Microbial Classification PDF

Microbial Classification Dr. Moroianu Study of phylogenetic relationships Taxonomy is the science of classifying organisms Shows degree of similarity among organisms Systematics, or phylogeny, is the study of the evolutionary history of organisms Three domains Eukarya...

Microbial Classification Dr. Moroianu Study of phylogenetic relationships Taxonomy is the science of classifying organisms Shows degree of similarity among organisms Systematics, or phylogeny, is the study of the evolutionary history of organisms Three domains Eukarya Animals, plants, fungi Bacteria Archaea Methanogens Extreme halophiles Hyperthermophiles 2 Phylogenetic tree 3 Taxonomic hierarchy Nomenclature identifies groups and further subgroups containing shared characteristics 4 Classifying & Identifying Microorganisms Classification: placing organisms in groups of related species Lists of characteristics of known organisms Identification: matching characteristics of an “unknown” organism to lists of known organisms Clinical lab identification Bergey’s Manual of Determinative Bacteriology provides identification schemes for identifying bacteria and archaea Approved Lists of Bacterial Names lists species of known classification 5 Methods: 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 6 Classification of Prokaryotes Prokaryotic species: a population of cells with similar characteristics Culture: bacteria grown in laboratory media Clone: population of cells derived from a single parent cell Variant: slight genetic differences with no functional change Strain: accumulated genetic differences, leading to changes in behavior or properties How do prokaryotes multiply? 7 Classification of Viruses Not a part of any domain; not composed of cells; require a host cell Viral species: population of viruses with similar characteristics that occupies a particular ecological niche 8 Archaea classification overview Distinct taxonomic grouping; lack peptidoglycan Extremophiles Halophiles Require salt concentration >25% Thermophiles Require growth temperature over 80C Methanogens Anaerobic and produce methane 9 Important contributions of Archaea Primarily acknowledged to be beneficial rather than harmful Invaluable to global ecosystems, the play a role in: Nutrient cycling Wastewater treatment Plant immunity Their ability to occupy extreme environments allows them to reach areas and nutrients no other organism could 10 Archaea and human health Archaea can be manipulated to produce various chemicals and drugs Source of Taq polymerase, the enzyme used in PCR Compose 1.2% of microbiome Reduce skin pH which increases defense against infection May produce compounds preventing cardiovascular disease Many benefits to using archaea for pharmacological processes due to ability to withstand extreme conditions, however for this same reason difficult to grow and culture 11 Bacteria classification overview Primarily* divided into two groups Gram positive Thick peptidoglycan cell well Purple Gram negative Thin peptidoglycan cell well Lipopolysaccharide wall (and associated endotoxins) Pink *Important to note, there are always exceptions and some species of bacteria do not fall neatly into one or the other group 12  Bacteria of medical importance at a glance Domain: Bacteria (Gram-Negative) Phyla Selected Classes Notes Proteobacteria Alphaproteobacteria Includes Ehrlichia, Agrobacterium and Rickettsia Betaproteobacteria Includes Bordetella and Burkholderia Gammaproteobacteria Includes Vibrio, Salmonella, Helicobacter,and Escherichia Deltaproteobacteria Includes Bdellovibrio Epsilonproteobacteria Campylobacter and Helicobacter Cyanobacteria Cyanobacteria Oxygenic photosynthetic bacteria Chlorobi Chlorobia Photosynthetic; anoxygenic; green sulfur bacteria Chloroflexi Chloroflexi Include anoxygenic, photosynthetic, nonsulfur bacteria Chlamydiae Chlamydiae Grow only in eukaryotic host cells Planctomycetes Planctomycetacia Aquatic bacteria; some are stalked Bacteroidetes Bacteroidetes Phylum members include opportunistic pathogens Fusobacteria Fusobacteria Anaerobic; some cause tissue necrosis and septicemia Spirochaetes Spirochaetes include pathogens that cause syphilis and Lyme disease Deinococcus-Thermus Deinococci Deinococcus and Thermus 13  Bacteria of medical importance at a glance Domain: Bacteria (Gram-Negative) Phyla Selected Classes Notes Proteobacteria Alphaproteobacteria Includes Ehrlichia, Agrobacterium and Rickettsia Betaproteobacteria Includes Bordetella, Neisseria and Burkholderia Gammaproteobacteria Includes Vibrio, Salmonella, Helicobacter,and Escherichia Deltaproteobacteria Includes Bdellovibrio Epsilonproteobacteria Campylobacter and Helicobacter Cyanobacteria Cyanobacteria Oxygenic photosynthetic bacteria Chlorobi Chlorobia Photosynthetic; anoxygenic; green sulfur bacteria Chloroflexi Chloroflexi Include anoxygenic, photosynthetic, nonsulfur bacteria Chlamydiae Chlamydiae Grow only in eukaryotic host cells Planctomycetes Planctomycetacia Aquatic bacteria; some are stalked Bacteroidetes Bacteroidetes Phylum members include opportunistic pathogens Fusobacteria Fusobacteria Anaerobic; some cause tissue necrosis and septicemia Spirochaetes Spirochaetes include pathogens that cause syphilis and Lyme disease Deinococcus-Thermus Deinococci Deinococcus and Thermus 14  Bacteria of medical importance at a glance Domain: Bacteria (Gram-Positive) Phyla Selected Classes Firmicutes Bacilli (Endospores) Staphylococcus Streptococcus Clostridia (Endospores) Lactobacillales Listeria Enterococcus Staphylococcus Streptococcus dd Tenericutes Mycoplasmas Actinobacteria Actinobacteria Mycobacterium 15 Key points for bacterial classification Gram negative: Proteobacteria- mythical Greek god Proteus, assume many shapes Largest taxonomic group of bacteria Contains many pathogens Cyanobacteria- photosynthesizing bacteria, play role in ecosystems Bacteroidetes- many opportunistic pathogens Gram positive: Firmicutes- contains many pathogens Bacillus and Clostridium produce endospores 16 Phylogenetic tree 17 Diversity in bacteria 18 Diversity in eukaryotes 19 Origin of Eukaryotes Endosymbiotic theory - proto-eukaryote engulfed a protomitochondrion, and this endosymbiont became an organelle, a major step in eukaryogenesis, the creation of the eukaryotes. 20 Classification of Eukaryotes Protista: a catchall kingdom for a variety of organisms; autotrophic and heterotrophic Grouped into clades based on rRNA Fungi: chemoheterotrophic; unicellular or multicellular; cell walls of chitin; develop from spores or hyphal fragments Plantae: multicellular; cellulose cell walls; undergo photosynthesis Animalia: multicellular; no cell walls; chemoheterotrophic 21  Kingdom fungi ~100,000 species of fungi documented Heterotrophic organisms- gain nutrients via absorption Saprophytic (feed on dead matter) or parasitic (feed on living host) The image we associate with fungi is their fruiting body (mushroom) Meant for sexual reproduction Large network of mycorrhizae beneath the surface 22 Mycology Mycology: the study of fungi Chemoheterotrophs Decompose organic matter Aerobic or facultative anaerobic 23 Fungi: Vegetative structures Vegetative structure means not associated with reproduction Molds and fleshy fungi (filamentous fungi) The fungal thallus (body) consists of hyphae filaments; a mass of hyphae is a mycelium Septate hyphae: contain cross-walls Coenocytic hyphae: do not contain septa Vegetative hyphae obtain nutrients while aerial hyphae are involved with reproduction 24 Vegetative structures of filamentous fungi 25 Vegetative structures of yeast Yeasts Nonfilamentous and unicellular Budding yeasts divide unevenly Fission yeasts divide evenly 26 Dimorphism in fungi Dimorphic fungi are fungi that have a yeast (or yeast-like) phase and a mold (filamentous) phase 27 Fungal lifecycle Fungi reproduce sexually and asexually via the formation of spores that detach from the parent and germinate into a new mold Asexual spores Produced via mitosis and cell division; formed by the hyphae of one organism Sexual spores Fusion of nuclei from two opposite mating strains Three phases of sexual reproduction 28  Fungal Spores Fungal spores are stress- resistant cells Survive extreme conditions (high temperatures, high exposure to UV radiation etc) Can remain dormant for up to 17 years Spores can survive for thousands of years frozen in permafrost Oldest viable spores believed to be 250 millions of years old 29 Sexual reproduction of fungi Plasmogamy- two cells fuse but nuclei do NOT fuse n+n Karyogamy- fusion of two haploid nuclei to form diploid nucleus Dikaryotic hyphae- product of plasmogamy, cells have two haploid nuclei and continue to grow mycelial network 30 Sexual reproduction of fungi Plasmogamy- two cells fuse but nuclei do NOT fuse n+n Karyogamy- fusion of two haploid nuclei to form diploid nucleus Dikaryotic hyphae- product of plasmogamy, cells have two haploid nuclei and continue to grow mycelial network 31 Sexual reproduction of fungi Plasmogamy- two cells fuse but nuclei do NOT fuse n+n Karyogamy- fusion of two haploid nuclei to form diploid nucleus Dikaryotic hyphae- product of plasmogamy, cells have two haploid nuclei and continue to grow mycelial network 32 Sexual reproduction of fungi Plasmogamy- two cells fuse but nuclei do NOT fuse n+n Karyogamy- fusion of two haploid nuclei to form diploid nucleus Dikaryotic hyphae- product of plasmogamy, cells have two haploid nuclei and continue to grow mycelial network 33 Largest living organism on EARTH 34 Largest living organism on EARTH The Armillaria ostoyae, or Humongous Fungus, covers 2385 acres (almost 4 square miles) 35 Fungal environments Grow better at pH of 5 Grow in high sugar and salt concentration; resistant to osmotic pressure Can grow in low moisture content, majority prefer high moisture Can metabolize complex carbohydrates Sensitive to UV Majority are mesophiles, growing between 25-30C (77-86F) 36 A medicine and a disease Penicillium fungi used to make penicillin, an antibiotic Tolypocladium inflatum produced cyclosporine which helps suppress the immune system for organ transplants Fungi can cause meningitis, lung disease, athletes food, and yeast infections Primary source of food spoilage (faster than bacteria) 37 Fungal influence on history Phytophthora infestans (fungus- like water mold) brought on the Irish Potato Famine from 1845- 1852 Salem witch trials in 1692 mostly started due to erratic behavior after consuming rye products with ergot fungus growing on it 38 Medically important fungi Microsporidia Zygomycota Ascomycota Basidiomycota 39 Microsporidia No sexual reproduction is observed, but probably occurs in a host No mitochondria Obligate intracellular parasites Infection ranges from asymptomatic to symptomatic infections that includes diarrhea, myositis, keratitis, and bronchitis 40 Zygomycota Conjugation fungi Coenocytic hyphae Produced asexually: sporangiospore Produced sexually: zygospore Forms when nuclei of two similar cells fuse 41 Ascomycota Sac fungi; septate hyphae Teleomorphic fungi Produce sexual and asexual spores Some are anamorphic Lost ability to sexually reproduce Produced asexually: conidiospore Produced sexually: ascospore Nuclei morphologically similar or dissimilar fuse in a saclike ascus 42 Basidiomycota Club fungi; septate hyphae Produced asexually: conidiospores Produced sexually: basidiospores Formed externally on a base pedestal called a basidium 43  Lichens Lichens as mutualistic combination of a green alga (or cyanobacterium) and fungus Alga produces and secretes carbohydrates; fungus provides holdfast Economic importance Dyes Antimicrobial (Usnea) Litmus Food for herbivores 44 Fungal relationship to humans Evolutionarily, fungi are more closely related to animals than they are to plants As a result, drugs that kill fungi are often dangerous and damaging to our own health 45  Fungal diseases Mycosis: fungal infection Systemic mycoses: deep within the body Subcutaneous mycoses: beneath the skin Cutaneous mycoses: affect hair, skin, and nails Superficial mycoses: localized (e.g., hair shafts) Opportunistic mycoses: fungi harmless in normal habitat but pathogenic in a compromised host 46 Economic benefits of fungi Saccharomyces cerevisiae: bread, wine, hepatitis B vaccine Trichoderma: cellulase Taxomyces: taxol Entomophaga: biocontrol Coniothyrium minitans: kills fungi on crops Paecilomyces: kills termites 47 Zombie apocalypse? Zombie ant fungus Cordyceps Ophiocordyceps unilateralis Insect pathogen Mind control Inspiration for the game The Last of Us 48 Fungi Review- Notable mention 49 Fungi Review- Zombie apocalypse? Zombie ant fungus Cordyceps Ophiocordyceps unilateralis Insect pathogen Mind control In a twist- there are pathogenic fungi infecting the zombie ant fungi!! 50 PLANT TO HUMAN FUNGI ARE HERE! Year 2023 we saw first case of a plant fungus infecting a human host Chondrostereum purpureum infected a 61yo mycologist Went to the doctor complaining of sore throat Doctors found hyphae growing in neck Sign of global warming affecting fungi 51 Protists clarification Groups of protists do not share a common ancestor with each other that is not also shared with plants, fungi, and animals Protists are a group of all the eukaryotes that are not fungi, animals, or plants 52 Visualization of phylogenetic tree 53 Algae- photosynthesizing protists Not a taxonomic group (mixed among other groups) Unicellular or filamentous photoautotrophs Lack roots, stems, and leaves Mostly aquatic Water is necessary for growth and reproduction All reproduce asexually Multicellular algae can fragment or reproduce sexually via alternation of generations 54 Selected phyla of algae Brown algae (kelp) Cellulose and alginic acid cell walls Multicellular and macroscopic Produce algin-thickener used in foods 55 Selected phyla of algae Red algae Have branched thalli Most are multicellular Harvested for agar and carrageenan Some produce a lethal toxin 56 Selected phyla of algae Green algae Cellulose cell walls Unicellular or multicellular Chlorophyll a and b Store starch Gave rise to terrestrial plants 57 Selected phyla of algae Diatoms Pectin and silica cell walls Unicellular or filamentous Store oil Produce domoic acid- cause neurological disease Contracted by swimming in saltwater affected by algal blooms 58 Selected phyla of algae Dinoflagellates Cellulose in plasma membrane Unicellular Neurotoxins (saxitoxins) cause paralytic shellfish poisoning Dinoflagellates are the most common cause of algal blooms in salt water 59