Planet of the Bacteria
by Stephen Jay Gould
interest in paleontology began in a childhood fascination with dinosaurs. I spent a
substantial part of my youth reading the modest literature then available for
children on the history of life. I well remember the invariant scheme used to divide
the fossil record into a series of "ages" representing the progress that supposedly
marked the march of evolution: the "Age of Invertebrates," followed by the Age of
Fishes, Reptiles, Mammals and, finally, with all the parochiality of the engendered
language then current, the "Age of Man."
I have watched various reforms in this system during the past 40
years. The language police, of course, would never allow an Age of Man any more, so
we could, at best and with more inclusive generosity, now specify an "age of humans"
or an "age of self-consciousness." But we have also come to recognize, with even
further inclusive generosity, that one species of mammals, despite our unbounded
success, cannot speak adequately for the whole. Some enlightened folks have even
recognized that an "age of mammals" doesn't specify sufficient equityespecially
since mammals form a small group of some 4,000 species, while nearly 1 million species
of multicellular animals have been formally named. Since more than 80 percent of these
million are arthropods and since the great majority of arthropods are insects, these
same enlightened people tend to label modern times as the "age of arthropods."
Fair enough, if we wish to honor multicellular creatures, but we
are still not free of the parochialism of our scale. If we must characterize a whole
by a representative part, we certainly should honor life's constant mode. We live now
in the "Age of Bacteria." Our planet has always been in the "Age of Bacteria," ever
since the first fossilsbacteria, of coursewere entombed in rocks more than
3 billion years ago.
On any possible, reasonable or fair criterion, bacteria areand
always have beenthe dominant forms of life on Earth. Our failure to grasp this
most evident of biological facts arises in part from the blindness of our arrogance
but also, in large measure, as an effect of scale. We are so accustomed to viewing
phenomena of our scalesizes measured in feet and ages in decadesas typical
Individual bacteria lie beneath our vision and may live no longer
than the time I take to eat lunch or my grandfather spent with his evening cigar.
But then, who knows? To a bacterium, human bodies might appear as widely dispersed,
effectively eternal (or at least geological), massive mountains, fit for all forms
of exploitation and fraught with little danger unless a bolus of imported penicillin
strikes at some of the nasty brethren. Consider just some of the criteria for
T I M E
The fossil record of life begins with bacteria, at least 3.5 to
3.6 billion years ago. About half the history of life later, the more elaborate
eukaryotic cell makes a first appearance in the fossil recordabout 1.8 to 1.9
billion years ago by best current evidence.
The first multicellular creaturesmarine algaeenter
the stage soon afterward, but these organisms bear no genealogical relationship to
our primary interest: the history of animal life. The first multicellular animals
do not enter the fossil record until about 580 million years agoafter about
five-sixths of life's history had already passed. Bacteria have been the stayers
and keepers of life's history.
I N D E S T R U C T I B I L I T Y
Let us make a quick bow to the flip side of such long domination
to the future prospects that match such a distinguished and persistent past.
Bacteria have occupied life's mode from the very beginning, and I cannot imagine a
change of status, even under any conceivable new regime that human ingenuity might
someday impose upon our planet.
Bacteria exist in such overwhelming number and such unparalleled
variety; they live in such a wide range of environments and work in so many
unmatched modes of metabolism. Our shenanigans, nuclear and otherwise, might easily
lead to our own destruction in the foreseeable future. We might take most of the
large terrestrial vertebrates with usa few thousand species at most.
I doubt that we could ever substantially touch bacterial diversity.
The modal organisms cannot be nuked into oblivion or very much affected by any of our
considerable conceivable malfeasances.
T A X O N O M Y
The history of classification for the basic groups of life is
one long tale of decreasing parochialism and growing recognition of the diversity
and importance of single-celled organisms and other "lower" creatures. Most of
Western history favored the biblically sanctioned twofold division of organisms into
plants and animals, with a third realm for all inorganic substancesleading
to the old taxonomy of "animal, vegetable, or mineral" in such venerable games as
This twofold division produced a host of practical consequences,
including the separation of biological research into two academic departments and
traditions of study: zoology and botany. Under this system, all single-celled
organisms had to fall into one camp or the other, however uncomfortably, and
however tight the shove of the shoehorn. Thus, paramecia and amoebae became
animals because they move and ingest food.
Photosynthesizing unicells, of course, became plants. But what
about photosynthesizers with mobility? And, above all, what about the prokaryotic
bacteria, which bear no key feature suggesting either allocation? But since
bacteria have a strong cell wall, and because many species are photosynthetic,
bacteria fell into the domain of botany. To this day, we still talk about the
bacterial "flora" of our guts.
By the time I entered high school in the mid-1950s, expansion
and enlightenment had proceeded far enough to acknowledge that unicells could not
be so divided by criteria of the multicellular world and that single-celled
organisms probably deserved a separate kingdom of their own, usually called
Twelve years later, as I left graduate school, even greater
respect for the unicells had led to further proliferation at the "lower" end.
A "five kingdom" system was now all the rage (and has since become canonical in
textbooks), with the three multicellular kingdoms of plants, fungi and animals
in a top layer (representing, loosely, production, decomposition and ingestion
as basic modes of life); the eukaryotic unicells, or Kingdom Protista, in a
middle layer; and the prokaryotic unicells.
Most proponents of this system recognized the gap between
prokaryotic and eukaryotic organizationthat is, the transition from
Monera to Protistaas the fundamental division within life, thus finally
granting bacteria their measure of independent respect, if only as a bottom
Starting in the mid-1970s, development of techniques for
sequencing the genetic code finally gave us a key for mapping evolutionary
relationships among bacterial lineages. We know how to use anatomy for drawing
genealogical trees of multicellular creatures more familiar to us. But we are so
ignorant of the bacterial world that we couldn't identify proper genealogical
divisions, and we therefore tended to dump all bacteria together into a bag of
little unicellular blobs, rods and spirals.
As nucleotide sequences began to accumulate for key segments
of bacterial genomes, a fascinating and unsuspected pattern emerged and has grown
ever stronger with passing years and further accumulation of evidence. This
group of supposed primitives, once shoved into one small bag for their limited
range of overt anatomical diversity, actually includes two great divisions, each
far larger in scope (in terms of genomic distinction and variety) than all three
multicellular kingdoms (plants,animals and fungi) combined!
Moreover, one of these divisions seemed to gather together, into
one grand sibship, most of the bacteria living in odd environments and working by
peculiar metabolisms under extreme conditions (often in the absence of oxygen) that
may have flourished early in Earth's historythe methanogens, or methane
producers; the tolerators of high salinities, the halophiles; and the thrivers at
temperatures around the boiling point of water, the thermophiles.
These first accurate genealogical maps led to the apparently
inescapable conclusion that two grand kingdoms, or domains, must be recognized
within the old Kingdom Monera(1) Bacteria, for most conventional forms that
come to mind when we contemplate this category (the photosynthesizing blue-greens,
the gut bacteria, the organisms that cause human diseases and therefore become
"germs" in our vernacular); and (2) Archaea, for the newly recognized coherence
of oddballs. By contrast, all eukaryotic organisms, the three multicellular
kingdoms as well as all unicellular eukaryotes, belong to a third great
evolutionary domain, the Eucarya.
The accompanying chart, adapted from the work of Carl Woese,
our greatest pioneer in this new constitution of life, says it all, with the
maximally stunning device of a revolutionary picture. We now have a system of
three grand evolutionary domainsBacteria, Archaea and Eucaryaand two
of the three consist entirely of prokaryotes: that is, "bacteria" in the
vernacular, the inhabitants of life's constant mode. Once we place two-thirds of
evolutionary diversity at life's mode, we have much less trouble grasping the
centrality of this location and the constant domination of life by bacteria.
For example, the domain of Bacteria, as presently defined,
contains several major subdivisions, and the genetic distance between any pair
is at least equal to the average separation between eukaryotic kingdoms such as
plants and animals.
Note, by contrast, the restricted domain of all three
multicellular kingdoms. On this genealogical chart for all life, the three
multicellular kingdoms form three little twigs on the bush of just one among
three grand domains of life. Quite a change in one generationfrom my
parents' learning that everything living must be animal or vegetable, to the
icon of my mature years: the kingdoms Animalia and Plantae as two little twigs
amid a plethora of other branches on one of three bushes, with both other
bushes growing bacteria, and only bacteria, all over.
U B I Q U I T Y
The taxonomic criterion, while impressive, does not guarantee
bacterial dominationand for a definite reason common to all genealogical
schemes. Bacteria form the root of life's entire tree. For the first 2 billion
years or so, about half of life's full history, bacteria alone built the tree of
life. Therefore, all multicellular creatures, as late arrivers, can only inhabit
some topmost branches; the roots and trunk must be exclusively bacterial.
This geometry does not make the case for calling our modern
world an "Age of Bacteria" because the roots and trunk might now be atrophied,
with only the multicellular branches flourishing. We need to show not only that
bacteria build most of life's tree but also that these bacterial foundations
remain strong, healthy, vigorous and fully supportive of the minor superstructure
called multicellular life. Bacteria, indeed, have retained their predominant
position and hold sway not only by virtue of a long and illustrious history but
also for abundant reasons of contemporary vigor. Consider two aspects of
1. Numbers. Bacteria inhabit effectively every
place suitable for the existence of life. Mother told you, after all, that
bacterial "germs" require constant vigilance to combat their ubiquity in every
breath and every mouthful, and the vast majority of bacteria are benign or
irrelevant to us, not harmful agents of disease. One fact will suffice: during
the course of life, the number of E. coli in the gut of each human being
far exceeds the total number of people that now live and have ever lived.
Numerical estimates, admittedly imprecise, are a stock in
trade of all popular writing on bacteria. The Encyclopaedia
Britannica tells us that bacteria live by "billions in a gram of rich
garden soil and millions in one drop of saliva." Writer Dorion Sagan and
biologist Lynn Margulis write in their book, Garden of
Microbial Delights, that "human skin harbors some 100,000
microbes per square centimeter" ("microbes" includes nonbacterial unicells,
but the overwhelming majority of "microbes" are bacteria.
I was particularly impressed with their statement about our
colonial status: "Fully 10 percent of our own dry body weight consists of
bacteria, some of which, although they are not a congenital part of our bodies,
we can't live without."
2. Places. Since the temperature tolerance and
metabolic ranges of bacteria so far exceed the scope of all other organisms,
bacteria live in all habitats accessible to any form of life, while the edges of
life's toleration are almost exclusively bacterialfrom the coldest puddles
on glaciers to the hot springs of Yellowstone Park, to oceanic vents where water
issues from the earth's interior at 480 degrees F (still below the boiling point
at the high pressures of oceanic bottoms).
At temperatures greater than 160 degrees F, all life is
bacterial. Thermophila acidophilum thrives at 140 degrees F, and
at a pH of 1 or 2, the acidity of concentrated sulfuric acid. This species,
found on the surface of burning coals and in the hot springs of Yellowstone
Park, effectively freezes to death below 100 degrees F.
U T I L I T Y
Importance for human life forms the narrowest of criteria for
assessing the role of any organism in the history and constitution of life, though
the conventional case for bacteria proceeds largely in this mode. I will therefore
expand a bit toward utility (or at least "intrinsicness") for all of life and even
for the Earth.
1. Historical. Oxygen, the most essential constituent of
the atmosphere for human needs, now maintains itself primarily through release by
multicellular plants in the process of photosynthesis. The Earth's original
atmosphere apparently contained little or no free oxygen, and this otherwise
unlikely element both arose historically and is now maintained by the action of
Plants may provide the major input today, but oxygen started to
accumulate in the atmosphere about 2 billion years ago, substantially before the
evolution of multicellular plant life. Bacterial photosynthesis supplied the
atmosphere's original oxygen and, in concert with multicellular plants, continues
to act as a major source of resupply today.
We could not digest and absorb food properly without our gut
"flora." Grazing animals, cattle and their relatives, depend upon bacteria in their
complex, quadripartite stomachs to digest grasses in the process of rumination.
About 30 percent of atmospheric methane can be traced to the action of methanogenic
bacteria in the guts of ruminants, largely released into the atmospherehow
else to say itby belches and farts.
In another symbiosis essential to human agriculture, plants
need nitrogen as an essential soil nutrient but cannot use the ubiquitous free
nitrogen of our atmosphere. This nitrogen is "fixed," or chemically converted into
usable form, by the action of bacteria like Rhizobium, living symbiotically in
bulbous growths on the roots of leguminous plants.
2. Current. We could also compile a long list of more
parochial uses for human needs and pleasures: the degradation of sewage to
nutrients suitable for plant growth; the possible dispersion of oceanic oil
spills; the production of cheeses, buttermilk and yogurt by fermentation (we make
most alcoholic drinks by fermentation of eukaryotic yeasts); the bacterial
production of vinegar from alcohol and of MSG from sugars.
More generally, bacteria (along with fungi) are the main
reducers of dead organic matter and thus act as one of the two major links in
the fundamental ecological cycle of production (photosynthesis) and reduction to
useful form for renewed production. (The ingesting animals are just a little blip
upon this basic cycle; the biosphere could do very well without them.) Sagan and
Margulis write in conclusion:
"All of the elements crucial to global lifeoxygen,
nitrogen, phosphorus, sulfur, carbonreturn to a usable form through the
intervention of microbes. . . . Ecology is based on the restorative decomposition
of microbes and molds, acting on plants and animals after they have died to
return their valuable chemical nutrients to the total living system of life on
N E W D A T A O N B A C T E R I A L
B I O M A S S
This range of bacterial habitation and necessary activity
certainly makes a good case for domination of life by the modal bacter. But one
claim, formerly regarded as wildly improbable but now quite plausible, if still
unproven, would really clinch the argument. We may grant bacteria all the above,
but surely the main weight of life rests upon eukaryotes, particularly upon the
wood of our forests. Another truism in biology has long proclaimed that the
highest percentage of the Earth's biomasspure weight of organically
produced mattermust lie in the wood of plants.
Bacteria may be ubiquitous and present in nearly uncountable
numbers, but they are awfully light, and you need several gazillion to equal the
weight of even a small tree. So how could bacterial biomass even come close to
that of the displacing and superseding eukaryotes? But new discoveries in the
open oceans and Earth's interior have now made a plausible case for bacterial
domination in biomass as well.
Bacteria dwell in virtually every spot that can sustain any
form of life. And we have underestimated their global number because we, as
members of a kingdom far more restricted in potential habitation, never
appreciated the full range of places that might be searched.
For example, the ubiquity and role of bacteria in the open
oceans have been documented only in the past 20 years. Conventional methods of
analysis missed up to 99 percent of these organisms because we could identify
only what could be cultured from a water sample, and most species don't grow on
most culture media. Now, with methods of genomic sequencing and other
techniques, we can assess taxonomic diversity without growing a large, pure
culture of each species.
Scientists had long known that the photosynthesizing
Cyanobacteria ("blue-green algae" of older terminology) played a prominent role
in the oceanic plankton, but the great abundance of heterotrophic bacteria
(nonphotosynthesizers that ingest nutrients from external sources) had not been
appreciated. In coastal waters, these heterotrophs constitute from 5 to 20
percent of microbial biomass and can consume an amount of carbon equal to 20 to
60 percent of total "primary production" (that is, organic material made by
photosynthesis)giving them a major role near the base of oceanic food
But Jed A. Fuhrman and his colleagues then studied the
biomass of heterotrophic bacteria in open oceans (by far the largest habitat on
Earth by area) and found that they dominate in these environments. In the
Sargasso Sea, for example, heterotrophic bacteria contribute 70 to 80 percent
of microbial carbon and nitrogen and form more than 90 percent of biological
In the late 1970s, marine biologists discovered the bacterial
basis of food chains for deep-sea vent faunas and the unique dependence of this
community upon energy from the earth's interior, rather than from a solar source.
Two kinds of vents had been described: cracks and small fissures with warm water
emerging at temperatures of 40 degrees to 70 degrees F and large conical sulfide
mounds, up to 30 feet in height, and spouting superheated waters at temperatures
that can exceed 600 degrees F.
Bacteria had long been identified in waters from small
fissures of the first category, but it was only in the early 1980s that John
Baross and his colleagues discovered a bacterial biota, including both oxidative
and anaerobic species, in superheated waters emanating from the sulfide mounds
(also known as "smokers").
They cultured bacteria from waters collected at 650 degrees F
and then grew vigorous communities in a laboratory chamber with waters heated to
480 degrees F at a pressure of 265 atmospheres. Thus, bacteria can (and do) live
in high temperatures (and pressures) of waters flowing beneath Earth's surface.
Then, in the early 1990s, several groups of scientists found
and cultured bacteria from oil drillings and other environments beneath oceans
and continents, thus indicating that bacteria may live generally in the Earth's
interior and not only in limited areas where superheated waters emerge at the
surface: from four oil reservoirs nearly two miles below the bed of the North
Sea and below the permafrost surface of Alaska's North Slope, from a Swedish
bore hole nearly four miles deep and from fourwells about a mile deep in
France's East Paris Basin.
Water migrates extensively through cracks and joints in
subsurface rocks and even through pore spaces between grains of sediments
themselves (an important property of rocks, known as "porosity" and vital to
the oil industry as a natural mechanism for concentrating underground
liquidsand, as it now appears, bacteria as well). Thus, although such
data do not indicate global pervasiveness or interconnectivity of subsurface
bacterial biotas, we certainly must entertain the proposition that much of
the Earth deep beneath our feet teems with microbial life.
We might ask one further question that would clinch the
case for underground ubiquity: Moving away from the specialized environments
of deep-sea vents and oil reservoirs, do bacteria also live more generally
in ordinary rocks and sediments (provided that some water seeps through
joints and pore spaces)? New data from the mid-1990s seem to answer this most
general question in the affirmative as well.
R.J. Parkes found abundant bacteria in ordinary sediments
of five Pacific Ocean sites at depths up to 1,800 feet. Meanwhile, the
Department of Energy, under the leadership of Frank J. Wobber, had been
digging deep wells to monitor contamination of groundwater from both
inorganic and potentially microbial sources (done largely to learn if bacteria
might affect the storage of nuclear wastes in deep repositories!). Wobber's
group, taking special pains to avoid the risk of contamination from surface
bacteria introduced into the holes, found bacterial populations in at least
six sites, including a boring in Virginia at 9,180 feet under the ground!
In 1995, T.O. Stevens and J.P. McKinley described rich
bacterial communities living more than 3,000 feet below Earth's surface in
rocks of the Columbia River Basalt in the northwestern United States. These
bacteria are anaerobic and seem to get energy from hydrogen produced in a
reaction between minerals in the basaltic rocks and groundwater seeping
Thus, like the biotas of the deep-sea vents, these bacteria
live on energy from the Earth's interior, entirely independent of the
photosynthetic, and ultimately solar, base of all conventional ecosystems. To
confirm their findings in the field, Stevens and McKinley mixed crushed basalt
with water free from dissolved oxygen. This mixture did generate hydrogen.
They then sealed basalt together with groundwaters containing the deep
bacteria. In these laboratory conditions, simulating the natural situation at
depth, the bacteria thrived for up to a year.
Following a scientific tradition for constructing humorous
and memorable acronyms, Stevens and McKinley have named these deep bacterial
floras, independent of solar energy and cut off from contact with surficial
communities, SLiME (for subsurface lithoautotrophic microbial ecosystemthe
second word is just a fancy way of saying "getting energy from rocks alone").
Jocelyn Kaiser, writing a comment for Science magazine on the work of
Stevens and McKinley, used a provocative title: "Can deep bacteria live on
nothing but rocks and water?" The answer seems to be yes.
When one considers how deeply entrenched has been the dogma
that most earthly biomass lies in the wood of our trees, this potentially greater
weight of underground bacteria represents a major revision of conventional
biology and quite a boost for the modal bacter.
Not only does the Earth contain more bacterial organisms than
all others combined (scarcely surprising, given their minimal size and mass); not
only do bacteria live in more places and work in a greater variety of metabolic
ways; not only did bacteria alone constitute the first half of life's history,
with no slackening in diversity thereafter; but also, and most surprisingly,
total bacterial biomass (even at such minimal weight per cell) may exceed all
the rest of life combined, even forest trees, once we include the subterranean
populations as well. Need any more be said in making a case for the modal
bacter as life's constant center of maximal influence and importance?
[ Stephen Jay Gould, "Planet of the Bacteria," Washington
Post Horizon, 1996, 119 (344): H1; Reprinted here with permission;
This essay was adapted from Full House,
New York: Harmony Books, 1996, pp. 175-192. ]
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