The Seafloor “Methane Filter” Takes Years to Regrow After Disruption

Disturbances to the seafloor, whether natural or unnatural, can upset the “microbial methane filter," a blanket of microbes that efficiently consumes methane seeping from the seafloor before it enters the water column. A new study uses a deep-sea mud volcano as a natural experiment to track how different microbial species colonize a new mud flow.

Each year, about 200 million tons of methane leak out from sediments and cold seeps along the seafloor, but that number could be far higher. Fortunately, up to 90 percent of this greenhouse gas never reaches the surface, thanks to a buried carpet of microbes that consume the methane to generate energy. A new, long-term study of a mud volcano eruption finds that this “microbial methane filter" can take years to re-form after a disturbance.

DCO Deep Life Community members Emil Ruff (University of Calgary, Canada), and Antje Boetius (Max Planck Institute for Marine Microbiology, Germany) used the eruption of a mud volcano to investigate how methane-consuming microbes colonize new mud flows. In a new paper in The ISME Journal [1], they describe the different waves of bacteria that inhabited mud flows, aged from zero to over five years. Now that they have established a rough timeline for the re-formation of the methane filter, the findings can be used to estimate methane release from seafloor disturbances such as deep-sea mining.

To understand how methane-consuming microbes, called methanotrophs, colonize the seafloor, the researchers needed to start with a clean slate. They couldn’t sterilize a portion of the seafloor, but they realized that a mud volcano, which spews methane and deep mud onto the seafloor, was the next best thing. “We know the mud coming out has a very different community than the surrounding seafloor,” said Ruff. “The idea was to follow the succession and see how the material from deeper layers is colonized and how long it takes for methanotrophic communities to establish.” The process would be similar to the succession that occurs after a volcanic eruption, where lichens colonize a new lava flow first, followed by mosses, shrubs and larger plants, to establish a mature ecosystem.

The researchers monitored the Håkon Mosby mud volcano, located on the seafloor north of Norway, using the Long-term Observatory of Mud volcano Eruptions (LOOME). The instrument sat close to its eruptive center, at the edge of the mud flow, where it took photos and collected measurements for one year, which enabled the researchers to estimate the speed of the mud flow. They could then collect sediment samples and calculate their ages based on how far each one was located from the center of the volcano. 

Once they could reliably assess how long the sediments were exposed to ambient conditions, the researchers used multiple approaches to understand the activities and identities of the microbes colonizing the mud flows at different times. They sequenced microbial DNA through a grant from the DCO’s Census of Deep Life, performed cell counts, and made biochemical measurements to see what compounds the microbes consumed to generate energy.

The analyses showed clear waves of microbial succession at the site. After a new mud flow, the deep microbes deposited at the surface die off within a year. Meanwhile, aerobic methanotrophs, which metabolize methane using oxygen, quickly colonize the new flows. These microbes are weedy species that disperse easily on bottom water currents. Within two to five years, however, anaerobic methanotrophs begin growing beneath the surface of the seafloor. These slow-growing microbes partner with bacteria to metabolize methane using sulfate. Since the anaerobic methanotrophs sit lower in the sediment, eventually they consume the methane before it reaches the aerobic methanotrophs at the surface, causing them to decline. The anaerobic reactions also generate considerable amounts of sulfide, which creates a new niche for sulfur-oxidizing bacteria at the seafloor. Their thick, white mats of cells signal the presence of a mature ecosystem. 

The discovery that it takes about five years at the Håkon Mosby mud volcano for a mature methane-consuming community to re-establish after a disruption may help explain why the methane filter near mud volcanoes and other gas seeps is less efficient than at more stable sites. The findings also suggest that protecting these communities from human disturbances may be one tactic for controlling methane emissions from the oceans. “If we know now that any deep-sea mining or bottom trawling can destroy these ecosystems, and they take many years to grow back, I think that’s an indication that we should probably think about preserving them,” said Ruff.

In November, Ruff will start his own lab at the Marine Biological Laboratory (USA) with a focus on microbial food webs within the seafloor. In his current research, he has turned his attention from methanotrophs to the organotrophs of the ecosystem, and is designing long-term experiments to look at microbes that consume dead cells,  also called necromass, in the sediment.

mud volcano caldera map
Thanks to a loan of SENTRY, an autonomous underwater vehicle from the Woods Hole Oceanographic Institution, the researchers created a high-resolution map of the seafloor across the mud volcano’s caldera, created from a mosaic of underwater images. It is one of the largest high-resolution images of the deep seafloor available to date. Credit: Ruff et al. and The ISME Journal


The LOOME observatory sat on the seafloor for one year, for the first extended study of a deep-sea mud volcano. In this image, the observatory sits on mature seafloor covered with white mats of sulfur-oxidizing bacteria, next to freshly erupted mud. Credit: SENTRY, Woods Hole Oceanographic Institution


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