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