First Methane-Exhaling Microbes Discovered in Earth's Subsurface

A new study has provided the first detailed records of methane-exhaling microbes living deep within the Earth's subsurface.

The study is headed by microbiologist James Holden of the University of Massachusetts Amherst. Holden proclaimed that evidence was slowly mounting for over 20 years about the biomass in the Earth's subsurface. He even argued that the evidence pointed to the possibility that the micro organisms living in the crust and marine sediments could total the amount of animals and plants on the surface.

"We're interested in the microbes in the deep rock, and the best place to study them is at hydrothermal vents at undersea volcanoes. Warm water flows bring the nutrient and energy sources they need," said Holden. "Just as biologists studied the different habitats and life requirements for giraffes and penguins when they were new to science, for the first time we're studying these subsurface microorganisms, defining their habitat requirements and determining how those differ among species. It's very exciting, and will advance our understanding of biogeochemical cycles in the deep ocean."

Holden added that because the study included methanogens, it could illuminate researchers into how terrestrial natural gas was formed. Methanogens are microbes that inhale and carbon dioxide to produce methane as waste.

"Models have predicted the habitability of the rocky environments that we're most interested in, but we wanted to ground truth into these models and refine them," Holden explains.

Graduate Student Helene Ver Eecke utilized a 2-liter bioreactor at U Mass Amherst where she could control hydrogen levels and grew pure cultures of hyperthermophilic methanogens from their study site. She also grew a commercially available hyperthermophilic methanogen species as a control alongside of the pure cultures. Eventually, she found that growth kinetics for the three organisms were about the same. All grew at the same rate when given equal amounts of hydrogen and had the same minimum growth requirements.

Holden concluded that the experiments established that "these methanogens need at least 17 micromolar of hydrogen to grow."

Among other experts brought on for the investigation were Julie Huber from the Marine Biological Laboratory on Cape Cod who provided molecular analyses of the microbes as well as David Butterfield and Marvin Lilley from the University of Washington who contributed geochemical fluid analyses.

Utilizing the research submarine Alvin, the researchers collected samples of hydrothermal fluids flowing from black smokers up to 350 degrees C (662 degrees F) and seeping out of ocean floor cracks at lower temperatures. The samples were taken from Axial Volcano and the Endeavour Segment, both long-term observatory sites along an undersea mountain range about 200 miles off the coast of Washington and Oregon and 1-1.5 miles below the surface. 

At the Axial site, they found hydrogen above their methanogen threshold for growth and obtained molecular, organism and geochemical evidence of on-going methanogenesis. At the Endeavour hydrogen levels were below the threshold and evidence for methanogenesis was largely non-existent.  Holden's group then analyzed these and confirmed the lower threshold of hydrogen concentration needed by these methanogens.

At the low-hydrogen Endeavour site, they found that a few hyperthermophilic methanogens can survive by feeding on the hydrogen waste produced by other hyperthermophiles.

"We hypothesized that the methanogens grow syntrophically with the hydrogen producing microbes, and it worked out that way in the lab with a strain from the site," said Holden. "So we have described a methanogen ecosystem that includes a symbiotic relationship between microbes, which in my mind highlights the strength of our multi-pronged team approach. It really paid off. We feel that more research coupling broad field measurements with laboratory experiments will be really fruitful in the future."

Support for the research was provided by the National Science Foundation, NASA Astrobiology Institute, and the National Oceanographic and Atmospheric Administration.