Unit 2: Taxonomy and Classification of Microbes PDF

Unit 2. Taxonomy and Classification of Microbes A summary of life on Earth through time and origin of the cellular...

Unit 2. Taxonomy and Classification of Microbes A summary of life on Earth through time and origin of the cellular domains. (a) At its origin, Earth was sterile and anoxic. Cellular life, in the form of Bacteria and Archaea, was present on Earth by 3.8 billion years ago (bya). The Unit 2: Taxonomy and Classification of Evolution of phototrophic bacteria called Microbes Cyanobacteria caused Earth’s PREPARED BY: BRENT JOY H. HERNANDO 1 atmosphere to become oxygenated over time. While the first evidence for oxygen Review: MICROBIAL APPLICATIONS in Earth’s appears 2.4 bya, current levels of atmospheric O2 were not achieved until 500–800 million years ago. (b) The three domains of cellular organisms are Bacteria, Archaea, and Eukarya. Bacteria and Archaea appeared first and Eukarya evolved later, diverging PREPARED BY: BRENT JOY H. HERNANDO 2 from the Archaea. LUCA, last universal Microorganisms have major impacts on common ancestor. the world in which we live. In the topics that follow, we will learn how microorganisms impact our health, the foods we eat, the water we drink, and even the air we breathe. Three Domains: Bacteria, Archeae, Eukarya Three Domains: Bacteria, Archeae, Eukarya PREPARED BY: BRENT JOY H. HERNANDO 5 Domain Archaea PREPARED BY: BRENT JOY H. HERNANDO 3 consists of five described phyla. All cells fall into one of three major Archaea have historically been associated groups: Bacteria, Archaea, or Eukarya. with extreme environments; the first isolates came from hot, salty, or acidic sites. These three major cell lineages are called domains, and all known cellular BUT NOT ALL Archaea are extremophiles. organisms belong to one of these three domains. PREPARED BY: BRENT JOY H. HERNANDO 6 Domain Archaea: Five Phyla Three Domains: Bacteria, Archeae, Eukarya PREPARED BY: BRENT JOY H. HERNANDO 7 PREPARED BY: BRENT JOY H. HERNANDO 4 Schematic representation of the phylogeny of the major taxonomic orders within the domain Archaea.  Five major archaeal phyla (studied in multicellularis' showing its spherical pure or highly enriched cultures) and morphology and the tightly bound cells. their most representative orders are Note the highly organized disposition of indicated in color, while other archaeal the cells. Bar, 2 μm. taxa are indicated in black. While (b) Light (upper right inset; bar, 10 μm) archaeal phyla are nearly as numerous and transmission electron microscopy of as Bacteria, far fewer Archaea have been the micro-organism deposited on nickel cultivated. grids and stained in a 2% Most described species of Archaea fall phosphotungstic acid solution in water. within the phyla Crenarchaeota and Microorganisms vary greatly in size and Euryarchaeota while only a handful of shape. species have been described for the Nanoarchaeota, Korarchaeota, and Thaumarchaeota. The root of the archaeal tree lies between these four branches though the exact position remains uncertain. PREPARED BY: BRENT JOY H. HERNANDO 11 Domain Archaea The smallest known microbe is the Methanogens- methane producing microbes circovirus (20 nm) and the largest shown Extremophiles Hyperthermophiles- with growth here is the bacterium Epulopiscium (700 temperature optima above 80 C Extreme Halophiles- requires 1.5 M (about mm), which represents a 35,000-fold 9%) or more (NaCl) for growth (Haloferax & Natronobacterium) diSerence in length! Acidophiles- grow best below pH 5.5 Alkaliphiles- pH optima of 8 or higher Certain protozoa can be even larger than Epulopiscium (>2 mm long) and are PREPARED BY: BRENT JOY H. HERNANDO 8 visible to the unaided eye. Methanogenesis is a globally important Included in the figure are Eukarya: process that has produced virtually all of Paramecium (300 um * 85 um), diatoms the natural gas on Earth and has a (Navicula, 50 um * 12 um), yeast significant eSect on climate because (Saccharomyces, 5 um), and methane is a strong “greenhouse gas” nanoflagellates (Cafeteria, 2 um); Bacteria: Epulopiscium (700 um * 80 Three Domains: Bacteria um), cyanobacteria (Oscillatoria, 10-um- diameter multicellular filaments), Bacteria have a prokaryotic cell structure. They are Magnetoglobus (multicellular aggregate, often thought of as undifferentiated single cells with a length that ranges from 0.5 to 10 um. 20 um diameter), Spirochaetes (2–10 um Although most bacteria are unicellular, some * 0.25 um), bacteria can differentiate to form multiple cell types and others are even multicellular (for example, Flexibacter (5–100 um * 0.5 um Magnetoglobus). filaments), PREPARED BY: BRENT JOY H. HERNANDO 9 Escherichia coli (2 um * 0.5 um), Pelagibacter (0.4 um * 0.15 um), and Candidatus Magnetoglobus multicellularis’, a multicellular, Mycoplasma (0.2 um); magnetotactic prokaryote from a hypersaline environment Archaea: Giganthauma (10-um- diameter multicellular filament), Ignicoccus (6 um), Nanoarchaeum (0.4 um), Haloquadratum (2 um), Methanosarcina (2 um per cell in packet); and viruses: PREPARED BY: BRENT JOY H. HERNANDO 10 Pandoravirus (1 um * 0.4 um), a) Scanning electron microscopy of T4 bacteriophage (200 nm * 90 nm), ‘Candidatus Magnetoglobus Influenza A virus (100 nm),  Tobacco mosaic virus (300 nm * 20 nm), Circovirus (20 nm). Smallest Bacteria Three Domains: Bacteria Read more at page 45 of Unit 1 of Madigan et al e-book PREPARED BY: BRENT JOY H. HERNANDO 14 PREPARED BY: BRENT JOY H. HERNANDO 12 Domain: Bacteria a Where only one number is given, this is the Among the Bacteria, 30 major phylogenetic lineages (called phyla) have at least one species that has been grown in culture. diameter of spherical cells. The values given are for the largest cell size observed in More than 90% of cultivated bacteria belong to one of only four each species. For example, for T. phyla: Actinobacteria, Bacteroidetes. Firmicutes, Proteobacteria, and namibiensis, an average cell is only about 200 mm in diameter. But on occasion, giant PREPARED BY: BRENT JOY H. HERNANDO 15 cells of 750 mm are observed. Likewise, an average cell of S. marinus is about 1 mm in Domain: Bacteria diameter. The species of Beggiatoa here is Actinobacteria- are Gram-positive bacteria with high G+C DNA content unclear, and E. fishelsoni, M. bavaricum, that constitute one of the largest bacterial phyla, and they are ubiquitously distributed in both aquatic and terrestrial ecosystems. and P. ubique are not formally recognized Firmicutes- include Gram-positive bacteria with a low DNA mol% G+C and have rigid cells walls containing muramic acid. names in taxonomy. For more on ultra-small Proteobacteria- A very large of group of Gram-negative bacteria (bacilli and cocci) with generally reactogenic LPS or LOS (Chs 2 and10) in their bacteria, see Explore the Microbial World outer membranes and five subdivisions (alpha, beta, gamma, delta and epsilon). “Tiny Cells.” Bacteroidetes- the second most populous in the human gut after Firmicutes (Gram-positive), with the predominance of the Bacteroides and Prevotella genera b Mycoplasma is a bacterium that lacks a cell wall and can thus take on many shapes PREPARED BY: BRENT JOY H. HERNANDO 16 (pleomorphic means “many shapes”). Largest Bacteria Major Phyla of Bacteria PREPARED BY: BRENT JOY H. HERNANDO 17 Some major phyla of Bacteria based on Epulopiscium fishelsoni Thiomargarita namibiensis PREPARED BY: BRENT JOY H. HERNANDO 13 Two very large Bacteria. (a) Epulopiscium 16S ribosomal RNA gene sequence fishelsoni. The rod-shaped cell is about 600 um comparisons. (a) Depicted are the major (0.6 mm) long and 75 um wide and is shown with phyla of Bacteria that have cultivated four cells of the protist Paramecium (a microbial species. The area of each wedge is roughly eukaryote), each of which is about 150 um long. proportional to the number of described (b) Thiomargarita namibiensis, a large sulfur cultivated species in each group. Analyses of chemolithotroph and currently the largest 16S rRNA gene sequences from natural known of all prokaryotic cells. Cell widths vary environments suggest there are more than 80 from 400 to 750 um. bacterial phyla. The bacterium Epulopiscium fishelsoni (Figure 1.6a; Figure 1.9), which is found in the gut of the surgeonfish, can be more than 75 um wide and 600 um long  Saccharomyces in b. Domain: Eukarya Plants, animals, and fungi are the most well-known groups of Eukarya. The first eukaryotes, however, were unicellular microbes. Microbial eukaryotes vary dramatically in size, shape, and physiology. Among the smallest are the nanoflagellates, which are microbial Prokaryote predators that can be as small as 2 mm long. vs In addition, Ostreococcus, a genus of green algae that contains species whose cells are only 0.8 mm in diameter, are smaller than many bacteria. Eukaryote The major lineages of Eukarya are traditionally called kingdoms instead of phyla PREPARED BY: BRENT JOY H. HERNANDO 18 PREPARED BY: BRENT JOY H. HERNANDO 23 Phylogenetic Tree of Eukarya PREPARED BY: BRENT JOY H. HERNANDO 21 The tree diagram provides a schematic PREPARED BY: BRENT JOY H. HERNANDO 24 view of phylogenetic relationships for five of the best-characterized Microbial Nomenclature supergroups within the Eukarya. Colors The science of classifying living beings is taxonomy. It originated more than 250 years are used to identify the supergroups in ago when Carl von Linné (also known as Linnaeus; 1701–1778), a Swedish botanist, laid down the basic rules for classification and established taxonomic categories, or taxa (singular: taxon). the tree. Dashed lines indicate both Nomenclature is the assignment of scientific names to the various taxonomic categories and individual organisms. primary endosymbioses of mitochondria Classification attempts the orderly arrangement of organisms into a hierarchy of taxa. Identification is the process of discovering and recording the traits or organisms so that and chloroplasts, and the secondary they may be recognized or named and placed in an overall taxonomic scheme. endosymbioses of red and green algae. Protists are common in all eukaryotic lineages except the Opisthokonta (Fungi PREPARED BY: BRENT JOY H. HERNANDO 25 and Animalia) and the plants. Microbial Nomenclature The method of assigning a scientific or specific name is called the binomial (two- name) system of nomenclature. The scientific name is always a combination of the generic (genus) name followed by the species name. Microbial The generic part of the scientific name is capitalized, and the species part begins with a lowercase letter. Both should be italicized (or underlined if using handwriting), as follows: Cell Staphylococcus aureus Structure The two-part name of an organism is sometimes abbreviated to save space, as in S. aureus, but only if the genus name has already been stated. PREPARED BY: BRENT JOY H. HERNANDO 26 PREPARED BY: BRENT JOY H. HERNANDO 22 Microbial Nomenclature Microbial cell structure. (a) (Left) Diagram of a prokaryotic cell. (Right) The source for nomenclature is usually Latin or Greek. If other languages such as English or French are used, the endings of Electron micrograph of Heliobacterium these words are revised to have Latin endings. The inspiration for names is extremely varied and often rather modesticaldum (Bacteria, cell is about 1 mm imaginative. Some species have been named in honor of a microbiologist who originally discovered the microbe or who has made outstanding in diameter) and Thermoproteus contributions to the fi eld. Other names may designate a characteristic of the microbe (shape, color), neutrophilus (Archaea, cell is about 0.5 mm a location where it was found, or a disease it causes. in diameter). (b) (Left) Diagram of a eukaryotic cell. (Right) Electron micrograph PREPARED BY: BRENT JOY H. HERNANDO 27 of a cell of Saccharomyces cerevisiae (Eukarya, cell is about 8 mm in diameter). In terms of relative scale, the bacterial cell in a is about the same size as the mitochondria of  Microbial Nomenclature Major Morphologies of Prokaryotic Cells “Bacillus” has two meanings in microbiology. As we have just used it, bacillus refers to a bacterial shape. When capitalized and italicized, it refers to a specific genus. For example, the bacterium Bacillus anthracis is the causative agent of anthrax. Bacillus cells often form long, twisted chains of cells. If a species is unknown, the abbreviation "sp." is used in place of the species name and is non-italicized. The abbreviation "spp." is similarly used to indicate a group of unknown species. Bacillus sp. Bacillus spp. Bacillus spp. PREPARED BY: BRENT JOY H. HERNANDO 28 PREPARED BY: BRENT JOY H. HERNANDO 33 Spiral bacteria have one or more twists; Microbial Nomenclature they are never straight. Bacteria that look like curved rods are called vibrios (Figure 4.4a). Others, called spirilla (singular: spirillum), have a helical shape, like a corkscrew, and fairly rigid bodies (Figure 4.4b). Yet another group of spirals are helical and flexible; they PREPARED BY: BRENT JOY H. HERNANDO 29 are called spirochetes (Figure 4.4c) Unlike the spirilla, which use propeller-like Microbial Nomenclature external appendages called flagella to move, spirochetes move by means of axial filaments, which resemble flagella but are contained within a flexible external sheath. Viruses PREPARED BY: BRENT JOY H. HERNANDO 30 WHERE DO THEY BELONG? Major Morphologies of Prokaryotic Cells Share your thoughts… PREPARED BY: BRENT JOY H. HERNANDO 34 Viruses are not cells, and they lack the cytoplasmic membrane, cytoplasm, and ribosomes found in all forms of cellular life. PREPARED BY: BRENT JOY H. HERNANDO 31 Viruses do not carry out metabolic processes; instead, they take over the metabolic systems of Major Morphologies of Prokaryotic Cells infected cells and turn them into vessels for producing more viruses. Unlike cells, which all have genomes composed of double-stranded DNA, viruses have genomes composed of DNA or RNA that can be either double- or single- stranded. https://microbenotes.com/bacterial-sizes-shapes- arrangement/ PREPARED BY: BRENT JOY H. HERNANDO 32  Viruses ARE NOT FOUND ON THE TREE OF LIFE They are obligate parasites. PREPARED BY: BRENT JOY H. HERNANDO 35 Microorganisms provide essential models that give us fundamental knowledge about life processes. Some microorganisms cause diseases which may result in death. Microorganisms that cause diseases are called pathogens. These pathogens infect other organisms and cause various signs and symptoms in the organism. Life Cycle of Virus PREPARED BY: BRENT JOY H. HERNANDO 36 REFERENCES: E-BOOKS: 1. Tortora, G.J.; Funke, BMichael T. Madigan_ Jennifer Aiyer_ Daniel H. Buckley_ W. Matthew Sattley_ David A. Stahl - Brock Biology of Microorganisms-Pearson (2021). Pearson Education. ISBN 10: 1-292- 40479-5 2.. R.; Case. C. L., 2016. Microbiology : an introduction 12th Edition. Pearson Education Inc., United States of America. ISBN 10: 0-321-92915-2; ISBN 13: 978-0-321-92915-0 (Student edition) 3. Cowan, M.K.,2012. MICROBIOLOGY: A SYSTEMS APPROACH, THIRD EDITION. The McGraw-Hill Companies, Inc. ISBN 978–0–07–352252–4 PREPARED BY: BRENT JOY H. HERNANDO 37 REFERENCES: WEBSITES: 1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4711186/ 2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4711186/ 3. https://www.sciencedirect.com/topics/immunology-and-microbiology/proteobacteria 4. https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/bacteroidetes 5. https://microbenotes.com/bacterial-sizes-shapes-arrangement/ PREPARED BY: BRENT JOY H. HERNANDO 38