An Introduction to Marine Biogeochemistry, 2

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Study Guide

An Introduction to Marine Biogeochemistry, 2nd ed.

Dr. Susan M. Libes

Table of Contents

Introduction 2

Math and Chemistry Topics to Review 3

Logarithms, Exponents and pH 4

Study Questions 6

Answers 5

Short Problems 4

Answers 5

Long Problems 4

Answers 5

Exam/Test Problems 4

Answers 5


This study guide is designed to aid the student in mastering the information presented in the accompanying text, “An Introduction to Marine Biogeochemistry”. The questions and problems in this guide are designed to help students be active learners. These materials are presented by chapter with a separate answer key.

Students should be able to answer the study guide questions after a first reading of the chapter. These questions are designed to focus attention on the overarching principles in each chapter and prepare students to participate in classroom discussions. Student should complete them by writing two to three sentence essays.
Three types of problems are included herein. The first are short and specific to individual chapters. They are designed to be completed in 15 to 20 minutes, making them amenable to use in the classroom. The short problems are meant to prepare students to undertake longer ones which integrate concepts covered in several consecutive chapters. The other two types of problems are longer and generally involve calculations based on data sets available in the peer-reviewed literature. The longest are designed to as homework or laboratory exercises. They typically require 1 to 2 hours to complete. For these, students will hopefully prefer to use a spreadsheet program for graphing or repetitive calculations. Once students have completed these problems, their learning can be assessed with the third type of problem, which is designed for exam and test use. These problems are of intermediate length and do not require the use of a spreadsheet program. They are intermediate in length and combine topics covered in several consecutive chapters.
Also included in this study guide are lists of chemistry and math topics and skills that students should have mastery of as a prerequisite to learning from the text. Some review materials can be found in Appendices 2, 3 and 4 in the text.

Susan Libes

Foundational Math Skills to Review

  1. Algebra

    1. Equation of a Straight Line

    2. Solving Simultaneous Equations

  1. Geometry

    1. Volume and Area of Basic Geometric Shapes

  1. Dimensional Analysis

    1. Unit conversions

    2. Use of compound units

  1. Reading Graphs and Tables

  1. Significant Figures

    1. Rules of Multiplication and Division

    2. Rules for Subtraction and Addition

  1. Metric Units

    1. Prefixes

  1. Exponential and Scientific Notation

  1. Logarithms

    1. Log, 10x

    2. Ln, ex

  1. Calculus

First order rate equations

Foundational Chemistry Topics to Review

  1. Stoichiometry

    1. Interconverting grams and moles

    2. Balancing Equations

    3. Concentration units

  1. Formula Naming Conventions, Structures and Symbols

    1. Atoms

    2. Molecules

    3. Ions

  1. Periodic Table

    1. Electronic Configuration

    2. Valence electrons and reactivity

    3. Classes of elements

    4. Periodic Trends

    5. Solubility Trends

  1. Electron Structure

    1. Electron-dot Diagrams

    2. Influence on formation of ions

  1. Composition

    1. Phases – Kinetic Theory of Matter

    2. Chemical vs Physical Changes and Properties

    3. Solids vs Solutes vs Solutions

    4. Density

    5. Solutions – concentration units

  1. Ideal Gas Law

  1. Redox Chemistry

    1. Oxidation Number Assignments

    2. Identification of Oxidizing and Reducing Agents in a Redox Reaction

    3. Use of Nernst Equation

  1. Thermodynamics: Definition and Computation of

    1. Enthalpy

    2. Heat Capacity

    3. Free Energy

    4. Entropy

    5. Energy requirements in spontaneous and nonspontaneous reactions

    6. Equilibrium Constants

    7. Calculation of equilibrium concentrations of gases and solutes

    8. Acid-Base Behavior

    9. Le Chatelier's Principle

    10. Solubility rules and calculations

  1. Kinetics

    1. Rate Laws

Study Questions

The following questions should be answered with a two to three sentence essay. The answers are presented at the end of this section of the study guide.

Chapter 1

The Crustal-Ocean-Atmosphere Factory

1. What important roles does water play on this planet?

2. Give an example of a biogeochemical cycle.

3. What features are commonly found in depictions of biogeochemical cycles?

4. What are some disadvantages in using a mechanistic model of biogeochemical cycles?

5. What are some advantages in using a mechanistic model of biogeochemical cycles?

6. What factors have to be considered when designing a sampling strategy for oceanographic research?

7. When did "modern" marine chemistry start and what motivated this?

8. Describe some of the over-arching trends in current marine research.

Chapter 2

The Waters of the Sea
Part I: The Hydrological Cycle

1. How much water is in the ocean?

2. Is the ocean in a steady state with respect to water?

3. What is the residence time of water in the ocean?

4. What fraction of the water leaving the ocean returns directly as rainfall?

5. Compute the turnover time of water in the ocean with respect to river runoff.

Part II: The Physicochemistry of Water

1. What physical behavior of water is highly unusual?

2. What causes this behavior?

3. Why does water form hydrogen bonds?

4. Why do oxygen and hydrogen form polar covalent bonds?

5. How does this bond contribute to water's behavior as a Universal Solvent?

6. What other behaviors of water are influenced by hydrogen bonding?

7. What effects does the high concentration of salt have on the physical behavior of seawater?

Chapter 3

Seasalt is more than NaCl
1. What's in seawater?

2. What is salinity?

3. How is it measured?

4. Why can salinity be computed from chlorinity?

5. What factors affect salinity?

6. What factors can cause exceptions to the Rule of Constant Proportions?

7. Is density directly proportional to salinity and temperatures? (Hint: Examine the form of the Equation of State of Seawater.)

8. Why can't the density of seawater be computed by simply summing the masses of water and salt as shown in Table 3.6?

Chapter 4

Salinity as a Conservative Tracer
Part I: Conservative Behavior

1. What is a conservative property?

2. Give an example of a conservative property.

3. How can you check that a solute in seawater is exhibiting conservative behavior?

4. What physical mechanisms are responsible for the transport of solutes in seawater?

5. What physical processes are mathematically described by Fick’s first law?

6. What can conservative tracers tell us about physical oceanographic processes (water movement)?

Part II: Tracers of Water Motion

1. What factors determine the vertical and horizontal density gradients in the ocean?

2. How do these gradients affect oceanic circulation?

3. What impact does this circulation have on the distribution of conservative properties?

4. How can conservative tracers be used to provide information on the rates of biogeochemical processes?
Chapter 5

The Nature of Chemical Transformations in the Ocean

Part I: The importance of chemical speciation

1. Why is it important to know the speciation of ions?

2. What types of ion species exist in natural waters?

3. What is the general technique used to calculate the speciation of ions?

4. Give some examples of ion speciation results presented in Chapter 5.

6. What special considerations have to be taken into account when calculating equilibrium ion speciation in seawater?

7. How are these considerations handled when computing ion speciation?

8. What data are needed to compute ion speciation?

Part II: Chemical speciation in seawater

1. Describe the major ion speciation of seawater.

2. Why are a greater percentage of the anions complexed than the cations?

3. What factors can influence ion speciation in seawater?

4. How does the speciation of trace metals compare to that of the major ions?

5. List the most important ligands that are present in seawater.

6. Give some examples of how organic matter can affect the speciation of ions in seawater.

7. How does speciation affect acids and bases in seawater?

8. How does speciation affect solids in seawater?

9. How does speciation affect redox reactions in seawater?

Chapter 6


Part I: Gas Solubility

1. What gases are present in seawater?

2. How did they get there?

3. Give some examples of gases whose concentrations are controlled by biological processes.

4. Are these gases conservative or nonconservative?

5. Give some examples of pollutant gases.

6. How can we detect and quantify the nonconservative behavior of gases in seawater?

7. What factors influence gas solubility?

8. What percent saturation should conservative gases exhibit?

9. What can cause deviations from 100% saturation even in conservative gases?

Part II: Exchange Rates

1. What can cause seawater to be 100% saturated?

2. Why might percent saturations vary over time?

3. What factors control the rates of gas exchange across the air-sea interface?

4. Give some examples of natural and unnatural barriers to gas exchange.

5. How can we quantify gas exchange rates?

Chapter 7

The Importance of Oxygen
Part I: Metabolism from the redox perspective
1. Why are redox reactions important in the marine environment?

2. What types of energy yielding reactions occur in the marine environment?

3. Why is aerobic respiration the dominant metabolic process?

4. Give some examples of metabolic processes which are redox reactions that require energy to proceed, i.e. they are not spontaneous.

5. What impact do these biologically driven redox reactions have on chemical speciation and vice versa?

6. How can the energy yields or requirements of these reactions be quantified?

7. How can the energy yields for these reactions be predicted?

8. What half reactions would you pick to get the largest energy yield?

9. What kinds of oxidation reactions can organisms use to obtain energy if organic matter is present?

10. What are these organisms called?

11. What kinds of redox reactions can organisms use to obtain energy without relying on organic matter?

12 What are these organisms called?

13. Why is O2 important?

14. How does the energy of sunlight get transmitted through the crustal-ocean factory?

15. How do organisms transfer redox energies within their cells?
Part II: Basics of Redox Chemistry

1. Under what environmental conditions are standard half-cell potentials defined?

2. Are these conditions common in the marine environment?

3. How can standard half-cell potentials be adapted to predict energy yields under non-standard conditions?

4. How can equilibrium speciation be computed from Eocell values?

5. Do any redox reactions reach equilibrium in the marine environment?

6. In cases where equilibrium is not reached, how can the value of K be used to predict ocean redox chemistry?

7. How can non-equilibrium speciation be predicted?

8. Why is this information often graphically presented as pε-pH diagrams?
Chapter 8

Organic Matter: Production & Destruction

1. How is organic matter formed in the ocean?

2. How is it destroyed?

3. What impact does this have on nutrients and O2?

4. What important impacts have plankton had on the crustal-ocean-atmosphere factory?

5. How can these impacts be quantified?

Chapter 9

Vertical Segregation of the Biolimiting Elements
1. What kinds of particles are created by marine organisms?

2. What is the elemental composition of these particles?

3. How does the formation of these particles affect the chemical composition of seawater?

4. What percentage of the nutrients entering the mixed layer is removed as sinking biogenic particles?

5. How much of this flux is lost from the ocean by burial in the sediment?

6. What percentage of the nutrients entering the mixed layer is lost from the ocean by burial in the sediment?

7. What effect does this have on the concentrations and residence times of the elements present in these particles?

8. What impact does the efficiency of particle recycling have on global marine productivity?

9. How is the Broecker Box Model used to estimate particle recycling efficiency?

10. What assumptions are this model built on?

11. Which elements are best described by this model?

Chapter 10

Horizontal Segregation

of the Biolimiting Elements

1. What can depth profiles tell us about global patterns of nutrient distributions?

2. What would happen to these distributions if global warming occurred?

3. What is different about distributions of elements contained in soft vs hard parts?

4. How can we check the hypothesis that particulate organic matter decomposition establishes the observed horizontal nutrient gradients?

Chapter 11

Trace Metals in Seawater

1. Why are trace metals important to marine life?

2. What are trace metals?

3. What are the sources of trace metals to the marine environment?

4. What are the sinks of trace metals to the marine environment?

5. Why are organisms important in the biogeochemical cycle of trace metals?

6. What geochemical evidence supports this?
Chapter 12


1. What are marine sediments made up of?

2. What is the source of the material that these sediments are made up of?

3. What can happen to the material that reaches the seafloor?

4. What effects do marine organisms have on sediments?

5. How can we quantify these biogeochemical processes?

Chapter 13

Classification of Sediments

1. Why is it important to have a classification scheme(s) for marine sediments?

2. What kinds of classification schemes are in common use?

3. What are the types of sediment as classified by location?

4. What are the types of sediment as classified by size?

5. What are the types of sediment as classified by sorting?

6. What are the types of sediment as classified by origin?

7. What are the types of sediment as classified by sedimentation rate?

8. What processes are responsible for transporting sediments into the ocean?

9. What processes are responsible for transporting sediments after they reach the seafloor?

10. What depositional conditions favor the formation of sediments best suited for paleoceanographic use?
Chapter 14

Clay Minerals and Other Detrital Silicates

1. What are clay minerals?

2. Why are clay minerals important?

3. How are clay minerals transported to (and within) the ocean?

4. How do these processes determine the distributions of the clay minerals in marine sediments?

5. How are clay minerals formed?

6. What types of clay minerals are produced?

7. What environmental conditions determine the types of clay minerals which are produced by weathering?

8. Describe the spatial distributions in surface sediments of the major types of clay minerals?
Chapter 15

Calcite, Alkalinity & the pH of Seawater
Part I: Calcareous Oozes

1. Why is the formation of calcareous sediments important in the crustal-ocean-atmosphere factory?

2. What kinds of organisms deposit calcareous hard parts?

3. What kinds of minerals do they deposit?

4. How should the production of these hard parts influence the distribution of calcareous oozes?

5. Does the global marine distribution pattern of calcareous oozes fit the pattern you would predict from the distribution of biological production of biogenic calcite?

6. What other factors, in addition to biogenic production, influence the formation of calcareous oozes?

7. Where would you expect the smallest and largest dilution by other particles to occur?

8. What factors influence the flux of calcareous tests to the sediments?

9. What factors influence the degree to which calcareous hard parts are preserved so that they can survive the trip to the seafloor and become buried in the sediments?

10. What factors influence the dissolution rates of calcareous hard parts in seawater?

11. What factors influence the seawater solubility of calcareous hard parts?

Part II: Quantifying Calcite Solubility

1. How can the tendency of a shell's dissolution be quantified?

2. How is Ωcalcite estimated from field measurements?

3. How does the Degree of Saturation of calcite vary with depth?

4. What causes these variations?

5. Why does the vertical profile of D vary from ocean to ocean?

6. What impact do these variations in D have on the global distribution of calcite in surface sediments?

7. What factors influence the dissolution rate of calcareous tests in seawater?

8. To review, what other factors determine the global marine distribution of calcareous sediments?
Chapter 16

Biogenic Silica
1. Why is the formation of siliceous oozes important in the crustal-ocean-atmosphere factory?

2. What other types of "siliceous" sediments accumulate on the seafloor?

3. What organisms deposit siliceous tests?

4. What factors control the productivity of these organisms?

5. What factors control the flux of biogenic silica to the seafloor?

6. What factors determine the burial rate of biogenic silica in the sediments?

7. What factors determine the percentage of biogenic silica in the sediments?

8. Where are the highest percentage siliceous sediments found and why?

Chapter 17

1. Why are evaporites important in the crustal-ocean-atmosphere factory?

2. What conditions are necessary for the formation of evaporites?

3. Where are/were these conditions found?

4. What minerals are produced?

5. How can you tell a marine from a terrestrial evaporite?

6. How do modern evaporites differ from the ancient salt giants?

7. What can evaporites tell us about the ocean's past?
Chapter 18

Iron-Manganese Nodules

and Other Hydrogenous Minerals
1. What is a hydrogenous mineral?

2. What are some examples of hydrogenous minerals?

3. Why are iron-manganese nodules important?

4. Where are they most abundant?

5. What do these nodules look like?

6. What are they composed of?

7. How do they form?

8. What role do microorganisms play in their formation?

9. Why don't they get buried?

10. What do we need to know before we can profitably mine them?

11. Why are phosphorites important?

12. What do we need to know before we can profitable mine them?

13. What is barite and how does it form?

14. What is glauconite and how does it form?

15. What is oolite and how does it form?

16. Are any of these hydrogenous minerals truly abiogenic in origin?

Chapter 19

Metalliferous Sediments

and Other Hydrothermal Deposits

1. What are the major types of sediments created by hydrothermal emissions?

2. Where are they located?

3. Do hydrothermal systems occur above sea level?

4. Why are hydrothermal systems important in the crustal-ocean-atmosphere factory?

5. How do they form?

6. How do they “die”?

7. What factors determine the composition of hydrothermal products?

8. How are elemental fluxes from hydrothermal processes estimated?

9. How do we know the temperature of hydrothermal fluids?

10. What kinds of low temperature venting have been observed?

11. What kinds of unique biota live at these vents?

12. What is the ecological importance of this marine life?

13. What are the ecological constraints on these communities?

14. How might these communities have evolved?

15. What factors enhanced the continuity of these communities?

Chapter 20



1. What factors are important in determining surface sediment distribution patterns?

2. What are the major sediment types?

3. What are their general distribution patterns?

4. What processes cause these patterns?
Chapter 21

Why Seawater is Salty but Not Too Salty
1. Why is it important to know what processes in the crustal-ocean-atmosphere factory stabilizes the major ion composition of seawater?

2. What are the sources and sinks of the major ions?

3. What evidence exists that the ocean is in (and has been in) steady state with respect to these ions?

4. Could this steady state be due to chemical reactions that are at equilibrium?

5. If equilibrium is not attained, then what causes the steady state?

6. What could (or has) caused changes in the salinity of seawater?

7. How can the ocean either buffer itself against these changes or exacerbate these changes in salinity?

8. What can residence times tell us about the geochemical behavior of an element in seawater?

9. How can we evaluate the impact of selected processes on the behavior of an element in seawater?

10. Explain why the long residence times of the major ions are responsible for the Rule of Constant Proportions.

11. Explain what phenomena are ultimately causing the ocean to have a salinity of approximately 35.
Chapter 22

Marine Organic Chemistry: An Overview
1. Why are organic compounds important in the crustal-ocean-atmosphere factory?

2. How are these compounds quantified and identified?

3. How are organic compounds created and destroyed by organisms?

4. What are the major classes of biomolecules and their monomers?

5. Which classes are enriched in nitrogen?

6. Which classes are enriched in phosphorus?

7. Which classes are enriched in sulfur?

8. Which classes are enriched in halogens?

9. What chemical characteristics are required for a biomarker to have paleoceanographic use?
Chapter 23

Production and Destruction

of Organic Compounds in the Sea
1. Why is DOM important in the crustal-ocean-atmosphere factory?

2. Why is POM important in the crustal-ocean-atmosphere factory?

3. What are the operational definitions of POM and DOM?

4. What is colloidal organic matter?

5. What are the relative abundances of POM and DOM?

6. What percentage of POM is alive?

7. What forms does detrital POM take?

8. How do plankton control the production and destruction of organic matter?

9. What organic compounds are phytoplankton composed of?

10. Describe how these compounds get biochemically altered after death of the phytoplankton.

11. What are some other sources of DOM?

12. How do humic materials form?

13. What is the fate of this high MW DOM?

14. What other types of high MW DOM are present in seawater?

15. What are the sources and fate of the low MW DOM?

16. Describe the vertical and horizontal distributions of POM and DOM in seawater.

17. Describe the vertical and horizontal distributions of POM and DOM in the sediments.
Chapter 24

The Marine Nitrogen and Phosphorus Cycles

1. Why is nitrogen important in the marine environment?

2. What are the chemical species of nitrogen in seawater?

3. What is the underlying cause of the complexity of the marine nitrogen cycle?

4. What role do phytoplankton play in this cycle?

5. What role do aerobic bacteria play?

6. What role do anaerobic bacteria play?

7. Describe the seasonal cycling of nitrogen at mid latitudes.

8. Describe the vertical and horizontal variations in concentration of the nitrogen species in seawater.

9. Repeat #8 for the sediments.

10. Is the nitrogen cycle in a steady state?

11. What are the major anthropogenic perturbations in the nitrogen cycle?

12. In what ways is iron important in the nitrogen and phosphorus cycles?

Chapter 25

The Marine Carbon Cycle

and Global Climate Change
1. Why is carbon important in the crustal-ocean-atmosphere factory?

2. What roles does the ocean play in this cycle?

3. What is the Greenhouse Problem?

4. What is the Greenhouse Effect?

5. What anthropogenic activities are causing the Greenhouse Problem?

6. What sinks are removing some of this carbon?

7. Why is the ocean such a good sink for CO2?

8. Where is it a source of CO2 to the atmosphere?

9. Describe some of the evidence for climate change that has been observed in the marine environment?

10. What could have caused past fluctuations in atmospheric CO2 levels?

11. What are some of the negative consequences of climate change to the oceanic carbon cycle?

12. What are some of the negative feedbacks in the oceanic carbon cycle?

13. What are some of the positive feedbacks in the oceanic carbon cycle?

14. How is the Greenhouse Problem leading to ocean acidification?

15. How is global climate change leading to increased ocean hypoxia?
Chapter 26

The Origin of Petroleum

in the Marine Environment
1. What is petroleum?

2. What is the ultimate source of the organic matter in petroleum?

3. What is the best organic source material for the formation of oil?

4. How does this organic matter become petroleum?

5. What is the difference in the petroleum yields from marine and aquatic organic matter?

6. What role do time and temperature play in petroleum formation?

7. What process acts to refine natural petroleum deposits?

8. What geological features are necessary for the accumulation of large deposits of petroleum that are sufficiently large and pure enough to be profitable for recovery?

9. Where in the marine environment would you look for economically significant deposits of petroleum?
Chapter 27

ORGANIC PRODUCTS FROM THE SEA: Pharmaceuticals, Nutraceuticals, Food Additives, and Cosmoceuticals
1. Why are marine organisms a likely source of novel drugs?

2. What observations are used to identify potential candidate organisms?

3. What are some examples of drugs and natural products now in use?

4. Why have so few marine drugs been brought to market thus far?

Chapter 28

Marine Pollution: The Oceans as a Waste Space
Part I: Defining Marine Pollution

1. Is marine pollution a significant problem?

2. What is a pollutant?

3. Why has the ocean been used as a dumpsite?

4. Why have we had such a bad track record in controlling marine pollution?
Part I: Types of Pollution

1. How can we classify pollutants?

2. What are some examples of contaminants?

3. What are some examples of pollutants?

4. What are some examples of pollutogens?
Part I: Policy Issues

1. Why are estuaries more polluted than the open ocean?

2. How would you characterize the current state of legal pollution control measures?

3. What are the options for the future of the oceans given current economic and political realities?

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