Global Biogeochemical Cycles and Biological Metabolism
I. Biogeochemistry & Biogeochemical Cycles A. Global cycles: nitrogen, water, carbon B. Carbon cycle through time
II. Biological Metabolism A. Redox reactions: basis of metabolism B. The metabolic pathways C. Microbial Habits
I. What is Biogeochemistry?
Biogeochemistry = the study of how the cycling of elements through the earth system (water, air, living organisms, soil and rock) is governed by physical, chemical, geological and biological processes
hydrosphere atmosphere biosphere pedosphere lithosphere
Key Names Vladimir Vernadsky (1863-1945): Russian scientist known as the “father of biogeochemistry”, invented the terms geosphere, biosphere, and “noosphere” G. Evelyn Hutchinson (1903-1991): famous limnologist (considered to be founder of limnology) (also studied the question of how biological species coexist)
1 Global Change and the N-cycle
“The nitrogen dilemma is not just thinking that carbon is all that matters. But also thinking that global warming is the only environmental issue. The weakening of biodivers- ity, the pollution of rivers... Smog. Acid rain. Coasts. Forests. It’s all nitrogen.” - Peter Vitousek
Global Change and the N-cycle Human alteration of N-cycle is LARGE (> 100% in fixation relative to the background rate of 90-140 Tg N/yr):
80 to No place on (terrestrial) 90 Tg earth unaffected 20 Tg by this 40 Tg
Vitousek et al., 1997
2 9 Atmospheric N2: 3.9 x 10
Reactive N (NOx, NH3)
Vege- tation: 4,000
Soils: 100,000
Units: Stocks (Tg N) or Flows (Tg N/yr)
9 Atmospheric N2: 3.9 x 10 Huge but inaccessible
Reactive N (NOx, NH3)
Vege- tation: 4,000
Soils: 100,000
Units: Stocks (Tg N) or Flows (Tg N/yr)
3 Atmospheric N : 3.9 x 109 2 Note big difference in N turnover Reactive N (NOx, NH ) times in 3 terrestrial vs. Marine biota Terrestrial: 4000/1200 = Vege- tation: 3-4 yrs 4,000 Marine: 300/8000= Soils: 2 weeks 100,000 Atmosphere: 3.9x109/~300 ≈ 107 years! Units: Stocks (Tg N) or Flows (Tg N/yr)
9 Atmospheric N2: 3.9 x 10 natural Nfixa- tion
Reactive N (NOx, NH3)
Vege- tation: 4,000
Soils: 100,000
Units: Stocks (Tg N) or Flows (Tg N/yr)
4 9 Atmospheric N2: 3.9 x 10
Human Reactive N (NOx, NH3) N fixa- tion
Vege- tation: 4,000
Soils: 100,000
Units: Stocks (Tg N) or Flows (Tg N/yr)
I. The Global water cycle
Atmosphere: 13,000
Freshwater available for interaction with terrestrial biosphere is small fraction
Ice: 33 x 106
Lakes: 230,000
Vegetation: 10,000
Soil water: Oceans: 120,000 1.350 x 109 groundwater: In km3 (pools) and 6 15.3 x 10 km3/yr (fluxes)
5 I. The Global water cycle
Atmosphere: 13,000
Atmospheric supply to Land (precipitation) is greater than land return ,000 11,000 1 1 to atmosphere 7 (evapotranspiration) Ice: 6
Precip: 33 x 10
Lakes: 230,000 Transpiration Vegetation: 10,000
Soil water: Oceans: 120,000 1.350 x 109 groundwater: In km3 (pools) and 6 15.3 x 10 km3/yr (fluxes)
I. The Global water cycle
Atmosphere: 13,000
40,000 Atmospheric supply to Land (precipitation) is greater than land return to ,000
,000 Opposite ,000 11,000 5 5 1 1 atmosphere
itis true over 7 42 38 the ocean (evapotranspiration) Ice: (precip < 6
Precip: 33 x 10 evapo- Precip: transpiration) Lakes: Evaporation: 230,000 Transpiration Vegetation: 10,000
Soil water: Oceans: 120,000 1.350 x 109 groundwater: In km3 (pools) and 6 15.3 x 10 km3/yr (fluxes)
6 I. The Global water cycle
Atmosphere: 13,000
40,000 Plants power water return to ,000 ,000 ,000 11,000 5 5 1 Ocean 1 atmosphere on water 7 land powers Ice: 6 land Precip: 33 x 10
Precip: 38 precip
Lakes: Evaporation: 42 230,000 Atmospheric Transpiration turnover Vegetation: time: 10,000 13,000/ 496,000 Soil water: = 0.026 yrs Oceans: 120,000 ≈ 1 week 1.350 x 109 groundwater: In km3 (pools) and 6 15.3 x 10 km3/yr (fluxes)
Facts about the global water cycle 496 x 103 km3 • Global precip: 385,000 (ocean) + 111,000 (land) 496 x 103 km3 510 x 106 km2 =097x10= 0.97 x 10-3 km
Earth surface area ≈ 1 meter of precip (global average) • Land area is 148 x 106 km2 111148 = 0.75 m average land precip – Comparison: Tucson gets 030m0.30 m, – tropical forests 2 or 3 m
7 Overview: The Modern Global carbon cycle (1990s)
Total FF . emissions
Total land- use change emissions
Values in black are natural, values in red are anthropogenic Note: 1990s values (IPCC 2007, Ch. 7)
8 What is residence time of C in atmosphere? One estimate is from land+ocean flux: 120+70=190; 597/190 ≈ 3yrs
BUT: this is not an estimate of removal rate to ocean of excess CO2 (2.2). Better: 597 / 2.2 = 270 years.
But in truth, for CO2, no single residence time.
Total FF . emissions
Total land- use change emissions
Values in black are natural, values in red are anthropogenic Note: 1990s values (IPCC 2007, Ch. 7)
Fun problem in global biogeochemistry: How likely is it that in your next breath, you will inhale at
least one molecule of nitrogen (N2) that Julius Caesar exhaled in his last breath?
(Julius Caesar, the famous Roman emperor, was assassinated on March 15, 44 BC by a group of Roman senators).
This requires some basic chemistry: 1 mole of air is 6.02 x 1023 molecules At STP, 1 mole occupies ~22 liters. Also helpful: whole atmosphere: 1.8 x 1020 moles of air
What is atmospheric mixing ratio of N2? What is N2 mixing time in the atmosphere? What is N2 residence time in the atmosphere?
9 First, the concentration, in the whole atmosphere, of
Caesar’s last-breath N2 molecules #'N moleculesin Caesar s last breath Concentration 2 #molecules in wholeatmosphere
3 N 1mol air 23 1610/L of air inbreath2 molecules mol 422air L air 21022 1.8 1020mols air / atmosphere 6 10 23 molecules / mol Next, the average number you inhale per breath = Concentration('2/)# moleculesCaesar s N molecules air molecules inhaled
221mol air 23 210 1L 610 molecules / mol 22 Lair 21022 2.710 22 5.45
So on average you inhale 5 molecules of Caesar’s-breath N2 in every breath!
II. What is Biological Metabolism?
Metabolism, simplified
oxygenic photosynthesis
H2O + CO2 CH2O + O2 Carbon in Reduced Carbon atmospheric Aerobic Respiration in organic matter CO2 (plant biomass & energy supply)
More generally:
autotrophy
- - e donor + CO2 CH2O + e acceptor
heterotrophy
10 Life is catalyzed Redox Reactions
• “Master variables” in soil & water chemistry: H+ and e-
• Control the direction, rate and endproducts of many reactions.
• Electron transfer reactions near earth’s surface are driven largely by C cycling:
• Photosynthesis: CO2(g) + H2O(l) CH2O(s) + O2(g)
•Respiration: CH2O(s) + O2(g) CO2(g) + H2O(l)
•Both are full, balanced redox reactions.
Oxidation-Reduction Reactions •A redox reaction involves the transfer of one or more electrons (e-) from one species to another.
Reduced Oxidized Oxidized Reduced + + Species A Species B Species A Species B
e- e- • The reaction proceeds in either direction,
depending on magnitude and sign of Gr (change in Gibbs free energy = energy stored or released)
11 Some Redox Definitions
• Oxidation: The loss of e- • Reduction: The gain of e- • Oxidized Species: – Oxidizing agent or “oxidant” in the reaction. – Atom or compound that oxidizes the other atom or compound. – The electron acceptor. –Is itself reduced (gains an e-) in the process. • Reduced Species: – RdReduc ing agent or “d“reduc tan t” – Atom or compound that reduces the other atom or compound. –The electron donor. – Is itself oxidized (loses an e-) in the process.
The full redox reaction:
Reduced Oxidized Oxidized Reduced + + Species A Species B Species A Species B
e- e- contains two half reactions, where each pertains to a given element that undergoes oxidation or reduction: Red A Ox A + m H+ (aq) + e-(aq)
Ox B + m H+ (aq) + e-(aq) Red B
12 Thermodynamics of Redox
•The e-'s represent a common currency for examin ing conditions of thermodynamic spontaneity and equilibrium when comparing reactions. • The thermodynamic spontaneity of the reaction is determneddetermined by the potential for e- to be transferred in one direction or another.
Half-Cell Conventions
• Half-Reaction: The elemental reaction used to describe a redox reaction. Normally written as a reduction:
- + • 0.25 O2 (g) + e (aq) + H (aq) 0.5 H2O (l)
• log K = 20.8
0 • Eh = standard half-cell potential (electromotive force) [V] = 0.059*log K • Describes the spontaneity of the reaction as written (tendency of reaction to occur, driving force) under standard state conditions of reactants and products. • Measure of affinity of an electron acceptor for electrons under standard conditions.
13 Standard Hydrogen Electrode
H2 = 1 atm Platinum electrode
+ - ½H2(g) H + e
aH+ = 1 0 Eh = 0.000 V Log K = 0.0
• Thus given free energy of formation for 0 compounds Eh
0 0 • ΔG r < 0 (Eh > 0): reduction has greater tendency to occur than does the + reduction of H (aq) to H2 (g) (under standard conditions).
14 Overall redox reaction in soil is sum of two half-reactions
+ - 2+ MnO2(s) + 4H (aq) + 2e Mn (aq) +2H2O (l); log K = 41.6 •is a reduction half-reaction. • This reaction must be combined (coupled) with another half-reaction that is inverted to represent an oxidation half-reaction. • No free electrons appear in balanced full redox reactions. • For example, the reduction of Mn(IV) to Mn (II) could be coupled with the oxidation of nitrite to nitrate (see next slide)
Summing two half reactions
+ - 2+ MnO2(s) + 4 H + 2 e Mn +2 H2O log K = 41.6 - - + - 2 x (0.5 NO2 + 0.5 H2O 0.5 NO3 + H + e ) log K = -28.4 ------
+ - 2+ - MnO2(s) + 2 H + NO2 Mn + NO3 + H2O log K = 13.2
Will this reaction proceed under standard conditions?
15 Terminal Electron Accepting Processes
• TEAPs refers to the fact that in natural aqueous systems, the availability of O2 to act as a terminal electron acceptor in respiration is limited by its availability.
• Other oxidizing agents are used as O2 becomes depleted. • The order of use of these alternati ve TEAPs is the same as that of their energetic yield.
Sequence of TEAPs is consistent with the decrease in energy yield per mole of organic matter oxidized.
16 Falkowski et al. (2008)
17 The change in Gibbs free energy G (and Eh) can be calculated for all pairs of redox reactions, giving theoretical thermodynamic energy yields.
Reactions that run “downhill” (release energy) offer opportunities to power metabolism, and hence, a possible hbithabit for life.
Falkowski et al. (2008)
18