Allies and Enemies: How the World Depends on Bacteria (22 page)

Microbial ecologists continually uncover new Earth-human—

bacteria relationships. Despite the importance of good bacteria in the

environment, microbial ecology is a new science compared with food

and medical microbiology.

During the Golden Age of Microbiology, battles against disease

inspired microbiologists more than finding out what grew in a clump

of dirt. Joseph Lister introduced aseptic techniques for surgical procedures, Edward Jenner developed the smallpox vaccine, and Florence Nightingale promoted hygiene practices for preventing infection. It may have seemed as if the only good bacterium was a dead bacterium.

Late in the Golden Age, botanists Martinus Beijerinck and Sergei

Winogradsky took roads less traveled by studying the beneficial bacteria of soil and water. In the Netherlands Beijerinck studied the symbiotic relationships between plants and bacteria. Winogradsky, from Russia, explored bacterial metabolism in soil and water.

Martinus Beijerinck was born in 1851 and grew up in modest surroundings as the son of a tobacco farmer. After pursuing an education in botany and agriculture, he became head of the Netherlands’ first 121

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laboratory devoted to industrial microbiology. At this position

Beijerinck investigated contagious viruses that infected tobacco plants and nitrogen-metabolizing bacteria that live in association with legume plants.

In 1888, Beijerinck discovered bacteria living inside small lumps

or nodules on the roots of Vicia and Lathyrus (yellow pea) plants.

Beijerinck performed the difficult tasks of isolating these bacteria from the nodules and growing them in his laboratory. He took on the painstaking process of formulating a nutrient mixture to favor the root nodule bacteria while inhibiting thousands of other bacteria in soil.

This method, called enrichment medium, remains a key part of environmental microbiology. Beijerinck spent several years piecing

together the metabolism of these bacteria (later to be named to the

genus Rhizobium) and their role in nature.

Martinus Beijerinck revealed what is now known to be a critical

step in the Earth’s nitrogen cycle: Rhizobium pulls nitrogen from the air, a process called nitrogen fixation, and converts the element into a form that legume plants (peas, beans, peanuts, and alfalfa) can use.

The plant incorporates the nitrogen into proteins, nucleic acids, and

vitamins, which a diversity of animal life then takes in for nutrition.

The Rhizobium-legume union represents symbiosis in which two unrelated organisms live in close association. In this case, the type of symbiosis is termed mutualism because both organisms cooperate in giving each a benefit. The root gives the bacteria a safe haven, and

Rhizobium supplies the plant with an essential nutrient. Not all types of symbiosis are as beneficial as mutualism:

·
Commensalism
—One organism benefits and the other

receives neither a benefit nor harm.

·
Amensalism
—One organism benefits by exerting a harmful

effect on another.

·
Parasitism
—One organism living on or in a host organism benefits at the expense of the second organism’s health.

Beijerinck also studied the sulfur cycle in soil bacteria. The step

called sulfate reduction occurs in anaerobic places in soil. Beijerinck devised methods for growing fastidious sulfate-reducing bacteria, a Chapter 6 · the invisible universe

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feat that other microbiologists had believed to be too difficult or even impossible.

Winogradsky, born 5 years after Beijerinck, enjoyed a more privileged upbringing. Young Sergei found classes in Greek and Latin “not only uninteresting and unpleasant, but depressing, both physically and mentally.” As he grew older he tried law, then music, but inspired by neither he turned to the natural sciences. In 1885, Winogradsky

took a position in botany at the University of Strasbourg and began at

once to study the sulfur-using bacterium Beggiatoa, the bacterium that shuttles between sunlit and dark layers in microbial mats.

Louis Pasteur offered Winogradsky a position at his famed

research institute in Paris, but the Russian declined, preferring to return to his homeland to build the microbiology profession there.

The Great War disrupted the progress of most professions; in 1917,

wealthy families such as Winogradsky’s barely escaped death at the hands of the Bolsheviks.

Winogradsky took a position at the University of Belgrade where

no science laboratories or even a library existed, but at least it pro—

vided some stability for his family. He perused the only scientific journal he could find, Centralblatt dür Bakteriolge and thus kept abreast with bacteriology research in Europe. Few microbiologists were examining in depth the bacteria of natural environments. He plunged into studies on the organism he knew best, Beggiatoa, examining the microbe’s use of iron compounds for energy. The Institut Pasteur called again, and this time Winogradsky accepted, perhaps tempted by the well-funded and stocked laboratories in Paris.

During his career, Winogradsky would discover at least eight new

bacterial species in addition to Beggiatoa: endospore-forming Clostridium pasterianum; the gliding, cellulose-digesting Cytophaga of freshwater, estuarine, and marine habitats; and nitrogen-metabolizing Nitrosococcus, Nitrosocystis, Nitrosomonas, Nitrosospira, and Nitrobacter. The five nitrogen-utilizing bacteria differed from those studied by Beijerinck: these bacteria live free in soil and run separate steps in the nitrogen cycle from those carried out by Rhizobium.

Like Beijerinck, Winogradsky studied the sulfur bacteria and

became the first microbiologist to isolate pure cultures of sulfur-oxidizing bacteria from soil. These bacteria turn the element sulfur 124

allies and enemies

into a usable inorganic form that Beijerinck’s bacteria then convert to a molecule useful to higher organisms. A bit of a Renaissance man of microbiology, Winogradsky also became the first bacteriologist to study biofilms in aqueous habitats, and he sparked interest among microbiologists in iron-metabolizing bacteria living in deep aqueous sediments.

Winogradsky continued writing on microbial ecology into his

nineties. His daughter Helen would join him at the institute and carry

on his work on nitrogen-using bacteria after his death at age 97.

Versatility begets diversity

Communities such as biofilms and microbial mats make life easier for

their members than living alone as a single cell. But all species of bacteria spend some part of their existence free from a microbial community.

Cells break away from communities when the density grows too high.

Motile cells escape toxins by themselves or migrate toward nutrients by using flagella, cilia, or twitching movements. During the periods of growth in which cells fend for themselves separate from a microbial

community, they often meet their toughest challenges for survival.

Bacteria grown in laboratories encounter few of the discomforts

found in nature. Rich nutrient broths, incubators set at perfect temperature, and culture vessels bathed in the bacteria’s preferred gas make laboratory life plush compared with life in soil or water. In the lab, bacteria grow faster and bigger than in nature.

Out in the real world bacteria confront scant nutrients, inadequate adherence sites, toxic chemicals, and predators. But with diversity comes versatility, and bacteria have developed a multitude of tactics to ensure their survival in the environment.

In nature, bacteria wage constant competition with protozoa,

algae, plants, insects, and worms for nutrients in the soil or natural

waters. Unlike these eukaryotes, bacteria become dormant, construct

an endospore, or select an alternative metabolism to ride out tough

conditions. When nutrients are few, bacteria hold cell size to a mini—

mum; cells that in the lab grow to three or four
ì
m in diameter might reach only one to two
ì
m in nature. This downsizing reduces the amount of nutrients a cell needs, increases the number of safe hiding

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places on surfaces, and might help bacteria to go airborne and thus

move to better environments. Small size also leads to faster reproduction so that a species survives in part by producing enormous numbers of progeny.

Single bacterial cells weather the harsh conditions in their environment and rejoin a community as soon as they can. Part of community-building involves the ability to stick to surfaces. Pathogens and nonpathogenic bacteria both rely on adherence as a key part of their survival mechanism. Like pathogens, environmental bacteria use tiny

appendages called fimbrae to attach to things such as rock, soil particles, leaves, or decomposing matter. On surfaces lacking a topography good for attachment, bacteria use electrical charges to help them stick.

Bacteria have a small negative charge on their outside due to the

chemistry of the carbon and phosphorus in their proteins and acidic

portions of the cell wall. In aqueous environments where most bacteria

live, the negative cell attracts positively charged molecules. A negatively charged cell therefore travels through the environment wrapped in a positively charged suit. The minerals in rock and soil also have a positive

charge. Organic matter in nature carries a negative charge like bacteria and also attracts its own suit of positive particles. Bacteria would seem to have no chance of adhering to a surface because of all the positive-positive repulsion. But matter behaves differently at the nanoscale level than it does at visible or microscopic sizes measured in micrometers.

At certain nanometer (nm) distances, positive-positive repulsion

prevents bacteria from sticking to positively charged objects. At about 10 nm from a surface, a pebble for instance, bacteria detect a small electrical attraction to the surface, but repulsion increases as a cell comes nearer to the pebble. The amount of repulsion wavers due to additional chemical forces existent between 10 nm and 2 nm from the

surface. If the cell manages to reach within 1 nm of the pebble, the

attractive forces win out and the cell can adhere.

Not only must bacteria overcome the competing chemical forces

that occur between 10 nm and 2 nm, they also must find a site not

already occupied by other cells, settle in a spot far from microbes secreting antibiotics, and locate a place that affords nutrients, light, and air.

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allies and enemies

Evading the action of natural antibiotics takes additional guile.

Most of the natural antibiotics in use today came from soil microbes.

Soil bacteria must resist not only the naturally produced antibiotics in their environment but also synthetic antibiotics that contaminate water coming from human-populated places. Chlorine-containing pollutants, toxic metals (such as mercury, cadmium, silver, and copper), and radioactive chemicals also harm bacteria except for the relatively small number of species that have adapted to these substances. As the amount of pollutants increases in soil, the number and diversity of bacterial species decrease. Adaptations, in fact, provide bacteria with their most powerful survival mechanism. Because of their fast reproductive rate, bacteria can make vital adaptations such as antibiotic resistance part of their genetic makeup more efficiently

than any other organism.

After overcoming the travails of starvation, lack of sites to live, and toxic substances, bacteria still must deal with predation. Protozoa roam aqueous environments in nature as they do inside the rumen, engulfing and digesting bacteria. A protozoal cell gobbles 1,000 to

10,000 bacteria for each cell division. Bacteria’s greatest defense against extinction is a reproductive rate faster than that of protozoa.

The size diversity of bacteria helps, too. Larger protozoa (100 to 1,000
ì
m in length) capture larger bacteria, leaving most of the small bacteria for small protozoa (5 to 100
ì
m in length). In many other areas of nature, organisms of similar type diversify the prey they target. Wolves target elk and leave smaller prey such as jackrabbits to the coyotes. This hierarchy of prey and predators ensures the survival

of biodiversity. In the microbial world, the protozoa size-to-prey size ratio is about ten to one. On rare occasions, however, protozoa try to take in food larger than their size with deadly consequences.