Scientists Piece Together Microbe’s Long History Through its Genome

Microbes that live in deep-sea hydrothermal vents offer a window into how early organisms survived on a young Earth. As these microbes evolved in response to the changing planet, the adaptations became recoded in their genomes. As a result, some modern vent microbes have a “mosaic genome” with both ancient and recent additions, which can reveal important details of their evolutionary history.

DCO Deep Life Community members Donato Giovannelli (Earth-Life Science Institute, Japan and Rutgers University, USA) and Stefan Sievert (Woods Hole Oceanographic Institution, USA), in collaboration with Costantino Vetriani (Rutgers University, USA) and colleagues, conducted a comprehensive analysis of the genome of Thermovibrio ammonificans, a heat-loving organism that lives off the chemical energy provided by deep-sea hydrothermal vents. The researchers used a “molecular archaeology” approach to distinguish between genes passed down from ancient ancestors and more recent acquisitions, to better understand how the microbe co-evolved with the changing planet. The researchers report their findings in a new paper in the journal eLife.

Vetriani’s lab first isolated the T. ammonificans bacterium from a black smoker hydrothermal vent chimney on the East Pacific Rise. It thrives in hot environments rich in volcanic gases such as hydrogen, carbon dioxide, and sulfur dioxide. “T. ammonificans is a modern organism that lives on the planet today, but in an environment that resembles conditions on early Earth,” said senior author Vetriani. “We can assume that some of the genetic or metabolic traits that are present today, may have been inherited from an ancestor that lived on early Earth.”

After realizing that T. ammonificans likely stemmed from a deep branch on the tree of life, Vetriani sequenced the genome with the help of the Joint Genome Institute. But it wasn’t until Giovannelli joined Vetriani’s lab that the group was able to use bioinformatics techniques to fully analyze that genome. The researchers combined comparative genomics approaches that draw evolutionary connections between T. ammonificans and related microbes, with physiological experiments, and proteomic analyses that look at all of the proteins expressed by the bacterium. Together, these techniques enabled the researchers to reconstruct the evolutionary history of the organism and determine its early metabolism.

The researchers identified many genes that had ancient origins, including five different genes coding for hydrogenases, which would enable the microbe to capture energy from hydrogen. Genes coding for enzymes that reduce sulfur to hydrogen sulfide also came from early ancestors.

As oxygen levels on Earth rose, the researchers suspect that T. ammonificans acquired genes to help it survive exposure to oxygen, which is toxic to the organism, and for reducing nitrate, the oxidized form of nitrogen, as part of its metabolism. The bacterium likely obtained key genes in these pathways by taking up DNA from other microbes.

“It’s like T. ammonificans, over time, had the chance—and threat—of adapting to new oxidizing conditions and it coped by exchanging DNA with its neighbor and getting new functions,” said Giovannelli. “The signal in the genome is so clear, it’s striking.” 

Perhaps the most surprising trait uncovered by the genomic analysis is that T. ammonificans appears to have enzymes for two different ancient metabolic pathways for converting carbon dioxide into bacterial biomass. In future work, the researchers plan to investigate whether the second, older pathway is still active and what conditions trigger the expression of each pathway. They also are sequencing related organisms to fill in existing evolutionary gaps.

Giovannelli plans to continue his exploration into the coevolution of biology and geology through time, in collaboration with Vetriani, in his new position as an EON research fellow at the Earth-Life Science Institute in Tokyo. Giovannelli is a member of the DCO Early Career Scientist Network and credits the DCO as playing an important role in his career development and his ability to forge connections across disciplines.

A transmission electron microscopy image of T. ammonificans. Credit: Costantino Vetriani
 
Donato Giovannelli (left), Costantino Vetriani (center), and colleagues work in the lab of the Atlantis research vessel during a hydrothermal vent sampling expedition. Credit: Donato Giovannelli

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