Microbial Oceanography Final - Thornton
gyres
What areas of the world have the least amount of chlorophyll?
orange
What color does chlorophyll illuminate?
nitrification and denitrification
What coupled processes explains chemical gradients of the ocean?
4000 - 6000 m
What depth of the ocean does the abyssal plain make up?
bacteria
What do HNFs feed on?
land air masses
dry
abyssal plane
lifeless flat deep area of the ocean
tsunami
long high sea wave caused by underwater earthquake
climate vs weather
long term vs short term changes in temperature, precipitation and wind
Tethys Ocean
Between Gondwanaland and Laurasia
Fossil/biogenic particles
Hard parts of dead organisms
hurricane origins: tropical depression
winds less than 61 km/hr
Are seaweed covered with bacteria?
yes many!
How much bacteria is in seawater?
you can get a few hundred colonies from 1 mL, very miniscule compared to marshes to assumed to be limited role
infralittoral zone
zone on a rocky shore that is open water Algal-dominated zone
Elser et al. Gross growth efficiency
- Herbivores consuming elemetally imbalanced food will exhibit strongly diminished efficiency of conversion of ingested carbon into new biomass = reduced GGE
Continental drift
All continents had once been joined in a single supercontinent, not sure what mechanism is
Indian Ocean
Ocean formed when Gondwanaland broke apart
pathogenic bacteria prefer warmer or colder water?
warmer water, like the human body
4 steps of Transportation and Deposition of Sediments
Weathering, erosion, transport and deport.
Decomposition of organic matter
covered with bacteria, fungal filaments and pennate diatoms
The name of the continent from 245 million years ago -- one big continent
Pangaea
How is the distribution of grain sizes measured from a sample?
with a distribution of size measurements; gravel, sand, mud
Species concept
works very well for animals but is less significant for microorganisms
ekman spiral
describes speed and direction of flow of surface waters at various depths
The most obvious way to group organisms
is by the SPECIES
Epifauna
live ON the surface of ocean floor. Star fish
Few ciliates
live in the black sand and below
foraminifera
settle 1-6 cm per 1000 years
diatom
shaped like a hockey puck settle 1-6 cm per 1000 years base of marine food chain
doldrums (trade winds) and horse lats (westerlies)
shift N in summer, S in winter
diatomaceous earth
siliceous ooze lithifies into diatomaceous earth commercal uses: pest control, agriculture, explosives
biomarkers
term- chemical fossils. Chemical traces in a sample that allows an assumption of the past.
export production
term- organic matter exported out of the euphotic zone into the deep ocean.
remineralization
term- organic matter turned back into CO2 (inorganic)
benthic
term- organisms that live on the bottom of the ocean
munchates
term- particles released during sloppy feeding by phytoplankton
submarine canyon
steep sided valley cut into the seafloor on a continental shelf
False, too much sun
T or F: The peak for photosynthesis is found at the surface of the ocean. Why?
denitrification
nitrogen cycle process- Reduction of nitrate to dinitrogen gas. NO3- ---> NO2- ---> N2 Nitrate ---> Nitrite ---> Dinitrogen
ammonification
nitrogen cycle process- Remineralization of organic matter producing ammonium. Organic NH3 ---> NH4+
5 Sediment Subcategories
Terrigenous, Biogenous, Hydrogenous, Volcanogenous, Cosmogenous
Solute
the substance being dissolved
What is mRNA used for inside cells?
to carry the instructions for making proteins to the ribosomes
What is the purpose of diffusion?
to even out concentrations
Extracellular molecules greater than 600 da (atomic mass unit, dalton) are generally
too big to be taken up by bacterial cells
harmful agal blooms
too high of levels of nitrogen can lead to what?
DOM
total DOC in the ocean is 6.6e17 gC, same as atmospheric CO2
doldrums
trade winds meet, pressure gradient decreases, little wind difficult to cross equator weather systems rarely cross hemispheres
Equatorial Currents
trade winds set water in motion in the tropics -flow westward, parallel to the equator -northern equatorial currents if north of the equator and southern equatorial currents flow south of the equator -from north or southern boundary of subtropical gyre
what is the TEP again?
transparent extracellular polyments;
Explain energy flow inside the ecosystem
energy flows in and out of ecosystems and higher trophic levels are dependant on primary production
Bioluminescence and how many organisms in benthic zone have this adaption?
used to distract prey, use as a warning and to communicate 99% of organisms in mesopalegic zone
Molecular Classification
using DNA structure and seuence, sometimes ribosomal DNA,
Rocky shore
very little sand, high wave energy and environmental extremes of temperatures, salinity, moisture, pH, dissolved oxygen, degree of predation, and food supply
Antonie Philips van Leeuwenhoek
• 1632 - 1723 • Dutch tradesman and early scientist. • 'Father of microbiology.' • Improved design of optical microscope and was the first person to observe and record observations of single celled microorganisms -'animacules.'
turbidites
turbidity currents - deposit materials further from coast than would be expected "underwater landslide"
where do we generally find the greatest biomass of benthic organisms?
under areas of upwelling
0.2 - 2 micrometers
How big are picoplankton?
What are important differences between a bacterium and an animal cell?
Prokaryotic: These cells are simple in structure No structured nucleus Exist as single-celled organisms Bacteria is both helpful and harmful to us and the environment. Example: Bacterial cells Eukaryotic: These cells tend to be larger than the cells of bacteria (prokaryotic) Have a defined nucleus Found in organisms made up of many cells Example: Plant and Animal cells
Salt Marsh
Swamp, build up of decaying plant matter, can protect against erosion
all directions
What direction does light come from in the sediment?
where do storms typically develop
at fronts
quantum vacuum
loaded nothing (different from absolute nothingness)
Terrigenous
products of weathering and volcanic ash
This summer, the __________________ was deployed
the 12th WHOTS mooring
how many hurricanes a year worldwide
~100
Eastern Boundary Currents
currents are turned by the Corilois effect and mand barriers towards the equator -carry cool water from high latitudes towards equator from eastern boundaries of subtropical gyres
what two types of organisms are involve in a hard corals symbiosis?
cnidarians and dinoflagellate
Why Alum is best method
- cheapest - longer lating - reduces alkalinity, must be applied with caution so pH isn't driven below 6
Artificial Circulation
- disrupting/preventing stratification using compressed air - oxidizes water in hypolimnion to form the oxidized microtone cap at the sediment-water interface - traps P in the sediments - prevents the clinograde oxygen curve from forming
Bacteria -->
simple, single celled life form in which there is no membrane bound nucleus of organelles ex: cyanobacteria
hydrothermal vents
sites where superheated water containing dissolved minerals and gases escapes through vents (smokers).
Phytoplankton
drifting photosynthetic microbes
glomar challenger 1983
drilled off del-mar-va-peninusula and found tektites
high pressure
dry climate, clear sky lats: horse lats, poles
deposit feeders
eat particles in lying sediments,
weather definition
day to day variations, short term state of atmosphere (minutes to weeks)
Benthic Decomposition Rates
decline with depth bust are still vital in abyssal plains due to their vast area
epipelic diatoms
What kind of organism move by releasing exopolymers and pull themself along like spiderman?
amino acids and proteins
What makes up DON (dissolved organic nitrogen)?
DNA
What makes up DOP (dissolved organic phosphorus)?
bacteria
What organism carries out nitrogen fixation? There's only one.
phytoplankton
What organisms accounts for the most organic carbon in the ocean?
78%
What percent of the atmosphere is made up of dinitrogen gas?
21%
What percentage of the atmosphere is made up of oxygen?
bacteria
What type of organism makes up about 50% of the total community respiration?
linear
What type of relationship do chlorophyll and exopolymers have?
sand
What type of sediment are ripples made of?
2.4 to 2.5 byo
When did free oxygen begin to accumulate in the atmosphere?
organic carbon increase
When measuring the productivity of heterotrophic bacteria (chemoheterotrophic bacteria), what does adding leucine determine?
cell division rate
When measuring the productivity of heterotrophic bacteria (chemoheterotrophic bacteria), what does adding thymidine determine?
survivalist
When the nutrient levels are higher than the Nitrogen:Phosphorus ratio the area is known as a __________.
bloomer
When the nutrient levels are lower than the Nitrogen:Phosphorus ratio the area is known as a __________. ex- Mississippi River
coasts
Where are there higher respiration rates: Coasts or open ocean?
coasts
Where is there a higher growth efficiency rate: Coasts or open ocean?
denser, colder water
Which can hold more dissolved inorganic carbon: denser, colder water OR warmer surface waters?
C12
Which form of Carbon is normal?
C14
Which form of Carbonis radioactive and used to measure photosynthesis?
nitrate
Which form of nitrogen is typically found in deep waters?
DMS
Which is released by stressed or lysed phytoplankton: DMSP or DMS?
nitrification
Which nitrogen cycle process explains why ammonium doesn't accumulate in deep waters?
no
Will Mg ever be a limiting factor on nitrogen fixation?
Upwelling
Wind-driven motion, cooler water
What gives coral its color?
Zooxanthellae An algae that lives within the coral Coral provides protection for the algae and the CO2 needed for photosynthesis Coral gains nutrients from the algae, which can allow it to live in nutrient-depleted waters
Where is new land always created or destroyed?
between the margins of lithospheric plates.
black smokers
a hydrothermal vent on the seabed that ejects super heated water containing much suspended matter, typically black sulfide minerals.
Gyre
a large horizontal circular moving loop of water 1= Subtropical gyre 2=Equatorial Countercurrents 3= sub polar gyre
Abyssal Plain
a large, flat, almost level area of the deep-ocean basin
Decomposing Zostera
a layer of decomposing sea grass
Periodic Table of Elements
a listing of known elements that highlights their common chemical and physical properties. Divided into periods, and columns called groups.
trench
a long narrow underwater ditch
what is temperature
a measurement of molecular motion
dredge
a metal frame with a collecting mesh bag behind it disturbed sample
Ribosome
a molecular machine that synthesizes protein
Polar molecule
a molecule exhibiting positive and negative charges on different ends of the the molecule
Electronegative
a molecule or part of a molecule with a negative charge
Electropositive
a molecule or part of a molecule with a positive charge
upwelling
a movement of water that brings stuff up
pH Scale
a numerical designation between 1 and 14 corresponding to the pH of acids and bases
Anthropogenic CO2
carbon dioxide released as a result of human activities; for example, the burning of fossil fuels
Sink in microbial loop?
carbon not passed at higher trophic levels, carbon is respired (low bacterial growth efficiency)
Link in microbial loop?
carbon passed to higher trophic levels (high growth efficiency)
neritic deposits: carbonate deposits
carbonate minerals containing CO3 marine carbonates primarily limestone (CaCO3, calcium carbonate) most limestone contain fossil shells (suggests biogenous origin) ancient marine carbonates constitutes 25% of all sedimentary rocks on earth
carnivores
carnivore issues -low pop. size, movement to patches of prey -locating prey -capture of prey -physiology limitations (depth, sensory) -feeding, while avoiding predation by other species
Sandy (2012)
cat 1 largest atlantic hurricane on record storm surge coincided w peak high tides in NY and Jersey severe coastal erosion extreme flooding 233 deaths, more than 68 bil in damages 2nd costliest hurricane after Katrina
seasons
caused by tilt, not changing distance of earth from sun 23.5 degree tilt closer or further to sun during the year
anticyclonic flow
clockwise around a low in the N Hemis counterclockwise around a low in the S Hemis
cold molecules
closer together
Observation
collection of scientific facts through observation and measurement
corals
colonial cnidarians that secrete skeletal stuctures of calcium carbonate. Create habitat for vast number of species. Greatest biodiversity of any marine community.
physical properties of the atmosphere
column of dense, cool air causes high pressure at surface, leads to sinking air column of warm, less dense air causes low pressure at surface, leads to rising air
comets
comets may still be bringing water to earth
Explain what happens to biomass and diversity depth decreases in the ocean
decreases toward the bottom increases toward the bottom
Ekman's Spiral
describes the speed and direction of flow of surface waters at various depths
horse lats
deserts, sinking air (dry)
SONAR
detects underwater objects using sound
surface currents
develop friction between winds and water only 2% of winds energy transferred to ocean surgace 100 knot wind creates 2 knot current
carbonate deposites: stromalites
fine layers of carbonate warm shallow ocean, high salinity cyanobacteria lived billions of years ago example: shark bay, australia
manganese nodule
fist sized lumps of manganese, iron, & other metals very slow accumulation rates commercial uses: cellphones, disk drives, batteries unsure why they aren't buried by seafloor sediments
Viral population
it's hard to count viruses, tbut there's a potential for decay by UV, ingestion by non-living particles, and digestion by enzymes.
Are most bacteria pathogenic?
it's not
hypoxia
lack of oxygen.
terrigenous
land origin gravel, sand, silt
land breezes
land to ocean
tectonic plates
large pieces of the earth's crust
biogenous marine sediments: macroscopic
large remains
tropical cyclones (hurricanes)
large rotating masses of low pressure strong wind, torrential rain classified by max sustained wind speed typhoons (N Pacific name) cyclones (Indian Ocean name)
continental shelf
large shallow area near the continents
jetstream
narrow, fast moving easterly air flow at middle lats below top of troposphere may cause unusual weather by steering air masses
Anions
negatively charged ions
Swimmers
nekton live in water column organisms capable of moving independently of the ocean currents
new
nitrate uptake indicates what kind of production: new or regenerated?
assimilation
nitrogen cycle process- Incorporation of reduced nitrogen into organic matter. NH4+ ---> Organic NH3
nitrification
nitrogen cycle process- Oxidation of ammonium to nitrate. NH4+ ---> NO2- ---> NO3- Ammonia ---> Nitrite ---> Nitrate
nitrogen-fixation
nitrogen cycle process- Reduction of dinitrogen to ammonium N2 ---> Organic NH3
cosmogenous marine sediments
space dust macroscopic meteor debris overall, insignificant proportion of marine sediments
white cliffs of dover
taller than statue of liberty 110 m
Supersaturated
when the concentration of a dissolved gas or substance exceeds the solubility for a given set of conditions.
Undersaturated
when the concentration of a substance is less than the saturation concentration
convergent plate boundary
when two plates collide and one plunges under the other
surface of sediments
where does cyanobacteria grow?
What are divergent boundaries?
where is plates separate (move away from each other) and new ocean basins are created. new crust is also created
antarctica
where is the most salicious ooze found? Which country?
nitrification
which nitrogen cycle process accoutns for the accumulatio of high nitrate concentrations in deep waters?
abyssal plain
which part of the ocean is the biggest ecosystem?
meiofauna 2
who are they? -20 phyla total -5 phyla only meiofauna adaptations -elongated/wormlike -reduce complexity (smooth) -increases structure of body covering -adhesive organs
Keeling Curve
the graph that depicts the rise in atmospheric carbon dioxide since the late 1950's
continental slope
the slope between the continental shelf and deep ocean floor (abyssal plane)
Practical Salinity Scale
the standard scale of measurement for salinity
Ries crater
theory of how life began- meteorite; found microbial-like tubules in rocks; impact from comet polymerized amino acids into peptide chains
round earth
uneven solar heating (different distribution of sunlight on earth)
Steady-state
unvarying in rate; when rates of flows of energy and matter in an ecosystem are constant
What is nitrate assimilation?
uptake of NO3- or NH4 incorporation into biomass
suspension feeders
use appendages to strain paticulate food matter from the water. Heterotrophs
chemosynthetic bacteria
use hydrogen sulfide that comes out of Black Smokers as an energy source to grow and reproduce. Primary producers. Exist independent of sunlight!
echolocation
use of sound waves and echoes to determine where objects are in space
curtis ebbesmeyer
used rubber ducks to look at current 1992-fell off boat in pacific
Why do most benthic organisms have some kind of bioluminescence?
used to communicate or used as a warning light, lures prey, mates and frightens predators
vibra coring
uses both gravity and vibration
behind
A shadow is found: in front of OR behind the ripple?
Flow Cytometry
In biotechnology, flow cytometry is a laser- or impedance-based, biophysical technology employed in cell counting, cell sorting, biomarker detection and protein engineering, by suspending cells in a stream of fluid and passing them by an electronic detection apparatus.
Future coast line prediction
No Boston, New York City, Philadelphia, Washington DC, Florida will be completely covered.
are polar regions becoming colder? are tropical regions becomming warmer?
No, heat transported by atmospheric and oceanic currents and redistributed via convection cell
The Gulf Stream carries warm water where?
North
Laurasia
North America, Europe, and Asia
Where is the Station ALOHA?
North Pacific Gyre
Whittaker's phylogenetic tree had five main branches, what were they?
Plantae Fungi Animals Protista Monera
Until the early 20th century the "tree of life" had two main branches, what were they?
Plantae and Animalia
Variations in Sea level
Pleistocene vs. Holocene
diatoms
Salicious ooze is produced by diatoms or coccolithophores?
Density of water (salinity/temp)
Saltier water = denser Hotter water = less dense
Global Distribution of Deep-Sea Sediments
Sand becomes sandstone; mud becomes either shale, if composed of clay minerals, or limestone, if composed of carbonate ooze.
rocky intertidal zone
The ________ , the band between the highest high-tide and lowest low-tide marks on a rocky shore, is one of Earth's most densely populated areas.
Covalent Bond
The chemical bond between the oxygen and hydrogen atoms. A type of bond that results from the sharing of electrons between hydrogen and oxygen.
Continental Rise
The gently sloping section of the continental margin located between the continental slope and the abyssal plain
Climate
Weather condition over a period of time
greenhouse gases
ex: CO2, .5% increase/year regulates temp too much causes problems
Deep-sea fans
Cone-shaped deposits
Aesthenosphere
Lower mantle and viscous
warm molecules
far apart
Vibro cholerae
gram negative, cholera, curved rods (beans)
Anoxygenic photosynthesis
• There are also anaerobic bacteria that do not generate oxygen when they photosynthesize, anoxygenic photosynthesis: • General equation for photosynthesis: 2H2A + CO2 + light → (CH2O) + H2O + 2A
Hadal Zone
Below bottom of the ocean floor
transform plate boundary
an area where plates slide side-to-side with each other
Diatoms
an important group: responsible for approximately 40 % of primary production in the oceans.
Each species has a scientific name that includes
2 parts; the genus and the species
cryptic species
2 things that look the same, but are different
How long are nanoplankton?
2 to 20 micrometers
Controlling 2ndary production
2. Secondary production; microbes are a source of food for marine organisms; indigestable larger marine organisms; degrade these compounds
at what rate does the mid atlantic ridge spread?
2.5 centimeters per year
latent heat of vaporization for water
540 calories
true
T or F: increased temperature leads to increased respiration
true
T or F: more bacterial production = more respiration.
cold
Low nitrogen fixation rates are associated with warm or cold oceans?
Higher viscosity leads to a higher or lower Reynold's number?
Lower. Viscosity really effects smaller organisms.
Corilois effect`
MOVING OBJECTS ON EARTH TO FOLOW CURVED PATTERNS -result of earths rotation to the east -Gaspard Gustave de Corilois, a French calculated it in 1835 -effects all moving objects, though more effect over longer distances --object in northern hemisphere moves to the right of its intended direction -object in the southern hemisphere will move to the left of it intended direction.
Size classification
Macrobenthos -shortest dimensions is >0.5mm Melobenthos -shortest dimensions is 0.1 - 0.5mm Microbenthos -shortest dimensions is <0.1mm
Fringing Reef
Most common type of reef that forms on the coastline
Reynolds Numbers (Re)
Motion through water is a function of two variables: momentum and viscosity Viscosity is very important when you're a microorganism Reynold's number is the rate of intertial force to viscous force acting on a body of interest (microorganism). The inertial force is the force that was necessary to accelerate the body to the speed it now possesses, or to stop the body now traveling at a constant speed under it's own inertia.
NHemisphere tilted more at sun
NH summer, SH winter
Topographic features
Physical features of land
Bathysgraphic features
Physical features of ocean
Which marine organisms compose most of the Earth's biomass, serve as the basis of the food chain, and create future oil reserves?
Phytoplankton
What would be the characteristics of a sequence of DNA/RNA that would make it suitable as a phylogenetic marker?
The properties that should be possessed by an ideal marker are as follows : (a) A single-copy gene may be more useful than multiple-copy gene; this condition is satisfied by the mitochondrial and nuclear genes; (b) As marker gene sequences are aligned prior to phylogenetic analysis, their alignment should be easy. The length of the same gene can vary among different members of taxa due to insertions or deletions because of which aligning their sequences may be difficult. However, regions with ambiguous alignments can be avoided specifically or secondary structure information may be applied; (c) The substitution rate should be optimum so as to provide enough informative sites. A gene evolving too fast may reach a state of saturation due to multiple substitutions. This problem can be enhanced by base composition bias since this makes it more likely that the second mutation at a particular site will be a reversion to the original state. For protein coding genes it may be the case that the synonymous substitution rate is too high even though very few non-substitutions have occurred; (d) Primers should be available to selectively amplify the marker gene. However, the primer should not be too universal as in that case it would lead to amplification of non-specific genes present as contaminants or contributed by symbionts; (e) A too much of base variation among the taxa, is not preferable which may not reflect the true ancestry [14]. The breakthrough in the study of the phylogeny of prokaryotes was achieved by Carl Woese and co-workers in the seventies [15,16]. They introduced rapid methods of comparative 16S rRNA sequence analysis and phylogenetic tree reconstruction. The results of these efforts provided, for the first time, insight into the phylogeny of prokaryotes and also established the three domains of life, popularly known as- "The Universal Tree of Life" - Archaea (formerly archaebacteria), Bacteria (formerly eubacteria) and Eukarya (eukaryotes)
hydromechanical and digging
burrowers of sediments use what two mechanisms?
burrowing
burrowers use hydromechanical and mechanical digging mechanisms to move through the sediment
burrowing 4
burrowing impacts the environment -increases water content of sediment if mud -increases grain size -alters vertical and 3-D mechanical, chemical structure
seafloor spreading and sediment accumulation
calc ooze deposited on MOR above CCD calc ooze covered and protected seafloor spreading moves calc ooze btwn CCD into deep water
E. coli
fecal coliforms, E.coli present in the water, help in digestion of the food;
Heterotrophic nanoflagellates
feed on bacteria, only about 10k in the water;
scavengers
feeds on dead animals falling from above
Taxonomy
grouping organisms into the following increasingly specific groups
How do the sizes of organisms living around the hydrothermal vents compare with other benthic organisms?
grow to be huge in size and can withstand temps from 36 degrees to 662 degrees
extrapolating
guessing based on known relationships
crust
hard out layer of the earth
ITCZ
intertropical convergence zone "doldrums" (equator)
solar wind
ionized particles; blew away nebular gases from sun
bottom grab sampler
it grabs a handful of sediment quick spot sample disturbed sample
What do ribosomes do?
it is the protein factory, makes proteins *all cells have these they are stuck to membrane and cytoplasm
What does it mean when grazing is 100%
it means that grazing is only limited by the bacteria present there
Hydrogenous
minerals precipitated from chemical compounds in seawater
significance of vapor
moderates global climate
marine air masses
moist
protoearth
molten ball of hot liquid rock; heat from deep in protoearth -> disintegration of atoms -> radioactivity
idealized 3 cell model
more complex in reality tilt of earth's axis and seasons lower heat capacity of continental rock v seawater uneven distribution of land and ocean
evolution of life
more data in the deep sea than anywhere else
Benthic sediment
more organic matter, more prokaryotes, and more respiration
terrigenous sediments
most at continental margins coarser sediements close to shore, finer sediments further from shore mainly mineral quartz (SiO2) eroded rock fragments from land, reflect comp of rock from which derived
storm surge
most dangerous part of hurricane
is flesh eating bacteria related to pollution?
mostly amputations and persistent lesions, incubation period is 12-72 hours
what is the tallest land elevation?
mount Everest at 8.85 kilometers
wind
moving air
downwelling
mvmt of surface water down moves warm, nutrient depleted surface water down not associated w productivities or abundant marine life
currents
named for direction in which they flow eastward current: moving to east, coming from west
winds
named from direction in which they are coming southerly: come from south, blowing North
Southern Hemi boundary
in southern hemisphere these currents from the southern part of subtropical gyres
Why is it important?
indiator of human presence; gives rashes/ infections, and upset stomaches; other give u cholera and mengingitis
energy resources: petroleum
petroleum ancient remains of microscopic organisms more than 95% of economic value of oceanic nonliving resources more than 30% of world's oil from offshore resources future offshore exploration will be intense oil spill potential
What are some characteristics and obstacles of life in the deep sea?
pitch black nearly freezing high pressure far from food source 90% are bioluminescent sparsely populated hydrothermal vent community issues: - temporary nature, fragile? - larvae of deep-sea hydrothermal vent species must travel great distances
Floaters
plankton live in water column no strong individual locomotion; dependent of ocean currents
The filters used to collect marine microorganisms for counting are usually made from :
polycarbonate
What is Agar made of?
polysaccharide from seaweed
RNA World Hypothesis
prevailing theory of how life began; need clay; nucleotides polymerize on clay and form RNA -> fold into ribozymes -> form phospholipids that absorb RNA so they can replicate
Ecological roels
primary production is regulated by 3 things: nutrients, light, and column structure
Thermocline
rapid change in heat/depth
chemical weathering: incongruent weathering
results in newly made clay minerals and dissolved ions
chemical weathering: congruent weathering
results in only dissolved ions
Carl Woese
revolutionized microbiology through his study of microbes He postulated that Monera was not a kingdom, but instead was made up of two domains: Archaea and Bacteria Woese did experiments where he extracted ribosomes and looked at their structure (using chromatography with ribosome fragments) and drew a tree of life based on that
salt marshes (estuaries)
rich in nutrients and have abundant sunlight. Very high primary production, yielding an abundant food supply to support many organisms
Why are more reefs and more biodiversity in the pacific than the atlantic?
ring of fire = volcanic islands!! = shallow water, clear water older ocean?
deserts
rising air now dry some rising air flows north, some flows south dry air descends at around 30 degrees N or South descending air flows N+S
population density
the number of individuals per unit area.
A marine heterotrophic protist (feeds on bacteria) is
5 micrometers; 5 times the length of the typical marine bacterium
Kiørboe (2008)
"Life is all about encounters. In the ocean, for example, phytoplankton cells need to encounter molecules of nutrient salts and inorganic carbon; bacteria need to encounter organic molecules; viruses need to encounter their hosts; predators need to encounter their prey; and males need to encounter females (or vice versa)."
The growth of bacteria can be ___________ limited.
"diffusion limited"
Expenditure _______________ as a power function of cell size
"expenditure increases as a function of cell size"
Plankton
"floaters" Live in the water column and drift with the current Some may be able to move themselves, but only weakly or vertically Includes phytoplankton (single-celled photosynthetic algae) And zooplankton-microscopic organisms (mostly animals) not capable of photosynthesis Bacterioplankton, too
Biological species concept
"groups of actually or potentially interbreeding natural populations, which are re-productively isolated from other such groups"
Aggregate from Pacific Ocean
"marine snow" continuous shower of mostly organic detritus from the upper layers of the water column sinking aggregates can create a hotspot, patches of high nutrients (ie not actually "hot", lol) a significant means of exporting energy from the light-rich photic zone to the aphotic zone below
For a cell at maximum size, the uptake must __________ the expenditure.
"the uptake must equal the expenditure"
nekton
(Swimmers) Swim within the water column, are able to determine their location within the ocean and often are migratory beings
Galapagos ridge
*Where deep sea vent communities were first discovered* an east-west arm of the spreading mid-ocean ridge system in the equatorial pacific ocean where seawater is heated as it circulates underground through fractured basalt rock.
What are the main features of coral reefs? (Where found? Why important?)
- "rain forests of the ocean - reefs provide both habitat and high primary production, high biodiversity - provide services: coastal erosion protection, tourism, fish nursery, pharmacueticals
Burns objective
- examine how max size of ingested particles changed with cladoceran size
Phytoplankton biomass
- has a pronounced seasonality - north polar water vs. temperate zones
How does N depressions change stoichiometry of TN and TP in lakes
- in areas of low N deposition the phytoplankton is N limited - in areas of high N deposition the phytoplankton is P limited
Why are benthic organisms used as environmental indicators?
- limited mobility so are unable to avoid adverse conditions - live in sediments where they are exposed to environmental stressors (chem. contaminants, low oxygen levels) - life spans are long enough to reflect the effects of environmental stressors - communities are taxonomically diverse so respond to multiple types of stress
Elser et al. Conclusion about histograms
- stoichiometry of the autotroph-herbivore interaction is unbalanced in both systems - C:N and C:P ratios of herbivores were lower than their potential foods especially in terrestrial foods
Mazumder and Havens conclusions about the role of grazers and their effects on chl
- there is potentially an important role of zooplankton grazers in determining hl and water transparency - recent invasion of subtropical lakes by large Daphnia may change the situation
Elser et al. purpose
- use the perspective of ecological stoichiometry to analyze factors affecting energy and material flows at the autotroph-herbivore interface in terrestrial and freshwater ecosystems
Great barrier reef
- worlds largest reef system - biggest living biological structure
Crust (Chemical composition)
-"thin skin" -surface to 20 mi deep -composed of low density rock (mostly silicate minerals known as Si and O) -2 types of crust= oceanic and continental
DOM is recycled when viruses lyse bacteria,
--
Western Intensification of Subtropical Gyres
-Apex (top) of the hill forming the subtropical convergence in a subtropical gyre is close to the western boundary of the gyre then the center -Western boundary currents of subtropical gyres are faster, deeper, and narrower than the eastern boundary currents-called western intensification - The western boundary currents of all subtropical gyres are western intensified, even in the southern hemisphere
Convergence surface water-down welling
-Current Convergence=occurs when the surface water moves towards one another -In north Atlantic the Gulf stream, Labrador current and east Greenland current all converge -When currents converge the water has no where to go except down wards Down welling- occurs a surface water sinks -Down welling area have low productivity
bacterial production?
-DNA formation -thymidine is needed for formation of DNA -bacteria are filtered out and counted with scintillation counter
What are the different habitat zones and which benthic organisms live there?
-Epifaunal/Infaunal -Rocky Shores/Sandy Shores (vertical zonation) Spray zone (rarely covered by water) High tide zone Middle tide zone Low tide zone (rarely exposed) -Coral, Mangrove -Shelves/slopes/rise -Deep Sea (abyssal plains) -Hydrothermal Vents
Ocean Currents and Climate
-Ocean surface currents effect the climate of nearby landmasses -warm surface currents warm the air and carry water vapor over the continents, which result in precipitation -Continental margins with warm currents offshore have a relatively warm, humid climate -Continental Margins with cold currents cools the air resulting in cool, dry air traveling over the continent and a dry climate -California
Mazumder and Havens findings: Secchi vs TP and Chl
-Secchi tranparency declines with Chl and TP - Secchi tranparancey at a given chl or TP concentration decreases from temperate LH to Temp SH to subtropical SH
Explain how chemosynthesis and photosynthesis similar
-Uses energy released by inorganic chemical reactions to produce food -uses solar energy to produce food
conditions for development of coral reefs
-Warm temperatures greater than 18 degrees celcius, between 30N and 30S latitude -shallow water to satisfy temperature and light requirements -clear water: light requirements -clean water: pollutants disrupt ecosystem and upset delicate balance between organisms. Also too many nutrients "kill coral reefs" -firm substrate: corals require a firm base
chemosynthetic bacteria
-are primary producers in this "sunless ecosystem" -bacteria use chemical energy released by oxidation of the H2S to turn the inorganic carbon into organic carbon
Intertidal (high to middle)
-barnacles and mussels -many mollusks -green algae and brown algae -many different feeding strategies represented -severe competition for space
deposit feeders
-feed upon sediment, within the sediment or at surface -head down deposit feeders feed within the sediment at depth, usually on fine particles, defecate at surface -surface browsers often feed on surface microorganisms such as diatoms
Continental Crust
-forms land masses -composed of igneous rock called GRANITE- lower density and lighter colored -most originates beneath surface as molten mamma and coals and hardens with earths crust.
Equatorial Countercurrents
-large volume of water moves westward due to north and south equatorial currents -water piles up on the western margins of the ocean basins and is not turned by the Corilois effect which is minimal at the equator -consequently average sea level may be 2 m higher on the western side of the ocean s than the eastern side - the water flows east under the influence of gravity, creating a narrow current that flows between and -Equatorial countercurrents most pronounced in the pacific arrangement of the m]land on the western side of the Pacific traps the water and due to the arrangements of the land and large size of the equatorial zone in the Pacific
Sub polar Gyres
-rotate in the opposite direction to subtropical gyres in that hemisphere -few of these than subtropical gyres -Atlantic ocean between Europe and Greenland or the Weddell sea off Antarctica -surface currents moving eastward as a result of the prevailing westerly's are driven by the polar easterlies once they reach sub polar latitudes
Particle size
-smaller holds more water -affected by current -affects oxygen supply -affects ability to burrow -affects damage to organisms living within the particles
oxygen issues
-soft sediment microzone -affected by biological activity -creates redox potential discontinuity RPD --boundary between chemically oxidizing and reducing processes
Characteristics of the habitat
-soft sediments are a mixture of inorganic particles, organic particles, and pore water -particle size and sorting are key factors
Coral reefs
-very luxuriant, complex, beautiful environments -can be huge (as long as the entire eastern coast of the USA in the case of the great barrier reef in Australia) -Framework constructed of the CaCO3 "houses" of the polyps
in notes, microbial loop and viral shunt
...
look at graphs on notes
...
Hadley Cells
0-30 degrees
Is it hard to see something like a micron?
0.5 to 2 million/ mL... hard to see something with a micron
Drinking water salinity:
0.6
changes in earths rotating velocity w latitude
0km/hr at poles more than 1600km/hr at equator
The length of a typical marine bacterium in the open ocean would be?
1 micro meter
knot
1 nautical mile/hr 1.15 land mi, 1.85 km
How much DOC is for bacteria?
1% of this is available to bacteria, this pool must turnover radpily; oldest DOC is 6000 years old. o Radiocarbon dating issues... some direct input from organic matter, compromises radiocarbon dating, whale carcasses ♣ Decrease for thousands of years; comes back to surface; o Averages!!!
What factors limit the upper and lower sizes of bacteria?
1) Surface area to volume ratio 2) Fragility of the cell membrane 3) Mechanical structures necessary for life
4 types of Shelf Sediment
1. Glacial Marine Sediments and Ice Rafting 2. Calcareous Sediments 3. Terrigeneous Sediments 4. Relict Sediments
Microbes controlling production...
1. It affects primary production; nutrients available through remineralization; they compete with phyto for inorganic nutrients
Important factors that control sedimentation on seafloor
1. Particle size (something like a boulder is going to take more to break down than a grain of sand. 2. Energy Conditions at site of deposition (tidal waves) 3. Flocculation or the ability of particles to clump together (sticky, clay, mud, silt)
life cycle of a star
1. average star -> red giant -> planetary nebula -> white dwarf 2. massive star -> red supergiant -> supernova ->black hole
water calorie amount
1.00
neritic sediment distribution
1/4 of ocean floor
Viral morphologies
10 million viruses per mL, most will infect bacteria and small phytoplankton;
How long do geologists estimate hydrothermal vents last before the hydrogen sulfide runs out?
100 years
How many micrometers are in one meter?
10^6
What is a realistic count for the number of bacteria in seawater from the surface of the ocean?
1x10^6 mL
how many types of weathering? names
2 physical and chemical
In the beginning there was only
2 kingdoms: plantae and animalia
Black Sea
2 layers • Anaerobic phototrophs (e.g. Chlorobium) are found in the Black Sea where there is anoxic water at the bottom of the euphotic zone.
SAR-11
25% of all pelagic bacteria
incongruent weathering ex:
2NaAlSi3O8 + 11H2O + 2CO2 -> 2Na + 2HCO3- + 4H4SiO4 + Feldspar water cd sodium ion bicarbonate ion silica Al2Si2O5(OH)4 clay (kaolinite)
what is the mean depth of the ocean?
3,790 meters
What is the typical size of zooplankter: copepods ?
3.5 mm long: 3500 times longer than our typical marine bacterium
pelagic sediment distribution
3/4 of ocean floor
A Blue Whale is
30 meters long, and 30,000,000 longer than our typical marine bacterium
albedo avg for earth
30%
biogenic ooze
30% or more tests
Ferrel Cells
30-60 degrees
Average depth of the ocean is:
3729 meters
Ocean basins: How many, which are they, size order
4, cover 71% of land, interconnected; Pacific, Atlantic, Indian & Arctic Southern ocean bigger than arctic, not a basin
How many CTD casts have been sent in to measure that characteristics of the ocena at ALOHA?
4,371
Aarchean Eon
4020-3500 bya; mantle much hotter; convection faster; plate tectonics faster; more subduction and smaller plates; much of initial crust is long gone
Polar Cells
60-90 degrees
how many m would ocean rise if all antarctic sea ice were to melt
63 m
What percentage of earth is covered by the global ocean?
70.8%
Continental shelf
8% of surface area Richest area of the ocean ends at 120-400m
past ocean pH
8.1
ocean pH before the industrial revolution
8.2
latent heat of fusion for water
80 calories
What is the mean land elevation?
840 meters
Ridges
A continuous series of underwater mountains
Submarine Canyon
A deep underwater valley with sharp sides
carbohydrates
A lot of organisms that live within the sediments store energy as ________
Caballing
A mix of two types of water with same density but different salinity/temperature creates higher density water that mixes and sinks Happens in all oceans
Claude ZoBell (1904 - 1989)
A research scientist at the Scripps Institution of Oceanography "The sea harbors an extensive population of bacteria, varying greatly in numbers and in the variety of their activities." Waksman, 1934 "...microorganisms are widely distributed in sea water and on the ocean floor, where they influence chemical, physiochemical, geological, and biological conditions." ZoBell, 1946 ZoBell synthesized his ideas into one of the first 'microbial oceanography' books: ZoBell CE (1946) Marine Microbiology: A Monograph on Hydrobacteriology. Chronica Botanica
Sea
A smaller body of salt water that is almost completely surrounded by by land
Gulf
A smaller body of salt water that is partially surrounded by land
Hypothesis
A tentative, testable statement about the natural world can be used to build more complex inferences and explanations
Trench
A very deep, wide valley that forms at a subduction zone
Seamount
A volcanic mountain that forms on the ocean floor
Theory
A well substantiated explanation of some aspect of the natural world that can incorporate facts, laws, logical inferences and tested hypotheses
Pacific-type margins
Active. Will widen over time through erosion.
hypoxia
Adaptations to __________: 1. Reduction of metabolic rates 2. blood pigments with higher O2 affinity 3. Air breathing through water filled branchial cavities
Advantages/Disadvantages to dispersal of planktonic larvae:
Adv: chance of larvae to land on the best substrate Disadv: heavy predation
Advantages/Disadvantages to direct development
Adv: protection of an adult Disadv: if adults is eaten, all the offspring are lost
All organisms within a category share
All organisms within a category share certain characteristics and evolutionary origins
environmental resistance
All the limiting factors that tend to reduce population growth rates and set the maximum allowable population size or carrying capacity of an ecosystem
Salinity
Amount of Salt and minerals in the water
leucine
An amino acid often used as an organic substrate to measure bacterial growth. Used to determine the organic carbon increase
Subduction Zone
An area where one plate of the ocean floor is sliding under another plate
What is an exopolymer?
An exopolymer is a biopolymer that is secreted by an organism into the environment (i.e. external to the organism). These exopolymers include the biofilms produced by bacteria to anchor them and protect them from environmental conditions.
Bioinformatics
An interdisciplinary field that develops methods and software tools for understanding biological data. As an interdisciplinary field of science, bioinformatics combines computer science, statistics, mathematics, and engineering to analyze and interpret biological data.
Gondwanaland
Ancient super continent that incorporated present day South America, Africa, Arctic, Madagascar, India, Antarctica, Austrailia
hydrogen sulfide
As you go deeper into the ocean Oxygen levels decline but ____ ____ levels increase.
Intentidal Zone
Area closest to shore, covered during high tide and exposed to air during high tide
Terrigeneous Sediments
Asia has biggest build up now. Amazon-Erosion of Andes mountains and deforestations. Monsoon region and rainforests. Deep sea sedimentation. Middle latitudes.
Continental Slope
At the egde of the contiental shelf, the ocean floor drops sharply downwards
5 Oceans
Atlantic Ocean, Pacific Ocean, Indian Ocean, Arctic Ocean, and Southern Ocean
Redfield Ration
Atomic ration in the ocean - 106C: 16N: 1P
Who they are: 3 domains of life
Baceria Archaea Eukarya
Tell me about bacterial growth
Bacteria use 20-50% of organic matter fixed at sea.
Phytoplankton and Bacteria Comparison
Bacterial production is about 10-25% of output compared to primary production. Bacterial growth is also important, uses about 20-50% of organic matter in the sea.
Turbidities
Beds of sediment laid down by turbidity currents.
Calcareous Sediments
Biogenic Sediment. Low latitudes.
Give examples of bivalves, cephalopods, and gastropods
Bivalves: Cephalopods: Gastropods:
Lagoon
Body of water composed brackish water-a mixture of salt & fresh
Benthos
Bottom dwelling creatures
Continental Rise
Bottom of slope, gradual drop
Benthic Zone
Bottom of the ocean
calcareous ooze
CCD warm shallow ocean saturated w CaCo3 scarce calcerous ooze below 5000 m in modern ocean ancient calcareous ooze at greater depths if moved by seafloor spreading
Calcium Carbonate Compensation Depth
CaCO3 shells are not preserved below CCD. Cold deep water very acidic. 4-5 km down.
coccolithophores
Calcareous ooze is produced by diatoms or coccolithophores?
What was the modern system of classification based on?
Carl Linnaeus in 1758 He set up the basics of the system
Terrigenous
Carried into the ocean from the land
emergent systems
Characteristics of ______ ______: 1. Arise from the interaction of many particles or agents. 2. Energy flows through the systems of particles/agents. 3. They manifest new patterns or behaviors by the individual agents.
Origin of Hydrogenous
Chemically precipitated from water. Chemical or biochemical reactions in seawater near the seafloor; manganese and phosphate nodules are examples
What phylum do humans belong to?
Chordata
Grain size and Bottom Energy
Clear relationship between particle size and energy of bottom currents (Erosion, deposition, transportation) High energy conditions vs. low energy conditions.
El Nino vs. La Nina
Cold vs Warm phases in the western Pacific ocean that effect weather
Chukchi Sea -- Alaska William L. Boyd Josephine W. Boyd
Cold, extreme bacteria Tried to count the bacteria in the ocean Carried out at Point Barrow Counts were low except for a brief period during the summer Counts weer similar on both fresh and seawater media, suggesting terrestrial origin
Pangea
Combined Gondwanaland and Laurasia
coasts
Composition of marine aerosols are mostly found in the: open ocean or coasts?
Theory of plate tectonics
Continental drift + sea floor spreading World is a bunch of major/minor plates
Ocean Basin
Continental rise to open ocean
Continental Margin
Continental shelf to rise
Structure of ocean floor - 4 parts
Continental shelf, continental slope, continental rise, abyssal plain
Origin of Terrigenous
Continents. Produced by the weathering of erosion of rocks on land; typically sands and mud.
La Nina
Cooling of the Pacific Ocean. Which is affected by the weather including Hurricane Season
in, out, in
Explain the water intake and output moving along a ripple. Going up, at the top, going down.
Coral Reefs
Coral reefs are built from a mutualistic relationship between photosynthetic algae and a marine invertebrate. The invertebrate provides a calcified home and feeds by extending small fan-like filters into the water, which catch food and capture sunlight. Other organisms find homes in and around the coral structure. Coral reefs are one of the most biologically productive ecosystems in the world, just behind tropical rainforests.
Viruses infect phytoplankton
Could solve the Red Tide probelm. Viral DNA is with you, once you have it once, you have it forever... waiting for you to get sick and you will
Lithosphere
Crust and upper mantle, rigid
So, if we can't grow them in the lab, how do we know anything about them?
Culture independent molecular techniques have revolutionized microbial ecology over the last 25 years
Gulf Stream
Current in the Atlantic Ocean. Moves from the Gulf of Mexico to England. It brings up warm water up to the coast and helps control the climate
Black Box of Unknowns Can't grow bacteria in a lab Can't count them accurately How do we solve this problem?
DNA Based Methods
Trenches
Deep cut in the ocean floor
Submarine Canyon
Deep cut to continental margin
Ocean Trench
Deep valley in the ocean floor that forms along a subduction zone
DART
Deep-ocean Assessment and Reporting of Tsunamis
Pressure
Deeper in the Earth you go higher the pressure
DGGE
Denaturing gradient gel electrophoresis (DGGE) is a technique used for separating DNA fragments according to their mobilities under increasingly denaturing conditions (usually increasing formamide/ urea concentrations). Data extracted from the DGGE gels can be used to construct a dendrogram to see how similar the different sampling sites were. This does not require the DNA to be sequenced, based on the pattern of bands on the gel. This is NOT a phylogenetic tree as it is sampling sites rather than taxa that are on the ends of the branches. Sequences run through databases (e.g. BLAST) to determine 'who' is there.
Density Stratification
Density: is a measure of how heavy something is for it's size. -The release of internal heat was so intense that Earth's surface became MOLTEN (a ball of hot liquid rock) -As this is happening, the elements in the planet are now separating based on their densities (how heavy they were) and formed layers (gravity did this because they all have different densities and formed layers)
Testing
Development of observations, experiments, and models to test the hypothesis
Burns' findings
Diameter of largest bead ingested increased with carapace length - the size of largest particle ingested was smaller for smaller species
ammonia, oxygen
Different processes take place in sediments during the day vs. the night: _______ taken up in the light, and given off in the dark. ________ produced in the light, and taken up at night (dark).
Divergent vs convergent plates
Divergent - ridges Convergent - trenches When oceanic plates collide, one is subducted, which is why they are younger - recycled
Seamounts
Diverse marine life due to hydrothermal vents with mineral rich water
no
Does nitrification require sunlight?
Oceanic Rigde
Each major ocean has a long chain of mountains
Microorganisms in random walks and diffusions
Each organism has different ways of moving, and they need to keep moving.
Early bacteria counting techniques
Early counts of bacteria in the ocean required researchers to make a dilution series of the sample and then 'plate it out' or grow it in a liquid broth.
What is ESME?
Earth System and Microbial Ecology laboratory -- Daniel Thornton Studies the: - ecology and physiology of diatoms - detection of harmful algal blooms - carbon and nitrogen cycling - effect of marine microorganism on atmospheric processes - exopolymers - microbial mats (modern and ancient)
75%
Earth's Surface is covered in water
Why do we group organisms together?
Ecologists group organisms together as it would be very complex to think about all individuals separately within an ecosystem.
Continental slope
Edge of a land mass - shelf break to sea floor, steep from 120-400 to ocean floor (3000-5000)
Chemosynthesis
Energy obtained from hydrogen sulfide rather sunlight Reflective of majority of primary producers
Canyons
Eroded by rivers, but the parts of the canyons that cut into the outer shelf and continental slope are too deep in the ocean ever to have been serially exposed. Most submarine canyons have been excavated by a combination of sediment slumping and turbidity currents that have deepens a gully or depression, on the sea bottom.
Nebular Hypothesis:
Evidence suggests the sun and the rest of the solar system formed about 5 billion years ago from a cloud of dust and gas aka Nebula. All bodies in the solar system formed from an enormous cloud of H and He. The bodies(became protoplanets after they cooled off) formed around a mass in the center (became the sun)
Culture independent techniques applied to Microbial Oceanography Characterization of communities based on small subunit ribosomal RNA genes: who is there
Example: application denaturing gradient gel electrophoresis (DGGE)
high , low at top, high
Explain the change in pressure gradients as you move along a ripple. Going up, ___ at top, going down
Limiting Factors
Factors that limit the growth of organisms, including temperature light, and dissolved substances.
Types of feeding mechanisms of benthos and what they are
Filter feeders, deposit feeders, scavengers
ID 3 feeding types of infaunal organisms
Filter feeding Deposit feeding (feed on detritus) Carnivorous feeding
Which method is commonly used to separate marine microorganisms from seawater?
Filtration
Pelagic Sediments
Fine-grained fallout of terrigenous and biogenic material that settles though the water column, particle by particle, much as snowflakes fall out of the sky and accumulate as a snow cover on land. 1. Inorganic-red clay (actually brown) 2. Biogenic -oozes (have to have 30% skeletal debris)
What is sand?
Finely divided rock and mineral material in a granular form
Ocean Zone
Five layers, Deeper you go temperature drops and pressure increases
Sediment removal
For lakes with significant P loading from sediments due to longterm eutrophication - reduces internal loading of P and N - Reduces undesireable phytoplankton blooms and growths of rooted aquatic plants
Convection
Force that makes magma in Earth's mantle move, due to heating and cooling
Hydrogenous
From chemical possess in seawater
Biogenous
From the shells and skeletons of living organisms
Origin of Volcanogenous
From volcanic eruptions. Ash is an example.
BLAST
Generally, > 98 % similarity of the sequence with the sequence of a known taxa in the database is required to determine taxonomic affiliation.
Importance of geological processes
Geological processes set the context within which ecology and evolution occur
Grain Size Categories
Gravel, sand, mud (mixture of silt and clay)
Hard coral vs. soft coral
HARD CORAL - secrete CaCO3 - symbiosis - multiples of 6 tentacles - stony corals SOFT CORAL - littel CaCO3 - 8 tentacles - feathery - often toxic - spiky spicules
What type of vents are for hot and cold seep environments?
HOT: - hydrothermal vents COLD: - brine seeps - springs of concentrated brine emerge from the rock - hydrocarbon seeps - subduction zone seeps
green sulfur bacteria use ___________________ as a reductant (electron donar) rather than water:
H_2_S
deep ocean curretns
Hard to measure -follow deep ocean currents using chemical tracers, which can be naturally occurring or intentionally added. -radioisotopes produced during the testing of nuclear weapon have been used as tracers -follow mass o water IF IT HAS A DISTINCTIVE TEMPERTAURE AND SALINITY
Glacial Marine Sediments and Ice Rafting
High latitudes. Delivered to the deep sea by icebergs. Debris dropped from melting icebergs. Polar regions.
Lateral Gene Transfer
Horizontal gene transfer (HGT) is the movement of genetic material between unicellular and/or multicellular organisms other than via vertical transmission (the transmission of DNA from parent to offspring.) HGT is synonymous with lateral gene transfer (LGT) and the terms are interchangeable. Ex: conjugation
2 - 20 micrometers
How big are HNFs? one size up from bacteria
0.2 - 2 micrometers
How big are bacteria?
little variability in salinity, a lot of variability in chemicals
How does salinity vary across the ocean? How does the distribution of chemicals (nitrate, ammonium, phosphate, silicate) vary across the ocean?
3.8 byo
How long has life been present on Earth?
10 ^ 15 grams
How many grams are in a petagram? (Pg)
4.6 byo
How old is the Earth suspected to be?
very
How productive are the microphytobenthos: very or little?
Pathalassic Ocean
Huge ocean surrounding pangea
burrowing 2
Hydromechanical -muscle contraction working against rigid, fluid filled chamber -penetration anchor to allow extension of body into sediment -terminal anchor to allow pulling of rest of body into the sediment Mechanical -displacement of sediment using hard digging structures --bivalve shells --crustacean limbs
Dune
Inclining to protect the coastline
For planktonic microorganisms:
Inertial forces (the amount of force it takes to stop something) are insignificant; because if you're a super tiny microorganism, it doesn't take much force to stop you. Water is viscous, like honey or tar 'Senses' operate over a limited range Seawater is very dilute. Challenging to find food and challenging to find mates/hosts.
Weather
Influence by the ocean. The sun heats the water and the water is moved by the equator
Estuary
Inlet area where salt water meets fresh water
inorganic
Is CO2 organic or inorganic?
yes
Is there life everywhere in the ocean?
What does the Gulf Stream do?
It redistributes heat from the equator, by carrying warm waters to the North Pole
Why are benthic organisms so diverse?
LOTS OF NICHES
Burns Methods
Laboratory experiment - feeding experiments of different sizes of cladocerans - fed range of sizes of microspheres, yeast, latex particles, and algae
Continental Shelf
Land at the edge of a continent gently slopes underwater
Subtropical Gyre
Large circular mobbing loops of water driven by the major wind belts -five subtropical gyres=north Atlantic gyre, south Atlantic gyre, north pacific gyre, south pacific gyre, Indianan ocean gyre -center of each gyre at a latitude of 30 n or south -rotate clockwise in the northern hemi =southern hemi rotate anticlockwise
Gyre
Large system of rotating, Ocean currents
emergent events
Life's origins can be thought of as a series of _______ ______, each of which increased the chemical complexity of the prebiotic Earth.
Specific groups
Life, Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species *hierarchial system
Elser et al. methods
Literature on C:N:P stoichiometry on hundreds of different plant and herbivore species - compared terrestrial caterpillar to Daphnia
Origin of Biogenous
Living things. Derived from hard parts of organisms such as shells and skeletal debris; typically lime (composed of calcium carbonate) and siliceous (composed of silica) muds.
What is the deepest point of the ocean?
Mariana trench at 11 kilometers
Density
Mass per unit volume, how much inside
Highest Density
Materials (heaviest like iron and nickel) concentrated in the core.
Pleistocene
Means last ice age. Shore lines were used out to sea level. Florida was super fat, there was no Massachusetts. Australia was larger, Indonesia was all connected. There was a land bride that you could migrate from Asia to North America. Last Glacial Maximum.
Holocene
Means present sea level. Ice sheets are letting now, sea level is rising. Global Warming.
phytoplankton
Nitrogen is a limiting factor on what type of organism?
new food web?
Microbial loop
Types of Marine Sediment
Mineral Particles and Fossil/biogenic particles
Site samples of nektobenthic, sessile epibenthic, and infauna organisms
Nektobenthic: live on bottom but can also move through water column (crabs) Sessile epibenthic: Attached to the bottom (coral) Infauna: live buried in the sediment (worms, bivalves..)
In what direction does diffusion flow:
Net movement of molecules ppr atoms from a region of HIGH concentration to a region of LOW concentration. Waste leaves a cell, while nutrients enter a cell.
The sea surface microlayer (SML) contains the _______________
Neuston
Scientific Method steps:
Observation --> Hypothesis --> Testing --> Theory
Oceanic crust vs continental crust
Oceanic crust is made of basalt: Relatively more dense, relatively thin, relatively young
Sea-floor spreading hypothesis
Oceanic crust, formed by volcanism, moves away from ridge, provides a mechanism for continental drift
Pelagic Zone
Open ocean
Bacteriology
Original investigations of applied techniques developed during the 19th and early 20th century in the field of 'bacteriology'. The early studies of bacteria were focused on the physiology and ecology of pathogens, i.e. medical microbiology. These methods are not suited to studying the vast majority of marine Bacteria and Archaea. Issues: nutrient rich media, unknown nutrient requirements, medium toxicity, slow growth rates, interactions with other microorganisms.
Origin of Cosmogenous
Outer space. Tend to be mixed into terrigenous and biogenic sediment.
ALOHA has been collecting data for ....
Over two decades
What is the largest ocean?
Pacific Ocean
Cosmogenous
Particals from outer space
Atlantic-type margins
Passive. Broad continental shelf as seafloor spreads and sediments build up. Subduction zone
Relict Sediments
Past fluctuations of sea level have stranded course sediments across the shelf. (Energy decreases as you go off shore). Most of the sedimentary cover of the continental shelves. 60-70 percent. No longer evident. Not in equilibrium with the present-day shelf environment.
inorganic
Phosphate, Ammonia, and Nitrate are all organic or inorganic?
What phyla make up the benthic organisms?
Porifera: sponges Cnidaria: jellyfish, corals, hydroids Ctenophora: comb jellies Mollusca: clams, snails, octopi Arthropoda: crabs, shrimp, lobsters Echinodermata: sea stars, brittle stars, sea urchins
Photic
Portion of zone with sunlight
Aphotic
Portion of zone without sunlight
LH vs SH
Presence and absence of dense populations of large-bodied Daphnia - Large/Small Herbivores - Subtropical lakes usually have SH not LH
What types of non-coral reefs are there?
REEF: a rock, sandbar, shipwreck lying just below the surface BIOTIC REEF: a biological structure (ex: oyster reef, sponges, worms)
Pycnocline
Rapid change in density
Halocline
Rapid change in salinity
Thermocline
Rapid change in temperature
Calculation for sedimentation rates
Rate=Distance/Time Residence Time=Mass of Reservoir/ Rate of Input (or Output)
Reynold's number formula
Re = ud/v u = flow velocity d = diameter v = viscosity of the fluid dimensions, so there are no units
RPD layer
Redox Potential Discontinuity Layer As oxygen concentration diminishes, anaerobic processes come to dominate. The transition layer between oxygen-rich and oxygen-poor layers is called the redox discontinuity layer and appears as a gray layer above the black anaerobic layers. *grey or gray* sand
Atoll Reef
Reef forms when the island has completely sunk beneath the ocean surface
Where is the 16s rRNA located?
Ribosomes
water
Ripples cause ____ to move in and out of the sediment.
Tide
Rising and falling of the ocean levels due to The gravitational pull of the moon
ID 4 major types of benthic habitats
Rocky shores Shallow oceans Sediment-covered shores Deep ocean
Transform
Scrape part each other in opposite direction, forms faults and cliffs
Sea water
Sea or Ocean, Ocean has a salinity of approximately 3.5% for every 1 liter of seawater its 35 grams of salt
Match shells with correct name.
See your notes sucka:)
Continental Shelves-sorting of gran sizes and transport.
Shallow and near a terrigenous source. Gentle Slope, bora, shallow. Bottom energy caused by waves, tides. As we move further away from the shelf the energy decreases.
Continental Slope
Sharp drop from shelf
Briefly describe the benthic environment of the deep ocean
Stable environments with minimal light Slow currents, cold temperatures, and constant high concentrations of oxygen.
Opening the Black Box The Molecular revolution
Started in the late 1970s, but molecular approaches really took off in microbial oceanography in the 1990s
Currents
Stream like movement in one direction. Can be water from the ocean, or air for heating and cooling or Electrons for electricity
Continental Rise
Stretching between the continental slope and the deep ocean floor
Ekman's Spiral
Surface angle move a ta 45 degree to the wind - However combing the movement of all the layers produce a net movement of water at an angle of 90 degrees from the wind - the average movement is called Ekman transport -Ekman transport is 90 degrees to the right of the wind direction in the northern hemisphere and 90 degrees to the left in the southern hemisphere
Deep Currents
Temp and salinity changes at surface cause high density water to form, which sinks. Dense water spreads beneath the surface , causing deep currents . vertical motion. Density driven
Temperature, salinity, density changes with depth
Temperature decreases Salinity increases Density increases
Elser et al. overview
Terrestrial compared to Freshwater ecosystems at autotroph-herbivore level
What are the four types of marine sediments based on origin? Give a brief statement of each.
Terrigeneous, biogeneous, hydrogenous, cosmosgeneous
Where is the ALOHA Cabled Observatory?
The ALOHA Cabled Observatory is located in the Pacific Ocean at 22 45'N, 158W, 4782m depth.
The super continent existed during
The Paleozoic and early Mezosoic era
The Abyss
The abyss exists at great depths in the ocean. For biomass and energy, abyssal organisms either scavenge on the steady rain of decomposing biomass from above, or in some areas of the world, derive nutrients from the heat and sulfide gases of thermal vents.
summer
The beach has a high accumulation of sand in the: summer or winter?
Challenges in "omics" studies?
The biggest challenge in 'omics' studies is how to handle the data; i.e. tools to analyze the GB to TB of data generated in each study, quality control tools, long term storage and archiving of the data, long term access to the data
warm oxygen rich / cold anoxic
The black sea is made up of two layers of water: 1 --------------------- 2
Abyssal Plain
The fairly level ocean floor that stretches to the middle of the ocean
Continental Shelf
The flat or gently sloping submerged part of the continent; extends from the shoreline out to the continental slope.
Inertial force
The inertial force is the force that was necessary to accelerate the body to the speed it now possesses, or to stop the body now traveling at a constant speed under it's own inertia.
Ocean floor
The land under the ocean
Great Plate Count Anomaly
The majority of bacteria species do not grow on synthetic bacteria, meaning we can't grow them in the lab. Many non-growers require growth factors from other bacteria, but the nature of these compounds is largely unknown.
The genus name
The name of the genus always starts with a capital letter and the whole name is in italics.
What is the Neuston?
The neuston is the name for the biological community that lives closely associated with the sea sirface 10 mm thick? Top 1000 micrometers (or 1 mm) of the ocean surface boundary layer where all exchange occurs between the atmosphere and the ocean
thymidine
The only nucleotide base that is in DNA and not RNA. Used to determine the cell division rate in heterotrophic bacteria productivity.
Continental Accretion
The process of growth by the gradual accumulation of additional layers of matter
Subduction
The processes of sliding under something
supralittoral zone
The splash zone above the highest high tide; not technically part of the ocean bottom
4 types of RNA
There are 4 types of RNA, each encoded by its own type of gene: mRNA - Messenger RNA: Encodes amino acid sequence of a polypeptide. tRNA - Transfer RNA: Brings amino acids to ribosomes during translation. rRNA - Ribosomal RNA: With ribosomal proteins, makes up the ribosomes, the organelles that translate the mRNA. snRNA - Small nuclear RNA: With proteins, forms complexes that are used in RNA processing in eukaryotes. (Not found in prokaryotes.)
High, because no photosynthesis
There are ____ nutrients found at the bottom of the ocean. Why?
Low, because it gets used up by phytoplankton
There are ______ nutrients found at the surface. Why?
higher
There is a _______ current speed the further away from sediment you are.
What important similarities in bacteria cells and animal cells?
They both have a cell membrane, ribosomes, and genetic information of some kind. They both have methods for reproduction.
Barrier Flat
Thick vegetation dune gives protection from wind and sea spray
Microbial loop
To what extent does microbial production get passed to larger metazoa (a LINK to higher trophic levels).
Continental Shelf
Top of margin
Bacterivory Methods to measure rats of grazing on bacteria Class 1?
Tracers. follow flurescently labeled or isotope-labeled bacteria into grazers
Thymidine uptake is linearly increasing with time
Tritriated thymidine, put into the DNA; it's not part of RNA- not taken up by euks or cyanobaceria, compare bacteria growth
A larger cube has a smaller surface area to volume ratio than a smaller cube
True
Sea water is not very viscous
True
what is heat
a form of energy
There are more major groups (phylums) in the oceans than on land
True
Warm water is less viscous than cold water
True
Canada
US... 2000 colonies/ 100 mL Non-contact 5000 colonies/ 100 mL Texas = 200 colonies/ 100mL, non-contact 2000/100mL
El Nino
Unusual heating of the Pacific Ocean which makes the weather patterns get affected
Mazumber and Havens method
Used data on TP, TN, Chl, Secchi for 420 lake years for temperate and subtropical lakes - regression analyses
Ocean
Varies in sanctity, temperature, and ocean
The ocean has a:
Vertical structure
Which one of these groups is most abundant (in terms of numbers of individuals) in the pelagic ocean?
Viruses
Mg, P, Fe, Mo, Co, V
What 6 elements does nitrogen fixation require?
no light, pressure, cold, no food
What are 4 possible reasons why there should NOT be life at the bottom of the ocean?
Carbon, Oxygen, Hydrogen
What are the 3 nutrients that are NOT limiting factors?
1. oxygen 2. denitirification 3. sulfate 4. methane
What are the 4 main layers of nutrients in sediments? 1 = surface 4 = deepest into the sediments 1 --> 4 declines in release of energy
nitrogen, phosphorus, sulfur, iron
What are the 4 major nutrients required for phytoplankton growth and production?
pressure gradients
_____ _____ change over the ripple.
Thalassiosira pseudonana
a 'lab rat' diatom grown in many labs as a model organism for studies on photosynthesis, diatom physiology etc.
Evaporation has ________ affect on the saltiness of water
a big
Hypoxia
a condition of low dissolved oxygen concentration in a body of water; typically, less than 2 milligrams per liter.
rift
a crack, split, or break
great rift valley
a deep canyon that runs the length of the mid Atlantic ridge
What is denaturing gradient gel electrophoresis (DGGE)?
a form of chromatography
Oxygen minimum zones
a region of the world ocean where the concentration of oxygen reaches a minimum at depth, cause by the biological utilization of oxygen at a rate faster than its resupply by physical processes
Microbial oceanography is
a relatively new field: integrating the principles of marine microbiology, microbial ecology and oceanography to study the role of microorganisms in the biogeochemical dynamics of natural marine ecosystems
Mid-Atlantic Ridge
a ridge slicing through the Atlantic ocean to the southwest coast of Africa
Carbonate
a solid form of carbon, such as calcium carbonate
continental crust
a solid layer of earth divided into large and small plates
Buffer
a substance that inhibits a change in pH
Water Column
a widely used expression for denoting an undefined volume of water from the surface to depth
Current ocean pH
about 7
low albedo
absorbing light and heat
Surface Current's
affected by movement in air, wind belt mostly, over the surface of the ocean. Run near surface and are horizontal currents. wind driven
Ecological stoichiometry
all organisms are composed of the same major elements: C, N, P - balance affects production, nutrient cycling, and food web dynamics
Culture independent techniques
allow us to determine which organisms are in-situ, even if they have never been grown in a lab. allow us to determine which processes are going on, or at least potentially going on, in-situ.
organic building blocks
amino acids, nitrogenous bases, fatty acids, sugars
regenerated
ammonium uptake indicates what kind of production: new or regenerated?
latent heat of fusion
amount of heat required to convert water to ice or ice to water - 80 calories
latent heat of vaporization
amount of heat required to convert water to vapor or vapor to water - 540 calories - in order to break all hydrogen bonds
hydrothermal vents
an opening in the sea floor out of which heated mineral-rich water flows.
What is anammox?
anaerobic ammonium oxidation (loosing N from the ocean)
Direct counts
are culture independent Direct microscopic counts were made of microbes on membrane filters and of microbes transferred from membrane filters to glass slides. Direct counts showed the presence of from 13 to 9,700 times as many bacteria as cultural methods. The dilution method and the microcolony membrane filter method gave counts 20 and 35 times higher, respectively, than did any of the macrocolony methods. Direct microscopic counts on membrane filters were approximately 150 times higher than plate counts, and the numbers of microbes transferred from membrane filters to glass slides were approximately 2,000 times higher than plate counts.
Substances
are matter that has a definite or constant composition and that exhibits distinctive properties.
Elements
are substances comprised of atoms of a single type that cannot be divided into other substances.
Compounds
are substances made up of the atoms of two or more elements that are chemically united in constant proportions.
Temporal variability in bacteria nad grazer abundance
bacteria goes up and grazers eat them, cyclic model;
Microbial diversity
bacteria, cyanobacteria, and archaea Euk = protozoans and fungi It's hard to ID species because high morphology and diversity
Spray zone to high tide zone
barnacles (filter feeding crustaceans), snails, limpets
circulation cells
basic units of vertical atmospheric circulation
buildup of calc ooze at MOR
bc above CCD lower pressure, warmer temps, less acidic, higher ph (less CO2) plates move, subsides, sinks if it dips below CCD, CaCO3 will dissolve if high productivity area, protective layer (silica (harder to dissolve), clay) doesn't dissolve
ocean sediments
bits of rock or mineral scattered over the sea floor
heat
body size and body shape both influence the degree of _______ stress and desiccation
sampling sediments instruments
bottom grab sampler dredge coring device
fronts
boundaries btwn air masses
divergent plate boundary
boundaries that pull apart two plates. Often cause sea floor spreading
Why do most benthic organisms have small or no air bladders?
bouyancy is not needed
inorganic CaCO3
change in pressure and temp brought up from sea floor by upwelling looks like flour
sediment type: hydrogenous
chemical percipates
gyre
circular flow of water in the ocean
eddy
circular mvmt of water formed along edge of a permanent current avg year, 10-15 rings form 150-300 km in diameter speed 1m/sec
Eukarya/Eucarya -->
complex organisms with membrane bound nuclei and other organelles in the cells (ex: mitochondira, chloroplasts) include both single celled and multicellular organisms (ex: plants, animals, fungi, protists)
Major Constituents
compounds present in the highest concentration For Example, sodium chloride (NaCl) and epsom salt (MgSO4, MgCl2)
Oceans formed about 4 billion years ago, when earth cooled long enough for water vapor to _______.
condense
continental rise
connect the continental slope to the abyssal plain
pelagic rain
constant rain of particles that settle to the ocean floor
cold front
contact where cold air mass moves into warmer area
Where is old land destroyed?
convergent plate boundaries
what are earth layers sorted by?
cool and sort by density (density stratification); inner core -> outer core -> mantle -> crust
Katrina (2005)
costliest and deadliest US hurricane cat 3, largest hurricane of its strength to make land fall in US history flooded New Orleans
cyclonic flow
counterclockwise around a low in N Hemis clockwise around a low in the S Hemis
lithogenous sediments
courser - gravel, sand, silt - settle very quickly finer - clay - slow to settle
hurricane anatomy
diameter usually less than 200km, larger can be 800km eye-low pressure center spiral rain bands w intense rainfall and thunderstorms
vibrio paramhaelyticus
diarrhea, cramps; oysters enter through open wounds
silica in biogenic sediments
diatoms (algae) photosynthetic, diatomaceous earth radiolarians (protozoans siliceous ooze
Long-term organic carbon cycle
dictates the storage of carbon in rocks, best represented by measurements of CO2 trapped in ice cores recoding hundreds of thousands of years.
Different winds cause surface currents to flow in ________ directions.
different
Changes in the global deep-water circulation pattern can:
dramatically and abruptly effect climate
filter feeders
draw water in through a siphon, filter out the particles and expel water. Clams, scallops
Conservative Elements
elements whose relative ratios do not vary regardless of the salinity
Grey Sand is the
equivalent of the RPD layer
limestone weathering
example of congruent weathering CaCO3 + H2O + CO2 -> Ca^2+ + 2HCCO3- calcite water carbon dioxide calcium ion bicarbonate ion florida sinkholes produced by dissolution of limestone by carbonic acid
Vibrio vulnificus
flesh eating, wounds 80k infections and 100 deaths
Direct Methods
floating device dropped into current and tracked through time. floating bottles fitted with radio-transmitters. Or measure from a fixed position (drift meter, flow meter)
sea buoy
floating instruments that show location, wave height, temperature and wind conditions at the surface
calcium carbonate in biogenous sediments
foramini fera (protozoans) calcareous ooze coccolithophones (algae) photosynthetic coccoliths (nano-plankton) rock chalk
energy resources: gas hydrates
gas hydrates resemble ice but burn when lit may form on sea floor sea floor methane supports rich community of organisms most deposits on continental shelf 2x as much organic carbon as all known fossil fuels 10000: value in billions of totns of carbon
Study slides 27-28 for biological pump and solubility pump
geez okay bossy
black smokers
geothermal vent on the sea bed that ejects super heated water containing nutrients and soot
Three things that affect ocean surface currents are...
global winds, the Coriolis Effect, and Continental deflections.
sediment texture
grain size proportional to energy of transportation and deposition
What can sand be made of?
gravel, silt, clay, quartz, mud,
Protist bacteriovores
grazing rates, fluorescent labelled bacteria; but they don't choose for that and couldn't track ingestion. Most bacterivores are small, under 5 um
density variation in the atmosphere
heat rises, so warm air rises cold air is dense, sinks
physical weathering
heat, water, ice, pressure makes small chunks and surface area
convection
heat/energy distribution
herbivores
herbivore issues -ability to mechanically attack plants -chemical defense of plants -feeding, while avoiding predation by other species
deep current
high density, cold water that flows deep in the ocean
tsunamis
high energy wave
spherical shape of earth: solar reflection
high lats (poles): comes in at an angle on the top and bottom, lots reflected, slant Low lats (equator): middle, direct, little reflected, concentrated
albedo in lats
high lats: more heat lost than gained ice has high albedo low solar say incidence low lats: more heat gained than lost
air alway flows from where to where? (Pressure)
high pressure to low pressure
gas hydrates/clathrates
high pressures squeeze chilled water and gas into ice-like solid methane hydrates most common
hurricane destruction
high winds intense rainfall storrm surge: increase in shoreline sea level
Reef crest
highest point- exposed at low tide
# things that have a higher viscosity than seawater:
honey, olive oil, and tar
magma
hot fluid or semi fluid material below or within the earth's crust from which lava and other igneous rock is formed by cooling.
#5 the "universal solvent"
hydrogen bonds negatives are attracted to positives, the water surrounds the other molecule in order to dissolve them
#1 unusually high freezing and boiling point
hydrogen bonds are really strong so you have to heat them more in order to break them - boiling you have to add heat in order to get the molecules to vibrate enough to freeze. the higher the molecular weight, the higher the freezing and boiling point
Larger molecules like polysaccharides, to be used as nutrients for microorganisms, must be
hydrolyzed outside of the bacterial cytoplasmic membrane by extracellular enzymes before the carbon can be transported into the cell and assimilated.
bonding in H2O's different phases
ice - complete hydrogen bonding liquid - incomplete hydrogen bonding vapor - no hydrogen bonds
Bays, gulfs, and seas will have higher salinity that other parts of the world's oceans because waters in these areas move ______ than other ocean areas.
less
hydrogenous/authigenic sediments
less common than litho/bio sediments, almost never dominent sediment type near hydrothermal vents, lots of metal ions are released into the water, and these ions oxidize/combine w silica and precipite out as dark, metal-rich sediment
iron manganese nodules
look like charcoal, grow on the sea floor grow about 1-10 mm per million years fragment of shell, shark tooth, fish ear bone, volcanic cinder grow in layers like an onion
arctic sea ice
lots of sea ice lowers earths albedo ice melts, albedo decreases-cycle
hurricane origins
low pressure cell winds feed water vapor air rises, low pressure deepens storm develops
Bacterial-viral loop in the food web
lysis of bacteria is taken up by bacteria, nutrients regenerated. o Some eaten by grazers, also go to primary producers o A small fraction goes to higher trophic levels...
magma vs lava
magma molten rock under crust; magma that reaches the surface
Nanoplankton?
main primary producers
quarks
make up protons and neurons
estuaries
many fish are born and grow up in __________, and later migrate to the open ocean
Why are reefs biodiverse?
many potential niches (specialization), complex structure, stability
pelagic deposits buildup: high productivity
many tests sinking tests accumulate as siliceous ooze
tidal cycle
marine predators are limited by _____ _____- usually limits predation to lower part
Lowest Density
materials (like rocky material) formed concentric spheres around the core (layers)
Cosmogeneous
materials fall from space
wentworth grain size scale
measure grain diameter (mm) of sediment 3 cats: gravel 256 mm (boulders) sand 1/4 mm (medium sand) mud 1/256 mm (clay)
What is porosity?
measure of empty spaces in a material, spaces filled with air, water and food
formation of the moon
meteor hit Earth; caused 24 hour day and spin on axis; moon formed by gravity
history of extraterrestrial impact
meteor shower impacts are still shown in the deep sea floor
cosmogenous sediments
meteorites from space tektites
responsible for most respiration?
microbes
Can you culture pelagic bacteria?
no you can't, need to only look at their environment. Look at genes and rDNA, SAR-11 is 25% of all pelagic bacteria, pelagibacter ubique
do viruses have metabolism?
no, they are purely reliant on host replication
problems with RNA hypothesis
nobody has made all 4 nucleotides; RNA too complex; RNA is unstable; couldn't randomly form large number of RNA sequences needed for catalytic activity; need ribosomes
important source of food?
non-living organic seawater
Western boundary
occur when an equatorial currents meets the land on the western side of an ocean basin -Corilois effect deflects currents away from equator -western boundary currents found on the western side of the ocean basin -carry warm water from the equator to higher latitudes -form western boundary of subtropical gyres
The significance of liquid
ocean medium for life universal solvent moderates global climate
Oceanographers used the Rubber Duck accident to study _________.
ocean surface currents.
sea breezes
ocean to land
what do hurricanes require
ocean water warmer than 25 C warm moist air coriolis effect season: June 1-Nov 20
Where are earth's most active volcanoes?
oceanic, continental convergence zones
what are the 3 types of convergent zones?
oceanic- continental convergence, oceanic- oceanic convergence, and continental- continental convergence zones
benefit of studying sediments
oceanographers deciper earth's history
Nearly all of the Earth's water is in ________.
oceans
Study slide 12 for microbial loop
okie dokie
Carbonic Acid
one of the forms of dissolved carbon dioxide in seawater protecting regions of the Pacific; a subduction zone off the coast of Oregon
Bicarbonate
one of the forms of dissolved carbon in seawater; a salt containing HCO3
What is formed by continental- continental convergence zones?
only partial subduction occurs therefore forming mountains
florida's coral reefs
only state in continental US to have extensive coral reef formations threatened from: - nutrients - visitors - pesticides, offshore oil, sediment from development, marine debris
gravity corers
only work with gravity very heavy tube
Benthic
organisms that live on the bottom or in sediments
ekman transport
overall water mvmt due to ekman spiral ideal transport is 90 degrees from the wind transport direction depends on hemisphere
Where do pearls come from?
oysters
deposit feeders - microbial stripping hypothesis
particulate organic matter is relatively indigestible and therefore microbial organisms are the main source of nutrition for deposit feeders
Drake passage
passage- Area between South America and Antarctica. Constricted area = faster currents = ripples in sediments on ocean floor.
Nitrate and phosphate nutrients
peak at 1,000 meters
DOM
pelagic bacteria feed on DOM, bacteria that use 20-50% of primary production; a lot of photosynthate must be a DOM
distribution of biogenous sediments
pelagic rain found on the abyssal plane
solar energy
primary source of earth energy: sun 1400 w/m^2 at top of atmosphere solar energy drives circulation of atmosphere and ocean and source of energy for almost all living organisms
deposit feeders
process mud, removing food particles. Sand dollars
FISH
process- Can be used to label different components of natural or experimental bacteria populations to see what species or strains of bacteria the HNF ate.
Long-term inorganic Carbon Cycle
processes involved i the formation and dissolution of carbon-containing rocks, such as limestones, over geologic time.
Sinks
processes that remove a substance or material from a reservoir
factors controlling distribution of biogenous sediments
productivity #of organisms in surface water above occean floor destruction skeletal remains (tests) dissolve in seawater at depth dilution deposition of other sediments decreases % of biogenous sediments
export ratio
ratio- export production --------------------------------- primary production
f-ratio
ratio- new production ----------------------------------------------- new + regenerated production
What is denitrification?
reduction, 2 steps 1. nitrate to nitrite 2. nitrite to N2 or N20
Chemical Properties
refer to characteristics of a substance on an atomic (microscopic) level that involve changes in the composition of a substance.
high albedo
reflective, lots of energy and sunlight reflected away
Most phytoplankton are
relatively easy to count as large and pigmented
Sidney Fox
repeated Miller's experiment in tide pools -> proteinoids -> protocells (look like primitive cells)- theory of how life began
latent heat
required amount of heat to cause a change in physical state
accretion
rocks spinning with gravity to form planets; condensation -> faster spinning
which kind of shoreline has the greatest biodiversity?
rocky shoreline with a large tidal range
eddy: warm core ring
rotates clockwise found on landward side of current
eddy: cold core ring (cyclonic eddy)
rotates counterclockwise forms on ocean side of current
Classifying Pelagic Bacteria
round, tubular, bent rods/ helices
Classifying Pelagic Bacteria
round, tubular, bent rods/ helices gram negative
what measures hurricane intensity
saffir-simpson scale of hurricane intensity 1-5 scale
Oceans have different _______ all over the world.
salinity
#4 unusual temperature and density behavior
salt water - as the temp goes up the density goes down. warm water is on top of colder water - because as water cools the molecules move more slowly, they can crowd together better fresh water - as the temp goes up the density does down, but only above 4 degrees c. below 4 degrees c the water is expanding and ice crystals are forming which forces water molecules apart
What is the microbial loop?
salvage pathway in which bacterioplankton repackage and reincorporate DOC back into the aquatic food web
grain size
sediment _____ _______ is important in determining the distribution of benthic organisms- increases with increasing energy
active herbivores (grazers)
seek out primary producers as food. Sea urchins, limpets
rocky intertidal
sessile organisms in this zone hang on tightly to rocks, often have low profiles and tough shells
coccolithophore
settle 1-6 cm per 1000 years
Archaea -->
simple single celled organisms that look like bacteria often found in extreme environments significant differences in biochemistry compared with bacteria and eukarya
What are prokaryotes?
single-celled organisms that lack any membrane-bound organelles
tektites
small glass beads that fall from the sky after impact
biogenous marine sediments: microscopic
small remains tiny shells/ tests settle thru water column mainly algae and protozoans
The main salt in ocean water is _________.
sodium chloride
Viral population
stick, digest, ingest, damaged by UV
what were earth's first reefs?
stromatolites (cyanobacteria)
Dr. Billy Glass
studies tektites
mid-ocean ridge
submerged mountain chain caused by magma due to divergent plate
Molecules
substances composed of two or more atoms, not all are considered compounds
incident electromagnetic radiation
sunlight
sediment type: cosmogenous
tektites
metabolism
term- Ability to manufacture biomolecular structures from matter scavenged from the surroundings and energy.
regenerated production
term- Nutrients are supplied by the recycling of nutrients that results from the remineralization of organic matter within the surface ocean. Supported by ammonia. Less Productive of the two primary production sources. Commonly found in subtropical gyres
Electrical Conductivity
the ability of a substance, such as seawater, to transmit an electrical charge.
What are examples of chemical and physical reactions in processes in the ocean?
the addition or removal of dissolved elements and the exchange of heat in seawater by hydrothermal vents.
Solubility
the amount of a solute that can be dissolved by a solvent under a given set of conditions
heat capacity
the amount of heat required to change the temperature of 1 gram of a substance by 1 degree c
Missing Carbon Problem
the apparent discrepancy between the amount of carbon released by human activities and the smaller amounts found in the atmosphere
the amount of CO2 in the ocean is the same as
the atmospheric amount fo carbon
inner core
the center of the earth, iron
Precipitating
the coming out of solution of a dissolved substance
Salinity
the concentration of salts in seawater
Principle of Constant Proportions
the constancy of the ratios of the major constituents regardless of the salinity
the history of climate
the deep sea floor is the best record fossil evidence geochemical analysis of CaC03
carbonate compensation depth
the depth that CaCO3 dissolves, just above the abyssal plane
Macronutrients
the dissolved chemical substances in greatest demand by photosynthetic organism
carrying capacity
the size of population that the community can support under a stable set of environment conditions
Continental Margin
the edge of the continent that is covered by the ocean includes the continental shelf, the continental slope, and the continental rise.
Alternative phyolgeny
the eocyte hypthesis 1984 a new ribosome structure indicates a kingdom with a close relationship to eukaryotes
Biogeochemical cycles
the exchanges and cycling of matter through biological, geological, and chemical processes.
outer core
the liquid layer surrounding the inner core
Biosphere
the living part of the world
Saturation Concentration
the maximum concentration of a solute that can be dissolved in a substance
Redfield Ratio
the near-constant proportions of C:N:P in seawater
pH
the negative log of the concentration of hydrogen ions in a solution
why do H2O molecules form
the oxygen and the hydrogen want to have a filled outer-shell so they share electrons
Electron orbitals
the positions occupied by electrons in an atom
Dissolving
the process whereby one substance is dissolved into another to form a solution
oceanic crust
the relatively thin part of the earth's crust that underlies the ocean basins.
Short-term organic carbon cycle
the reservoirs and processes involved in the transformation and exchange of newly fixed organic carbon
Geosphere
the rocky part of the world
Chemistry is defined as...
the science of the composition, structure, properties, and behavior of matter.
mantle
the second top layer of the earth's core, made of molten rocks (magma)
Continental Slope
the steeply inclined section of the continental margin located between the continental rise and the continental shelf
Carbon cycle
the storage and transfer of carbon among various living and nonliving earth reservoirs; both short- and long-term carbon cycles are recognized
Chemical Oceanography
the study of the chemistry of the world ocean
Solvent
the substance into which other substances are dissolved
Residence Time
the time that a dissolved substance spends in a particular reservoir
Osmotrophy
the uptake of dissolved organic compounds by osmosis for nutrition many microorganisms receive most, if not all, of their nutrients from the surrounding water
hydrothermal vents
theory of how life began- where seafloor is spreading; iron sulfide world; iron sulfide can catalyze both oxidation-reduction reactions and polymerizations of amino acids; works at high temperatures and pressures like deep-sea vents;
Why do Nitrate and phosphate nutrients peak at 1000 meters?
there is no light at 1,000 meters so the nutrients are not absorbed
marine sediments acronym
tlbhcv to, like, be honest, aubrey can't very
fore-reef zone (outer slope)
to a depth of 10-20 meters- steep, rigged masses of large corals and some large fish ~20-30 meters more delicate species of coral occur ~Below 30-50 meters reef growth is patchy because light levels are very reduced ~Below 50 meters slope drops off rapidly into deep water
The most important function of the ocean is ....
to absorb and hold energy from sunlight.
burrowing 3
type of sediment is important -larger particles --send 62-200um --grains not compressible --need force to move particles and water -smaller particles --mud/clay <62um --organic polymers cause adhesion between the grains --behaves with elastic properties --burrowing causes cracks, sediment weakens --water flows in, burrowing causes more water --Thixotropy - sediment become less resistant as you exert more force
Down welling
vertical movement of water to deeper parts of the ocean . Usually associated with low primary productivity. Important carries oxygen from surface water to the deep
Upwelling
vertical movement of water to the surface. water usually cold, rich in nutrients. High Primary productivity when the nutrients rich water is carried up into the light. Primary Production provides food for other organisms such as fish
upwelling
vertical mvmt of water upwelling= mvmt of deep water to surface cold nutrient rich water rising to surface produces high productivities and abundant marine life
Earth's temp and gg's
w/o: -18 C w: 15 C
Brownian motion
water molecules or gas molecules can push and actually move bacterium cells or other very small organisms *For bacteria < 0.6 µm in diameter, Brownian motion makes steering impossible.
#3 unusually high latent heat of fusion and vaporization
water needs a lot more energy to change states
Hydrogen bonds
weak chemical bond formed between the electronegative oxygen atom of one water molecule and the electropositive hydrogen atom of another water molecule.
Yellow Sand is
well oxygenated
earth spins in what direction
west to east counterclockwise
low pressure
wet climate, overcast skies lats: polar front, equatorial doldrums
easily accessible
what does labile DOM mean?
cell suicide
what is autoatalytic cell death?
Eastern Boundary Current
wide (>1000km) shallow (0.5km) slow (10s of km/day) moving cold water to equator ex: California, Canary, Peru, Western Australian Current
ekman spiral factors
wind coriolis effect
surface current
wind and Coriolis effect creates shallow ocean current
ocean currents
wind driven: mainly more water, horizontal, down to 1 km only 10% of ocean currents gravity/density driven: moves water vertically, mixes water masses
hurricane origins: tropical storm
winds 61-120 km/hr
DGGE Steps in the method
• Collection of environmental samples. • Extract and crudely purify DNA. • Design primers to amplify selected regions of DNA. • Amplify selected regions of DNA using PCR (polymerase chain reaction). • Separate the PCR products by running DGGE gels (type of chromatography). • Sequence analysis of selected DGGE bands to determine the order of the nucelotides in the selected DNA fragment (i.e. order of the 'le1ers' in the DNA code). • Analysis of the sequence data to identify the taxonomic affiliation of the organisms from which the DNA was originally extracted (BLAST search).
How can we identify different taxa of prokaryotes without growing them?
• DNA sequences that define the genotype give rise to an organism's phenotype - who it is. • Could use nucleic acids (DNA and/or RNA) as a 'barcode' to identify an organism. • Woese and Fox (1977) used 16S RNA. "16S RNA is a subunit of the ribosome. • Ribosome is used to translates DNA into proteins. •Ribosomes are complex structures composed of ribonucleic acid (RNA) and proteins - ribonucleoprotein.
BBL --> Benthic Boundary Layer
Contributes those portions of sediment and water columns that are affected directly in the distribution of their properties and processes by the presence of the sediment-water interface
SHemisphere tilted more at sun
NH winter, SH summer
Mineral Particles
Weathering of rocks on land.
Cations
dissolve ions with a positive charge
Hydrated
surrounded by water water molecules
fossils
term- remains of microorganisms and trace fossils.
pile of DOM
what would happen if there wasn't a microbial loop?
Poretsky et al. 2009 Day/Night differences
• 75,558 putative mRNA reads from the day transcriptome and 75,946 from the night transcriptome at Station ALOHA. • Cyanobacteria contributed 54 % of the transcripts, greater than expected by abundance (35 % cell counts, 21 % of 16S rRNA sequences). • Indicates that Cyanobacteria were the most active component of the community, both during the day and at night. • Relative abundance of transcripts changes between day and night, e.g. more photosynthesis transcripts during the day and cell repair at night. • Transcriptome a good indicator of which biogechemically significant processes are occurring.
Issues to think about with counting
• Both dead and live prokaryotes stain with fluorescent nucleic acid dyes such as DAPI. • Sample preservation. • Delicate cells (e.g. small protists) hard to count. • Direct counts tell you very little, if anything, about activity. • Direct counts of prokaryotes tell you nothing about who they are.
Valence
the number of single bonds that can be formed by an element
Improving counts
• Direct counting of marine 'bacteria', using a counting slide and transmitted light under the microscope is unreliable. Marine bacteria are very small and basically transparent. • Indirect counts, based on growing the 'bacteria', significantly underestimate abundance. • Two innovations led to a better method for directly counting marine microorganisms: Track etched polycarbonate filters and fluorescent dyes that bind to nucleic acids.
Genome of a diatom: Armbrust et al. (2004)
• Extracted DNA from a CULTURE of T. pseudonana grown from a single cell. • Used shotgun sequencing with 14 x coverage.
Molecular Methods Summary
• Fluorescent nucleic acid stains (e.g. DAPI) can be used to stain microorganisms to enable direct counts using an epifluorescence microscope or flow cytometer. • The gene that codes for 16S RNA (18S RNA in eukaryotes) can be used to determine which microorganisms are present in a system. This has revolutionized our understanding of microbial diversity and distribution in the ocean (examples we used were DGGE and FISH) • Whole genome sequencing of specific organisms has helped elucidate the physiology, biogeochemical significance, and evolutionary history of important taxa. • Metagenomics has been used to determine both who is there and what they can potentially do in entire ecosystems (e.g. Sargasso Sea). • Metatranscriptomics has been used to look at what genes a biological community is expressing. This will help us understand what processes are actually active in an ecosystem and how they are regulated. • The new technologies associated with molecular methods have enabled researchers to open up the 'black box' of microbial ecology in the ocean, reinvigorating a field that was essentially stalled until the late 1980s.
Louis Pasteur (1822 - 1895)
• French chemist and microbiologist who is generally considered to have founded the field of 'medical microbiology' • Germ theory, pasteurization
Key questions in Microbial Oceanography
• Who is there? • How abundant are they? • What are they doing? • How active are they? Answering these questions was very difficult prior to the development of molecular techniques in the late 1970s onwards
The final twigs and leaves of a tree of life are the
species
Grouping marine organisms
• By where they live (e.g. plankton, benthos, neuston) • By size. • By what they do (e.g. autotrophs and heterotrophs) • By trophic level • By who they are (classification and phylogenetics)
Ferdinand Cohn (1828-1898)
• German biologist who studied algae, spores, and bacteria • Classified bacteria into four groups by shape (sphericals, short rods, threads, and spirals). • Showed Bacillus can form endospores when subjected to conditions unsuitable for growth.
Heinrich Hermann Robert Koch (Robert Koch) (1848 - 1910).
• German medical doctor. • Isolated bacteria that cause diseases such as tuberculosis (TB), chlolera, anthrax. • Won Nobel Prize for medicine in 1905 for work on TB. • Developed Koch's postulates for determining whether an organism causes a disease.
For diffusive supply, uptake ___________ with ____________
"uptake increases linearly with the cell radius"
DOc in the food chain
(DOC) is returned to higher trophic levels via its incorporation into bacterial biomass, and then coupled with the classic food chain formed by phytoplankton-zooplankton-nekton.
Alum
- Applied to lake surface, floc settles quickly through water column - Aluminum sulfate - inactivates sediment P by forming Al bound P that is not biologically available - Reduces internal loading of P
Mazumder and Havens findings: Chl vs TP
- Chl increases as a function of TP in temperate and subtropical lakes - Temperate SH and subtropical lakes are similar - Temperate LH lakes had less chl per TP than subtropical SH or temperate SH lakes - TP-chl relationships are sigmoidal for all three types of lakes
Mazumder and Havens findings: Chl vs TN
- Chl increases as a function of Tn in temperate and subtropical lakes - N didn't explain a greater proportion of hl variance in subtropical lakes compared with temperate lakes
Elser et al. Herbivore histograms
- Herbivorous insects and zooplankton had similar mean C:N, C:P and N:P ratios in the two habitat types
What types of organisms' lifestyles make up the benthos?
- Infauna: Plants, animals and bacteria of any size that live in the sediment (micro, meso, macro) - Epifauna: attached to the hard bottom or substrate (to rocks, reefs, debris) and live on the sediment surface - Demersal: Bottom-feeding or bottom-dwelling fish that feed on the benthic infauna and epifauna
Elser et al. N:P ratios
- N:P ratio didn't vary as greatly between terrestrial and FW habitats as it did in C:N - biomass composition for N and P were similar --> may indicate the prevalence of N-limitation in lakes is greater than thought
Elser et al. C:Nutrient rations
- The base of the terrestrial and freshwater food web differ dramatically in C:Nutrient raise - Mean C:N and C:P ratios of foliage of terrestrial autotrophs were more than 3x higher than freshwater sexton - Nutrient poor, c-rich structural carbohydrates in vascular plant tissue
Geostrophic Currents
- Water pile sup in the middle of subtropical gyres as a result of the clockwise rotation of surface water due to Ekman transport, this is called a Subtropical Convergence -hill of water may be up to 2 m high - water flows down the hill of the subtropical convergence in response to gravity -Corilois effect oppose gravity, deflecting water to the right in a curved path into the hill -When the effect of gravity and the Corilois effect balance then a geostrophic current results, which moves in a circular path around the hill -path of ideal geostrophic flow - Path of actual geostrophic flow
Hypolimnetic withdrawal
- pump out deepest water - changes the depth at which water leaves the lake - Hypolimnetic DO increases and epilimnetic P decreases - used for stratified lakes with anaerobic hypolimnion that restricts the habitat for fish
What are the different environments of a reef?
- reefs found in warm, shallow, clear water and nutrient-poor environments - coral structure grows upward when land subsides or sea level rises Fringing (no lagoon) Platform Barrier Atoll zones of coral reef- [lagoon] back reef, reef crest, fore reef (buttress zone)
What two organisms make up coral and of what benefit are they to each other?
- reefs made up of individuals (colony of polyps) possessing tentacles with nematocysts to capture prey - polyps secrete calcium carbonate exoskeleton - most corals contain symbiotic algae, zooxanthellae, that are dinoflagellate (protist: single cell algae) - symbiosis!!! - cnidaria provide shelter and nutrients for zooxanthellae - photosynthesis provides O2 and organic carbon and aids in CaCO3 precipitation by removing CO2 - sucessful but VULNERABLE (both organisms need right light, and right and stable temp)
Elser et al Conclusion implications of stoiciometry
- the C:N:P requirements of organisms varies with producer and consumer species - The bottom up effects are complex
Mantle (Chemical composition)
-below crust -has largest volume of the 3 layers -down to 1800 mi deep -composed of high density iron and magnesium silicate rock
Mesosphere (physical properties)
-beneath asthenosphere -down to 1800 mi deep is the middle and lower mantle -is rigid
Asthenosphere (physical properties)
-beneath lithosphere -is plastic and can flow when a gradual force is applied -62 mi to 430 miles deep -is the base of upper mantle
Core (Chemical composition)
-beneath mantle -1800 mi to center of the earth 3960 mi deep -composed of higher density metal (Fe and Ni mostly)
Core (Inner and Outer)
-beneath mesosphere -Outer core is liquid and can flow -inner core is rigid
How do you determine differences between prokaryotes?
-cell shape and morphology -colony shape and morphology -determine metabolic potential
active suspension feeders - issues
-concentration of particles - saturation and even clogging --mussels -current velocity and ability to create current, and keep siphon erect -selection of high-quality particles
How do prokaryotes transform DOC?
-convert from mostly labile to refractory -photodegredation and other abiotic processes also involved
Lithosphere (Physical properties)
-cool, rigid, outermost layer -surface to 62 mi deep -includes crust and top portion of mantle -is brittle and can shatter easily if pressure is applied *it's plates are the ones involved in plate tectonics
Proto Earth
-larger than today's earth -No oceans -no life -composition was the same throughout/no layers -lots of meteorites (rocks) were hitting it **Proto earth condensed and contracted and cooled off so it began to shrink. As it cooled it stratified (layered) which is known as density Stratification.
Oceanic Crust
-lies under ocean basins -composed of igneous rocks called BASALT-high density (heavy) and it's dark colored -originates as molten magma and comes to surface during underwater seafloor eruptions
Middle intertidal to subtidal
-many different feeding strategies represented -crabs, starfish -anemones, sea urchins, oysters, worms, lobster -kelp and red algae
living on the benthos
-need hard surface -need attachment mechanism -must deal with drag -mobile organisms usually align with current and have some attachment mechanism --low body form --suckers --muscular foot
Fridtjof Nanasen
-noticed a artic ice moved 20-40 degrees to rights o the wind blowing across the surface - water in the northern hemisphere behaves the same way. on the southern Hemisphere water moves to the left of the wind direction
meiofauna
-organisms that live within the grains of sand -interstitial organisms aka meiofauna -move among grains but do not displace them --not truly burrowing
passive suspension feeders - issues
-orientation in current -current velocity - pressure drag -particle concentration - saturation of feeding structure
What is nitrification?
-oxidation, 2 steps carried out by 2 types of bacteria 1. ammonium to nitrite, ammonium oxidized 2. nitrite to nitrate, nitrite oxidized further
What is the impact of the surface area to volume ratio?
1) As a cell increases in size, the surface changes to the power of 2, while the volume chances to the power of 3, so much more. The bigger a cell is, the more volume it has compared to its surface. The ratio surface area to volume gets much smaller as the cell increases in size. 2) Because cells must get their supplies through their membranes. If the surface:volume ratio gets too small, there is not enough membrane to get all their supplies anymore. Also, the distances within the cell get to big to get everything everywhere. Compare it to a city that keeps on growing and growing. At some point there is not enough food to feed the population, and not enough freeways to get people everywhere. 3). Some animal cells overcome this problem because they have microvilli: many small folds in their membranes, which increase their surface area. An egg needs to store a lot of food, and is not very metabolically active, so it can probably afford to be bigger.
What is life? or What are certain attributes of life?
1) Reproduction (instructions to make itself); Genetics, DNA, RNA, contianing information of some kind. 2) Homeostasis 3) Metabolism (energy, chemical processes) 4) A purpose, a function, a niche; an ability to "die" or cease to exist 5) Ability to grow, change, or evolve 6) Autonomy
Sand Layers
1) Yellow Sand 2) Grey Sand 3) Decomposing Zostera 4) Black Sand
The earth is a(n)
1) ocean dominated planet 2) integrated system
Whittaker's five kingdom system
1) plantae 2) fungi 3) animalia 4) protista --> single celled eukarya 5) monera --> bacteria
Process of sedimentation in the Deep Sea
1. Bulk Emplacement (Large quantities of sediment are transported to the deep-sea floor as a mass rather than as individual grains.) 2. Fallout of fine-grained terrigenous sediment and biogenic material (pelagic/bottom sediment) 3. Formation of hydrogenous material
Biogenic Oozes
1. Calcareous oozes (organisms secret CaCO3-foraminifera) 2. Silicous oozes (organisms secrete SiO2 remains of diatoms and radiolaria)
Chemical composition: What are the 3 layers of earth?
1. crust 2. mantle 3. core
Deep sea
1. incredible pressures and cold temperatures, no light, very little food 2. very slow rates of bacterial degradation and recolonization 3. mostly muds so are mainly deposit feeders 4.creatures- generally small with a low population density
impact of supernova shock wave hitting our nebula
1. might have triggered condensation of our nebula 2. caused condensing mass to spin 3. heavy atoms absorbed from supernova
Mazumder and Havens objective
1. test nutrient-chl relationships for subtropical and temperate lakes - similar for similar grazer communities 2. examine if stronger TN-chl relationships in subtripcal lakes and stronger TP-chl relationships for temperate laeks 3. test subtropical and temperate lakes for producing similar TP-secchi and Chl-Secchi relationships for small zooplankton dominated systems
water's unusual properties (list)
1. unusually high freezing and boiling point 2. unusually high heat capacity 3. unusually high latent heat of fusion and vaporization 4. unusual temperature - density behavior 5. "the universal solvent" 6. light in water - why is the ocean blue?
Soft substrates
1. vertical zonation less obvious and quality of environment determined mostly by size, shape, and organic content of sediments. 2. lots more infauna than on shore rocky substrate ~Deposit-feeders like sand dollars, sea cucumbers and worms ~Filter feeders (also called suspension-feeders like clams (sandy or coarser sediments)
Now in modern day, we know there are closer to
2 million bacteria in the ocean
How is life distributed in the ocean and why?
98% of ocean's species are benthic, 2% pelagic The pelagic environment is fairly uniform, placing less pressure on organisms for adaptation than in the benthic world, where things are always changing environmentally
What is the issue with bacteria in the lab?
>99% of Bacteria and Archaea cannot be grown in cultures. This means that their physiology and ecology cannot be investigated in the laboratory.
Rift Valley
A deep valley that forms where two plates move apart
Selman Waksman (1888 - 1973)
A soil microbiologist who developed the Department of Marine Bacteriology at the Woods Hole Oceanographic Institution. Received Nobel Prize for his work on soil microbiology and the discovery of several antibiotics in 1952.
Fluorescent nucleic acid stains
Acridine Orange (AO) (N,N,N',N'-Tetramethylacridine-3,6-diamine) DAPI (4',6-diamidino-2-phenylindole) SYBR Green 1 N',N'-dimethyl-N-[4-[(E)-(3-methyl-1,3- benzothiazol-2-ylidene)methyl]-1-phenylquinolin-1- ium-2-yl]-N-propylpropane-1,3-diamine
Advantages/disadvantages to Asexual reproduction
Adv: solves the problem of finding a mate disadv: lacks the adaptability provided by variety in a gene pool
Turbidity currents
Agents of transport to the deep sea. Powerful bottom currents are sediment-laden slurries that, under the influence of gravity, move rapidly downslope as turbulent underflows that push aside less dense water.
zooxanthellae
Algae that lives within coral in a cooperative relationship Gives coral its color
Deep Ocean Basin
Begins at edge of continental margin and extends under deepest parts of the ocean; consists of the abyssal plain and all the ocean floor formations.
Barrier Reef
Begins to form when an island starts to sink but is not completely submerged
If a bacterium is an osmotroph in the ocean, do you think it's better to be small or big?
Better to be small, no chance of not being able to fulfill it's energy requirements for necessary functions
Bacterivory Methods to measure rats of grazing on bacteria Class 2?
Community manipulations. - At natural contact rates growth is cancelled by grazing - Reduce contacts between predator and prey - At zero contacts 'true' growth rate can be determine because there is zero grazing - Decrease in growth rate with increasing contacts is the grazing rate
Conjugation
Conjugation is a method of horizontal gene transfer. The gene transfer occurs when a conjugation tube forms between ANY two bacteria (same or different species). In the gut, this happens between E. coli all the time - same or different species.
What is meant by culture-dependent approaches to microbial ecology? How about culture-independent approaches? Which approach is better?
Culture-dependent approaches rely on growing prokaryotes. Culture independent methods rely on molecular methods to study microbes within their environments.
Equatorial Upwelling
Current Divergence= occurs when currents move away from an area -South east trade wind slow across the equator and Ekman Transport causes water to veer to the right (northward), north of the equator and veer to the left (southward)south of the equator -This creates a divergence of surface currents along the geographical equator and upwelling of cold, nutrient rich water - Equatorial upwelling common in Pacific and creates areas of high productivity and rich fishing grounds
What is cytometry used for?
Cytometry is the measurement of the characteristics of cells. Variables that can be measured by cytometric methods include cell size, cell count, cell morphology (shape and structure), cell cycle phase, DNA content, and the existence or absence of specific proteins on the cell surface or in the cytoplasm.
Abyssal plain
Flat, with submarine volcanoes called seamounts
Diffusion Limited Aggregation
Diffusion-limited aggregation (DLA) is a growth model used to predict bacterial growth. It creates complex, multi-branched forms, and can be applied to any system where diffusion is the main method of particle transportation. DLA can be observed in bacterial growth on agar plates, in dendrites, dust balls, electrodeposition, and mineral deposits. [9] A DLA pattern begins with a seed molecule at the origin of the lattice. A "random walker" molecule diffuses from far away in a random pattern of motion. It stops once it reaches a space adjacent to the seed molecule, and another random walker is launched. In a DLA lattice, a molecule that sticks out of a main branch will be emphasized by new growth, not be rounded or smoothed over. Nodes are more likely to catch wandering particles because they three facets available for growth, compared to a molecule in the branch, which only has one available facet. [5]
Disease
Disease = big impact on marine systems; pathogens to oysters
Estuaries and Salt Marshes
Estuaries and salt marshes are unique because they represent the interface between a river ecosystem and a coastal marine ecosystem. Organisms must adapt to the salinity of the water that fluctuates with the tides. The river brings large amounts of nutrients into shallow water that allows photosynthetic algae to be highly productive. Young crustaceans and juvenile fish eat the algae and live among the grasses that grow along the shore. Like mangrove swamps, estuaries trap and filter sediment. As the sediment accumulates, the estuary becomes a salt marsh ecosystem, such as those found in the southeastern Atlantic seaboard. Both estuaries and salt marshes are important habitats for migratory birds. In the salt marsh, a rich spongy soil builds up as the marsh snags detritus and decaying organisms. Near the water, mudflats are a microbial soup, with crabs and other invertebrates feeding from the organic material. Low wave action allows small particles to settle here, so little oxygen can penetrate into the mud. Bacteria undergo anaerobic digestion, which involves the reduction (adding hydrogen) of carbon or sulfur, rather than oxidation (adding oxygen). As a result, the marshes produce methane (natural gas) and hydrogen sulfide (which smells like rotten eggs).
Oceanic Zone
Extends from the continental shelf to the end of the continental slope
Neritic Zone
Extends from the intentidal zone to the continental shelf
Abyssal Plains
Flat ocean bottom
FSC, in relation to flow cytometry
Flow cytometers detect Fluorescence emission at a 90 degree angle to the exciting light beam. Forward Scatter (FSC) A parameter measuring light scattered less than 10 degrees as a cell passes through the laser beam. The FSC measurement is related to cell size.
What do fluorescent dyes do?
Fluorescent dyes enable researchers to count bacteria and viruses in water samples - revealing high concentrations of both
FISH
Fluorescent in situ hybridization FISH stands for fluorescent in situ hybridization. It is a culture-independent technique that is used to visualize certain types of prokaryotes within a sample. A fluorescent probe is used that targets the 16S rRNA gene of a prokaryote. The probe can be specific for one type of microbe like bacteria or archaea. The probe can be "universal" useful for detecting all prokaryotes. Only the cells with the FISH probe will fluoresce under the epifluorescent microscope. You can count prokaryotes using FISH. • Can tell you 'who' is there and how abundant they are. • Can relate the abundance of different components of the microbial population to total abundance. • You can choose 'who' you count. • You can design probes to be very general (e.g. Archaea) or specific down to the species level. • Limitation: you have to know 'who' you are looking for. FISH cannot be used to look for unknown taxa as you cannot design a probe for the totally unknown. • Limitation: you can't look for everything at once .
Hydrostatic pressure
Hydrostatic pressure is the pressure that is exerted by a fluid at equilibrium at a given point within the fluid, due to the force of gravity. Hydrostatic pressure increases in proportion to depth measured from the surface because of the increasing weight of fluid exerting downward force from above. It does NOT limit microbial activity
1 atmospheric pressure
If you go down 10 meters in the ocean what is the change in pressure?
What is metagenomics? Why is this a culture-independent approach used in microbial ecology studies?
In metagenomics the approach is to determine the sequence of DNA isolated from an environment. The hope is that you will discover novel organisms and genes that could not be determined using culture-dependent methods. In metagenomics, you don't need to grow any organisms. You just extract the DNA and use high throughout sequencing facilities to determine the DNA sequence. • Metagenomics is a holistic approach that can tell us 'who' is there and what they can POTENTIALLY do. It can tell us something about how an ecosystem works and enable us to make predictions about biogeochemical processes. • However, all the data comes from the genome. Therefore we do not know if the processes indicated by certain genes or collections of genes are actually occurring in situ. • No information on rates of process (would still need to measure rates of processes such as community respiration or photosynthesis).
more
Is there more or less nitrogen and phosphorus at the bottom of the ocean compared to the surface?
Mangrove Swamps
Mangrove swamps occur near the shore where highly adapted, salt-secreting trees grow with their roots in the water. Like coral reefs and kelp holdfasts, the mangrove roots provide a home for marine invertebrates and small fish. Bacteria that live among the sediments trapped in the roots digest toxins that flow through, so mangrove swamps serve as a kind of filter in coastal areas. Eventually the trees grow close enough together where a terrestrial community is able to establish itself on top of the roots. Mangroves are found in the Caribbean, Southeast Asia, Africa, and tropical islands throughout the world.
Why study Microbial Oceanography?
Microorganisms play a significant role (often the dominant role) in the 'economy of the sea' (Karl 2007). • Photosynthetic microorganisms (Eukarya and Bacteria) use solar energy to fix the organic matter that fuels almost all heterotrophic processes in the ocean. • Life in the ocean is dominated, both in terms of biomass and metabolism, by microorganisms from all three domains of life (Bacteria, Archaea, Eukarya). • Observations need to be made at multiple levels of system organization to understand life in the Ocean: genomes to biomes, multiple temporal and spatial scales. Understand and to be able to predict the effects of climate change on the ocean (e.g. global warming and ocean acidification). • To better understand and predict the factors affecting resources and other ecosystem services provided by marine microorganisms (e.g. fisheries management). • Understand biodiversity (how many species, where those species are located, metabolic diversity etc.) • Curiosity: Understand how marine ecosystems function and how they are structured, understand global biogeochemical cycles, origin and evolution of life, the Earth system.
Observational basis for Sea-floor spreading hypothesis
Mid-ocean ridges with geological activity Rocks nearer ridge are younger Sea floor rocks have magnetic bands
nitrogen, oxygen
Mirror Image- More ____ the deeper you go into the ocean, then levels out. Less _____ the deeper you in the mesopelagic zone then more when you get deeper into the ocean.
Support for the Endosymbiotic theory
Mitochondria Have DNA Mitochondria and chloroplasts have striking similarities to bacteria cells. They have their own DNA, which is separate from the DNA found in the nucleus of the cell. And both organelles use their DNA to produce many proteins and enzymes required for their function. A double membrane surrounds both mitochondria and chloroplasts, further evidence that each was ingested by a primitive host. The two organelles also reproduce like bacteria, replicating their own DNA and directing their own division. *shared genetic information at some point in time
Coriolis Effects
Movement of the air and water. Northern Hemisphere moves clockwise. Southern Hemisphere moves Counter-clockwise
5 subtropical gyres
N atlantic S Atlantic N Pacific S Pacific Indian Ocean
most hurricanes where?
N pacific, bangladesh regularly SE Asia affected often Hawaii
What is nitrogen fixation? What is it controlled by?
N2 to organic nitrogen, controlled by diazotrophs
autotrophs
Nitrifying bacteria are _______ like phytoplankton.
Convergent
Oceanic-to- co-continental crust come together, forms trenches
Divergent
Oceanic-to-oceanic crust move apart, forms mid-ocean ridge
Name the five oceans
Pacific, Atlantic, Indian, Southern, Arctic
Molecular Markers Nuclear ribosomal genes
Ribosomal RNA is considered as the best target for studying phylogenetic relationship because, it is universal and is composed of highly conserved as well as variable domains. The ribosomes consist of rRNA and proteins. In all organisms the ribosome consists of two subunits, the small ribosomal subunit (SSU) contains a single RNA species (the 18S rRNA in eukaryotes and the 16S rRNA in others) As Woese & Fox (1977) said: • Component of all self-replicating systems. • Sequence changes slowly with time. • Easy to isolate. Also: • Sequence needs to be long enough to have the resolution to distinguish species.
Ross Sea, Antarctica
Ross Sea: - Water - Ice - Water underneath the ice water/ice slushy There are lots of microhabitats Objective: examine protistan diversity in an extremely cold environment using molecular methods. • Phototrophic and heterotrophic protists are ubiquitous in cold environments, where they play an important role in nutrient cycling and food webs. • Traditional microscopic methods are limited as they require distinctive morphological features to distinguish between taxa. Great for large protists with distinctive features (e.g. diatoms), but many protists are small (< 20 µm diameter) without distinctive morphological features. • Many protists don't preserve very well, so can't look at a sample later. • Warming up of Antarctic protists kills them rapidly (e.g. moving to lab inside a ship) and characteristics, such as swimming behaviour, are often used in traditional identification methods. • Can the molecular methods commonly used to assess Bacterial and Archaeal diversity from environmental samples also be used to determine Antarctic protistan diversity
Guyots
Single underwater flat mountain
Seamounts
Single underwater pointed mountain
Size is used as a what?
Size is used as a way of classifying plankton as samples are usually connected using different sized nets and filters
Brachish
Slightly salty water mixes with ocean water
V. Walfrid Ekman
Swedish physicist , developed a circulation model at he Ekman Spirals that explained Nansen's observation in accordance with the Corilois effect
Intertidal Ecosystem
The intertidal zone represents the region between low and high tides. Organisms must adapt to the forces of moving water and waves, and the periodic exposure to both open air and salt water immersion. The food chain is based on organic nutrients that become washed ashore and are digested by decomposers, hearty algae that cling to rocky outcroppings, and invertebrates that are able to protect themselves from the changes in abiotic factors by either burrowing in sand or living behind a protective coating. Clams, for example, employ both strategies. Worms, protozoa, and bacteria live between the grains of sand on the intertidal beach, while filter-feeders, such as clams, mussels, and crabs, feed on them. Hardy species of starfish and sea anemones will inhabit tide pools and envelop a passing invertebrate.
Endosymbiotic theory: origins of Eukarya
There is compelling evidence that mitochondria and chloroplasts were once primitive bacterial cells. This evidence is described in the endosymbiotic theory. How did this theory get its name? Symbiosis occurs when two different species benefit from living and working together. When one organism actually lives inside the other it's called endosymbiosis. The endosymbiotic theory describes how a large host cell and ingested bacteria could easily become dependent on one another for survival, resulting in a permanent relationship. Over millions of years of evolution, mitochondria and chloroplasts have become more specialized and today they cannot live outside the cell. Eukarya --> an amalgam of Archaea and Bacteria All Chloroplasts are from bacterium?
Who is the father of Biogeochemistry?
Vladimir Ivanovich Vernadsky, he reinforced the importance of living processes in the cycling of the elements
fluctuating salinity
What are the environmental conditions which predominate in a salt marsh?
new production and regenerated production
What are the two components of primary production? Two processes.
nitrogen fixation and lightening
What are the two natural inputs of nitrogen into the nitrogen cycle?
ammonium and nitrite oxidation
What are the two steps of nitrification? What two elements get oxidized?
mouth of mississippi and underneath sediments
What are two examples of oxygen limited habitats?
cloud condensation nuclei
What does CCN stand for? hint = droplets that affect the weather
Dissolved Organic Matter
What does DOM stand for?
heterotrophic nanoflagellates
What does HNF stand for? Type of organism.
sea surface microlayer
What does SML stand for? It is delicate to disturbances.
refraction
What happens to light in sediment?
sticks sediment down into place not allowing it to move
What important thing does biofilm do to the sediment?
polymers
What is biofilm made up of?
amount of carbon in need for respiration and production
What is the Bacterial Carbon Demand (BCD)?
proportion of the bacterial carbon used for production
What is the Bacterial Growth Efficiency (BGE)?
106 C : 16N : 1P
What is the Redfield Ratio? _____ C : ______ N : _____ P
getting material from the surface to the deep ocean
What is the biological carbon pump important for?
hydrogen sulfure + water + CO2 + oxygen --> sugar + sulfuric acid
What is the chemical reaction formula for Chemosynthesis?
temperature
What is the dissolving of CO2 dependent on?
biological pump
Which Carbon pump does this? 1. Strips inorganic nutrients and carbon from surface waters during the formation of organic matter. 2. Organic matter sinks out of the euphotic zone, into deep water where the majority is remineralized. 3. The remainder sinks to the ocean floor. 4. Most of the organic matter that reaches the seafloor is remineralized, with only some being buried in the sediments to become oil.
DMSP
Which osmolyte is found inside many phytoplankton and when broken down has the potential to create new aeorsols that can act as cloud condensation nuclei?
nitrogen and phosphorus
Which two nutrients effect the cycling of Carbon?
shorter
Which wavelength is absorbed into the sediments: longer or shorter?
longer
Which wavelength is re-emmitted from the sediment: longer or shorter?
estuary, run off from land
Which would you expect to have higher levels of Carbon: estuary or mariana's trench? Why?
Stanley Miller
Who conducted an experiment that exposed a mixture of gases and water to UV light and sparks that ended with the production of organic molecules like amino acids.
because samples are taken around a ship which is made of iiron
Why are iron (Fe) levels overestimated in the ocean?
phosphorus is a limiting nutrient
Why does nitrogen disappear before phosphate?
1. too dilute 2. inconsistent nutrient levels across the ocean 3. not digestible
Why hasnt dissolved organic matter been eaten by bacteria? 3 part answer
less harsh of conditions
Why is there higher growth efficiency rates on coasts?
What is WHOTS?
Woods Hole Oceanographic Institution Hawaii Ocean Time-series (WHOTS) The interactions that occur between the ocean and the atmosphere influence much of the processes and properties of each system separately. Woods Hole Oceanographic Institution (WHOI) and HOT collaborate to study these interactions at the WHOI Hawaii Ocean Time-series Site (WHOTS). A buoy has been deployed each summer since 2004 with meteorological instruments above the surface and oceanographic instruments moored below in the upper ocean. The objective of this project is to provide long-term data on fluxes between the air and sea including heat, fresh water and chemical fluxes at Station ALOHA, representing the North Pacific Subtropical Gyre.
bolide
a big ball of something moving as fast as a high velocity bullet
Ecological Stoichiometry
a branch of science that examines and interprets the ratios of elements in ecosystems.
Anoxia
a complete absence of dissolved oxygen
What are hot spots?
a phenomenom where magma rises over a fixed matle plume which create chains of island moving away from the hot spot.
coring device
a pipe you force into the ground gravity corers vibra coring
Base
a substance that accepts protons in a chemical reaction, raising the pH: common examples include baking soda and ammonia
Acid
a substance that donates protons in solution, lowering the pH: common examples include vinegar and battery acid.
plate tectonics
a theory explaining the structure of the earth's crust and many associated phenomena as resulting from the interaction of rigid lithospheric plates that move slowly over the underlying mantle.
gyre
any large system of rotating ocean currents, particularly those involved w large wind movements
`intertidal zone
area between high and low tides high productivity and high biodiversity Organisms must be able to withstand dessication, wave shock, and drastic temp and salinity changes
earth rotation
around an eliptical path (not perfect circle)
neritic deposits
around coastal dominated by lithogenous sediment, may contain biogenous sediment
why is photosynthate production used by bacteria? what form?
as DOM, 20-50% of all production is for bacteria. sometimes from 1%, others release up to 80%, average is 13%
coriolis effect
as earth rotates, different latitudes travel at different speeds change in the speed w latitude causes coriolis effect causes moving objects to follow curved paths in N hemis, curvature to right in S hemis, curvature to left changes with latitude no coriolis effect at equator max effect at poles greatest effect on objects that move long distances across lats (N to S) point on equator has further to travel in a day (bc its wider)
metallic sulfides
became solid a hydrothermal vent change in temp black smokers
Earth's internal structure:
because of density stratification, Earth became a layered sphere based on 2 things: chemical composition and Physical properties.
Bottom Dwellers
benthos live on the ocean floor -epifauna (epibenthic): live on top of sea floor surface, either free-moving or attached -infauna
Northern or southern boundary currents
between 30 to 60 latitudes the prevailing westerly's direct water in a n easterly direction across an ocean basin
calcareous ooze: CCD
calcite compensation depth depth where CaCo3 readily dissolves rate of supply = rate at which the shells dissolve
major ocean upwelling regions (6)
california equatorial peru canary benguela somalia
pollution history
can tell what polluted waters and how long it has been there
What is the base of the food chain in the deep sea normally and at vents and seeps?
chemosynthesis communities: have autotrophy food chain base: hydrogen sulfide or methane oxidizing bacteria as primary producers -whalefalls can have a huge impact upon the seafloor - localized and highly episodic - lots of organic matter in a whale carcass
The seawater effluent from the vents contains high concentrations of hydrogen sulfide (H2S) which supports huge populations of...
chemosynthetic bacteria
sea level history
chip fletcher studied sea level history shows the changes over time sea level rising
volcanogenous marine sediments
comes from volcanoes...ash distributed in marine by wind, streams, submarine gravity flows, ocean currents, and sea ice
warm front
contact where warm air mass moves to colder area
metal sulfides
contains: iron nickel copper zinc sulfur associated w hydrothermal vents
what parts of the sea floor have terrigenous sediments?
continental shelf and continental rise
Stanley Miller experiment
created atmospheric condition of primitive earth and zapped with lightening; created organic building blocks
hydrogenous sediments
created by a change in temp, change in pressure, and change in pH inorganic CaCO3 Metalic sulfides iron manganese nodules
Theory
describes the culmination of many scientific investigations
#6 light in water
differential penetration of visible wavelenghts blue can go 2oo+ meters, all other things appear gray because longer wavelengths don't go down as far. red goes down 1-3 meters
sea and land breezes
differential solar heating is due to different heat capacities of land and water
pressure drag
directional force of water movement may rip apart support structures or dislodge holdfasts
chicxulub impact crater
discovered by oil company near yucatan peninsula, mexico happened 65 million years ago 200km across
How do benthos reproduce?
dispersal of planktonic larvae, direct development, asexual reproduction
Minor Constituents/Trace elements
dissolved substances in seawater whose concentration is less than 1 part per million
The ink sac on an octupus or squid is used for what purpose?
distracts prey
storms
disturbances w strong winds and precip
What are the 3 types of boundaries?
divergent boundaries, convergent boundaries, and transform boundaries
marine sediment
eroded rock particles and fragments transported to ocean deposit by settling thru water column
bioerosion
erosion of rocks, coral, etc by living organisms like fish or sea urchians
if earth were flat?
even distribution of sunlight
impact ejecta
everything that was displaced from the crater
why do we care about the ocean sediments
evolution of life the history of climate pollution history sea level history history of extraterrestrial impact
suspension feeders
feed on small particles -low Reynolds number within a chamber -higher Re outside passive versus active suspension -passive; sit in current, planar, bush shaped -active; create current flow, cilia interacts
pelagic deposits buildup: low productivity
few silica sinking silica tests dissolve
non rotating earth
fictional, nonspinning earth air would rise at equator (low pressure) air would sink at poles (high pressure) air would flow high to low
relationship of fine grained quartz and prevailing winds
fine grained clay particles from wind can make up ~38% of deep sea sediment
seagrasses
flowering plants (angiosperms) that grow entirely underwater. They may tolerate or require various conc. of salt. High primary productivity. Provide important habitat for marine species. Stabilize sediment
Continental rise
formed by sediments pushed from continental shelf
supernova
forms elements heavier than iron; generate shock waves
ringwoodite
forms under very high pressure and temperature in transition zone; comes up during outgassing
Benthic animals
found at all depths and on all substrates, there are many more species that in pelagic realm Epifauna- Live on or attached to bottom (rocks/firm seds) Infauna live in bottom (soft seds mud/sand)
Aquatic pathogens
found worldwide, main killer in poor places; there is a lot of death from dehydration and Vibrio cholerae
greenhouse effect
fourier, 1827 gases: H2O, CO2, CH4(methane), N2O(nitrous oxide), O3(ozone), CFCs
albedo
fraction of incident electromagnetic radiation reflected by a surface
mangrove wetlands
habitat and nesting sites for birds. Nursery for young fish and invertebrates. Rich source of nutrients for many organisms
biogenous marine sediments
hard remains of once-living organisms shells, bones, teeth commonly either calcium carbonate (CaCO3; calcite) or silica (SiO2 or SiO2 x nH2O) usually planktonic (freefloating)
convection current
hot fluids that rise and cold fluid that fall
CLAW hypothesis and cloud albedo
hypothesis + _________: 1. Increase in DMS emissions from the ocean ---> increase in CCN ---> increase in cloud concentration and cloud albedo. 2. High cloud albedo would decrease the amount of solar radiation reaching Earth's surface ---> cooler Earth? 3. Change in the composition and abundance of phytoplankton --> affects how much DMSP is produced. TOTAL = Climate feedback loop
CLAW hypothesis
hypothesis of how microorganisms regulate the Earth as a system- Activity of phytoplankton regulates cloud formation over the ocean. Lots of clouds --> less sunlight penetrating the ocean surface --> phytoplankton can't photosynthesis very fast.
ooze
if 30% or more of sediment made up of biogenic material
ocean circulation
important: transports 20% of latitudinal heat (equator to poles) transports nutrients and organisms influences weather and climate influences commerce
Northern Boundary Hemisphere
in Northern hemi compromise the northern parts of subtropical gyre
larger
in a rocky intertidal community, the __________ species dominates lower down
Seamounts
individual underwater mountains of volcanic material
tropics
intense radiation at equator warms air warm air rises, collecting moisture air cools as it rises, moisture condenses and falls as rain lots of rain in tropics
Atmospheric oxygen is a molecule because...
it normally exists in a diatomic state, meaning that two oxygen atoms are bound to each other in the gaseous state.
Average salinity of the ocean:
it varies between 33 and 38
air masses
large volumes of air w distinct properties
Ocean surface temperature varies with _______ and _______.
latitude and time of year (seasons).
Bacterial biomass
less organic matter with larger cells; Carbon per cell is 20 femtograms C (e-15 gC)... 1 billion cells only 1 ugC per liter
Earth's surface layers:
lithosphere consists of crust and top mantle 1) Oceanic Crust 2)Continental Crust
Infauna
live IN sediment and rocks. Razor clams
herbivore 2
microphages -graze on thin layer of microalgae -radula -limpets, chitons, snails macrophages -tear apart and feed on macroalgae -crustaceans, urchins
sediment type: biogenous
microscopic planktonic organisms
hydrogenous/authigenic sediments: minerals
minerals precipitate directly from sea water manganese nodules phosphates carbonates metal sulfides small proportion of marine sediments distributed in diverse environments
evaporites
minerals that form when sea water evaporates restricted open ocean circulation high evaporation rates
Ekman's Model
model assumes that a uniform column of water is set in motion by wind blowing across its surface - the water at the very surface moves in a direction 45 degrees to the rights of the wind direction ( northern Hemisphere) -The thin layer at the top moves and sets in motion other layers below it, passing the wind energy down through the water column - current speed decrease with depth -Corilois effect increase curvature to the right ( left in the southern Hemisphere) -below a certain depth there will be no water motion as friction will consume all the energy imparted by the usually at a depth at 100 m
significance of ice
moderates global climate
Western Boundary Currents
narrow (<100km) deep (up to 2 km) fast (hundreds of km/day) moving warm water to poles ex: Kuroshio, Gulf Stream
atmosphere makeup
nitrogen: 78.1% oxygen: 20.9% CO2: 0.039% argon: 0.9% all others: trace
Surface current s
occur above within and above the PYCNOCLINE to a depth of 1 Km and only effect 10% of oceans volume -2% of energy transferred ; so a 50 know wind creates a 1 knot surface current - 1 knot= 1 nautical mile per hour =1.85 km -h -no continental land masses the currents would follow one wind belt -
rocky shore vertical zonation
organism types are generally hard-bodied at surface and are soft-bodied with depth Rocky shore - low and sub-tidal zone: brief or no exposure to air (bivalves, anemones, starfish, sea squirts, crabs, sea cucumbers), must tolerate high energy - spray and high tide zone: organisms can survive drought - benthic algae: no roots, some with holdfasts (seaweed) Sandy Shore - beaches, salt marshes, mud flats (mainly infaunal) - less vertically differentiated - inhabitants can bury during low tide - worms, crabs, starfish, sea cucumbers, bivalves, crabs, arthropods - due to erosion, all must be capable of finding new dwellings
abiogenesis
origin of life
Primary production is dependant on?
primary prodution isdependant on decomposers
Big Bang
quarks -> cools and forms protons and neurons -> keeps cooling and forms hydrogen and helium -> contraction- formation of heavier elements -> galaxies made of nebula -> contraction under gravity -> stars -> supernova -> even heavier elements and shock waves
longwave radiation
radiation emitted from earth gg's only absorb long wave radiation
Adaptions of benthic organisms
respiratory feeding appendages, expandable mouths and bodies, air bladders are small and missing as bouyancy is not needed, evisceration(expelling) internal organs to escape predators
biodiversity
sand beaches and cobble beach communites have very low_____________ because of wavew shock, desiccation, highly unstavle and abrasive habitat. The species that do thrive are very abundant, feeding on plankton and food particles washed in by waves
measure currents with
satelites floats (neutrally buoyant) ADCPs Acoustic Doppler Current Profiler buoys
Where are mollusks typically live?
sea floor
transparent exopolymer particles
term- What polysaccharides are the important glue that sitcks particles together to form marine snow.
What are three different ways to describe sediment?
size, shape, and sorting
biogeneous
skeletal and fecal remains from life
biogenous sediments
skeletons and shells CaCO3 - chalk - macro = snails, clams, coral, sand dollars, starfish, echinoderms. micro = coccolithophore (plant), foraminifera (animal) SiO2 - quartz glass - macro = some glass sponges. micro = diatom (plant), radiolarian (animal)
DOC can also be obtained by eating crap
sloppy feeding,
chemical weathering
soil ph, temp, precip, mineral composition of rock respiration H2O + CO2 =H2CO3 (carbonic acid)
sediment type: lithogenous
solid products of weathering and erosion
The ability of the ocean to take up atmospheric CO2 is controlled by what?
solubility pump (solubility of CO2) and biological pump (photosynthesis and respiration)
What is the DOM used for?
some of that material is used to make the TEP, transparent extracellular polyments
Estuaries
some of the most productive habitats on earth due to shallowness, abundance of nutrients and low wave energy. ~~Nurseries and spawning grounds for many marine organisms!
sedimentary structure
sorting of particles -constant current leads to well sorted -heterogenous current leads to poorly sorted ripples -can be large scale - tens of meters, bars -can be very small scale - millimeters, ripples -unidirectional currents --steep slope down current -bidirectional currents (tides) --ripples can be reestablished with each tidal change
Intermediate disturbance hypothesis
species diversity increases with moderate disturbance, but not too much
intertidal
species higher in ________ generally more tolerant of dessication, reduced feeding, hypoxia, and extreme temp swings
What are examples of reef-building organisms?
sponges, cnidarians, worms, stromatolites
viscous sublayer
term- velocity = 0 due to the drag of the sediment. water does not move at this area.
climate definition
statistical weather info that describes variation of weather at a given place fro specific time period (approx 30 years)
What sediment type is most of the US coast made of? Why?
terrigeneous because it is created by weathering and ash
Nonconservative Elements
substances dissolved in seawater whose concentration varies independently of salinity
Ionic Compounds
substances made up of a cation and anion held together by an ionic bond
Biologically important nutrients
substances necessary for the growth of phytoplankton
keys to pelagic deposits buildup
sunlight and nutrients are key silica secreting organisms only live in sunlit surface waters
The two kinds of currents are _________ and _______.
surface currents, deep currents
filter feeders
suspension feeders, goes through water column
new production
term- Nutrients are supplied from external sources, upwelling, or mixing of nutrients from the thermocline. Supported by nitrate. Common in productive ecosystems.. fishing.
marine snow
term- Organic matter than sticks together (gel). Is a form of downward flux for organic matter, therefore supports the ecosystems of the deep ocean.
consortia
term- Organisms living in the same environment working together.
ecological stoichiometry
term- The balance of multiple chemical substances in ecological interaction and processes. The study of this balance. Helps understand how ecosystems work.
benthic boundary layer
term- Thin layer of sediment and water column that directly interact. Contributes those portions of sediment and water columns that are affected directly in the distribution of their properties and processes by the presence of the sediment-water interface.
genetic mechanisms
term- Transfer of biological information from one generation to the next.
global distribution of sediments (the map)
terrigenous accumulates fastest - any time on the shelf biogenous - pelagic rain - silica, CaCO3 - mid ocean ridge deep sea clays - abyssal plane
classification of marine sedments by origin
terrigenous/lithogenous biogenous hydrogenous (authigenic) cosmogenous volcanogenous
Fundamental unit of classification
the "species" there are loads of species within the same genus
The Coriolis Effect causes the Earth's air and ocean surface currents to curve as a result of ___________.
the Earth's rotation on its axis.
Direct counting
the bacteria are super super small (less than 1 micrometer); you can stain them black or with nucleic acids, or use epifluorescence mi
Coriolis Effect
the force of the earth spinning on the currents in the ocean
sea-floor spreading
the formation of new areas of oceanic crust, which occurs through the up welling of magma at mid ocean ridges and its subsequent outward movement on either side.
Marine Carbonate System
the forms of dissolved carbon dioxide in seawater and the changes in their concentration and equilibrium in response to pH and biological uptake
Atmosphere
the gaseous part of the world
Hydrosphere
the watery part of the world
When is bacteria better at growing than phyto?
there is more bacteria biomass in the tropics, less than phyto in the poles/ atlantic. Bacterial production is high in pacrific, low in tropics and ross sea. Growth rate is higher in arctic
Where do continents and ocean basins exist?
they exist on the lithosperic plates (the first very thin layer of earth) that move relative to each other.
what is formed by oceanic- oceanic convergence zones?
they form trenches (one plate will be subducted), volcanoes and islands
What happens to sediment as they mature?
they slowly harden into rock and preserve the shapes of the organisms????
How can humans get exposed to this?
they swallow the seawater, eat raw food, open wounds
estuaries
this community is more prone to pollution from urban and agricultural areas.
Micronutrients
those dissolved substances required in small amounts by autotrophs
In the past, bacteria in the ocean were
thought to be in very little amounts
interstitial animals
tiny creatures that live in the spaces between sand grains. One of the more abundant species on sand beaches.
What is formed by oceanic- continental convergence zones?
trenches, mountains, and volcanoes
What is coral bleaching? What causes it?
under stress, corals mat expell their zooxzn., causing a lighter or completely white appearance... if prolonged, death of polyps is followed CAUSED BY: - - *water too warm* (1-2 degrees) (global warming) - *ocean acidification* - solar irradiance (due to decreased ozone?) - disease (pathogens) - pollutants (nutrients, sediments) - over-fishing
Mid ocean ridges
underwater mountain ranges that form along a crack in the oceans crust; where sea floor spreading occurs
sea mount
underwater mountain that does not reach sea level
marine sediments mixtures
usually mix of different sediment types typically 1 sediment type dominates in different area of sea floor
Ideal Conditions
very rare - the movement of the currents deviates from the angles discussed above -example shallow coastal water Ekman's transport may be in almost the same direction as the wind - in open ocean the surface currents move at an angle slightly less than 45 degrees from the direction of the wind and Ekman transport is about 70 digress from the wind direction
Beaches
very sparsely populated because of severe instability and high wave energy ~a few crabs and fast burrowing clams
water vapor
warm air: more water vapor, low pressure cold air: less water vapor, high pressure
terrigenous sediments: agents of transport
water (river-transported sediement) wind (wind-blown dust - aolinan transport) ice (ice-rafted rocks) gravity (turbidity currents)
what is the standard for calories
water - 1.00
pelagic zone deposits
water column siliceous ooze accumulates in high productivity areas silica tests no longer dissolved by seawater when buried by other tests
Currents
water in the ocean, transfer heat to different parts of the planets tot he other, like winds -energy drives ocean currents that is produced by the sun -surface currents affect the climate of coastal continental regions -they also effect living organism by transporting nutrients to surface water and oxygen to deep water.
#2 unusually high heat capacity
water is the hardest to heat up, requires the most energy
ammonification
what nitrogen cycle process must occur before nitrification can take place?
nitrogen fixation
what process of the nitrogen cycle makes nitrogen biologically available on the planet?
cratons
what's left of the first small continents; oldest found rocks on earth are in Canada
what are transform boundaries?
when 2 plates slide past each other instead pushing into each other or pulling away from each other an example is the san andreas fault
low tide
when do organisms move vertically out of the sediment to the surface?
outgassing
where water on earth came from; water vapor comes out of volcanoes; rained for 2.5 million years (so water came from ringwoodite stored in transition zone between upper and lower mantle)
hurricane origins: tropical cyclone/hurricane
winds above 120 km/hr
True plants
with seeds and flowers are much rarer and include mangroves, eelgrass, marsh grass, turtle grass, etc
Plants- seaweeds
~Large algae = primitive plants ~Dependent on sunlight so they are confined to shallow coastal areas where they can attach to the bottom but still get enough light to photosynthesize ~Anchored to the bottom by holdfast (not a root) ~Blade=leaf-like portion of seaweed ~Color depends on dominant pigment which varies with depth
DGGE Conclusions
• Lot of uniqueness (endemism) even within one microhabitat; however samples from within one microhabitat were more similar to one another than to other microhabitats. • Method does not provide a full characterization of the complex protistan assemblages in each sample, just dominant components. • Different dominant species in sea ice and water. • Some groups obviously underrepresented, such as diatoms. Did the cells get broken open to extract DNA?
DNA extraction
• Need to smash open the cells collected on the filter; use a mixture of mechanical and chemical cell disruption. • Crudely separate DNA from everything else using a solvent extraction step. • Precipitate DNA and separate by centrifugation. End up with a pellet of DNA resuspended in pure water.
Sergei Winogradsky (1856 - 1953)
• Russian (born in Kiev, Ukraine) who worked in Russia and France. • Microbiologist, ecologist, soil scientist. • Make a good case that he was the first 'microbial ecologist' and 'biogeochemist' in the modern sense. • Pioneering work on biogeochemistry. • Discovered chemolithoautotrophy by studying nitrifying bacteria. AKA "chemosyhtesis" --> the basis for hydrothermal vents
What is ALOHA?
• Station ALOHA was established in 1988. Initial 5 year program was A Longterm Oligotrophic Habitat Assessment (ALOHA). • Now lots of research is done at this site under the Hawaiian Ocean Timeseries (HOT). Focus on how biology, chemistry, and physics interact to affect biogeochemical processes. • Station ALOHA is actually a 10 km diameter (6 miles) circle of ocean centered at 22° 45'N, 158° 00' W, approximately 100 km north of Oahu, Hawaii. • Used as a representative site for the oligotrophic pelagic ocean (subtropical gyres). One of the largest habitats on Earth. On June 6th, 2011, the observatory, a collection of instruments at Station ALOHA 4700 m below the sea surface, established communications and power connection with Oahu providing rare oceanographic data for several years to come. The observatory has hydrophones for listening to the ocean and a camera for watching it. The dissolved oxygen content, salinity, temperature and current profile of the water are constantly recorded and communicated to land. A retired AT&T telephone cable makes this connection between Station ALOHA and Oahu. The constant and long-term data from ACO will be analyzed to discover patterns of ocean circulation, ocean-atmosphere interactions, seismology, climate change and other oceanographic topics.
Metatranscrriptomics and Transcriptomics
• Transcriptomics - study of the complete set of RNA transcripts produced by the genome. • Includes study of mRNA, tRNA, rRNA, and any other form of RNA in the cell. • Generally, RNA molecules are smaller than DNA, they are single stranded, and turnover rapidly (mRNA turns over on a Qmescale of seconds to hours). • Messenger RNA (mRNA) carries the transcript from the genomic DNA to the ribosome. The ribosome translates the transcript (i.e. the mRNA) to make the protein encoded in the original gene located in the genomic DNA. • mRNA does not hang around in cells for very long, therefore the measurement of mRNA inside a cell is a good indicator that the gene associated with that mRNA is being expressed. • For example, the presence of mRNA encoding for a specific enzyme would indicate that the cell is currently making that enzyme. • If that enzyme (or other protein) is associated with a particular process, then it strongly suggests that the process is active. • The presence of a gene in the DNA may tells us that the organism has the potential to do something, but it does not tell us if it is doing it now. • Transcriptomics can give us very little information on actual rates of process.
Primers
• Used primers that had previously been established as good for the amplification and sequencing of eukaryote small subunit rRNA genes. • Remember, they are interested in the genes that code for the small subunit RNA genes, not the ribosomes themselves. They use the term 'small subunit ribosomal DNA (srDNA). • Used very general primers (e.g. eukaryotes) and primers specific to certain eukaryotes taxonomic groups groups (e.g. diatoms).
