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!

10. 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

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
article.php/534.html

14. Fungus-like Animal-like protists Water molds Slime molds
Capable of ingesting their food.
Found among many different groups, so not good for taxonomy.

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

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.

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 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

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

24. 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

25. 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.

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... 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 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
bn106.htm /fungi/parasol.htm