Hadesarchaea: a New Archaeal Class of Cosmopolitan Deep Microbes

The deep biosphere encompasses a variety of ecosystems, from the marine subsurface to crevices in continental crust.

These niches are characterized by different physical and chemical conditions, which in turn influence their microbial inhabitants. In a new paper in Nature Microbiology, a team of researchers including several DCO Deep Life scientists describes a new class of Archaea, which thrive in a variety of subsurface settings [1].

The team, led by Brett Baker (University of Texas Austin, USA), used shotgun sequencing (a similar technique was used to decode the human genome) to obtain genomes from sediments from the hot springs of Yellowstone National Park and the White Oak River estuary. The Archaea they found are part of a class previously known as SAGMEG (South-African Gold Mine Miscellaneous Euchyarchaeal Group), and are very closely related to organisms found in the Lost City hydrothermal vent field and other deep locales. 

“These new genomes belong to a class of microbes specialized for survival beneath the surface, so we called them ‘Hadesarchaea’, after the ancient Greek god of the underworld,” said Baker.

These microbes have not been grown in the laboratory, therefore little was known about how they survive in the subsurface. This analysis provided significant insight into their lifestyles in deep environments. Baker and his colleagues found that the Hadesarchaea have relatively small genomes of, on average, 1.5 megabase pairs (compared to 2 megabase pairs in an average Archaea species), and the genes encoded therein are similarly streamlined. The authors suggest this reduction in genome and gene size allows the Hadesarchaea to survive despite low nutrient availability.

These microbes are also experts at scavenging carbon from their environment, harboring the genes necessary to fix inorganic carbon. They also have the genetic potential to utilize chemical energy in the form of molecular hydrogen. These traits are essential for life in the absence of sunlight..

How this important and ubiquitous class of microbes fits into the deep biosphere ecosystem is an important next question.

“We are in the process of sequencing dozens of other subsurface microorganisms, which will enable us to obtain a highly resolved foodweb and understand the roles of Hadesarchaea in subsurface ecosystems.” said Baker

Baker’s co-authors include DCO Deep Life Co-Chair Kai-Uwe Hinrichs (University of Bremen, Germany) and Deep Life scientists Cassandre Lazar (University of Bremen, Germany), the Ettema Laboratory (Uppsala University, Sweden), and Andreas Teske (University of North Carolina, USA).

Image: The hot spring in Yellowstone National Park from which Baker's team collected sediment samples. Credit: Dan Coleman.

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