Deep Science

Dark Life: Biology

Shewanella putrifaciens exhibiting filamentous connections known as "nanowires." The nanowires are a recently discovered physiological behavior common to most microorganisms and represent a response to adverse environmental stress. The nanowires provide conduits for energy sharing and communication between individual cells.
Source: Uri Gorby-Pacific Northwest National Laboratory

The surprising discovery of deep subsurface microbial communities in the mid-1980s launched a new and rapidly expanding subdiscipline within biology, known as geomicrobiology. In geomicrobiology, the fields of geology, geophysics, hydrology, geochemistry, biochemistry, and microbiology have merged to study how life on this planet interacts with the earth's geology, how life may have originated and how life evolved over billions of years. Dark life–those organisms that thrive underground in the absence of sunlight–comprises 50 percent of the earth's biomass, is responsible for many geological phenomena, degrades our wastes and produces some of our energy. Yet many questions remain regarding dark life–questions that can only be answered by going underground.


Since the 1980s scientists have gained insight into the diversity and limits of life underground based on information from boreholes and from piggybacking on mining operations. They have discovered microbial life at depths of four to five kilometers and at temperatures of 60°C. Microbes recovered from hot springs and deep-sea hydrothermal vents can live at temperatures of about 120°C. Studies of petroleum reserves indicate that above 80° these reserves are not degraded by biological action. Does subsurface life reach down to depths where the temperatures are 100° or 120° or even more? Such a search would require drilling under aseptic conditions that are far more stringent than previous drilling programs have attempted. Drilling from an underground facility where the ambient rock temperature is 50°C brings scientists more than one-third of the way toward their goal, and they can control air circulation and water filtration to reduce the contamination associated with surface drilling.

Biofilm: Black fluid emanating from a heavily corroded bore-hole at 3.1 km depth in the Mponeng gold mine in South Africa. The black fluid is due to "nanoparticles" of iron sulfide precipitated by thermophilic anaerobic sulfate-reducing bacteria and the corrosion is due to thermophilic aerobic sulfide and iron-oxidizing bacteria.
Source: Duane Moser-Pacific Northwest National Laboratory
Biologists filtering water samples
Biologists filtering water samples from a borehole at 2.7 km depth in the Driefontein gold mine in South Africa. The borehole extends to a depth of 3.5 km and contains a novel thermophilic microorganism that had not been previously encountered.
Source: Duane Moser-Pacific Northwest National Laboratory


Earth's deep, hot subsurface habitats differ from other high-temperature environments such as deep-sea hydrothermal vents and hot springs, because they are completely isolated from biological communities that rely on photosynthesis, earth's atmosphere, or the oceans. Far below the earth's surface, dark life relies instead on nonphotosynthetic biogeochemical processes that allow microbes to survive under extreme conditions and force them to interact with the environment. They do this by dissolving minerals, degrading petroleum and consuming gases for energy and nutrients. They may have the ability to detect chemically the presence of a nearby energy source and swim toward it. They precipitate minerals and produce gases, thereby changing the rock's porosity and permeability, but normally at rates a million times slower than those of surface life. Given enough time, however, microorganisms secreting sulfuric acid can carve enormous chambers in limestone, like those of the Carlsbad Caverns. The extent to which microbes can alter the subsurface environment in general is not well understood and undoubtedly depends on many variables, including time. The only way to unravel these secrets is to perform microbial experiments in an underground laboratory with access to a large rock volume for a long time. By understanding how microorganisms can alter the subsurface under natural conditions, we learn how we can manipulate them for practical applications.


Surface life evolves by a variety of processes including random mutations and exchange of genetic information between organisms in response to environmental change. The sequences for entire genomes for many common bacteria and certain extremophilic organisms have revealed that they have acquired functional capabilities from other microorganisms and that pieces of genetic code are derived from viruses. Complete genome sequences have become powerful tools in unraveling the evolutionary construction of a microorganism. In an evolutionary interpretation of the microbial tree based on all available sequences of entire genomes, the bacterial lineages common to the deep subsurface communities appear to be among the most ancient in the bacterial kingdom. Is this because they have evolved very little over billions of years? In the deep subsurface, microorganisms may live isolated existences, and their environment changes very little on time scales typical for surface life. In an underground laboratory, experiments designed to alter the subsurface environment by changing the temperature, salinity or pH, for example, and supplying exogenous DNA in the form of viruses or bacteria, can decipher the evolutionary steps that led to the construction of a bacterial genome. Discovering how this dark life has adapted to thrive in heat, pressure, and high salinity at depth in our own planet can inform our understanding of how surface life evolves here, as well as of the potential for life on other planets.


Deep subsurface environments mimic in many respects the surface environment of the ancient earth before the evolutionary development of photosynthesis pumped oxygen into earth's atmosphere. Thus, deep subsurface microbial processes are the closest living record of life as it existed on the ancient earth. Because current theories for the origin of life do not require the intervention of sunlight, and because the surface environment of the early earth was constantly subjected to the sterilizing effects of meteorite bombardment, life could conceivably have begun in the subsurface. Currently bench-top experiments have explored various aspects of life's origins, but performing such experiments underground could provide critical new clues to how life made the transition from a cluster of prebiotic molecules into a single cellular entity with nucleic acid.

Microbial biofilm forming on gold crystals
Microbial biofilm forming on gold crystals found in rock specimens collected from a South African mine. Experiments utilizing bacteria instead of toxic chemicals to chelate and precipitate gold from mining water represent an active area of research in South Africa.
Source: Gordon Southam-University of Western Ontario
Microbial biofilm
Microbial biofilm collected from 2 km depth in a platinum mine in South Africa. This biofilm contains star shaped bacteria that have never before been seen. The phylogenetic relationship of these bacteria to known organisms and their function are currently under intense study.
Source: Gordon Southam-University of Western Ontario


Recent investigations of the microbial communities inhabiting hot springs have uncovered microorganisms with surprising attributes. Known as "nanobacteria," they represent a new limb on the tree of life. Such surprises may also exist in the deep subsurface where the world of DNA-based life forms is less abundant or even absent, but all the conditions required for life exist. As in the case of searching for earth's deepest life forms, the search for exotic forms of life will require careful aseptic procedures and highly sensitive detection methods, best provided by an underground laboratory. The search for new forms of dark life may also offer insights into how to search for life beneath the surface of Mars and could have significant implications for NASA's Mars exploration program over the next 15 years.


To address these questions, biologists need a dedicated program and facility for large-scale, long-term subsurface sampling and experiments. So far, nearly all microbiological studies of the terrestrial subsurface have relied either on shallow (less than 30 meters deep) arrays of boreholes or on deeper drilling and coring studies that piggy-backed on petroleum and natural-gas exploration. Others have relied on excavations and drilling within active mines, making them secondary to the exigencies of mine operations.

The few deeper boreholes drilled exclusively for biology are still relatively shallow (less than 500 meters) due to cost constraints. Moreover, boreholes yield limited data, because borehole sampling is inherently one dimensional. An array of boreholes provides three-dimensional data, but to be useful for microbial experiments they would need a spacing of 1 meter, which, at a depth of 2 kilometers, is difficult to achieve by surface drilling. Perhaps most problematic is the unavoidable contamination of samples by surface microbes resulting from the drilling mud used when drilling from the surface. Drilling from underground tunnels with filtered water in a controlled environment greatly reduces this problem. While underground laboratories for biological studies do exist outside the U.S., they are for the most part shallow and primarily devoted to other purposes such as waste storage and mining and provide only short term access. A dedicated, deep-underground laboratory in the U.S. would allow the four-dimensional access (three space dimensions plus time) that biologists need for discoveries of the nature of life under the unique conditions of the deep subsurface.

A key requirement for the investigation of indigenous microbial processes at a deep underground laboratory will be long-term access to rock environments free from contamination by prior or ongoing mining activities. Rock strata targeted for indigenous microbial experiments must be free from exposure to mine air or water, which alter the microbiology and chemistry of the native environment in ways that compromise the validity of scientific results. Mining environments carry with them considerable microbial and chemical "noise," background materials introduced during mining. By tunneling into pristine rock strata and aseptically drilling and sealing boreholes, biologists can install experimental facilities for detecting clean, clear signals from underground life.

DUSEL Information
NSF - The National Science Foundation