Geobiology Flashcards
(L1)
What are the three domains of life?
Eukarya, bacteria, archea
What is the phylogenetic tree based off of?
rRNA and distance between common ancestors
What are microbes?
Bacteria and archea
Who developed a way to relate different organisms by seperarating RNA in 1977?
Carl Woese
What is the morphology of each domain?
Eukaryote- Multi-cellular (over 10mm), diverse shape
Bacteria- Unicellular (1-5micrometers), limited shape
Archea- Unicellular (1-5micrometers), limited shape
What is the structure of the nucleus of each domain?
Eukaryote- Membrane-bound
Archea- No membrane
Bacteria- No membrane
What are the main structures in prokaryotes?
Cell wall, cell membrane, DNA, nucleoid, cytoplasm with ribsomes.
What are the main structures in Eukaryote?
Golgi apperatus, lysosome, nucleus, endoplasmic reticulum, mitochondrion, cell membrane.
How diverse is each domain?
Eukaryote- not very diverse
Archea- diverse, incredibly diverse metabolisms, millions of cells/ml in most aquatic systems, global biomass is 60-100x the size of plant biomass.
Bacteria- Diverse-same as archea, incredibly important agents of biogeochemical change.
What type of locations can extremophiles inhabbit?
Salt ponds, lava, frozen lakes etc.
What are the five requirements for life?
Stable enviroment, liquid water, nutrients, carbon source, energy source.
What happens to enzyme proteins when they exceed an optimum temperature?
They denature
What happens to enzyme proteins when they fall too far below optimum temperature?
They freeze
What is a Psychrophile?
Cold lover
What is the optimum temperature for Psychrophiles?
<15C
Why is this helpful?
Over 80% of Earth is below 15C.
What is a hyperthermophile?
Super heat lover
Where can we find the hyperthermophile that can live in the hottest temperature (300C)?
Black smoker hydrothermal vents
Where are the highest growth rates?
In specimens where the generation time is slowest.
Where can microbes be found below 0C?
Growing between ice crystals in the pore spaces of ice,
What is the lowest temperature that cell activity has been recorded?
-25C
What do microbes do to inhibit ice crystal formation?
They secrete compounds
Name a bacteria that optimumly grows in extreme halite conditions.
Halobacterium Salinarium
What are acidophiles?
Acid lovers- thrive at pH3 by maintaing their cytoplasm at the same pH as their neutophilic relatives
What pH is the cytoplasm of Acidophiles?
Neutral
A change in 1 pH unir is a _x change in hydrogen ion?
10
What are the two types of acidophiles that can be found in Rio Tinto?
Streamers ad Veils
What is the equation used to describe the oxidation of such acidophiles?
4Fe2+ +O2 +4H+ -> 4Fe3+ + 2H2O
What eukaryotes can be found in Rio Tinto?
Green algae
What process do they undergo?
Photosynthesis
(L2)
What are two requirements for life make up metabolism?
Carbon source and energy source
What are two carbon sources?
CO2 or organic matter
What are the two energy sources?
Sunlight and chemicals
What does autotroph mean?
Self-nutrition
Name some autotrophs.
Oak tree, cyanobacteria
What is the energy source for chemotrophs?
Electrochemical energy produced by coupling electron flow between chemicals in the enviroment.
What are two electron sources>
Lithotroph and Organotroph
Give the carbon and energy source for photoautotrophs.
C-CO2, E-sunlight
Give the carbon and energy sources for photoheterotrophs.
C-Organic compounds, E- sunlight
Give the carbon and energy sources for chemoheterotrophs,
C-Organic compounds, E- organic compounds
Give the carbon and energy sources for chemoautotrophs.
C-CO2 and E-inorganic compounds
What are the two types of photosynthesis?
Oxygenic and anoxygenic
Why was oxygen a critical steo in evolutionary history?
It is a potent source of energy, toxic and damages DNA, PROTEINS AND LIPIDS.
What is the electron potential (V or Eo)?
Tendancy of a substance ro become ozidised or reduced
What does a negative Eo correspond with?
Electron donation
What is Gibbs Free Energy?
Eo acceptor- Eo donor
What part of the electrochemical series has strong e-donors?
Top
What is the oxidation half-equation for aerobic respiration,
C₆H₁₂O₆ -> 6CO₂ + 24e ⁻
What is the reduction equation for aerobic respiration?
6O₂ + 24e⁻ -> 6H₂O
What is the oxidation half-equation for anaerobic respiration?
CH₃CO₂⁻ -> 2CO₂ + 8e⁻
What is the reduction half-equation for anaerobic respiration?
SO₄²⁻ + 8e⁻ -> H₂S
Give some common e-acceptors for chemoautotrophy.
O2, Fe3+, SO₄²C
What is the oxdation half-equation for chemotrophic Fe-oxidiation?
4Fe²⁺ -> Fe³⁺ + 4e⁻
What is the reduction half-equation for chemotrophic Fe-oxidation?
O₂ + 4e⁻ + 4H⁺ -> 2H₂O
What bacteria is important in AMD?
Acidithiobaccilus ferrooxidans
(L3)
What is a system science?
The framework for thinking about complex interactions on Earth,
What is a system?
A set of interconnecting parts that function together as a complex whole.
What are the 3 components?
A resevoir of matter (marine bicarbonate, atmosphere of CO2), an attribute (a state-T or P) and a subsystem (defined at various scales)
What are the Earth’s subsystems?
Geosphere, hydrosphere, biosphere, atmosphere,
??anthrosphere??
What are couplings?
Components of a system that can be linked.
What is a feedback?
A self-perpetuating mechanism of change and response to that change
When does feedback occur?
When the couplings change or respond to disturbances in the system.
Is the water vapor effect a positive or negative feedback effect and why?
Negative, warming -> water vapour -> clouds -> albedo -> warming decreases
Is the ice-albedo effect a positive or negative feedback and why?
Positive, ice cover -> Warming -> ice cover ->albedo -> Warming increases
What does perturbation mean?
Disturbance to the system
How is a stable equilibrium created?
Modest disturbances (perturbations) return the system to equilibrium (negative feedback)
What does positive feedback do to perturbation?
It increases the effect of perturbatio
What is the global carbon cycle important for?
Global climate (CO₂, CH₄), global redox (CO₂ and O₂ fixation), evolution of life (all of the above)
What is primary productivity?
The amount of organic carbon produced per unit time over a unit area of Earth’s surface
What is a Giga ton of carbon in metric tons?
1 billion metric tons 10¹²
Which of reservoir contains most carbon?
Limestone in sedimentary rocks (40,000,000Gt C)
What is biomass?
The total mass of organic carbon living in organisms in a particular reservoir (terrestrial vs marine)
Give an example of marine primary producers
Phytoplankton (free floating photosyntheic microorganisms) which include diatoms and coccolithophorids)
Give an example of marne chemoheterotrophs.
Zooplankton (including foraminifera and radiolarians)
Give the oxidation part of aerobic respiration
C6H12O6 -> 6CO2 + 24e-
Give the reduction part of aerobic respiration
CO2 + 24e- -> 6H2O
What is Gibbs free energy?
The change in free energy during a reaction at standard conditions
What does negative gibbs energy mean?
The reaction is exergonic
What does positive gibbs energy mean?
The reaction is endergonic
Describe the biogeochemical zonation in marine conditions.
As depth increases, oxygen decreases, nitrate decreases, Mn2+ increases, Fe2+ increases until it precipitates, FeS2 increases, CH4 increases.
How does electron potential relate to gibbs free energy?
deltaG=nFdeltaE where F = faraday constant (96.48kJ/V)
(L4)
How can we calculate the residence time?
Total mass is reservoir/rate of supply (or removal)
How do CO2 atmospheric levels stay constant?
The input and output are constant
What are the seasonal imbalances of CO2?
More photosynthesis than respiration during spring. More respiration during winter.
What is the relative number of atoms in living phytoplankton?
Carbon-106 Nitrogen-16 Phosphorus-1
What is the nutrient profile in seawater?
Concentrations depleted in the surface, increases with depth
Where does regeneration and the biological pump occur?
Deep water
What processes occur at the ocean surface?
Photosynthesis, fecal-pellet production, oxygen production
What processes occur in the deep ocean?
Respiration (decomposition), release of nutrient and oxygen consumption
Where is the oxygen minimum zone and why is it low in oxygen?
Between 1 and 1000m from surface. O2 production in photic zone and O2 consumption at depth.
Why are oxygen levels so high in deep waters?
Because regeneration occurs by cold O2 rich deep waters
Globally, where are nutrient concentrations highest and lowest?
Lowest in open ocean water and highest in upwelling region or in areas of high coastal runoff.
What are the inorganic/oxidised carbon reservoirs?
a) CO2 in the oceans
b) atmospheric CO2
c) CO₃²⁻ in the oceans
d) Marine Carbonate sediments
e) HCO₃₋ in the oceans
f) Limestone in sedimentary rocks
What happens when CO2 dissolves in seawater?
It forms carbonic acid (H2CO3)
What influences the distribution of different forms of carbon in the sea (Carbonic acid/bicarbonate/carbonate)?
The pH (hydrogen ion concentration)
Which form of carbon is dominant in low pHs?
Carbonic acid
Which form of carbon is dominant in medium pHs?
Bicarbonate
Which form of carbonate is dominant is high pHs?
Carbonate
What pH is seawater?
8
What pH is unpolluted rainwater?
5-6
How does the ocean buffer itself with the influence of fossil fuels?
H₂CO₃ ->H⁺ + HCO₃⁻
H⁺ + CO₃²⁻ -> HCO₃⁻
CO₂ + H₂O + CO₃²⁻ -> 2HCO₃⁻
(precipitation of Carbonate sediments)
How do we calculate the saturation of seawater?
omega= (Ca²⁺)(CO₃²⁻)/Kₛₚ If Omega >1, seawater is supersaturated and the mineral will precipitate, if its less than 1 then the mineral should disolve.
What is the lysocline?
The depth at which CaCO₃ dissolution begins
What is the calcium compensation depth?
The depth at which there is no CaCO₃ preservation
What are the long term effects of the inorganic carbon cycle?
The formation of carbonate sedimentary rocks
What is the equation for chemical weathering?
CO₂ + H₂O -> H⁺ + HCO₃⁻
What are the products of carbonate weathering?
Ca²⁺ and 2HCO₃⁻
What are the products of silicate weathering?
Ca²⁺ + 2HCO₃⁻ + SiO₂ + H₂O
Why is the input and output of the carbonate-silicate geochemical cycle the same despite them not being related?
Because both temperature and net precipitation relate to CO2. (Inorganic Carbon cycle diagram)
(L6)
What is the importance of nitrogen and phosphorus in biomolecules?
They are required by all living organisms for the synthesis of essential compounds such as DNA and RNA, amino acids and proteins.
What is the ulitimate source and sink of Nitrogen?
The atmosphere and loss back to the atmosphere
What is the ultimate source of P and sink of P?
From minerals and via complex diagenetic cycling in sediments.
Where is most nitrogen fixated?
On land (7x10^15 moles) and in surfave ocean (1x10^15 moles)
How many molecules of ATP are required to reduce atmospheric N2 to N(NH4+)?
16
Look at Marine Biological Pump
Why is NO3- depleted at the surface?
Uptake by organisms.
What happens as you increase in depth to the NO3- content?
It becomes enriched due to release.
What happens to nitrate in sediment?
it becomes denitrified
What is dentrification?
The dominant process by which fixed nitrogen is lost from the biosphere back to the atmosphere
Where does dentrification occur?
in sub-oxic marine sediments and oxygen minimum zones.
What is the electron acceptor for dentrification?
Chemoheterotrophic respiration of organic matter with nitrate.
Why is nitrogen important for paleo-biogeochemical reconstruction?
Because it has two stable isotopes (15N and 14N) and the isotope ratios of Norg reflects cycling processes
How is nitrogen stored in soils?
Either organically as N2 or as NH4+ incorporated into clays
Why does phosphate increase with depth?
Because of the biological pump and regeneration in deep waters.
Which sea has the higher level of phosphate?
Pacific.
How is phosphorus taken to the sea floor?
With sediment and organic matter (binds strongly to Fe- and Mn- oxides in oxygenated water and sinks
What happens to phosphorus in anoxic environments?
Look at Feedbacks between P and O2
Phosphate is released into the water column during early diagenesis.
Give the positive feedback loop promoting oxygen anoxia
Phosphate upwelling -> Primary productivity -> Corg, nutrient export to deep water -> oxygen consumption -> phosphate upwelling
Give the negative feedback loop regulating the global phosphorus cycle.
Phosphate upwelling -> primary productivity -> Corg, nutrient export to deep water -> Corg burial in sediments -> Net O2 which does not lead to phosphate upwelling
Which mineral-nitrogen or phosphate- limits primary productivity the most?
Both do, however N has an unlimited resource where P relies on abiotic weathering delivery. REDFIELD RATIO N:P+ 16:1
When are N2 fixing organisms at an advantage?
When N:P<16 and plenty of trace metals exist.
What is the importance of Fe in HNLC (High nutrient low chlorophyll)?
Fe is a micro-nutrient, used in enzymes for N2 fixation. High productivity areas receive Fe in the form of dust eg from the Sahara Desert
What does limiting the metal ion content do?
Increase the drawdown of CO2 in HNLC areas.
