Chapter 15: Microbial Evolution, Systematics and Taxonomy Introduction

Chapter 15 (pages 608-637) focuses on the genetic diversity found within the groups of microorganisms and how the diversity is thought to have arisen. It is clear that few, if any, locations on the earth's surface are not colonized by bacteria. Changes in the genetic constitution of microbes can lead to the evolution of new types of microorganisms. Although most genetic alterations are deleterious to the microbe, some changes that confer new properties on the cell may be beneficial in specific environments. Therefore, the interaction between genetic variability and environmental selection has produced the diversity of microbes that have developed during the earth's history.

The earth is about 4.6 billion years old. At that time, the earth must have been very hot, but there is evidence that liquid water was present 3.8 billion years ago. Microbial fossils have been found in rocks less than or equal to 3.5 billion years old.

At this time, there was no O2 in the atmosphere, so the first microbes must have been anaerobes. Furthermore, the earth was hotter than at present, so they were probably thermophilic. It is thought that a variety of organic compounds, including polymers, were formed by chemical reactions driven by ultraviolet radiation and lightning discharges.

The aggregation of polymeric molecules is hypothesized to have given rise to a cell capable of metabolism and self-replication. The rich supply of organic compounds present in the environment were used for energy generation, probably by fermentation. These could also be used for biosynthesis. Subsequent mutation and selection would yield new organisms with greater biosynthetic capacities.

The evolution of porphyrins was probably a key step, because, with these, electron transport phosphorylation could occur, so that for the first time non fermentable organic compounds could be used as energy sources, via anaerobic respiration.

The next step may have been development of photosynthetic pigments, such as the chlorophylls. Using anoxygenic photosynthesis, organisms could arise which were not dependent for energy upon the organic compounds produced by chemical reactions.

The occurrence of oxygenic photosynthesis fundamentally changed the earth and its evolution. The accumulation of atmospheric O2 led to the formation of the ozone barrier to prevent intense ultraviolet radiation from reaching the earth. This meant organisms could exist over the entire surface of the earth. The presence of oxygen provided the conditions for the evolution of aerobic prokaryotes, eukaryotic cells, and subsequently the metazoans, higher animals, and plants.

For over 80% of the time during which life has existed on earth, that life consisted solely of microorganisms.

From the first cell that originated life on earth, three lines of descent were established. These are the Bacteria, Archaea, and Eukarya (See Figures 15. 7 and 15.12). Present-day eukaryotic cells are descended from the Eukarya line. The cytoplasmic organelles, mitochondria and chloroplasts, found in eukaryotic cells were derived from prokaryotic endosymbionts (an aerobic heterotroph and a phototroph, respectively) which entered cells of the nuclear line while the Eukarya were evolving. The endosymbiont supplied the eukaryote with energy, and in return received nutrients and a protected environment. With time, the endosymbiont lost the genetic capability to exist independently.

Phylogeny is the study of the evolutionary relationships among organisms. The phenotypic characteristics of microbes have provided little information on microbial phylogeny. Recently, sequence comparisons between macromolecules of homologous function in different species have permitted an analysis of evolutionary distance. The study of 16S ribosomal RNA has been exceptionally useful in this regard.

This method presumes that the longer the period of time since two organisms had a common ancestor, the greater the number of differences in sequence between a macromolecule of similar function which they both contain. The macromolecule chosen for study should be broadly distributed among organisms, have the same function in each, and not evolve so rapidly that similarities between distantly related organisms cannot be recognized.

Ribosomal RNA molecules are extremely well suited for this type of analysis. In addition to their universal distribution and constant function, they are easily purified from cells and can now be easily sequenced, using DNA primers to highly conserved sequences and the enzyme reverse transcriptase. Furthermore, some regions of the molecule have evolved rapidly while others have changed more slowly; this permits evolutionary distances to be calculated between both closely and distantly related species.

Phylogenetic trees are constructed from 16S RNA sequences by computer analysis of the sequence differences between each pair of organisms for which data exist. The computer algorithm arranges the organisms on a branching tree, spaced in a way to provide the best fit to all of the pair-wise sequence comparisons.

The 16S RNA sequences have allowed analysts to identify signature sequences that are unique to particular groups of organisms. In the future, as more are identified, these sequences may become useful for identifying unknown organisms.

The analysis of microbial phylogeny derived from ribosomal RNA sequences has led to many interesting insights. These include the following. (1) There are two lines of prokaryotic cells, the Bacteria and Archaea, which are no more closely related to each other than they are to the Eukarya line. (2) Different lineages have evolved at different rates; for example, the Archaea have evolved relatively slowly and the eukaryotic line has evolved rapidly. (3) Eukaryotic mitochondria and chloroplasts arose from endosymbiotic bacteria.

Bacteria can be divided into twelve groups that have been defined on the basis of ribosomal RNA analysis (rRNA). Most groups (similar to phylums) contain a variety of physiological and morphological types of bacteria. This reinforces the idea that phenotypic characteristics are inadequate to define evolutionary relationships between microbial species.

There are three groups of Archaea, two of which contain methanogens, while another contains sulfur-dependent organisms. This last group is composed of extreme thermophiles that require elemental sulfur for optimal growth. For most members, the sulfur serves as an electron acceptor in anaerobic respiration. Evolution of the eukaryotic line was characterized by periods of rapid evolution interspersed with eras of slow evolution. The accumulation of O2 in the atmosphere about 1.5 billion years ago seems to correspond to a period of rapid evolution.

Differences among the primary kingdoms: The cell walls of Bacteria contain peptidoglycan. Most Archaea have glycoprotein in their cell walls. Eukaryotic cell walls (when present) have neither of these compounds but may contain cellulose or chitin.

The lipids of Archaea are unique in that they are ether-linked molecules, whereas in Bacteria and eukaryotes there are ester links between glycerol and the fatty acids.

The types and subunit complexity of RNA polymerase differ among organisms in the three kingdoms. Bacteria have a single RNA polymerase that consists of four different subunits. Archaea have at least two types of RNA polymerase, and these enzymes contain 8-10 polypeptides. Eukaryotic cells contain at least three different polymerases; the most prevalent type contains 10-12 polypeptides.

Protein synthesis in Bacteria and Archaea occurs on 70S ribosomes, whereas eukaryotic ribosomes are larger. Formylmethionine is always the first amino acid incorporated into Bacterial proteins; in eukaryotes and Archaea, an unmodified methionine is inserted by the initiator tRNA. Inhibitors of Bacterial protein synthesis generally do not affect the process in organisms from the other two kingdoms. Conversely, diphtheria toxin inhibits protein synthesis in all organisms except Bacteria.

Bacterial taxonomy relies on phenotypic characteristics to classify organisms, and is useful for the practical identification of unknown strains. The primary taxonomic unit is the species, which is defined by the phenotypic characteristics of a collection of similar strains. Culture collections contain type strains to serve as standards of the characteristics attributed to a particular species.

In conventional taxonomy, some characteristics are given special emphasis. These include the Gram stain, cell morphology, and the presence of cell structures such as endospores. In numerical taxonomy, all phenotypic characteristics are given equal weight in classifying strains.

Bergey's Manual of Systematic Bacteriology contains the phenotypic characteristics used to classify bacteria by conventional taxonomy, and keys that can be used to identify unknown strains from their phenotypic characters.

Some analyses of nucleic acids have been used in conventional taxonomy. These include measurements of DNA base composition and nucleic acid hybridization.

DNA base composition can only prove that organisms are unrelated. The ratio of bases in DNA can vary over a wide range. If two organisms have different DNA base compositions, they are not related. However, organisms with identical base ratios are not necessarily related, because the nucleotide sequences in the two organisms could be completely different.

Hybridization between the total DNA of two organisms is useful for detecting relationships between closely related organisms. Different genera rarely exhibit any DNA sequence homology. Strains of the same species should have homology values above 60-70 percent.

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