Microbial Diversity - Phylogenetics PDF 2023

MICR1010 MICROBIAL DIVERSITY: PHYLOGENETICS Lecturer: Dr. Stacy Stephenson-Clarke EMAIL: [email protected]  Three Domain System All organisms evolved from cells that formed over 3 billion years ago. The DNA passed on from ancestors is described as conserve...

MICR1010 MICROBIAL DIVERSITY: PHYLOGENETICS Lecturer: Dr. Stacy Stephenson-Clarke EMAIL: [email protected]  Three Domain System All organisms evolved from cells that formed over 3 billion years ago. The DNA passed on from ancestors is described as conserved. The Domain Eukarya includes the kingdoms Fungi, Plantae, and Animalia, as well as protists. The Domains Bacteria and Archaea are prokaryotes. Phylogenetic Tree  Grouping organisms according to common properties:  Fossils  Genomes  Mutations accumulated in the genomes serve as a molecular clock  Groups of organisms evolved from a common ancestor  Each species retains some characteristics of its ancestor  Microbial Diversity 4 Classification  The organization of organisms into progressively more inclusive groups on the basis of either phenotypic similarity or evolutionary relationship.  This is done through systematics, the study of the diversity of organisms and their evolutionary relationships Taxonomy  The science of classifying organisms  Shows degree of similarity among organisms  Organisms are characterized, named and classified according to several defined criteria 5  Microbial Diversity 6 Scientific Nomenclature  Application of formal rules for naming organisms  It follows the Binomial Nomenclature used throughout biology to consistently and accurately name organisms  Genus  Species epithets (species) Microbial Diversity 7 Nomenclature  The terms used are Latin or Latinized Greek derivations  They are set print in italics Example There are over 100 species of the genus Bacillus Examples of species in the genus: Lactobacillus lactis Lactobacillus acidophilus Lactobacillus brevis Making Scientific Names Familiar The Taxonomic Hierarchy Microbial Diversity 10 Nomenclature  Nomenclature is subjected to specific rules  These are regulated by the Bacteriological Code -The international Code of Nomenclature of Bacteria  The Bacteriological Code deals only with procedures for assigning names to organisms, not with the issues of taxonomic methods or interpretation  Approved Lists of Bacterial Names lists species of known classification  Classifying Microbial Diversity 11  International Committee on Systematics of Prokaryotes (ICSP) - Oversees the nomenclature and taxonomy of Bacteria and Archaea as well as give guidance to subcommittees that meet to establish and revise standards for description of new species in the different groups of prokaryotes  Bergey’s Manual and The Prokaryotes - Classification system used by microbiologists to describe the physiology, enrichment, isolation and cultivation of Bacteria and Archaea - provides identification schemes for identifying bacteria and archaea Methods of Classifying and Identifying Microorganisms  Morphological characteristics: useful for identifying eukaryotes; tell little about phylogenetic relationships  Differential staining: Gram staining, acid-fast staining; not useful for bacteria without cell walls  Biochemical tests: determine presence of bacterial enzymes One type of Rapid Identification Method for Bacteria One tube containing media for 15 biochemical tests is inoculated with an unknown enteric bacterium. After incubation, the tube is observed for results. Phenylalanine Arabinose Ornithine Adonitol Glucose Lactose Sorbitol Dulcitol Urease Citrate Lysine Indole V–P Gas H2S The value for each positive test is circled, and the numbers from each group of tests are added to give the code number. Comparing the resultant code number with a Code Number Microorganism Atypical Test Results computerized listing shows that the organism in the tube is Citrobacter freundii. 62352 Citrobacter freundii Citrate 62353 Citrobacter freundii None Methods of Classifying and Identifying Microorganisms in 14 Taxonomy Morphology Staining characteristics Nutritional properties Metabolic properties Habitat/Ecology Methods of Classifying and Identifying Microorganisms in Taxonomy 15 16 Genotypic Methods used in Bacterial Taxonomy  DNA Sequencing (DNA base composition)  Guanine + cytosine %  GC + AT = 100%  Two organisms that are closely related have similar amounts of various bases  Online databases (NCBI Genome Database)  DNA Fingerprinting  Electrophoresis of restriction enzyme digests of an organism's DNA  Comparing fragments from different organisms provides information on genetic similarities and differences  Nucleic acid hybridization  Measures the ability of DNA strands from one organism to hybridize with DNA strands of another organism  Greater degree of hybridization, greater degree of relatedness  Hybridization of >70% indicates same species DNA-DNA Hybridization Phylogenetic Relationships of Prokaryotes Domain Bacteria  Proteobacteria vs Nonproteobacteria  From the mythical Greek god Proteus, who could assume many shapes  Gram-negative  Chemoheterotrophic  Largest taxonomic group of bacteria  Five classes (alpha-, beta-, gamma-, delta-, epsilonproteobacteria) Bacterial Diversity 22 Four Major Divisions  1. Organisms with a Gram –ve type of cell wall  2. Organisms with a Gram +ve type of cell wall  3. Organisms lacking cell wall  4. Organisms whose cell walls lack peptidoglycan  23 Prokaryotes with Gram -ve cell walls Spirochetes 24  Gram –ve  Coiled, flexible cell wall (flexuous in shape)  Unique motility mechanism via axial filaments  Widespread in aquatic environments and in animals  Many are difficult or impossible to cultivate  Classification based on morphology and ability to cause disease  Treponema pallidum (syphilis)  Leptospira interrogans (excreted in animal urine - leptospirosis) Treponema pallidum 25 Leptospira interrogans 26  27 Gram-ve Aerobic rods and cocci represent a large and diverse group of prokaryotes Pseudomonads (Key genera: Pseudomonas) 28  Gram –ve  Straight or slightly curved rods  Obligately Aerobic  Chemo-organotrophs  Wide variety of organic compounds as energy source (metabolically diverse)  Motile by a polar flagella  Respiratory metabolism, never fermentative  Oxidase +ve , catalase +ve  Often produces pigments Pseudomonad 29 (Key genera: Pseudomonas)  Can be found in soil or water  Capable of breaking down xenobiotics eg pesticides and toxic chemicals  Very important in bioremediation  P. aeruginosa (opportunistic pathogen), causes urinary and respiratory tract infection  P. aeruginosa primarily found in soil Pseudomonad 30 (Key genera: Pseudomonas) TEM preparation of Pseudomonas sp Pseudomonad Bioremediation 32 Rhizobium and 33 Bradyrhizobium  Rods  Aerobic/microaerophilic  Non-sporeforming  Motile by one polar flagellum  Commonly pleomorphic under adverse growth conditions  Chemoorganotrophic  Fix nitrogen in the roots of leguminous plants Azotobacter 34  Gram –ve  Large rods  Obligately aerobic  Some strains motile by peritrichous flagella  Free living N2 fixing bacteria (N2 biogeochemical cycle)  Inhabits alkaline soil  Metabolizes carbon compounds oxidatively  Acids and other fermentative products are never produced Azotobacter 35 Azotobacter vinelandii  36 Facultative aerobic Gram-ve rods: represented by Enterobacteria and Vibrios Enteric Bacteria 37 (Escherichia coli, Salmonella, Enterobacter, Shigella, Klebsiella, Proteus, Yersinia)  Gram –ve  Straight rods (non-sporulating)  Non motile or motile by peritrichous rods  Facultative aerobes  Ability to ferment glucose  Catalase +ve ; oxidase –ve Enteric Bacteria 38  Inhabits the intestine of humans and other animals  E. coli: indicator of fecal contamination; causes foodborne disease, urinary infection, newborn Meningitis  S. enteritidis: common form of foodborne illness, gastroenteritis, food poisoning  Salmonella typhi: typhoid fever Enteric Bacteria (cont’d) 39  Shigella  Causes bacillary dysentery  Klebsiella  K. pneumoniae causes pneumonia  Serratia  Produces red pigment  Common cause of nosocomial infections  Proteus  Swarming motility; colonies form concentric rings  Yersinia  Y. pestis causes plague  Transmitted via fleas  Erwinia  Plant pathogens Proteus mirabilis Flagella Proteus mirabilis with peritrichous A swarming colony of Proteus flagella mirabilis, showing concentric rings of growth Bdellovibrio  Gram-negative  Comma-shaped rods  Obligate aerobe  Motile by single polar flagellum surrounded by a sheath  Inhabits soil, sewage, freshwater and marine water  Predators: attacks other Gram-negative bacteria Vibrio 42  Gram –ve  Rods or curved rods  Facultatively aerobic  Oxidase-positive  Found mainly in aquatic, marine, brackish or freshwater habitats  Genera include Vibrio, Aliivibrio and Photobacterium (bioluminescent)  Vibrio cholerae: cholera in humans  Vibrio parahaemolyticus: gastroenteritis from raw fish, shellfish and crustaceans Vibrio parahaemolyticus 43 Vibrio cholerae  45 Sulphate - and Sulphur-Reducing Bacteria  Sulphate - and Sulphur - reducing bacteria 46 (Key genera: Desulfovibrio)  Gram –ve  Obligate anaerobes  Anaerobic respiration  Utilizes S or SO42- as final electron acceptors  H2S is the product of sulfate or sulfur reduction   Widespread in aquatic and terrestrial environments that have become anoxic due to microbial decomposition  47 Obligate Intracellular Parasites (Rickettsia, Chlamydia) Rickettsias 48 (Rickettsia, Wolbachia)  Gram –ve  Coccoid or rod-shaped  Unable to reproduce outside of a host cell (obligate intracellular parasite)  Found in blood sucking arthropods (ticks, flea and insects)  Causes typhus fever and spotted fever such as Rocky mountain spotted fever Rickettsias 49  Rickettsias Slime layer Scattered Chicken rickettsias embryo cell Nucleus Rickettsias grow only within a host cell, such as the chicken Masses of embryo cell shown rickettsias in here. Note the scattered nucleus Rickettsias within the A rickettsial cell that cell and the compact has just been released masses of rickettsias from a host cell in the cell nucleus. Rickettsias 51 Rickettsia 52 (e.g. Wolbachia)  Gram –ve  Rod-shaped  Unable to reproduce outside of a host cell  Live in insects (arthropods) and other animals   Affects reproduction of insects  Causes male killing, feminization, pathenogenesis (development of unfertilized eggs) Wolbachia 53 Wolbachia are red inside the cells of this fruit fly embryo. Wolbachia: Male killing and 55 feminization of infected arthropods In an infected pair, only female hosts can reproduce. Males Females Neither infected Uninfected offspring Male infected No offspring Female infected Infected offspring Both infected Infected offspring Wolbachia Unfertilized female infected Infected female offspring Chlamydia 57  Gram –ve  Spherical  No peptidoglycan in the cell wall; grow intracellularly  Do not parasitize blood sucking arthropods  Form an elementary body that is infective Chlamydia 58  C. trachomatis: urethritis and genital tract disease (most common sexually transmitted disease)  C. psittaci: Pneumonia (psittacosis or parrot fever) Cells of C. trichomatis attached to 59 human fallopian tube tissues A damaged fallopian tube containing C. trachomatis cell legion 60  Chlamydias The elementary bodies Elementary body The bacterium’s infectious are released from the form, the elementary host cell. body, attaches to a host cell. Nucleus The reticulate bodies begin to convert back to elementary bodies. The host cell phagocytizes the elementary body, Host cell housing it in a vacuole. Vacuole forming Vacuole Reticulate body The reticulate body divides The elementary body successively, producing reorganizes to form a multiple reticulate bodies. reticulate body. Life cycle of the chlamydias, which takes about 48 hours to complete © 2013 Pearson Education, Inc.  62 Anoxygenic Phototrophic Bacteria (Purple Bacteria) Purple Sulfur bacteria 63 (Key Genera: Chromatium, Thiocapsa)  Gram –ve  Anaerobes  Phototrophs  Bacteriochlorophylls instead of chlorophyll, variety of carotinoids  Variety of colours Purple Sulfur bacteria 64  Utilizes H2S as an electron donor in photosynthesis 2H 2S + CO 2 ⎯⎯ ⎯ light →(CH 2O) + H 2O + 2S0  Does not produce O2 as a by-product of photosynthesis  Found in illuminated anoxic zones of lakes and other aquatic habitat where H2S accumulates such as sulfur springs Purple Sulfur bacteria 65 Purple sulphur bacteria 67 Selected Characteristics of Photosynthesizing Bacteria  69 Oxygenic photosynthetic bacteria Cyanobacteria 70  Gram –ve  Unicellular, filamentous forms  Oxygenic phototrophs  Liberate O2 during photosynthesis  Unique accessory pigments called phycobiliproteins  Many cyanobacteria have the ability to fix nitrogen (may contain heterocysts)  Gas vesicles that provide buoyancy  Widespread in nature Cyanobacteria Heterocysts Filamentous cyanobacterium The unicellular, nonfilamentous showing heterocysts, in which cyanobacterium Prochlorococcus nitrogen-fixing activity is located may be the world’s most abundant photosynthetic organism. (Electron micrograph courtesy of Claire Ting, Williams College)  72 Chemolithotrophic Bacteria  Sulphur oxidizing bacteria 73 (Thiobacillus sp, Beggiatoa)  Gram –ve  Aerobic rods  Grows in aquatic sediments  Chemoautotrophic  oxidize H2S to S0 for energy Methanotrophs and Methylotrophs 74  Gram –ve  Various shapes  Aerobes  Uses methane or other one-carbon sources as electron donors  Widespread in aquatic and terrestrial environments wherever stable sources of methane are present  Methylotrophs are organisms that can grow using one-carbon organic compounds  Endosymbionts of deep-sea vent mussels Electron micrograph of Methanotrophic 75 bacteria (Key genera: Methylmonas, Methylobacterium) Contains extensive internal membrane systems for methane oxidation  76 Prokaryotes with Gram +ve cell wall  77 Non-Sporulating Gram +ve Bacteria Staphylococcus  Gram-positive  Spherical/cocci-shape as grapelike clusters  Chemoheterotrophs  Facultative aerobes  Commonly found on the skin  S. aureus causes wound infections, is often antibiotic resistant, and produces an enterotoxin Streptococcus 79  Gram +ve  Aerotolerant anaerobes  Spherical/coccoid in chains  Catalase –ve  Homo-fermentative (produces lactic acid only, no gas formed)  Some members are pathogenic (S. pneumoniae) – produce enzymes that destroy tissue (haemolysin, collagenase)  Some are beneficial (Lactococcus sp used in dairy industry) Streptococcus 80  Some are beneficial (Lactococcus sp used in dairy industry) Lactobacillus 81  Gram +ve  Rods  Aerotolerant anaerobes  Can be hetero- or homo-fermentative  Common in dairy products (yogurt, sauerkraut), pickles  Produce lactic acid from simple carbohydrates  Resistant to acidic conditions  Colonize the body but rarely pathogenic Lactococcus sp vs 82 Lactobacillus sp  83 Spore-forming Gram + ve bacteria  Clostridium 84  Gram +ve  Rods  Obligate anaerobes  Endospore-producing  Found primarily in soil  Can be pathogenic to humans  C. tetani: causes tetanus  C. botulinum: causes botulism  Clostridium sp can fix N2  Clostridium sp can also produce butanol and acetone Tetanus caused by 85 Clostridium tetani Bacillus 86  Gram +ve  Rods (chains)  Aerobic or facultatively aerobic  Endospore-producing rods  Found primarily in soil  B. thuringiensis (insect pathogen used as biocide)  B. cereus (food poisoning)  B. anthracis (anthrax, can be fatal if inhaled) Endospore case This Bacillus cereus cell is shown emerging from the endospore. B. anthracis 88  B. anthracis 89 Forearm of a Section of brain patient  90 Gram +ve bacteria that lack cell wall  91 Mycoplasmas  Phylogenetically related to Gram +ve  Lack cell wall  Can be coccoid in shape  Can be aerobic or anaerobic  Can be found in soil or sewage  Can cause human and plant diseases  Mycoplasma pneumoniae : pneumonia Gram +ve bacteria that lack cell wall 92 (Phytoplasma)  Gram +ve  Lacks cell wall  Can be round or filamentous  Found in plants  Has been known to cause lethal yellowing disease in coconuts Phytoplasma: Lethal Yellowing 93 Actinobacteria 94 (Key genera: Streptomyces)  Gram +ve  Strict aerobes  Undergo filamentous growth  Produces spores  Have antibiotic-producing properties (e.g. chloramphenicol, tetracycline)  Found primarily in soils (alkaline or neutral) Streptomyces 96