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Chapter 2. Earth as a Microbial Habitat

Chapter 2. Earth as a Microbial Habitat

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Crust (5−70 km)




Inner core

2867 km

2200 km

1250 km

FIGURE 2.1 Diagrammatic cross section of the Earth. Radii of core and mantle drawn to scale.



North American
















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Major crustal plates of the Earth.

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Earth as a Microbial Habitat
















ia mantin


a Tr


id g





Tren ga



In d








Atlantic− In













ril ch Aleuti






P a c if



ctic R




t Pacif







tl a n


t i c idge

Convection resulting from the thermal gradients in the plastic rock of the asthenosphere is believed

to be the cause of movement of the crustal plates (Kerr, 1995; Wysession, 1995; Ritter, 1999). In

some locations this movement may manifest itself in a collision of plates and in other locations in

plates of nearly equal density sliding past one another along transform faults. In still others, interacting plates may partially slide over one another in a process of crustal convergence called subduction

where a denser oceanic plate slides below a lighter continental plate. Either of the last two processes

may lead to formation of a trench–volcanic island arc system. Island arc systems result from a sedimentary wedge formed by the oceanic plate. In subduction, the resulting arc system may eventually

accrete to the continental margin as a result of the movement of the subducting oceanic plate in the

direction of the continental plate (Van Andel, 1992; Gurnis, 1992).

Oceanic plates grow along oceanic ridges, the sites of crustal divergence. Two examples of

such divergence are represented by the Mid-Atlantic Ridge and the East Pacific Rise (Figure 2.3).

The older portions of growing oceanic plates are destroyed through subduction with the formation

of deep-sea trenches, such as the Marianas, Kurile, and Phillipine trenches in the Pacific Ocean

and the Puerto Rico Trench in the Atlantic Ocean. Growth of the oceanic plates at the midocean

ridges is the result of submarine volcanic eruptions of magma (molten rock from the deep crust or

upper mantle). This magma gets added to opposing plate margins along a midocean ridge, causing

adjacent parts of the plates to be pushed away from the ridge in opposite directions (Figure 2.4).

The oldest portions of the interacting oceanic plates are consumed by subduction more or less in

proportion to the formation of new oceanic plate at the midocean ridges, thereby maintaining a

fairly constant plate size.

Volcanism occurs not only at midocean ridges but also in the regions of subduction where the

sinking crustal rock undergoes melting as it descends toward the upper mantle. The molten rock

may then erupt through fissures in the crust and contribute to mountain building at the continental









FIGURE 2.3 Major midocean rift systems (thin continuous lines) and ocean trenches (heavy continuous

lines) (A, Philippine Trench; B, Marianas Trench; C, Vityaz Trench; D, New Hebrides Trench; E, Peru–Chile

Trench; F, Puerto Rico Trench). The East Pacific Ridge is also known as the East Pacific Rise.

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Volcanic mountain

Coastal mountain range

Midocean ridge

Rift zone


Oceanic plate



Oceanic plate










Schematic representation of sea floor spreading and plate subduction. New oceanic crust is

formed at the rift zone of the midocean ridge. Old oceanic crust is consumed in the subduction zone near a

continental margin or island arc.

margins (orogeny). It is plate collision and volcanic activity associated with subduction at continental margins that explain the existence of coastal mountain ranges. The origin of the Rocky

Mountains and the Andes on the North- and South American continent, respectively, is associated

with subduction activity, whereas Himalayas are the result of collision of the plate bearing the Indian

subcontinent with that bearing the Asian continent.

Volcanic activity may also occur away from crustal plate margins, at the so-called hot spots. In the

Pacific Ocean, one such hot spot is represented by the island of Hawaii with its active volcanoes. The

remainder of the Hawaiian island chain had its origin at the same spot where the island of Hawaii

is presently located. Crustal movement of the Pacific Ocean plate westward caused the remaining

islands to be moved away from the hot spot so that they are no longer volcanically active.

The continents as they exist today are thought to have derived from a single continental mass,

Pangaea, which broke apart less than 200 million years ago as a result of crustal movement. Initially

this separation gave rise to Laurasia (which included present-day North America, Europe, and most

of Asia) and Gondwana (which included present-day Africa, South America, Australia, Antarctica,

and the Indian subcontinent). These continents separated subsequently into the continents we know

today, except for the Indian subcontinent, which did not join the Asian continent until some time

after this breakup (Figure 2.5) (Dietz and Holden, 1970; Fooden, 1972; Matthews, 1973; Palmer,

1974; Hoffman, 1991; Smith, 1992). The continents that evolved became modified by accretion

of small landmasses through collision with plates bearing them. Pangaea itself is thought to have

originated 250–260 million years ago from an aggregation of crustal plates bearing continental landmasses including Baltica (consisting of Russia, west of the Ural Mountains; Scandinavia; Poland;

and Northern Germany), China, Gondwana, Kazakhstania (consisting of present-day Kazakhstan),

Laurentia (consisting of most of North America, Greenland, Scotland, and the Chukotski Peninsula

of eastern Russia), and Siberia (Bambach et al., 1980). Mobile continental plates are believed to

have existed as long as 3.5 billion years ago (Kroener and Layer, 1992). The Earth seems to have had

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Earth as a Microbial Habitat




Tethys Sea


225 × 106 years ago

180 × 106 years ago

135 × 106 years ago

65 × 106 years ago

Continents today

FIGURE 2.5 Continental drift. Simplified representation of the breakup of Pangaea to present time.

(Reproduced from Dietz RS, Holden JC, J. Geophys. Res., 75, 4939–4956, 1970. With permission.)

a crust as early as 4.35–4.4 eons ago—the age of the Earth being 4.65 eons (Amelin, 2005; Harrison

et al., 2005; Watson and Harrison, 2005; Wilde et al., 2001).

The evidence for the origin and movement of the present-day continents has been obtained from

at least three kinds of studies: (1) paleomagnetic and seismic examinations of the Earth’s crust;

(2) comparative sedimentary analyses of deep-ocean cores obtained from drillings by the Glomar

Challenger, an ocean-going research vessel; and (3) paleoclimatic studies (Bambach et al., 1980;

Nierenberg, 1978; Vine, 1970; Ritter, 1999). Although the separation of the present-day continents

with the breakup of Pangaea had probably no significant effect on the evolution of prokaryotes (they

had pretty much evolved to their present complexity by this time), it did have a profound effect on

the evolution of metaphytes and metazoans (McKenna, 1972; Raven and Axelrod, 1972). Flowering

plants, birds, and mammals, for example, had yet to establish themselves.

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The biosphere, the portion of the Earth that supports life, is restricted to the uppermost part of the

crust and to a certain degree the lowermost part of the atmosphere. It includes the land surface,

that is, the exposed sediment or soil and rock and the subsurface to a depth of 1 km and more,

and the sediment surface and subsurface on the ocean floor (Ghiorse and Wilson, 1988; Parkes

et al., 1994; Pedersen, 1993; Pokrovskiy, 1961; van Waasbergen et al., 2000; Wellsbury et al., 2002).

The sediment, soil, and rock at and near the surface of the crust are sometimes referred to as the

lithosphere by ecologists (however, see Section. 2.1 for geologists’ definition of this term). The

biosphere also includes the hydrosphere, the freshwater and especially the marine water that cover

a major portion of the Earth’s crust. The presence of living microorganisms has been demonstrated

in groundwater samples taken at a depth of 3500 m from a borehole in granitic rock in the Siljan

Ring in central Sweden (Szewzky et al., 1994). The water from this depth contained thermophilic,

anaerobic fermenting bacteria related to Thermoanaerobacter and Thermoanaerobium species and

one strain related to Clostridium thermohydrosulfuricum but no sulfate-reducing or methanogenic

bacteria. The bacteria that were cultured grew in a temperature range of 45–75°C (65°C optimum)

at atmospheric pressure in the laboratory. In continental crust, the temperature has been estimated

to increase by ∼25°C km−1 of depth (Fredrickson and Onstott, 1996). Using this constant, the

in situ temperature at a depth of 3500 m should be ∼87.5°C, which is higher than the maximum

temperature tolerated by the cultures isolated by Szewzky et al. (1994) when grown under laboratory conditions, but well within the temperature range of hyperthermophilic bacteria (recently

found maximum growth temperature was ∼121°C; Kashefi and Lovley, 2003). Within a very limited range, elevated hydrostatic pressure to which microbes would be subjected at great depths may

increase their temperature tolerance slightly, as suggested by the observations of Haight and Morita

(1962) and Morita and Haight (1962). Clearly, temperature and hydrostatic pressure are important

determinants of the depth limit at which life can exist within the crust. Other limiting factors are

porosity and the availability of moisture (Colwell et al., 1997).

Unlike the lithosphere, the hydrosphere is inhabited by life at all water depths, some as great as

11,000 m—the depth of the Marianas Trench. In marine sediments, microbial life has now been

detected at depths of >500 mbsf (meters below sea floor) (Parkes et al., 1994; Cragg et al., 1996).

Bacterial alteration of the glass in ocean basalts has been seen to decreasing extents for 250–500 mbsf

(Torsvik et al., 1998; Furnes and Staudigel, 1999). In some parts of the hydrosphere, some special

ecosystems have evolved whose primary energy source is geothermal rather than radiant energy from

the sun (Jannasch, 1983). These ecosystems occur around hydrothermal vents at midocean rift zones.

Here heat from magma chambers in the lower crust and upper mantle diffuses upward into overlying

basalt, causing seawater that has penetrated deep into the basalt to react with it (see Figure 17.17 for

diagrammatic representation of this process). This seawater–basalt interaction results in the formation

of hydrogen sulfide and in the mobilization of some metals, particularly iron and manganese and in

some cases some other metals such as copper and zinc. The altered seawater (now a hydrothermal


n charged with these dissolved metals is eventually forced up through cracks and fissures in

the basalt to enter the overlying ocean through hydrothermal vents. Autotrophic bacteria living free

around the vents or in symbiotic association with some metazoa at these sites use the hydrogen sulfide

as an energy source for converting carbon dioxide into organic matter. Some of this organic matter

is used as food by heterotrophic microorganisms and metazoa at these locations (Jannasch, 1983;

Tunnicliffe, 1992). The hydrogen sulfide–oxidizing bacteria are the chief primary producers in these

ecosystems, taking the place of photosynthesizers such as anoxygenic photosynthesizing bacteria,

cyanobacteria, algae, and plants—the usual primary producers of Earth. Photosynthesizers cannot

operate in the location of hydrothermal vent communities because of the perpetual darkness that prevails at these sites (see also Section 19.8).

Not all submarine communities featuring chemosynthetic hydrogen sulfide oxidizers as primary

producers are based on hydrothermal discharge. On the Florida Escarpment in the Gulf of Mexico,

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Earth as a Microbial Habitat


ventlike biological communities have been found at abyssal depths around hydrogen sulfide seeps

whose discharge is at ambient temperature. The sulfide in this instance may originate from an adjacent carbonate platform containing fluids with 250‰ dissolved solids and temperatures up to 115°C

(Paul et al., 1984).

In some other locations, such as at the Oregon subduction zone or at some sites of the Florida

Escarpment, methane of undetermined origin expelled from the pore fluids of the sediments, rather

than hydrogen sulfide, is the basis for primary production on the seafloor. Metazoa share in the carbon fixed by free-living or symbiotic methane-oxidizing bacteria (Kuhn et al., 1986; Childress et al.,

1986; Cavanaugh et al., 1987) (see also Chapter 22).

Finally the biosphere includes the lower portion of the atmosphere. Living microbes have been

recovered from it at heights as great as 48–77 km above the Earth’s surface (Imshenetsky et al.,

1978; Lysenko, 1979).

Whether the atmosphere constitutes a true microbial habitat is very debatable. Although it harbors viable vegetative cells and spores, it is generally not capable of sustaining growth and multiplication of the organisms because of lack of sufficient moisture and nutrients and because of lethal

radiation, especially at higher elevations. At high humidity in the physiological temperature range,

some bacteria may, however, propagate to a limited extent (Dimmick et al., 1979; Straat et al.,

1977). The residence time of microbes in air may also be limited, owing to their eventual fallout. In

the case of microbes associated with solid particles suspended in still air, the fallout rate may range

from 10−3 cm s−1 for particles in a 0.5 µm size range to 2 cm s−1 for particles in a 10 µm size range

(Brock, 1974, p. 541). Even if it is not a true habitat, the atmosphere is nevertheless important to

microbes. It is a vehicle for spreading microbes from one site to another; it is a source of oxygen for

strict and facultative aerobes; it is a source of nitrogen for nitrogen-fixing microbes; and its ozone

layer screens out most of the harmful ultraviolet radiation from the sun.

Although the biosphere is restricted to the upper crust and the atmosphere, the core of the Earth does

exert an influence on some forms of life. The core, with its solid center and molten outer portion, acts

like a dynamo in generating the magnetic field surrounding the Earth (Strahler, 1976, p. 36; Gubbins

and Bloxham, 1987; Su et al., 1996; Glatzmaier and Roberts, 1996). Magnetotactic bacteria can align

themselves with respect to the Earth’s magnetic field because they form magnetite (Fe3O4) or greigite

crystals (Fe3S4) in special membrane vesicles, magnetosomes, in their cells that behave like compasses.

Although it has been thought that their ability to sense the Earth’s magnetic field enables the cells to

seek their preferred habitat, which is a partially reduced environment (Blakemore, 1982; DeLong et al.,

1993), this interpretation appears to be too simplistic (Simmons et al., 2006) (see also Chapter 16).



The surface of the Earth includes the lithosphere, hydrosphere, and atmosphere; all of which are

habitable by microbes to a greater or lesser extent and constitute the biosphere of the Earth.

The structure of the Earth can be separated into the core, the mantle, and the crust. Of these, only

the upper part of the crust is habitable by living organisms. The crust is not a continuous solid layer

over the mantle but consists of a number of crustal plates afloat on the mantle, or more specifically

on the asthenosphere of the mantle. Some of the plates lie entirely under the oceans. Others carry

parts of a continent and an ocean. Oceanic plates are growing along midocean spreading centers,

whereas old portions of these plates are being destroyed by subduction under or by collision with

continental plates. The crustal plates are in constant, albeit slow, motion owing to the action of convection cells in the underlying mantle. This plate motion accounts for continental drift.


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of Life

3 Origin

and Its Early History



The Earth is thought to be ∼4.54 × 109 years old (∼4.6 eons) (Jacobsen, 2003). One accepted view

holds that it was derived from an accretion disk that resulted from gravitational collapse of interstellar matter. A major portion of the matter condensed to form the Sun, a star. Other components

in the disk subsequently accreted to form planetesimals of various sizes. These in turn accreted to

form our Earth and the other three inner planets of our solar system, namely, Mercury, Venus, and

Mars. All four of these planets are rocky. As accretion of the Earth proceeded, its internal temperature could have risen sufficiently to result ultimately in separation of silicates and iron, leading to a

differentiation into mantle and core. Alternatively, and more likely, a primordial rocky core could

have been displaced by a liquid iron shell that surrounded it. Displacement of the rocky core would

have been made possible if it fragmented as a result of nonhydrostatic pressures, causing the inner

core to become surrounded by a hot, well-mixed mantle or rock material in a catastrophic process.

Whichever process actually took place, much heat must have been released during this formational

process, resulting in outgassing from the mantle to form a primordial atmosphere and, possibly,

hydrosphere. It has been suggested recently that bombardment of the early Earth by giant comets

that consisted of water ice and cosmic dust introduced much of the water on the Earth’s surface (see,

for instance, Delsemme, 2001; Broad, 1997; Robert, 2001). All of this is thought to have occurred

in a span of ∼108 years. Recent evidence suggests the presence of liquid water at the Earth’s surface

as long ago as 4.3 eons before the present (BP) (Mojzsis et al., 2001).

As the planet cooled, segregation of the mantle components is thought to have occurred and a

thin crust to have formed by 4.0–3.8 eons ago. Accretion by meteoritic (bolide) bombardment is

believed to have become insignificant by this time. Results from very recent geophysical investigations involving zircon thermometry suggest that the Earth developed a crust as early as 4.35 eons

ago and that the process of plate tectonics originated in less than 100 million years (Myr) thereafter

(Watson and Harrison, 2006; Wilde et al., 2001). Previous estimates of the origin of crustal plates

ranged from 3.8 to 2.7 eons ago. Protocontinents may have emerged at this time to be subsequently

followed by the development of true continents. (For earlier views on the details about these early

steps in the formation of the Earth, see Stevenson, 1983; Ernst, 1983; Taylor, 1992.) How and when

did life originate on this newly formed Earth?



According to the panspermia hypothesis, life arrived on the planet as one or more kinds of spores

from another world. This view finds some support in laboratory studies published by Weber and

Greenberg (1985). Their studies employed spores of Bacillus subtilis, a common soil bacterium,

enveloped in a mantle of 0.5 µm thickness or greater derived from equal parts of H2O, CH4, NH3,

and CO (presumed interstellar conditions). The mantle shielded the spores from short ultraviolet

(UV) radiation (100200 àm wavelength) in ultrahigh vacuum (<1 ì 106 torr) at 10 K, but not from

long UV radiation (200–300 µm). From experimentally determined survival rates of the spores,

the investigators calculated that if spores were enveloped in a mantle of 0.9 µm thickness having a

refractive index of 0.5, which would protect them from short- and long-wavelength UV radiation,


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they could survive in sufficient numbers over a period of 4.5–45 Myr in outer space to allow them

to travel from one solar system to another. Spores could have entered outer space in high-speed

ejecta as a result of collisions between a life-bearing planet and a meteorite or comet (Weber and

Greenberg, 1985).

Instead of individual spores coated in a mantle of H2O, CH4, NH3, and CO arriving on the Earth’s

surface, it is possible that spores were carried inside ejecta of rock fragments generated by a meteorite impact on another planet that harbored life (Cohen, 1995; Nicholson et al., 2000; Nisbet and

Sleep, 2001). As shown in other chapters of this book (e.g., Chapter 9), microbial life is known to

exist inside some rocks on the Earth, and thus the idea of viable spores inside ejecta of rock fragments is not preposterous. If such rock fragments are large enough, shock-induced heating and pressure through meteorite impact and the acceleration that an ejected rock fragment would undergo

immediately after meteorite impact could be survived by bacterial spores inside the rock fragment

(for more details see Nicholson et al., 2000). Enclosure in a protective film or in a salt crystal is

thought to enable spores to survive the dehydrating effect of high vacuum of space (see Weber and

Greenberg, 1985; Nicholson et al., 2000). Enclosure in a rock fragment is thought to protect spores

sufficiently not only from UV radiation but also from cosmic ionizing radiation to survive interplanetary travel (Nicholson et al., 2000; Fajardo-Cavazos and Nicholson, 2006). Furthermore, spores in

a large rock fragment should be able to survive entry into and penetration of the Earth’s atmosphere

and subsequent impact on the Earth. Breakup of the entering rock fragment due to aerodynamic

drag in the lower atmosphere would ensure scattering of the inoculum at the Earth’s surface (see

Nicholson et al., 2000 for more detail).

Despite the possibility that life on Earth could have originated elsewhere in the universe, a more

widely held view is that life began de novo on Earth.


For life to have originated de novo on Earth, the existence of a primordial nonoxidizing atmosphere

was of primary importance. There is still no common agreement as to whether Earth’s primordial

atmosphere was reducing or nonreducing. Its constituents may have included H2O, H2, CO2, CO,

CH4, N2, and NH3 (see Table 4.3 in Chang et al., 1983), and HCN (Chang et al., 1983). The exact

composition of Earth’s early atmosphere will have changed as time progressed. Photochemical reactions and reactions driven by electric discharge (lightening) in the atmosphere, interaction of some

gases with mineral constituents at high temperature, and escape of the lightest gases (e.g., hydrogen)

into space (Chang et al., 1983; Schopf et al., 1983) could be the causes of this change. Two opposing

views have been expressed on how life may have arisen de novo on Earth, the organic soup theory

and the surface metabolism theory (Bada, 2004).





An older view, and one that is still much favored, is that life arose in a dilute aqueous, organic soup


h that covered the surface of the planet. This view arose from the proposals of Haldane (1929)

and Oparin (1938) (see also Nisbet and Sleep, 2001; Bada and Lazcano, 2003). According to this

view, the biologically important organic molecules in the soup were synthesized by abiotic chemical interactions among some of the atmospheric gases, driven by heat, electric discharge, and light

energy (see, for instance, discussion by Chang et al., 1983). If, as Bada et al. (1994) have theorized,

the surface of the early Earth was frozen because the sun was less luminous than it was to become

later, bolide impacts could have caused episodic melting, during which time the abiotic reactions

took place. Alternatively, it is possible that few or none of the early organic molecules in the organic

soup were formed on Earth, but were mostly or entirely introduced on the Earth’s surface by collision with giant comets. Whatever the origin of these molecules, special polymeric molecules that

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