Survey of the Microbial World

Survey of the Microbial World

Unit 3: 5 days

February 24th and 25th: Prokaryotes

• Important manuals divide bacteria based on several criteria:– Gram stain reaction– Cellular morphology– Oxygen requirements– Nutritional properties

• Many rRNA discoveries are helping to classify bacteria better

Classification

• Three major domains:

Archaea

• Highly diverse with respect to morphology, reproduction, physiology, and ecology

• Grow in extreme habitats– Anaerobic– Hypersaline– High temps

Archaea

• Cell walls do not contain peptidoglycan• Differ from bacterial cell walls in structure• Membrane lipids have branched chain

hydrocarbons connected to glycerol by ether links– Bacteria and eukaryotes

have glycerol connected to fatty acids through ester bonds

Archaea

• Some can synthesize methane• Have unique glucose catabolism and pathways

for CO2 fixation• Have distinguishable tRNA, ribosomes,

elongation factors, and RNA polymerases

Archaea

• Five major types:– Methanogenic archaea– Sulfate reducers– Extreme halophiles– Cell wall-less archaea– Extreme thermophiles

• Two official phyla:– Crenarchaeota– Euryarchaeota

Crenarchaeota

• Extremely thermophilic• Sulfur metabolizers• Frequently acidophiles• S may be used as an electron

acceptor in anaerobic respiration, or as an electron donor for lithotrophs

• Most are strict anaerobes• Found in geothermally

heated soil and water that is rich in sulfur

Euryarchaeota

• Contains 5 major groups:– Methanogens– Halobacteria– Thermoplasms– Extreme thermophilic S metabolizers– Sulfate reducers

Methanogens

• Strict anaerobes• Obtain energy through

synthesis of methane• Several unusual cofactors

involved in methanogenesis

Halobacteria

• Aerobic chemoheterotrophs• Require at least 1.5 M NaCl for growth• Found in salt urns, salt lakes, and salted fish

• Halobacterium salinarium can carry out photosynthesis without chlorophyll (uses a different pigment)

Thermoplasma

• Thermophilic• Grows in hot, acid coal refuse piles• Survives even without a cell wall

• Picrophilus can grow at pH 0

Thermococci

• Extremely thermophilic organisms• Can reduce sulfur to sulfide

Sulfate Reducers

• Many extreme thermophiles• Some use a variety of electron donors to

reduce sulfate

These archaea are being used to clean heavy metal waste from nuclear reactors

Bacteria

• Four major divisions:– The Deinococci and Nonproteobacteria Gram

Negatives– The Proteobacteria– The Low G and C Gram Positives– The High G and C Gram Positives

Deinococci and Nonproteobacteria Gram Negatives

• Order Deinococcales:– Aerobic– Gram positive– Cocci and rods– Unusually high resistance

to desiccation and radiation

Deinococcus radiodurans


• Photosynthetic bacteria:– Cyanobacteria carryout oxygenic photosynthesis• Very similar mechanism to the eukaryotic process

– Purple and green bacteria use anoxygenic photosynthesis• Bacteriochlorophyll pigments allow them to live in

deeper, anaerobic zones of aquatic habitats

Cyanobacteria and Purple Bacteria


• Phylum Planctomycetes:– Lack peptidogylcan in their cell walls

• Phylum Chlamydiae:– Nonmotile– Coccoid– Reproduce within the cytoplasmic vacuoles of

their host cells– Energy parasites


• Phylum Spirochaetes:– Slender, long, helical bacteria– Motile due to axial filament

• Phylum Bacteriodetes:– Obligate aerobes– Chemoheterotrophic– Nonsporing– Variable shapes

Proteobacteria

• General characteristics:– Largest and most diverse group– Gram negative– Often called the purple bacteria– No obvious overall pattern of morphology or

metabolism– Divided into 5 classes

Proteobacteria

• Class Alphaproteobacteria:– Purple nonsulfur bacteria can grow anaerobically

as photoorganoheterotrophs– Also aerobically as chemoorganoheterotrophs– Rickettsias are obligate

intracellular parasites– Rhizobium carries out

nitrogen fixation• Oxidize either ammonia

or nitrite to nitrate

Proteobacteria

• Class Betaproteobacteria:– Neisseria contains nonmotile, aerobic cocci that

usually occur in pairs• Colonize mucous membranes

– Buckholderia are aerobic rods• Almost always have a polar flagella

– Some have sheaths– Some are chemolithotrophic

Proteobacteria

• Class Gammaproteobacteria:– Largest subgroup– Some grow in long filaments or trichomes– Have gliding motility– Some use methane as their carbon source– Contains:• Pseudomonas – soil bacteria, pneumonia• Vibrionaceae – cholera, in raw shellfish• Enterobacteriaceae – human pathogen• Pasteurellaceae – domestic animal pathogens

Proteobacteria

• Class Deltaproteobacteria:– Anaerobic– Can use sulfur as electron acceptots– Bdellovibrio is a bacteria parasite• Grows in their periplasmic space

Proteobacteria

• Class Epsilonproteobacteria:– Smallest of the proteobacteria classes– Contain two important pathogenic genera:• Campylobacter• Helicobacter

– Microaerophilic – Motile– Helical of vibroid

Low G and C Gram Positives

• Phylum Firmicutes:– Class Clostridia– Class Mollicutes– Class Bacilli


• Class Clostridia:– Anaerobic– Rods– Form endospores– Responsible for

botulism, food spoilage, and putrefaction


• Class Mollicutes:– Mycoplasmas are actually Gram negative– Grow on agar to resemble fried eggs– Smallest bacteria capable of self-reproduction– Lack cell walls

• Why are they located in this section rather than with the other gram negative bacteria?


• Class Bacilli:– Divided into 2 orders• Bacillales and Lactobacillales

– Several important genera • Bacillus – food poisoning and anthrax• Thermoactinomyces – alergic reactions that lead to

Farmer’s Lung• Lactobacillus – carries out lactic acid fermentation• Leuconostoc – used in cheese and buttermilk

production

High G and C Gram Positives

• General characteristics:– Form branching usually non-fragmenting hyphae– Asexual spores• Called conidiospores

– Several distinctively different cell wall types

• Phylum is Actinomycetes


• Suborder Actinomycineae:– Irregular in shape– Nonsporing– Rods– Cause disease in cattle an humans


• Suborder Corynebacterineae:– Mycobacterium form rods or filaments that readily

fragment– Cell walls have a high lipid content and mycolic

acids– Acid-fast– Contain several important human pathogens– Some form aerial mycelia with spores


• Suborder Propionibacterineae:– Common skin and intestinal inhabitants– Important in cheese making– Causative agents of acne vulgaris


• Suborder Streptomycineae:– Important decomposers of complex organic

material– Produce useful antibiotics– Some are pathogenic to plants and animals


• Suborder Bifidobacteriales:– Irregular rod– Anaerobic– One of the first colonizers of the intestinal tract of

babies

February 27th: Fungi

• Widespread in the environment• Major limitation to growth are often water

and temperature range• Secrete enzymes outside of their body and

then absorb the digested food molecules• Eukaryotic, spore bearing, absorptive nutrition• No chlorophyll• Cell walls usually contain chitin

Importance

• Important decomposers• All heterotrophic• Play a role in many industrial processes• Used as research tools

Structure

• The body, or vegetative structure, of a fungus is called a thallus

• Fungi are grouped into molds or yeasts based on the development of the thallus

Structure

• Yeast:– Unicellular fungi that have a single nucleus– Asexual or budding reproduction– Sexual spore formation

• Mold:– Consist of long branched filaments of cells, called

hyphae, which form a tangled mass called a mycelium

– Mycelium can produce reproductive structures

Structure

• Some fungi alternate between mold and yeast forms in their lifecycle

• This is called being dimorphic

Fungi Structure

Nutrition

• Most are saprophytes• Grow best in moist dark habitats• Chemoorganoheterotrophic• Usually aerobic

• Some yeasts are fermentive

Reproduction

• Asexual reproduction often occurs in the fungi by production of spores that are easily dispersed

• Sexual reproduction is initiated by the fusion of hyphae of different mating strains– In some fungi the nucleus of the two conjoined

hyphae immediately fuse to form a zygote– In others the two nuclei stay separate, but divide

synchronously, and may fuse later

Fungi Lifecycle

Fungal Divisions

• Zygomycetes:– Coenocytic (multinucleate cells)– Saprophytic (decomposer)– Includes bread mold, Rhizopus stolonifer– Conjugation involves + and – strains

• Basidiomycetes:– Called the club fungi

Fungal Divisions

• Ascomycetes:– Called the sac fungi– Sac-shaped reproductive structure called an ascus

• Deuteromycetes:– Also called ‘fungi imperfecta’– They have no know sexual phase• Therefore imperfect

Slime Molds and Water Molds

• The plasmodial (acellular) slime molds move about as a multinucleate plasmodium

• When food or water is scarce, they form sporangia from which spores are produced


• The cellular slime molds consist of a vegetative stage called a myxamoeba

• These feed until their nutrients are exhausted, then the cells come together to form a moldlike multicellular structure called a sorocarp

• The sorocarp produces haploid cells that germinate when conditions are favorable

Slime Mold Pictures


• The chytrids are a group of terrestrial and aquatic fungi that produce motile zoospores – These have a single, posterior, whiplash flagella


• The oomycota (water molds) are characterized by the production of motile spores and production of resistant sexual spores

Additional Fungi Pictures

Fungal Diseases

• Systemic mycoses – infections within the body, typically begin in the lungs from inhalation of spores

• Subcutaneous mycoses – under the skin infections, spores enter through puncture wounds

• Yeast infections are common in the urinary tract and vaginal canal

• Most are opportunistic

Fungal Infection

March 5th: Algae, Protozoa, and Multicellular Parasites

• Algae – eukaryotic photoautotrophs

• Protozoa – unicellular, eukaryotic, chemoheterotrophs

• Helminths – parasitic worms of the phyla Platyhelminthes and Nemartoda

• Arthropods – (as vectors) animals from the phylum Arthropoda

Algae

• Most live in aquatic ecosystems• Reproduce asexually by cell division and

fragmentation• Many algae are sexual as well• Produce oxygen• Classified by structures and pigments

Algae Anatomy

Types of Algae

• Red algae grow deep in the ocean, can absorb blue light

• Green algae have chlorophyll a and b, store starch

• Multicellular algae include: Brown, Red, and Green

Types of Algae• Diatoms are unicellular and have silica in their

cell walls– Some produce a neurotoxin

• Dinoflagellates produce a neurotoxin that can cause paralytic shellfish poisoning and ciguatera

Types of Algae

• Euglenoids have a semi-rigid cell membrane and one flagellum– They are unicellular

Importance

• Algae produce most of the world’s oxygen

• Responsible for petroleum reserves

• Often symbiotic

Protozoa

• Unicellular• Chemoheterotrophic• Found in soil and water• Also as normal microbiota in animals

» Giardia lamblia

Types of Protozoa

• Entamoeba, Naegleria, and Acanthamoeba are parasitic amoeboflagellates that use pseudopods for motility

• Parasitic amoeboflagellates that use flagella include:– Giardia lamblia – intestinal infection– Trichomonas vaginalis – urogenital infections – Trypanosomes – blood transmitted by insect

vectors

Types of Protozoa

• Only one ciliate is parasitic to humans– Balantidium coli – form of dysentery

• Plasmodium causes malaria– Asexual reproduction occurs in red blood cells and

the liver of humans– Sexual reproduction takes place in the intestines

of the female mosquito

• Lots of others cause lots of diarrhea

Helminths

• Multicellular animals• A few are parasites in humans• The anatomy and lifecycle of a helminth is

modified for parasitism– The adult stage is found in the definitive host– Each larva stage requires an intermediate host

• Can be monoecious or dioecious

Platyhelminths

• Flatworms• Dorsoventrally flattened• Some may lack a digestive system• Some have a sucker which allows them to

attach to a host• Eggs often hatch into free swimmers• These enter an intermediate host

Platyhelminths

• Typically the flatworm bores out of its intermediate host

• They are then eaten by a definitive host

Tapeworm Anatomy

Circle of Life

• Beef tapeworm– Cattle are intermediate hosts– Humans are definitive hosts

• Pork tapeworm– Humans can be definitive or intermediate host

• Echinococcus granulosus– Humans are intermediate hosts– Dogs, wolves, and foxes are the definitive host

Nematodes

• Roundworms• Have a complex digestive system• Infect humans with their eggs:– Pinworms– Ascaris lumbricoides

• Infect humans with their larvae:– Hookworms– Trichinella spiralis– Anisakis worms

Pinworms

Ascaris lumbricoides

Hookworms

Trichinella spiralis

Anisakis worms

Arthropods

• Joint legged animals• Include ticks and insects• Often vectors for parasites

• Elimination of vector borne diseases is best accomplished by control or eradication of the vectors

March 11th: Viruses

• Either:– Exceptionally complex aggregations of nonliving

chemicals– Exceptionally simple living microbes

Viruses

• Contain: – A single type of nucleic acid– Protein coat– Sometimes a lipid, protein, and carbohydrate

envelope

• Obligatory intracellular parasites• Must use the cells synthesizing machinery to

replicate

Viruses

• Host range – refers to the spectrum of cells in which a virus can multiply

• Most viruses only infect one type of cell in one species

• Determined by the specific attachment site on the cell’s surface and the availability of host cellular factors

Viruses

• Viral size is determined by electron microscopy

• They range from 20 to 14,000 nm in length

• Viruses must be grown in living cells• The easiest viruses to grow are

bacteriophages

Viral Structure

• A virion is a complete, fully developed, viral particle – Composed of nucleic acid surrounded by a protein

coat

• The nucleic acid to protein relation is anywhere from 1% to 50%

Viral Structure

• The protein coat surrounding the nucleic acid is called the capsid

• Composed of subunits called capsomeres– Can be a single type of protein or many

• Some capsids are enclosed by envelopes – Made from protein, lipids, and carbohydrates

• Some envelopes are covered with carbohydrate-protein complexes called spikes

Viral Structure

• Helical viruses resemble long rods, and their capsids are long cylinders surrounding the nucleic acid– Ebola

Viral Structure

• Polyhedral viruses are many sided, usually the capsid is an icosahedron– adenovirus

• Enveloped viruses are covered by an envelope and are roughly spherical– Highly pleomorphic– Some are helical (influenza)– Some are polyhedral

(herpes simplex)

• Complex viruses have complex structures– E.g. many bacteriophages have a polyhedral

capsid, with a helical tail attached

Viral Structure

Taxonomy of Viruses

• Classification is based on:– Type of nucleic acid– Replication strategy– Morphology

• Family names end in –viridae• Genus names end in virus• Species names have not been assigned

Identification

• Serological tests are used most often to identify viruses

Viral Multiplication

• Viruses do not contain enzymes for energy production or protein synthesis

• To multiply a virus must invade a host cell and direct the cell’s metabolic machinery

Multiplication of Bacteriophages

• During a lytic cycle a phage causes the death and lysis of a host cell

• Some viruses can insert their nucleic acid into the nucleic acid of the host cell– This is called lysogeny

• During the attachment phase of the lytic cycle, sites on the phage’s tail fibers attach to complimentary receptor sites on the bacterial cell


• In penetration, phage lysozyme opens a portion of the bacterial cell wall, the tail sheath contracts to force the tail core through the cell wall, and the phage DNA enters the bacterial cell

• The capsid is discarded outside


• In biosynthesis, transcription of phage DNA produces mRNA coding for necessary proteins

• Phage DNA is replicated, and capsid proteins are produced

• During the eclipse period, separate phage DNA and protein can be found


• During maturation, phage DNA and capsids are assembled into complex viruses

• During release, phage lysozyme breaks down the bacterial cell wall, and the phages are released


• The time from absorption to release is called burst time – 20 to 40 mins

• Burst size is the number of newly formed phages that are released from a single cell – 50 to 200


• During the lysogenic cycle, the phage DNA is integrated into the bacterial DNA, and each subsequent cell division includes a replication of the bacteriophage DNA

Multiplication of Animal Viruses

• Attach to the plasma membrane• Penetration occurs by endocytosis or fusion• DNA is put into the nucleus, where

transcription occurs• Capsid and other proteins are produced in the

cytoplasm

DNA Animal Viruses

• Adenoviridae (Kennel Cough)• Poxviridae • Herpesviridae • Papovaviridae (HPV)• Hepadnaviridae (Hep B)

RNA Viruses

• Multiplication of RNA viruses occurs in the cytoplasm

• Retroviridae uses reverse transcriptase to transcribe DNA from RNA

• Some are released through budding of the host cell plasma membrane

Viruses and Cancer

• Some viruses have been linked to cancers in humans

• HPV is the most well known

Latent Viruses

• A viral infection that stays in the host for long periods of time without causing symptoms

• E.g. herpes and shingles

Exceptions to the Rule

• Viroids– Common in plants– Potato spindle tuber viroid disease

• Prions– CJD– Mad cow– Kuru

Survey of the Microbial World

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