ocean-atmosphere through time
DESCRIPTION
Ocean-atmosphere through time. Lyons, 2008, Science 321, p. 923-924. From Reinhard et al., 2009, Science Vol.326, p. 713. Earth’s Oceans @ 2.5 Ga. From Reinhard et al., 2009, Science Vol.326, p. 713. Geomicrobiology. Classification of life forms: - PowerPoint PPT PresentationTRANSCRIPT
Ocean-atmosphere through time
Lyons, 2008, Science 321, p. 923-924.
From Reinhard et al., 2009, Science Vol.326, p. 713
Earth’s Oceans @ 2.5 Ga
From Reinhard et al., 2009, Science Vol.326, p. 713
Geomicrobiology
• Classification of life forms:– Eukaryotic = Plants, animals, fungus, algae,
and even protozoa– Prokaryotic = archaea and bacteria
• Living cells can:– Self-feed– Replicate (grow)– Differentiate (change in form/function)– Communicate – Evolve Can purely chemical systems do these things?
All of these things? Why do we care to go through this ?
Tree of life
Diversity
• There are likely millions of different microbial species
• Scientists have identified and characterized ~10,000 of these
• Typical soils contain hundreds- thousands of different species
• Very extreme environments contain as little as a few different microbes
Characterizing microbes
• Morphological and functional – what they look like and what they eat/breathe– Based primarily on culturing – grow microbes
on specific media – trying to get ‘pure’ culture
• Genetic – Determine sequence of the DNA or RNA – only need a part of this for good identification
• Probes – Based on genetic info, design molecule to stick to the DNA/RNA and be visible in a microscope
Environmental limits on life• Liquid H2O – life as we know it requires liquid
water• Redox gradient – conditions which limit this?• Range of conditions for prokaryotes much
more than that of eukaryotes – inactive stasis• Spores can take a lot of abuse and last very
long times• Tougher living = less diversity
• Closer to the limits of life – Fewer microbes able to function
Profiles and microbial habitats
O2
H2S
Concentration
dept
h Fe2+
H2S
O2
Org. C Org. C
1
2 3
4
Life requires redox disequilibrium!!
Phototrophic mats - PSB• Purple sulfur bacteria mats
– Respond to light level changes in minutes position in sediment and water column can vary significantly!
Purple sulfur bacteria mats
-800
-700
-600
-500
-400
-300
-200
-100
0
0 500 1000 1500 2000
H2S(aq) Concentration (M)
Dep
th (
mic
ron
s)
Cell Metabolism
• Based on redox reactions– Substrate (food) – electron is lost from this
(which is oxidized by this process)– that electron goes through enzymes to
harness the energy for the production of ATP
– Electron eventually ends up going to another molecule (which is reduced by this)
The Redox ladder
H2O
H2
O2
H2O
NO3-
N2 MnO2
Mn2+
Fe(OH)3
Fe2+SO4
2-
H2S CO2
CH4
Oxic
Post - oxic
Sulfidic
Methanic
Aerobes
Dinitrofiers
Maganese reducers
Sulfate reducers
Methanogens
Iron reducers
The redox-couples are shown on each stair-step, where the most energy is gained at the top step and the least at the bottom step. (Gibb’s free energy becomes more positive going down the steps)
Redox gradients and life
• Microbes harness the energy present from DISEQUILIBRIUM
• Manipulate flow of electrons
O2/H2O
C2HO
Nutrition value
• Eukaryotes (like us) eat organics and breathe oxygen
• Prokaryotes can use other food sources and acceptors
Microbes, e- flow
• Catabolism – breakdown of any compound for energy
• Anabolism – consumption of that energy for biosynthesis
• Transfer of e- facilitated by e- carriers, some bound to the membrane, some freely diffusible
Exergonic/Endergonic
• Thermodynamics tells us direction and energy available from coupling of 2 half-reactions
• Energy available = -G0 = exergonic
• Organisms use this energy for life!!
Evening Primrose Cinder Pool
Temp 82.8 89.7pH 5.42 4.03
mg/L mg/LCa 10 6.3Mg 0.43 0.017Sr 0.029 0.021Ba 0.076 0.019Na 330 430K 36 65Li 1.1 5.6F 3.1 5.5Cl 390 670Br 1.1 2.2Si 240 370B 7.8 12Al 10 0.71Mn 0.2 0.0005Cu 0.0005 0.004Zn 0.012 0.0005Cr 0.001 0.0005
C(2) 0.0005 0.002Ni 0.01 0.01Cd 0.0005 0.0005Pb 0.016 5.00E-05Be 0.001 5.00E-05V 0.001 0.0005Se 0.00015 0.00015As 1.7 2.6
Fe(3) 2.01 0Fe(2) 2.55 0.043
S52- 13.4-51.51 7.4-161
SO4 17002 432
S2O3 4.481 1
H2S 2.111 0.5-0.581
NH4 No Data 1.83
H2 No Data 0.0343
Calculating Potential Energy Thermodynamic Modeling
∆Gr = ∆Gr ۫ + RTlnQ
∆Gr ۫ = Σ vi,r * ∆Gi ۫ (products) - Σ vi,r * ∆Gi ۫ (reactants)
Q = π ai vi,r(products)- π ai
vi,r(reactants)
R = 8.3141 J/mol*K (Gas Constant)
T = 85 C
• Example
2 S5-2 + 2 H+ = 2 HS- + S8
∆Gr ۫ = ((HS-)2 + (S)) -(( S5-2)2 + (H+)2)
∆Gr ۫ = -101.64 kJ/mol
Species ∆Gi Formation
S -2.04
S5-2 58.13
H+ 0
HS- 8.33
Calculating Potential Energy Thermodynamic Modeling
Q = ((HS-)2 * S)/(( S5-2)2 * (H+)2)
Q = 2.46E-9 kJ/mol
Species log activity activity
S5-2 -8.71 1.95E-09
HS- -9.479 3.32E-10
H+ -1.771 0.016943
S 0 1
∆Gr = ∆Gr ۫ + RTlnQ
∆Gr = -101.64 + 8.3141*358.15*ln(2.46E-9)
∆Gr = -160.17 kJ/mol for 4 electrons
∆Gr/e- = -40 kJ/mol
NAD+/NADH and NADP+/NADPH• Oxidation-reduction reactions use NAD+ or
FADH (nicotinamide adenine dinucleotide, flavin adenine dinucleotide).
• When a metabolite is oxidized, NAD+ accepts two electrons plus a hydrogen ion (H+) and NADH results.
NADH then carries
energy to cell for other uses
• transport ofelectrons coupledto pumping protons
glucosee-
CH2O CO2 + 4 e- + H+0.5 O2 + 4e- + 4H+ H2O
Proton Motive Force (PMF)
• Enzymatic reactions pump H+ outside the cell, there are a number of membrane-bound enzymes which transfer e-s and pump H+ out of the cell
• Develop a strong gradient of H+ across the membrane (remember this is 8 nm thick)
• This gradient is CRITICAL to cell function because of how ATP is generated…
HOW IS THE PMF USED TO SYNTHESIZE ATP?• catalyzed by ATP
synthase
BOM – Figure 5.21
Other nutrients needed for life
• Besides chemicals for metabolic energy, microbes need other things for growth.– Carbon– Oxygen– Sulfur– Phosphorus– Nitrogen– Iron– Trace metals (including Mo, Cu, Ni, Cd, etc.)
• What limits growth??
Nutrients• Lakes are particularly sensitive to the amount of
nutrients in it:– Oligotrophic – low nutrients, low photosynthetic activity,
low organics clear, clean…– Eutrophic – high nutrients, high photosynthetic activity,
high organics mucky, plankton / cyanobacterial population high
• Plankton growth:• 106 CO2 + 16 NO3
- + HPO42- + 122 H2O + 18 H+ +
trace elements + light C106H263O110N16P1 + 138 O2 (organic material composing plankton)– This C:N:P ratio (106:16:1) is the Redfield Ratio– What nutrients are we concerned with in Lake
Champlain?
Nutrient excess can resultin ‘blooms’
• Lake Champlain– Phosphorus
limited?– Algal blooms– What controls P??
Nutrient cycling linked to SRB-IRB-
MRB activity
Blue Green Algae blooms
FeOOH
PO43- PO4
3-
PO43-PO4
3-
Org C + SO42-
H2SFeS2
PO43- PO4
3-
PO43-
PO43-
Sulfate Reducers