Allies and Enemies: How the World Depends on Bacteria (2 page)

survival. Unlike any other type of cell in biology, bacteria do these things using the simplest cell in biology. What about viruses, which are often described as the simplest biological beings in existence? The science of microbiology has adopted viruses mainly because viruses are microscopic and biological. But viruses cannot perform all the functions that would make them a living thing: a life cycle, metabolism, and interaction with the environment. Viruses depend entirely on living cells for their survival. A single virus particle dropped into even the most comfortable environment would be a lifeless speck with no capabilities of its own.

Various theories have been put forth to explain the origin of viruses in relation to bacteria. Viruses may have descended from a primitive form of nucleic acid, meaning deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). RNA carries information inside cells just

as DNA carries genes. RNA interprets the code in DNA’s genes and

uses this information to assemble cellular components. RNA would

be a likely candidate for originating viruses because its structure is simpler than DNA’s; DNA contains two long chains that make up its

molecule and RNA has only one chain. Perhaps ancient RNA

directed the early processes of building more complex molecules such as a nucleic acid wrapped in protein, the basic structure of a virus. (A protein is a long strand of amino acids folded into a specific shape.) A second contrasting theory views viruses as self-replicating pieces of RNA or DNA cast out from early bacteria. The pieces somehow became enveloped in protein and thus turned into the first virus.

Microbiologists have also considered a scenario in which evolution reversed and bacterial cells regressed by shedding much of their cellular structure until only nucleic acid surrounded by protein remained. The theories fall into and out of favor, but one thing is certain: bacteria and viruses share a very long history on Earth.

Fungi, protozoa, algae, plants, and all animal life, including

humans, belong to the Domain Eukarya. The cells that make up

eukaryotes have internal structures called organelles. The organelles

give eukaryotic cells an orderliness that bacteria lack and help refine the basic activities of the cell: building compounds, breaking down compounds, and communicating with other cells. But managing a lot of infrastructure also requires extra work. During cell reproduction,

each organelle must be allocated to the two new cells. In sexual

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allies and enemies

reproduction, a eukaryote needs another eukaryotic cell to propagate

the species. Members of Domain Bacteria and bacterialike microbes

in Domain Archaea split in half by binary fission without the worries

of managing organelles, which bacteria and archaea lack. (Archaea are indistinguishable from bacteria in a microscope, and many scientists, even microbiologists, lump the two types of microbes together.) Before people knew of the existence of bacteria, they put bacteria

to work making or preserving foods and decomposing waste. Although

humanity’s relationship with bacteria extends to humans’ earliest history, studies of these cells began in earnest only 200 years ago, and

the major discoveries in bacterial evolution emerged in the past 50 years. Bacterial genetics bloomed in 1953 when James Watson, Francis Crick, and Rosalind Franklin studied a thick, mucuslike substance from Escherichia coli and thus determined the structure of DNA.

Bacteriology required microscopes to improve before this science

could advance. Van Leeuwenhoek provided a starting point, but others refined the instrument, particularly van Leeuwenhoek’s British

contemporary Robert Hooke. Hooke invented a way to focus light on

specimens to make the magnified image easier to study. By the 1800s,

microbes had captured the imagination of scientists and microbiology

would enter a period from 1850 to the early 20th century called the

Golden Age of Microbiology. By the close of the Golden Age, microbiologists had solved a number of health and industry problems related to bacteria. Microbiology’s eminent Louis Pasteur would raise the stature of microbiologists to veritable heroes.

The emergence of electron microscopy in the 1940s enabled

microbiologists to see inside individual bacterial cells. This achieve—

ment plus the studies on DNA structure and replication launched a

new golden period, this time involving cellular genetics. By learning

how bacteria control and share genes, geneticists moved beyond

simply crossing red flowering plants with white. Genetics reached the molecular level. Some electron microscopes now produce

images of atoms, the smallest unit of matter. With these abilities, scientists have uncovered the fine points of cell reproduction. Genetic engineering, biotechnology, and gene therapy owe their development to the first microscopic studies on cell organization.

Microbiologists also peer outward from bacterial cells to entire ecosystems. Ecologists have discovered bacteria in places no one thought a creature could live, and the bacteria do not merely tolerate these places, they thrive. Many of the surprises have come from extremophiles that live in environments of extraordinary harshness, by human standards, where few other living things can survive.

Industries have mined extremophiles for enzymes that work either at

extremely hot or frigid conditions. Polymerase chain reaction (PCR),

for example, relies on an enzyme from an extremophile to run reactions between a range of 154°F and 200°F. PCR replicates tiny bits of

DNA into millions of copies in a few hours. By using the enzyme (called restriction endonuclease) from extremophiles, microbiologists

can track disease outbreaks, monitor pollution, and catch criminals.

Bacteria recycle the Earth’s elements and thereby support the

nutrition of all other living things. Bacteria feed us and clean up our wastes. They help regulate the climate and make water drinkable.

Some bacteria even release compounds into the air that draw moisture droplets together to form clouds. But most people overlook the

benefits of bacteria and focus instead on what I call the “yuck factor.”

“Are bacteria really everywhere?” “Is my body crawling with bacteria

right now?” “Is
E. coli
on doorknobs?” The answers are yes, yes, and yes. To a microbiologist, this is a wonderful thing.

Bacteria thrive on every surface on Earth, and almost all bacteria

possess at least one alternative energy-generating system if the preferred route hits a snag. And if some bacteria do not thrive, they at

least develop mechanisms that allow them to ride out catastrophe.

The apparent indestructibility of bacteria may fuel the fear people have toward them. We fear infectious disease, resistant superbugs, and the high mortalities that bacteria have already caused in history.

Pathogens in fact make up a small percentage of all bacteria, yet if

asked to name ten bacteria in 15 seconds, almost everyone would tick

off the names of pathogens.

I am here to improve the public image of bacteria. Bacteria

can and do harm people, but this happens almost exclusively when people make mistakes that let dangerous bacteria gain an advantage.

The benefits we receive from bacteria far outweigh the harm. By

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allies and enemies

understanding the wide variety of Earth’s bacteria, people can put some of their fears aside and appreciate the vital contributions of these microbes. The bacterial universe may at first glance seem invisible. But as you get to know the bacteria that influence your life each day, they become easier to see even if they truly remain invisible.

Bacteria have been called “friendly enemies,” but I think that sends

the wrong message. Bacteria are powerful friends. We will never defeat bacteria, nor do we want to. Like most friends with lots of power, it is best to respect them, treat them well, and keep them close.

1

Why the world needs bacteria

What is a bacterium? Bacteria belong to a universe of single-celled

creatures too small, with rare exceptions, to be seen by the unaided

eye, but exist everywhere on Earth. Being small, simple, and many

confers on bacteria advantages that allow them to not only survive but

also to affect every mechanism by which the planet works. Bacteria

influence chemical reactions from miles above the Earth’s surface to

activities deep within the Earth’s mantle.

Bacteria range in size from
Thiomargarita namibiensis
, which reaches 750 micrometers (
ì m) end to end and is visible to the naked eye, to
Francisella tularensis
measuring only 0.2
ì
m in diameter.

Since 1988, microbiologists have explored a new area involving

“nanobacteria.” These microbes measure 0.05
ì
m in diameter or one—

thousandth the volume of a typical bacterial cell. Excluding these unusual giants and dwarfs, most bacteria are between 0.5 and 1.5
ì m in diameter and 1 to 2
ì
m long, or less than one-twentieth the size of

the period at the end of this sentence. The volume of bacterial cells

ranges from 0.02 to 400
ì
m3. One of many advantages in being small

involves the ability to sense environmental changes with an immedi—

acy that large multicellular organisms lack.

Bacterial simplicity can deceive. The uncomplicated structure

actually carries out every important biochemical reaction in Earth’s

ecosystems. Bacteria have an outer cell wall that gives them their distinctive shapes (see Figure 1.1) and overlays a membrane, which holds in the watery cytoplasm interior and selectively takes in nutrients, restricts the entry of harmful substances, and excretes wastes.

This membrane resembles the membranes of all other living things.

That is, it is consists of a bi-layer of proteins and fats that communicates with the aqueous environment and confines the cell contents to 7

8

allies and enemies

the cell interior. Inside the membrane bi-layer proteins and fats line

up in a way that hydrophilic or water-attracting portions of the compounds face out or into the cytoplasm, and hydrophobic compounds

point into the membrane. The character of membrane fats enables them to assemble spontaneously if put into a beaker of water. The ease with which membranes assemble likely helped the first cells to develop on Earth.

Figure 1.1 Bacteria shapes. Cell shape is hardwired into bacteria genetics.

No animal life adheres as strictly to a standard shape as bacteria and algae called diatoms. (Courtesy of Dennis Kunkel Microscopy, Inc.)

The bacterial cytoplasm and membrane hold various enzymes

that keep the cell alive. Bacterial deoxyribonucleic acid (DNA), the

depository of information formed over the millennia, appears in the

cytoplasm as a disorganized mass (seen only with an electron microscope), but it actually contains precise folds and loops that decrease

chapter 1 · why the world needs bacteria

9

the chances of damage and facilitate repair. Tiny protein-manufacturing particles called ribosomes dot much of the remainder of the

cytoplasm.

Bacteria require few other structures. Motile bacteria have

whiplike tails called flagella for swimming, photosynthetic cyanobacteria contain light-absorbing pigments, and magnetotactic species, such as Aquaspirillum magnetotacticum , contain a chain of iron magnetite particles that enable the cells to orient toward Earth’s poles. These micro-compasses help Aquaspirillum migrate downward in aqueous habitats toward nutrient-rich sediments.

Though tiny, bacteria occupy the Earth in enormous numbers.

Microbiologists estimate total numbers by sampling soil, air, and water and determining the bacterial numbers in each sample, and then extrapolating to the size of the planet with the aid of algorithms.

Guesswork plays a part in these estimates. Bacteria exist 40 miles above the Earth and 7 miles deep in the ocean, and most of these places have so far been inaccessible. The total numbers of bacteria reach 1030. Scientists struggle to find a meaningful comparison; the

stars visible from Earth have been estimated at “only” 7 × 1022. The

mass of these cells approaches 2 × 1015 pounds, or more than 2,000

times the mass of all 6.5 billion people on Earth. Of these, the overwhelming majority lives in the soil.

Bacteria can stretch the limits of our imagination with small size

and massive numbers. Both of these attributes help bacteria, and by

the biological processes they carry out, bacteria also ensure that humans survive.

Tricks in bacterial survival

Bacteria and bacterialike archaea survive challenging conditions

through the benefit of adaptations accrued in evolution. Survival techniques might be physical or biochemical. For example, motility in bacteria serves as an excellent way to escape danger. In addition to flagella that help bacteria swim through aqueous environments, some bacteria can glide over surfaces, and others start twitching frantically to propel themselves. Certain bacterial species develop impregnable shells

called endospores. Others use biochemical aids to survival to counter

the effects of acids, bases, salt, high or low temperature, and pressure.

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allies and enemies

A large number of bacteria use a modified version of a capsule for

protection. The cells build long, stringy lipopolysaccharides, which are polysaccharides (sugar chains) with a fatty compound attached and which extend into the cell’s surroundings. The bacteria that make these appendages, called O antigens, construct them out of sugars rarely found in nature. As a consequence, protozoa that prey on bacteria do not recognize the potential meal and swim past in search of “real” bacteria.

Archaea seem to be Earth’s ultimate survivors because of the

extreme environments they inhabit. Archaea and bacteria both

belong to the prokaryotes, one of two major types of cells in biology,

the other being more complex eukaryotic cells of algae, protozoa, plants, and animals. Because archaea inhabit extreme environments

that would kill most terrestrial animal and plant life, the archaea are sometimes thought of as synonymous with “extremophile.” The outer

membrane of archaea living in boiling hot springs contain lipid (fat—

like) molecules of 30 carbons or more, larger than most natural fatty

compounds. These lipids and the ether bonds that connect them sta—

bilize the membrane at extremely high temperatures. News stories often tell of new bacteria found at intense pressures 12,000 feet deep

on the ocean floor at vents called black smokers. These hydrothermal

vents spew gases at 480°F, release acids, and reside at extreme pressures, so any organisms living there would truly be a news item. The

organisms living near black smokers are usually archaea, not bacteria.

Archaea also dominate habitats of high salt concentration, such as salt lakes, or places completely devoid of oxygen, such as subsurface sediments. Because of the difficulty of getting at many archaea and their aversion to growing in laboratory conditions, studies on archaea trail

those completed on bacteria.

Some bacteria also survive in the same extreme conditions favored

by archaea. The aptly named
Polaromonas
inhabits Antarctic Sea ice where temperatures range from 10°F to –40°F by slowing its metabolism until it reproduces only once every seven days. By comparison, E. coli grown in a laboratory divides every 20 minutes.
Polaromonas is a psychrophile or cold-loving microbe.
Thermus aquaticus is the opposite, a thermophile that thrives in hot springs reaching 170°F by synthesizing heat-stabile enzymes to run its metabolism. Enzymes of chapter 1 · why the world needs bacteria

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mesophiles, which live in a comfortable temperature range of 40°F to

130°F, unfold when heated and thus lose all activity. Mesophiles include the bacteria that live on or in animals, plants, most soils, shallow waters, and foods. The bacteria that live in harsh conditions that mesophiles cannot endure are the Earth’s extremophiles.

The genus
Halococcus
, a halophile, possesses a membrane-bound

pump that constantly expels salt so the cells can survive in places like the Great Salt Lake or in salt mines. Barophilic bacteria that hold up under intense hydrostatic pressures from the water above are inexorably corroding the
RMS Titanic
12,467 feet beneath the Atlantic.

These barophiles contain unsaturated fats inside their membranes that make the membrane interior more fluid than the fats in other bacterial membranes. Unsaturated fats contain double bonds between some of the carbon atoms in the chainlike fat rather than single bonds

that predominate saturated fats. At pressures of the deep ocean, normal membrane liquids change into the consistency of refrigerated butter, but the special membrane composition of barophiles prevents such an outcome that would render the membrane useless. A later

chapter discusses why red-meat animals store mainly saturated fats and pork and chicken store more unsaturated fats.