02 - bacteria and archaea

is morphology and phenotype sufficient enough to distinguish prokaryotic species from one another?

no

what is an OTU?

operational taxonomic unit - a category used to classify prokaryotic organisms based solely on dna sequence similarity

why do we use OTUs?

because you need to consider both dna sequence similarity and phenotypes but most microbes cant be cultured in a lab so looking for phenotypes is hard, so we use OTUs.

is OTUs used to classify prokaryotes?

no; OTUs are not directly used to classify prokaryotes. dna sequencing is used to group microbes into OTUs based on sequence similarity

what is the 16S rRNA gene?

encodes the ribosomal RNA (~1500 nt long) in the small subunit of prokaryotic ribosomes

what are ribosomes made of?

made of ribosomal proteins and rRNA

where is 16S rRNA gene found?

in all prokaryotes

what is one thing we know about the similarity of 16S rRNA gene sequence?

the more similar the 16S rRNA gene sequence, the more closely related those organisms are

what is the 16S rRNA gene sequence used for?

used to distinguish bacteria from archaea and to distinguish different prokaryotic species

how are prokaryotic species defined?

with dna sequencing categorized into OTUs; sometimes phenotypes alone aren’t enough

what are the three domains of life? what experiment led to this conclusion?

archaea, bacteria, and eukarya; the experiment was the 16S rRNA led by Woese

what is the 16S rRNA?

what base pairs with the messenger rna with the shine series to initiate translation in bacteria

how do archaea and bacteria differ?

differ in chemical properties of cell wall and membrane, bacteria is sensitive to antibiotics and archaea is not sensitive to many, bacteria include animal and plant pathogens while archaea do not

how is the traditional prokaryotic “species” definition different from an OTU species?

traditional involves phenotypic review and the OTU just relies on dna sequencing

what are some characteristics of cyanobacteria?

oxygenic photosynthesis, the original producers of atmospheric O2, ancestors of chloroplasts (in plants and algae), and they have unicellular and filamentous forms

what are the types of proteobacteria?

alpha, beta, gamma, delta, epsilon, and zeta

what is alphaproteobacteria?

include bacteria that live with plants (Agrobacterium tumefaciens, Rhizobia)

what is betaproteobacteria?

include pathogens Bordatella pertussis, Neisseria gonorrhoeae, and Neisseria meningitidis

what is gammaproteobacteria?

include enterobacteria (including E. coli and Salmonella), vibrios (including Vibrio cholerae), and pseudomonads (including Pseudomonas aeruginosa)

what is epsilonproteobacteria?

include Helicobacterpylori

is proteobacteria gram negative or positive?

negative

what are firmicutes?

low gc content in genomes; gram positive in phylum but include mycoplasmas

what do firmicutes include?

include endospore-forming bacteria in the bacilli and clostridia classes; includes pathogens such as staphylococcus aureus, streptococcus pyogenes, and listeria monocytogenes; also lactobacillus species

what are bacteroidetes?

gram negative rods that may be obligate aerobes, facultative aerobes, obligate anaerobes

what do bacteroidetes include?

includes the genus bacteroids, a major component of the gut human microbiota

where do bacteroids thetaiotamicron live? what do they do?

in the large intestine and specializes in breaking down polysaccharides

what are actinobacteria?

gram positive; high gc content in genomes

what do actinobacteria include?

streptomyces genus (soil bacteria, filamentous, many species of streptomyces produce antibiotics)

what are two examples of achaea phyla

crenarchaeota and euryarchaeota

what does creanarchaeota include? what do they metabolize? where do they live?

thermoacidophiles that live in hot springs; metabolize sulfur; live in the ocean in non-extreme environments

what does euryarchaeota include?

methanogens (methane producers) and extreme halophiles (grow in high salt conditions)

how were archaea discovered

carl woese used 16S rRNA sequencing to show that some microbes thought to be bacteria were actually a separate domain of life