52 Chapter 2 diversity of the microbial world
FIG. 2-10 Brown rot of an apricot.
fortunately many are also plant pathogens, causing great losses of agricultural crops. We sometimes use chemical fungicides to protect many cultivated plants (FIG. 2-10). A few also cause human diseases such as athlete's foot, histoplasmosis, coccidioidomycosis, and yeast (Candida) infections.
The classification of fungi is based primarily on their sexual reproductive spores (FIG. 2-11). Some sexual spores of fungi are formed within a specialized structure known as the ascus. Such spores are called ascospores and the fungi that produce them are called ascomycetes. Another major group of fungi, the ba-sidiomycetes, produce sexual spores on a specialized structure known as the basidium. A mushroom is such a basidium. The spores produced by basidomycetes are called basidiospores. Other fungi, known as the deuteromycetes or fungi imperfecti, have no known sexual reproductive phase. As far as we know, they are restricted to asexual means of reproduction. The fungi imperfecti include Penicillium and Aspergillus, two of the more common fungi that we may observe growing on foods such as bread.
Fungi are composed of eukaryotic cells, may be unicellular or multicellular, often form filaments, usually have cell walls, and typically form reproductive spores.
Fungi are classified primarily based on their sexual means of reproduction.
To distinguish among species of yeasts, we employ a few morphological (structural) observations and numerous metabolic characteristics. The procedure for identifying the unicellular yeasts is very similar to that employed for identifying bacteria. For the filamentous fungi, on the other hand, we rely almost entirely on morphological observations. We use the same basic approach used in identifying plants. Mushroom-producing fungi, for example, are identified based on visual appearance (FIG. 2-12). Great
FIG. 2-11 The classification of fungi is based largely on spore formation. Various types of spores and fruiting bodies are formed by different fungi. Basidomycetes form spores on basidia; ascomycetes form spores within asci; fungi imperfecti do not form sexual reproductive spores.
FIG. 2-12 The ink cap mushroom Coprinus atrameutarius.
care should be taken in identifying mushrooms. Some mushrooms are edible but others that may look quite similar are deadly poisonous. Even experts have sometimes been fooled and have died after eating mushrooms that they improperly identified.
SURVEY OF MICROORGANISMS 53
Algae
Algae are eukaryotic photosynthetic microorganisms that contain chlorophyll and utilize light energy to generate their chemical energy They are the only eukaryotic photosynthetic microorganisms. As such, they are the microorganisms most closely related to the plants. They also are able to produce oxygen (02) from water. Many of the characteristics used in the classification of algae have been adapted from botanists. These characteristics tend to be those that can be observed. They are generally not metabolic characteristics that must be experimentally determined. The major groups of algae are identified by their characteristic colored pigments and cell morphologies. The major groups of algae include the green algae, euglenoids, golden and yellow-green
algae, cryptomonads, and dinoflagellates.
The diatoms are unicellular algae that have cell walls containing silicon. They are quite beautiful when seen through the microscope (FIG. 2-13). The euglenoid algae, dinoflagellates, and many green algae are also unicellular. Some green algae are multicellular but do not form structures nearly as complex as the brown and red algae. As examples, the green alga Volvox forms a multicellular colonial aggregation of cells and the green alga Spirogyra produces a multicellular filament (FIG. 2-14).
Algae are photosynthetic eukaryotic microorganisms.
Most algae are nonpathogens.
54 С H A P T E R 2 DIVERSITY OF THE MICROBIAL WORLD
Some organisms that have traditionally been classified as algae, namely the red and brown algae, produce complex macroscopic multicellular structures. The kelps, for example, are brown algae that often reach lengths of 50 meters. Kelps have holdfasts, which are rootlike structures that make them plantlike. They are clearly not microorganisms and have been appropriately reclassified as plants instead of algae.
Protozoa
The protozoa for the most part are unicellular, non-photosynthetic eukaryotic organisms. They generally lack a cell wall. Many of the protozoa are motile, meaning they are able to move. Since at one time all organisms that moved were considered animals, protozoa have been studied largely by zoologists. The protozoa have heterotrophic metabolism, meaning that they obtain cellular energy from organic substances such as proteins. Protozoa tend to engulf their food sources, a characteristic that makes them similar to higher animals. Many of the characteristics used in classifying protozoa are analogous to the morphological characteristics used in describing animals.
Protozoa are eukaryotic heterotrophic microorganisms that are classified on the basis of morphological characteristics, especially their means of locomotion.
Motility is a major characteristic traditionally used in classifying protozoa. It is still very important in the latest classification system proposed in 1980. Some protozoa, the Sarcodina, form extensions of their cells known as pseudopodia, or false feet (FIG. 2-15). By forming pseudopodia, these protozoa move from
place to place increasing their chances of encountering food. This group includes the genus Amoeba. Amoeba is an amorphous organism that moves and engulfs food particles by extending its cytoplasm. Unlike the Sarcodina, the cells of the Ciliophora are covered by numerous hairlike projections, called cilia. Cilia beat continuously, either propelling the protozoan cell or moving food to the protozoan so that it can be engulfed. Paramecium is a common example of a ciliate protozoan (FIG. 2-16). The cilia of Paramecium propel it from one place to another and drive food toward its "mouthlike" region.
FIG. 2-16 Colorized micrograph of the protozoan Didini-um (green) consuming the protozoan Paramecium (yellow).
Yet other protozoa, the Mastigophora, have fla-gella that emanate from one end of the protozoan cell. They propel the cell. Giardia is a flagellate protozoan that infects the human gastrointestinal tract and causes severe diarrhea. It is becoming an increasing health problem in the United States (FIG. 2-17).
FIG. 2-15 Micrograph of the protozoan Amoeba proteus, which moves by extending its cytoplasm to form false feet. (225 x).
SURVEY OF MICROORGANISMS 55
FIG. 2-17 Colorized micrograph of Giardia lamblia, a protozoan that is one of the most common causes of gastrointestinal infections.
Another protozoan group that traditionally has been recognized is the Sporozoa. Members of the Sporozoa generally are nonmotile, produce spores during their life cycles, and grow only on or in a host organism from which they derive nutrition.
In the protozoan classification system proposed in 1980, the Sporozoa were reclassified into several smaller groups based on morphological characteristics. Many of these characteristics can only be observed with an electron microscope. Various other protozoa were also placed into these smaller groups regardless of their means of locomotion. For example, Plasmodium—the protozoan genus that includes the species that cause malaria—was placed into the group Apicomplexa because it produces a small umbrella-like structure at the end of the cell.
The classification of protozoa now includes electron microscopic observations of previously unseen morphological characteristics.
SUMMARY
Evolution of Microorganisms (pp. 25-30)
Microorganisms evolved from abiotically formed micelles.
As microorganisms evolved they altered their surroundings, permitting new forms of life to develop.
Classifying Microorganisms (pp. 25-30)
Early Classification Systems (p. 26)
Early classification systems were based on observable characteristics of microorganisms, such as shape and motility.
The species is the fundamental unit used in classifying all organisms.
Modern Classification Systems (pp. 26-29)
Modern classification systems attempt to reflect evolutionary relationships.
The contemporary classification system of Woese, which is based on genetic analyses at the molecular level, recognizes three primary Kingdoms: archaebac-teria (primitive specialized prokaryotes), eubacteria (common prokaryotes or "true bacteria"), and eu-karyotes (all other cellular organisms, including plants, animals, protozoa, algae, and fungi).
Survey of Microorganisms (pp. 30-55)
Acellular Nonliving Microorganisms—Viruses, Viroids, and Prions (pp. 30-33)
The acellular microorganisms include the viruses, viroids, and prions.
Viruses have two parts: a protein coat (the capsid) and a hereditary molecule, which may be DNA or RNA.
Viroids are composed of only RNA.
• Prions are infectious proteins.
Prokaryotes—Eubacteria and Archaebacteria (p. 33-50)
The eubacteria and archaebacteria are prokaryotic cells.
Like other organisms, bacteria are named using a binomial system of genus and species.
The major groups of bacteria are distinguished based on morphological, metabolic, and genetic characteristics.
The bacteria are described in Bergey's Manual, which is revised periodically.
Eukaryotes (pp. 51-55) Fungi (pp. 51-52)
The fungi are heterotrophic eukaryotic microorganisms.
Fungal cells commonly have cell walls.
Some fungi form multicellular filamentous growths called mycelia and others are unicellular (yeasts).
The fungi are classified into major groups based on their modes of reproduction and, in particular, the reproductive spores they produce.
Algae (pp. 53-54)
The algae are photosynthetic eukaryotic microorganisms.
The major groups of algae are defined based on their characteristic pigments and cell morphologies.
Protozoa (pp. 54-55)
The protozoa are heterotrophic microorganisms.
The cells of protozoa generally lack cell walls.
The major groups of protozoa are classified based on their means of motility or on specialized morphological characteristics.
56 CHAPTER 2 DIVERSITY OF THE MICROBIAL WORLD
CHAPTER REVIEW
Review Questions
Why is it hard to classify microorganisms by their evolutionary relationships?
Compare and contrast the classification systems of Linnaeus, Haeckel, Whittaker, and Woese.
How do viroids differ from viruses?
What are prions? Why are prions different from other living organisms?
What are the main characteristics of organisms in each of the Kingdoms in the five-Kingdom system of classification?
How are bacteria named?
What is Bergey's Manual?
How do humans differ from bacteria?
What are some of the morphological and physiological characteristics that have been used to classify bacteria?
What are the main features of the endosymbiont theory of evolution?
What are the modern methods used to classify organisms?
What were the characteristics of the first microorganisms?
How could life have evolved on Earth? Could life have evolved on other planets? If so, how?
What are the differences between classification and identification. How can clinical laboratories identify pathogens based on only 20 tests?
Why has the proposal by Carl Woese for three primary Kingdoms (eubacteria, archaebacteria, and eu-karyotes) upset many traditional plant and animal biologists?
Balows A, HG Truper, M Dworkin, W Harder, K-H Schleifer: 1992. The Prokaryotes, ed. 2, New York, Springer-Verlag.
A comprehensive set of volumes on the prokaryotes that is a valuable
reference for information on the properties of specific bacteria. Cairns-Smith AG: 1985. The first organisms, Scientific American 252(6):90-100.
Presents an alternative theory for the origin of life, arguing that clay,
not primordial soup, provided the fundamental materials from which
life arose. Chang ST and PG Miles: 1984. A new look at cultivated mushrooms, BioScience 34:358-362.
A fascinating account of the rapidly growing industry that produces
these fungi. Courtenay В and HH Burdsall Jr: 1982. A Field Guide to Mushrooms and Their Relatives, New York, Van Nostrand Reinhold.
Excellent identification manual, illustrating and describing more
than 350 species of ascomycetes and basidiomycetes. Dickerson R: 1978. Chemical evolution and the origin of life, Scientific American 239(3):70-86.
Explains the chemical changes thought to have occurred during the
evolution of life. Diener TO: 1982. Viroids: minimal biological systems, BioScience 32:38-44.
Describes the studies that established the existence of viroids.
Dyer BD and R Obar (eds.): 1985. The Origin of Eukaryotic Cells,
New York, Van Nostrand Reinhold.
Considers the question of what initiated the development of mitochondria, chloroplasts, and organelles of motility and espouses a belief in the endosymbiont theory to explain these processes.
Fox GE et al: 1980. The phylogeny of prokaryotes, Science 209:457-
463.
Describes the relationships of the prokaryotes, particularly the Archaebacteria.
Holt J (ed.): 1994. Bergey's Manual of Determinative Bacteriology, ed.
9, Baltimore, Williams & Wilkins.
The most recent volume of Bergey's Manual describes the characteristics of bacteria and provides valuable diagnostic tables to aid in the identification of bacteria.
Horgan J: 1991. In the beginning... Scientific American 264(2):116-
125.
Reviews recent theories inspired by Stanley Miller's 1953 experiments on the origin of life; discusses when, where, and how life began.
Joyce GF: 1992. Directed molecular evolution, Scientific American
267(6):90-97.
An interesting examination of the underlying molecular basis of evolution.
Krieg NR and J Holt (eds.): 1984. Bergey's Manual of Systematic
Bacteriology, 4 Volumes. Baltimore, Williams & Wilkins.
CHAPTER REVIEW 57
The comprehensive volumes o/Bergey's Manual is an invaluable resource, giving the descriptions of bacteria. Margulis L and KV Schwartz: 1988. Five Kingdoms: An Illustrated Guide to the Phyla of Life on Earth, New York, W.H. Freeman.
A catalog of the diversity of the world's living organisms, describing with profuse illustrations all major groups of organisms—100 phyla belonging to the five Kingdoms proposed by Robert Whittaker. Margulis L: 1984. Early Life, Boston, Jones & Bartlett.
Presents the author's views on the origins of life. Margulis L: 1982. Early Life, Boston, Science Books International. Short treatise on the evolution of life on earth, presenting an overview of the genesis of living organisms and their life processes. Margulis L: 1981. Symbiosis in Cell Evolution, San Francisco, W.H. Freeman.
Extensive arguments for the endosymbiotic theory of eukaryotic origins, that mitochondria, chloroplasts, and other organelles were acquired by eukaryotes from symbiotes. Margulis L: 1970. Origin of Eukaryotic Cells; Evidence and Research Implications for a Theory of the Origin and Evolution of Microbial, Plant, and Animal Cells on the Precambrian Earth, New Haven, Connecticut, Yale University Press.
Presents the author's views on the origin and evolution of cells based on the endosymbiotic origin of specific eukaryotic organelles. Margulis L and KV Schwartz: 1982. Vive Kingdoms: An Illustrated Guide to the Phyla of Life on Earth, New York, W.H. Freeman. Catalog of the diversity of life on earth, especially valuable for its treatment of the bacteria. Palleroni NJ: 1983. The taxonomy of bacteria, BioScience 33:370-377.
Reveals the methods by which bacteria are classified. Prusiner SB: 1984. Prions, Scientific American 251(3)50-59.
Introduction to prions, disease-causing agents that contain no DNA or RNA and yet are able to reproduce within cells. Schopf JW (ed.): 1983. Earth's Earliest Biosphere: Its Origin and Evolution, Princeton University Press.
A collection of articles by experts on the evolution of early forms of life and the geochemical evidence of the kinds of metabolism they conducted. Schopf JW: 1978. The evolution of the earliest cells, Scientific American 239(3):110-138.
Argues that the earliest cells gave rise to the oxygen in the atmosphere on which modern life depends. Shapiro JA: 1988. Bacteria as multicellular organisms, Scientific American 258(6):82-89.
Laboratory grown bacteria can form complex multicellular communities, differentiating into various cell types and forms. Skerman VBD: 1967. Order out of confusion: a case for a systematic approach to microbiology, Impact of Science on Society 17:225-244.
Reviews the history of microbiology in order to show the general basis on which the description of microorganisms is founded and how it is constantly changing. Skerman VBD, V McGowan, PHA Sneath: 1989. Approved Lists of Bacterial Names, Washington, D.C.; American Society for Microbiology.
Includes all valid names of bacteria that have been adequately described and, if cultivatable, for which there is a type, neotype, or reference strain available. Whittaker RH and L Margulis: 1978. Protist classification and the Kingdoms of organisms, Biosystems 10(l-2):3-18.
Some insights on the five-Kingdom system. Whittaker RH: 1969. New concepts of kingdoms of organisms, Science 163:150-160.
The proposal for the five-Kingdom classification system. Woese CR: 1981. Archaebacteria, Scientific American 244(6):98-122. Insights on early evolution and the archaebacteria and the author's revolutionary new three-Kingdom classification system based on genetic analyses.