7

Bacterial and Viral Genetic Systems

Humans like to think that that we rule the world, but we are clearly in a minor position compared with bacteria. Bacteria first evolved some 3.5 billion years ago, 2 billion years before the first eukaryotes appeared (some evidence suggests that bacteria evolved even earlier). Today, bacteria are found in every conceivable environment, including boiling springs, highly saline lakes, and beneath more than 2 miles of ice in Antarctica. They are found at the top of Mt. Everest and at the bottoms of the deepest oceans. They also exist on and in us—in alarming numbers! Within the average human gut, there are approximately 10 trillion bacteria, ten times the total number of cells in the entire human body. No one knows how many bacteria populate the world, but one analysis conducted by scientists in 1998 estimated that the total number of living bacteria on Earth exceeded 5 million trillion trillion (5 × 10³⁰).

Not only are bacteria numerically vast, they also constitute the majority of life’s diversity. The total number of described species of bacteria is less than 10,000, compared with about 1.4 million plants, animals, fungi, and single-celled eukaryotes. But the described species of bacteria greatly underrepresent true microbial diversity. Species of bacteria are typically described only after they have been cultivated and studied in the laboratory. Because only a few species are amenable to laboratory culture, the identification and study of most bacteria was impossible until the 1970s, when molecular techniques for analyzing DNA became available. These techniques opened up a whole new vista on microbial diversity and revealed several important facts about bacteria. First, many of the relationships among bacteria that microbiologists had worked out on the basis of physical and biochemical traits turned out to be incorrect. Bacteria once thought to be related were in fact genetically quite different. Second, molecular analysis showed that members of one group of microbes—now called the archaea—were as different from other bacteria (the eubacteria) as they are from eukaryotes. Third, molecular analysis revealed an astounding number of different types of bacteria.

In 2007, Luiz Roesch and his colleagues set out to determine exactly how many types of bacteria exist in a gram of soil. They collected soil samples from four locations: Brazil, Florida, Illinois, and Canada. From these soil samples, they collected and purified bacterial DNA. Using this DNA, they determined the sequences of a gene that is present in all bacteria, the 16S rRNA gene. Each bacterial species has a unique 16S rRNA gene sequence, so they could determine how many types of bacteria existed in each soil sample by counting the different types of DNA sequences.

178

Roesch’s results were amazing. The estimated number of different eubacterial species in each gram of soil ranged from 26,140 in Brazil to 53,533 in Canada. Many unusual bacteria were detected that appeared dissimilar to all previously described groups of bacteria. Another interesting finding was that soil from agricultural fields harbored considerably fewer species than did soil from forests.

This study and others have demonstrated that bacterial diversity far exceeds that of multicellular organisms, and undoubtedly, numerous groups of bacteria have yet to be discovered. Like it or not, we truly live in a bacterial world.

In this chapter, we will examine some of the genetic properties of bacteria and viruses and the mechanisms by which they exchange and recombine their genes. Since the 1940s, the genetic systems of bacteria and viruses have contributed to the discovery of many important concepts in genetics. The study of molecular genetics initially focused almost entirely on their genes. Today, bacteria and viruses are still essential tools for probing the nature of genes in more complex organisms, in part because they possess a number of characteristics that make them suitable for genetic studies (Table 7.1).

The genetic systems of bacteria and viruses are also studied because these organisms play important roles in human society. Bacteria are found naturally in the mouth, in the gut, and on the skin, where they are essential to human function and ecology. They have been harnessed to produce a number of economically important substances, and they have immense medical significance, causing many human diseases. In this chapter, we focus on several unique aspects of bacterial and viral genetic systems. Important processes of gene transfer and recombination will be described, and we will see how these processes can be used to map bacterial and viral genes. TRY PROBLEM 12