Biologists have long recognized that species can be grouped into hierarchical assemblages. These units are linked by lines of descent; that is, all species that make up a higher category share a common ancestor. species are grouped into genera. (Our species is grouped, along with the extinct human forms, into the genus Homo. This means that all species of Homo, including Homo sapiens, Homo erectus, and Homo habilis, among others, have a common ancestor.) Genera are grouped into families, families into orders, orders into classes, classes into phyla, and phyla into kingdoms. The kingdoms have always been defined as the highest level, so they are not grouped into any higher unit. The earliest practitioners of this system, which was developed by the great swedish naturalist Carl Linnaeus in the eighteenth century, first recognized only two king doms: animals and plants. As biologists invented and mastered microscopes and came to understand plants better, they increased the number of kingdoms to five: the kingdoms Animalia, Plantae, Fungi, Protozoa, and Bacteria. But the discovery of the archaea changed all of that. They are so different that they have required scientists to devise an entirely new taxonomic category of life.
The archaea have long been overlooked because they closely resemble bacteria. But once molecular biologists were able to analyze their DNA, it became clear that these tiny cells were as different from bacteria as bacteria are from the most primitive protozoans. This led University of Illinois biologist Carl Woese to propose a new category of life, the domain, which he placed above kingdoms. In this scheme, the five kingdoms are spread over three domains: Archaea, Bacteria, and a new category called Eucarya, which includes the plants, animals, protists, and fungi.
The domain Archaea is itself subdivided into two previously unrecognized kingdoms: the kingdom Crenarchaeota, made up of heat-loving forms, and the kingdom Euryarchaeota, which includes a few thermophiles but is composed mainly of forms that produce the organic compound methane (swamp gas) as a biological by-product of their metabolism. Most archaeans are "anaerobic"; they can live only in the absence of oxygen. This characteristic makes them prime candidates for the first life on Earth, because the newly formed Earth had no free oxygen.
Although many types of archaeans have been found in hot-water settings, it is clear that they can live in other subterranean settings, including within solid rock itself. The first clue that life might exist hundreds to thousands of meters below Earth's surface came in the 1920s, when geologist Edson Bastin of the University of Chicago began to wonder why water extracted from deep within oil fields contained hydrogen sulfide and bicarbonates. Bastin knew that both of these compounds are commonly created by bacterial life, yet the water coming from the oil wells was from environments that seemed far too deep and hot to support any sort of bacterial life discovered up to that time. Bastin enlisted the aid of microbiologist Frank Greer, and together they succeeded in culturing bacteria recovered from this deep water. Regrettably, their findings were dismissed by other scientists of the time as being due to contamination from the oil pipes, and this first interdisciplinary venture linking the fields of geology and microbiology languished, its provocative discovery ignored for more than 50 years.
The possibility that life was present deep within our planet was finally taken seriously when scientists began studying groundwater around nuclear waste dumps in the 1970s and 1980s. As ever-deeper boreholes were drilled, microbial life was routinely found at depths long thought to be too great to support life of any kind. But were the microbes found at these depths actually living there, or were they contaminants from surface regions that were picked up by the sampling equipment on its journey down? This question was not answered until 1987, when an interdisciplinary team of scientists assembled by the United States Department of Energy built a special coring device capable of drilling deep into the rock and extracting samples with no possibility of contamination. Three 1500-foot-deep boreholes were drilled at a government nuclear research laboratory near Savannah River, South Carolina. Samples brought to the surface were analyzed for microbes, and it was quickly discovered that microbial life did indeed exist at these depths and that it was rich in both number of species and number of individuals. A new habitat for life had been discovered, and the pioneering work of Bastin and Greer had been confirmed.
It is generally acknowledged that the cataloguing of Earth's species is far from complete—that many species of all groups of life, not just ex-tremophiles, wait to be discovered. Less well known is that our understanding of the habitats occupied by life on this planet may be equally incomplete; the new extremophile discoveries beneath Earth's surface are proof of that. In this age of satellite surveys and global travel, it seems incongruous that there could be vast unexplored regions harboring unknown life, but this is certainly the case. Aside from Jules Verne's imaginative and prophetic novel Journey to the Center of the Earth, humankind has little penetrated the last frontier and the region that may hold the single largest mass of life inhabiting the planet: deep in Earth's crust.
With the discovery of deep life in South Carolina, many teams began probing ever deeper underground, trying to find the lower limit of life within the crust of Earth itself. Soon they learned that subterranean microbes could be found in most geological formations; the deep bacterial and archaean world thus appears ubiquitous under the surface. The greatest depth from which these life forms have so far been recovered is about 3.5 kilometers, at temperatures of 167°F. At such great depths, however, the population density of the microbes is low. They can live in many rock types, including both sedimentary and igneous rocks. Temperatures increase in a planet as one descends deeper into the crust. Archeans may inhabit a wide range of rock types even several miles beneath Earth's surface. Cornell University geologist Thomas Gold has gone so far as to suggest that the combined biomass of microorganisms beneath Earth's surface may be several times that of all organisms—great and small, complex and simple—living on the surface above. If so, microorganisms are by far the most numerous organisms on Earth!
The maximum depth at which extremophiles have been found to live is constantly being revised. In 1997 the record was 2.8 kilometers, but soon a mine located in South Africa yielded specimens from a depth of 3.5 kilometers. The basic requirements of the inhabitants of this "deep biosphere" are water; pores, in the source, of sufficient size to allow the presence of the deep microbes; and nutrients. Because the extremophiles are adapted for pressure they are virtually unaffected by the high pressures encountered at these great depths.
The nutrients used by these deep-living extremophiles come from the rocks they live in. In sedimentary rock, nutrients derive from organic material trapped at the time of the rock's deposition. The deep-biosphere microbes (the microbes living in sedimentary rock) then utilize this material for the energy and organic matter necessary for life. Oxidized forms of iron, sulfur, and manganese are also utilized as nutrients. Living in sedimentary rock thus poses no great hardship for certain archaeans and bacteria. Living in igneous rock, however, is a more difficult proposition.
Igneous rock, such as basalt (the rock that forms when lava cools and solidifies) has no (or very little) constituent organic matter. It was therefore a major surprise when scientists in Washington state discovered flourishing communities of microbes living in ancient basaltic rock in the Columbia River basin. Microbiologists Todd Stevens and James McKinley from Batelle Laboratory discovered in the 1980s that many of the bacteria they found in these rocks were manufacturing their own organic compounds, using carbon and hydrogen taken directly from hydrogen gas and carbon dioxide dissolved in the rock. They produced methane as a by-product of their synthesis, so they acquired the name methanogens. These archaea are thus autotrophs, organisms that can produce organic material from inorganic compounds. Co-occurring heterotrophic or organic-consuming microbes then ingest some of the organic material produced by these autotrophic organisms. This is (like the deep-sea vent community) an ecosystem totally independent of solar energy—independent of the surface and of light. These particular communities have been dubbed—perhaps appropriately—the SLiME communities, for "subsurface Hthoautotrophic microbial ecosystem." Because their presence in these dark, sometimes hot regions of Earth's crust tells us that sunlight is not necessary to sustain life, their discovery is one of the most important ever made about the range of environments that can support life. It means that even a far-distant and relatively cold planet such as Pluto could conceivably support life in the warm, inner portions of its crust. Planets and moons far from a star may have frigid surfaces, but their interiors are warm with heat from radioactive decay and other processes.
The deep-rock microbe communities can be trapped within their host rock for millions of years. They first get into the igneous rock via flowing groundwater, but in some instances this groundwater is cut off, and yet the deep microbes persist and thrive. Samples from the Taylorsville region of Texas are thought to be 80 million years old and have grown and evolved at exceedingly slow rates. They became trapped in the hard igneous rock during the heyday of the dinosaurs and remained there, living without any contact with the rest of Earth's life, until humans released them by digging deep wells. Some of these microbes have adapted to very low levels of nutrients and tolerate extended periods of starvation.
Extremophiles are not only adapted to hot and high-pressure conditions. Other groups are found in conditions thought too cold for life. All animal life eventually ceases at below-freezing temperatures. When the bodies of animals are cooled below the freezing point, they can enter a state of suspended animation, but the metabolic functions do not continue. Some extremophiles, however, circumvent this. Microbiologist James Staley of the University of Washington discovered a new suite of extremophiles living in icebergs and other sea ice. This habitat was long considered too cold to harbor life, yet life has found a way to live in the ice. This particular finding is as exciting and as relevant to the astrobiologist as the heat-loving ex-tremophiles, for many places in the solar system are locked in ice. other ex-tremophiles relish chemical conditions inimical to more complex life, such as highly acidic or basic environments or very salty seawater.
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