1. Background in Biogeochemistry
Definition of Ecological Biogeochemistry--study of the biological and chemical transformations and fluxes of elements and compounds in populations, communities, ecosystems of the Earth.

2. Background in Biogeochemistry
Elements can be separated into reservoirs or pools and transfers among these pools are measured by fluxes. The content of the pool is controlled by fluxes in and out of the reservoirs and transformations within the reservoir. The actual delineation of reservoirs and fluxes depends on scale of measurement both with respect to time and pace.
Some definitions:
Reservoir (box, compartment)--An amount of matter or energy defined by certain physical, chemical ,or biological characteristics that, under the particular consideration, can be considered as reasonably homogenous.
Flux--The amount of matter or energy transferred from one reservoir to another per unit time.

3. Background in Biogeochemistry
Source--The flux of matter or energy into a reservoir.
Sink--The flux of matter or energy out of a reservoir.
Budget--A balance of all sources and sinks of a reservoir.

4. Background in Biogeochemistry
A mean residence time “” can be defined such that:
= amount in reservoir/sum of all fluxes (pool/mass input or mass output).
If the reservoir amount is constant, it is in steady state. The assumption of steady state is often very important and useful especially for very large reservoirs. It is very difficult to detect divergence from steady state of large reservoirs over a short period.
The analysis or depiction of the interconnections reservoirs and fluxes of a biogeochemical component is termed a cycle.

5. Background in Biogeochemistry

6. Background in Biogeochemistry
Some aspects of element composition and behavior are illustrated in Table 1.
The major elements include Si, C, Al and Ca.
T = pool/mass input or mass output

7. (units of 1020 moles and 106 years)
Table 1. Oxidation State, Abundance and Residence Times of Major Elements
(units of 1020 moles and 106 years)
Element
Oxidation State(s)
Hydrosphere
(Ocean) (-H2O)
Pool T
Lithosphere
Pool T
Atmosphere
Pool T
Biosphere
Pool T
Total Si +4
0.0014
0.016
220
450 C
0.033
0.088 61
0.19
0.0042
0.078 Al +3 57
504 Ca +2
0.15
1.2 50
351 Mg
0.82 15 25
381 26 Na +1
7.1
193
125
288 22 Fe
+3, +2 17
481 Cl -1
8.2
305
5.9
218 14 K 13
399 S
+6, +4, +2, 0, -2
0.42
4.9
242
5.3 N
+5, +4, +3, +2, +1, 0, -3
0.7
2.7
3.5 P +5
0.27 O
-2, 0
0.387
0.38

8. Background in Biogeochemistry (cont.)
Most of the major elements are largely found in the lithosphere (solid part of the Earth including the crust and outer mantle ~ 100 km) and exhibit long residence times in this pool.
For the most part, the atmosphere (the mass of air surrounding the Earth) and biosphere (regions of the surface and atmosphere of the Earth where living organisms exist) are minor element pools.
Only for N is the atmosphere a significant pool.
For some elements, a significant fraction of the mass is found in the oceans (Na, Cl, S).
Some elements exhibit more than one oxidation state and therefore can participate in redox (oxidation-reduction) reactions (e.g. C, Fe, S, N, O).

9. Acid-Base Chemistry Acid—a substance that increases [H+] in water.
Base—a substance that increases [OH-] in water.
pH = -log10 [H+] in moles L-1
For pure water at 24C: [H+] [OH-]= [10-7][10-7] = 10-14
pH = 7

10. pH Scale

11. Acid-Base Chemistry (cont.)
Major ionic solutes
Cations (positively charged ions)
Basic - Ca2+, Mg2+, K+, Na+ largely derived from cation supply in the lithosphere
Acidic - H+, Al3+, Fe3+ occurs under acidic conditions
Reduced - Fe2+, Mn2+ occurs under reducing conditions (sediments, wetlands)

12. Acid-Base Chemistry (cont.)
Anions (negatively charged ions)
Strong acid anions - SO42-, NO3-, Cl- (strongly dissociated with H+)
Weak acid anions - HCO3-, CO32-, An- (organic anions)
Basic - OH-
CB - sum of basic cations
(often expressed in eq L-1 or molc L-1)
= 2[Ca2+] + 2[Mg2+] + [Na+] + [K+]
CA - sum of strong acid anions
= 2[SO42-] + [NO3-] + [Cl-]

13. Acid-Base Chemistry (cont.)
Dissolved inorganic carbon (DIC) = CT
[H2CO3*] + [HCO3-] + [CO32-]
The distribution of inorganic carbon species is a function of pH (see figure).
H2CO3* = H+ + HCO3- ; pKa1 = 6.3
HCO3- = H+ + CO32- ; pKa2 = 10.3

15. Acid-Base Chemistry (cont.)
An important measurement of the acid-base status of waters is acid neutralizing capacity or alkalinity.
ANC = [HCO3-] + 2[CO32-] + n[An-] + [OH-] - [H+]
= the ability of a system to neutralize inputs of strong acid.
HCO3- + H+ = H2CO3*
CO H+ = H2CO3
OH- + H+ = H2O
ANC = CB - CA

16. Acid-Base Chemistry (cont.)
An important concept is electroneutrality.
All solutions (and systems) must be electrically neutral.
ci - concentration of ionic solute
zi - charge
2[Ca2+] + 2[Mg2+] + [Na+] + [K+] + [H+] =
2[SO42-] + [NO3-] + [Cl-] + [HCO3-] + 2[CO32-] + n[An-] + [OH-]
Rearranging
ANC= [HCO3-] + 2[CO32-] + n[An-] + [OH-] - [H+]
= 2[Ca2+] + 2[Mg2+] + [Na+] + [K+] - 2[SO42-] - [NO3-] - [Cl-]
= CB - CA

17. Acid-Base Chemistry (cont.)
Increases in Ca2+ by weathering of minerals increases ANC.
CaCO3 + H+ = Ca2+ + HCO3-
Inputs of H2SO4 from acid rain decreases ANC.
H2SO4 = 2H+ + SO42-
Any process which affects the concentration of ionic solutes changes ANC.
There is a non-linear relationship between ANC and pH (see figure).
e.g., ANC production is an important indicator of the abiotic fixation or removal of CO2.

19. Acid-Base Chemistry (cont.)
Weathering is an important process by which CO2 is fixed from the atmosphere.
NaAlSi3O8(s) + H2O + CO2 = Na+ + HCO3- + Al(OH)3(s) + 3H4SiO4
(albite)
This HCO3- is transported by rivers to the oceans.
A budget for bicarbonate of the ocean is shown in Table 2 (from Berner and Berner).

20. Table 2. The Oceanic Bicarbonate Budget (rates in Tg HCO3- yr-1)
Present-Day Budget
Inputs
Outputs
Rivers
1980
CaCO3 deposition:
Biogenic pyrite formation
145
Shallow water
1580
Deep sea
1340
Total
2125
2920
Budget for Past 25 Million Years
Inputs
Outputs
Rivers
1980
CaCO3 deposition:
Biogenic pyrite formation 73
Shallow water
730
Deep sea
1340
Total
2053
2070
Note: Tg = 1012g. Replacement time for HCO3 (river input only) is 83,000 years.

21. Acid-Base Chemistry (cont.)
There are two budgets presented.
The first is the current budget.
The second is the budget over the past 25 MY.
Note that the major inputs of HCO3- are riverine inputs and biogenic pyrite formation. About 7% of the total HCO3- inputs is associated with SO42- reduction.
2CH2O + SO42- = H2S + 2HCO3-
Also remember: Ca2+ + HCO3-  CaCO3 + H+

22. Organic S Compounds
Organic Matter
Bacteria
H2S
Dissolved SO42-
Bacteria
Iron Minerals
Pyrite FeS2

23. Acid-Base Chemistry (cont.)
The sink of HCO3- inputs to the oceans is precipitation of CaCO3.
Ocean water is not oversaturated with respect to the solubility of CaCO3 over the entire depth.
The upper waters are oversaturated while the lower waters are undersaturated.
The reason for this pattern is that the solubility of CaCO3 increases with increasing depth due to increases in pressure (see figure). Also, solubility increases with temperature. At the average ocean depth, the pressure is 400 atm. Under these conditions, CaCO3 is about twice as soluble as at the surface.

25. Acid-Base Chemistry (cont.)
Also, the production of CO2 from respiration of organic matter facilitates the dissolution of CaCO3.
What happens with increasing [CO2]?
About 83% of the precipitated CaCO3 redissolves at depth.
CO2 + H2O + CaCO3 = Ca2+ + HCO3-

26. Acid-Base Chemistry (cont.)
Note that the current ocean is not at steady-state with respect to inputs of HCO3-. Over the short-term, HCO3- is being depleted, sediment deposition exceeds inputs. At the current rate of deposition, all of the HCO3- in the ocean would be removed in 200,000 yr. This condition would never exist, as the ocean would eventually become undersaturated with respect to the solubility of CaCO3 and precipitation would stop.
The condition of elevated CaCO3 deposition to sediments has only been occurring during the past 11,000 yr. This condition is due to the rapid post-glacial rise of sea level over the continent of shelves.
Role of the biota: coral reefs, forminifera, etc.

28. Redox Chemistry Redox reactions involve the transfer of electrons.
All redox reactions must be coupled and require an electron donor and electron acceptor.
e.g.
CH2O + H2O = CO e- + 4H+
O e H+ = 2H2O
CH2O + O2 = CO2 + H2O
Redox reactions are often characterized in stoichiometric half reactions.
e.g. Fe3+ + e- = Fe2+

29. Redox Chemistry (cont.)
This reaction can be written as a mass law.
where K is a thermodynamic equilibrium constant.
If we take the logarithm of this expression. or
pe = - log[e-] and is the indicator of the redox status of the system.
oxidizing conditions - high or positive pe values (high K)
reducing conditions - low or negative pe values (low K)

30. Redox Chemistry (cont.)
Only a few elements dominate redox reactions in natural waters.
Major redox elements - C, N, O, S, Fe, Mn
The most important electron donor in natural waters is organic matter.
The electron acceptor that is coupled with the electron donor (organic matter) is variable. It depends on the quantity and energetics of the electron acceptor.
Redox reactions in the natural environment can be thought of as an electron titration. The source of electrons is the electron donor (organic matter). These electrons are released to electron acceptors in order of their electron affinity or energetics.

31. peo = standard electron activity
Log K
pe0
pe0w
Aerobic respiration
¼O2 + H+ + e- = ½H2O
20.75
13.75
Denitrification
NO3- + 6/5 H+ + e- = 1/10 N2 + 3/2 H2O
21.05
12.65
Mn reduction
½MnO2(s) + 2H+ + e- = ½Mn2+ + H2O
20.8
6.8
Fe reduction
Fe(OH)3(s) + 3H+ + e- = Fe2+ + 3H2O
16.0
-5.0
SO42- reduction
cSO42- +9/8 H+ + e- = cHS- + ½H2O
4.25
-3.6
Methanogenesis
cCO2(g) + H+ + e- = cCH4(g) + ¼ H2O
2.9
-4.1
peo = standard electron activity
Peow = standard electron activity in water at pH =7.0 for 25C

32. Redox Chemistry (cont.)
The energy yield of these electron acceptor reactions decreases as a function of energetic yield (electron activity). So, O2 is the preferred electron acceptor. When O2 is consumed, electrons are transferred to NO3- and so on.
Note that when the electron acceptor O2 is in excess, conditions are aerobic (i.e. Earth's surface).
When the quantity of electron donor (organic matter) exceeds the quantity of electron acceptor (O2), then anaerobic conditions result.
These conditions occur in wetlands or in lake sediments.

34. Redox Chemistry (cont.)
If photosynthetic products were oxidized completely by respiration, the atmosphere would be devoid of O2.
Photosynthesis is a critical process in generating O2. Light energy is converted to chemical energy.
The electron cycle is responsible for the partitioning of an oxidizing atmosphere and reducing lithosphere.

36. Methods Water Column Monitoring – 1981, 1989, 1990, 1991, 2000 O2 NO3-
NH4+
SO42-
(H2S)T
Fe2+
CH4
Alkalinity pH
DIC – calculated from alkalinity, pH, temperature
Sediment Traps – 10m – 1989, 1990, 1991
POC

39. Rates of Solute Accumulation (+) or Loss (-) in the Hypolimnion of Onondaga Lake
Constituent
Rate (mmol m-2d-1)
Year
1981
1989
1990
1991
DIC 35 32 49 42
NH4+
5.3
11.8
10.9
10.0 O2
-62
-63
-41
-48
NO3- -
-8.8
-4.7
-5.4
Fe2+
0.9
1.6
1.1
SO42-
-11.2
-11.0
-7.0
H2S
16.5
9.9
14.7
13.5
CH4*
15.7 (10.5)
14.5 (9.7)
18.1 (12.1)
* Includes ebullitive loss, assumed to be 33% of total; soluble component in parentheses.

40. Effective Equilibrium Constants of Aquatic Redox Couples
Reaction
pe0
pe0w (pH = 7)
¼O2 + H+ + e- = ½ H2O
20.75
13.75
1/5 NO3- + 6/5 H+ + e- = 1/10 N2(g) + 3/5 H2O
21.05
12.65
½ MnO2(s) + 2H+ + e- = ½ Mn2+ + H2O
20.8
6.8
Fe(OH)3(am) + 3H+ + e- = Fe2+ + 3H2O 16
-5.0
1/8 SO /4 H+ + e- = 1/8 H2S(g) + ½ H2O
5.25
-3.5
1/8 CO2 (g) + H+ + e- = 1/8 CH4 + ¼ H2O
2.9
-4.1

41. Oxygen Reduction DIC Equivalents per Mole O2: -1
(CH2O)106(NH3)16H3PO O2 106 CO NH3 + H3PO H2O
Denitrification DIC Equivalents per Mole NO3-: -1.25
(CH2O)106(NH3)16H3PO HNO3 106 CO NH3 + H3PO N H2O
Manganese Reduction DIC Equivalents per Mole Mn: 0.5
(CH2O)106(NH3)16H3PO MnO H+ 106 CO NH3 + H3PO Mn H2O
Iron Reduction DIC Equivalents per Mole Fe2+: 0.25
(CH2O)106(NH3)16H3PO FeOOH H+ 106 CO NH3 + H3PO Fe H2O
Sulfate Reduction DIC Equivalents per Mole H2S: -2
(CH2O)106(NH3)16H3PO SO CO NH3 + H3PO S H2O
Iron & Sulfate Reduction DIC Equivalents per Mole SO42-: -2.25
(CH2O)106(NH3)16H3PO FeOOH SO H+ 106 CO NH3 + H3PO FeS H2O
Methanogenesis DIC Equivalents per Mole CH4: 1
(CH2O)106(NH3)16H3PO4 53 CO NH3 + H3PO CH4
Fermentation DIC Equivalents per Mole C: 0.5
(CH2O)106(NH3)16H3PO CO NH3 + H3PO C2H5OH
Humification DIC Equivalents per Mole C: 0.5
(CH2O)106(NH3)16H3PO CO2 + ( C2H5OH)35.3 (NH3)16 H3PO4

44. Organic Carbon Budget 1987-92
Rate
(mmol C m-2 d-1) %
Organic C Inputs (Sediment Traps) 62
100
DIC Release (Water Column) 41 66
CH4 (Water Column) 16 26
Total C Release 57 92
Net Sediment C Accumulation 5 8
Organic C Burial (Sediments)

45. Hypolimnion Electron Budget 1987-92
Rate
(meq m-2d-1) %
Electron Donor (Sediment Traps)
248
100
Electron Acceptors (Water Column) O2 69 28
NO3- 18 7
Fe3+
0.79
<1
SO42- 49 20
CH4 41 16
Total Electron Acceptors Measured
178 72
Net Electron Transfer to Sediments 70
Net Electron Burial in Sediments (Sediments)
105

46. Fluxes Electron Acceptors (meq m-2 d-1)
Comparison of Hypolimnetic Electron Budgets During Summer Stratification
Lake
Fluxes Electron Donor
(meq m2d-1)
Fluxes Electron Acceptors (meq m-2 d-1) O2
NO3-
Fe3+
SO42-
CH4
Total
Bleltham Tarm
154
18 (49)
7.3 (20) ND
0.85 (2)
10.7 (29)
36.8
Dart’s
18.8
15.2 (81)
2.8 (14)
0.4 (2)
0.7 (4) -
Mirror 40
9.2 (69)
0 (0)
0.43 (3)
1.5 (20)
2.3 (17)
13.4
L226
15.2 (30)
4.2 (8)
0.97 (2)
8.1 (16)
23 (45)
51.8
L227 84
1.6 (5)
0.3 (1)
0.6 (2)
8.8 (28)
20.1 (64)
31.3
L223
2.7 (10)
1.8 (7)
9.1 (34)
12.8 (48)
26.8
Onondaga Lake
240
69 (39)
18 (10)
0.79 (<1)
49 (27)
41 (23)
178