BIO3124 Bacteria 2023 Student Microbiology PDF

Bacteria BIO3124 General microbiology Textbook Chapter 3 Openstax Microbiology Chap 3 Art by David Goodsell (E.coli) Chapter 3 Overview § A synopsis of the bacterial cell § The cell membrane and transport § The cell envelope and cytoskeleton § How bacterial cells divide § The nucleoid: structure...

Bacteria BIO3124 General microbiology Textbook Chapter 3 Openstax Microbiology Chap 3 Art by David Goodsell (E.coli) Chapter 3 Overview § A synopsis of the bacterial cell § The cell membrane and transport § The cell envelope and cytoskeleton § How bacterial cells divide § The nucleoid: structure and expression § Specialized structures: vesicles, nanotubes, pili, and more § Bacterial flagella and chemotaxis 2 Morphology: Size of microorganisms Three domains of life: Bacteria Archaea Eukarya (protists (algae and protozoa), fungi, molds) Helminths (multicellular but microscopic) Viruses and other acellular microbes (virions and prions) Chap 1.3 Morphology: shapes How do bacteria know what shape they have to be? What molds their shape? Morphology: Cell arrangements Figure 3.14 General structure of a bacterium A typical bacterial cell contains: • a cell membrane, • chromosomal DNA that is concentrated in a nucleoid and extrachromosomal DNA called plasmids • ribosomes, • and a cell wall. Some prokaryotic cells may also possess flagella, pili, fimbriae, and capsules. Features of the cytoplasm Structure Composition Function Nucleoid DNA, RNA, protein Genetic information storage and gene expression Extra chromosomal DNA DNA Variable, encode non-chromosomal genes for a variety of functions Enzymes Protein Replication of the genome, transcription Metabolism, Cell signaling Regulatory factors Protein, RNA Control of replication, transcription, and translation Ribosomes RNA, protein Translation (protein synthesis) Cell inclusions Various polymers Storage or reservoir Gas vesicles Protein Buoyancy Magnetosomes Protein, lipid, iron Orienting cell during movement Cytoskeleton Protein Guiding cell wall synthesis, cell division, and possibly partitioning of chromosomes during replication Modified from ©2018 John Wiley & Sons, Inc. 3.2 Membrane Molecules and Transport • Membrane Lipids • Membrane Proteins • Molecules Cross the Cell Membrane 3.2 The Cell Membrane (plasma membrane is the same) Lipid bilayer • Separate in/out • Fluidity Membrane proteins • Integral or peripheral • Transport • Osmosis • Energy (cell respiration) • Sensing • Secretion Membrane Lipids Charged head Hydrophobic tail FIGURE 3.5 Phospholipids. A. Phosphatidylglycerol consists of glycerol with ester links to two fatty acids, and a phosphoryl group linked to a terminal glyceride. B. Phosphatidylethanolamine contains a glycerol linked to two fatty acids, and a phosphoryl group with a terminal ethanolamine. The ethanolamine carries a positive charge. Membrane Lipid Diversity Microorganisms live in vary different environments (hot, cold, salty, etc.), membrane lipid diversity helps to respond to these conditions. • Cardiolipin (diphosphatidylglycerol) • • • Palmitic and oleic acid • • Saturated or unsaturated, add fluidity to the membrane in cold temp. Cyclopropane fatty acid • • • Localizes to the cell poles Binds certain environmental stress proteins, such as a protein that transports osmoprotectants when the cell is under osmotic stress Stiffens the cell membrane wikipedia The conversion of unsaturated fatty acids to cyclopropane is an important process for Mycobacterium tuberculosis pathogenesis Hopanoids • Cholesterol Stabilizes membranes like cholesterol wikipedia 11 Membrane Lipids: Hopanoids Figure 3.8 Hopanoids add strength to membranes. Hopanoids limit the motion of phospholipid tails, thus stiffening the membrane. Hopanoids Cell membrane function • Polar and charged molecules must be transported. • Transport proteins accumulate solutes against the concentration gradient • Holds transport proteins in place • Generation of proton motive force 3.3 The Envelope and Cytoskeleton • The Cell Wall Is a Single Molecule • Cell Envelope of Bacteria • Cell Envelope—Gram-Positive • Cell Envelope—Gram-Negative • Mycobacterial Cell Envelope • Bacterial Cytoskeleton The Cell Wall Is a Single Molecule § The cell wall (or envelope) confers shape and rigidity to the cell and helps it withstand turgor pressure. § The bacterial cell wall (or envelope), consists of a single interlinked macromolecule. • Like a flexible mesh bag or scaffold • This mesh is made of peptidoglycan. • 100+ distinct peptidoglycans have been described 15 Cell wall function In prokaryotic cells, the cell wall provides some protection against changes in osmotic pressure, allowing it to maintain its shape longer. The cell membrane is typically attached to the cell wall. Rigid sugar-protein coat Figure 3.16 Peptidoglycan Structure Rigid layer that provides strength typically composed of: • alternating modified glucose • N-acetylglucosamine and N-acetylmuramic acid in β-1,4 linkages • amino acids • L-alanine, D-alanine, D-glutamic acid, and either L-lysine or diaminopimelic acid (DAP) Can be destroyed by lysozyme • enzymes that cleave glycosidic bond between sugars • found in human secretions, major defense against bacterial infection http://library.open.oregonstate.edu/micr obiology/chapter/bacteria-cell-walls/ How peptidoglycan are arranged to form the wall Gram - Gram + Sugar backbone Bridge between 2 peptides Copyright ©2018 John Wiley & Sons, Inc. A. Peptidoglycan crosslinking in E. coli B. Peptidoglycan crosslinking in S. aureus Note: Amino acids have two forms that are mirror opposites, D and L, of which only the L form is incorporated by ribosomes into protein. The D-form amino acids, however, are used by microbes for many nonprotein structural molecules. Peptidoglycan Structure – cont’d § Peptidoglycan is unique to bacteria. • Thus, the enzymes responsible for its biosynthesis make excellent targets for antibiotic. – Penicillin inhibits the transpeptidase that cross-links the peptides. – Vancomycin prevents cross-bridge formation by binding to the terminal D-Ala-D-Ala dipeptide. • Unfortunately, the widespread use of such antibiotics selects for evolution of resistant strains. 19 Peptidoglycan Structure – cont’d § Growth of peptidoglycan occurs via a synthesis complex that extends the chains of amino-sugars. § So-called penicillin-binding proteins catalyze the formation of peptide cross-bridges. § Overall direction of cell wall extension is organized by a protein complex that includes MreB (actin homologue). 20 Peptidoglycan Growth in Different Species § Bacterial species differ in where they synthesize new peptidoglycan in their growing cell walls: • In dispersed zones • At the septum • At the poles 21 Cell Envelope: Gram-positive and Gram-negative Gram positive Gram negative Stains Blue with Gram stain Stains Pink with Gram stain S-layer is not part of the cell wall per say, but an outer layer present in some Bacteria and Archaea. 22 Gram stain Most well established method for distinguishing bacterial morphology and cell wall composition Gram + retain the crystal violet dye but Gram – do not. A counterstain is added (fuchsine or safranin) and whilst Gram + stay violetblue, Gram - retain the red of the safranin. http://stanleyillustration.com/latestwork/2015/2/8/ngoo8tdfmqo4tyh0v ksu37vqroxnvs Exoenzymes: Digests nutrients that are too large to pass Has multiple layers of peptidoglycan threaded by teichoic acids Teichoic Acid: • Glycopolymer • Neg. charged (helps generate proton motive force) • Rigidity, cell shape • Protects against high temp. or high salt conditions • Protects against antibiotics (Abx) like β-lactams • lipoteichoic acids: teichoic acids covalently bound to membrane lipids LPS consists of core polysaccharide: • O-polysaccharide • and lipid A Multiple serotype exist and defines the O- in bacterial serotype: Ex. E.coli O157:H7 H is for flagellar protein. Sometimes K is used for capsular polysaccharide antigens. Other Differential Stains § Acid-fast stain: carbolfuchsin used to stain Mycobacterium species § Spore stain: malachite green used to detect spores of Bacillus and Clostridium § Negative stain: colors the background, which makes capsules more visible 26 Acid-fast bacteria Acid-fast stained M. tuberculosis sputum Hydrophobic layer (mycolic acids are lipids) Looks light blue with Gram stain but bright pink with special stain Pathogen Recognition and Innate Immunity, Akira et al., Cell 124, 783–801, February 24, 2006 Why so much detail for these structures? *The cell wall is ESSENTIAL for most bacteria* Antimicrobials target cell structures and cell processes • Antibiotics are for bacteria only • Antimicrobials include drugs against viruses, fungi and parasites. • Bactericidal KILLS bacteria • Bacteriostatic INHIBITS growth • Nosocomial infection: acquired in hospital care Antibacterial drug targets Subject of your first Cases study! Important to know what is targeted by antimicrobials Openstax Microbiology Chap 14.3 How antibiotic resistance happens Resistance is a genetically acquired tool to resist the toxic effects of an antibiotic. The organisms’ genome is changed, and the genetic material can be shared with other microbes (mostly same species, but cross-species sometimes). From CDC website https://www.cdc.gov/drugresistance/about.html https://www.youtube.com/watch?v=plVk4NVIUh8 Why is it such a problem? • People die of infectious diseases (not even drug resistant ones) ALL THE TIME! • If all these infectious agents became drugs resistant, then we are back to the medieval ages of medicine! Planet wise, 25% of deaths are attributable to microbial infections 11 to 12 millions of deaths per year WHO 2016 Ischaemic heart disease and stroke are the world’s biggest killers, accounting for a combined 15.2 million deaths in 2016 (26.7% of all deaths). Lower respiratory infections remained the deadliest communicable disease, causing 3.0 million deaths worldwide in 2016. The death rate from diarrhoeal diseases decreased by almost 1 million between 2000 and 2016, but still caused 1.4 million deaths in 2016. In 2012 0.1/10 death < 15 yo 4/10 death < 15 yo 7/10 death > 70 yo 2/10 death > 70 yo 6.5 millions of children deaths < 5 ans. 99% of those in low-income countries. CDC’s biggest threats list (2013) https://www.cdc.gov/drugresistance/biggest_threats.html Urgent threats: Serious threats: • C.difficile • Multidrug resistant Acinetobacter • Carbapenem-Resistant Enterobactericeae (CRE) • Drug-resistant Campylobacter • Neisseria gonorrhoeae • Extended Spectrum Enterobacteriaceae (ESBL) • Fluconazole-resistant Candida • Vancomycin-resistant Enteroccocus (VRE) • Multidrug resistant Pseudomonas Aeruginosa • Drug-resistant Non-Typhoidal Samonella • Drug-resistant Salmonella Serotype Typhi • Drug-resistant Shigella Don’t memorize this! • Methicillin-resistant Staphylococcus Aureus (MRSA) • Drug-resistant Streptococcus pneumonia • Drug-resistant Tuberculosis Concerning threats: • Vancomycin-resistant S. aureus • Erythromycin-resistant Group A Streptococcus • Clindamycin-resistant Group B Streptococcus Clostridium difficile 223900 Hospitalization/year 2019 AR threats report From 2013 -2019 13,000 Carbapenem-resistant Enterobacteriaceae (CRE) bacteria Stable 2013-2019 Neisseria gonorrhoeae Fact sheet: https://www.cdc.gov/drugresistance/pdf /drug-resistant-gonorrhea-508-final.pdf Drug-resistant infections nearly doubled to 550,000 from 2013 to 2019 Antibiotic resistance monitoring in Canada Canadian Antimicrobial Resistance Surveillance System Report 2022 Antibiotic resistance monitoring in Canada 42.8% 5.6% 18% Non-GP/FP and non-physiscian: dentist, nurse practitioners, optometrists, pharmacists, veterinarians Canadian Antimicrobial Resistance Surveillance System Report 2022 Canadian Antimicrobial Resistance Alliance (CARA) The Canadian Antimicrobial Resistance Alliance (CARA) started the CAN-R project in 2007 to track antimicrobial resistance across Canadian hospitals. • Link: http://can-r.com/study.php?study=canw2018&year=2018 Back to our cell surface structures… …next class. I hope we made it this far! Chapter 3 Overview § A synopsis of the bacterial cell § The cell membrane and transport § The cell envelope § Other cell surface structures § The cytoskeleton § How bacterial cells divide § The nucleoid: structure and expression § Specialized structures: vesicles, nanotubes, pili, and more § Bacterial flagella and chemotaxis 43 Other cell surface structures Glycocalyces • not considered part of cell wall because these do not confer significant structural strength • polysaccharide layers (may be thick or thin, rigid or flexible) • Capsules • Tightly attached, tight matrix; visible if treated with India ink • Slime layer • loosely attached, easily deformed (e.g., Leuconostoc) • assist in attachment to surfaces • role in development and maintenance of biofilms • virulence factors: protect against phagocytosis • prevent dehydration/desiccation Acinetobacter calcoaceticus The capsular material surrounding these bacteria (Acinetobacter calcoaceticus) is revealed in a suspension of India ink and viewed through a light microscope (magnified about 2,500×). From W.H. Taylor and E. Juni, “Pathways for Biosynthesis of a Bacterial Capsular Polysaccharide,” Journal of Bacteriology (May 1961) https://www.britannica.com/science/bacteria/Capsules-and-slime-layers Cell surface structures § S-layer • An additional protective layer commonly found in free-living Grampositive and Gram-negative bacteria and archaea • Crystalline layer of thick subunits consisting of protein or glycoprotein • May contribute to cell shape and help protect the cell from osmotic stress 45 Cell surface structures Fimbriae and pili • filamentous protein structures ~2–10 nm wide • Fimbriae enable organisms to stick to surfaces or form pellicles (thin sheets of cells on a liquid surface). Source: Khan Academy • Pili are typically longer, and fewer (1 or a few) found per cell than fimbriae. • Conjugative/sex pili facilitate genetic exchange between cells (conjugation). • Type IV pili adhere to host tissues and support twitching motility (e.g., Pseudomonas and Moraxella). Figure 3.30 The bacterial cytoskeleton shapes bacteria • Implicated in cell division • Shapes the morphology of the cell FtsZ: tubulin-like protein MreB: actin-like protein Crescentin: filament-like protein Skin and bones: the bacterial cytoskeleton, cell wall, and cell morphogenesis. Matthew T. Cabeen and Christine Jacobs-Wagner, The Journal of Cell Biology, Vol. 179, No. 3, November 5, 2007 381–387 Bacterial cytoskeleton • Necessary for the movement of ParM: actin-like protein molecules to the right location within the cell Example of Par system: • Segregates a dividing chromosome to both polls of the cell in preparation for cell division. • Also segregates extrachromosomal DNA such as plasmids. Plasmid partitioning system (wiki) 3.4 Bacterial Cell Division • Cell Division by Septation • DNA Is Organized in the Nucleoid • DNA Replication Regulates Cell Division 3.4 Bacterial Cell Division § Bacterial cell division, or fission, requires highly coordinated growth and formation of all the cell’s parts. • Unlike eukaryotes, prokaryotes synthesize RNA and proteins continually while the cell’s DNA undergoes replication. § Bacterial DNA replication is coordinated with the cell wall expansion and ultimately the separation of the two daughter cells. § Bacteria do not undergo mitosis or meiosis. 50 Cell Division by Septation § As DNA synthesis terminates, the cell divides by a process called septation, the formation of the septum. § The septum grows inward from the sides of the cell, at last constricting and sealing off the two daughter cells. § FtsZ subunit assembly circles around the septum in a “treadmilling” pattern, stepwise around the cell, that directs septal growth. Figure 9.3 Openstax Microbiology 51 Cell Division by Septation – cont’d § Septation requires rapid biosynthesis of all envelope components, including membranes and cell wall. § The overall process of septation is managed by a protein complex called the divisome. • One component of the divisome is FtsZ, which polymerizes to form the Z-ring. § To avoid the “guillotine” of the cell, septation is coordinated with DNA replication. 52 DNA Is Organized in the Nucleoid Microbiology OpenStax, Chap 3.3 Prokaryotic cells have a nucleoid region that extends throughout the cytoplasm and is not enclosed by a membrane. 53 DNA Is Organized in the Nucleoid – Cont’d In most bacterial species, the DNA is attached to the envelope at the origin of replication, on the cell’s equator. In prokaryotes, translation is tightly coupled to transcription. • The ribosomes bind to mRNA and begin translation even before the transcription of the mRNA strand is complete. 54 DNA Replication Regulates Cell Division § In prokaryotes, a circular chromosome begins to replicate at its origin, or ori site. § Two replication forks are generated, which proceed outward in both directions. • At each fork, DNA is synthesized by DNA polymerase, with the help of accessory proteins. – This protein complex is called the replisome. § As the termination site is replicated, the two forks separate from the DNA. § Completion of replication triggers Z-ring formation. 55 DNA Replication FIGURE 3.28 (Part 1) Replisome movement within a dividing cell. The DNA origin-of-replication sites (green) move apart in the expanding cell as the two replisomes (yellow) stay near the middle, where they replicate around the entire chromosome, completing the terminator sequence last (red). As the terminator sequence nears completion, FtsZ proteins assemble the Z-ring organizing septum formation. Source: Top 2 insets: Ivy Lau et al. 2003. Mol. Microbiol. 49:731. Bottom inset: Jackson Buss et al. 2015. PLoS Genet. 11(4). 56 DNA Replication FIGURE 3.28 (Part 2) Replisome movement within a dividing cell. The DNA origin-of-replication sites (green) move apart in the expanding cell as the two replisomes (yellow) stay near the middle, where they replicate around the entire chromosome, completing the terminator sequence last (red). As the terminator sequence nears completion, FtsZ proteins assemble the Z-ring organizing septum formation. Source: Top 2 insets: Ivy Lau et al. 2003. Mol. Microbiol. 49:731. Bottom inset: Jackson Buss et al. 2015. PLoS Genet. 11(4). 57 DNA Replication Regulates Cell Division 58 3.5 Cell Asymmetry, Membrane Vesicles, and Extensions • Bacterial Cell Differentiation • Growth Asymmetry and Polar Aging • Membrane Vesicles • Membrane Extensions and Nanotubes 3.5 Cell Polarity, Membrane Vesicles, and Nanotubes § Even superficially symmetrical bacilli such as E. coli show underlying chemical and physical asymmetry. • Such as possession of a chemoreceptor array at the “forward” pole § Other species, such as Caulobacter crescentus, develop different structures at either pole, and their cell division generates two different cell types. § And many kinds of bacteria extend their cytoplasm in surprising ways. 60 Bacterial Cell Differentiation Some bacteria generate two kinds of daughter cells: one stationary (sessile) and one mobile (swarmer). • Example: the flagellum-to-stalk transition of the bacterium Caulobacter crescentus 61 Growth Asymmetry and Polar Aging § The actual process of cell division itself determines that the poles of each daughter cell differ chemically from each other. • Polar aging is increased by stress. § A major form of asymmetrical growth is endospore formation by Firmicutes such as Bacillus and Clostridium species. • Endospores can remain dormant but viable for thousands of years. 62 Extracellular Membrane Vesicles and Nanotubes Surprisingly, microbial cells export bits of cytoplasm in membrane vesicles. These carry proteins and nucleic acids (RNA,DNA). Both Gram – and Gram + bacteria can shed membrane vesicles. 63 Extracellular Membrane Vesicles and Nanotubes – Cont’d § Some bacteria and archaea can form membrane extensions that merge directly with the membranes of neighboring organisms. • These nanotubes allow bacteria to directly share proteins and mRNA useful under hostile conditions, such as when exposed to antibiotics. 64 3.6 Specialized Structures • Thylakoids, Carboxysomes, and Storage Granules • Pili and Stalks • Rotary Flagella • Endospores 3.6 Specialized Structures: Thylakoids Thylakoids: extensively folded intracellular membranes found in photosynthetic bacteria 66 3.6 Specialized Structures: carboxysome Carboxysome: polyhedral bodies packed with the enzyme Rubisco for CO2 fixation 67 3.6 Specialized Structures: Gas vesicles Gas vesicles: protein-bound gas-filled structures that increase buoyancy 68 3.6 Specialized Structures: cell inclusions • Inclusions function as energy reserves, carbon reservoirs, and/or have special functions. • Enclosed by thin membrane • Reduces osmotic stress • Carbon storage polymers • glycogen: glucose polymer • poly-β-hydroxybutyric acid (PHB): lipid polymer, stored as lipid droplets. • PHB is produced by species of Bacillus and Pseudomonas. • Industrially, PHB has also been used as a source of biodegradable polymers for bioplastics. • Other types of stored energy or material Cell inclusions or storage granules 69 3.6 Specialized Structures: Pili § Pili (also called fimbriae) are straight filaments of pilin protein. • Used in attachment § Gram-negative enteric bacteria use sex pili for conjugation. Openstax, Microbiology, Chap. 3.3. 70 3.6 Specialized Structures: stalks and holdfast § Stalks are membraneembedded extensions of the cytoplasm. Stalk § Tips secrete adhesion factors called holdfasts. C. crescentus Holdfast Wagner, Jennifer K, PNAS, 2006. https://doi.org/10.1073/pnas.0602047103 Cell motility Several modes of locomotion: • Flagella, Archaella, and Swimming Motility • Gliding Motility • Chemotaxis and Other Taxes Rotary flagella and Swimming Motility Flagellar and flagellation • In bacteria • long, thin appendages (15–20 nm wide) • different arrangements: polar, lophotrichous, amphitrichous, peritrichous Figure 3.32 Microbiology OpenStax Flagella structure Rotation! helical in shape consists of several components Filament composed of flagellin. reversible rotating machine increase or decrease rotational speed relative to strength of proton motive force • Note: flagella rotate either clockwise (CW) or counterclockwise (CCW) relative to the cell. • • • • • Is this a Gram-negative or Gram-positive bacterial cell? Chemotaxis § Chemotaxis is the movement of a bacterium in response to chemical gradients. § Attractants cause CCW rotation. • Flagella bundle together • Push cell forward • “Run” § Repellents (or absence of attractants) cause CW rotation. • Flagellar bundle falls apart. • “Tumble” – Bacterium briefly stops, then changes direction. Figure 3.33 Microbiology Openstax Movement of flagellated bacteria - Chemotaxis Attractant concentration increases and prolongs run = more likely to run toward chemoattractant Chemotaxis Animation 77 Chemotaxis and other taxes • Taxis: directed movement in response to chemical or physical gradients • chemotaxis: response to chemicals • phototaxis: response to light • aerotaxis: response to oxygen • osmotaxis: response to ionic strength • hydrotaxis: response to water • monitor/sample environment with chemoreceptors that sense attractants and repellents Endospores Bacterial cells are generally observed as vegetative cells, but some genera of bacteria have the ability to form endospores, structures that essentially protect the bacterial genome in a dormant state when environmental conditions are unfavorable (not to be confused with the reproductive spores formed by fungi). Figure 3.19 Endospores Structure and features • many layers: exosporium (outermost), spore coats, cortex, core wall • contains dipicolinic acid and is enriched in Ca2+, both form the calcium-dipicolinic acid (DPA) complex • DPA complex help the cells to cope with dehydration and stabilize DNA • Core contains small acid-soluble spore proteins (SASP), which bind and protect DNA and function as carbon and energy source for outgrowth. • Core also contains the cytoplasmic membrane, cytoplasm, ribosomes and other cellular essentials. Endospores Figure 3.20 • Formed during endosporulation or sporulation (again, not to be confused with the reproductive spores formed by fungi) • Highly differentiated cells resistant to heat, harsh chemicals, and radiation • Survival structures to endure unfavorable growth conditions • “Dormant” stage of bacterial life cycle • Ideal for dispersal via wind, water, or animal gut • Present only in some gram-positive bacteria, (e.g., Bacillus and Clostridium), none in archaea, suggesting this process evolved in bacteria after split. Endospore Formation Animation 82 Bacterial taxonomy Bacteria are named using a binomial system: Escherichia coli Genus Species Taxonomic level Example Phylum Proteobacteria Class Gammaproteobacteria Order Enterobacteria Family Enterobacteriaceaea Genus Escherichia Species coli Genus: group of closely related species Species: group of organisms sharing common features while differing considerably from other organisms Strain vs serotype • Strain: Distinct subtype of species that differs genetically, and often phenotypically, from other subtypes. • Serotype (or serovar): Strain identified by serotyping (identifying surface antigens particular to a subspecies) Escherichia coli O147:H7 Genus Species Strain or serotype Escherichia coli BL21 Genus Mus musculus BALB/c Genus Species Influenza A virus Influenza virus A H1N1 Species Strain Bacteria Strain Genus Animal Species Virus Strain or serotype Serotyping Study.com Bacteria Patient serum Agglutination means patient is infected (has developed Ab against bacteria) Two serotypes 1a and 1b with antigens 2a and 2b on surface, which are recognized by two distinct antibodies, 3a and 3b, respectively Wikipedia Bacterial taxonomy Bacteria are typically classified according to shared characteristics: • • • • • • Morphology (colony appearance on a plate) Gram colouring Size and shape (rod or coccus, single, chain or cluster, …) Presence of structures (such as magnetosomes or flagella) Metabolic traits (energy source, enzymatic capacities,…) DNA sequence Bacterial taxonomy • 84 phyla identified so far • Only 32 of these have been described on the basis of strains in cultivation • 90% of strains in cultivation belong to one of only four phyla: • • • • Firmicutes Proteobacteria Bacteroidetes Actinobacteria Sample of known bacterial phyla For more info, see chapter 18 in your textbook. Copyright ©2018 John Wiley & Sons, Inc. Next class: Archaea