Researchers Discover Salt-Loving Methanogens

Two previously overlooked archaeal strains fill an evolutionary gap for microbes.

By Abby Olena | May 26, 2017

A hypersaline salt lake in southeastern Siberia with halite crystal deposition; the red color is due to a high density of haloarchaea in the brines.DIMITRY SOROKINMany strains of archaea are capable of living in environments with high salt concentrations, and others are able to produce methane, but only a few can do both. In a study published today (May 26) in Nature Microbiology, researchers identified and cultured two lineages of methane-generating archaea that thrive in salty lakes. The two strains—part of a class the authors named “Methanonatronarchaeia”—appear to be most closely related to the Halobacteria, a class of archaea found in salt-rich environments worldwide.  

“The halophilic archaea had long been suspected to have evolved from a lineage of methanogens, and this new lineage is the missing link confirming this hypothesis,” William Whitman, a microbiologist at the University of Georgia who did not participate in the study, wrote in an email to The Scientist. “This work is of great value and an important development.” 

Dimitry Sorokin, a microbial ecologist at the Russian Academy of Sciences in Moscow, and his colleagues showed previously that the sediment in soda lakes in southern Siberia contained DNA with two different versions of a gene unique to methanogens, but that were only distantly related to the same gene in known microbes. In order to find the organisms the genes belonged to, the researchers isolated 11 strains of archaea from highly alkaline and salty soda lakes, and three from non-alkaline salt lakes.

To culture the strains successfully, the team grew them at high salt concentrations and temperatures and added a form of iron sulfide, a mineral that is found in the sediments where these microbes grow.

The researchers observed the production of methane in the cultures only when they provided both formate and methanol or trimethylamine, two substrate combinations used in the methyl-reducing pathway of methanogenesis. They concluded that the two archaeal lineages likely use this pathway instead of three alternative methanogenesis pathways commonly used by other archaea.

The authors compared representative genomes of the two lineages to each other, as well as to the genomes of other archaea. These comparisons suggested that the common ancestor of archaea was a methane-producer, a hypothesis that others have explored as well. They also found genomic evidence that this class of archaea copes with high salt concentrations by transporting potassium ions into their cells, rather than by excluding salt, behavior that is more similar to halophilic archaea than to other methanogens.

A hypersaline soda lake in southeastern Siberia, near Altai

This study details the “finding of an unusual methane-producing microorganism in that it is only distantly related to all the others that we know of,” said James Ferry, a microbiologist at Pennsylvania State University who was not involved in the work.

In order to confirm that the two lineages do use the methyl-reducing pathway of methanogenesis, the group would need to isolate and characterize relevant enzymes, and create a genetic system in which they could manipulate genes, Ferry said. The authors “were only able to speculate on the more detailed mechanism of growth based on what was known about [other] organisms that have the similar growth characteristics,” he added.

Sorokin explained that another open question is how the organisms use iron sulfide, since it doesn’t appear to get into their cells. But the future direction that most interests him is understanding how this class of archaea functions in the environment.

“The main question now is how they compete,” Sorokin said. In sediment incubation experiments, the team found that “as soon as the conditions are right, [these organisms] immediately jump to domination of 90 percent of the community, but of course how it goes on in the native setting, I still don’t know,” he explained.

“We know that there are many ancient lineages in the prokaryotic world that have never been cultured and haven’t been fully explored,” said Whitman. “This is a good example of how studying these lineages provides much more detail about the early evolution of life.”

D.Y. Sorokin et al., “Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis,” Nature Microbiology, doi:10.1038/nmicrobiol.2017.81, 2017.

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Avatar of: James H

James H

Posts: 6

May 30, 2017

Researchers Discover Salt-Loving Methanogens


1. As a scientist it would have been good to see the equations and structures of the compounds . It saves so many words and is intuitive.

2. Para 5: it mentions 'three alternative pathways'. This is poor English and inaccurate: you can only have ONE alternative.


James Hooper



Avatar of: James V. Kohl

James V. Kohl

Posts: 531

May 30, 2017

“The main question now is how they compete,” Sorokin said.

Others have shown that competition is nutrient energy-dependent and pheromone controlled in the context of changes that link angstroms to ecosystems in all living genera.

See: Scientists investigate how the sense of smell works in bacteria

...the signaling and inactive states differ only very slightly at the nitrate-binding site – by 0.5-1 angstroms, which is approximately one fifth of the size of the ion itself (1 angstrom is 10-10 meters). However, when this ion binds to the sensor, it causes huge changes in the protein: The helices of different monomers begin to move in different directions, like pistons. These “pistons” transmit the small change of 0.5-1 angstroms through the membrane, and their outer ends shift by approximately 2.5 angstroms in different directions. Inside the cell, in the HAMP domain, these shifts are converted into the rotation of two parts of NarQ relative to each other. Ultimately, the positions of the output helices change by as much as 7 angstroms, thus completing the signal transmission.

I'm not sure how this level of energy-dependent signal transmission can be linked to increasing organismal complexity via the evolution of one or two innate immune systems. But that appears to be the attempt made in the journal article.

For example, Figure 6 attests to the complexity of the "evolution of microbial methanogenesis" by placing everything into the context of energy-dependent thermodynamic cycles of RNA-mediated protein folding chemistry, which are biophysically constrained by the physiology of reproduction in species from microbes to humans.

Two complete CRISPR-Cas / innate immune systems in HMET1 compared to none in AMET1 help to explain why an excess number of genes for anti-parasitic defense appear to have been created in the context of food energy-dependent lifestyle differences. The lifestyle differences indicate that HMET1 is subject to much more nutrient stress and social stress that causes virus-driven energy theft in the context of stronger pressure from mobile elements than in AMET1.

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