Prokaryotic microbial diversity

1. Prokaryotic microbial diversity • Taxonomy • Study of the classification of living things • Bacterial taxonomy has been difficult • Species concept does not work • Ideally, classify by evolutionary relationship • Until recently, classification methods similar to identification methods • Morphology, etc.: shape, size, arrangement • Gram stain • Biochemical characteristics, e.g. aerobe

2. Relatedness is determined from DNA • Since 1960s, molecular techniques used to help determine relatedness • %G + C • DNA-DNA hybridization • Sequence of rRNA genes • Whole genome sequencing • rRNA gene sequences revealed the 3 domains • Archaea, Eubacteria, Eukaryota • Further genetic analysis shows family relationships • Gram negative and Gram positive difference is real.

3. Archaea: Archaebacteria • Different from Eubacteria because • rRNA genes different • Not peptidoglycan, but similar substance in cell walls • Odd branched lipids; other differences too. • Don’t cause disease • Classified into 3 groups by rRNA analysis • Some grow in normal environments, some are extremophiles. Examples of extremophiles: • Hyperthermophiles and acid loving species • Halophiles grow in very high NaCl concentrations • Methanogens: strict anaerobes, produce methane

4. Representative Eubacteria • Phototrophs • Autotrophic, use sunlight energy • Green sulfur, Green non-sulfur, Purple Sulfur, Purple non-sulfur • Bacteria use only 1 photosystem, do not produce oxygen • The “sulfur bacteria” can use reduced sulfur compounds as H donors for making sugar from CO2 • Color relates to pigments • Cyanobacteria: blue green “algae” • Similar to chloroplasts, release oxygen gas

5. Gram positive bacteria • Clostridium: rod shaped, spore forming • Strict anaerobes, ferment, make toxins • Mycoplasma: pleomorphic • Has no cell wall, stains pink, sterols in membranes • Bacillus: rod shaped spore former • Common in soil, some cause disease • Listeria: short rod • Psychrotrophic, causes disease • Lactobacillus: small fermenting rods • Helpful normal microbiota

6. Gram positive bacteria-2 • Streptococcus and Enterococcus • Round, fermenting, in chains, can cause disease • Staphylococcus: round, in clusters • Faculatative anaerobe, some cause disease • Corynebacterium: short rods in odd arrangements • Some normal microbiota, one causes disease • Mycobacterium: poorly staining rods • Have mycolic acids; cause disease or environmental • Actinomycetes: family of filamentous bacteria • Includes Streptomyces, maker of antibiotics

7. Gram Negative Bacteria • Wide variety with many families • 5 groups of “Proteobacteria” w/ Greek letters • Includes common environmental species, some that can’t make ATP, aerobes, anaerobes, disease causers • Pseudomonads: aerobic with great range of different C sources that can be used. • Enteric bacteria: facultative anaerobes, many of which can cause disease • Chlamydia: obligate parasites that cause disease • Spirochaetes: internal flagella, cause disease • Bacteroides and Cytophaga: much different genera with similar rRNA sequences.

8. Eukaryotic Microbial Diversity • Early attempts at taxonomy: all plants and animals • Whitaker scheme (late 20th century) • Five kingdoms • Modified by Woese’s work on rRNA • Three Domains, one of which is Eukaryotes • Protista: the grab bag Kingdom • Always recognized as a highly diverse group • In new schemes, split into 7 kingdoms • Since the application of molecular biology, taxonomy of all things constantly changing.

9. Eukaryotes vs. prokaryotes • Eukaryotes are larger • Eukaryotes have membrane-bound organelles • Nucleus, mitochondria, membrane systems • Larger size requires functional compartments • Mitochondria once bacteria? So same size! http://www.earthlife.net/images/eury-cell.gif

10. Microbial eukaryotes • Animals • Parasitic worms; studied by Parasitologists • Fungi • Yeasts and molds, studied by Mycologists • Several types can cause human disease • Protists • Unicellular eukaryotes with many different characteristics. Also studied by Parasitologists. • Some cause human disease • Plants: not of particular interest other than hosts

11. Kingdom Protista • Highly diverse group of organisms • Size range from 5 µm to several meters (kelp) • Defined more by what they aren’t • Nutrient/energy acquisition ranges from photosynthesis to predatory to detrivores • Important in many food webs • Provide link between bacteria and larger organisms library.thinkquest.org/ 12413/protist.html

12. Some protozoal terminology • Macronucleus and micronucleus • Two type of nuclei differing in size and function. • Cyst: a resting stage similar to a spore with a thick wall and low level of metabolism. • Trophozoite: stage in life cycle during which the microbe is feeding and growing. • Merozoite: Small cells with a single nuclei produced during schizogony. • Large, multinucleated cell undergoes cytokinesis to produce multiple daughter cells (merozoites)

13. Plant-like Protists • Contain chloroplasts • Representatives • Diatoms (right). • Diatomaceous earth = fossilized diatoms: abrasives and slug repellants. • Red, brown, yellow algae • Seaweed, source of agar • Dinoflagellates • Neurotoxins and red tide http://www.bhikku.net/archives/03/img/diatoms.JPG www.enviroliteracy.org/ article.php/534.html

14. Fungus-like • Water molds • Slime molds Animal-like protists Capable of ingesting their food. Found among many different groups, so not good for taxonomy. http://en.wikipedia.org/wiki/Slime_mold http://ar.geocities.com/seti_argentina/estamos_solos/ameba.jpg

15. Breaking up the Protista: various algae, slime molds, and Protozoa • What are the characteristics of Protozoa? • Unicellular eukaryotes • Lack a cell wall • Require moist environments (water, damp soil, etc) • Great amounts of diversity • Locomotion: float, cilia, flagella, pseudopodia • Nutrition: chemoheterotrophs, photoautotrophs, either • Simple to complex life cycles, reproduction • Different cell organelles, some lack mitochondria

16. How to classify? • Cell ultrastructure and molecular analysis becoming the main methods used for classification. • Suggests that several kingdoms would be appropriate. • Alternative scheme, keep the kingdom Protista, classify protozoa into several phyla • Your text: • 4 groups of protozoa • Algae • Slime molds • Water molds

17. Classification of Protozoa Alveolates Ciliates Apicomplexans Dinoflagellates Amoebae Shelled and unshelled Euglenozoa Ameobae Euglenoids Kinetoplastids Archaezoa Diplomonadida Parabasala http://www.jracademy.com/~mlechner/archive1999/paramecium.JPG

18. Protozoa: details and examples • Alveolates • Possess alveoli: small membrane-bound cavities of unknown function (classification by ultrastructure) • Ciliates: move by cilia, short flagella-like appendages • Includes disease-causing Balantidium • Apicomplexans: have a complex of specialized organelles at the apices (corners, tips) of the cells • Generally have complex life cycles • Include Plasmodium (malaria), Toxoplasma (toxoplasmosis).

19. Apicomplexans Complex structure of organelles involved in infection. http://cgdc3.igmors.u-psud.fr/microbiologie/apicomplexans_fichiers/image002.jpg

20. Alveolates continued • Dinoflagellates • Large group of plantlike protozoa, have photosynthetic pigments (chlorophylls), cellulosic cell walls, store sugars as starch. • RNA sequences show relationship to other aveolates, not to plants. • Large portion of fresh water and marine plankton • Some encased in silica • Some bioluminescent or produce red pigments • Some produce dangerous neurotoxins

21. Amoebae • Amoebae have 2 main characteristics • Move and feed using pseudopodia • Cytoskeleton aids extension of cell membrane, cytoplasmic streaming. • Lack mitochondria • Some have loose shells; some form cysts. • Fossilized shells major component in some limestones. • Some “ameobae” are classified in another group. • Entamoeba: example of disease-causing amoeba.

22. Euglenozoa • United by similar RNA sequences • Not particularly similar otherwise. Have mitochondria. • Amoebae: move by pseudopodia • Including disease-causing Naegleria and Acanthameoba • Euglenoids: Euglena and similar microbes • Photoautrophs, but: no cell walls, motile by flagella and other means, store paramylon instead of starch, and can grow heterotrophically in the dark. Not plants! • Kinetoplastids: mitochondrial DNA forms kinetoplast • Includes Trypanosma, a pathogen

23. Archaezoa • Lack mitochondria and some other organelles • Thought to be old, hence the name (“Archae-”) • But have mitochondrial genes in nucleus. • Diplomonadida: 2 nuclei plus flagella • Includes pathogen Giardia, forms cysts, causes diarrhea • Parabasala: Single nucleus plus parabasal body. • Wood digesting microbe of termite gut. • Trichomonas, inhabits vagina, potential STD http://www.mhhe.com/socscience/sex/common/ibank/ibank/0149.jpg

24. Algae • Green algae • Ancestors of plants • Red algae • Mostly marine • Source of food thickeners carrageenan and agar • Chrysophyta (golden algae, diatoms, etc) • Diatoms: major component of phytoplankton • Diatomaceous earth as abrasives, gardening tools • Brown algae • Common seaweeds, kelps http://habitatnews.nus.edu.sg/news/chekjawa/ria/photos/r119.jpg

25. Water Molds and Slime Molds • Water molds • Similar to fungi except for 4 major differences; • 2 of 4: cellulose, not chitin in cell wall; motile spores • Phytophthora: Irish potato blight, sudden oak death • Slime molds • Acellular slime molds: The Blob, giant multi-nucleated cell; reproduces into amoebae that are amphibious • Cellular slime molds, e.g. Dictyostelium: unicellular, aggregate into slug-like structure, model for primitive development and differentiation.

26. Fungi • Mycology: the study of fungi • Fungi are mostly saprophytes, all heterotrophs • Saprophytes: decay non-living organic matter • Fungi are the kings of decomposition • Heterotrophs: use pre-formed organic matter • Not autotrophs, not photosynthetic • Fungi grow into, through their food • Release extracellular enzymes, break down polymers into LMW compounds for transport

27. Fungi terminology and structure • Hypha (singular) hyphae (plural): thread • Hyphae may be partially separated into cells or not at all (ceonocytic). • Cytoplasm is continuous throughout hypha • Mycelium (plural mycelia): a mass of hyphae • Like a bacterial colony except really all one organism. • Some fungi are molds, some are yeasts • Yeasts are oval, unicellular • Dimorphic: able to grow as either form. • Typical of some disease-causing fungi

28. Impacts of Fungi • Disease: mycosis (plural mycoses) • Superficial (on hairs, nails) • Cutaneous (dermatophytes, in skin (athlete’s foot) • Subcutaneous (deeper into skin) • Systemic (in deeper tissues, usually via lungs) • Opportunists: serious disease when immune system is depressed. • Antibiotic production • Penicillium, Cephalosporium • Decomposition; Food industry (soy sauce)

29. Classification of fungi • By sexual reproductive structures • Fungi reproduce both asexually and sexually • Deuteromycota = Fungi Imperfecti • No longer a valid classification • Contained fungi that couldn’t be coaxed into having sex • Through morphological and molecular means (e.g. DNA analysis), being distributed into the other 3 phyla of fungi.

30. Classification-2 • Zygomycota: produce zygospores • Example: Rhizopus • Fusion of hyphae (haploid) of opposite mating types produces zygospore (diploid). • Zygospore produces a zygosporangium with haploid spores that are released. • Asexually, sporangium containing spores. sporangia Zygospore botit.botany.wisc.edu/ images/332/Zygomycota/Z...www.butte.cc.ca.us/.../ fungi.unks.html

31. Classification-3 • Ascomycota: the sac fungi • Sexual spores produced inside an ascus (sac) • Asexual spores are called conidiospores or conidia (singular conidium) • Many types of common molds are ascomycetes. Ascus conidia fungus.org.uk/ nwfg/ascus.htm inseto.rc.unesp.br/.../ fungos%20e%20micoses.htm www.ent.iastate.edu/.../ aspergillus_ear_rot.html

32. Classification-4 • Basidiomycota: the club fungi or mushrooms • After extensive growth of hyphae, opposite mating types fuse and above ground mushroom is formed. • Sexual spores are called basidiospores; asexual conidia can also be formed. Close-up of gills www.birdsasart.com/ bn106.htm www.fishing-in-wales.com/. ../fungi/parasol.htm