Introducing Hydrothermarchaeota: a group of microbes living in hydrothermal fluids

Researchers used cutting-edge molecular methods to describe a group of subseafloor microbes that thrive in the hot, oxygen-free fluids flowing through Earth’s crust.

It’s tough for microbes to make a living in the cold, dark sediments beneath the seafloor. Hydrothermal vents, however, are an oasis for subseafloor life. A variety of organisms thrive on the hot, chemical-rich fluids that percolate through these environments.    

DCO Deep Life Community members Stephanie Carr (formerly of Bigelow Laboratory for Ocean Sciences, now at Hartwick College, USA) Ramunas Stepanauskas, Beth Orcutt, (both at Bigelow Laboratory for Ocean Sciences, USA), and Sean Jungbluth (DOE Joint Genome Institute, USA), and colleagues have described a group of microbes that make their home in hydrothermal fluids, called Hydrothermarchaeota. The researchers report their discovery in a new paper in The ISME Journal [1].

Hydrothermarchaeota live in such an extreme environment that they have never been cultivated in a laboratory for study. Researchers bypassed the problem of cultivation with genetic sequencing methods including single cell genomics, a suite of novel techniques to detect and sequence individual cells. They found that Hydrothermarchaeota may obtain energy by processing carbon monoxide and sulfate, which is an overlooked metabolic strategy. The microbes use energy from this process to build their own organic compounds, in a form of chemosynthesis.

“The majority of life on Earth is microbial, and most microbes have never been cultivated,” said Orcutt. “These findings emphasize why single cell genomics are such important tools for discovering how a huge proportion of life functions.”

Carr and Student
Stephanie Carr works with a student to process deep-sea samples aboard the R/V Atlantis. A recent study found that a group of unusual microbes living below the seafloor provides clues to the evolution of life on Earth, and potentially other planets. Credit: Beth Orcutt/Bigelow Laboratory for Ocean Sciences 

Analyzing Hydrothermarchaeota genomes revealed that these microbes belong to the group of single-celled life known as archaea. They evolved early in the history of life on Earth, as did their unusual metabolic processes. These observations suggest that the subsurface ocean crust is an important habitat for understanding how life evolved on Earth, and potentially other planets.

The researchers also found genetic evidence that Hydrothermarchaeota have the ability to move on their own. Motility offers a valuable survival strategy for the extreme environment they call home, which has a limited supply of nutrients essential to life. 

“Studying these unique microbes can give us insights into both the history of Earth and the potential strategies of life on other planets,” said Carr. “Their survival strategies make them incredibly versatile, and they play an important, overlooked role in the subsurface environments where they live.”

In 2011, Orcutt and other scientists sailed to the flank of the Juan de Fuca Ridge, a mid-ocean ridge off the coast of Washington where two ocean plates are separating and generating new oceanic crust. They used Woods Hole Oceanographic Institution’s deep-diving robot Jason to travel 2.6 kilometers to the seafloor and collect samples of the fluid that flows through the deep crust. 

These crustal fluids contained microbes that no one had studied. Working in partnership with the Department of Energy’s Joint Genome Institute, the researchers sorted and analyzed the microbes in the Single Cell Genomics Center at Bigelow Laboratory. Stepanauskas directs this cutting-edge research facility. These analyses yielded insights into the genetic blueprints of Hydrothermarchaeota, their relationship to other archaea, and the strategies they have evolved to survive in the subseafloor.

The researchers will build upon this discovery when they return to the Juan de Fuca Ridge in May 2019 to continue investigating the extreme microbes thriving below the seafloor. Orcutt and several other Bigelow Laboratory researchers will use ROV Jason to further explore the subseafloor environment, with funding from the National Science Foundation and NASA.

“The microbes living ‘buried alive’ below the seafloor are really intriguing to us, since they can survive on low amounts of energy,” Orcutt said. “We hope that our experiments on these weird microbes can show how they do this, so we can imagine how life might exist on other planets.”

The National Science Foundation, the NASA Astrobiology Institute, the DOE Joint Genome Institute, and the Center for Dark Energy Biosphere Investigations (C-DEBI) provided funding for this research.


Main image: Scientists use the deep-diving robot Jason to collect water samples from oceanic crust at a subseafloor observatory off the coast of Washington. Credit: Woods Hole Oceanographic Institution, courtesy of University of California, Santa Cruz, U.S. National Science Foundation, ROV Jason dive J2-711, 2013, AT26-03 cruise chief scientist Andrew Fisher

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