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

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.

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

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

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

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

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.

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.

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

Microbial eukaryotes Animals Fungi Protists 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

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

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)

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

Fungus-like Animal-like protists Water molds Slime molds 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

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

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

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

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).

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

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

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.

Euglenozoa Amoebae: move by pseudopodia 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

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

Algae Green algae Red algae Chrysophyta (golden algae, diatoms, etc) 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

Water Molds and Slime 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.

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

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

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)

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.

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

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

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