Fundamental Hydro-Biogeochemistry
Preface
Author
1
Introduction
1.1
Biogeochemistry applied to excess nutrients in rural aquatic environments
1.2
Ecologically engineered systems treated as black boxes
1.3
Biogeochemical processes in pollution flows
1.4
Scope of this book
1.5
Exercises
2
Life’s secrets for storing energy
2.1
The five fundamental requirements of life
2.2
Electron allocation onto CHONSP
2.3
Electronegativity as a powerful tool to allocate electrons
2.4
Dioxygen: the ‘electron kleptomaniac’ molecule
2.5
Fully Oxidized forms of CNSP
2.6
Oxidation versus Reduction
2.7
A gradient of oxidation and reduction states on inorganic and organic molecules
2.8
Examples of electrons stored on organic molecules
2.9
Summary on electron allocations
3
Functional groups of biochemical importance
3.1
Hydrocarbon chains
3.1.1
Alkanes
3.1.2
Unsaturated hydrocarbons
3.1.3
Aromatic hydrocarbons
3.2
Functional groups from alkane chain oxidation
3.2.1
Hydroxyl and sulfanyl functional groups
3.2.2
Methyl, Methylene, and Ethyl functional groups
3.2.3
Phosphoryl functional group
3.2.4
Amine functional group
3.2.5
Carbonyl and acyl functional groups
3.2.6
Alcohol functional group
3.2.7
Thiol functional group
3.2.8
Alkyl amines
3.2.9
Aldehyde functional group
3.2.10
Ketone functional group
3.2.11
Carboxyl functional group
3.2.12
Amide functional group
3.2.13
Methoxy functional group
3.3
Functional groups from bonding of functionalized organic molecules
3.3.1
Ester functional group
3.3.2
Thioesters
3.3.3
Phosphoesters
3.3.4
Ether functional group
3.3.5
Disulfide functional groups
3.3.6
Hemiacetal and hemiketal functional groups
3.3.7
Anhydride and phosphoanhydride functional groups
3.4
Summary on functional groups and important radicals
4
Life’s secrets to make complex organic molecules
4.1
Polymers of simple monomers
4.2
Carbohydrates
4.2.1
Monosaccharides
4.2.2
Dissacharides
4.2.3
Polyssaccharides or glycans
4.2.4
Other important carbohydrates
4.3
Proteins
4.4
Nucleic Acids and Nucleotides
4.4.1
Nucleotides as monomers of nucleic acids
4.4.2
DNA and RNA
4.5
Lipids
4.5.1
Overview of fatty acid- or acyl-based lipids
4.5.2
Lipids as key to cell membrane structure and function
4.5.3
Fatty acids: lipids of their own and primary common building blocks
4.5.4
Glycerolipids for energy storage
4.5.5
Glycerophospholipids or phospholipids for cell membranes
4.5.6
Sphingolipids use sphingosine as backbone/fatty acid
4.5.7
Saccharolipids in bacterial membranes
4.5.8
Summary about the acyl-based-lipids
4.5.9
Overview of the isoprene-based lipids
4.5.10
Prenol or isoprenoid lipids
4.5.11
Sterol lipids
4.5.12
Summary about the isoprene-based lipids
4.5.13
Other notable lipids
4.6
Phenolics and polyphenols
4.6.1
The impermeable world of phenolics
4.6.2
Unavailable energy onto phenolic molecules
4.6.3
Monomeric phenols
4.6.4
Lignins
4.7
Alkaloids
4.8
Glucosinolates
5
Energy generation and aerobic respiration
5.1
Generating energy: transfer of electrons
5.1.1
Activation energy barrier
5.1.2
Electron transfer during methane combustion
5.2
Generating energy without combustion: ATP or the energy currency of the cell
5.3
The ATP manufacture: substrate-level versus oxidative phosphorylation
5.4
Respiration: providing most ATP thanks to exogenous electron acceptors and oxidative phosphorylation
5.4.1
Oxidative phosphorylation through molecular mechanical forces
5.4.2
Creating a proton gradient as a source of proton flow
5.4.3
A compartment to accumulate protons
5.4.4
A supply of protons for the intermembrane space: proton pumps
5.4.5
Electron transfer molecules that power the proton pumps
5.4.6
Transfer of electrons from the Organic Carbon to an electron acceptor
5.4.7
Oxygen reduction and oxidative phosphorylation
5.5
Respiration electron flow schemes
5.5.1
Aerobic respiration schemes for organotrophs
5.6
Glycolysis: an ancient way to produce ATP from glucose by substrate-level phosphorylation
5.6.1
Substrate-level phosphorylation
5.6.2
Energy investment and energy pay off phases of glycolysis
5.6.3
Electrons fate and electron transfer molecules
5.7
The citric acid or Krebs cycle as an efficient way to transfer high energy electrons
5.7.1
Oxidation of pyruvate as a preliminary step
5.7.2
Transfer of all electrons to NAD
+
and FAD
5.7.3
Summary of respiration
5.8
Fermentation or staying alive without exogenous electron acceptor
6
Capturing and storing energy: photosynthesis
6.1
Requirements to store energy on organic molecules
6.2
No need to reinvent the wheel for the production of ATP and the transfer of electrons
7
Anabolism and the sources of nutrients for organisms
7.1
Requirements to store energy on organic molecules
7.2
No need to reinvent the wheel for the production of ATP and the transfer of electrons
8
The classical collection of electron donors and acceptors
8.1
The theoretical vertical sequence of respiratory processes in wetland soils
8.2
An aerobic layer near the soil-water interface
8.2.1
Oxygen supply and demand at the sediment water interface
8.3
Respiration in the anaerobic zone of the soil
8.4
A denitrification layer below the aerobic layer
8.5
Manganese and Iron oxides reductions
8.6
Sulfate reduction
8.7
The methanogenesis oddity
8.8
Fermentation in wetland and stream sediment
8.9
First summary on the electron acceptor chain in wetland soils
8.10
Supply and demand of electron acceptors and of the byproducts of Organic Matter oxidation
8.10.1
Demands drive downward fluxes of dioxygen, nitrate and sulfate
8.10.2
Supply of byproducts of organic matter oxidation
8.10.3
Nitrification
8.10.4
Gas bubble formation
8.10.5
Oxidation of upward moving reduced sulfur
8.10.6
Oxidation of upward moving
\(Mn^{2+}\)
and
\(Fe^{2+}\)
8.10.7
Moving of Dissolved Organic Carbon
9
The not so classical electron donors and acceptors
9.1
DNRA
9.2
Anammox
9.3
Nitrification-denitrification
9.4
Chemilithotrophic denitrification
10
Nutrient concentration levels in rural and suburban environments
10.1
Level of dissolved oxygen concentrations in open waters
10.1.1
The supply and demand of O
2
in water
10.2
Level of nutrient concentrations in natural undisturbed streams
11
Applied thermochemistry: acid-base equilibria
11.1
The Brønsted–Lowry acid–base theory
11.2
Acid-base equilibrium parameters
11.2.1
K
A
11.2.2
pK
A
11.3
Self-ionization of water
11.4
Strong vs. weak acids
11.5
Mono- and polyprotic acids mole fractions
11.5.1
Triprotic acid example
11.5.2
Generalized polyprotic acid mole fractions
11.5.3
Graphical illustration of mole fractions of ecologically relevant weak acids
11.6
Equilibrium calculations using a graphical method
11.6.1
Logarithm of concentrations as a function of pH
11.6.2
Graphical approach to calculate pH for a monoprotic acid
11.6.3
Graphical approach to calculate pH for a triprotic acid
11.6.4
Dissolved CO
2
and carbonates in a closed system
12
Applied thermochemistry: Oxido-Reduction equilibria
12.0.1
The transfer of electrons in organotrophic denitrification
12.0.2
Some outside the box redox reactions
13
Dissolved gases in water
13.1
Henry’s law and the dissolution of gases in water
13.1.1
Equivalence between gas partial pressures and dissolved concentration
13.1.2
Many different units to express gas solubility
13.2
Solubility of gases as a function of temperature {#sol-f-temp)}
13.3
Actual solubility values of water in equilibrium with the atmosphere
13.4
Solubility of gases as a function of pressure
13.4.1
Dalton’s law of partial pressures
14
Respiration kinetics at the sediment-water interface
14.1
The spatial scale of redox sequence in wetlands
14.2
Deriving of
\(O_2\)
microprofile equation in sediment
14.3
Equation of the downward flux at the sediment-water interface (10 points)
15
References
16
Introduction to hydrographs, chemographs, concentrations, and loads
16.1
Hydrographs as the basic hydrologist tool
16.1.1
Characteristics of a hydrograph
16.1.2
Actual hydrograph over an entire year
16.1.3
Calculating water fluxes or cumulative flow volumes
16.1.4
Evaluating the importance of rare high flow events: flow duration curves
16.1.5
Flow duration curves as flow exceedance curves
16.2
Chemographs and concentration levels
17
Glossary
17.1
A
17.1.1
Aerobic respiration
17.1.2
Anaerobic respiration
17.1.3
Ammonia
17.1.4
Ammonium
17.1.5
Ammonium nitrate
17.1.6
Anoxic waters
17.2
B
17.2.1
Benthic
17.3
C
17.3.1
Carbon dioxide
17.3.2
Carbonates
17.3.3
Catabolism
17.4
D
17.4.1
Denitrification
17.4.2
Dihydrogen sulfide
17.5
E
17.5.1
Electron Donating Group (EDG) and Electron Withdrawing Group (EWG)
17.5.2
Eutrophication
17.6
F
17.6.1
Fischer projection
17.7
G
17.7.1
Greenhouse gases
(GHG)
17.8
H
17.8.1
Haber-Bosch process
17.8.2
Haworth Projection
17.8.3
Hydrogen Sulfide
17.9
L
17.9.1
Lithotrophs
17.9.2
Limiting factor
17.10
M
17.10.1
Methane
17.10.2
Mineralization
17.11
N
17.11.1
Nitrate
17.11.2
Nitrous Oxide
17.12
O
17.12.1
Oligotrophication
17.12.2
Oxidation
17.12.3
Oxidation state
17.13
P
17.13.1
Phosphate
17.14
R
17.14.1
Reactive nitrogen
17.14.2
Redox
17.14.3
Redox couple
17.14.4
Redox half-reactions
17.14.5
Reduction
17.15
S
17.15.1
Skeletal formula
17.15.2
Structural formula
17.15.3
Sulfate
17.16
T
17.16.1
Trophic names
Appendix
A
Appendix A
A.1
Quick guide on atom orbitals and Lewis dot structure
A.1.1
Electron orbitals
A.2
Orbitals hybridization
A.3
σ and π bonds
A.4
sp
3
hybridization examples
A.4.1
Methane
A.4.2
The water molecule
A.4.3
Ammonia and Ammonium
A.4.4
Sulfate
A.4.5
Phosphate
A.5
sp
2
hybridization examples
A.5.1
Nitrate
A.5.2
Nitrite
A.6
sp
hybridization examples
A.6.1
Carbon dioxide
A.6.2
Dinitrogen
A.7
Example of no hybridization
A.7.1
Dihydrogen sulfide
A.8
Lewis dot structures
A.8.1
Valence electrons and octet rule
A.8.2
Building Lewis dot structures
A.9
Molecular orbitals
A.9.1
Binding and antibinding regions
A.9.2
Bonding and antibonding orbitals
A.9.3
Molecular orbital diagrams
A.10
Exercises
B
Appendix B: Equilibrium Constants at 25°C
B.1
Equilibrium reactions in the H
2
O-H
2
-O
2
system
B.2
Equilibrium reactions in the CO
2
-H
2
O system
B.3
Equilibrium reactions for nitrogen species
B.4
Equilibrium reactions for phosphorus species
B.5
Equilibrium reactions for sulfur species
References
Published with bookdown
Fundamental Hydro-Biogeochemistry for Ecological Engineering and Environmental Sciences
Chapter 9
The not so classical electron donors and acceptors
Chapter summary:
9.1
DNRA
9.2
Anammox
9.3
Nitrification-denitrification
9.4
Chemilithotrophic denitrification