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Oil and Gas Seeps: Microbial Elevators through Ocean Sediments

Citation: Chakraborty, A., Ruff, S. E., Dong, X., Ellefson, E. D., Li, C., Brooks, J. M., McBee, J., Bernard, B. B., Hubert, & C. R. J. (2020). Hydrocarbon seepage in the deep seabed links subsurface and seafloor biospheres. PNAS, 117(20), 11029-11037. https://doi.org/10.1073/pnas.2002289117

Since the beginning of the COVID-19 pandemic, it’s become clear to the public that the movement of microscopic life helps shape the world we live in. A team of scientists from the University of Calgary and the Marine Biological Laboratory in Woods Hole, MA have discovered that ocean sediments are no exception. Populations of microorganisms from hundreds to thousands of meters below the seafloor may have a secret conduit to the surface: oil and gas seeps. And their movement may be affecting carbon cycling in the deep ocean.

The Hidden Majority

Figure 1: The deep seafloor – a seemingly barren environment, but teeming with life and energy in comparison to the subsurface hundreds to thousands of meters below it. (Image Source: NOAA)

It is estimated that one third of all microorganisms on Earth live in sediments and rocks below the seafloor (Figure 1). This large figure may be surprising given the lack of light and energy that exists there, but oceans cover roughly three quarters of the Earth’s surface, and the material beneath it stretches down for many kilometers. An enormous, three-dimensional home therefore exists for subsurface microbes to inhabit, and for this reason, they’re known as “the hidden majority.” Scientists believe that as sediment and other material drifts down from the water above, microbes at the seafloor are slowly buried, and end up in the subsurface. (Here, we distinguish between “seafloor” habitats just below the surface of the sediment, where there’s comparatively more energy available, and “subsurface” habitats hundreds to thousands of meters below that.) Burial is so slow (on the order of tens to hundreds of thousands of years) that subsurface microbial populations become isolated from their seafloor counterparts, and evolve to be quite distinct. The team of scientists wondered whether oil and gas seeps, which transport fluids rich in oil and gas from the subsurface to the seafloor, could transport microbes as well – effectively mixing two isolated populations.

Sampling Microorganisms in Sediments

Figure 2: Map of this study’s 172 sampling locations in the eastern Gulf of Mexico (Chakraborty et al., 2020).

To investigate, the team collected seafloor sediments from 172 locations at the bottom of the Eastern Gulf of Mexico (Figure 2). By analyzing their individual oil and gas (or hydrocarbon) content, they found that 11 of the 172 locations were active oil and gas seeps. To determine whether there was evidence for a microbial “elevator” from the subsurface at these 11 locations, the scientists extracted all the genetic material from the sediments, and sequenced one specific gene. This gene – the 16S rRNA gene – encodes for the small subunit of a ribosome (Figure 3), and is commonly used to identify microbial species because it’s present in all known bacteria and archaea. Just as home genetic tests can help determine how related two people are, the sequence of the 16S rRNA gene can determine how related two microorganisms are. And because the gene’s sequence doesn’t evolve very quickly, it can be used to pinpoint a specific microbial species with startling accuracy. The team examined all the microorganisms living at each location, and analyzed their data to identify patterns in microbial abundance.

Figure 3: The 16S rRNA gene encodes the small subunit (blue) of a ribosome. Ribosomes translate genetic sequences into proteins, and are therefore present in all known bacteria and archaea. (Image Source: Wikimedia Commons)

Microbial Transport Affects Carbon Cycling

Figure 4: Percent abundances of Atribacteria (orange), Aminicenantes (tan), Sulfurovum (blue), and Thermoprofundales (green) in seafloor sediments within gas-positive and gas-negative locations (A and B), visualized in violin plots. Abundances are much higher in gas-positive locations. Internal box and whisker plots indicate the minimum, lower quartile, upper quartile, and maximum values (Chakraborty et al., 2020).

The scientific team found that in locations without oil and gas seeps, microorganisms were representative of the general seafloor population. In the 11 locations with active oil and gas seeps, however, the microorganisms they found were unlike those inhabiting the rest of the seafloor. Instead, they were known inhabitants of the subsurface realm. These microbes included the groups Atribacteria, Aminicenantes, Sulfurovum, and Thermoprofundales (Figure 4), which have slow growth rates and metabolic capabilities that support their subsurface origin. Furthermore, there was a statistically-significant separation between the two types of locations (with and without oil and gas seeps) in terms of their entire microbial community composition.

This finding is important, because many of these subsurface microorganisms are incredibly efficient at consuming oil and gas. Without them, the oceans would be chock full of hydrocarbons, and greenhouse gases like methane would be released to the atmosphere more quickly. The existence of a microbial elevator at seeps also increases the biodiversity of seafloor environments, and allows subsurface microbes to impact carbon cycling in the deep ocean.

More and more, we’re discovering that microscopic life affects our planet in subtle ways. In the marine environment, these impacts will be important to document and monitor in the face of major climate change.

I’m a PhD candidate in Earth System Science at Stanford University, and I study how microbes in deep ocean sediments produce and consume greenhouse gases. I’m a native of the landlocked state of Minnesota, so I’ve always been fascinated by the ocean. When I’m not in the lab, I love to race triathlons, forward “The Onion” articles to friends and family, and hike with my hound dog Banjo.


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