Insights into the Marine Deep Biosphere: Deep Biosphere Activity

Theme 1 Deep Biosphere Activity | Theme 2 Extent of Life | Theme 3 Limits of Life | Theme 4 Evolution and Survival

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Theme 1: Activity in the Deep Subseafloor BiosphereCdebi

The Center for Dark Energy Biosphere Investigations (C-DEBI) is a multi-year research initiative sponsored by the National Science Foundation. This initiative and the projects it encompasses span many institutions and have four intertwining themes. Here, we present material on the first of these themes, Activity in the Deep Subsea Biosphere. First, however, what is the center all about?

The world we live in is dominated by microbial life. You can’t see them, but microorganisms are all around us. Everything living thing depends on them in one fashion or another. Many natural processes that we take for granted, such as plants growing from sunlight, and the decomposition of waste, result from microbial activity. Microbes provide essential nutrients, vitamins and other essential molecules for human and animal diets. They even regulate oxygen and carbon dioxide in the air. Microbial organisms both produce and consume huge amounts of greenhouse gases like carbon dioxide and methane. On a global scale, even “small” shifts in microbial activity can change Earth’s entire climate.

Although microbial processes are essential to life on Earth, scientists don’t know some of the most basic biological details about many of these organisms: who, what, and where are they?

In this world of unanswered questions about microbes, an enormous new habitat has recently come to light as scientists’ explore the distant reaches of Earth–the deep biosphere. As it turns out, there are vast numbers of microbes living below the surface of the land, below the seafloor, and into the very crust of the Earth itself.

What new forms of life live there? How do they survive so far from light and under such extreme pressures and temperatures? Will their discovery change the way we look for life elsewhere? What useful species and biological, chemical, and physical processes might we find there, such as new ways to make energy, store carbon, or treat wastewater? C-DEBI addresses these questions and more.


The first C-DEBI theme, or avenue of investigation, is Microbial Activity in the Deep Subseafloor Biosphere. The deep subseafloor biosphere refers to all the life underneath the ocean; not deep in the ocean or living on the bottom of the ocean, like fish, but many feet and even miles below that. In the past decade, researchers have discovered that these distant subseafloor environments contain a substantial amount of biomass, as measured by carbon content. One of the big questions for scientists is how many of those cells are actually alive and active, as opposed to inert. It may sound as though this is veering off into the domain of philosophy, but there is great scientific significance to the answer to this question.

What does it matter if there is a lot of organic material in the deep subseafloor if it’s just sitting there and not doing anything? “Dead” is one way to describe the microbes in this situation, and while it certainly attracts attention to use this descriptor, “death” is very hard to define, let alone measure, in microbes. This research theme, therefore, addresses the fundamental question of how much of the microbial life in these subseafloor environments is actually biologically active.

As many microbes live in the sediment beneath the seafloor as live in the ocean above[i]. However, this significant microbial biomass is small when compared to the total reservoir of carbon buried in the deep biosphere, which is about 100,000 times the amount in the atmosphere[ii].  Because active microorganisms in the subseafloor may either produce OR consume the buried organic carbon, there is potential for a huge impact on Earth’s oceans and, ultimately, atmosphere. These impacts could occur naturally, due to microbial activity over time. They could also change due to human influences, or affect human projects, such as proposed carbon capture and storage projects[iii]. In short, we cannot take for granted that everything that is buried is completely unchanging. Hence there is growing interest in understanding the activity of microbes in the deep biosphere.

While the question about subseafloor microbial life activity is straightforward, the answer is elusive. It’s pretty easy to tell if a person or a plant is alive, but single-celled organisms like bacteria have no breath, no pulse, and no heart. Determining whether a microorganism is living or not is surprisingly difficult, especially when it is buried deep beneath the seafloor.

A multinational team of researchers recently addressed this technologically and conceptually difficult question recently. Fronted by Bente Lomstein in Denmark, the research project addressed three kinds of cells found deep below the bottom of the ocean: those that are permanently inactive (“necromass”), those temporarily inactive (“spores”), and those active on some level, even if barely so (“vegetative biomass”).

Tolkien fans might relate the barely-active microorganisms to the Ents from the Lord of the Rings series. Tree-like creatures that live for eons, Ents can take hours just to say “hello.” Similarly, using the measurements described by Lomstein and colleagues, researchers calculated that bacterial and archaeal communities in the sediments of the deep biosphere metabolize at Ent-like rates; doing in thousands of years what an active laboratory culture might do in days.

Getting samples from this dark realm, one thousand feet or more below the seafloor, is no easy task, however. In this case, researchers used samples obtained by the R/V JOIDES Resolution, one of only two dedicated scientific drillships currently in operation and the only one operated by the United States.

Researcher, professor and C-DEBI member, Dr. Steven D’Hondt, University of Rhode Island, has in his office a small collection of drill bits and corers— the kinds used to power through layers of mud and rock found below the seafloor. This particular piece, from a piston core, was sacrificed in order to obtain precious rock samples. On another expedition, a different piece of equipment was likewise decommissioned after hitting a beer can on the bottom of the ocean. D’Hondt says the can wasn’t his.

In spite of great obstacles, scientific drilling of the seafloor has successfully retrieved many samples of mud and rock from around the world. Lomstein and her colleagues analyzed some of these samples using a technique known to NASA scientists and pharmaceutical companies alike: the analysis of the L/D ratios found in the organic molecules that make up proteins (amino acids). The L/D ratio refers to the shape of a molecule (chirality – see [iv]). Organic molecules twist to either the left or the right. Consequently, an otherwise identical compound can appear in two different forms, called levo, for left, and dextro, for right, which are similar in all respects except that they are mirror images of each other. Interestingly, amino acids, which form proteins essential for life, are almost all levo, or L, molecules. Over time, molecules will spontaneously flip back and forth until they reach an even mix of L and D forms, unless organisms spend energy to keep them in the same “L” form (maintenance).

Leaves provide a useful analogy for this process. Plants use energy to make sure that their leaves are oriented upward to face the sun; but when a plant goes dormant for the winter, or when it dies, the leaves fall off and get all jumbled up. When you look at a pile of leaves on the ground, some might face up but some will face down. Similarly, when we look at amino acid molecules that have not been maintained, we find an even mix of L and D.

Lomstein et al. looked at the L/D ratios of amino acids in deep biosphere samples. One would expect to see all L molecules if the community were 100% alive and biologically active, or half L and half D if the microbes were inactive or dead. They found that L amino acids accounted for around 75% of the total, on average – so the amino acids reflect a community that is not totally active, but far from inactive. Given that one might have assumed a completely inactive biosphere (although not all have done so[v]), this is groundbreaking news. This material from the subseafloor, which has been buried for millions of years—dust that washed off the Americas before humans ever migrated there, or, as with some samples, sediment swept out to sea before Lucy and early hominids ever walked the face of Earth – contain some active microbes.

By eking out a living on next to nothing, and doing it for a very long time, these remarkable microbes defy our expectations about how life behaves. Compared with familiar growth rates like bacteria in yogurt that grows in days, or tomato plants that grow in weeks, or children who grow up in a dozen years, these deeply buried microbes might experience little change over the course of millennia. This remarkable persistence not only impacts the way we think about evolution and the time scales of environmental change on Earth, but also makes us wonder if microbes are able to persist over incredibly long periods of time in less favorable locations, such as Mars.

Other projects and ongoing work in this research theme:


For more information:

Paper link for Lomstein et al.

C-DEBI website

This backgrounder was written by John Kirkpatrick, a post-doctoral fellow at the University of Rhode Island Graduate School of Oceanography, as part of the education and outreach efforts for C-DEBI.

[i]Kallmeyer, J., Pockalny, R., Adhikari, R. R., Smith, D. C., & D’Hondt, S. (2012). Global distribution of microbial abundance and biomass in subseafloor sediment. Proceedings of the National Academy of Sciences of the United States of America, 109(40), 16213–6. doi:10.1073/pnas.1203849109

[ii] Based on Pilson, “An Introduction to the Chemistry of the Sea” (1998) Prentice Hall: Upper Saddle River, NJ: Chap. 7 (p. 102 – 155).

[iii] The topic of carbon storage in the deep subsurface is an ongoing topic of investigation; see e.g.,

[iv] For a more detailed explanation with visual examples, see:

[v] See e.g. (and citations therein)