Chapter 26: Bacteria and Archaea: The Prokaryotic Domains

24 Pages·2009·2.75 MB·English

PART SEVEN THE EVOLUTION OF DIVERSITY
26
Life on a strange planet
I
t must have been quite a shock when Thomas “Grif” lated that red algae might account for the red coloration,
Taylor’s Antarctic exploration team first spotted Blood but in the 1960s geologist Robert Black discovered that
Falls in 1911. The blood-red falls were certainly a sur- the water’s color arises from iron oxides that come from
prise in the snowy, icy terrain. What could possibly cause a the underlying bedrock. With the methods then available,
red waterfall in Antarctica? biologists could not detect any living organisms in the
A few million years ago, the Taylor Glacier (which now cold, saline, iron-rich water.
bears the explorer’s name) moved above a pool of salty A half-century later, biologists were better equipped to
water, trapping the pool under 400 meters of ice. The study microscopic life in strange places. By then it was
harsh environment in the resulting enclosed subglacial also possible to amplify and sequence genes from single
sea could hardly seem more hostile to life. It is extremely microbes, and to place these gene sequences into the
cold; there is no light and virtually no oxygen; and salt framework of the tree of life to identify and classify the
concentrations are several times higher than seawater. In microbes. Microbiologist Jill Mikucki and her colleagues
short, it is not a place one might expect to find a diverse used these techniques on water samples from Blood Falls,
living ecosystem. and reported in 2009 that the falls contain an unusual
Some water is able to seep out of this subglacial sea. ecosystem of at least 17 different species of bacteria. The
This water is stained a dark, rusty red, and it spills from the bacteria survive by metabolizing minute amounts of or-
head of Taylor Glacier to form Blood Falls. Taylor specu- ganic matter trapped in the subglacial sea, using sulfate
and iron ions as catalysts and
electron acceptors.
The presence of living organ-
isms in Blood Falls confirms that it
is hard to find a place on or even
near the surface of the Earth that
does not contain populations of
prokaryotes. There are prokaryotes
in volcanic vents, in the clouds, in
environments as acidic as battery
acid or as alkaline as household
ammonia. There are species that
can survive below the freezing
point and above the boiling point
A Splash of Color in a Frozen World
of White Antarctica’s Blood Falls is
the outflow of a subglacial sea that
contains an unusual ecosystem of
bacteria that rely on sulfate and iron
ions for metabolism.
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CHAPTER OUTLINE
26.1 How Did the Living World Begin to Diversify?
26.2 What Are Some Keys to the Success of
Prokaryotes?
26.3 How Can We Resolve Prokaryote Phylogeny?
26.4 What Are the Major Known Groups of
Prokaryotes?
26.5 How Do Prokaryotes Affect Their Environments?
26.6 Where Do Viruses Fit into the Tree of Life?
26.1 How Did the Living World
Begin to Diversify?
You may think that you have little in common with unicellular
prokaryotes. But multicellular eukaryotes like yourself actually
Prokaryotes Can Take the Heat Entire ecosystems of
share many attributes with Bacteria and Archaea. For example,
prokaryotes create the beauty of Morning Glory Pool, a hot
all three of you:
spring in Yellowstone National Park. Cyanobacteria impart the
“morning glory blue” color. Archaea live in the intensely hot •conduct glycolysis
regions of the pool’s interior. •use DNAas the genetic material that encodes proteins
•produce those proteins by transcription and translation
using a similar genetic code
of water. There are more prokaryotes living on and in- •replicate DNAsemiconservatively
side our bodies than we have human cells. The prokary- •have plasma membranes and ribosomes in abundance
otes are masters of metabolic ingenuity, having devel-
These features support the conclusion that all living organ-
oped more ways to obtain energy from the environment isms are related to one another. If life had multiple origins, there
than the eukaryotes have. They have been around much would be little reason to expect all organisms to use overwhelm-
ingly similar genetic codes or to share structures as unique as
longer than other organisms, too.
ribosomes. Furthermore, similarities in DNAsequences of uni-
Prokaryotes are by far the most numerous organisms
versal genes (such as those that encode the structural compo-
on Earth. Late in the twentieth century, it became appar- nents of ribosomes) confirm the monophyly of life.
ent to microbiologists that all prokaryotes are not most Despite the commonalities found across all three domains,
major differences have evolved as well. Let’s first distinguish
closely related to one another. Two prokaryotic lineages
between Eukarya and the two prokaryotic domains. Note that
diverged early in life’s evolution: Bacteria and Archaea.
“domain” is a subjective term used for the largest groups of life.
An early merging between members of these two There is no objective definition of a domain, any more than there
groups is thought to have given rise to the eukaryotic is of a kingdom or a family.
lineage, which includes humans.
The three domains differ in significant ways
Prokaryotic cells differ from eukaryotic cells in three important
ways:
IN THIS CHAPTER we will discuss the distribution of •Prokaryotic cells lack a cytoskeleton and a nucleus, so they do not
prokaryotes and examine their remarkable metabolic diver- divide by mitosis.Instead, after replicating their DNA(see
sity. We will describe the difficulties involved in determin- Figure 11.2), prokaryotic cells divide by their own method,
binary fission.
ing evolutionary relationships among the prokaryotes
•The organization of the genetic material differs.The DNAof the
and will survey the surprising diversity of organisms in
prokaryotic cell is not organized within a membrane-
each domain. We will discuss how prokaryotes can have
enclosed nucleus. DNAmolecules in prokaryotes (both
enormous influence on their environments. Finally, we will bacteria and archaea) are often circular. Many (but not all)
discuss the evolutionary origin and diversity of viruses and prokaryotes have only one main chromosome and are effec-
tively haploid, although many have additional smaller
their relationship to the rest of life.
DNAmolecules, called plasmids, as well (see Section 12.6).
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538 CHAPTER 26 | BACTERIA AND ARCHAEA: THE PROKARYOTIC DOMAINS
TABLE 26.1
The Three Domains of Life on Earth
DOMAIN
CHARACTERISTIC BACTERIA ARCHAEA EUKARYA
Membrane-enclosed nucleus Absent Absent Present
Membrane-enclosed organelles Absent Absent Present
Peptidoglycan in cell wall Present Absent Absent
Membrane lipids Ester-linked Ester-linked Ester-linked
Unbranched Branched Unbranched
Ribosomesa 70S 70S 80S
Initiator tRNA Formylmethionine Methionine Methionine
Operons Yes Yes No
Plasmids Yes Yes Rare
RNA polymerases One Oneb Three
Ribosomes sensitive to chloramphenicol and streptomycin Yes No No
Ribosomes sensitive to diphtheria toxin No Yes Yes
a70S ribosomes are smaller than 80S ribosomes.
bArchaeal RNA polymerase is similar to eukaryotic polymerases.
•Prokaryotes have none of the membrane-enclosed cytoplasmic or-
partners (one ancestor that was related to modern archaea, and
ganelles—mitochondria, Golgi apparatus, and others—that are
another that was more closely related to modern bacteria). Oth-
found in most eukaryotes. However, the cytoplasm of a
ers view the divergence of the early eukaryotes from the archaea
prokaryotic cell may contain a variety of infoldings of the
as a separate and earlier event than the later endosymbiosis of
plasma membrane and photosynthetic membrane systems
the bacterium (the origin of mitochondria). In either case, some
not found in eukaryotes.
genes of eukaryotes are more closely related to those of archaea,
Aglance at Table 26.1will show you that there are also major while others are more closely related to those of bacteria. The
differences (most of which cannot be seen even under an elec- tree of life therefore contains some merging of lineages, as well
tron microscope) between the two prokaryotic domains. In as the predominant diverging of lineages.
some ways archaea are more like eukaryotes; in other ways they The common ancestor of all three domains had DNAas its
are more like bacteria. (Note that we use lowercase when refer- genetic material, and its machinery for transcription and trans-
ring to the members of these domains and uppercase when re- lation produced RNAs and proteins, respectively. This ancestor
ferring to the domains themselves.) The structures of prokary- probably had a circular chromosome.
otic and eukaryotic cells are compared in Chapter 5. The basic Three shapes are particularly common among the bacteria:
unit of an archaeon(the term for a single archaeal organism) or spheres, rods, and curved or helical forms (Figure 26.2). A
bacterium(a single bacterial organism) is the prokaryotic cell. spherical bacterium is called a coccus(plural cocci). Cocci may
Each single-celled organism contains a full complement of ge- live singly or may associate in two- or three-dimensional arrays
netic and protein-synthesizing systems, including DNA, RNA,
and all the enzymes needed to transcribe and translate the ge-
netic information into proteins. The prokaryotic cell also con-
Last common ancestor
tains at least one system for generating the ATPit needs. of today’s species
Endosymbiotic origin Endosymbiotic origin
Genetic studies clearly indicate that all three domains had a of mitochondria of chloroplasts
Very ancient
single common ancestor. For a major portion of their genome,
prokaryotes
eukaryotes share a more recent common ancestor with Archaea BACTERIA
than they do with Bacteria (Figure 26.1). However, the mitochon- Origin
dria of eukaryotes (as well as the chloroplasts of photosynthetic of life EUKARYA
eukaryotes, such as plants) originated through the endosymbio-
sis of a bacterium, as described in Section 5.5. Some biologists
ARCHAEA
prefer to view the origin of eukaryotes as a fusion of two equal
yourBioPortal.com Ancient Time Present
GO TO Animated Tutorial 26.1•The Evolution of 26.1 The Three Domains of the Living World All three domains
the Three Domains
share a common prokaryotic ancestor.
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26.2 | WHAT ARE SOME KEYS TO THE SUCCESS OF PROKARYOTES? 539
26.2 Bacterial Cell Shapes This composite, colorized micrograph
shows the three common types of bacterial morphology. Spherical cells
Helical are called cocci; the acid-producing cocci shown here in green are a
bacteria species of Enterococcus from the mammalian gut. The rod-shaped bacilli
(orange) are represented by Escherichia coli, also a resident of the gut.
Leptospira interrogansis a helical (spiral) bacterium and a human
pathogen.
Cocci
Bacilli
26.2 What Are Some Keys to the
Success of Prokaryotes?
0.50 μm
If success is measured by numbers of individuals, the prokary-
otes are the most successful organisms on Earth. Individual bac-
as chains, plates, blocks, or clusters of cells. Arod-shaped bac- teria and archaea in the oceans number more than 3 ×1028. This
terium is called a bacillus(plural bacilli). The spiral form (like a stunning number is perhaps 100 million times as great as the
corkscrew), or helix(plural helices), is the third main bacterial number of stars in the visible universe. In fact, the bacteria liv-
shape. Bacilli and helices may be single, form chains, or gather ing in your intestinal tract outnumber all the humans who have
in regular clusters. Among the other bacterial shapes are long ever lived.
filaments and branched filaments. Prokaryotes are unicellular organisms, although many form
Less is known about the shapes of archaea because many of multicellular colonies that contain many individual cells. These
these organisms have never been seen. Many archaea are known multicellular associations are not cases of true multicellular
only from samples of DNAfrom the environment, as we de- organisms, however, because each individual cell is fully viable
scribe in Section 26.4. However, the morphology of some species and independent. These associations arise as cells adhere to one
is known, including cocci, bacilli, and even triangular and another after reproducing by binary fission. Associations in the
square-shaped species; the latter grow on surfaces, arranged form of chains are called filaments. Some filaments become
like sheets of postage stamps. enclosed in delicate tubular sheaths.
Archaea, Bacteria, and Eukarya are all products of billions of
years of mutation, natural selection, and genetic drift, and they
Prokaryotes generally form complex communities
are all well adapted to present-day environments. None is
“primitive.” Their last common ancestor probably lived 2 to 3 Prokaryotic cells and their associations do not usually live in iso-
billion years ago. The earliest prokaryotic fossils date back at lation. Rather, they live in communities of many different species
least 3.5 billion years, and they indicate that there was consid- of organisms, often including microscopic eukaryotes. (Micro-
erable diversity among the prokaryotes even during the earli- scopic organisms are often collectively referred to as microbes.)
est days of life. Some microbial communities form layers in sediments, and oth-
ers form clumps a meter or more in diameter. While some mi-
crobial communities are harmful to humans, others provide im-
26.1 RECAP
portant services. They help us digest our food, break down
municipal waste, and recycle organic matter in the environment.
Bacteria and archaea are highly divergent from each
Many microbial communities tend to form dense biofilms.
other and are only distantly related on the tree of life.
Upon contacting a solid surface, the cells secrete a gel-like sticky
Eukaryotes received ancient evolutionary contribu-
polysaccharide matrix that then traps other cells (Figure 26.3).
tions from both of these prokaryotic lineages.
Once this biofilm forms, it is difficult to kill the cells. Pathogenic
• What are the principal differences between the (disease-causing) bacteria are difficult for the immune system—
prokaryotes and the eukaryotes? See pp. 537–538 and modern medicine—to combat once they form a biofilm. For
and Table 26.1 example, the film may be impermeable to antibiotics. Worse,
some drugs stimulate the bacteria in a biofilm to lay down more
• Why don’t we group Bacteria and Archaea together in
matrix, making the film even more impermeable.
a single domain? See p. 538 and Table 26.1
Biofilms form on contact lenses, on artificial joint replacements,
and on just about any available surface. They foul metal pipes
and cause corrosion, a major problem in steam-driven electricity
The prokaryotes were alone on Earth for a very long time, generation plants. The stain on our teeth that we call dental
adapting to new environments and to changes in existing envi- plaque is also a biofilm. Fossil stromatolites—large, rocky struc-
ronments. They have survived to this day, in massive num- tures made up of alternating layers of fossilized microbial biofilm
bers and incredible diversity, and they are found everywhere. and calcium carbonate—are the oldest remnants of early life on
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540 CHAPTER 26 | BACTERIA AND ARCHAEA: THE PROKARYOTIC DOMAINS
(A) Signal (B)
Free-swimming prokaryotes molecules
Other organisms
Binding to surface are attracted to the
signal molecules.
Matrix
Helical and spherical
Signal
organisms are
molecules Single-species biofilm
trapped in the matrix.
Irreversible attachment
100 μm
26.3 Forming a Biofilm (A) Free-swim-
ming bacteria and archaea readily attach
themselves to surfaces and form films stabi-
lized and protected by a surrounding matrix.
Once the population size is large enough, the
Growth and division, developing biofilm can send chemical signals
formation of matrix
that attract other microorganisms. (B) Scan-
ning electron micrography reveals a biofilm of
plaque on a used toothbrush bristle. The
Mature biofilm matrix of dental plaque consists of proteins
from both bacterial secretions and saliva.
Earth (see Figure 25.4). Stro-
matolites still form today in
some parts of the world.
Biofilms are the subject of TOOLS FOR INVESTIGATING LIFE
much current research. For ex-
ample, some biologists are 26.4 The Microchemostat
studying the chemical signals Using techniques from microfluidic engineering, biologists can monitor the dynamics of extremely
small bacterial populations. The photograph shows six microchemostats on a chip. Each of the six is
that bacteria in biofilms use to
equipped with input ports for growth and flushing media, and a number of output ports (diagram).
communicate with one an-
Tiny valves, controlled by a computer, direct flow. Samples are removed through the output ports and
other. By blocking the signals are analyzed to record changes in the bacterial population.
that lead to the production of
the matrix polysaccharides, re-
searchers may be able to pre-
In continuous circulation mode, medium containing
vent biofilms from forming. cells is pumped around the growth chamber loop
Ateam of bioengineers and (green) as the cells multiply.
Flushing
chemical engineers recently medium
devised a sophisticated tech- (input)
nique that enables them to
Growth
monitor biofilm development medium
Valves
in extremely small popula- (input)
tions of bacteria, cell by cell.
Supply
They developed a tiny chip channels
housing six separate growth
chambers, or “microchemo-
stats” (Figure 26.4). The tech-
niques of microfluidics use
microscopic tubes and com-
Pump
puter-controlled valves to di-
rect fluid flow through com-
Output ports
plex “plumbing circuits” in Valves can be adjusted to admit
fresh growth medium and collect
the growth chambers.
cells at an output port.
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26.2 | WHAT ARE SOME KEYS TO THE SUCCESS OF PROKARYOTES? 541
walls of archaea is a key difference between the two prokary-
Prokaryotes have distinctive cell walls
otic domains.
Many prokaryotes have a thick and relatively stiff cell wall. It To appreciate the complexity of some bacterial cell walls, con-
is quite different from the cell walls of land plants and algae, sider the reactions of bacteria to a simple staining process. Atest
which contain cellulose and other polysaccharides, and from called the Gram stainseparates most types of bacteria into two
those of fungi, which contain chitin. The cell walls of almost distinct groups, Gram-positive and Gram-negative. Asmear
all bacteria contain peptidoglycan(a cross-linked polymer of of cells on a microscope slide is soaked in a violet dye and
amino sugars), which produces a meshlike structure around the treated with iodine; it is then washed with alcohol and counter-
cell. Archaeal cell walls are of differing types, but most contain stained with a red dye (safranine). Gram-positive bacteriaretain
significant amounts of protein. One group of archaea has the violet dye and appear blue to purple (Figure 26.5A). The al-
pseudopeptidoglycanin its cell wall; as you can probably guess cohol washes the violet stain out of Gram-negative cells; these
from the prefix pseudo, pseudopeptidoglycan is similar to, but cells then pick up the safranine counterstain, so Gram-nega-
distinctly different from, the peptidoglycan of bacteria. The tive bacteriaappear pink to red (Figure 26.5B).
monomers making up pseudopeptidoglycan differ from and For most bacteria, the Gram-staining results are determined
are differently linked than those of peptidoglycan. Peptido- by the chemical structure of the cell wall. AGram-negative cell
glycan is a substance unique to bacteria; its absence from the wall usually has a thin peptidoglycan layer, and outside the
peptidoglycan layer the cell is surrounded by a second, outer
membrane quite distinct in chemical makeup from the plasma
membrane (see Figure 26.5B). Between the inner (plasma) and
(A)
Gram-positive bacteria have a uniformly dense outer membranes of Gram-negative bacteria is a periplasmic
cell wall consisting primarily of peptidoglycan.
space. This space contains proteins that are important in
digesting some materials, transporting others, and de-
Outside of cell
tecting chemical gradients in the environment.
AGram-positive cell wall usually has about five times
Cell wall as much peptidoglycan as a Gram-negative wall. This
(peptidoglycan)
thick peptidoglycan layer is a meshwork that may serve
some of the same purposes as the periplasmic space of the
Gram-negative cell wall.
The consequences of the different features of prokary-
Plasma otic cell walls are numerous and relate to the disease-caus-
membrane
10 μm ing characteristics of some bacteria. Indeed, the cell wall
is a favorite target in medical combat against pathogenic
Inside of cell
bacteria because it has no counterpart in eukaryotic cells.
Antibiotics such as penicillin and ampicillin, as well as
(B)
Gram-negative bacteria have a very thin other agents that specifically interfere with the synthesis
peptidoglycan layer and an outer membrane. of peptidoglycan-containing cell walls, tend to have little,
Outside of cell if any, effect on the cells of humans and other eukaryotes.
Outer
membrane
of cell wall Prokaryotes have distinctive modes of locomotion
Periplasmic space Although many prokaryotes cannot move, others are
motile. These organisms move by one of several means.
Peptidoglycan
layer Some helical bacteria, called spirochetes, use a corkscrew-
like motion made possible by modified flagella, called ax-
Periplasmic space
ial filaments, running along the axis of the cell beneath the
outer membrane (Figure 26.6A). Many cyanobacteria and
5 μm Plasma
membrane a few other groups of bacteria use various poorly under-
Inside of cell stood gliding mechanisms, including rolling. Various
aquatic prokaryotes, including some cyanobacteria, can
26.5 The Gram Stain and the Bacterial Cell Wall When treated with Gram
move slowly up and down in the water by adjusting the
stain, the cell walls of different bacteria react in one of two ways. (A) Gram-posi-
tive bacteria have a thick peptidoglycan cell wall that retains the violet dye and amount of gas in gas vesicles(Figure 26.6B). By far the
appears deep blue or purple. (B) Gram-negative bacteria have a thin peptidogly- most common type of locomotion in prokaryotes, how-
can layer that does not retain the violet dye but picks up the counterstain and ever, is that driven by flagella.
appears pink to red.
Prokaryotic flagellaare slender filaments that extend
singly or in tufts from one or both ends of the cell or are
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distributed all around it (Figure 26.7). Aprokaryotic fla-
GO TO Web Activity 26.1•Gram Stain and Bacteria
gellum consists of a single fibril made of the protein fla-
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542 CHAPTER 26 | BACTERIA AND ARCHAEA: THE PROKARYOTIC DOMAINS
(A)
Axial filaments
Cell wall
Outer
membrane
50 nm
(B)
Gas Flagella 0.75 μm
vesicles
26.7 Some Prokaryotes Use Flagella for Locomotion Multiple
flagella propel this Salmonellabacillus.
the genetic sense of the word), but this genetic exchange is
not directly linked to reproduction as it is in most eukaryotes.
If conditions are favorable, some prokaryotes can multiply
very rapidly. The shortest known prokaryote generation times
are about 10 minutes, although these rapid rates of replication
0.4 μm usually are not maintained for long. Under less optimal condi-
tions, generation times often extend to many hours or even sev-
26.6 Structures Associated with Prokaryote Motility (A) A spiro-
eral days. Bacteria living deep in Earth’s crust may suspend
chete from the gut of a termite, seen in cross section, shows the axial
their growth for more than a century without dividing, then
filaments used to produce a corkscrew-like motion. (B) Gas vesicles in
a cyanobacterium, visualized by the freeze-fracture technique. multiply for a few days before once again suspending growth.
Prokaryotes can communicate
gellin, projecting from the cell surface, plus a hook and basal Prokaryotes can send and receive signals from one another and
body responsible for motion (see Figure 5.5). In contrast, the fla- from other organisms. One communication channel they em-
gellum of eukaryotes is enclosed by the plasma membrane and ploy is chemical. Another is physical, with light as the medium.
usually contains a circle of nine pairs of microtubules surround- Bacteria release chemical substances that are sensed by other
ing two central microtubules, all containing the protein tubulin, bacteria of the same species. They can announce their availabil-
along with many other associated proteins. The prokaryotic fla- ity for conjugation, for example, by means of such signals. They
gellum rotates about its base, much like a propeller, rather than can also monitor the density of their population. As the density
beating in a whiplike manner, as a eukaryotic flagellum or cil- of bacteria in a particular region increases, the concentration
ium does. of a chemical signal builds up. When the bacteria sense that their
population has become sufficiently dense, they can commence
activities that smaller densities could not manage, such as form-
Prokaryotes reproduce asexually, but genetic
ing a biofilm (see Figure 26.3). This density-sensing technique
recombination can occur
is called quorum sensing.
Prokaryotes reproduce by binary fission, an asexual process Like fireflies and many other organisms, some bacteria can
(see Figure 11.2). Recall, however, that there are also processes— emit light by a process called bioluminescence. Acomplex, en-
transformation, conjugation, and transduction—that allow the zyme-catalyzed reaction requiring ATPcauses the emission of
exchange of genetic information between some prokaryotes light but not heat. Often such bacteria luminesce only when a
without reproduction occurring. So prokaryotes can exchange quorum has been sensed. The bioluminescent spots present in
and recombine their DNAwith other individuals (this is sex in some deep-sea fishes are produced by colonies of biolumines-
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26.2 | WHAT ARE SOME KEYS TO THE SUCCESS OF PROKARYOTES? 543
plasts—that are endosymbiotic descendants of bacteria, as
described in Section 5.5.
The long evolutionary history of bacteria and archaea, dur-
ing which they have had time to explore a wide variety of habi-
tats, has led to the extraordinary diversity of their metabolic
Arabian Peninsula “lifestyles”—their use or nonuse of oxygen, their energy
sources, their sources of carbon atoms, and the materials they
release as waste products.
ANAEROBIC VERSUS AEROBIC METABOLISM Some prokaryotes
can live only by anaerobic metabolism because molecular oxy-
gen is poisonous to them. These oxygen-sensitive organisms
are called obligate anaerobes. Other prokaryotes can shift their
metabolism between anaerobic and aerobic modes (see Chap-
Horn ter 9) and thus are called facultative anaerobes. Many faculta-
of Africa Bioluminescent tive anaerobes alternate between anaerobic metabolism (such
Vibrio
as fermentation) and cellular respiration as conditions dic-
tate. Aerotolerant anaerobes cannot conduct cellular respira-
tion but are not damaged by oxygen when it is present. By def-
inition, an anaerobe does not use oxygen as an electron acceptor
for its respiration.
At the other extreme from the obligate anaerobes, some
Indian Ocean prokaryotes are obligate aerobes, unable to survive for extended
periods in the absenceof oxygen. They require oxygen for cellu-
lar respiration.
26.8 Bioluminescent Bacteria Seen from Space In this satellite
photo, legions of bioluminescent Vibrio harveyiform a glowing patch NUTRITIONAL CATEGORIES All living organisms face the same
thousands of square kilometers in area in the Indian Ocean, off the Horn
nutritional challenges: they must synthesize energy-rich com-
of Africa. Compare their blue glow with the white light of cities in eastern
pounds such as ATPto power their life-sustaining metabolic re-
Africa and the Middle East.
actions, and they must obtain carbon atoms to build their own
organic molecules. Biologists recognize four broad nutritional
categories of organisms: photoautotrophs, photoheterotrophs,
cent bacteria. On land, some soil-dwelling bioluminescent bac- chemolithotrophs, and chemoheterotrophs. Prokaryotes are rep-
teria produce eerily glowing patches of ground at night. resented in all four groups (Table 26.2).
How is bioluminescence useful to a prokaryote? One fairly Photoautotrophsperform photosynthesis. They use light as
well understood case is that of some bacteria of the genus Vib- their energy source and carbon dioxide (CO ) as their carbon
2
rio. These bacteria can live freely, but they truly thrive inside the source. Like green plants and other photosynthetic eukaryotes,
guts of fish. Inside the fish, they may attach to food particles the cyanobacteria, a group of photoautotrophic bacteria, use
and then can be expelled as waste along with particulate mat- chlorophyll aas their key photosynthetic pigment and produce
ter. Reproducing on the particles, a bacteria population increases
until a glowing particle attracts another fish, which ingests the
bacteria along with the particle—giving the bacteria a new TABLE 26.2
home and food source for a while. In this case, Vibrioare both
How Organisms Obtain Their Energy and Carbon
communicating with another species and enhancing their own
nutritional status. In the Indian Ocean off the eastern coast of NUTRITIONAL CATEGORY ENERGY SOURCE CARBON SOURCE
Africa, Vibriosometimes concentrate over such a large area (sev-
eral thousand square kilometers) that their bioluminescence is Photoautotrophs Light Carbon dioxide
visible from space (Figure 26.8). (found in all three
domains)
Photoheterotrophs Light Organic
Prokaryotes have amazingly diverse
(some bacteria) compounds
metabolic pathways
Chemolithotrophs Inorganic Carbon dioxide
(some bacteria, substances
Bacteria and archaea outdo the eukaryotes in terms of meta-
many archaea)
bolic diversity. Although much more diverse in size and shape,
Chemoheterotrophs Organic Organic
eukaryotes draw on fewer metabolic mechanisms for their
(found in all three compounds compounds
energy needs. In fact, much of the eukaryotes’ energy metab-
domains)
olism is carried out in organelles—mitochondria and chloro-
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544 CHAPTER 26 | BACTERIA AND ARCHAEA: THE PROKARYOTIC DOMAINS
oxygen gas (O ) as a by-product of noncyclic electron transport Finally, chemoheterotrophsobtain both energy and carbon
2
(see Section 10.1). atoms from one or more complex organic compounds that have
There are other photosynthetic groups among the bacteria, been synthesized by other organisms. Most known bacteria and
but these use bacteriochlorophyllas their key photosynthetic pig- archaea are chemoheterotrophs—as are all animals and fungi
ment, and they do not release O . Indeed, some of these pho- and many protists.
2
tosynthesizers produce particles of pure sulfur, because hydro-
gen sulfide (H S) rather than H O is their electron donor for NITROGEN AND SULFUR METABOLISM Key metabolic reactions in
2 2
photophosphorylation (see Section 10.2). Bacteriochlorophyll many prokaryotes involve nitrogen or sulfur. For example, some
molecules absorb light of longer wavelengths than the chloro- bacteria carry out respiratory electron transport without using
phyll molecules used by all other photosynthesizing organisms. oxygen as an electron acceptor. These organisms use oxidized
As a result, bacteria using this pigment can grow in water un- inorganic ions such as nitrate, nitrite, or sulfate as electron ac-
der fairly dense layers of algae, using light of wavelengths that ceptors. Examples include the denitrifiers, bacteria that release
are not absorbed by the algae (Figure 26.9). nitrogen to the atmosphere as nitrogen gas (N ). These normally
2
Photoheterotrophsuse light as their energy source but must aerobic bacteria, mostly species of the genera Bacillus and
obtain their carbon atoms from organic compounds made by Pseudomonas, use nitrate (NO –) as an electron acceptor in place
3
other organisms. Their “food” consists of organic compounds of oxygen if they are kept under anaerobic conditions:
such as carbohydrates, fatty acids, and alcohols. For example,
2 NO –+ 10 e–+ 12 H+→N + 6 H O
compounds released from plant roots (as in rice paddies) or 3 2 2
from decomposing photosynthetic bacteria in hot springs are Nitrogen fixersconvert atmospheric nitrogen gas into a chemi-
taken up by photoheterotrophs and metabolized to form build- cal form (ammonia) usable by the nitrogen fixers themselves as
ing blocks for other compounds; sunlight provides the neces- well as by other organisms, especially land plants:
sary ATPthrough photophosphorylation. The purple nonsul-
N + 6 H →2 NH
fur bacteria, among others, are photoheterotrophs. 2 3
Chemolithotrophs(also called chemoautotrophs) obtain their All organisms require nitrogen in order to build proteins, nu-
energy by oxidizing inorganic substances, and they use some cleic acids, and other important compounds. Nitrogen fixation
of that energy to fix CO . Some chemolithotrophs use reac- is thus vital to life as we know it. This all-important biochemi-
2
tions identical to those of the typical photosynthetic cycle, but cal process is carried out by a wide variety of archaea and bac-
others use alternative pathways to fix CO . Some bacteria oxi- teria (including cyanobacteria) but by no other organisms, so
2
dize ammonia or nitrite ions to form nitrate ions. Others oxi- we depend on these prokaryotes for our very existence. We de-
dize hydrogen gas, hydrogen sulfide, sulfur, and other materi- scribe the details of nitrogen fixation in Chapter 36.
als. Many archaea are chemolithotrophs. Ammonia is oxidized to nitrate in soil and in seawater by
Deep-sea hydrothermal vent ecosystems are dependent on chemolithotrophic bacteria called nitrifiers. Bacteria of two gen-
chemolithotrophic prokaryotes that are incorporated into large era, Nitrosomonasand Nitrosococcus, convert ammonia to nitrite
communities of crabs, mollusks, and giant worms, all living at ions (NO –), and Nitrobacteroxidizes nitrite to nitrate (NO –).
2 3
a depth of 2,500 meters—below any hint of sunlight. These bac- What do the nitrifiers get out of these reactions? Their me-
teria obtain energy by oxidizing hydrogen sulfide and other tabolism is powered by the energy released by the oxidation
substances released in the near-boiling water flowing from vol- of ammonia or nitrite. For example, by passing the electrons
canic vents in the ocean floor. from nitrite through an electron transport chain (see Section 9.3),
Nitrobactercan make ATP, and using some of
this ATP, can also make NADH. With this
ATPand NADH, the bacterium can convert
The alga absorbs strongly in the Bacteria with bacteriochlorophyll CO and H O to glucose.
2 2
blue and red wavelengths, shading can use long-wavelength (infrared)
the bacteria living below it. light, which the algae do not absorb,
for their photosynthesis.
High
Ulva sp.
n (green alga)
o
pti
or
s
b
a
e
v
ati Purple sulfur
el bacteria
R 26.9 Bacteriochlorophyll Absorbs Long-
Low Wavelength Light The chlorophyll in Ulva, a
green alga, absorbs no light of wavelengths longer
than 750 nm. Purple sulfur bacteria, which contain
300 400 500 600 700 800 900 1000 bacteriochlorophyll, can conduct photosynthesis
Wavelength (nm) using longer wavelengths.
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© 2010 Sinauer Associates, Inc.
26.3 | HOW CAN WE RESOLVE PROKARYOTE PHYLOGENY? 545
26.2 RECAP ably less than 1 percent of living prokaryote species. Further-
more, this work provided little insight into how prokaryotic or-
Prokaryotes have established themselves everywhere ganisms evolved—a question of great interest to microbiologists
on Earth. They may form communities called biofilms and evolutionary biologists. Only recently have systematists de-
that coat materials with a gel-like matrix. Prokaryotes veloped the appropriate tools to produce classification schemes
have distinctive cell walls and modes of locomotion, that make sense in evolutionary terms.
communication, reproduction, and nutrition.
The nucleotide sequences of prokaryotes reveal
• How do biofilms form and why are they of special inter-
their evolutionary relationships
est to researchers? See pp. 539–540 and Figure 26.3
• Describe bacterial cell wall architecture. See p. 541 Analyses of nucleotide sequences of ribosomal RNA(rRNA)
and Figure 26.5 genes provided the first comprehensive evidence of evolution-
ary relationships among prokaryotes. For several reasons, rRNA
• How are the four nutritional categories of prokaryotes
is particularly useful for evolutionary studies of living organ-
distinguished? See pp. 543–544 and Table 26.2
isms:
• Explain why nitrogen metabolism in the prokaryotes is •rRNAis evolutionarily ancient, as it was found in the
vital to other organisms. See p. 544
common ancestor of life.
•No free-living organism lacks rRNA, so rRNAgenes can
be compared throughout the tree of life.
We noted earlier that only recently have scientists appreciated
•rRNAplays a critical role in translation in all organisms,
the huge distinctions between Bacteria and Archaea. How do
so lateraltransferof rRNAgenes among distantly related
researchers approach the classification of organisms they can’t
species is unlikely.
even see?
•rRNAhas evolved slowly enough that gene sequences
can be aligned and analyzed among even distantly
26.3 How Can We Resolve
related species.
Prokaryote Phylogeny?
Comparisons of rRNAgenes from a great many organisms have
As detailed in Chapter 22, classification schemes serve three pri- revealed the probable phylogenetic relationships from through-
mary purposes: to identify organisms, to reveal evolutionary out the tree of life. Databases such as GenBank contain rRNA
relationships, and to provide universal names. Classifying bac- gene sequences from hundreds of thousands of species—more
teria and archaea is of particular importance to humans because than any other gene sequences.
scientists and medical technologists must be able to identify bac- Although these data are helpful, it is clear that even distantly
teria quickly and accurately; when the bacteria are pathogenic, related prokaryotes sometimes exchange genetic material. In
lives may depend on it. In addition, many emerging biotech- some groups of prokaryotes, analyses of multiple gene se-
nologies (see Chapter 18) depend on a thorough knowledge of quences have suggested several different phylogenetic patterns.
prokaryote biochemistry, and understanding an organism’s How could such differences among different gene sequences
phylogeny allows biologists to make predictions about the dis- arise?
tribution of biochemical processes across the wide diversity of
prokaryotes.
Lateral gene transfer can lead to discordant gene trees
As noted earlier, prokaryotes reproduce by binary fission. If we
The small size of prokaryotes has hindered
could follow these divisions back through evolutionary time,
our study of their phylogeny
we would be tracing the path of the complete tree of life for bac-
Until about 300 years ago, nobody had even seenan individual teria and archaea. This underlying tree of relationships, repre-
prokaryote; these organisms remained invisible to humans un- sented in highly abbreviated form in Appendix A, is called the
til the invention of the first simple microscope. Prokaryotes organismal (orspecies)tree. Because whole genomes are repli-
are so small that even the best light microscopes don’t reveal cated during asexual binary fission divisions, we expect phylo-
much about them. It took the advanced microscopic equipment genetic trees constructed from most gene sequences to reflect
and techniques of the twentieth century (see Figure 5.3) to open these same relationships (see Chapter 22).
up the microbial world. From early in evolution to the present day, however, some
Until recently, taxonomists based prokaryote classification genes have been moving “sideways” from one prokaryotic
on observable phenotypic characters such as shape, color, motil- species to another, a phenomenon known as lateral gene trans-
ity, nutritional requirements, antibiotic sensitivity, and reaction fer. Mechanisms of lateral gene transfer include transfer by plas-
to the Gram stain. When biologists learned how to grow bac- mids and viruses and uptake of DNAfrom the environment by
teria in pure culture on nutrient media, they learned a great deal transformation. Lateral gene transfers are well documented, es-
about the genetics, nutrition, and metabolism of those species pecially among closely related species; some have been docu-
that could be cultured. However, these species represent prob- mented even across the three primary domains of life.
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any form without express written permission from the publisher.
© 2010 Sinauer Associates, Inc.