Domain Bacteria PDF

23-10-2024 Domain Bacteria Dr Jitendra 1 Including phyla of Bacteria known only from 16S ribosomal RNA (rRNA) gene sequences retrieved from the environment, over 80 phyla can be distinguished. However, only about 30 of th...

23-10-2024 Domain Bacteria Dr Jitendra 1 Including phyla of Bacteria known only from 16S ribosomal RNA (rRNA) gene sequences retrieved from the environment, over 80 phyla can be distinguished. However, only about 30 of these contain species that have been characterized in laboratory culture. Remarkably, more than 90% of cultivated genera and species of Bacteria originate in only four phyla: Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes 2 1  23-10-2024 Figure 16.1 Some major phyla of Bacteria based on 16S ribosomal RNA gene sequence comparisons. (a) Depicted are the major phyla of Bacteria that have cultivated species. The area of each wedge is roughly proportional to the number of described cultivated species in each group. Analyses of 16S rRNA gene sequences from natural environments suggest there are more than 80 bacterial phyla. of Proteobacteria. Differences between the size of the red and green bars indicate the degree to which members of each group are common in natural environments but difficult to cultivate in isolation. Note that the abscissa is a log scale. 3 (b) Numbers of cultured and characterized species (green bars) and known 16S rRNA gene sequences (phylotypes, red bars) for each of the 29 major bacterial phyla that have at least one type species in pure culture. Also shown are related data for the different classes 4 2  23-10-2024 Proteobacteria The Proteobacteria are by far the largest and most metabolically diverse phylum of Bacteria. More than a third of characterized species of Bacteria originate within this group, and Proteobacteria constitute the majority of known bacteria of medical, industrial, and agricultural significance. As a group, the Proteobacteria are all gram-negative bacteria. They show an exceptionally wide diversity of energy-generating mechanisms, with chemolithotrophic, chemoorganotrophic, and phototrophic species. Indeed, only a few types of metabolism do not occur within the Proteobacteria, including methanogenesis, which is only in Archaea 5 Figure 16.2 Phylogenetic tree and metabolic links of some key genera of Proteobacteria. Phylogeny of representative genera of Proteobacteria as revealed by analysis of 16S rRNA gene sequences. Note how identical metabolisms are often distributed in phylogenetically distinct genera, suggesting that horizontal gene flow has been extensive in the Proteobacteria. Some organisms listed may have multiple properties; for example, some sulfur chemolithotrophs are also iron or hydrogen chemolithotrophs, and several of the organisms listed can fix nitrogen. 6 3  23-10-2024 Based on 16S rRNA gene sequences, the phylum Proteobacteria can be divided into six classes: Alpha-, Beta-, Gamma-, Delta-, Epsilon-, and Zetaproteobacteria Each class contains many genera with the exception of the Zetaproteobacteria, which is composed of a single characterized species, the marine iron-oxidizing bacterium Mariprofundus ferrooxydans 7 Despite the phylogenetic breadth of the Proteobacteria, species in different classes often have similar metabolisms. For example, phototrophy and methylotrophy occur in three different classes of Proteobacteria, and nitrifying bacteria span four classes of Proteobacteria. This suggests that horizontal gene flow has played a major role in shaping the metabolic diversity of the Proteobacteria 8 4  23-10-2024 9 Alphaproteobacteria With about one thousand described species, the Alphaproteobacteria are the second largest class of Proteobacteria. The Alphaproteobacteria contain extensive functional diversity, Most species are obligate aerobes or facultative aerobes and many are oligotrophic, preferring to grow in environments that have low nutrient concentrations. There are 10 well-characterized orders within the Alphaproteobacteria, but the vast majority of species fall within the Rhizobiales, Rickettsiales, Rhodobacterales, Rhodospirillales, Caulobacterales, and Sphingomonadales 10 5  23-10-2024 11 12 6  23-10-2024 13 Betaproteobacteria With about 500 described species, the Betaproteobacteria are the third largest class of Proteobacteria. The Betaproteobacteria contain an immense amount of functional diversity A total of six orders of Betaproteobacteria have many characterized species: Burkholderiales, Hydrogenophilales, Methylophilales, Neisseriales, Nitrosomonadales, and Rhodocyclales 14 7  23-10-2024 Gammaproteobacteria: The Gammaproteobacteria are the largest and most diverse class of Proteobacteria, containing nearly half of all characterized species in the phylum. The class contains more than 1500 characterized species and at least 15 well-characterized order. Its species have diverse metabolic and ecological characteristics and include many well-known human pathogens. Species can be phototrophic (including the purple sulfur bacteria, chemoorganotrophic, or chemolithotrophic, and can have either respiratory or fermentative metabolisms. Members of this group often grow rapidly in laboratory media and can be isolated from a wide diversity of habitats 15 Enterobacteriales The Enterobacteriales, commonly called the enteric bacteria, comprise a relatively homogeneous phylogenetic group within the Gammaproteobacteria and consist of facultatively aerobic, gram-negative, nonsporulating rods that are either nonmotile or motile by peritrichous flagella. The oxidase test and the catalase test are common assays used to characterize bacteria , and these tests can be used to discriminate enteric bacteria from many other Gammaproteobacteria. The oxidase test is an assay for the presence of cytochrome c oxidase, an enzyme present in many respiring bacteria. The catalase test assays for the enzyme catalase, which detoxifies hydrogen peroxide and is commonly found in bacteria able to grow in the presence of oxygen 16 8  23-10-2024 Enteric bacteria are oxidase-negative and catalase-positive. They also produce acid from glucose and reduce nitrate but only to nitrite. Enteric bacteria have relatively simple nutritional requirements and ferment sugars Among the enteric bacteria are many species pathogenic to humans, other animals, or plants, as well as other species of industrial importance. Escherichia coli, the best known of all organisms, is the classic enteric bacterium ars to a variety of end products 17 18 9  23-10-2024 19 20 10  23-10-2024 Firmicutes, Tenericutes, and Actinobacteria The Actinobacteria include the actinomycetes, a huge group of primarily filamentous soil bacteria. One distinguishing feature of the Actinobacteria is that their genomic DNA typically has a high frequency of GC base pairs, and as a result they are also called the high G C gram-positive bacteria. The Tenericutes include cells that lack a cell wall, and the Firmicutes include the endospore-forming bacteria, lactic acid bacteria, and several other groups. In contrast to the Actinobacteria, the genomes of Firmicutes generally have a low GC content, and as a result, they are also called the low G C gram-positive bacteria. 21 22 11  23-10-2024 Firmicutes: Lactobacillales KEY GENERA: Lactobacillus, Streptococcus The order Lactobacillales contains the lactic acid bacteria, fermentative organisms that produce lactic acid as a major end product of metabolism. These organisms are used widely in food production and preservation. Lactic acid bacteria are nonsporulating, oxidase- and catalase-negative rods or cocci that show an exclusively fermentative metabolism. All lactic acid bacteria produce lactic acid as a major or sole fermentation product. Members of this group lack porphyrins and cytochromes; thus they do not carry out oxidative phosphorylation and obtain energy only by substrate-level phosphorylation. However, unlike many anaerobes, most lactic acid bacteria are not sensitive to oxygen (O2) and can grow in its presence; thus they are called aerotolerant anaerobes 23 24 12  23-10-2024 Streptococcus and Other Cocci USEFUL Streptococcus species have a characteristic cell morphology of cocci in chains or tetrads and so are readily resolved from the rod- shaped lactobacilli. As producers of lactic acid, other streptococci play important roles in the production of buttermilk, silage, and other fermented products Heterofermentative Leuconostoc also produce the flavoring ingredients 25 PATHOGENS Enterococcus includes streptococci that are primarily of fecal origin and can be human pathogens. Species of the genera Peptococcus and Peptostreptococcus are obligate anaerobes that ferment proteins rather than sugars Streptococci have been divided into two groups of related species: the pyogenes subgroup, characterized by Streptococcus pyogenes, the cause of strep throat, and the viridans subgroup, characterized by Streptococcus mutans, the major cause of dental caries 26 13  23-10-2024 Firmicutes: Nonsporulating Bacillales and Clostridiales Listeria monocytogenes is most noteworthy because it causes a major foodborne illness, listeriosis there are two major species, Staphylococcus epidermidis, a nonpigmented, nonpathogenic organism usually found on the skin or mucous membranes, and Staphylococcus aureus, a yellow- pigmented species that is most commonly associated with pathological conditions including boils, pimples, pneumonia, osteomyelitis, meningitis, and arthritis. Some S. aureus strains are resistant to multiple antibiotics (so-called MRSA strains) and are fierce pathogens that can cause extensive tissue damage 27 Staphylococcus Staphylococcus (Figure 16.20) is a facultative aerobe that shows a typical respiratory metabolism but can also grow fermentatively. Cells typically grow in clusters and produce acid from glucose both aerobically and anaerobically. Staphylococcus species are catalase-positive, and this permits their distinction from Streptococcus and some other genera of lactic acid bacteria. Staphylococci are relatively resistant to reduced water potential and tolerate drying and high salt (NaCl) fairly well 28 14  23-10-2024 29 30 15  23-10-2024 Firmicutes: Sporulating Bacillales and Clostridiales All endospore-forming bacteria are gram-positive species of Bacillales or Clostridiales. The ability to form endospores evolved only once in a common ancestor of the Bacillales, Clostridiales, and Lactobacillales. However, many Bacillales and Clostridiales and the entire order Lactobacillales are unable to form endospores. The capacity to make endospores requires many genes and has not been acquired by horizontal gene transfer 31 The two genera about which most is known are Bacillus, species of which are aerobic or facultatively aerobic, and Clostridium, which contains species that are obligately anaerobic and fermentative. All endospore forming bacteria are ecologically related because they are found in nature primarily in soil. 32 16  23-10-2024 Even those species that are pathogenic to humans or other animals are primarily saprophytic soil organisms and infect animals only incidentally. Indeed, the ability to produce endospores should be advantageous for a soil microorganism because soil is a highly variable environment in terms of nutrient levels, temperature, and water activity 33 Tenericutes: The Mycoplasmas KEY GENERA: Mycoplasma, Spiroplasma The Tenericutes, which contain the single class Mollicutes, are bacteria that lack cell walls (mollis is Latin for “soft”) and are some of the smallest organisms known. This group is often called the mycoplasmas because Mycoplasma, a notable genus containing human pathogens, is the best-characterized genus in the phylum. Although they do not stain gram-positively (because they lack cell walls), mycoplasmas are phylogenetically related to the Firmicutes. Mycoplasmas typically live within animal and plant hosts and this may eliminate the need for a gram-positive cell wall. 34 17  23-10-2024 Mycoplasmas resemble protoplasts (bacteria treated to remove their cell walls), but they are more resistant to osmotic lysis and are able to survive conditions under which protoplasts lyse. This ability to resist osmotic lysis is at least partially determined by the presence of sterols, which make the cytoplasmic membrane of mycoplasmas more stable than that of other bacteria 35 Actinobacteria: The other major group of gram-positive bacteria is the Actinobacteria, which form their own phylum within the Bacteria. The Actinobacteria contain rod-shaped to filamentous and primarily aerobic bacteria that are common inhabitants of soil and plant materials. For the most part they are harmless commensals, species of Mycobacterium (for example, Mycobacterium tuberculosis) being notable exceptions. Some are of great economic value in either the production of antibiotics or certain fermented dairy products. 36 18  23-10-2024 Corynebacterium and Arthrobacter The main genera of coryneform bacteria are Corynebacterium and Arthrobacter. The genus Corynebacterium consists of an extremely diverse group of bacteria, including animal and plant pathogens and saprophytes. Some species, such as Corynebacterium diphtheriae, are pathogenic (diphtheria) 37 Propionic Acid Bacteria The propionic acid bacteria (genus Propionibacterium) were first discovered in Swiss (Emmentaler) cheese, where their fermentative production of CO2 produces the characteristic holes. In addition, the propionic acid they produce is at least partly responsible for the unique flavor of the cheese The bacteria in this group are grampositive anaerobes that ferment lactic acid, carbohydrates, and polyhydroxy alcohols, producing primarily propionic acid, acetic acid, and CO2 38 19  23-10-2024 Actinobacteria: Mycobacterium Mycobacteria are common in soils and most are harmless, but the genus Mycobacterium contains several notable humanpathogens, chief among them Mycobacterium tuberculosis, the cause of tuberculosis Species are rod-shaped bacteria that at some stage of their growth cycle possess the distinctive staining property called acid-fastness. This property is due to the presence of unique lipids called mycolic acids, found only in species of the genus Mycobacterium, on the surface of the mycobacterial cell. Mycolic acids are a group of complex branched-chain hydroxylated lipids covalently bound to peptidoglycan in the cell wall; the complex gives the cell surface a waxy, hydrophobic consistency 39 40 20