Scientists from Berkeley have discovered a new choanoflagellate species in Mono Lake, which forms multicellular colonies and hosts a microbiome, offering new perspectives on the evolution of multicellular organisms.

The salty, arsenic- and cyanide-contaminated waters of Mono Lake in the eastern Sierra Nevada are an extremely hostile environment. Aside from the numerous brine shrimp and the black clouds of alkali flies, very few organisms live there.

Now researchers from University of California, Berkeley have discovered a new creature in the salty shallow waters of the lake that could give scientists insight into the animals’ origins over 650 million years ago.

Discovery of choanoflagellates

The organism is a choanoflagellate, a microscopic, single-celled life form that can divide and develop into multicellular colonies, similar to the way embryos develop in animals. However, it is not a species of animal, but a member of a sister group of all animals. As the closest living relative of animals, the choanoflagellate is a crucial model for the leap from single-celled to multicellular life.

Surprisingly, it has its own microbiome, making it the first known choanoflagellate to establish a stable physical relationship with bacteria rather than just eating them, making it one of the simplest organisms known to have a microbiome.

Choanoflagellates: A bridge in evolution

“Very little is known about collared flagellates, and there are interesting biological phenomena that we can only gain insight into by understanding their ecology,” says Nicole King, a professor of molecular and cellular biology at UC Berkeley and a Howard Hughes Medical Institute (HHMI) investigator who studies collared flagella as a model of what early life looked like in the prehistoric oceans.

Choanoflagellates are usually only visible under a microscope and are often ignored by aquatic biologists, who instead focus on macroscopic animals, photosynthetic algae or bacteria. But their biology and lifestyle can provide insights into creatures that lived in the oceans before animals evolved, and from which animals eventually evolved. This species in particular could shed light on the origin of the interactions between animals and bacteria that led to the human microbiome.

“Animals evolved in oceans that were full of bacteria,” King said. “If you think about the tree of life, all organisms alive today are related to each other over the course of evolution. So by studying organisms alive today, we can reconstruct what happened in the past.”

King and her colleagues at UC Berkeley described the organism they called Barroeca Monosierra, after the lake — in an article published in the magazine mBio.

The newly named species Barroeca monosierra was discovered in Mono Lake. Colonies of these organisms consist of numerous identical cells (cyan), each with flagella (green) that allow them to propel themselves through the water. This choanoflagellate colony hosts its own microbiome (red), something never seen before in these organisms. The extracellular matrix that the bacteria interact with is shown in white. Image credit: Davis Laundon and Pawel Burkhardt, Sars Centre, Norway; Kent McDonald and Nicole King, UC Berkeley

Insights from a surprising discovery

Nearly 10 years ago, then-UC Berkeley student Daniel Richter returned from a climbing trip in the eastern Sierra Nevada with a vial of Mono Lake water he had casually collected along the way. Under the microscope, it was teeming with choanoflagellates. Aside from brine shrimp, alkali flies, and various nematode species, few other life forms have been described in the lake’s inhospitable waters.

“It was just packed with these big, beautiful colonies of choanoflagellates,” King said. “I mean, they were the biggest we’d ever seen.”

The colonies, consisting of what appeared to be approximately 100 identical choanoflagellate cells, formed a hollow sphere that swirled and rotated as the individual cells moved their flagella.

“One of the interesting things about them is that these colonies have a shape that resembles the blastula – a hollow ball of cells that forms early in an animal’s development,” King said. “We wanted to learn more about that.”

At the time, however, King was busy studying other species of choanos, as she calls them, and so the Mono Lake choanos languished in the freezer until some students revived and stained them to study their unusual, doughnut-shaped chromosomes. Surprisingly, there were also DNA in the hollow colony, where there should not be any cells. After further investigation, doctoral student Kayley Hake determined that they were bacteria.

The study of choanoflagellates and bacteria

“The bacteria were a big surprise. It was just fascinating,” King said.

Hake also discovered binding structures within the spherical colony, the so-called extracellular matrix, which were secreted by the choanos. Only then did Hake and King realize that these might not be the remains of bacteria that had eaten the choanos, but bacteria that lived and grazed on the substances secreted by the colony.

“Nobody has ever described a choanoflagellate that had a stable physical interaction with bacteria,” she said. “In our previous studies, we found that choanos responded to small bacterial molecules swimming through the water, or that the choanos ate the bacteria, but there was no case of them doing anything that could potentially be a symbiosis. Or in this case, a microbiome.”

Future research and implications

King teamed up with Jill Banfield, a pioneer in metagenomics and professor of environmental science, policy and management and earth and planetary sciences at UC Berkeley, to find out what types of bacteria were in the water and in the choanos. Metagenomics involves sequencing all of the DNA from an environmental sample to reconstruct the genomes of the organisms living there.

After Banfield’s lab identified the microbes in Mono Lake’s water, Hake created DNA probes to find out which ones were also in the choanos. The bacterial populations were not identical, King said, so apparently some bacteria survive better than others in the oxygen-poor lumen of the choanoflagellate colony. Hake found that they were not there by chance; they were growing and dividing. Perhaps they were escaping the lake’s toxic environment, King mused, or perhaps the choanos were breeding the bacteria to eat them.

Much of this is speculation, she admits. Future experiments should reveal how the bacteria interact with the choanoflagellates. Previous work in her lab has already shown that bacteria act as an aphrodisiac and stimulate mating in choanoflagellates, and that bacteria can encourage single-celled choanos to form colonies.

For her, Mono Lake’s choanoflagellates will become another model system in which she can study evolution, just like the choanos that live in wading pools on the island of Curaçao in the Caribbean – her current focus – and the choanos in pools at the North and South Poles. But obtaining more samples from Mono Lake could be a challenge. During a recent visit, only six out of 100 samples contained these energetic microorganisms.

“I think there is a lot more that needs to be done about the microbial life of Mono Lake because it is the foundation for everything else in the ecosystem,” King said. “I am excited about B. monosierra as a new model to study the interactions between eukaryotes and bacteria. And I hope it tells us something about evolution. But even if not, I think it’s a fascinating phenomenon.”

Reference: “A large colonial choanoflagellate from Mono Lake hosts live bacteria” by KH Hake, PT West, K. McDonald, D. Laundon, J. Reyes-Rivera, A. Garcia De Las Bayonas, C. Feng, P. Burkhardt, DJ Richter, JF Banfield and N. King, August 14, 2024, mBio.
DOI: 10.1128/mbio.01623-24

The work is supported by HHMI and the National Science Foundation.