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
Life requires
redox
disequilibrium!!
3
2
depth
O2
H2S
Fe2+
4
H2S
1
Org. C
Concentration
Org. C
Phototrophic mats - PSB
• Purple sulfur bacteria mats
0
-100
-200
Depth (microns)
– Respond to light level changes
in minutes  position in
sediment and water column
can vary significantly!
Purple sulfur bacteria mats
-300
-400
-500
-600
-700
-800
0
500
1000
1500
H2 S(aq) Concentration (M)
2000
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
O2
Oxic
Aerobes
H2O
NO3- Dinitrofiers
Post - oxic
N2
MnO2
Mn2+
Maganese reducers
Fe(OH)3
Fe2+
Sulfidic
Iron reducers
SO42H2S
Methanic
Sulfate reducers
CO2
CH4
Methanogens
H2O
H2
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
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 halfreactions
• Energy available = -DG0 = exergonic
• Organisms use this energy for life!!
Evening Primrose Cinder Pool
Temp
82.8
89.7
pH
5.42
4.03
mg/L
mg/L
10
6.3
Mg
0.43
0.017
Sr
0.029
0.021
Ca
Ba
0.076
0.019
Na
330
430
K
36
65
Li
1.1
5.6
Calculating Potential Energy
Thermodynamic Modeling
∆Gr = ∆Gr ۫ + RTlnQ
F
3.1
5.5
Cl
390
670
Br
1.1
2.2
Si
240
370
B
7.8
12
Al
10
0.71
Mn
0.2
0.0005
Cu
0.0005
0.004
Zn
0.012
0.0005
Cr
0.001
0.0005
C(2)
0.0005
0.002
Ni
0.01
0.01
Cd
0.0005
0.0005
Pb
0.016
5.00E-05
Be
0.001
5.00E-05
V
0.001
0.0005
Se
0.00015
0.00015
2.6
As
1.7
Fe(3)
2.01
0
Fe(2)
2.55
0.043
S5
2-
13.4-51.5
1
7.4-16
∆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)
1
SO 4
17002
432
S2 O 3
4.481
1
H2 S
2.111
0.5-0.58
NH4
No Data
1.83
H2
No Data
0.0343
1
T = 85 C
Calculating Potential Energy
Thermodynamic Modeling
• Example
2 S5-2 + 2 H+ = 2 HS- + S8
Species
∆Gi Formation
S
-2.04
S5
-2
58.13
H+
0
HS-
8.33
∆Gr ۫ = ((HS-)2 + (S)) -(( S5-2)2 + (H+)2)
∆Gr ۫ = -101.64 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
Q = ((HS-)2 * S)/(( S5-2)2 * (H+)2)
Q = 2.46E-9 kJ/mol
∆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
glucose
• transport of
electrons coupled
to pumping protons
CH2O  CO2 + 4 e- + H+
0.5 O2 + 4e- + 4H+  H2O
e-
Proton Motive Force (PMF)
• Enzymatic reactions pump H+ outside the
cell, there are a number of membranebound 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 result
in ‘blooms’
• Lake Champlain
– Phosphorus
limited?
– Algal blooms
– What controls P??
Nutrient cycling
linked to SRB-IRBMRB activity
PO43-
PO43-
PO4
Org C + SO42-
FeS2
FeOOH
H2S
PO43-
3-
PO43-
Sulfate Reducers
PO43-
PO43- PO43Blue Green Algae blooms