At first sight, stromatolites may seem unremarkable. The stromatolite formations found in Shark Bay, Western Australia, do resemble dark, sediment-covered stones resting in shallow waters. However, they are rich in history through their layers of microbial life, whose interactions have occurred over time and are most likely indicative of a major occurrence in the timeline of Earth’s evolution.
A collaboration of researchers from The University of New South Wales, The University of Technology Sydney, and the University of Melbourne, reveals a previously undiscovered archaeon associated with a bacterium within one of these living fossils. It demonstrates an example of cellular cooperation that could have provided a fundamental pathway for the evolution of complex lifeforms.
Stromatolites likely represent not only a cradle for the early evolution of microbial organisms’ interactions with one another, but also a model to understand how complex eukaryotic organisms may have arisen from these interactions in a long-term evolutionary progression.
Although this idea as to how complex life originated may be a bold one, it builds on an age-old question. Approximately 2.3 billion to 2.1 billion years ago, it is believed that the first eukaryotic cells came into existence through a close association between an archaeal cell and a bacterium. Eventually, as the bacterial partner became an essential organelle in the eukaryotic cell, the mitochondrion, this close association or cooperation between the two cells directly contributed to the development of mitochondria as the energy-producing organelle for the eukaryote.
Since the first discovery of the Asgard archaea, often described as close relatives of the archaeal ancestor of eukaryotes, scientists have long speculated that the archaeal partner of the first eukaryotic cell was related to this group. This idea is based on various molecular and sequencing analyses.
Researchers studying a microbial habitat unique to Hamelin Pool, located within Shark Bay, a World Heritage Site often described as a model for the early Earth, discovered the Asgard archaeon Nerearchaeum marumarumayae using samples obtained from subsurface layers of ancient microbial mats. The microbial mats found in Hamelin Pool consist of thickly layered structures. In these environments, microorganisms share biological compounds for metabolic processing and utilize changing elements of the microbiome, including high salinity and periodic decay of dissolved oxygen, to survive.
To enrich for and isolate Nerearchaeum marumarumayae, the research team identified a sulfur-reducing bacterium that repeatedly grew in association with it in the lab. The fact that they could not isolate the archaeon in a pure culture for several years suggests that it had a mutual dependence on the sulfur-reducing partner for survival, according to researcher John Burns.
Through optimization and exploration of new potential organisms, researchers were able to push the project forward after five years of experimentation. They used an electron cryo-tomography technique that produced high-resolution 3D images of structures within Nerearchaeum marumarumayae at very small scales. This allowed the research team to visualize the build-up of thin cylindrical projection structures, or “tubes,” connecting to a sulfur-reducing partner.
As a working model of early partnership systems between archaea and bacteria, this study has helped to solidify understanding of early life evolutionary processes and the initial development of cellular complexity.
This recent discovery of an archaeon’s unique characteristics is not to be confused with an ordinary microorganism without distinctive features. Researchers observed coccoidal-shaped cells that had varied morphological extensions, including clusters of vesicular buds, large tubular cytoplasm, and strands of external fiber. Some cells appear as many jointed units joined together by filamentous structures.
The outer surface of the cells also differs in appearance from that which is typically evident in archaea. It exhibits an irregular-shaped outer layer comprised of spherical globules. Inside the cells, investigators noted other peculiarities, such as structures resembling encapsulin proteins or thermosome-like structures involved in thermal response regulation.
The genomic study revealed another aspect regarding the cells. Their genomes encode proteins associated with the complexity of cell surfaces, cellular membrane associations, and cytoskeletal activity. Some of these are homologous to proteins expressed in eukaryotes that are involved with intracellular membrane system function and intracellular vesicle transport. Researchers also employed deep learning techniques to predict the structural characteristics of proteins expressed by these microorganisms.
“Using deep learning methods to forecast the protein structure profile of these microbes is thrilling as it provides insight into earlier primitive cellular processes, which would later be essential to the evolution of higher-order species,” stated Associate Professor Kate Mitchie of The University of New South Wales.
Based on these structures, the research group has hypothesized a potential mechanism of partnerships between archaea and bacteria. The proposed model suggests that archaeal cells would use fermentative pathways to convert organic compounds into hydrogen and other fermentation products. These products would then support bacteria in their utilization of electron acceptors for metabolic activity.
It is likely that the bacterium provides vitamins, amino acids, fatty acids, trehalose, and other compounds that the archaeon needs. In exchange, the archaeon may provide cytoplasmic space or metabolic outputs that support the bacterium.
Most of this remains an informed reconstruction rather than a complete map of how the two microorganisms interact. The authors of the paper make it clear that some of the inferences made through genomic and proteomic analyses will require experimental validation.
The fact that there is a physical connection between the two is nevertheless important. “This is an important milestone in the ongoing quest for the origins of eukaryotic life forms,” says Debbie Ghosal, associate professor of microbiology at The University of Melbourne.
“This discovery brings us a few steps closer to understanding how the complexities of eukaryotic cells arose from more simple microbial life forms.”
While some aspects of the discovery are clear, there are still others that the authors do not fully understand, such as the function of the intercellular tubes connecting the two microorganisms. The authors suggest that the connections likely result from some type of symbiotic relationship, such as syntrophic or inhibitory interactions. However, they acknowledge that this remains speculative.
There are also uncertainties about the possible function of a number of cytoskeletal proteins encoded within the archaeon. While some are similar to those found in other Asgard archaea, the authors state that their roles in relation to the observed cellular structures are not yet known. The researchers relied largely on enriched cultures, which limits certainty about every specific interaction between these microorganisms.
Research on how eukaryotes evolved has led scientists to propose that the structures and behaviors seen in microbial mats in Shark Bay today resemble those of ecosystems that were common during the Proterozoic Eon. This is the period when eukaryotes began to appear. These mats were tightly packed and cooperative environments, suggesting that early cellular complexity may have developed in similar settings.
As Associate Professor Iain Duggin from The University of Technology Sydney said, “one could say we are slowly coming up from the depths of the ocean.” When naming the archaeon, Nerearchaeum marumarumayae, he drew on a metaphor that reflects its significance to his culture and that of the Malgana people. Kymberly Oakley, described as a leading expert in the Malgana language, and Malgana elders were consulted to ensure the respectful use of the name.
Shark Bay is not just a scientific archive but also a cultural landscape managed by Traditional Owners who have been connected to the area for thousands of years, long before the term “modern biology” came into use.
Burns explained that the research is important not only for its scientific value but also for demonstrating collaboration across disciplines. It also highlights the impact of climate change and human activity on the microbial ecosystems of Shark Bay.
Although the research does not provide a definitive answer to the question of where complex life originates, it offers a valuable reference point for further study. Researchers can now examine a modern archaeal-bacterial partnership formed in a mat ecosystem that may resemble ancient environments.
This provides insight into how cells formed and how early partnerships may have developed. It also reinforces the importance of preserving fragile ecosystems like those in Shark Bay.
By protecting these environments, researchers may continue to uncover clues about how complex cells eventually gave rise to plants, animals, and humans.
Research findings are available online in the journal Current Biology.
The original story “Newly discovered Asgard microbe could explain the origins of complex life on Earth” is published in The Brighter Side of News.
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