what are the guidlines for compenstion on bioprospecting
requires prior informed consent form source country, sharing benefits and promoting sustainable use of biodiversity.
what is a new class of antibiotics
archeocins
where are the Korarchaeota found
yellowstone hotspring
What is the smallest organism known and how big is it?
nanoarchaeum, 400nm diameter
Explain how the nanoarchaeum is an obligate symbiont
it is an obligate sybiont with another archaen ignioccus, it must be in contact wit ingnicoccus to survive
Do archaea have viruses?
yes.
What is an example of the archaea viruses
STIV.
What was the first archaeophage described?
STIV
what type of enviornment does it prefer?
Acidic hyperthermal enviornment
All currently known archaeophage have what type of DNA?
dsDNA
Are Archaephage monophyletic?
we dont know yet, but we can say no for now bc its branched off myoviridae
what evidence supports the primordial hypothesis?
the fact that viruses from different domains are similar suggests that viruses may have evolved prior to LUCA
what is the eocyte hypothesis?
that crenarchaeota are sister to eukaryotes not euryarchaeota
with the eocyte hypothesis what two ways are beleived that crenarchaeota developed a nucleaus?
spontaneaous origin, endosymbiotic origin with gram negative bacterisum the aquired the crenarchaeota endosymbiont which later becaome nucleus
Name the 6 steps to cloning a DNA molecule.
DNA extraction
PCR
Ligation to plasmid
transformation of E. Coli
E. Coli culture on antibiotic medium
Individual colonies sequenced
After sequencing what is done in order to identify a DNA molecule
BLAST analysis
what is the problems that arise from phylogenetic analysis
some DNA does not have universal markers
what is an alternative to cloning?
sanger sequencing
name and explain the three methods of the phylogenetic analysis
neighbor joining which looks a the percentge of similarity.
Parsimony seeks the tree with the least evolutionary step
Likelihood based methods looks at the actual data to seek the most likely hypothesis.
Explain the Sanger sequence
ssDNA is mixed with primer and mixed with DNA polymerase, dNTPs, replications terminatiors and primerss for replication. they replicated, they are loaded onto a gel and electrophoresis is done,
What is the noncloning based second generation method
pyrosequencing
Summarize the Fierer et al study.
they clonned SSUrDNA for bacteria (16s), archaea (16s) and fungi (18s), clones genomes of vurs sampled soil, Found that there is higher diversity of viruses and bacteria vs archaea, fungi, Higher diversity of Praries bacteria and viruses relative to the rainforest.
The human body hosts how many species of bacteria
100k
How long does it take for a child to stabilize its flora?
1 to 6 months depending if a child was born c section or non c- section
Chilren who are breast fed have primaryly what type of bacteria, gram positive or gram negativce
gram positive
T/F formula fed babies have a less incidence of E. coli and low diversity of microbes
False, Babies who are fomula fed have higher incidence of proteobacteria and higher diversity of microbes overall
T/F E.coli is the dominate bacteria in human body
false it is the most common but not dominant
what is the bacillus shape? what does streptobacillus mean?
rod shaped. chain of rods
name 2 examples of bacillus bacteria.
E.coli and anthrax bacteria
what is the coccus shaped bacteria.
They are sphereical
what shape is staphylococcus?
graped shaped
what is the name of tbe bacteria that is formed into a cube with the round shaped coccus cells.
sarcina
what is an example of a disease that is caused by coccus bacteria?
gonorrhea
what coccus bacteria causes tooth decay
streptococcus
what shape of bacteria is part of out normal flora but also causes hospital acquired infection, food poisoning and toxic shock syndrome?
stapylococcus aureus.
what bacteria is part of out normal flora on our skin? what shape is it?
micrococcus luteus, it is sarcina shaped
what are comma shaped bacteria called?
vibrio
what is the largest and most physiologically diverse clade of bacteria?
Proteobacteria
T/F All Proteobacteria are gram positive
False they are all gram negative
T/F Proteobacteria are polyphyletic
False they are monophyletic
what are the5 major divisions of proteobacteria?
alpha, beta, gamma, delta, epsilon
what are the 4 groups of proteobacteria covered?
Purple phtotrophic bacteria, nitrifying bacteria, methanotrophs and methyltrophs, and spirilla
what are the two functional groups of purple phototrophic bacteria.
purple sulfur bacteria, puple non sulfu bacteria
All Purple phototrophic bacteria carry out what type of phtotsynthesis?
Anoxygenic
what pigments are used in the anoxygenic photosynethesis of purple phototrophic bacteria
bacteriochlorophylls and carotenoid
Purple Sulfur bacteria use ______ are electron donor and _______ is stored inside of cells and are phylogenetically united in _________ proteobacteria and are found commonly in _________
Hydrogen sulfide, sulfur, gamma, merimetic lakes
spirilium proteobacteria look like
have ridged spiral shape
what is meromictic lakes
lakes with permanet stratification (no mixing)
T/F Purple non sulfur bacteria can use Hydrogen sulfide.
true
purple nonsulfur bacteria are __________ and do not require light. They use _____ to obtain C. They represent _____ and ______ proteobacteria.
photoheterophic, organic molecules, alpha and beta
what are the proteobacterial chemolithotrophs
nitrifying bacteria
what are the two functional groups of nitrifying bacteria
______ is converted to ________ in nitrite oxidizing bacteria
Nitrate, nitrite.
what are the three groups of proteobactieral chemolithotrophs
Nitrifying bacteria, sulfur and iron oxidizing bacteria and hyrdogen oxidizing bacteria
what is an example of sulfur-iron oxidizing bateria? where does is live? what type of shape does it have?
beggioatoa. sulfur springs. filamentous
what source of E does the Beggiatoa use.
sulfur.
T/F Beggiatoa are mixotropic
False they are generally chemolitothrophs but some are mixotrophic and can switch to chemoorganotrophy
Hydrogen oxidizing bacteria belong to what groups of proteobacteria?
alpha, beta and gamma
what is the theory of endosymbiosis?
a seperate prokaryotic organism is taken into a eukaryotic cell
what are the 6 chracteristic of the bacteria phylum
Prokaryotic cells
peptidoglycan cell wals
ester linkage in membrane
Simple RNA polymerase
Protein Synthesis
Unique SSUrDNA sequences
Archae do not share all characteriscts except
that they do have prokaryotic cells
Eukaryontes do not share all characterictsic with bacteria except
they have ester linkages in the membrane lipids
what are the 2 funcitonal classifications of bacteria
Gram posistive and Gram negatice
what is the difference between gram positive and gram negative bacteria?
gram positive have a cell wall that is mainly peptidoclycan and they retain the gram stain color. Gram Negative do not retain the gram stain color and there out wall does not contain much peptidoglycan. they have two layers to outer membrane it have inner phospholipid layer and out lipopolysaccharide layer
T/F Gram negative bacteria have porins which are little pores in the outer membrane
true
what is the sister group of the gram positive bacteria?
cyanobacteria
What is polytomy?
when there are many branching off events that happen at the same time
what is the earliset arising bacteria
aquifex
T/F proteobacteria are monophyletic
true
T/F Alpha and Beta proteobacteria are monophyletic but the rest are not
False they are all monophyletic
Explain the species accumulation curve
It shows the species richness of a given species sample
what are shared characteristics of the all the bacterial lineages?
SSUrDNA, Common ancestor, gram negative
what is the sister group of the alpha proteobacteria?
whe dont know because they all branch out at the sam etim
what are the 7 major proteobacteral chemoorganotrophs
