Microbes Overview

1. Microbes Overview

2. Course content • Prokaryotes Archaea Bacteria • Eukaryotes (microbial Protists) Fungi Algae Protozoa • Viruses

3. 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.

4. 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)

5. 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

8. Binomial System of Nomenclature • devised by Carl von Linné (Carolus Linnaeus) • each organism has two names • genus name – italicized and capitalized (e.g., Escherichia) • species epithet – italicized but not capitalized (e.g., coli) • can be abbreviated after first use (e.g., E. coli)

9. Techniques for Determining Microbial Taxonomy and Phylogeny • classical characteristics • morphological • physiological • biochemical • ecological • genetic

12. Ecological Characteristics life-cycle patterns symbiotic relationships ability to cause disease habitat preferences growth requirements

13. Molecular Characteristics nucleic acid base composition nucleic acid hybridization nucleic acid sequencing genomic fingerprinting amino acid sequencing

15. The prokaryotes: Domain Archaea and Domain Bacteria

16. 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.

17. The Archaea

18. 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

19. 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)

20. 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

21. 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

22. 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

23. 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 oxidizingorganic compounds or H2 while reducingsulfates to sulfides. In a sense, they "breathe" sulfate rather than oxygen - eg. Archaeoglobus

24. Bacteria

25. 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.

27. 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

28. 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)

29. Acetobacter Agrobacterium infect plant

30. 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)

31. 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)

32. 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)

33. 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.

34. Clostridia • Eg. Clostridium – anaerobic, form endospores, rod shape, gram +ve • pathogenic bacteria causing gangrene, tetanus, botulism, and diarrhea

35. 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

36. 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 Streptococcus Bacillus

37. 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 • Actinomycetesresemble 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

38. THE EUKARYOTES : FUNGI, ALGAE, PROTOZOA

39. 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)

40. 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

43. Acquire nutrients by absorption. Secrete enzyme to break large organic mol. Into simple mol. • Reproduction of fungi – sexual & asexual

44. Asexual reproduction Several ways : • Transverse fission - Parent cell undergo mitosis, divide into daughter cell by formation of new cell wall • Budding – after mitosis, one daughter nucleus is sequestered in a small bleb that is isolated from parent cell by formation of cell wall

45. 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

46. conidiospores sporangiospores Chlamydiospores

47. Arthrospores conidiospores chlamydospores Blastospores sporangiospores

48. 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

50. Classification of fungi 1) Zygomycota • Coenocytic molds – zygomycetes • produce sporangiospores (asexual) and zygospores (sexual) • e.g. Black bread mold Rhizopus nigricans