Allies and Enemies: How the World Depends on Bacteria (3 page)

The acidophile
Helicobacter pylori
that lives in the stomach withstands conditions equivalent to battery acid of pH 1 or lower by secreting compounds that neutralize the acid in their immediate surroundings. Even though an acidophile lives in strong acids that would burn human skin, it remains protected inside a microscopic cocoon of

about pH 7. Additional extremophiles include alkaliphiles that live in

highly basic habitats such as ammonia and soda lakes; xerophiles occupy habitats without water; and radiation-resistant bacteria survive gamma-rays at doses that would kill a human within minutes.

Deinococcus
, for instance, uses an efficient repair system that fixes the damage caused to the DNA molecule by radiation at doses that would kill a human. This system must be quick enough to complete

the repair before
Deinococcus
’
s
next cell division.

All bacteria owe their ruggedness to the rigid cell wall and its main component, peptidoglycan. This large polymer made of repeat—

ing sugars and peptides (chains of amino acids shorter than proteins

and lacking the functions of proteins) occurs nowhere else in nature.

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allies and enemies

Peptidoglycan forms a lattice that gives species their characteristic shape and protects against physical damage. A suspension of bacteria

can be put in a blender, whipped, and come out unharmed.

Archaea construct a cell wall out of polymers other than peptidoglycan, but their cell wall plays the same protective role. Furthermore, because archaea have a different cell wall composition than bacteria, they resist all the antibiotics and enzymes that attack bacterial cell walls. This quirk would seem to make archaea especially dangerous pathogens to humans, but on the contrary, no human disease has ever been attributed to an archaean.

In a microscope, bacteria present an uninspiring collection of

gray shapes: spheres, rods, ovals, bowling pins, corkscrews, and boomerangs. Microbiologists stain bacteria with dyes to make them

more pronounced in a light microscope or use advanced types of microscopy such as dark field or phase contrast. Both of these latter

methods create a stunning view of bacteria illuminated against a dark

background.

When bacteria grow, the cell wall prevents any increase in size so

that bacterial growth differs from growth in multicellular organisms.

Bacteria grow by splitting into two new cells by binary fission. As cell numbers increase, certain species align like a strand of pearls or form clusters resembling grapes. Some bacteria form thin, flat sheets and swarm over moist surfaces. The swarming phenomenon suggests bacteria do not always live as free-floating, or planktonic, beings but can form communities. In fact, bacterial communities represent more than a pile of cells. Communities contain a messaging system in which identical cells or unrelated cells respond to each other and change their behavior. This adaptation is called quorum sensing.

Quorum sensing begins when cells excrete a steady stream of signal molecules resembling amino acids. The excreted signal travels about 1
ì m so that neighboring cells can detect it with specific proteins on their surface. When the receptors clog with signal molecules, a cell gets the message that other cells have nudged too close; the population has grown too dense. The proteins then turn on a set of

genes that induce the bacteria to change their behavior. Different types of bacterial communities alter behavior in their own way, yet throughout bacteriology communities offer bacteria a superb survival

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mechanism. Some communities swarm, others cling to surfaces, and

yet others can cover a pond’s surface and control the entire pond ecosystem.

Bacterial communities

Swarm cells start growing like any other bacterium on laboratory-prepared nutrient medium. (Media are liquids or solids containing gel-like agar that supply bacteria with all the nutrients needed for growth.) They metabolize for a while, split in two, and repeat this until nutrients run low. Rather than halting the colony’s growth, swarm cells signal each other to change the way they reproduce. The swarmer
Proteus
develops a regular colony when incubated, each cell about three ì m in length. After several hours, cells on the colony’s outer edge elongate to 40 to 80
ì m and sprout numerous flagella. Ten to 12 flagellated cells team up and then squiggle away from the main

colony. By forming teams of cells lined up in parallel, 50 times more

flagella power the cells forward than if one
Proteus
headed out on its

own. Several millimeters from the main colony, the swarmers stop and again begin to reproduce normally. As generations of progeny grow, they build a ring of Proteus around the original colony, shown in Figure 1.2. At a certain cell density in the ring, Proteus repeats the swarming process until a super-colony of concentric rings covers the entire surface. When two swarming
Proteus
colonies meet, they do not overrun each other. The two advancing fronts stop within a few ì
m of each other, repelled by their respective defenses.
Proteus
produces an antibacterial chemical called bacteriocin. The specific bacteriocin of each swarmer colony protects its turf against invasion.

Other swarmer bacteria use hairlike threads called pili rather

than flagella, and cast their pili ahead to act as tethers. By repeatedly contracting, the cells drag themselves forward to up to 1.5 inches per hour. Petri dishes measure only 4 inches across, but if dishes were the size of pizzas, swarm cells would cover the distance.

Communities such as biofilm grow on surfaces bathed in moisture. Biofilms cover drinking water pipes, rocks in flowing streams,

plant leaves, teeth, parts of the digestive tract, food manufacturing lines, medical devices, drain pipes, toilet bowls, and ships’ hulls.

Unlike swarming colonies, biofilm contains hundreds of different

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allies and enemies

species, but they too interact via quorum sensing. (Bacteria that merely attach to surfaces such as skin are not true biofilms because

they do not coalesce into a community that functions as a single entity.) Biofilm begins with a few cells that stick to a surface by laying down a coat of a sticky polysaccharide. Other bacteria hop aboard and build the diverse biofilm colony.

Figure 1.2 The swarming bacterium
Proteus mirabilis. Proteus
swarms outward from a single ancestor cell and forms concentric growth rings with each generation. (Courtesy of John Farmer, CDC Public Health Image Library) Biofilms facilitate survival by capturing and storing nutrients and

excreting more polysaccharide, which protects all the members

against chemicals such as chlorine. Eventually fungi, protozoa, algae,

and inanimate specks lodge in the conglomeration of pinnacles and

channels. When the biofilm thickens, signals accumulate. But

because many different species live in the biofilm, the signals differ.

Some bacteria stop making polysaccharide so that no more cells can

join the community. The decrease in binding substance causes large

chunks to break from the biofilm, move downstream, and begin new

biofilm. (This constant biofilm buildup and breakdown causes great

fluctuations in the number of bacteria in tap water. Within a few hours tap water can go from a few dozen to a thousand bacteria per

milliliter.) Meanwhile, other bacteria ensure their own survival by

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increasing polysaccharide secretion, perhaps to suffocate nearby

microbes and reduce competition.

Pathogens likely use similar strategies in infection by turning off

polysaccharide secretion. With less polysaccharide surrounding the bacteria, the cells can reproduce rapidly. Then when pathogen numbers reach a critical level in the infected area, polysaccharide secretion returns to quash competitors.

A second type of multispecies community, the microbial mat, functions in complete harmony. Microbial mats lie on top of still waters and are evident by their mosaic of greens, reds, oranges, and purples from pigmented bacteria. Two types of photosynthetic bacteria dominate microbial mats: blue-greenish cyanobacteria and purple sulfur-using bacteria. During the day, cyanobacteria multiply and fill the mat’s upper regions with oxygen. As night falls and cyanobacteria slow their metabolism, other bacteria devour the oxygen. Purple bacteria prefer

anoxic conditions, so they live deep in the mat until the oxygen has been depleted. In the night, the purple bacteria swim upward and feast on organic wastes from the cyanobacteria. The sunlight returns, and

the purple bacteria descend to escape the photosynthesis about to replenish the upper mat with oxygen. As they digest their meal, these

bacteria expel sulfide compounds that diffuse to the top layer. There,

sulfur-requiring photosynthetic bacteria join the cyanobacteria (and some algae) in a new cycle. An undisturbed mat literally breathes: absorbing oxygen and emitting it, expelling carbon dioxide and inhaling it one breath every 24 hours. Microbial mats’ diurnal cycle makes them a distinctive microbial community.

Communities are mixtures of species within an ecosystem. Ecosystems contain living communities that interact with the nonliving things around them: air, water, soil, and so on. Bacteria participate in every phase of ecosystem life, but to learn about bacteria microbiologists must remove them from the environment and study one species at a time in a laboratory. A collection of bacterial cells all of the same species is called a population, or in lab talk a pure culture.

Microbiologists learn early in their training the tricky job of keeping all other life out of a pure culture by using aseptic technique.

Aseptic—loosely translated as “without contamination”—technique

requires that a microbiologist manipulate cultures without letting in

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allies and enemies

any unwanted bacteria. They accomplish this by briefly heating the

mouth of test tubes over a Bunsen burner flame, similarly flaming metal inoculating loops, and learning to keep sterilized equipment from touching unsterilized surfaces. Surgeons follow the same principles after they scrub up for surgery.

Under the microscope

For the two centuries following van Leeuwenhoek’s studies, microscopes improved, but microbiologists still needed a way to distinguish cells from inanimate matter in a specimen. They tested a variety of chemical dyes on bacteria with usually unsatisfactory results. In 1884, Danish physician Hans Christian Gram formulated through trial and error a stain for making bacteria visible in the tissue of patients with respiratory infection. On a glass slide, Gram’s recipe turned some of the bacteria dark purple and others pink. The new method served Gram’s purposes for diagnosing disease, but he had no notion of the

impact the Gram stain would have on bacteriology.

The Gram stain divides all bacteria into two groups: gram-positive and gram-negative. This easy procedure serves as the basis

for all identifications of bacteria from the sick, from food and water, and from the environment. Every student in beginning microbiology

commences her education by learning the Gram stain.

Bacteria with thick cell walls of peptidoglycan retain a crystal violet-iodine complex inside the wall. These cells turn purple and are

termed gram-positive. Other species cannot retain the stain-iodine complex when rinsed with alcohol. These gram-negative cells

remained colorless, so Gram added a final step by soaking the bacteria in a second stain, safranin, that turned all the colorless cells pink.