Allies and Enemies: How the World Depends on Bacteria (5 page)

Prior to the new rRNA classifications, biology students had been taught five-, six-, and even eight-kingdom classifications for organiz—ing all plants, animals, and microbes. When I took my first biology classes, the five-kingdom system being taught looked like this: · Monera, containing the bacteria

· Protista, containing protozoa and algae

· Plantae, containing green plants descended from algae

· Fungi descended from specific members of the Protista

· Animalia descended from specific members of the Protista

Bacteria

Archaea

Eukarya

Animals

Entoamoebae Slime

molds

Diatoms

Fungi

Chloroflexus

Methanothermus Halophiles

Plants

Methanococcus

Ciliates

Purple bacteria

Thermoproteus

Chloroplast

Pyrodictium Thermococcus

Flagellates

Cyanobacteria

Flavobacteria

Trichonomads

Thermotogales

Microsporidia

Aquifex

Diplomonads

Common Ancestor

Figure 1.4 The three domains. Classification of the world’s organisms does not remain static; new technologies constantly force taxonomists to reevaluate and reclassify species.

chapter 1 · why the world needs bacteria

23

New technologies for classifying organisms have yet to end confusion that ensues when attempting to organize the world’s biota, and for good reason. Taxonomists and philosophers have been trying to figure out organisms’ relationships to each other since Aristotle’s first attempts. Additionally, since the emergence of DNA analysis in the 1970s, geneticists have discovered more diversity in biota but also a

dizzying amount of shared genes, especially among bacteria. The rRNA analysis introduced by Woese showed the degree to which different species shared genes. The studies revealed a significant amount of horizontal gene transfer, which is the appearance of common genes across many unrelated species.

The evolutionary tree we all learned in which families, genera, and species branched from a major trunk does not depict horizontal

gene transfer. The evolutionary tree may look more like a bird’s nest

than an oak. Nowhere may that be truer than in the bacteria. Gene

sharing or gene transfer is now known to take place in bacteria, and

possibly archaea, more than ever before imagined. In 2002, the 16S rRNA system became further refined by focusing on certain pro—

tein-associated genes. But as biologists dig deeper into the genetic makeup of bacteria, they find more shared genes. Some microbiologists have begun to think that the term “species” makes no sense when speaking about bacteria. Currently, if two different strains of bacteria have less than 97 percent identical genes determined by 16S rRNA analysis, then they can be considered two different species. Some microbiologists suggest that only a 1 percent difference

in genes differentiates species, not 3 percent.

When microbiologists first developed the bacterial groups known

today as species, they let common characteristics of bacteria guide them. Gram reaction, nutrient requirements, unique enzymes, or

motility served as features for putting bacteria into various species.

Modern nucleic acid analysis has shown whether the traditional classification system still makes sense. With a high percentage of shared genes among bacteria and the ease with which diverse cells transfer

genes around, some microbiologists have suggested that classifying bacteria by species is futile. It seems as if all bacteria belong to one mega-species, and different strains within this species differ by the genes they express and the genes they repress. By classifying bacteria

24

allies and enemies

into a single species, all bacteria would obey the definition for a species first proposed by Ernst Mayr in 1942: Members of the same species interbreed and members of different species do not.

Genetic analysis has blurred the lines between bacterial species

so that the criteria used to classify other living things cannot apply to bacteria. To preserve their sanity, microbiologists need some sort of taxonomic organization so that they can speak the same language when discussing microbes. The traditional methods of grouping bacteria according to similar characteristics have turned out to be the handiest method regardless of DNA results. Microbiologists use the same classification and naming system for bacteria as used for all other life. The system has changed little since botanists in the mid—1800s, Carl Linnaeus being the most famous, developed it. Species

classification and naming uses binomial nomenclature to identify every species by a unique two-part Latin name.

Bacteria of the same genus share certain genes, quite a few as mentioned, but different species have a few unique genes. For example, Bacillus is the genus name of a common soil bacterium. The genus contains several different species: Bacillus subtilis (shortened to B. subtilis), B. anthracis, B. megaterium, and so on. If I were a bacterium, my name would be Maczulak anne or M. anne.

To name a new bacterium, microbiologists have several conventions at their disposal. All that matters is that the new name be different from all other names in biology. Table 1.1 shows common naming conventions.

Table 1.1 Origins of bacteria names

Naming Method

Example

Reason for the Name

A historic event

Legionella

Cause of a new disease that occurred

pneumophila

at a Legionnaires convention in 1976

Color

Cyanobacterium

Blue-green color

Cell shape and

Streptococcus

Long, twisting chains (strepto-) of

arrangement

pyogenes

spherical (-coccus) cells

Place of discovery

Thiomargarita

Found off the coast of Namibia

namibiensis

Discoverer

Escherichia coli

Discovered by Theodor Escherich

in 1885

chapter 1 · why the world needs bacteria

25

Table 1.1 Origins of bacteria names

Naming Method

Example

Reason for the Name

In honor of a famous Pasteurella

Genus named for Louis Pasteur

microbiologist

multocida

Unique feature

Magnetospirillum

Spiral-shaped bacteria with magnet—

magnetotacticum

containing magnetosomes inside

their cells

Extreme growing

Thermus aquaticus

Grows in very hot waters such as hot

conditions

springs

Bacterial names will likely never be replaced regardless of scientific advances in classifying and reclassifying the species. Medicine, environmental science, food quality, manufacturing, and biotechnology depend on knowing the identity of a species that causes disease or contamination or makes a useful product. As microbiology fine-tunes

its focus from the biosphere to the human body, species identity becomes more important.

The bacteria of the human body

Ten trillion cells make up the human body, but more than ten times

that many bacteria inhabit the skin, respiratory tract, mouth, and intestines. Microbiologists are fond of pointing out that if all of a person’s DNA were mixed with the body’s entire bacterial DNA, that person would be genetically more bacterial than human.

About 1,000 different species belonging to 200 genera live on the

body rather than in it. An animal’s body is a tube. The skin comprises

the tube’s outer surface, and the gastrointestinal tract from mouth to

anus makes up the inner surface. The body’s interior of blood, lymph,

and organs normally contain no bacteria; these places are sterile.

Urine and sweat exit the body as sterile fluids. In plants by contrast, bacteria live on but also inside the plant body.

The skin holds habitats that vary in moisture, oils, salts, and aeration. The scalp, face, chest and back, limbs, underarms, genitals, and feet make up the skin’s main habitats, and each of these contains smaller, distinct living spaces. The entire skin surface has about one million bacteria on each square centimeter (cm2) distributed unevenly

26

allies and enemies

among the habitats; the dry forearms contain about 1,000 bacteria per

cm2, and the underarms have many millions per cm2.

Microbiologists sample skin bacteria by pressing a cylinder about

the size of a shot glass open at both ends against the skin to form a

cup, and then pouring in a small volume of water. By agitating the

liquid and gently scraping the skin with a sterile plastic stick the microbiologist dislodges many of the bacteria. But no method or the strongest antiseptics remove all bacteria from the skin: The skin is not sterile. Staphylococcus, Propionibacterium, Bacillus, Streptococcus, Corynebacterium, Neisseria, and Pseudomonas dominate the skin flora.

Figure 1.5 Staphylococcus aureus. A common and usually harmless inhabitant of skin, S. aureus can turn dangerous given the opportunity. This species can infect injuries to the skin, and the MRSA strain has become a significant antibiotic-resistant health risk. (Courtesy of BioVir Laboratories, Inc.) Some of these names are familiar because they also cause illness, and yet a person’s normal bacteria pose no problem on healthy, unbroken skin. The native flora in fact keep in check a variety of

chapter 1 · why the world needs bacteria

27

transient bacteria collected over the course of a day. Some of these

transients might be pathogenic, but they do not settle permanently on

the skin because the natives set up squatters’ rights by dominating space and nutrients, and producing compounds—antibiotics and similar compounds called bacteriocins—that ward off intruders. Such silent battles occur continually and without a person’s knowledge.

Only when the protective barrier breaks due to a cut, scrape, or burn

does infection gain an upper hand. Even harmless native flora can turn into opportunists and cause infection because conditions change in the body. Immune systems weakened by chemotherapy, organ

transplant, or chronic disease increase the risk of these opportunistic infections:

·
Staphylococcus
—Wound infection

·
Propionibacterium
—Acne

·
Bacillus
—Foodborne illness

·
Streptococcus
—Sore throat

·
Corynebacterium
—Endocarditis

·
Pseudomonas
—Burn infection

Anaerobic bacteria do not survive in the presence of oxygen, but

they make up a large proportion of skin flora. Though the skin receives a constant bathing of air, anaerobes thrive in miniscule places called microhabitats where oxygen is scarce. Chapped and flakey skin and minor cuts create anaerobic microhabitats. Necrotic tissue associated with major wounds also attracts anaerobes, explain—ing why gangrene (caused by the anaerobe Clostridium perfringens) and tetanus ( C. tetani) can develop in improperly tended injuries. Of normal anaerobes inhabiting the skin, Propionibacterium acnes (the cause of skin acne), Corynebacterium, Peptostreptococcus, Bacteroides, and additional Clostridium dominate.