Prescott's Principles of Microbiology PDF

wiL75233_fm_i-xiv.indd Page i 11/28/07 10:28:45 AM epg /Volumes/ve401/MHIY034/mhwiL1%0/wiL1fm Prescott’s Principles of MICROBIOLOGY...

wiL75233_fm_i-xiv.indd Page i 11/28/07 10:28:45 AM epg /Volumes/ve401/MHIY034/mhwiL1%0/wiL1fm Prescott’s Principles of MICROBIOLOGY Joanne M. Willey Hofstra University Linda M. Sherwood Montana State University Christopher J. Woolverton Kent State University wiL75233_ch17_381-404.indd Page 381 11/21/07 5:34:49 PM luxminarayan /Volumes/ve401/MHIY034/mhwiL1%0/wiL1ch17 Microbial Evolution, 17 Taxonomy, and Diversity Chapter Glossary oligonucleotide signature sequences Short, conserved nucleotide sequences that are specific for a phylogenetically defined group of organisms. phenetic system A classification system that groups organ- isms together based on the similarity of their observable characteristics. phylogenetic or phyletic classification systems A classifi- cation system based on evolutionary relationships rather than the general similarity of characteristics. phylogenetic tree A graph made of nodes and branches, much like a tree in shape, that shows phylogenetic and evolutionary relationships between groups of organisms. polyphasic taxonomy An approach in which taxonomic The stromatolites shown here are layered rocks formed by incorpora- schemes are developed using a wide range of phenotypic tion of minerals into microbial mats. Fossilized stromatolites indicate and genotypic information. that microorganisms existed early in Earth’s history. RNA world The hypothesis that the first replicating entity was endosymbiotic hypothesis The hypothesis that mitochondria an RNA molecule. and chloroplasts arose when bacteria established an endo- strain Microbes that are descendants of a single, pure micro- symbiotic relationship with ancestral cells and then evolved bial culture. A single species may have many strains. into organelles. systematics The scientific study of organisms with the G ⴙ C content The percent of an organism’s genome that ultimate objective of characterizing and arranging them consists of guanine and cytosine (G ⫹ C); a parameter that is in an orderly manner; often considered synonymous with used in taxonomic analysis. taxonomy. genotypic classification The use of genetic data to construct taxon A group into which related organisms are classified. a classification scheme for the identification of an unknown taxonomy The science of biological classification; it con- species or the phylogeny of a group of microbes. sists of three parts: classification, nomenclature, and melting temperature (Tm) The temperature at which double- identification. stranded DNA becomes single stranded; determined by the universal phylogenetic tree A phylogenetic tree that G ⫹ C content of the genome. considers the evolutionary relationships among organisms natural classification A classification system that arranges from all three domains of life: Bacteria, Archaea, and organisms into groups whose members share many charac- Eucarya. teristics. What’s in a name? That which we call a rose by any other name would smell as sweet.... —W. Shakespeare Perhaps the most fascinating aspect of the microbial world is its ex- of microbial evolution and taxonomy. This is followed by a five-chapter traordinary diversity. It seems that almost every possible shape, size, (18–22) survey of the most important procaryotic groups. Our survey of physiology, and life-style can be found. In this section of the text, we fo- microbial diversity then moves to an introduction of eucaryotic microor- cus on microbial diversity. Chapter 17 introduces the general principles ganisms and finally that of viruses (chapters 23 and 24, respectively). 381 wiL75233_ch17_381-404.indd Page 382 11/5/07 12:26:52 PM epg /Volumes/ve401/MHIY034/mhwiL1%0/wiL1ch17 382 Chapter 17 Microbial Evolution, Taxonomy, and Diversity possible solution to this problem was suggested in 1981 when 17.1 MICROBIAL EVOLUTION Thomas Cech discovered self-splicing RNA in the protist Biological diversity is usually thought of in terms of plants and Tetrahymena. Three years later, Sidney Altman found that animals; yet the variety of microbial life forms is huge and largely RNaseP in Escherichia coli is an RNA molecule that cleaves unexplored. Consider the metabolic diversity of microorganisms— phosphodiester bonds. RNA molecules that possess catalytic this alone suggests that the number of habitats occupied by activity are called ribozymes, and to some, the ability of RNA microbes vastly exceeds that of all larger organisms. How has to catalyze biochemical reactions suggests a precellular “RNA microbial life been able to radiate to such an astonishing level of world,” a term coined by Walter Gilbert in 1986. This hypoth- diversity? To answer this question, one must consider microbial esis posits that the first self-replicating molecule was RNA, evolution. The field of microbial evolution, like any other scien- which is capable of storing, copying, and expressing genetic tific endeavor, is based on the formulation of hypotheses, the information, and possesses enzymatic activity as well. In this gathering and analysis of data, and the reformation of hypotheses version of early life, various forms of molecules were assem- based on newly acquired evidence. That is to say, the study of bled and destroyed over roughly half a billion years, until microbial evolution is based on the scientific method. To be sure, ultimately an entity, or probiont, something like modern RNA it is sometimes more difficult to amass evidence when consider- enclosed in a lipid vesicle was generated (figure 17.2). ing events that occurred millions, and often billions, of years ago, > The Proteobacteria somes of the protist Trichomonas vaginalis; and (3) the primitive (chapter 20) genome found in the hydrogenosomes of the protist Nyctotherus ovalis encodes components of a mitochondrial electron trans- port chain. Taken together, these data suggest that mitochondria The Endosymbiotic Origin of and hydrogenosomes are aerobic and anaerobic versions of the same ancestral organelle. Mitochondria and Chloroplasts Finally, the endosymbiotic theory put forth by Lynn In contrast to the unresolved origin of the nucleus, the endo- Margulis and her colleagues combines elements of the endo- symbiotic hypothesis is generally accepted as the origin of symbiotic origin of mitochondria with the genome fusion mitochondria and chloroplasts. That endosymbiosis was respon- hypothesis. The serial endosymbiotic theory (SET) calls for sible for the development of these organelles (regardless of the the development of eucaryotes in a series of discrete endo- exact mechanism) is supported by the fact that both organelles symbiotic steps. This theory suggests that motility evolved have bacterial-like ribosomes and most have a single, circular first through endosymbiosis between anaerobic spirochetes chromosome. Indeed, inspection of figure 17.4 shows that mito- and another anaerobe. Next, nuclei are thought to have formed chondria and chloroplasts belong to the bacterial lineage. by the development of internal membranes. These early nucle- Important evidence for the origin of mitochondria comes from ated forms would have been similar to modern protists with the genome sequence of the -proteobacterium Rickettsia hydrogenosomes. The endosymbiotic events needed for the wiL75233_ch17_381-404.indd Page 388 11/5/07 12:27:06 PM epg /Volumes/ve401/MHIY034/mhwiL1%0/wiL1ch17 388 Chapter 17 Microbial Evolution, Taxonomy, and Diversity Archaeon Bacterium Archaeon Smaller bacterium DNA 1. A symbiotic association occurred between two procaryotic species. The two cells fused with DNA each other to make a 1. A larger archaeal cell single cell. engulfed a smaller bacterial cell and established an endosymbiotic relationship. 2. Over time, archaeal genes involved with metabolism and lipid biosynthesis were lost. Bacterial genes involved 2. Genes from with transcription and endosymbiont were translation were also transferred to host cell. lost. 3. This event may have 3. Endosymbiosis of a resulted in bacterium resulted in mitochondria, or the formation of mitochondria may have mitochondria. The arisen via a second endomembrane system endosymbiotic event. created the nucleus and The endomembrane other organelles such as system created the the ER and Golgi. nucleus and other organelles such as the ER and Golgi. 4. A second endosymbiosis event involving cyanobacteria resulted 4. A subsequent in chloroplasts. endosymbiosis event involving cyanobacteria resulted in chloroplasts. Eucaryotic cells: Eucaryotic cells: Eucaryotic cells: Eucaryotic cells: Animals, fungi, and some protists Plants and algae Plants and algae Animals, fungi, and some protists (a) Origin from symbiotic relationship (b) Origin from endosymbiotic relationship Figure 17.5 The Genome Fusion Hypothesis for the Origin of Eucaryotic Cells. Evolutionary Processes evolution of mitochondria are thought to have occurred later, giving rise to early fungi and animal cells, with subsequent Clearly figure 17.4 demonstrates the astounding level of microbial endosymbiotic events leading to the development of chloro- diversity reflecting hundreds of millions of years of evolution. The plasts and plants. application of Darwin’s theory of natural selection to microbial wiL75233_ch17_381-404.indd Page 389 11/5/07 12:27:09 PM epg /Volumes/ve401/MHIY034/mhwiL1%0/wiL1ch17 17.2 Introduction to Microbial Classification and Taxonomy 389 evolution requires special consideration. Anagenesis, also known as microevolution, refers to small, random genetic changes that 17.2 INTRODUCTION occur over generations to slowly drive either speciation or extinc- TO MICROBIAL tion, both of which are forms of macroevolution. Neither CLASSIFICATION microevolution nor macroevolution occur at a constant rate. Instead, the fossil record shows that the slow and steady pace of AND TAXONOMY evolution is periodically interrupted by rapid bursts of speciation Microbiologists are faced with the daunting task of understand- driven by abrupt changes in the environment. This phenomenon is ing the diversity of life forms that cannot be seen with the naked called punctuated equilibria and was introduced by Niles eye but can live seemingly anywhere on Earth. One of the first Eldredge and Steven Jay Gould. The theory of punctuated equilib- tools needed to survey this level of diversity is a reliable clas- ria is one important reason why evolutionary distance, as measured sification system. Taxonomy (Greek taxis, arrangement or by the similarity of genes in living organisms, provides little or no order, and nomos, law, or nemein, to distribute or govern) is information regarding when evolutionary divergence occurred. defined as the science of biological classification. In a broader Procaryotic evolution results in the generation of microbial sense, it consists of three separate but interrelated parts: classi- diversity upon which selective processes determine the devel- fication, nomenclature, and identification. Once a classification opment of new species. Recall that genetic diversity in the scheme is selected, it is used to arrange organisms into groups Archaea and the Bacteria must occur asexually. Thus heritable called taxa (s., taxon) based on mutual similarity. Nomenclature genetic changes in these organisms are introduced principally is the branch of taxonomy concerned with the assignment of by two mechanisms: mutation and horizontal (lateral) gene names to taxonomic groups in agreement with published rules. transfer (HGT). Genome sequencing has revealed that HGT, Identification is the practical side of taxonomy—the process of particularly in the form of transposon- and phage-mediated determining if a particular isolate belongs to a recognized taxon gene transfer (transduction), appears to be more important and, if so, which one. The term systematics is often used for than once thought. In addition, model studies designed to taxonomy. However, many taxonomists define systematics in assess competition between microbial populations has led to more general terms as the scientific study of organisms with the some surprising observations. It had been thought that very ultimate object of characterizing and arranging them in an small genetic differences between microbial populations of the orderly manner. Any study of the nature of organisms, when the same species were of little evolutionary significance. However, knowledge gained is used in taxonomy, is a part of systematics. laboratory experiments demonstrate that when selection is Thus systematics encompasses disciplines such as morphology, applied, very small genetic differences can result in one popu- ecology, epidemiology, biochemistry, molecular biology, and lation overtaking another. These recent analyses help illuminate physiology. the potential mechanisms by which the vast level of microbial One of the oldest classification systems, called natural diversity came about and will help guide future studies. classification, arranges organisms into groups whose members