exam 2 Flashcards
culturing
(on agar plate)
adv:
-inexpensive
-have isolates to work with for future studies (freezing them)
disadv:
-“not yet culturable” microbes
-difficult to distinguish strains/species based on morphology or chemical tests- shape, size, color is all the same
gut- 70% culturable
ocean-17% culturable
-on plates, can have a couple colonies but have thousands of cells in the coloniesm and we do not understand the interactions- widely unculturable
SSU rRNA
Woese’s method
rRNA is ubiquitous
conserved- in all life- human and e.coli share about 50% identity
has multiple variable regions, good for discrimination
Woese’s method- primitive method of sequencing
grow cells in isotope 32PO4 so DNA and RNA are labelled, collect pellets;isolate total RNA
then separate the 16S rRNA using gel electrophoresis
use RibonuvleaseT1 RNA to cleave the single-stranded RNA after guanine residues
resulting oligonucleotides are separated and sequences by the 2-dimensional electrophoresis and compared to synthesized dinucleotides with known sequences
phylogenetic tree construction
1) extract DNA from organisms/communtiy
2) PCR amplify SSU or rRNA (or portion) using universal primers (they recognize many dofferent 16S molecules)
3) sequence
4) align sequences so homologous residues line up
5) count differences between sequences
6) construct tree that most accurately represents all the pairwise differences
“relatedness map”
problems with 16sRNA based methods
16 S rRNA based methods do not capture eukaryotes and viruses
the internal transcribed spacer regions as well as the 18S rRNA (SSU in eukaryotes) gene have been used to characterize eukaryotes
Internal transcribed spacer (ITS) refers to the spacer DNA situated between the small-subunit ribosomal RNA (rRNA) and large-subunit rRNA genes in the chromosome
viruses are harder due to their vast diversity (ex RNA vs DNA, ss vs ds)
-they don’t make their own proteins, are obligate parasites, hard to distinguish spacers using 18S- uses ITS
study of individuals in ecology, concepts
3 concepts of what an individual is in ecolog
1) numerical:
- countable, independent unit
- colony forming unit
- fluorescent stains- can show chains of cells
2) genetic
- genet-a single genetic unit- works well for lions but not clonal organisms
- ramets-an individual colony/clone
3) ecological
- follows individuals through its life cycle from birth to death
- binary fissions- have identical offspring
- this is important for organisms that demonstrate changes in morphology, ploidy or other
benefits of biodiversity in science/biological systems
- natural products such as drugs
- productivity of ecosystem services
- stability of communities involved in ecosystem services
- resistance of invasion of natural communities
- diversity in the natural world enriches our lives
diversity-productivity relationship
productivity is diffcult to measure/define
relationship unclear for microbes
tropical forest: productivity increases with species diverstiy
temperate forest: productivity increases with diversity up to a certain point before decreasing as diversity increases
agriculture: productivity decreases as species diversity increases (highest productivity with low diversity)
ways of estimating diversity
1) richness (s)- number of species per unit of area
- comparing species across space and time gives imp insights into communities,
- limitation- all species are given the same weight
2) diversity indices- integrates abundance
ex: shannon and simpson index
both say that higher diversity when more species are present
higher diversity when eveneess in abundance is greater
3)refraction curves- estimate species richness from sampled communities
plot the number of species as a function of number of samples
the more individuals sampled, the more species found
refraction curves are the plots of the average number of species found in each sample given multiple resampling
slop- the steeper the slope, the higher the predicted richness, and the larger the sampling required to find the most species
4)community phylogenies
-based on phylogenetic methods using sequence data
-potentially provides insights into functional groups
-uniFrac distace metric
limited ability to estimate diversity
-has more potential for comparing diversity between systems
shannon index
H= pi ln pi
s=number of species
pi= relative abundance of each species- # of individs divided by # of total individs
the higher the number, the more diverse
simpson index
s- number of species
ni= number of organisms of species i
N= total number of all individuals
the lower the number the more diverse
caveats with all techniques
1) issues of species concepts
2) sampling design difficult
- size of samples
- number of samples
3) difficult to detect rare species
4) changes across temporal and spatial scales
- changes over hours and days
- changes over space
ex: lakes
competitive exclusion theory
2 species with similar resource requirements can’t coexist in same community, one will be more efficient and drive the other toward local extinction
community interactions
1) competitive exclusion theory
2) resource partitioning
3) top-down versus bottom up interactions
4) island biogeography
5) intermediate disturbance hypothesis
metagenomics use
can find novel genes for resistance such as antibiotic resistance in soil reservoirs
functional metagenomics: extract DNA from a colony, sequence it, fragment it and combine it with a vector, put the vector in lab microbial hosts and see what it does
metagenomics allows us to observe changes over time, but we can only tell the relative abundance of each microbe compared to the other microbes present, and we cannot tell just from metagenomic data whether strains are harmful or not
parasitism
Importance of parasites
Estimated 50% of described species are Estimated 50% of described species are parasitesparasites
Almost every major taxonomic group Almost every major taxonomic group includes members that are parasitesincludes members that are parasites
Likely nearly 100% of organisms are Likely nearly 100% of organisms are host to parasites
Importance of parasites
Heavily influence different ecological Heavily influence different ecological levelslevelsddPopulation dynamicsPopulation dynamicsddCommunity ecologyCommunity ecologyddEcosystemsEcosystems
Thought to be a driving force shaping Thought to be a driving force shaping biological diversitybiological diversity
Selection agent favoring sexual Selection agent favoring sexual recombination
