Ch 4: Microbial Diversity

how long have bacteria been around for?

3 billion years

what occurred that caused a massive die-off of early organisms?

changes in the atmosphere → presence of oxygen

vast prokaryotic diversity

~30,000 named prokaryote species

• gram negative

• gram postive

• deeply branching bacteria

• archaea

gram negative bacteria

proteobacteria

• alphaproteobacteria

• betaproteobacteria

• gammaproteobacteria

• deltaproteobacteria

• epsilonproteobacteria

non-proteobacteria

spirochetes

chlamydia

CFP group

gram positive bacteria

low-GC content (Firmicutes)

high-GC content (Actinobacteria)

alphaproteobacteria

• gram negative; proteobacteria

• includes many oligotrophs

  • capable of living in low nutrient environments

  • ex. deep oceanic sediments, glacial ice, deep undersurface soil

• includes several obligate intracellular parasites (can only grow inside a host cell)

  • ex. Rickettsia rickettsii — causes Rocky Mountain fever

• Caulobacter crescentus

  • move species for studying cell division

• Rhizobium species

  • fix nitrogen in root nodules of legumes

betaproteobacteria

• gram negative

• eutrophs — require large amounts of organic nutrients

• includes Bordetella and Neisseria

gammaproteobacteria

• gram negative

• most diverse group of proteobacteria

• includes E. coli (most important model bacterium)

• pathogens

  • Salmonella typhus, Legionella pneumophila, Vibrio cholera, Haemophilus influenza

deltaproteobacteria

includes sulfate-reducing bacteria & soil scavengers

• ex. Myxobacteria form multicellular colonies with different cellular roles, something unusual among bacteria

epsilonproteobacteria

• microaerophilic → likes small amounts of oxygen

• includes Campylobacter & Helicobacter

chlamydia

• gram negative

• many obligate intracellular pathogens & some symbionts

• Chlamydia trachomatis begins infection of host when metabolically inactive elementary bodies enter an epithelial cell

spirochetes

• gram negative

• thin, highly motile via axial filaments

• Borrelia burgdorferi → lyme disease

• move by a corkscrew motion and can traverse dense tissue

CFB group

• gram negative

• Cytophaga → motile aquatic

• Fusobacterium → human mouth pathogens

• Bacteroides → human intestine mutualistic bacteria

phototrophic bacteria

• use sunlight as primary source of energy

• contains both proteo- and nonproteobacteria

• color variations are common

low G+C content (Firmicutes)

• gram positive

• many species produce spores

• fewer GC nucleotides, faster growth — harder to break GC bond

examples of Firmicutes

• Clostridium

  • pathogens, obligate anaerobes

  • gas gangrene, tetanus, botulism

  • C. difficile causes drug-resistant infection

• staphylococcus aureus

  • common hospital-acquired drug resistant infection

• Streptococcus pneumonia

  • respiratory pathogen

• Lactobacillus

  • commensal with humans & fermenters

high G+C content (Actinobacteria)

• gram positive

• can live in environments of higher temps or of greater variations

• most live in soil; some aquatic, some produce spores

examples of Actinobacteria

• Mycobacterium

  • contain a waxy coat (mycolic acid) that naturally blocks some antibiotics

  • cause tuberculosis, leprosy

• Corynebacterium

  • causes diphtheria

  • industrially important for things like glutamate production

• Bifidobacterium

  • beneficial gut microbe — found in yeast

• Streptomyces

  • source of majority of naturally occurring antibiotics

deeply branching bacteria

• few ancient groups are only distantly related to other modern bacteria

• adapted to the harshest conditions on the planet — resembling condition thought to dominate the earth when life first appeared

• Acetothermus paucivorans — deeper branching bacterium

Archaea

• also unicellular prokaryotes

• cell walls of not contain peptidoglycan

• found in any habitat

  • some grow at moderate temps

  • many extremophiles — heat, salt, acid

• no significant human pathogens

  • some are commensals (part of microbiome)

• produce methane

endosymbiont theory

eukaryotes have many similarities to archaea, but mitochondria have similarities to proteobacteria

• maybe bacterium could use oxygen, while archaeon used byproducts

supporting evidence of the endosymbiotic theory

• mitochondria & chloroplasts divide → but they cannot divide outside of eukaryotes

• eukaryotes cannot make them from scratch

• each maintains its own DNA & ribosomes → separate from the main eukaryotic counterparts

• mitochondria/chloroplast genes are closely related to bacterial genes

• double membrane → thought to be a relic of phagocytosis

microbial communities

• in labs microbes grown as pure cultures

• prokaryotes live in a community (group of interacting populations of organisms)

population

group of individual organism belonging to the same biological species & limited to a certain geographic region

symbiosis

cooperative or competitive interactions between populations

• 5 different relationship types

5 types of symbiotic relationships

• mutualism

• amensalism

• commensalism

• neutralism

• parasitism

mutualism

both populations benefit

• sometimes both populations depend on each other — neither can thrive alone, need each other to survive

mutualism: aphids & Buchnera aphidicola bacteria

• aphids eat sap that is deficient in some amino acids

• bactria colonizes the aphid gut & synthesizes the necessary amino acids

amensalism

one organism harms another, without (immediate) gain to itself — not helped or hurt

examples of amensalism

• Streptomyces produce antibiotics that kill other bacteria

• during fermentation, some microbes acidify their environment, preventing growth of competitors

• Staphylococcus epidermis produces bacteriocins that kill other bacteria on the skin

commensalism

one organism benefits, the other is neither harmed nor helped

example of commensalism

Staphylococcus epidermis & other bacteria consume dead skin — host (human) is unharmed

neutralism

symbiotic organism are unaffected by their coexistence

*difficult to prove

example of neutralism

• dormant spores in the soil have no effect on other bacteria or plants

• metabolically inactive endospores

  • share soil with active bacteria with no apparent interaction until conditions change

parasitism

parasite benefit at the expense of the host

• most pathogens fit this description