Introduction
In the mid-1600s, Europe’s population had been decimated by three centuries of bubonic plagues. The deadliest had been the Black Death, killing one-third of the population between 1347 and 1352. Between each epidemic European cities repopulated and rebuilt their commerce. In Amsterdam, the Dutch had ceded dominance of the seas to England but retained a central role in European finance and the trade routes. Glass, textiles, and spices moved by the ton through the Netherlands’ ports.
After apprenticing in Amsterdam, cloth merchant Antoni van Leeuwenhoek returned to his birthplace Delft to start his own business and capitalize on the growing economy. Needing a way to assess fabric quality and compete with established clothiers, van Leeuwenhoek experimented with glass lenses of various thicknesses to magnify individual threads. More than 75 years earlier, eyeglass makers Zacharias Janssen and his father, Hans, had put multiple lenses in sequence to amplify magnification and in doing so invented the first compound microscope. Van Leeuwenhoek used mainly single lenses, but he formed them with precision, enabling him to observe the microscopic world as no one had before.
Van Leeuwenhoek continued tinkering with new microscope assemblies and word spread of the clever new invention. More for hobby than for science, he studied various items from nature. Using a magnification of 200 times, van Leeuwenhoek spied tiny objects moving about in rainwater, melted snow, and the plaque sampled from teeth. He described the microscopic spheres and rods in such detail that scientists reading his notes three centuries later would recognize them. Van Leeuwenhoek called the minute creatures “animalcules” and introduced the first studies of the microscopic world. The animalcules would someday be known as bacteria, and van Leeuwenhoek would be credited with creating the science called microbiology.
Bacteria are self-sufficient packets of life, the smallest independently living creatures on Earth. Although bacteria derive clear benefits from living in communities, they do well in a free-living form called the planktonic cell. Bacteria as a group are not bound by the constraints that marry protozoa to aqueous places, algae to sunshine, and fungi to the soil.
The key to understanding microbes is to understand the cell. A cell is the simplest collection of molecules that can live. Life can be harder to define. Life has a beginning, an aging process, and an end, and during this span it involves reproduction, metabolism, and some sort of response to the environment. Biologists think of cells as the most basic unit of life in the way that an atom is the basic unit of chemistry.
Microbiology encompasses all biological things too small to be seen with the unaided eye. Mold spores, protozoa, and algae join bacteria in this world, each with attributes that would appear to give them advantages over the other microbes. Mold spores, for instance, are hardy, little spiked balls that withstand drought and frost and travel for miles on a breeze. Many bacteria do something similar by forming a thick-walled endospore that can outlast a mold spore by centuries. Protozoa meanwhile stalk their nutrition, which often comes in the form of bacteria. Why hunt a hundred different nutrients when you can swallow one bacterial cell for dinner? But bacteria roll out their own version of predation. Certain bacteria form cooperative packs that conserve energy as they roam their environment, searching for other bacteria to eat. Finally, algae appear to hold an ace because they produce their own food by absorbing solar energy and using it to power photosynthesis. But bacteria rise to the challenge here, too. Some bacteria live cheek-by-jowl with algae at the water’s surface and carry out the same photosynthesis. Other bacteria exist at greater depths and use the scarce light rays that filter through the water’s surface layer. Give bacteria the power of speech and they might say, “Anything you can do I can do better.”
Bacteria as a group live everywhere, reproduce on their own without the need for a mate, and depend on no other cells for their 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 most 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 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 achievement 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 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.