Mono Lake is a stunning yet unforgiving habitat, with waters high in salt and arsenic that only support brine shrimp, alkali flies, and not much else. Recently, researchers have made an exciting discovery of an unexpected inhabitant, a microscopic organism known as a choanoflagellate, which forms colonies that have their own distinct bacterial microbiomes. This creature, related to the common ancestor of all animals, could provide valuable insights into the evolutionary connections between animals and bacteria, and how multicellular organisms emerged.
Located in the Eastern Sierra Nevada, Mono Lake is famous for its striking tufa formations, plentiful brine shrimp, and dark swarms of alkali flies, all uniquely equipped to thrive in its salty waters tainted with arsenic and cyanide.
Researchers from the University of California, Berkeley, have identified another peculiar creature residing in the lake’s salty shallows—one that could reveal secrets about the origins of animal life dating back over 650 million years.
This organism is a choanoflagellate, a tiny, single-celled entity capable of replication and forming complex multicellular colonies, much like how animal embryos develop. Although it is not classified as an animal, it stands as a close relative, making it a vital model for understanding the transition from single-celled to multicellular life.
Interestingly, it hosts its own microbiome, marking it as the first known choanoflagellate to sustain a stable biological relationship with bacteria, rather than just consuming them. This positions it as one of the simplest known organisms that maintains a microbiome.
“There is still so much to learn about choanoflagellates; we can only gain insights into many fascinating biological phenomena by understanding their ecology,” said Nicole King, a UC Berkeley professor of molecular and cell biology and a Howard Hughes Medical Institute (HHMI) investigator who examines choanoflagellates to recreate what early life might have been like in ancient oceans.
Typically only observable under a microscope, choanoflagellates are often overlooked by aquatic biologists, who prefer to study larger animals or visible algae and bacteria. Yet, their biology and way of life can provide clues about the early aquatic organisms that predated animals and eventually led to their evolution. This specific species could illuminate the beginnings of relationships between animals and bacteria that ultimately shaped the human microbiome.
“Animals evolved in oceans teeming with bacteria,” noted King. “When considering the tree of life, every surviving organism is linked through evolutionary history. By examining today’s organisms, we can reconstruct past events.”
King and her team from UC Berkeley documented this organism, naming it Barroeca monosierra, in a paper published digitally on August 14 in the journal mBio.
A stunning colony
Almost a decade ago, then-graduate student Daniel Richter returned from a climbing expedition in the Eastern Sierra Nevada with a sample of water from Mono Lake. Upon inspection through a microscope, he discovered a vibrant community of choanoflagellates. Except for brine shrimp, alkali flies, and various nematode species, few other life forms have been documented in the lake’s challenging conditions.
“The vial was bursting with large, beautiful choanoflagellate colonies,” remarked King. “They were the biggest we had ever encountered.”
The colonies appeared as hollow spheres composed of nearly 100 identical choanoflagellate cells that rotated and moved as each cell propelled itself with its flagella.
“One intriguing aspect is that these colonies resemble a blastula—a hollow sphere of cells formed early during animal development,” King noted. “We wanted to investigate further.”
At that time, however, King was preoccupied with other choanoflagellate species, and the Mono Lake samples were frozen away until some students revived and stained them to examine their unusual, doughnut-shaped chromosomes. Surprisingly, DNA was found within the hollow colony where no cells were expected to exist. Graduate student Kayley Hake later identified these as bacteria.
“The presence of bacteria was an incredible surprise. It was truly captivating,” King expressed.
Hake also discovered connective structures known as the extracellular matrix within these spherical colonies, secreted by the choanoflagellates.
It then occurred to Hake and King that these might not just be remnants of bacteria consumed by the choanoflagellates, but rather bacteria living and feeding on substances secreted by the colony.
“No one had previously reported a choanoflagellate engaging in a stable physical interaction with bacteria,” she stated. “In earlier studies, we found that choanoflagellates reacted to small bacterial molecules floating in the water or were consuming the bacteria, but there was never an observation of potential symbiosis or microbiomes like this.”
King collaborated with Jill Banfield, a groundbreaking metagenomics researcher and UC Berkeley professor in environmental science, policy, and management, as well as earth and planetary science, to identify the bacterial species present in the lake water and within the choanoflagellates. Metagenomics allows for the sequencing of all DNA in an environmental sample to reconstruct the genomes of its inhabitants.
Once Banfield’s lab pinpointed the methanogens in Mono Lake, Hake formed DNA probes to check which ones were also found in the choanoflagellates. King noted that the bacterial populations differed, indicating that some bacteria had adapted better to survive within the oxygen-deprived environment of the choanoflagellate colony. Hake concluded that these bacteria were not just appearing by chance; they were thriving and multiplying. It’s possible they were escaping the pond’s toxic conditions, or perhaps the choanoflagellates cultivated them for food, King speculated.
Much of this remains conjecture, she acknowledges. Future experiments should unveil the nature of the bacteria-choanoflagellate interactions. Past research in her lab has shown that bacteria can act as stimulants for mating in choanoflagellates and can encourage single-celled choanoflagellates to cluster into colonies.
For King, the choanoflagellate from Mono Lake will serve as another model system for studying evolution, similar to choanoflagellates found in splash pools on Curaçao in the Caribbean—her current major research interest—and those in polar regions. Obtaining more samples from Mono Lake may pose a challenge; during a recent visit, only six out of 100 samples contained these vibrant microorganisms.
“I believe there is still much to discover regarding microbial life in Mono Lake, as it is fundamental to understanding the ecosystem,” King remarked. “I’m enthusiastic about B. monosierra as a new model for exploring interactions between eukaryotes and bacteria. I hope it will provide insights into evolution, but regardless, it is a captivating phenomenon.”
In addition to King, Banfield, Hake, and Richter, the paper includes contributions from UC Berkeley co-authors former doctoral student Patrick West, electron microscopist Kent McDonald, and postdoctoral fellows Josean Reyes-Rivera and Alain Garcia De Las Bayonas. This research has received support from HHMI and the National Science Foundation.
