Asgard Archaea

Tania Ghosh

2nd October, 2020

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Introduction

 

Asgard or Asgardarchaeota is a proposed superphylum consisting of a group of archaea that includes Lokiarchaeota, Thorarchaeota, Odinarchaeota, and Heimdallarchaeota A representative of the group was cultivated. The Asgard superphylum represents the closest prokaryotic relatives of eukaryotes, which possibly emerged from an ancestral lineage of Asgardarchaeota after assimilating bacteria through the process of symbiogenesis.

Scientific Classification

Domain:    Archaea

Kingdom:  Proteoarchaeota

Superphylum:  Asgard (archaea) (Katarzyna Zaremba-Niedzwiedzka, et al. 2017)

 

Discovery

The discovery of archaea in the late 1970s led scientists to propose that the tree of life diverged long ago into three main trunks, or ‘domains’. One trunk gave rise to modern bacteria; one to archaea. And the third produced eukaryotes. But debates soon erupted over the structure of these trunks. A leading ‘three-domain’ model held that archaea and eukaryotes diverged from a common ancestor. But a two-domain scenario suggested that eukaryotes diverged directly from a subgroup of archaea. the argument over where eukaryotes came from has matured. Many on both sides agree that the origin of eukaryotes probably involved a step known as endosymbiosis. This theory, championed by the late biologist Lynn Margulis, holds that a simple host cell living eons ago somehow swallowed a bacterium, and the two struck up a mutually beneficial relationship. These captive bacteria eventually evolved into mitochondria — the cellular substructures that produce energy — and the hybrid cells became what is now known as eukaryotes. The nature of the engulfing cell is where the two camps diverge. As the three-domain adherents tell it, the engulfer was an ancestral microbe, now extinct. According to Forterre, it was a “proto-eukaryote” — “neither a modern archaeon nor a modern eukaryote”. In this model, there were several major splits in early evolution. The first happened billions of years ago when primeval organisms gave rise to both bacteria and an extinct group of microbes. This latter group diverged into archaea and the group that became eukaryotes. In the two-domain world, however, a primeval organism gave rise to bacteria and archaea. And the organism that eventually swallowed the fateful bacterium was an archaeon. That would make all eukaryotes a sort of overachieving branch of the archaea — or, as some scientists call it, a ‘secondary domain’. According to nature.com, in 2015, a group led by Thijs Ettema, an evolutionary microbiologist at Uppsala University in Sweden at the time, published DNA sequences for Lokiarchaeota, found in sediments dredged up five years earlier1. Within two years, Ettema’s team and other researchers had announced the discovery of three new archaeal phyla related to the Lokis5,6. The entire grouping of new phyla was named Asgard after the realm of the Norse gods.

Relationship with eukaryotes

These newly discovered archaea have genes that are considered hallmarks of eukaryotes. And deep analysis of the organisms’ DNA suggests that modern eukaryotes belong to the same archaeal group. If that’s the case, essentially all complex life — everything from green algae to blue whales — originally came from archaea. Until recently, scientists who sought to identify the bacteria or archaea in a particular habitat had to grow the organisms in the lab. Now, researchers can assess microbial diversity in a sample of water or soil by fishing out the DNA and analyzing it using mathematical tools, a technique called metagenomics. Using the latest powerful modeling techniques, they have created a forest of evolutionary trees detailing the familial relationships among archaea. The results, in many cases, place eukaryotes within the archaeal ranks.

 

Characteristics

The Asgard archaea are tiny in size, but they have proved to be mighty. They have reinvigorated debate about the true number of life’s domains. And they are providing tantalizing hints about the nature of the cells that gave rise to the first eukaryotes — at least to two-domain proponents. Like their namesake, Lokiarchaeota and their kin evade easy description. They are unquestionably archaea, but their genomes include a smorgasbord of genes that are similar to some found in eukaryotes. Loki DNA, for example, contains genetic instructions for actins, proteins that form a skeleton-like framework in eukaryotic cells. Evolutionary modeling reinforced the tight linkage between the Asgard archaea and eukaryotes. The trees built by Ettema’s team place all eukaryotes in the Asgard group.

Is it culturable?

The strange organism was first plucked from the 2,500-meter-deep Omine Ridge off the coast of Japan, where it was buried in deep-sea mud, according to Science. To mimic the harsh conditions of the seabed, microbiologist Hiroyuki Imachi of the Japan Agency for Marine-Earth Science and Technology and his colleagues built a bioreactor to contain the seafloor muck and continually bathe it in methane gas. Five years later, they scraped samples into glass tubes filled with various nutrients and waited. A year later, they detected microbes growing in one of the samples that resembled bacteria, superficially, but were genetically distinct. These were the Asgard archaea they had hoped for. Over the next six years, they worked to isolate and culture pure samples of the organism, which they found takes between 14 and 25 days to double its cells in culture. In comparison, most bacteria double in under an hour. Finally, the researchers produced a pure sample of Prometheoarchaeum syntrophicum, which they named for the Greek god Prometheus who sculpted humans from the mud. Although not yet published in a peer-reviewed journal, the paper has already earned praise from prominent leaders in the field. According to scientists, it was one of the slowest dividing organisms. With the cultured microbe in hand, the researchers sequenced its full genome and confirmed the existence of eukaryote-like genes. They also observed that the microbe usually grows in tandem with a second, methane-producing archaeon, with whom it fosters a symbiotic relationship. Prometheoarchaeum breaks down amino acids and supplies its partner with energy in the form of hydrogen, which might otherwise impede Asgard's growth, according to Science. 

Images captured with an electron microscope revealed that Prometheoarchaeum develops lengthy appendages with multiple branches, according to Nature. The authors suggest the microbe may have used the tentacles to grab hold of oxygen-producing organisms. 

With the cultured microbe in hand, the researchers sequenced its full genome and confirmed the existence of eukaryote-like genes. They also observed that the microbe usually grows in tandem with a second, methane-producing archaeon, with whom it fosters a symbiotic relationship. Prometheoarchaeum breaks down amino acids and supplies its partner with energy in the form of hydrogen, which might otherwise impede Asgard's growth, according to Science. Images captured with an electron microscope revealed that Prometheoarchaeum develops lengthy appendages with multiple branches, according to Nature. The authors suggest the microbe may have used the tentacles to grab hold of oxygen-producing organisms. 

 

The Asgard way of living 

The genomes of Asgard is a new class of rhodopsin, suggesting a phototrophic lifestyle. Copper and arsenic resistance has also been identified within its genomes. Asgard archaea are mostly exposed to the anoxic environment as well as inorganic and organic carbon sources, nitrogen, and sulfur. Glycolysis appears to be ubiquitous in Asgard Archae with all the genomes only lacking hexokinase. Lokiarchaeota was shown to be hydrogen dependent, anaerobic autotrophic archaeon who has a complete THMPT-WL pathway to fix carbon dioxide. The Wood–Ljungdahl pathway, or the reductive pathway acetyl-CoA, is the largest carbon fixation pathway in anaerobic conditions. Evidence of nitrogen cycling was seen in Heimdallarchaeota, having both nitrite and nitrate reductase. All Asgard Archaea encode for both sulfate adenyltransferase and phosphoadenosine phosphosulfate reductase, showing evidence of sulfate cycling. They also have the capability to reduce arsenic with arsenic reductase and efflux arsenite through an arsenite transporter.

Conclusion

Many researchers are using data from these archaea to formulate a better picture of the eukaryotic precursor. It might already have had some features typical of eukaryotes before it took in the mitochondrial predecessor. Elusive though the microbes might be, one team has captured what it says are the first images of Asgard organisms. Pictures of one type show rounded cells, each containing a compacted bundle of DNA that resembles that defining feature of all eukaryotes, a nucleus. But the overall picture is still unclear. Lokiarchaeota and their relatives emerge from the shadows, two-domain supporters would like them to settle the long-standing debate over the origin of complex life. But that could take a while. In the meantime, scientists would continue researching this elusive microbe and find out more information about them which might help us to understand a lot more about our system in the long run.

References

  1. Watson, T. (2020, June 30). Fournier gangrene. Retrieved September 13, 2020, from https://en.wikipedia.org/wiki/Fournier_gangrene

  2. "Asgard archaea illuminate the origin of eukaryotic cellular complexity" (PDF). Nature. 541 (7637): 353–358. Bibcode:2017Natur.541..353Zdoi:10.1038/nature21031ISSN 1476-4687. PMID 28077874

  3. Fournier, G., & Poole, A. (2018, July 27). A Briefly Argued Case That Asgard Archaea Are Part of the Eukaryote Tree. Retrieved September 13, 2020, from https://www.frontiersin.org/articles/10.3389/fmicb.2018.01896/full

  4. Lanese, N. (2019, August 12). Elusive Asgard Archaea Finally Cultured in Lab. Retrieved September 13, 2020, from https://www.google.com/amp/s/www.the-scientist.com/news-opinion/elusive-asgard-archaea-finally-cultured-in-lab--66264/amp

About the Author

Tania Ghosh, studies Biotechnology in St. Xavier's College Kolkata.