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 (μm) end to end and is visible to the naked eye, to Francisella tularensis measuring only 0.2 μm in diameter. Since 1988, microbiologists have explored a new area involving "nanobacteria." These microbes measure 0.05 μm 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 μm in diameter and 1 to 2 μm 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 μm3. One of many advantages in being small involves the ability to sense environmental changes with an immediacy 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 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.
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 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 x 1022. The mass of these cells approaches 2 x 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.
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 (fatlike) molecules of 30 carbons or more, larger than most natural fatty compounds. These lipids and the ether bonds that connect them stabilize 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 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.
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 repeating sugars and peptides (chains of amino acids shorter than proteins and lacking the functions of proteins) occurs nowhere else in nature. 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 μm 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 mechanism. Some communities swarm, others cling to surfaces, and yet others can cover a pond's surface and control the entire pond ecosystem.