CHAPTER 12Prokaryotic Diversity: The Bacteria

The Phylogeny of Bacteria  Overview

• Nearly 7000 species of prokaryotes are known. Figure 12.1 gives a phylogenetic overview of Bacteria.

• 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).

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

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.

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

The Nitrifying Bacteria

• Chemolithotrophs are prokaryotes that can oxidize inorganic electron donors and in many cases use CO2 as their sole carbon

source.

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

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

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).

• 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.

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

• 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.

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.

• 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).

Methanotrophs and Methylotrophs

• 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.

• 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.

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

Pseudomonas and the Pseudomonads

• Pseudomonads include many gram-negative chemoorganotrophic aerobic rods; many nitrogen-fixing species are phylogenetically closely related.

• 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.

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

• 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.

Acetic Acid Bacteria

• The acetic acid bacteria are phylogenetically related to pseudomonads and are characterized by an ability to oxidize ethanol to acetate aerobically.

Free-Living Aerobic Nitrogen-Fixing Bacteria

• A variety of organisms inhabit soil and are capable of fixing N2 aerobically (Table 12.12).

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.

Enteric Bacteria

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

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

• 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.

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

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

• Figure 12.25 shows a simple key to the main genera of enteric bacteria.

Vibrio and Photobacterium

• Vibrio and Photobacterium species are marine organisms; some species are pathogenic, others are bioluminescent.

Rickettsias

• The rickettsias are obligate intracellular parasites, many of which cause disease. Rickettsias are deficient in many metabolic functions and obtain key metabolites from their hosts.

• Characteristics of rickettsias are given in Table 12.17.

Spirilla

• Spirilla are spiral-shaped, chemoorganotrophic prokaryotes widespread in the aquatic environment. The genera Helicobacter and Campylobacter are pathogenic spirilla. Spirilla are distributed among all five subdivisions of the Proteobacteria.

• Bdellovibrio organisms have the unusual property of preying on other bacteria, using as nutrients the cytoplasmic constituents of their hosts (Figure 12.34b).

• Table 12.18 lists characteristics of the genera of spiral-shaped bacteria.

Sheathed Proteobacteria: Sphaerotilus and Leptothrix

• Sheathed bacteria are filamentous Proteobacteria in which individual cells form chains within an outer layer called the sheath.

Budding and Prosthecate/Stalked Bacteria

• Budding and prosthecate bacteria are appendaged cells that form stalks or prosthecae used for attachment or nutrient absorption and are primarily aquatic.

• Table 12.19 lists characteristics of stalked, appendaged (prosthecate), and budding bacteria.

• Figure 12.38 illustrates the contrast between cell division in conventional bacteria and in budding and stalked bacteria.

• Two well-studied budding bacteria are closely related phylogenetically: Hyphomicrobium, which is chemoorganotrophic, and Rhodomicrobium, which is phototrophic. These organisms release buds from the ends of long, thin hyphae.

• The hypha is a direct cellular extension of the mother cell (Figure 12.39) and contains cell wall; cytoplasmic membrane; ribosomes; and, occasionally, DNA.

• One common stalked bacterium is Caulobacter. Figure 12.41 shows stages in the Caulobacter cell cycle beginning with a swarmer cell.

Gliding Myxobacteria

• The fruiting myxobacteria are rod-shaped, gliding bacteria that aggregate to form complex masses of cells called fruiting bodies. Myxobacteria are chemoorganotrophic soil bacteria that live by consuming dead organic matter or other bacterial cells.

• Table 12.20 gives the classification of the fruiting myxobacteria.

• The life cycle of a typical fruiting myxobacterium is shown in Figure 12.47.

Sulfate- and Sulfur-Reducing Proteobacteria

• Sulfate- and sulfur-reducing bacteria are a large group of delta Proteobacteria unified by their physiological process of reducing either SO4

2– or S0 to H2S under anoxic conditions.

• Two physiological subgroups of sulfate-reducing bacteria are known: group I, which is incapable of oxidizing acetate to CO2, and

group II, which is capable of doing so.

• Table 12.21 lists characteristics of some key genera of sulfate- and sulfur-reducing bacteria.

Phylum 2 and 3: Gram-Positive Bacteria and Actinobacteria 

Nonsporulating, Low GC, Gram-Positive Bacteria: Lactic

Acid Bacteria and Relatives

• Distinguishing features of major gram-positive cocci are given in Table 12.22.

• The "low GC," gram-positive Bacteria are a large phylogenetic group that contains rods and cocci, sporulating and nonsporulating species.

• One important difference between subgroups of the lactic acid bacteria lies in the pattern of products formed from the fermentation of sugars. One group, called homofermentative, produces a single fermentation product, lactic acid.

• The other group, called heterofermentative, produces other products, mainly ethanol plus CO2, as well as lactate (Table 12.23). Figure

12.53 summarizes pathways for the fermentation of glucose by a homo- and a heterofermentative organism.

• Table 12.24 gives differential characteristics of streptococci, lactococci, and enterococci.

Endospore-Forming, Low GC, Gram-Positive Bacteria: Bacillus,

Clostridium, and Relatives

• Production of endospores is a hallmark of the key genera Bacillus and Clostridium. Gram-positive Bacteria are major agents for the degradation of organic matter in soil, and a few species are pathogenic.

• Table 12.25 lists major genera of endospore-forming bacteria.

• Table 12.26 shows characteristics of representative species of bacilli.

• Table 12.27 gives characteristics of some groups of clostridia.

• One group of clostridia ferments cellulose with the formation of acids and alcohols, and these are likely the major organisms decomposing cellulose anaerobically in soil. The biochemical steps in the formation of butyric acid and butanol from sugars are well understood (Figure 12.58).

• Another group of clostridia obtains energy by fermenting amino acids. Some species ferment individual amino acids; others ferment only amino acid pairs. In this situation, one functions as the electron donor and is oxidized, the other acts as the electron acceptor and is reduced.

• This type of coupled amino acid decomposition is known as the Stickland reaction (Figure 12.59).

• One group of endospore-formers, the heliobacteria, is phototrophic.

Cell Wall–Less, Low GC, Gram-Positive Bacteria: The Mycoplasmas

• The mycoplasma group contains organisms that lack cell walls and contain a very small genome. Many species require sterols to strengthen their membranes, and several are pathogenic for humans, other animals, and plants.

• Major characteristics of mycoplasmas are shown in Table 12.28.

High GC, Gram-Positive Bacteria (Actinobacteria): Coryneform and

Propionic Acid Bacteria

• High GC, gram-positive Bacteria include such organisms as Corynebacterium, Arthrobacter, Propionibacterium, and Mycobacterium. They are mainly harmless soil saprophytes.

• The propionic acid bacteria were first discovered in Swiss cheese, where their fermentative production of CO2 results in the

characteristic holes. Figure 12.68 shows the enzymatic reactions leading from glucose to propionic acid.

Actinobacteria: Mycobacterium

• The genus Mycobacterium consists of rod-shaped organisms that at some stage of their growth cycle possess the distinctive staining property called acid-fastness.

• This property results from the presence on the surface of the mycobacterial cell of unique lipids called mycolic acids, found only in the genus Mycobacterium.

• M. tuberculosis is the causative agent of the disease tuberculosis.

•M. tuberculosis cells have a lipid-rich, waxy outer surface layer that requires special staining procedures (the acid-fast stain, Figure 12.69) to observe the cells microscopically.

Filamentous Actinobacteria: Streptomyces and Other

Actinomycetes

• The streptomycetes are a large group of filamentous, gram-positive Bacteria that form spores at the end of aerial filaments.

• Many clinically useful antibiotics such as tetracycline and neomycin have come from Streptomyces species (Table 12.31).

• Streptomycete spores are produced by the formation of cross-walls in the multinucleate sporophores, followed by separation of the individual cells directly into spores (Figure 12.74).

• Figure 12.75 illustrates various types of spore-bearing structures in the streptomycetes.

Phylum 4: Cyanobacteria and Prochlorophytes

• Cyanobacteria comprise a large and morphologically heterogeneous group of phototrophic Bacteria. Cyanobacteria differ in fundamental ways from purple and green bacteria, most notably in that they are oxygenic phototrophs.

• Cyanobacteria represent one of the major phyla of Bacteria and show a distant relationship to gram-positive Bacteria.

• Some filamentous cyanobacteria form heterocysts, which are rounded, seemingly empty cells, usually distributed regularly along a filament or at one end of a filament.

• Oxygen in Earth's atmosphere is thought to have originated from cyanobacterial photosynthesis.

Prochlorophytes and Chloroplasts

• Cyanobacteria and prochlorophytes are oxygenic phototrophic prokaryotes. Prochlorophytes differ most clearly from cyanobacteria in that prochlorophytes contain chlorophyll b or d and lack phycobilins.

Phylum 5: Chlamydia 

• Chlamydias are extremely small parasitic bacteria that cause a variety of human diseases. Figure 12.85 shows the infection cycle of chlamydia.

• Chlamydias contain a very small genome and are apparently deficient in many metabolic functions.

Phylum 6: Planctomyces/Pirellula 

Planctomyces: A Phylogenetically Unique Stalked Bacterium

• The Planctomyces group contains stalked, budding bacteria.

• This phylum contains a number of morphologically unique bacteria including the genera Planctomyces, Pirellula, Gemmata, and Isosphaera. The best studied of these has been Planctomyces.

Phylum 7: The Verrucomicrobia 

Verrucomicrobium and Prosthecobacter

• The Verrucomicrobia are distinguished by their multiple prosthecate cells.

• Members of the Verrucomicrobia share with other prosthecate bacteria the presence of peptidoglycan in their cell walls and are aerobic to facultatively aerobic bacteria, capable of fermenting various sugars.

Phylum 8: The Flavobacteria Bacteroides and Flavobacterium

• The flavobacteria contain a variety of gram-negative Bacteria motile by either flagella or by gliding and associated with animals, food, and the soil.

• The genus Bacteroides contains obligately anaerobic, nonsporulating species that are saccharolytic, fermenting sugars or proteins, depending on the species, to primarily acetate and succinate as fermentation products.

• The genus Bacteroides contains obligately anaerobic, nonsporulating species that are saccharolytic, fermenting sugars or proteins, depending on the species, to primarily acetate and succinate as fermentation products.

• Bacteroides are normally commensals, found in the intestinal tract of humans and other animals.

Phylum 9: The Cytophaga Group

• The Cytophaga group includes a variety of obligately aerobic chemoorganotrophic bacteria in soil, water, hot springs, and thermal environments.

Phylum 10: Green Sulfur Bacteria 

Chlorobium and Other Green Sulfur Bacteria

• Green sulfur bacteria are obligately anaerobic anoxygenic phototrophs that produce unique structures called chlorosomes. These organisms can grow at very low light intensities and oxidize H2S to

S0 and SO42–.

• Consortia containing phototrophic green bacteria and a nonphototrophic central cell are common in sulfidic aquatic environments.

Phylum 11: The Spirochetes 

• Spirochetes are tightly coiled, motile, helical prokaryotes that contain both free-living and pathogenic species.

Phylum 12: Deinococci 

Deinococcus/Thermus• Deinococcus is a key genus in a major lineage of Bacteria. Deinococcus radiodurans is the most radiation resistant of all known organisms.

• The lipids of Thermomicrobium contain 1,2-dialcohols instead of glycerol and have neither ester nor ether linkages (Figure 12.100).

Phylum 13: The Green Nonsulfur Bacteria 

Chloroflexus and Relatives

• Chloroflexus is a key genus in a major lineage of Bacteria. Chloroflexus is an anoxygenic phototroph that shows photosynthetic properties characteristic of both purple bacteria and green bacteria.

• In addition to Chloroflexus, other phototrophic green nonsulfur bacteria include the thermophile Heliothrix and the large-celled mesophiles Oscillochloris and Chloronema.

Phylum 14–16: Deeply Branching Hyperthermophilic

Bacteria Thermotoga and

Thermodesulfobacterium

• Thermotoga and Thermodesulfobacterium are hyperthermophiles, growing at high temperature, and each spearheads a major lineage of Bacteria.

Aquifex, Thermocrinis, and Relatives

• Aquifex is another hyperthermophile that heads a major lineage of Bacteria. Aquifex and Thermocrinis are H2-oxidizing

chemolithotrophs; Thermotoga and Thermodesulfobacterium are both anaerobic chemoorganotrophs.

Phylum 17 and 18: Nitrospira and Deferribacter 

Nitrospira, Deferribacter, and Relatives

• Nitrospira and Deferribacter each form their own phylum.

• Nitrospira oxidizes NO2– to NO3

– and grows

autotrophically. Despite this close physiological relationship to the classical nitrifying bacteria, Nitrospira is phylogenetically quite distinct from them.

• Also, Nitrospira lacks the extensive internal membranes found in species of nitrifying Proteobacteria.

• The genus Deferribacter forms its own distinct lineage and is composed of species that specialize in anaerobic energy metabolism. Other genera in this group include Geovibrio and Flexistipes; the latter genus is an obligately anaerobic and fermentative bacterium.