NORTHAMPTON — A Smith College lab has discovered a microscopic protist species living inside the shells of amoebas, a phenomenon researchers say has never been recorded in 200 years of study.
Arcellinida, or shelled amoebas, live in freshwater and wetlands across the globe. These predator organisms were first discovered in the 1880s, but their fossils date back more than 730 million years. Today, scientists track amoebas as bioindicators due to their high sensitivity to environmental changes or water contaminants.
From 2016 to 2024, Smith College biology professor Laura Katz and her lab sampled shelled amoebas across New England wetlands to document their biodiversity. Early on, lab members noticed something unexpected under the microscope: a worm-shaped organism called a flagellate swimming inside an amoeba’s shell.
After repeatedly seeing this phenomenon in amoebas along a single stream in Acadia National Park in Maine, the researchers realized this was not a coincidence, but a symbiosis. This finding was published in the Journal of Eukaryotic Microbiology in September.
“People have been studying these things for hundreds of years, and nobody ever saw what our lab discovered,” Katz said.
Relationships between microorganisms and other species are well documented, like gut bacteria digesting food in human intestines or algae giving coral their color. But Katz said these interactions were once thought to be an exception, not a rule. This newfound relationship between a flagellate and an amoeba adds to the growing body of evidence that interactions between microbes and other species are more common than researchers previously understood.
“We know lots of microbes interact with bacteria, but to have this amoeba interacting with the flagellate, on the one hand, was really new,” Katz said. “On the other hand, it’s part of this world we’re in where really species just don’t tend to live alone.”
Under Katz’s guidance, Godwin Ani, a doctoral candidate in the University of Massachusetts Amherst’s Organismic and Evolutionary Biology program, and Giulia Ribeiro, a postdoctoral researcher at Smith, identified the flagellate as a type of prokinetoplastid that appears to be parasitic to its host.
In the lab
On the second floor of Smith College’s Burton Hall on a recent fall day, Ribeiro walked over to the takeout containers stacked within a brightly lit box. She opened the container to reveal a tightly packed web of red moss. Within the moss, the amoebas are invisible to the human eye. They cannot be grown in the lab, so the researchers wash them off the moss and onto a plate to put under the microscope.
The microorganisms quickly become stressed once removed from their habitat. So Ani and Ribeiro brought their equipment to Maine, setting up a makeshift lab in their motel room.
“If we bring them back, they’ll be stressed,” Ani said. “They’ll start expressing some genes which are unrelated to the flagellates.”
Back at Smith College, Ani analyzed the complete RNA transcripts of the amoebas and flagellates, a study called transcriptomics. Using EukPhylo, an evolutionary history pipeline that Katz developed in her lab, Ani placed the species on “the Tree of Life” to deduce its classification. He previously completed a similar evolutionary history process for a newly identified “fire amoeba,” which can withstand temperatures up to 63 C, or 145 F.
Ribeiro corroborated Ani’s data by analyzing the gene expression of their amoeba samples. She has been studying these amoebas for most of her research career, previously working under one of Katz’s former doctoral students in Brazil.
“When we first saw it (the flagellate), we did not have these single-cell techniques,” Katz said. “We tried some other methods, but we really couldn’t get very far (until) the combination of the single-cell molecular work with the backbone biometric review.”
Only 8% of the 125 samples collected contained the flagellate. This particular study includes amoebas from the Hawley Bog in Hawley; Harvard Forest in Petersham; Orono Bog in Bangor, Maine and Big Heath Bog in Acadia National Park.
Under the microscope, bright green speckles appear on the body of amoebas. Ribeiro identifies these as algae, one of the amoeba’s favorite snacks. It is not uncommon for a larger single-celled predator to eat or absorb smaller species into its cytoplasm, Ani said. Microbiologists theorized our mitochondria — where a cell breaks down food into energy — were once single-celled organisms.
“It’s more surprising because we expect the amoeba to engulf the flagellate,” Ribeiro said. “Amoebas engulf anything smaller than them to feed on. So why is the flagellate still alive? That’s surprising.”
The research does not conclude any definitive relationship between the flagellate and Arcellinida, but the scientists speculate the flagellate is using the shell for protection from the changing environment. Ribeiro also observed the amoeba showed signs of a stress response when the flagellate was present.
“The flagellates are always touching the amoeba, so they are probably causing some stress in the amoeba,” Ribeiro said. “This interaction is probably not great for the amoeba.”
The Organismic and Evolutionary Biology program is an interdisciplinary, interinstitutional program based out of UMass. Single-celled organisms make up most eukaryotic species, but Ani notes that microorganisms are vastly understudied.
With so few researchers dedicated to the field, many undergraduate researchers at Smith College helped collect the data used in this study over the course of many semesters. Ribeiro said research like this would be far more challenging without the dedication of these students.
“Sometimes we don’t have the time to be at the microscope looking at these organisms and trying to learn new things, and we have all of these undergraduates all around here, and they spend a lot more time than us doing that,” Ribeiro said. “It’s one of the ways where we find these kinds of things when people are really sitting and looking.”
