The crust beneath the seafloor is a vast but remote habitat, peppered with poorly studied microbes in its deep, dark crevices. Scientists have tapped into subsurface aquifers to study the organisms living in the fluids, but determining what kinds of microbes cling to the rock is a much more challenging endeavor. Ocean drilling expeditions bring up rock cores full of microbes, but these samples tend to be contaminated with drilling fluids. To sample the biofilms living within the rocks, researchers decided to go fishing for them, using different rocks types as bait.
In a new paper  in Frontiers in Microbiology, Deep Life Community Members Gustavo Ramírez (University of Rhode Island, USA), Beth Orcutt (Bigelow Laboratory for Ocean Sciences, USA), and colleagues analyzed the biofilms that grew on rocks placed in the path of subsurface water flow. They discovered that the attached communities were sourced from rare free-swimming microbes in the same environment, and that temperature played a large role in determining which microbes colonized the rocks.
“We can’t just look at fluids and think that we’re getting the full structure of the microbial community of the crust,” said Ramírez. “The community that grows on the collected rock has a different structure and different dominant organisms from what we find in the fluids. You have to look at both parts to understand what is living in the crust.”
To grow these biofilms in as close to their natural habitat as is possible, the researchers took advantage of boreholes previously drilled into the seafloor at the Juan de Fuca Ridge flank in the Pacific Ocean, off the coast of Washington and British Columbia. In 2010, Integrated Ocean Drilling Program scientists plugged up these boreholes and converted them into observatories, complete with submerged instruments to measure temperature and pressure, and wellheads for subsurface fluid sampling. They also equipped boreholes at a crustal site in the Atlantic Ocean called North Pond.
At the Juan de Fuca observatories, Orcutt and colleagues installed Flow-through Osmotic Colonization Systems (FLOCS), which contain sterilized crushed or polished sections of different rock types and sit within the flow path of subsurface fluids. The late Katrina Edwards, a DCO scientist and former mentor to co-authors Ramírez, Garber, and Orcutt, initiated the work. In 2010 the researchers deployed three FLOCS at varying depths up to almost 300 meters beneath the seafloor, where fluids are 65 degrees and oxygen-free. In 2013 they also installed two at the wellheads, where the subsurface fluids cool down to 2 degrees Celsius. They collected all the FLOCS in 2014 and studied the biofilms that colonized them.
Through extensive DNA sequencing, the team analyzed and compared the different communities. The researchers took several steps to remove DNA sequences resulting from contamination, which is a common problem for Deep Life Community members when sequencing DNA from environments with low numbers of cells. Then they compared the resident organisms to microbes identified in fluids from this site and at North Pond.
Studies of natural biofilms in subseafloor crust have shown community differences due to the different rock types, but in this study, the major factor affecting community composition appeared to be the temperature of the surrounding fluids. The researchers found that rare free-swimming microbes were capable of colonizing the rock, as well as organisms known to live far away in the Atlantic Ocean crust. “That was a result we were not expecting,” said Orcutt. “It suggests that there’s some commonality to members of the deep biosphere in this ecosystem.”
Currently, the research team is analyzing the results from FLOCS deployed at North Pond. In May 2019 the team returned to Juan de Fuca to measure how fast individual species within the community grow and metabolize. They hope that the results of this work will illuminate how communities of microbes, both free-swimming and attached, make a living and cycle carbon in this giant, deep, dark ecosystem.
In honor of her work exploring the lives of microbes beneath the seafloor and their contribution to global geochemical cycles, Orcutt will receive the Asahiko Taira International Scientific Ocean Drilling Research Prize. Founded in 2014, the award is named for the past president of the Japan Agency for Marine-Earth Science and Technology (JAMSTEC). Starting in 2014, the American Geophysical Union and the Japan Geoscience Union have awarded the prize to a single early- or mid-career scientist who has demonstrated “outstanding transdisciplinary research accomplishment in ocean drilling.” Orcutt will receive the award at the 2019 AGU Fall Meeting in San Francisco.