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Biological Oceanography II
Info from the second half of the course
154
Biology
Graduate
12/11/2010

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Term
Coral Reefs
Definition
Most diverse ecosystem, 18 deg C and up, 32-42ppt. Atlantic reefs = 10k-20k yrs, Great Barrier = 2 mil yrs, Pacific = 60 mil yrs.
Term
zooxanthelle
Definition
Dinoflagellate that has symbiotic relationship with coral
Term
Coral Taxonomy
Definition
Class Anthozoa, subclasses Hexacorallia, Octocorallia(deep sea)
Term
Coral reef fish
Definition
Colorful, diverse, highly specialized
Term
Parrot fish
Definition
grabs algae from corals, breaks off coral and sand helps digestion
Term
Angelfish
Definition
Pomacanthidae, have spine below gills
Term
Triggerfish
Definition
Locking dorsal fin spines, strong jaws, eat sand dollars, young live in sargassum
Term
Surgeon fish
Definition
Poisonous blade close to tail fin, eats chlorophytes, phaeophytes, rhodophytes(in sand), and zooplankton
Term
Napoleon wrasse
Definition
Large, friendly, slow, coral reef fish
Term
Tridacna
Definition
Giant clam, largest bivalve mollusc, 400lbs, 5ft across. Also has zooxanthellae as endosymbiont
Term
Moray eel
Definition
Strong jaw, bacteria clean teeth
Term
Coral reef competition
Definition
Intense space competition, chemical warfare between corals
Term
Coral reef reproduction
Definition
Highly synchronized in lunar cycles, between polychaetes and corals
Term
Coral Endosymbiosis
Definition
With Zooxanthellae. CO2, ammonium, phosphorus from coral polyp. Photosynthetic sugars, amino acids from algae.
Term
Coral food
Definition
Coral feed on zooplankton - use nematocysts and mucous nets, still need zooxanthellae to survive
Term
Coral Primary Production
Definition
1500-5000 gC m-2 y-1, highest gross, comparable to open ocean
Term
Coral f-ratio
Definition
Less than .1, most primary production comes from recycled nutrients
Term
Fringing Reef
Definition
Reef that is along the coast
Term
Barrier Reef
Definition
Land sinks, leaving deep open water between reef and land. Approx 50-70km to mainland from reef
Term
Atoll
Definition
Reef surrounding island, but island sinks
Term
reef flat
Definition
(back reef), shallow depth, coral rock and sand. Area with largest temp/sal variation
Term
Reef Crest
Definition
Highest point of reef, exposed to air at low tide
Term
Reef slope
Definition
(fore reef) Outside of reef crest, contains largest corals, slopes downward to include sea whips, soft corals, and sponges below 20m
Term
Acanthaster planci
Definition
Crown of thorns starfish - eats corals, threat to them
Term
Nematocysts
Definition
Stinging cells to capture prey
Term
Coral bleaching
Definition
Organisms within corals die, leaving them white
Term
Mangrove Tree genera
Definition
Rhizophora (red), Avicennia (black), Laguncularia (white), Bruguiera
Term
Mangrove swamps (mangals)
Definition
Salty, low O2, no waves, soft mud
Term
Viviparous
Definition
'live birth', mangrove seedlings stay on trees then drop off
Term
Mangrove Primary Production
Definition
350-500 gC m-2 y-1, low compared to corals
Term
Mangrove tree adaptation
Definition
Bendy, cable like roots, salty leaves
Term
Organisms on Mangrove roots
Definition
periwinkles, barnacles, oysters, ascidians, sponges, sea anemones, polychaetes, bryozoans, hydrozoan polyps, crabs
Term
Sea grasses
Definition
Flowering plants w/ seeds, need light, have actual roots, produce own environment, trap sediments
Term
Posidonia
Definition
Largest sea grass, found up to 50m deep in clear water
Term
Thalassia
Definition
Turtle grass, found in Caribbean, tropical
Term
Seagrass reproduction
Definition
Need to be fertilized under water, pollen in packets or attached to threads, negatively buoyant seeds, most often it vegetatively regenerates a new shoot
Term
Rhizome
Definition
horizontal layer near bottom of sea grasses. Shoots come out the top, roots out the bottom.
Term
Benthic - pelagic coupling
Definition
Most benthic communities are in aphotic zone, depend on falling organic matter from pelagic. Many organisms use both zones during different life stages
Term
Zonation
Definition
Organisms grouped in distinct bands at different tidal levels.
Term
Keystone species
Definition
Species whose activities disproportionately affect patterns of species occurrence and distribution
Term
Pisaster
Definition
Keystone species of rocky shores, starfish
Term
Kelp as plants
Definition
Blades and holdfasts, no roots/leaves. Fastest growing plant, up to 60 cm/day. Reproduce via spores.
Term
Sea otter
Definition
Keystone species in N. Pacific kelp forests
Term
(a)hermatype
Definition
(non) reef building corals
Term
Homeostasis
Definition
Stoichiometry of consumer organism based on what they eat. Strict homeostasis means stoichiometry doesn't change. No homeostasis = you are what you eat.
Term
Phosphorus and growth
Definition
P is high in Nucleic Acids and ribosomes - low in proteins, lipids, and carbohydrates, so it is linked to growth
Term
Redfield Ratio
Definition
C:N:P = 106:16:1, 'emergent property'
Term
f ratio
Definition
new production over new plus regenerated production
Term
measuring f ratio
Definition
15N uptake (in form of NO3) over 14C uptake in primary production
Term
Photosynthetic Quotient
Definition
Moles of O2 produced by phytoplankton divided by moles of CO2 taken up.
Term
PQ values
Definition
carbohydrates: PQ = 1
lipids: PQ = 1.2
Protein from NO3: PQ = 1.8
Protein from NH3: PQ = .8
Because NO3 must be reduced more than NH4 and more O2 is released when NO3 is used.
Term
f ratio values
Definition
F-ratio is highest in coastal and upwelling regions, lowest in coral reefs.
Term
Thorium 234
Definition
Half life is 21.4days, produced by decay of U238. Th234 taken up by particles, can be measured to indicate particle flux
Term
ef ratio
Definition
Export production over primary production
Term
Particle export modes
Definition
marine snow, ballast, fecal pellets, active transport, carcasses
Term
Biological pump
Definition
Carbon flux, uses rotary pump, archimedian pump, reciprocating pump, and carbonate pump
Term
non-biological carbon pump
Definition
solubility pump, DOM advection, changes of seawater alkalinity
Term
Rotary pump
Definition
Circulation of material in microplankton food web
Term
Archimedian Pump
Definition
flux of fecal material and marine snow due to gravity
Term
Reciprocating pump
Definition
actively migrating organisms release CO2 and defecate at depth
Term
Carbonate Pump
Definition
sinking of calcifying organisms
Term
POC
Definition
Particulate Organic Carbon - 7 GtC yr-1 flux from surface to deep ocean
Term
DOM
Definition
Dissolved Organic Matter - cutoff either at .2, .45, or .7 microm (depending on filter). Better to overshoot.
Term
POM
Definition
Particulate Organic Matter - affected by gravity, greater than .7 microm in size, ex: marine snow.
Term
DOM age
Definition
Average age of DOM is approx 6000 yrs
Term
DOM characteristics
Definition
(C,N,P) - mostly proteins, lipids, polysaccharides. Some are chromogenic.
Term
Chromogenic
Definition
Referring to DOM. Either is colored or fluoresces in the visible spectrum when excited. Can be measured using color techniques.
Term
DOM sources
Definition
extracellular release, zooplankton grazing - messy eaters, excretion, egestion; allochthonous input through rivers, viral lysis
Term
labile
Definition
DOM degrades in hours to weeks
Term
semi-labile
Definition
DOM degrades in months to years
Term
refractory
Definition
DOM degrades in decades to millenia - larger refractory pool in Atlantic than in Pacific
Term
DOC concentrations
Definition
Deep ocean - 34 microMolar
Surface - more than 90 microMolar
Term
Total DOC
Definition
700 Pg C(pentagrams Carbon), but note that total DIC is 38,000 Pg C.
Term
Ocean conveyor belt
Definition
Water sinks in N. Atlantic and Antarctica, comes back up in N. Pacific and Indian. Recirculation time is about 1000-1600 yrs.
Term
DOM molecular weight
Definition
HMW (high molecular weight) is on average more reactive than LMW (low mw).
Term
DON
Definition
Dissolved organic nitrogen. 83-90% of total N, much lower refractory than DOC. No relationship between N-fixation and DON.
Term
DOM/DOC facts
Definition
-Net production of DOM in Ross Sea, Greenland, N. Atlantic. -DOC accumulates most at high PP. -Oxidation of 1% of DOM would be greater than burning all fossil fuels. -Bacterial growth efficiency = 15-30% on DOC. -Bacterial Production = 10% of PP, based on DOM after bloom.
Term
Colloids
Definition
Finely divided matter between 1 and 1000nm in diameter. Step between DOM and POM. Chemically different than surrounding water.
Term
Marine snow types
Definition
Initial matrix is either phytoplankton exudates or appendicularian houses.
Term
Marine snow facts
Definition
- 'oasis of life' = enriched bacteria concentrations. -'blanket of death' = smothers benthic organisms. -increased role of cyanobacteria at high marine snow abundance.
Term
DOM vs. POM
Definition
DOM floats with water currents, POM sinks.
Term
Types of distribution
Definition
uniform(low chi-square), random(med chi-s), patchy (most common, high chi-s)
Term
Physical patchiness
Definition
Produced by turbulence, horizontal displacement, internal waves, langmuir circulation
Term
Biological patchiness
Definition
Produced by growth, nutrient patchiness, grazing, swarming, vertical migration
Term
Langmuir vortices
Definition
Oppositely spinning vortices, create surface streaks parallel to wind direction. Particles congregate in between vortices.
Term
Diel vertical migration
Definition
Generally descend during day to not be seen by predators, then return to surface at night to feed.
Term
Reverse vertical migration
Definition
Surface during the day because your predators are down during the day, then down at night to escape predators.
Term
Tidal vertical migration
Definition
Migrate down at ebb tide to get carried back in, then up to surface.
Term
Biological thin layers
Definition
Coherent horizontal layers of organisms between few cm to few m thick
Term
Creating thin layers (biologically)
Definition
Phytoplankton growth, cohesion and aggregation, sinking, pathogens/parasites, grazing, predation, mortality, behavior
Term
Creating thin layers (physically)
Definition
Circulation patterns, mixing, shear, turbulence, internal waves
Term
Particle plumes
Definition
Sinking POM leaves a stream of particles in its wake - creates patchiness
Term
Martin Curve
Definition
Determines particle flux. Fz = F(100)*(z-100)^(-b). F = flux, z = depth, b = .858 - empirical parameter
Term
Abyssal Plane, physical characteristics
Definition
60% of ocean floor, avg depth = 4500m, desert in terms of faunal distribution, <3 deg C, 33-35ppt, O2 near saturation
Term
Abyssal Plane, some organisms
Definition
Fish(rattails, sharks, hagfish), Echinoderms(brittle stars, sea stars, sea cucumbers, sea urchins, crinoids), Sea pens, Stalked sea squirt, Crustacea(amphipohds, isopods), Annelids (sedentary and motile polychaetes)
Term
Hydrothermal vents
Definition
warm/diffuse(5-100deg) or superheated plume(250-400deg) w/ dissolved minerals. Low O2, high hydrogen sulfide(H2S)
Term
Riftia
Definition
(Vestimentifera - Annelida). 85cm/yr, up to 1.5m long with 3m long tube. Has symbiotic bacteria. Hemoglobin of blood carries both O2 and H2S.
Term
Hyrdrothermal vents (marine life)
Definition
clams, polychaetes, shrimp (Atl.), specialized plankton, meiofauna(nematodes, copepods), aolluscs, annelids, crustaceans
Term
Pompej worm
Definition
Alvinella pompejana - lives in hydrothermal vents, up to 80 degC, 'hottest' animal on earth.
Term
Cold seeps
Definition
Subduction zones, seeps sulfur and methane, sometimes in shallower water. Limpets graze on bacterial mats, low species diversity, influences metal content of water.
Term
trophically dilute
Definition
Mesopelagic zone - low food density, periods of starvation, long life cycles
Term
silvered sides
Definition
mirrors on mid water fish (oarfish, sardines, tuna) - crystal panels that reflect light as if it passed through the fish
Term
counter shading
Definition
Dark dorsally, light ventrally - hard to see from top/bottom, but not perfect because reflected light is not as strong as downwelling light.
Term
bioluminescence
Definition
Fish glow, at mid/deep water, to match the ambient light, as sensed by eyes and sensors.
Term
Fishing gear
Definition
purse seine, midwater trawl, bottom trawl, flatfish beam trawl, scallop dredge, drift gill net, set gill net, long line, fish trap, fish pot
Term
Fish population limiting factors
Definition
Egg production, recruitment, natural mortality, fishing pressure
Term
Ricker Curve
Definition
Model for spawner-recruit relationship. R=aSexp(-bs). R=recruits, s=spawner, a= density independent parameter, b = density dependent parameter.
Term
Counting fishes
Definition
2 methods: Tag/recapture, Estimate population size from fisheries catch data.
Term
Tag/Recapture
Definition
T/N = R/C #tagged/population size = # recaptured/catch size
Term
Tag/Recapture assumptions
Definition
catch spots are unbiased estimate of stock, fish are randomly caught, tags do not cause mortality, tagged fish mix evenly with population
Term
law of diminishing returns
Definition
The fewer fish there are, the harder it will be to catch them (CPUE goes down)
Term
CPUE
Definition
Catch per unit effort - should be proportional to population - can't compare between fisheries though. A change in method leading to a higher CPUE does not mean there is a higher population
Term
Leslie plot
Definition
Total catch on x axis, CPUE on y axis, interpolate to x intercept = population.
Term
MSY
Definition
Maximum Sustainable Yield - point of max CPUE, more effort leads to a lowering of CPUE. Cannot determine point of MSY without overshooting it.
Term
MSY bad assumptions
Definition
1. CPUE rise falsely interpreted as increase in stock size. 2. stock behaves the same each year, same recruit rate. 3. assumes environment doesn't change.
Term
Aging techniques
Definition
Scales - annual marker, otoliths(ear bones) - daily/annual marker, clam shells - annual growth rings
Term
Collapse of Atl. Cod
Definition
3 reasons. 1. Overestimation of abundance, underestimation of mortality. 2. Ability to catch fish at low abundances. 3. Increased discarding and nonreporting of small fish.
Term
Bycatch
Definition
Species not targeted by fishers are caught anyways - small fish of same species, wanted and unwanted fish of other species. Total annual bycatch = 26%.
Term
fishing down the food web
Definition
Fisheries continually target smaller and smaller species after they've fished out the larger ones.
Term
Regime shift
Definition
Rapid shift in organization of ecosystem - change of dominant species (ex: anchovies and sardines)
Term
Year Class Strength
Definition
Strength of a given year class determined by survival through a critical period very early in life cycle.
Term
Mis-match hypothesis
Definition
Marine fishes time reproduction so larval development matches high productivity periods.
Term
Stable Ocean hypothesis
Definition
First feeding larvae require abundance of food, so patches of local food are very important b/c need is higher than average ocean abundance.
Term
hydrographic containment
Definition
Mating convention where fish will return to same place to spawn because currents carry larvae into suitable waters for survival.
Term
North Atlantic Oscillation (NAO)
Definition
Pressure diff btwn Portugal and Iceland. High NAO = strong winds pushing gulf stream, warmer water northwards, cooler summers, warmer winters in Europe. Low = opposite basically.
Term
ENSO
Definition
El Nino Southern Oscillation - El Nino = weak trade winds, less upwelling, east ward flow and expansion of warm water pool. La Nina = opposite, more upwelling and nutrients.
Term
Greenhouse gases
Definition
Carbon Dioxide, methane, Nitrous oxide, CFCs, water.
Term
Non-greenhouse 'gases'
Definition
particles inhibit green house effect
Term
CO2 Facts
Definition
6.5 Gt from fossil fuels, increase of 1.3 Gt per year, 1.7-2 Gt C dissolves in ocean
Term
Seal level change
Definition
Caused by: land and tectonic movements, extraction of terrestrial ground water, expanding warmer ocean water, melting ice sheets/glaciers
Term
response to CO2 - equilibrium times
Definition
CO2 emissions - 0-100 yrs, CO2 stabilization - 100-300 yrs, Temp stabilization - few centuries, Sea level rise due to thermal expansion - centuries to millenia, sea level rise due to ice melting - several millenia
Term
Iron fertilization
Definition
Add iron to HNLC regions - increase PP to take up excess CO2. Won't actually make a difference.
Term
Ocean-climate feedback mechanisms
Definition
Albedo, ice ages = more iron, more ice = no deep water forming = continuing ice age, melting permafrost = more CO2 = more melting
Term
Milankovitch cycles
Definition
Glacial/inter glacial cycles - seen by more 18O in water when ice forms
Term
Carbon storage places
Definition
Atmosphere - 720 GtC, Ocean - 38k GtC, Rocks - 60,000,000 GtC, organic carbon - 15,000,000 GtC
Term
Estuary types
Definition
Fan shaped delta, bird foot delta, Estuarine delta
Term
Estuaries
Definition
High PP, heavily urbanized, extensive agriculture, strong salinity gradients, environmental problems, low diversity of species
Term
Estuarine Turbidity Maximum (ETM)
Definition
Entrapment zone - point where 1ppt isohaline intersects bottom (salt wedge), high zooplankton, turbidity, chl a
Term
Chesapeake Bay
Definition
3 mi wide at Annapolis, 30 mi at Potomac, 3600 species, avg 21 ft deep, lost oyster beds.
Term
San Francisco Estuary
Definition
Diked islands, agricultural delta region, high irrigation, important species - striped bass, Pacific herring
Term
X2
Definition
Distance from Golden Gate to where Salinity is 2 ppt - proxy for flow, relates to fish production
Term
Pollution aggregation
Definition
on sea bottom (attached to particles), on pycnoclines, water surface (sea surface microlayer - neuston)
Term
Hydrocarbons
Definition
Pollutant.
Naturally - seeps, rivers, volcanoes, atmosphere, bacteria.
Human - transportation, production, aerosols
Term
Heavy Metals
Definition
Pollutant (Lead, mercury, cadmium, arsenic, copper)
Natural - Volcanoes, rivers, sediments, weathering of rocks.
Human - industrial and municipal effluents
Term
Nutrients (as pollutant)
Definition
Pollutant
Natural - rivers, upwelling, atmosphere, bacterial decomposition
Human - municipal effluents, agricultural fertilizers
Term
Synthetic chemicals
Definition
Pollutant
Human only - manufacturing, transportation, agricultural fertilizers, pesticides
Term
Oil Spill fate
Definition
Atmospheric oxidation, spreading - tar balls, adsorbed to particles, degradation/assimilation by benthos, chemical breakdown, bacterial degradation, assimilation by plants, mixing into sediment
Term
Oil Clean up
Definition
Detergents, Steam, Do Nothing (Best!), bioremediation (fertilize beaches)
Term
Effects of Effluents
Definition
cells - poisoning, cellular damage
organisms - behavioral changes, reduced reproduction, reduced immune response
population - changes in age, size, recruitment, mortality, biomass
community - changes in richness, distribution, trophic interactions, adaptation
Term
Sewage impacts
Definition
Discharge trapped in estuaries, gives large P and N input, dense plankton blooms, oxygen depletion causes hypoxia and anoxic zones
Term
DDT
Definition
Pesticide, banned in Western countries, used at small levels in Africa to fight malaria
Term
Ocean dredging effects
Definition
changes hydrography, increase turbidity, resuspends buried toxins, lose benthic organisms
Term
Ocean mining
Definition
Manganese nodules - very slow growing, phosphorite nodules, metal deposits and sediments - dredging these causes high turbidity and toxic levels of metal in water
Term
Invasive species
Definition
Non-endemic species, take over new area. Ex: Japanese oyster
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