Quiz #1 Vocabulary Flashcards
probe
-short length of DNA that can be labelled to hybridize to a complementary molecule
redfield ratio
- fixed ratio of elements in ocean
- C:N:P = 106:16:1
synechococcus
- prevalence varies seasonally
- autofluoresce
- photosynthetic
- very common, one of the first studied
- cyanobacterium
- nitrogen fixer
thermohaline circulation
- occurs in polar climates
- cold water forms ice, leaves salt behind
- surrounding water is very salty and cold (so denser) and sinks, fresher water is pulled in to replace it
- dense water moves along the seafloor, creates deep-ocean currents
- transports nutrients, O2, CO2, etc…
FISH
- fluorescence in situ hybridization
- probe is labelled with a fluorescent dye, will bind to ribosomal RNA
- fix cells, use probe, wash away excess dye, hybridize them
- now, only those cells that the probe attached to are marked fluorescently
- helpful for distinguishing between groups, like bacteria and archaea
dead zones
- 85% of the freshwater flow into the Gulf of Mexico comes from the US and 64% of this originates from the Mississippi River: Leads to Dead Zones with very low oxygen
- large influx of nutrients, they get decomposed by bacteria, process consumes oxygen, region is left anoxic
NifH
-major protein in nitrogen fixation
order of ions in the sea
Cl> Na >SO4>NO3->Fe(3+)
the great plate count anomaly
- orders of magnitude of cultures go from 10, 100, 1000, 10000, etc…
- 10 is too few but 1000 is too many
- difficult to get a plate with an appropriate number of colonies to count
niskin bottles
- used to collect water at specific depths
- sample the water column
most probable number method
- plate counts to know how many bacteria are in seawater
- a statistical method used to estimate the viable numbers of bacteria in a sample by inoculating media in 10-fold dilutions
flow cytometer
-direct count method
-forces the cells through a very narrow tube, almost single file
-a light source shoots through at them, scatters light & fluoresces (bigger cells scatter more light)
can indicate cell size and cell count
euphotic zone
- the depths to which light can penetrate
- photosynthesis occurs here
- same as photic zone
primer
- short length of DNA used to initiate synthesis of a new DNA strand
- universal or specific
- can be used to duplicate desired gene
RT-PCR
- take mRNA, do reverse transcriptase, gives you complementary DNA
- run standard PCR on the cDNA, gives an amplified double stranded DNA fragment
- do this when the DNA you want to replicate is in the form of RNA to start
core genome
- represents the genes present in all strains of a species
- typically includes housekeeping genes for cell envelope or regulatory functions
- accessory/variable genome is genes not present in all strains
metatranscriptome
-gene expression of microbes within natural environments
gyre/gyres
- created by circular movement of currents
- transports nutrients and microbes
- creates niches
light quality
- light color
- blue penetrates furthest, red goes shallowest
upwelling/ekman pumping
- at coast, wind pushes water offshore
- new water comes up from deep to replace it, this new water is very nutrient rich
- causes influx of nutrients
thermocline
- rapid decline in temperature between surface water and deep water
- roughly 250-1000m
compensation depth
-depth at which net photosynthesis = net respiration
garbage patches
- accumulation of trash in the ocean because of gyres
- creates a niche
bioavailability
- whether the compound is in a form where an organism can currently use it or not
- EX: iron can be found as colloids or bound by organic ligands, cannot be taken up in these cases
