Lecture 4. Chemistry and Biogeochemical Cycling
A. Chemicals Dissolved in Water
In addition to water (and its component hydrogen and hydroxyl ions) lakes typically contain a variety of
dissolved substances, including gases (e.g. carbon dioxide, nitrogen and oxygen) and dissolved salts (e.g.
various ions).
Most Common Ions
calcium, Ca+2
magnesium, Mg+2
bicarbonate, HCO3-
Other Ions
sodium, Na+
potassium, K+
sulfate, SO4-2
chloride, Clnitrate, NO3phosphate, PO4-3
silicate, SiO4-2
Salinity (mg∙L-1) is defined as the total concentration of ions dissolved in water and is measured as
specific conductance (conductivity), the ability of water to conduct electricity. Conductivity increases as
the salt content of the water increases. A similar expression, total dissolved solids, includes inorganic
and organic salts plus nonionized substances. Finally, hardness refers to the levels of calcium and
magnesium in the water.
B. Solubility of Gases
Atmospheric gases, such as carbon dioxide, nitrogen and oxygen dissolve in water.
[T] Bottle of coke
Water can hold more of these gases under pressure and at lower temperatures. At the temperatures
commonly experienced in lakes (0-35 C) the oxygen concentration varies by more than a factor of 2.
[T] Oxygen = f (temperature); Dodson, Figure 2.4, p. 33
Water can hold several times its saturation concentration. Photosynthetic activity when the water
column is experiencing quiescent conditions can lead to supersaturation.
A condition of
supersaturation is ultimately relaxed through the formation of bubbles.
[T] Bottle of coke
[T] Bubbles on algae
The solubility of gases also depends on the concentration of solutes, i.e. salts, in the water.
[T] Salting out effect
The saturation concentration of oxygen at 4 C is 13.1 mg∙L-1 in freshwater and 8.6 mg∙L-1 in salt water.
B. pH, Alkalinity and the Carbonate System
Water molecules dissociate yielding hydrogen ions (H+) and hydroxyl ions (OH-),
H 2O  H   OH 
The ion product (Kw) for water,
K w   H   OH    1x1014
@ 25 C
and, since the concentration of hydrogen ions must equal the concentration of hydroxyl ions, the
concentration of each is 10-7. Remembering that pH is defined as –log[H+], we find that pure water
would have a pH of 7 at 25 °C. Depending on the concentrations of other chemicals in water, the
hydrogen ion concentration (pH) may vary widely. While the majority of temperate and tropical lakes
have a pH between 7 and 9, bog lakes, rich in organic acids, can have pH levels of 2-6 and desert lakes,
saturated with carbonates, can reach a pH of 10. pH plays an important role in mediating water
chemistry and in establishing the limits of growth for aquatic organisms.
Dissolved inorganic carbon (DIC) is a collection of chemical species that includes carbon dioxide,
carbonic acid, bicarbonate and carbonate and which is often referred to as the carbonate system. DIC
enters lakes through the dissolution of carbon dioxide from the atmosphere and carbonate minerals in
the watershed.
When carbon dioxide dissolves in water it participates in a series of reactions yielding the various
inorganic carbon species –
CO2  H 2O  H 2CO3  H   HCO3  H   CO3
The position along this reaction continuum depends on the scarcity of hydrogen ions. Initially, carbonic
acid is formed. If hydrogen ions are scarce, the carbonic acid will dissociate to form bicarbonate ion.
Further scarcity of hydrogen ions leads to the dissociation of bicarbonate ion to form carbonate ion.
This is an equilibrium reaction and the relative abundance of the various inorganic carbon species varies
with pH.
[T] Dissolved inorganic carbon = f (pH); Dodson, Figure 10.2, p. 234
Because this is an equilibrium reaction, the extraction of carbon dioxide through photosynthesis causes
the reaction to move to the left, consuming hydrogen ions and raising the pH. This also increases the
carbonate ion concentration, sometimes to the point that the solubility product of calcium carbonate is
exceeded, precipitating a white, chalk-like material called marl. In lakes, such precipitation events are
termed a whiting.
[T] Whiting; Dodson, Figure 10.3, p.236
At night (and in the hypolimnion) photosynthesis is absent and respiration leads to a net production of
carbon dioxide, lowering the pH. The interplay of photosynthesis and respiration forms what is called a
diel cycle, not only in pH, but in oxygen as well (production, photosynthesis; consumption, respiration).
Acids enter the water through the dissolution of carbon dioxide and through the deposition of nitric acid
(internal combustion engines) and sulfuric acid (coal combustion). The ability to absorb hydrogen ions
when acid is added is termed acid neutralizing capacity (ANC) or alkalinity which is defined as –
Alk  [ HCO3  2[CO3 ]  [OH  ]  [ H  ]
Waters that are able to absorb significant amount of acids without changing pH are said to be well
buffered. The inorganic carbon system is the primary buffering system in lakes, although organic acids
may serve this role in bog lakes.
Pure water in contact with the atmosphere becomes a weak solution of carbonic acid as it takes up
carbon dioxide from the air, yielding a pH of 5.65. Here, some of the carbonic acid has broken down
into bicarbonate and hydrogen ions, but at this pH bicarbonate levels are low and carbonate levels
negligible.
[T] Dissolved inorganic carbon = f (pH); Dodson, Figure 10.2, p. 234
This water has a low alkalinity (ANC) and poor buffering capacity. Alkalinity is added to lakes when
carbonates are dissolved from limestone (CaCO3) bedrock in the watershed. This increases the ANC of
the lake and makes it less vulnerable to the impacts of acid deposition. Watersheds dominated by
granitic bedrock provide little additional ANC and it is these that experience the negative effects of acid
deposition. Here, the acids in rain titrate the lake water, reducing the lake’s buffering capacity over
time until it is exhausted and the pH drops rapidly.
D. Organic Carbon
In addition to DIC, carbon is present in lakes as organic carbon (DOC). The energy that governs the
metabolism of lakes is derived from the solar energy utilized in photosynthesis and fixed in molecules of
organic carbon. The organic carbon in lakes may originate from terrestrial vegetation within the
watershed (allochthonous sources) or from aquatic vegetation (algae, macrophytes) within the lake
(autochthonous sources). Most (>95%) of the organic matter produced in the drainage basin is
decomposed, with little being stored permanently. Export of organic matter resistant to decomposition
is largely as dissolved organic matter (e.g. humic and fulvic acids).
[T] Humic acid structure
[T] Humic acids in lake water
Organic carbon occurs in particulate (POC) and dissolved (DOC) phases. All organisms, living and nonliving are composed of organic matter and thus contribute to the particulate organic carbon (POC) pool.
The non-living component includes dead and decaying organisms or organism parts and excreted
material and is collectively termed particulate detritus. POC is progressively broken down into smaller
and smaller particles and ultimately solubilized to yield dissolved organic carbon (DOC). Other sources
of DOC in lakes include the refractory humic and fulvic acids received from the watershed, excretion of
organic molecules by organisms in the lake and generation of the gas methane (CH4) through
decomposition of organic matter in the sediments.
DOC is often further partitioned into labile (available for decomposition) and refractory (unavailable for
decomposition) fractions. Labile DOC participates in a series of redox reactions in which the organic
carbon compounds are metabolized yielding the chemical energy stored via photosynthesis. A redox
reaction is one in which electrons are transferred, and in the case of microbially-mediated reactions,
yielding energy to the organism mediating the reaction. Each redox reaction includes an electron donor
(here, organic carbon represented as C(H2O)) and electron acceptor (several are available). The general
form of the reaction is,
C ( H 2O)  EA  CO2  RS  
Where EA is the electron acceptor and RS represents a reduced species. Consider this generalized
representation applied to with oxygen as the electron acceptor,
C ( H 2O)  O2  CO2  H 2O  
Now, let’s look at this as two half reactions,
C ( H 2O)  CO2
C (0)  C (4)
O2  CO2
O2 (0)  O2 (4)
In the terminology of redox reactions, a substance that donates electrons (becomes more plus) is said to
be oxidized and a substance that accepts electrons (becomes more minus) is said to be reduced. Here,
organic carbon, the electron donor is oxidized and oxygen, the electron acceptor is reduced.
The metabolism (decomposition, mineralization, oxidation, BOD) of DOM with oxygen as the electron
acceptor is termed aerobic respiration. Where oxygen is not available to perform this function, e.g. in
the sediments and in the hypolimnion of productive lakes in summer and occasionally winter, alternate
electron acceptors are utilized.
[T] redox series
The alternate electron acceptors are utilized in the order of the thermodynamic favorability of their
respective reactions as shown in the table above. While this is generally conceived of as a time series,
the sequential utilization of alternative electron acceptors occurs with depth in lake sediments.
[T] redox in sediments
The decomposition of organic matter, particularly in sediments, has dramatic effects on water quality,
including –





depletion of oxygen (directly, by heterotrophic oxidation);
depletion of oxygen (indirectly, by subsequent oxidation of Fe2+, Mn2+, H2S and CH4);
fouling of drinking water supplies (Fe, Mn precipitates); and
production of toxic H2S
mediation of ammonia, phosphorus and mercury release
[T] redox applications
Note that even refractory DOC may participate in this process where the complex macromolecules
characteristic of humic and fulvic acids are broken down into smaller moieties through photolysis
making the products available for further decomposition.
As we leave organic carbon, it is important to recognize the significance of this biogeochemical cycle in
capturing and recycling the energy reserves present in the lake ecosystem.
[T] Carbon cycle
As an example of this, remember the depletion of organic matter and the attendant increase the
relative contribution of clays to the sediment with depth in Portage Lake sediments.
E. Oxygen
Oxygen is required to support all life in lakes, with the exception of those bacteria which function via the
alternate electron acceptors discussed above. A key feature of oxygen dynamics in lakes is the concept
of a saturation concentration which varies with temperature and salinity, as discussed previously.
[T] oxygen saturation
The primary source of oxygen for lakes is the atmosphere. Conditions of undersaturation and
oversaturation are corrected through the process of reaeration, i.e. the transfer of oxygen into or out of
the water. We quantify reaeration as,
dO2
 ka  (O2, sat  O2,measured )
dt
where ka is the reaeration rate coefficient (d-1) and is equal to,
ka 
Kl
H
where Kl is the oxygen mass transfer coefficient (m·d-1) and H is depth (m). Kl, in turn, is a function of
wind speed, e.g.
Kl  0.864 U w
where Uw is wind speed (m·s-1). The reaeration rate coefficient varies with temperature as described by
a theta function,
ka,T  ka,20  (T 20)
The other important oxygen source for lakes is photosynthesis,

CO2  H 2O 
 C ( H 2O)  O2
Oxygen is consumed through aerobic respiration,
C ( H 2O)  O2  CO2  H 2O  
and through the oxidation of reduced species end products, e.g. Fe2+, S2- and CH4.
F. Nitrogen
The primary components of the nitrogen cycle in lakes are,
nitrogen gas
N2
sources: atmosphere and denitrification
activity: nitrogen fixation
impact: none
ammonia/ammonium
NH 3 / NH 4
sources: loads, direct excretion and DON decomposition
activity: nitrification
impact: plant nutrient (marine), toxic; oxygen demand
nitrite
NO2
sources: nitrification intermediate; transient
activity: nitrification
impact: toxic; oxygen demand
nitrate
NO3
sources: loads, precipitation, nitrification
activity: nitrification, denitrification
impact: plant nutrient (marine)
DON/PON
R  NH 2
sources: loads, biosynthesis/decomposition of organic matter
activity: ammonification
impact: none
[T] amino acid structure
[T] nitrogen cycle
Nitrogen is the growth-limiting nutrient for plants in marine waters, but it is difficult to assign a major
role for this element as it participates in so many important biogeochemical pathways.
G. Phosphorus
Weathering of bedrock, e.g. apatite (Ca5(PO4)3(OH)0.33F0.33Cl0.33) is the primary natural source of
phosphorus. Discharges from wastewater treatment plants and runoff from watersheds receiving
phosphorus fertilizers represent important anthropogenic sources. Phosphorus is subject to interactions
with calcium, magnesium, iron and aluminum (clays) that retard its movement from the watershed to
lakes.
Phosphorus is the growth-limiting nutrient for plants in fresh waters.
[T] nutrient limitation
[T] the divided lake
It is important to understand the way that phosphorus partitions in lake water as that process influences
its management, biogeochemical cycling and impact on the environment.
[T] phosphorus forms
H. Iron
Iron in lakes may be present in the ferrous (Fe2+, anoxic) or ferric (Fe3+, oxic) states. The most common
species of iron in lakes are the ferrous and ferric hydroxides,
Fe(OH )2
Ksp  1x1014
Fe(OH )3 1x1038
which have markedly different solubility products. Thus, changes in redox can have a great impact on
the solubility of iron compounds and the mobilization of chemical species, especially phosphorus.
[T] phosphorus accumulation in the hypolimnion
Like nitrogen and phosphorus, iron has shown potential for limitation of algal growth.
I. Sulfur
Sulfur is introduced to lakes (usually as sulfate, SO4) through the geochemical weathering of bedrock
material, especially calcium sulfate (gypsum, CaSO4). Sulfate also reaches lakes as acid deposition. Once
in the lake, sulfur participates in a suite of microbially-mediated reactions … most notably sulfate
reduction with the generation of the toxic gas, hydrogen sulfide. Dissolved sulfide exerts and oxygen
demand, yielding sulfate, when exposed to oxygen.
J. Silicon
Silicon is moderately abundant in lakes and is an important nutrient for siliceous algae, e.g. diatoms.
Thus the availability of silicon has an impact on patterns of algal succession and production. Silica is
often depleted from the surface waters of eutrophic lakes.