New Advances in Understanding Microbes in the Marine Deep Biosphere

Underlying the bottom of Earth’s oceans is sediment containing layers of aging organic matter built up over millions of years.

In this sediment lives a largely unknown ecosystem of microbes, the marine deep biosphere, which depends on nutrients and energy from the sediment. The physical and chemical composition of sediment varies dramatically. However, the precise relationships between sediment variation over time and microbial diversity are unclear. In two new papers from DCO Deep Life scientists John Kirkpatrick, Emily Walsh, Steven D’Hondt (all at the University of Rhode Island, USA) and colleagues address the preservation of ancient microbiota trapped in the sediment over time [1] and identify new factors controlling microbial diversity in sediment ecosystems [2].

In the first paper, recently published in Geology [1], they report using molecular fossils in marine sediment to distinguish between ancient DNA accumulated from the surface world and the signatures of ongoing life that lives buried under layers of sediment – in this case up to 1.4 million years of it.

“We know that a large fraction of the carbon in the marine deep biosphere settled there from the surface world,” said co-author John Kirkpatrick (University of Rhode Island, USA). “Usually that carbon, and the nitrogen and phosphorus with it, gets transformed and re-purposed. What we were interested in, though, was trying to figure out how long traces of intact DNA molecules stuck around for. It was a lot longer than we thought.”

To look at microbial diversity, many deep life scientists use high throughput DNA sequencing technology. Samples from deep below the seafloor contain vanishingly small numbers of microbial cells, but modern sequencing techniques can produce incredibly large datasets from a tiny amount of biomass. As expected, from a sample at the seafloor there were signs of photosynthetic life – plankton that had sunk from the sunlit ocean. Surprisingly, however, while those sequences declined to a vanishingly small fraction of the community over time -  the decline took a hundred thousand years or more – they never disappeared completely.  

“The vast majority of the DNA buried in the subsurface reflects microbial communities that live there, making their way with whatever energy sources and material they have at hand,” D’Hondt said. “However if you look closely enough, even after a million years buried under the seafloor, you can find ancient DNA there that gives us clues about where it came from and what was going on at the surface all those years ago.”   

The second paper, published in the journal Applied and Environmental Microbiology [2], directly addresses the microbes living in the marine subsurface and the factors that are shaping this community. Emily Walsh and her colleagues looked at samples collected at three open ocean sites (in the Bering Sea and equatorial Pacific) and one continental margin site (Indian Ocean). At each of these sites the authors assessed microbial diversity at increasing depths below the seafloor and found that at each site diversity decreased at varying rates relative to depth. However, by accounting for the different sediment accumulation rates of the different sites, they found that diversity declines similarly with age at all sites, reaching relatively low levels once the sediment is a few hundred thousand years old.

The authors determined this dependence on sediment age is related to organic-matter degradation rates. At the sediment surface, there are more varieties of bacteria and the microbial ecosystem is more active, using newly deposited organic matter as an energy source. Deeper in the sediment, however, this activity declines, along with bacterial diversity.

The authors suggest this indicates an active battle for survival in the marine deep biosphere. As energy supplies become scarce, better-adapted microbes out-compete their neighbors.

“It’s a pretty tough environment for most microbes,” Walsh said. “As the sediment ages, and respiration slows down, most kinds of microbes appear to die off. It’s unclear if there are actually any real winners here, or just kinds that are ‘losing’ more slowly.”


Images: Top Left: Diatoms such as the one highlighted here (white arrow) can be prolific in Arctic waters, where they form the base of the food chain. Many of them sink to the seafloor and are buried in sediment, but more than just the frustule remains. In this image, the DNA is stained green, but the chloroplasts fluoresce pink on their own. Small snippets of DNA from inside these chloroplasts were detected in sediment up to and over a million years old [1]. The ubiquitous green dots seen elsewhere in this image are other microbes, which are quite diverse at the seafloor but undergo extreme selection as time passes [2]. Credit: Brice Loose. Lower Right: It looks like “just mud”, but million-year old sediment like this example from the Equatorial Pacific is an evolutionary battleground. A microbial community that is initial diverse at the seafloor becomes shadows of its former selves, as respiration decreases and time passes; by the time the community has been isolated as long as this example, more than ¾ of the microbial taxa initially present will have disappeared [2]. Credit: John Kirkpatrick.

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