Insights Into the Marine Deep Biosphere: Extent of Life

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 2: Extent of LifeCdebi

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 second of these themes, Extent of Life. 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.

 

C-DEBI’s second theme, or avenue of investigation, is Extent of Life: Biomes and the Degree of Connectivity. Given the fundamental role of microbes in life as we know it, one might expect scientists to have some idea of where different types of microbes are found and maybe even why they’re there. Yet specialists in the field of microbiology struggle to understand why, in some cases, nearly identical organisms live a world apart. How can identical bacteria exist thousands of miles away from each other, even when we know the width of a human hair is enough to divide entire microbial populations?

Just as mathematicians struggled with Fermat’s last theorem for hundreds of years[1], so have microbiologists over the last century tried to prove or disprove a very basic idea: everything is everywhere. According to this postulate, it is the environment that chooses which microbes thrive and which fail. If this is true, then every square inch of Earth is a seething struggle for survival on a microscopic level, where the winner or group of winners in any given spot could be as varied as the bacterium that makes your yogurt, the cyanobacterium that produces oxygen, or the metal-loving microbe that thrives on rust. The characteristics of the species that become the microbial victors have enormous implications for everything from agriculture to health to the oil and gas industry.

Deep biosphere scientists are uniquely qualified to address the question of whether everything is everywhere because their studies focus on communities of microorganisms buried deep below the surface of the Earth. Here, these organisms are isolated from the surface world, and, researchers think, they also have to be highly specialized to survive conditions of high pressure and little food. Furthermore, many of these communities have been buried for millions of years–microbial dinosaurs, in effect. If ever there were a place where you wouldn’t expect to find everything, this would be it.

Now that scientists know one can find something just about everywhere in the deep subsurface, researchers working on the Extent of Life theme are addressing questions about the origin, selection, and connectivity of these different communities. If there are similarities between isolated communities, how did they become similar? How did these organisms arrive in separate, isolated locations?

While most of the deep biosphere is far below the ocean bottom, in some places such as seeps where methane “leaks” directly into the ocean from deep inside the sediment, samples can be collected that allow scientists to infer processes happening deeper into the Earth. While sampling locations like this are relatively accessible, they still require highly specialized equipment; here, Dr. Biddle is shown inside the deep submersible Alvin. Three people can (barely) fit into the 82 inch sphere— note the other pair of legs crammed into the foreground!

In a recent paper examining the unique nature of the deep biosphere, lead author Jennifer Biddle of the University of Delaware points out that using genomic analysis–the analysis of an organism’s entire set of DNA–can help more precisely identify the types or groups of organisms found in the subseafloor[2].

This is significant because the variety of subseafloor microbes is staggering. For example, while two different organisms may appear as identically-shaped dots under a microscope, analysis of the millions of basepairs of DNA that make up their genome may tell us that one requires oxygen while the other may be a strict anaerobe for which oxygen is toxic. For microbial worlds that can contain millions or billions of members in a single spoonful of sediment, it is no mean feat to determine these differences (indeed, it has only been made possible by tremendous advances in computing power).

Even when it is impossible to precisely identify and name all the specific species, these large-scale genetic analyses can shed light on the capabilities and metabolisms of whole communities. Some traditional microbiology studies are similar to analyzing the names in the white pages of a telephone book: is O’Malley the most common name, or Santos, or Tanaka? New analytical approaches, however, are more similar to the way the yellow pages organize information about a community’s abilities: is there a bricklayer? A Thai restaurant? An autobody shop?

Being buried for thousands or millions of years, deeper and deeper layers of sediment can record the inputs and effects of ocean and sediment processes from many years ago just as tree rings can document past changes. In this ancient sediment, do we find the same genes as in modern samples? Have they diverged and evolved into something else? Or have the organisms and their genes been preserved in their original ancient state, like a woolly mammoth in ice?

Dr. Biddle’s work has recently been complemented by a study from a collaborative Spanish and American group, which used a worldwide dataset to compare communities based on composition (the white pages) versus function (the yellow pages)[3]. Rather than comparing old, buried samples to surface, fresh samples, this study led by Albert Barberán compared massive DNA datasets from different places on the globe to ask similar questions. When comparing different samples, do we see the same microbes everywhere, just acting differently, or do we find different organisms acting similarly?

The Barberán study found that one does, in fact, need to consider the genomes of organisms, and not simply the name or lineage of that species, in order to understand what is truly different about a coastal community versus an open ocean community. In other words, some of the big differences between coastal and open ocean microbes appear to be communities that can act differently – even if the cast of characters seems highly similar. Deep biosphere scientists like Dr. Biddle then wonder if the same trends hold true over time – between today’s fresh sediment and those million-year-old sediments.

Genomic analyses may be able to tell us not only whether everything is everywhere, but also whether the same “everythings” exist across samples separated by millennia as well as thousands of miles of distance. In this sense, researchers may soon be answering questions we previously thought only a time traveler could ask.

Other projects in this research theme:

For more information:

C-DEBI website

Jennifer Biddle Lab

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.


[1] Fermat stated a theory in 1637 that is correct, but couldn’t be proven until 1995; he wrote that it is impossible for an + bn = cn, if n is greater than 2. For a detailed discussion of Fermat’s Theorem, see e.g. http://www.pbs.org/wgbh/nova/physics/andrew-wiles-fermat.html

[2] Biddle, J. F., Sylvan, J. B., Brazelton, W. J., Tully, B. J., Edwards, K. J., Moyer, C. L., Heidelberg, J. F., and Nelson, W. C. (2011). Prospects for the study of evolution in the deep biosphere. Frontiers in microbiology 2, 285.

[3] Barberán, A., Fernández-Guerra, A., Gohannan, B. J. M., and Casamayor, E. O. (2012) Exploration of community traits as ecological markers in microbial metagenomes. Molecular Ecology 21, 1909 – 1917. doi: 10.1111/j.1365-294X.2011.05383.x