From Germ tom Genome: WhatIs a Microbe?

From early childhood, we hear that we are surrounded by microscopic organisms, or "germs," that we can not see. What are microbes? Our modern concept of a microbe has deepened through two major research tools: advanced microscopy and the sequencing of gnomic DNA. Microscopy is covered in Chapter 2, and microbial genetics and genomics are presented in Chapters 7-12.

A Microbe Is a Microscopic Organism

A microbe is commonly defined as a living organism that requires a microscope to be seen. Microbial cells range in size from millimeters (mm) down to 0.2 micrometer (pm),

and viruses may be tenfold smaller (Table 1.1). Some microbes consist of a single cell, the smallest unit of life, a membrane-enclosed compartment of water solution containing molecules that carry out metabolism. Each microbe contains in its genome the capacity to reproduce its own kind. Our simple definition of a microbe, however, leaves us with contradictions.

■ Super-size microbial cells. Most single-celled organisms require a microscope to render them visible and thus fit the definition of a microbe. Nevertheless, some species of protists and algae, and even some bacterial cells, are large enough to see with the naked eye. The marine sulfur bacterium Thiomargarita namibiensis, called the sulfur pearl of Namibia, grows as large as the head of a fruit fly (Fig.1.4). Even more surprising, a single-celled plant, the "killer alga" Caulerpa taxifolia, spreads through the coastal waters of California. The single cell covers many acres with its leaflike cell parts.

 ■ Microbial communities. Many microbes form complex multi cellular assemblages, such as mushrooms, kelp's, and boffins. In these structures, cells are differentiated into distinct types that complement each others function, as in multi cellular organisms. And yet, some multi cellular worms and arthropods
require a microscope to see but are not considered microbes.

 ■ Viruses. A virus consists of a non cellular particle containing genetic material that takes over the metabolism of a cell to generate more virus particles. Some viruses consist of only a few molecular parts, whereas others, such as the Mimi virus infecting amebas (also spelled "amoebae"), show the size and complexity of a cell. Although viruses are not fully functional cells, the Mimi virus genome shows that it evolved from a cell.

In practice, our definition of a microbe derives from tradition as well as genetic considerations. In this book, we consider microbes to include prokaryotes (cells lacking a nucleus, including bacteria and archaea) as well as certain classes of eukaryotes (cells with a nucleus) that include simple multi cellular forms: algae, fungi, and protists (Fig. 1.5). The bacteria, archaea, and eukaryotes known as the three domains diverged from a common ancestral cell. We also discuss viruses and related infectious particles (Chapters 6 and 11).

ORIGIN AND DISCOVERY

Life on Earth began early in our planet's history with microscopic organisms, or microbes. Microbial life has since shaped our atmosphere, our geology, and the energy cycles of all ecosystems. A human body contains ten times as many microbes as it does human cells, including numerous tiny bacteria on the skin and in the digestive tract. Throughout history, humans have had a hidden partnership with microbes ranging from food production and preservation to mining for precious minerals. Yet throughout most of our history, humans were unaware that microbes even existed. To study these unseen organisms required a microscope, first developed in the 1600s. In the nineteenth century the "golden age" of microbiology microscopes revealed the tiny organisms at work in our bodies and in our ecosystems. The twentieth century saw the rise of microbes as the engines of biotechnology. Microbial discoveries led to recombinant DNA and revealed the secrets of the first sequenced genomes.         In 2008, the Phoenix Mars lander arrived at the north pole of the planet Mars (Fig. 1.1). The lander carried scientific instruments to study the history of water in Martian soil and search for evidence of microbial life. Its robotic instruments tested the soil for life-supporting elements such as carbon, nitrogen, phosphorus, and hydrogen. The discovery of surface water in the form of frost supported the possible existence of living microbes. Why do we care whether microbes exist on Mars? The discovery of life beyond Earth would fundamentally change how we see our place in the universe. The observation of Martian life could yield clues as to the origin of our own biosphere and expand our knowledge of the capabilities of living cells on our own planet. As of this writing, the existence of microbial life on Mars remains unknown, but here on Earth, many terrestrial microbes remain as mysterious as Mars. Barely 0.1% of the microbes in our biosphere can be cultured in the laboratory; even the digestive tract of a newborn infant contains species of bacteria unknown to science. Our "exploration rovers" for microbiology include, for example, new tools of microscopy and the sequencing of microbial DNA. On Earth, the microscope reveals microbes through out our biosphere, from the super heated black smoker vents at the ocean floor to the subzero ice fields of Antarctica. Bacteria such as Escherichia coli live in our intestinal tract, while algae and cyanobacteria turn ponds green (Fig. 1.2). Protists are the predators of the microscopic world. And viruses such as influenza virus cause disease, as do many bacteria and protists. Yet before microscopes were developed in the seventeenth century, we humans were unaware of the unseen living organisms that surround us, that float in the air we breathe and the water we drink, and that inhabit our own bodies. Microbes generate the very air we breathe, including nitrogen gas and much of the oxygen and carbon dioxide. They fix nitrogen for plants, and they make vitamins, such as vitamin B12. In the ocean, microbes produce biomass for the food web that feeds the fish we eat; and microbes consume toxic wastes such as oil from the Deepwater Horizon spill in 2010. At the same time, virulent pathogens take our lives. Despite all the advances of modern medicine and public health, microbial disease remains the number one cause of human mortality. history of fresh news on ORIGIN AND DISCOVERY In the twentieth century, the science of microbiology exploded with discoveries, creating entire new fields such as genetic engineering. The promise and pitfalls were dramatized by Michael Crichton's best selling science fiction novel and film The Andromeda Strain (1969; filmed in 1971). In The Andromeda Strain, scientists at a top-secret laboratory race to identify a deadly pathogen from outer space or perhaps from a biowarfare lab (Fig. 13A). The film prophetically depicts the computerization of medical research, as well as the emergence of pathogens, such as the human immunodeficiency virus (HIV), that can yet defeat the efforts of advanced science.
       Today, we discover surprising new kinds of microbes deep underground and in places previously thought uninhabitable, such as the hot springs of Yellowstone National Park (Fig. 1.3B). These microbes shape our biosphere and provide new tools that impact human society. For example, the use of heat-stable bacterial DNA polymerase (a DNA-replicating enzyme) in a technique called the polymerase chain reaction (PCR) allows us to detect minute amounts of DNA in traces of blood or fossil bone. Microbial technologies led us from the discovery of the double helix to the sequence of the human genome, the total genetic information that defines our species. In Chapter 1, we introduce the concept of a microbe and the question of how microbial life originated. We then survey the history of human discovery of the role microbes play in disease and in our ecosystems. Finally, we address the exciting century of molecular microbiology, in which microbial genetics and genomics have transformed the face of modern biology and medicine.