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).