Transcript Eukaryotic Microbial Diversity

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
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Relatedness is determined from DNA
• Since 1960s, molecular techniques used to help
determine relatedness
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%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.
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Archaea: Archaebacteria
• Different from Eubacteria because
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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
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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
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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
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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
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Gram Negative Bacteria
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• 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.
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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
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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
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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
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Some protozoal terminology
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• 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
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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
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Breaking up the Protista:
various algae, slime molds, and Protozoa
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What are the characteristics of Protozoa?
Unicellular eukaryotes
Lack a cell wall
Require moist environments (water, damp soil, etc)
Great amounts of diversity
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Locomotion: float, cilia, flagella, pseudopodia
Nutrition: chemoheterotrophs, photoautotrophs, either
Simple to complex life cycles, reproduction
Different cell organelles, some lack mitochondria
How to classify?
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• 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:
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4 groups of protozoa
Algae
Slime molds
Water molds
Classification of Protozoa
• Alveolates
– Ciliates
– Apicomplexans
– Dinoflagellates
• Amoebae
– Shelled and unshelled
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• Euglenozoa
– Ameobae
– Euglenoids
– Kinetoplastids
• Archaezoa
– Diplomonadida
– Parabasala
http://www.jracademy.com/~mlechn
er/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).
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Apicomplexans
Complex structure of
organelles involved in
infection.
http://cgdc3.igmors.upsud.fr/microbiologie/apicomplexans_fichiers/image002.jpg
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Alveolates continued
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– 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.
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Euglenozoa
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– 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
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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
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.
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Fungi
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• 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
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• 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
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• Disease: mycosis (plural mycoses)
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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
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• 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
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• 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
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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.
Closeup of
gills
www.birdsasart.com/ bn106.htm
www.fishing-in-wales.com/. ../fungi/parasol.htm
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