The prokaryotes comprise a diverse array of microscopic organisms. To explore their diversity, let's first consider how they are classified and some of the difficulties involved in doing so.
The nucleotide sequences of prokaryotes reveal their evolutionary relationships
Why do biologists want to classify bacteria and archaea? There are three primary motivations for classification schemes: to identify unknown organisms, to reveal evolutionary relationships, and to provide universal names (see Chapter 25). Scientists and medical technologists must be able to identify bacteria quickly and accurately—when the bacteria are pathogenic, lives may depend on it.
Until recently, taxonomists based their classification schemes for the prokaryotes on readily observable pheno-typic characters such as color, motility, nutritional requirements, antibiotic sensitivity, and reaction to the Gram stain. Although such schemes have facilitated the identification of prokaryotes, they have not provided insights into how these organisms evolved—a question of great interest to microbi-ologists and to all students of evolution. The prokaryotes and the protists (see Chapter 28) have long presented major challenges to those who attempted phylogenetic classifications. Only recently have systematists had the right tools for tackling this task.
Analyses of the nucleotide sequences of ribosomal RNA have provided us with the first apparently reliable measures of evolutionary distance among taxonomic groups. Riboso-mal RNA (rRNA) is particularly useful for evolutionary studies of living organisms for several reasons:
► rRNA is evolutionarily ancient.
► No living organism lacks rRNA.
► rRNA plays the same role in translation in all organisms.
► rRNA has evolved slowly enough that sequence similarities between groups of organisms are easily found.
Let's look at just one approach to the use of rRNA for studying evolutionary relationships.
Comparisons of rRNAs from a great many organisms revealed recognizable short base sequences that are characteristic of particular taxonomic groups. These signature sequences, approximately 6 to 14 bases long, appear at the same approximate positions in rRNAs from related groups. For example, the signature sequence AAACUUAAAG occurs about 910 bases from one end of the small subunit of ribo-somes in 100 percent of the Archaea and Eukarya tested, but in none of the Bacteria tested. Several signature sequences distinguish each of the three domains. Similarly, the major groups within the bacteria and archaea possess unique signature sequences.
These data sound promising, but things aren't as simple as we might wish. When biologists examined other genes and RNAs, contradictions began to appear and new questions arose. Analyses of different nucleotide sequences suggested different phylogenetic patterns. How could such a situation have arisen?
Lateral gene transfer muddied the phylogenetic waters
It is now clear that, from early in evolution to the present day, genes have been moving among prokaryotic species by lateral gene transfer. As we have seen, a gene from one species can become incorporated into the genome of another. Mechanisms of lateral gene transfer include transfer by plasmids and viruses and uptake of DNA by transformation. Such transfers are well documented, not just between bacterial species or ar-chaeal species, but also across the boundaries between bacteria and archaea and between prokaryotes and eukaryotes.
A gene that has been transferred will be inherited by the recipient's progeny and in time will be recognized as part of the normal genome of the descendants. Biologists are still assessing the extent of lateral gene transfer among prokaryotes and its implications for phylogeny, especially at the early stages of evolution.
Figure 27.8 is an overview of the major clades in the domains Bacteria and Archaea that we will discuss further in this chapter. This phylogeny is based on the evidence that is currently available, but keep in mind that a new picture is likely to emerge within the next decade, based on new nu-cleotide sequence data and new information about the currently understudied archaea.
Mutations are a major source of prokaryotic variation
Assuming that the prokaryote groups we are about to describe do indeed represent clades, these groups are amazingly complex. A single lineage of bacteria or archaea may contain the most extraordinarily diverse species; on the other hand, a species in one group may be phenotypically almost indistinguishable from one or many species in another group. What are the sources of these phylogenetic patterns?
Although prokaryotes can acquire new alleles by transformation, transduction, or conjugation, the most important sources of genetic variation in populations of prokaryotes are probably mutation and genetic drift (see Chapter 23). Mutations, especially recessive mutations, are slow to make their presence felt in populations of humans and other diploid organisms. In contrast, a mutation in a prokaryote, which is
Common ancestor of all of today's organisms
27.8 Two Domains:A Brief Overview This abridged summary classification of the domains Bacteria and Archaea shows their relationships to each other and to the Eukarya.The relationships among the many clades of bacteria, not all of which are listed here, are unresolved at this time.
haploid, has immediate consequences for that organism. If it is not lethal, it will be transmitted to and expressed in the organism's daughter cells—and in their daughter cells, and so on. Thus, a beneficial mutant allele spreads rapidly.
The rapid multiplication of many prokaryotes, coupled with mutation, natural selection, and genetic drift, allows rapid phenotypic changes within their populations. Important changes, such as loss of sensitivity to an antibiotic, can occur over broad geographic areas in just a few years. Think how many significant metabolic changes could have occurred over even modest time spans, let alone over the entire history of life on Earth. When we introduce the proteobac-teria, the largest group of bacteria, you will see that its different subgroups have easily and rapidly adopted and abandoned metabolic pathways under selective pressure from their environments.
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