Quiz #1 General Knowledge Flashcards
the oceans - percentages
- 71% of Earth’s surface
- 90% of biosphere
- 50% of primary production
size classes
femto (0.01-0.2 microns) pico (0.2-2 microns) nano (2-20 microns) micro (20-200 microns) (all prefixes go before "plankton")
coriolis effect
- currents are deflected to the right in the northern hemisphere and the left in the southern
- helps shape gyres
importance of circulation
-creates distinct ecological environments (niches) of different temperatures, nutrients, etc.
light
- energy for phototrophs and heat
- angle of incidence varies with latitude and season
Major elements of marine life
- nitrogen (proteins, DNA/RNA)
- phosphorous (DNA/RNA)
- carbon (lipids, proteins, carbs)
- silicon (SiO2: silica frustules)
iron
- insoluble in seawater
- essential but occurs in trace amounts
- introduced by weathering/dust
- HNLC zones are limited by iron
IronEx
- experimental addition of iron to HNLC zones to see if it would cause great phytoplankton growth
- it did
net tows
- Used to collect cells using a fine mesh net dragged through the water (bigger microbes)
- sample the water column
grab sampler
- sample the sediment
- doesn’t preserve the layers
- like a claw machine
corer
- sample the sediments
- layers represent depth below sea floor
- preserves layers
manned submersibles
- sample deep sea
- EX: Alvin
autonomous undersea vehicle (AUV)
-sample deep sea
the environmental sample processor
- designed for autonomous, remote sample collection and processing
- designed for shipboard and subsurface in situ applications
enrichment
- culture dependent
- duplicate as closely as possible a particular environment (light, temperature, salinity, pressure, etc.)
- design growth medium to enrich for a particular type of organism and exclude others
- EX: grow on media with and without NH4+ to see if the organism can fix nitrogen (will still grow as well as w/ nitrogen if it can)
counting/isolation techniques
- agar or silica gel plates or tubes (spread, streak, pour)
- fluorescence activated cell sorter (FACS)
- dilution methods
spread plate
-leads to surface colonies only
pour plate
- surface and subsurface colonies
- better for culturing some strains because being fully surrounded by media can be a better representation of seawater
dilution series
-plate different amounts of the sample on several plates to find the optimal dilution for counting
limitations
- Most fit organism for a particular set of chosen conditions becomes dominant although it may have been a minor component of the original community (Remedy: dilute inoculum, then enrich)
- Difficulty of duplicating natural environment in the laboratory
direct counts
- microscope
- cells made fluorescent with dye
- cells are naturally autofluorescent
major parameters for fluorescent cells
- excitation wavelength
- emission wavelength
-determined by light source and microscope filters
16s rRNA
- Universally distributed (all prokaryotes)
- Some regions are highly conserved (allow isolation of this molecule from others)
- Some regions have more variability (distinguish ones organism from another)
- Large database
signature sequences
- short stretches of oligonucleotides unique to certain groups of organisms
- Because of their exclusivity they can be used to design phylogenetic probes
- Universal primers
archaea
- low prevalence at surface, so assumed to be unimportant in marine microbio
- there is a depth where they are as prevalent as bacteria
- ~1/2 of cells in ocean
Environmental DNA Clone Bank
- 1 16S gene/plasmid
- 1 unique plasmid/colony
- using plasmids to clone DNA
- Sequence each plasmid
secondary antibodies
- for detecting protein markers of an enzyme’s activity
- label with fluorescent dye, will attach to the antibodies defending against an antigen
- can be highly specific but need to purify antigens and create antibodies
isotopes
-forms of an element that differ in atomic weight (differ in the number of neutrons)
MAR
- microautoradiography
- can help identify cells that are missed with other techniques
- tracks metabolic activity
how are genomes from a single organism sequenced
-assembled from many fragments by aligning sections that are the same
ecogenomics
-more difficult to piece together fragments of DNA in real world because many different species present
annotation
- converting DNA sequences into potential genes
- assigning function (compare to other proteins/ databases about proteins)
- mostly done by machine, humans still need to check and resolve errors
