1. Ocean-atmosphere through time
Lyons, 2008, Science 321, p

2. From Reinhard et al., 2009, Science Vol.326, p. 713
Highly
reactive iron (FeHR) is defined as the sum of
pyrite iron (FePY) and iron in phases that are
reactive to hydrogen sulfide (H2S) on short
diagenetic time scales, such as ferric oxides
(Feox), magnetite (Femag), and iron present as
carbonate (Fecarb).
From Reinhard et al., 2009, Science Vol.326, p. 713

3. Earth’s 2.5 Ga
From Reinhard et al., 2009, Science Vol.326, p. 713

4. Geomicrobiology

5. 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 ?

6. Tree of life

7. 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

8. 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

9. 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

10. Profiles and microbial habitats
Life requires redox disequilibrium!! O2 O2 3 2
Fe2+
depth
H2S 4
H2S 1
Org. C
Org. C
Concentration

11. Phototrophic mats - PSB
Purple sulfur bacteria mats
Respond to light level changes in minutes  position in sediment and water column can vary significantly!

12. 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)

13. The Redox ladder
H2O H2 O2
NO3- N2
MnO2
Mn2+
Fe(OH)3
Fe2+
SO42-
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)

14. Redox gradients and life
Microbes harness the energy present from DISEQUILIBRIUM
Manipulate flow of electrons
O2/H2O
C2HO

15. Nutrition value Eukaryotes (like us) eat organics and breathe oxygen
Prokaryotes can use other food sources and acceptors

16. 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

17. Exergonic/Endergonic
Thermodynamics tells us direction and energy available from coupling of 2 half-reactions
Energy available = -DG0 = exergonic
Organisms use this energy for life!!

18. Calculating Potential Energy Thermodynamic Modeling
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 = J/mol*K (Gas Constant)
T = 85 C

19. Calculating Potential Energy Thermodynamic Modeling
Example
2 S H+ = 2 HS- + S8
Species
log activity
activity
S5-2
-8.71
1.95E-09
HS-
-9.479
3.32E-10 H+
-1.771 S 1
Species
∆Gi Formation S
-2.04
S5-2
58.13 H+
HS-
8.33
Q = ((HS-)2 * S)/(( S5-2)2 * (H+)2)
Q = 2.46E-9 kJ/mol
∆Gr ۫ = ((HS-)2 + (S)) -(( S5-2)2 + (H+)2)
∆Gr ۫ = kJ/mol
∆Gr = ∆Gr ۫ + RTlnQ
∆Gr = *358.15*ln(2.46E-9)
∆Gr = kJ/mol for 4 electrons
∆Gr/e- = -40 kJ/mol

20. 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

21. glucose e-
transport of
electrons coupled
to pumping protons
CH2O  CO2 + 4 e- + H+
0.5 O2 + 4e- + 4H+  H2O

22. 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…

23. HOW IS THE PMF USED TO SYNTHESIZE ATP?
catalyzed by ATP synthase
BOM – Figure 5.21

24. 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??

25. 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 CO NO3- + HPO H2O + 18 H+ + trace elements + light  C106H263O110N16P 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?

26. Nutrient excess can result
in ‘blooms’

27. Lake Champlain
Phosphorus limited?
Algal blooms
What controls P??

28. Nutrient cycling linked to SRB-IRB-MRB activity
Blue Green Algae blooms
FeOOH
PO43-
Org C + SO42-
H2S
FeS2
Sulfate Reducers