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Microbes Overview Course content Prokaryotes Archaea Bacteria Eukaryotes (microbial Protists) Fungi Algae Protozoa Viruses Introduction Taxonomy is the science of the classification of organisms, with the goal of showing relationships among organisms. Taxonomy also provides a means of identifying organisms. How would you classify? Types of classification: natural (Carolus Linnaeus, members share same characteristics) phenetic (based on similarities of biological and morphological characters); phylogenetic (considers differences and similarities of evolutionary processess) genotype (comparision of genetic similarity between organisms, 70% homologous belong to the same species) Taxonomic Ranks microbes are placed in hierarchical taxonomic levels with each level or rank sharing a common set of specific features highest rank is domain within domain - phylum, class, order, family, genus, species epithet, some microbes have subspecies Binomial System of Nomenclature devised by Carl von Linné (Carolus Linnaeus) each organism has two names name – italicized and capitalized (e.g., Escherichia) species epithet – italicized but not capitalized (e.g., coli) genus can be abbreviated after first use (e.g., E. coli) Techniques for Determining Microbial Taxonomy and Phylogeny classical characteristics morphological physiological biochemical ecological genetic Ecological Characteristics life-cycle patterns symbiotic relationships ability to cause disease habitat preferences growth requirements Molecular Characteristics nucleic acid base composition nucleic acid hybridization nucleic acid sequencing genomic fingerprinting amino acid sequencing The prokaryotes: Domain Archaea and Domain Bacteria Bergey’s Manual of Systematic Bacteriology 1923,David Bergey (prof of bacteriology) published a classification of bacteria for identification of bacterial (and archaea) species. Bergey’s Manual categorizes bacteria into taxa based on rRNA sequences. Bergey’s Manual lists identifying characteristics such as Gram stain reaction, cellular morphology, oxygen requirements, and nutritional properties. The Archaea Archaea Scientist identified archaea as a distinct type of prokaryotes based on its unique rRNA sequence Reproduce by : binary fusion, budding or fragmentation Cells shape : cocci, bacilli, spiral, lobed, cuboidal etc Not causing disease to humans/animals Cell wall contain proteins, glycoproteins, lipoproteins, polysaccharides Very high/low temp/pH, concentrated salts or completely anoxic (extreme environments) Archae are either gram +ve or gram –ve Classified into two phylum : 1) Crenarchaeota – most thermophyllic and many acidophiles and sulfur dependent; anaerobes e.g. Thermoproteus and Sulfobolus 2) Euryarchaeota – 5 major physiologic groups (the metanogens, the halobacteria, the thermoplasms, extremely thermophilic S°reducers and sulfate-reducing) The Methanogens - strict anaerobes - obtain energy by converting CO2, H2, methanol to methane or methane & CO2 - eg. Methanobacterium, Methanococcus - methanogenesis * last step in the degradation of organic compounds *occurs in anaerobic environments e.g., animal rumens e.g., anaerobic sludge digesters e.g., within anaerobic protozoa The Halobacteria - extreme halophiles - aerobic chemoorganotrophs (use organic compound as energy sources) - dependent on high salt content - cell wall dependent on NaCl, they disintegrated when [NaCl] < 1.5M - dead sea The Thermoplasms - lack cell walls - but plasma membrane strengthen by diglycerol tetraether, lipopolysaccharides, and glycoproteins - grow best at 55-59°C, pH1-2 - eg. Thermoplasma Extremely Thermophillic So-Reducers - strictly anaerobic - can reduce sulfur to sulfide - grow best at 88-100°C - motile by flagella - eg. Thermococcus Sulfate-reducing - irregular garm –ve coccoid cells cell walls consist of glycoprotein subunits - extremely thermophilic optimum 83°C isolated from marine hydrothermal vents - obtain their energy by oxidizing organic compounds or H2 while reducing sulfates to sulfides. In a sense, they "breathe" sulfate rather than oxygen - eg. Archaeoglobus Bacteria Domain Bacteria Bacteria are essential to life on Earth. We should realize that without bacteria, much of life as we know it would not be possible. In fact, all organisms made up of eukaryotic cells probably evolved from bacterialike organisms, which were some of the earlist forms of life. The Proteobacteria Largest group of bacteria. More than 500 genera gram-negative, some motile using flagella Most are facultative/obligate anaerobes Share common 16s rRNA sequence 5 distinct classes of proteobacteria (α,β, ε, ɣ,δ) : - Alphaproteobacteria - Betaproteobacteria - Gammaproteobacteria - Deltaproteobacteria - Epsilonproteobacteria Alphaproteobacteria Gram -ve Most are oligotrophic (capable of growing at low nutrient levels) Example of alphaproteobacteria ; 1) Most purple nonsulfur phototrophs are in this group (use light energy and CO2 and do not produce O2) 2) Nitrifying bacteria e.g. Nitrobacter (oxidize NH3 to NO3 by a process called nitrification) 3) Pathogenic bacteria eg. Rickettsia (typhus), Brucella (brucellosis), Ehrlichia (ehlichiosis) 4) Beneficial bacteria eg. Acetobacter and Caulobacter (synthesize acetic acid); Agrobacterium (used in genetic recombination in plants) Acetobacter Agrobacterium infect plant Betaproteobacteria Gram –ve oligotrophic (capable of growing at low nutrient levels) Differ with alphaproteobacteria in rRNA sequence Example of betaproteobacteria : 1) nitrifying bacteria eg. Nitrosomonas 2) pathogenic species, Neisseria (gonorrhea), Bordetella (whooping cough) 3) Thiobacillus (ecologically important), Zoogloea (sewage treatment) Gammaproteobacteria – largest class purple sulfur bacteria – obligate anaerobes that oxidize hydrogen sulfide to sulfur intracellular pathogens (Legionella, Coxiella), methane oxidizers (Methylococcus), facultative anaerobes that utilize glycolysis and the pentose phosphate pathway (Escherichia coli), pseudomonads –aerobes that catabolize carbohydrates (Pseudomonas, and Azomonas) Deltaproteobacteria Sulfate reducing microbes Eg. Desulfovibrio (important in the sulfur cycle) Myxobacteria – gram negative, soil-dwelling bacteria , dormant myxospores; common worldwide in the soils having decaying plant material or dung Epsilonproteobacteria Gram-negative rods, vibrios, or spiral Include important human pathogens Eg. Campylobacter (causes blood poisoning) The Gram Positive Bacteria In Bergey’s Manual, gram-positive bacteria (able to form endospore) are divided into those that have : - low G + C ratio (base pair in genome below 50%) - high G + C ratio Low G + C gram-positive bacteria include 3 groups clostridia, mycoplasms, Gram-positive Bacilli and Cocci High G + C gram-positive bacteria include mycobacteria, corynebacteria, and actinomycetes. Clostridia Eg. Clostridium – anaerobic, form endospores, rod shape, gram +ve pathogenic bacteria causing gangrene, tetanus, botulism, and diarrhea Mycoplasmas Facultative or obligate anaerobes lack cell walls Gram +ve (previously under gram negative category until nucleic acid sequences proved similarity with gram positive organisms) When culture on agar, form ‘fried egg’ appearance bcoz cell in the center of the colony grow into the agar while those around the spread outward Usually associated with pneumonia and urinary tract infections Fried egg appearance Gram positive Bacilli and Cocci Eg. Bacillus – form endospores, flagella (B.licheniformis synthesis antibiotic. B.anthracis cause anthrax) Eg. Lactobacillus – nonsporing rods, nonmotile, produce lactic acid as fermentation product. Mostly found in human mouth, intestinal tract, stomach. Protect body from pathogens Streptococcus – nonmotile, cocci associated in pairs and chain. Cause pneumonia, scarlet fever Bacillus Streptococcus High G+C gram-positive bacteria Include Corynebacterium, Mycobacterium and Actinomycetes that have a G+C ratio > 50% in the phylum Actinobacteria, which have species with rod-shaped cells Corynebacterium store phosphates in metachromatic granules. C. diptheria causes diphtheria Mycobacterium cause tuberculosis and leporosy. It has unique resistant cell walls containing mycolic acids. Hence, acid fast stain (for penetrating waxy cell walls) is used for its identification Actinomycetes resemble fungi as they produce spores and form filaments; important genera: Actinomyces found in human mouths; Nocardia useful in degradation of pollutants; and Streptomyces produces antibiotics THE EUKARYOTES : FUNGI, ALGAE, PROTOZOA FUNGI Organisms in kingdom fungi include molds, mushrooms, yeasts Fungi are aerobic or facultatively anaerobic (yeast), chemoheterotrophs, spore-bearing, lack chlorophyll Most fungi are decomposers, and a few are parasites of plants and animals Some fungi – cause disease (mycoses) Some fungi – essential to many industries (bread, wine, cheese, soy sauce) Characteristics of Fungi Body/vegetative struc. of fungi – Thallus Thalli of yeast – small, globular, single cell Thalli of mold – large, composed of long, branched, threadlike filaments of cell called hyphae that form mycelium Hyphae - septate - Aseptate (coenocytic) Fungi grow best in the dark, moist habitats Acquire nutrients by absorption. Secrete enzyme to break large organic mol. Into simple mol. Reproduction of fungi – sexual & asexual Asexual reproduction Several ways : 1) Transverse fission - Parent cell undergo mitosis, divide into daughter cell by formation of new cell wall 2) Budding – after mitosis, one daughter nucleus is sequestered in a small bleb that is isolated from parent cell by formation of cell wall 3) Asexual spore formation - filamentous fungi produce asexual spores through mitosis and subsequent cell division. several types of asexual spores : 1) Sporangiospores form inside a sac called sporangium 2) Chlamydospores form with a thickened cell wall inside hyphae 3) Conidiospores (conidia) produced at the tip or side of hyphae, not within sac 4) Blastospores produced from vegetative mother (hyphae) cell by budding 5) Arthrospores hyphae that fragment into individual spores conidiospores sporangiospores Chlamydiospores Arthrospores conidiospores chlamydospores Blastospores sporangiospores 4) Sexual reproduction in fungi Fungal mating type designated as + and –. 4 basic steps : 1) Haploid (n) cells from + and – thallus fuse, form dikaryon (cell with both +&- nuclei) 2) pair of nuclei within a dikaryon fuse to form one diploid (2n) nucleus 3) meiosis of the diploid restores the haploid state 4) haploid nuclei partitioned into + and - spores Classification of fungi 1) Zygomycota Coenocytic molds – zygomycetes produce sporangiospores (asexual) and zygospores (sexual) e.g. Black bread mold Rhizopus nigricans 2) Ascomycota Septate hyphae Form ascospores within sac-like structure call asci (sexual) Form conidiospores in asexual reproduction Eg Penicillium 3) Basidiomycota septate hyphae produce basidiospores (sexual), some produce conidiospores (asexual) Eg mushrooms, puffballs, stinkhorns Protozoa Eukaryotic, unicellular and lack of cell wall Motile (cilia, flagella, pseudopodia) Grow in moist habitats Some are in group of Planktonic (floating free in lakes, ocean and form the basis of aquatic food chain) Some protozoa can produce a cyst that provides protection during adverse environmental conditions Asexuall reproduction by binary fission, schizogony/multiple fission Sexually reproduction by conjugation 1)Nucleus undergoes mitosis 2)Cytoplasm divides by cytokinesis Schizogony/multiple fission Classification of protozoa Grouping based on locomotive structure do not reflect genetic relationship. 7 taxa of protozoa : alveolates, cercozoa, radiolaria, amoebozoa, eglenozoa, diplomonads, and parabasalids Alveolates Have small membrane cavities called alveoli beneath cell surface. 3 groups : ciliates (have cilia), apicomplexans (pathogen to animal), dinoflagellates (have flagella) Cercozoa Unicellular, called amoeba Move & feed by pseudopodia Have snail-like shells of calcium carbonate Radiolaria Amoeba that have ornate shells composed of silica Amoebozoa Have lobe-shaped pseudopodia, no shell Eg Acanthamoeba, Naegleria Eglenozoa move by means of flagella and lack sexual reproduction; they include Trypanosoma Diplomonad Lack mitocondria, golgi bodie Have 2 nuclei and multiple flagella Giardia Algae Simple eukaryotic, phototrophic organisms, like plants Carry out photosynthesis using chlorophyll Most live in aquatic environments Characteristic of Algae Unicellular or simple multicellular (thalli) Thallus of seaweed (large marine algae) are complex, with holdfast (attached to rock), stemlike stipes and leaflike blades Algae reproduce sexual and asexual (fragmentation & cell division) Classification of algae Classify according to their structure and pigment : - red algae - brown algae – cell wall composed of cellulosa & alginic acid - green algae - diatoms – silica cell wall composed of two halves called frustules that fit together like petri dishes frustule DIATOMS VIRUSES Characteristics of Viruses Viral disease – SARS, AIDS, influenza, herpes, common cold Viruses – miniscule, infectious agent with simple acellular organization and pattern of reproduction Viruses can exist – extracellular or intracellular Virion (complete virus particle) consist of : - nucleocapsid (composed of 1 or more DNA or RNA, held within capsid) - in some viruses – envelope (phospholipid membrane) Capsid - build by few types of protein = protomer - 3 types – helical, icosahedral, complex symmetry Virus structure Different types of virus Helical Icosahedral Types of capsids Helical Complex symmetry Virus size range 10-1000nm Most virus infect only particular host’s cells Eg. HIV only infect T lymphocytes (a type of white blood cell) Some viruses infect many kinds of cells in many different hosts Eg. Rabies can infect most mammals Viruses are obligatory intracellular parasites. They multiply by using the host cell’s synthesizing machinery to cause the synthesis of specialized elements that can transfer the viral nucleic acid to other cells Viral replication Virus cannot reproduce themselves bcoz: - have no genes for all enzyme needed for replication - have no ribosomes for protein synthesis Viruses dependent of host’s organelles and enzymes to replicate Virus replication – Lytic replication Lytic replication of bacteriophage Consist of 5 stages – attachment, entry, synthesis, assembly, release 1) Attachment – structure responsible for attachment to host = tail fiber. Attachment is dependent on chemical attraction and precise fit between T4 tail and protein receptor on E.coli cell wall 2) Entry – T4 release lysozyme to weaken peptidoglycan of E.coli cell wall. T4 inject genome into E.coli, leaving T4 coat outside. 3-4) Synthesis – viral enzyme degrade the bacterial DNA. E.coli start synthesis new viruses. T4 DNA is transcribed, producing mRNA which is translated to T4 protein (component of tail and head, lysozyme) 5) Assembly – T4 components are assemble in spontaneous manner to form mature virion 6) Release – newly assembled virions are released from the cell as lysozyme completes its work on the cell wall Lytic replication takes about 25min can produce 100-200 new virions each cycle