubes just in case. “I just carried it from hotel room to hotel room and stuck it in the minifridge, when there was a minifridge,” he says.

When he returned to school, the sludge became part of his undergraduate project looking for unknown species of marine amoebas called vampyrellids (SN: 11/2/15). The name may conjure nightmares, but even two of More’s ferocious finds look less jaw-and-claw and more bed-and-breakfast. They resemble a fried egg.

Though vampyrellid body plans vary, in this case, the egg’s “white” is the structure that breaks through the outer covering of prey to harvest the nutritious insides. Watching a small algal cell caught by the vampyrellid reveals the predator pressing against the algal cell until the victim stops moving, draining the dying cell’s innards in five to 10 minutes.

More’s single sample of collected sand ended up providing at least seven visibly different kinds of vampyrellid amoebas. Placopus melkoniani and P. pusillus, fried-egg vampyrellids now named as new species, hunt by rolling forward. Their outer membranes move “like a conveyor belt,” More says, or the treads on a tank. “You can see all their cell contents inside also rotating as the outer membrane rotates, which is almost beautiful,” he says.

In 2021, that same vacation sample delivered a third new species. More, by then a graduate student in systematics and evolution at the University of Alberta in Edmonton, Canada, and colleagues named that new species Sericomyxa perlucida, meaning “transparent silken slime.” It looks like a road-killed badminton shuttlecock but with exquisitely delicate tufts. And it was not just a new species in a new genus but also represented a whole new family.

Any ornithologist or mammalogist would have been thrilled with the results. But in the giddy frontier of protist discovery, “I was disappointed,” More says. “I was so determined that I was going to find an environmental lineage where no one had seen anything before.”

When Swedish botanist Carl Linnaeus, the 18th century founder of Western science’s biological naming system, studied single-celled organisms, he was limited to looking. He named relatively few single-celled organisms and put most in a genus he eventually called Chaos. Today’s biologists have many more high-tech tools at their disposal, but the evolution of life on Earth still looks chaotic. One cell of a type of protist called a cryptomonad has seven separate sets of genes, according to research reported this year. Three of the extra sets come from little organs descended from long-ago free-living cells, two from symbiotic bacteria that had apparently become essential and another from a virus hitchhiking in one of the bacteria.

“We’re an aberration,” says Maureen O’Malley, a philosopher of microbiology at the University of Sydney, as one multicellular earthling talking to another. In the modern view of life, single-celled microbes — protists among them — dominate the planet. Big multicellular life-forms now look like the rare, outlier freaks. A 2018 comparison estimates that Earth’s protists account for twice the gigatons of carbon as all the animals put together. Add in other microbes, and together they hold 40 times the biomass.

Earth was entirely a microbe’s world for some 2.5 billion years or more, the majority of life’s history, O’Malley points out. We big multicellulars evolved on the backs of microbe innovations. Just a few examples: The oxygenated atmosphere came from cyanobacteria photosynthesizing 2.7 billion years ago. Even today an estimated half of the oxygen we breathe comes from microbial sources, not from plants. And plants’ ability to generate oxygen came from engulfing the microbial technology we know as chloroplasts.

Termites “eat” wood thanks to the protists packed into their guts. Tomato plants grow better with more of the predatory protists in the soil around their roots. Bobtail squid get the glow in their light organs from engulfed bacteria. Tsetse flies can’t sustain milk-feeding for their bizarre live-birthed young without specialized live-in bacteria to provide B vitamins. The list goes on and on for influential microbes. They shaped the world and keep us alive in it.

O’Malley sums up microbes as “the dominant life-forms not only in today’s world, but also in all past eras of the living Earth.” For bird watchers, wildflower lovers and nature enthusiasts of all stripes, truly seeing these invisibly small creatures for the first time can be like realizing dark matter exists. And not only that it exists, but that it makes up so much more of the universe than the supposed ordinary stuff.

New discoveries of protists and other microbial species and their ways of living are creating a very different view and appreciation for life in all its forms. With a few quirky exceptions — including us — to be an earthling is to be microscopic.

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