CHAPTER 12 Prokaryotic Diversity: The Bacteria

1. CHAPTER 12 Prokaryotic Diversity: The Bacteria

2. The Phylogeny of Bacteria Overview Nearly 7000 species of prokaryotes are known. Figure 12.1 gives a phylogenetic overview of Bacteria.

4. The Proteobacteria consist of five clusters containing several genera. Each cluster is designated by a Greek letter: alpha, beta, gamma, delta, or epsilon (Table 12.1).

7. Physiologically, Proteobacteria can be phototrophic, chemolithotrophic, or chemoorganotrophic.

8. Phylum 1: Proteobacteria, Purple Phototrophic Bacteria Purple bacteria are anoxygenic phototrophs that obtain carbon from CO2 + H2S (purple sulfur bacteria) or organic compounds (purple nonsulfur bacteria). • Purple nonsulfur bacteria are physiologically diverse, and most can grow as chemoorganotrophs in darkness. The purple bacteria reside in the alpha, beta, and gamma subdivisions of the Proteobacteria.

9. Table 12.2 gives genera and characteristics of purple sulfur bacteria. Table 12.3 gives genera and characteristics of purple nonsulfur bacteria.

12. The Nitrifying Bacteria Chemolithotrophs are prokaryotes that can oxidize inorganic electron donors and in many cases use CO2 as their sole carbon source.

13. Several reactions are involved in the oxidation of inorganic nitrogen compounds by chemolithotrophic nitrifying bacteria (Figure 12.9).

15. Characteristics of the nitrifying bacteria are listed in Table 12.4.

17. Sulfur- and Iron-Oxidizing Bacteria The ability to grow chemolithotrophically on reduced sulfur compounds is a property of a diverse group of Proteobacteria (Table 12.5).

19. Some sulfur chemolithotrophs are obligate chemolithotrophs, which must use inorganic instead of organic compounds as electron donors. Carboxysomes are often present inside the cells of obligate chemolithotrophs.

20. Other sulfur chemolithotrophs are facultative chemolithotrophs, in the sense that they can grow either chemolithotrophically (and thus also as autotrophs) or chemoorganotrophically.

21. Most species of Beggiatoa, however, can obtain energy from the oxidation of inorganic sulfur compounds but lack enzymes of the Calvin cycle. Thus, they require organic compounds as carbon sources. Such organisms are called mixotrophs.

22. Hydrogen-Oxidizing Bacteria A wide variety of bacteria can grow with H2 as the sole electron donor and O2 as the electron acceptor using the reduction of O2 with H2 as their energy metabolism.

23. All hydrogen-oxidizing bacteria contain one or more hydrogenase enzymes that bind H2 and use it either to produce ATP or as reducing power for autotrophic growth (Table 12.6).

25. Methanotrophs and Methylotrophs • Two classes of methanotrophs are known, each having a number of structural and biochemical properties in common. Methanotrophs reside in water and soil and can also exist as symbionts of marine shellfish. Methylotrophs are prokaryotes able to grow on carbon compounds that lack carbon-carbon bonds. Some methylotrophs are also methanotrophs, able to grow on CH4. • Two classes of methanotrophs are known, each having a number of structural and biochemical properties in common. Methanotrophs reside in water and soil and can also exist as symbionts of marine shellfish.

26. Table 12.7 lists substrates used by methylotrophic bacteria, and Table 12.8 gives some characteristics of meganotrophs.

29. Pseudomonas and the Pseudomonads • The distinguishing characteristics of the pseudomonad group are given in Table 12.9. Also listed in this table are the minimal characteristics needed to identify an organism as a pseudomonad. Pseudomonads include many gram-negative chemoorganotrophic aerobic rods; many nitrogen-fixing species are phylogenetically closely related.

31. Many pseudomonads, as well as a variety of other gram-negative Bacteria, metabolize glucose via the Entner-Doudoroff pathway (Figure 12.17c).

33. Species of the genus Pseudomonas and related genera are defined on the basis of phylogeny and various physiological characteristics, as outlined in Tables 12.10 and 12.11.

36. Acetic Acid Bacteria The acetic acid bacteria are phylogenetically related to pseudomonads and are characterized by an ability to oxidize ethanol to acetate aerobically.

37. Free-Living Aerobic Nitrogen-Fixing Bacteria A variety of organisms inhabit soil and are capable of fixing N2 aerobically (Table 12.12).

39. Neisseria, Chromobacterium, and Relatives This group of beta and gamma Proteobacteria comprises a diverse collection of organisms, related phylogenetically as well as by Gram stain, morphology, lack of motility, and aerobic metabolism. • The genera Neisseria, Moraxella, Branhamella, Kingella, and Acinetobacter are distinguished as outlined in Table 12.13.

41. Enteric Bacteria The enteric bacteria are a large group of facultative aerobic rods of medical and molecular biological significance.

42. Table 12.14 gives the phenotypic characteristics used to separate the enteric bacteria from other bacteria of similar morphology and physiology.

44. One important taxonomic characteristic separating the various genera of enteric bacteria is the type and proportion of fermentation products produced by anaerobic fermentation of glucose.

45. Two broad patterns are recognized, the mixed-acid fermentation and the 2,3-butanediol fermentation (Figure 12.24).

48. Tables 12.15 and 12.16 outline the key diagnostic reactions used to distinguish key genera of enteric bacteria.