Courses & Content

Terrestrial Biogeochemistry

The objective of this course is to introduce you to the concepts and important topics in terrestrial biogeochemistry. We will begin with an analysis of where, when and how energy and elements arrived on plant earth. From here we will consider the basic metabolic pathways of early life on earth and their effect on the atmosphere and lithosphere. We will then consider the basic mechanisms underlying the biogeochemical transformation of carbon, nitrogen, phosphorus and other rock-derived elements. The spatial scale of our analysis will include small plots (m2) to regions (km2) and the entire globe. The temporal scale of analysis will include seconds to years to eons. We will, when appropriate, consider the biogeochemistry of aquatic and marine ecosystems. A major theme for this course is the effect of human activity on biogeochemical cycles, and environmental change. The foundations for the course are lectures, readings from the text, readings from the scientific literature, and discussions.


WH Schlesinger & ES Bernhardt. 2013. Biogeochemistry: An Analysis of Global Change. 3rd Edition. Academic Press, New York.


Syllabus: Biogeochemistry, Class Syllabus 2015

Lectures (Powerpoint Files)

Lecture 1 & 2 Introduction and Origins – Chapter 1 & 2

Lecture 3, Atmosphere Structure and Circulation

Lecture 4, Atmospheric Aerosols and Deposition

Lecture 5, Biogeochemical Reactions in Troposphere & Stratosphere

Lecture 6, Lithosphere, Hawaii P Limitation

Lecture 7, Weathering & Soil Development

Exam I Study Guide 2015

Lecture 8, Photosynthesis

Lecture 9 NPP & NEP

Lecture 11 Decomposition

Lecture 12 Principles of Kinetics and Soil C Cycling

Lecture 13, Biogeochemical Cycling N Mineralization

Lecture 14 N Losses Gas & Leaching Fluxes

Lecture 15 Intrasystem Cycling

Exam II Study Guide

Lectures 18 & 19 Wetlands

Lecture 20 Atmospheric CO2 Sources & Sinks

Lecture 21, Evidence for a Terrestrial C Sink

Lecture 22 Smoking Gun for Atm CO2

Lecture 23, Atmospheric CH4

Lecture 24, Global N Cycle

Lecture 25 Global P Cycle

Exam III Review Questions

Drake et al 2011 Ecology Letters


Chapter Problem Sets

These problems can be challenging so let me offer a few useful tidbits of advice:
1. In most instances you will need to obtain numbers directly from the tables in the text. Often, but not always, that number will be found in the corresponding chapter. In some cases, however, you will need to look to tables in other chapters. Be adventurous.
2. Some problems may lead you to question whether you’ve found the “correct” number. This is actually a common problem in life and environmental sciences due to a variety of factors. If you come across this situation, be sure to justify your choice of number. For example, are you considering the quantity of carbon on the Earth’s crust, or are you considering the inventory on the planet as a whole? Citing the source of information you have in a calculation will aid my understanding of the approach in your answer.
3. Most problems require that you interpret your result in words. That is, what does this tell you about a particular type of biogeochemical transformation. Be sure to interpret your answer.
4. All problems must be typed and handed in hard copy. Use Word [or similar] and when necessary use the equation editor tool to type up more complex equations. Having the ability to type equations is an important skill. Develop it!


Chapter 2 Problems [page 48]:
Undergraduates: 2.1 & 2.4
Graduate Students: 2.1, 2.2, 2.4, 2.5 [optional: 2.3]

Hints for Chapter 2 Problems:

2.1 The inventory of volatile C is presented as both C and CO2 in Table 2.3. You must convert CO2 [in units of 1019g] into a mass of C by the mass ratio of C to CO2.


Chapter 3 Problems [page 91]:
Undergraduates: 3.1, 3.2 & 3.5
Graduate Students: 3.1 through 3.5

Hints for Chapter 3 Problems:

3.5 To solve this question you must convert moles of NH3 to liters of NH3. To begin,  calculate the density of ammonia gas at standard temperature and pressure (STP). Recall that the density (D) of a gas in units of g / liter is calculated as:

D = Mass*P / RT

, and at STP pressure (P)  = 1 atm, temperature(T) = 273 K, & R (universal gas constant) = 0.0821. Calculate the molar mass of NH3 and you should get a density of 0.760 g / liter.

To estimate volume, simply divide the mass of NH3 by its density (=22.4L).

Be sure to track your unit conversions!


Chapter 4 Problems [page 133]:

Undergraduate Students: Problems 4.1 & 4.2

Graduate Students: All problems [4.1-4.4]

Hints to Solving the Problems [note: there is often more than 1 approach to solving these problems, so you may use these hints, nor not, as you wish].


a. Calculate the input of precipitation from the atmosphere. Remember that 100cm/yr is the input over any amount area, so you can scale this up to the volume of water per unit area [e.g., L/ha] recalling that 1ha = 10,000 cm2. You will find it easiest if for precipitation inputs you calculate units of L/ha/yr.

b. Calculate separate input rates of Mg from precipitation and weathering [units of kg/ha/yr is recommended].

c. Recall that streamflow is 50% of precipitation. Use this knowledge to estimate watershed area from which you can estimate the rate of Mg loss in streamflow in units of kg/ha/yr.

d. From these calculations you should be able to identify the small discrepancy in the budget and provide a proximate explanation for its occurrence.


Chapter 5 Problems [page 172, Due 10/26/2015]:

Undergraduate Students: Problems 5.3 & 5.4

Graduate Students: All problems [5.1-5.4]


Chapter 5 Problem Hints

5.1          Use units of umol cm-2 s-1

CO2 flux entering the leaf will be given by the general expression:

Flux = (ca-ci)/resistance

, where resistance is either 5 sec cm-1 or 10 sec cm-1

For H2O vapor pressure [VP] in the atmosphere, use the information at engineering toolbox dot com. Show how you calculated VP in units of g m-3. Then calculate the flux for water vapor.

Finally, calculate WUE


5.2          Use units of mol CO2 yr-1

Given, the shape of the tree is a cone with diameter at base of 50cm, height 15m and thickness of outermost ring of wood at 2mm, calculate the volume of wood that is actively respiring. Here, it may be useful to estimate this volume as the difference of two cones one subtending the other with the subtending cone 2mm less in diameter.

Next, calculate leaf area supported by the 2mm-diameter tree ring. Here again, it may be useful to estimate leaf area from the difference in cross-sectional area of the two cones at their base. Then, calculate the rate of photosynthesis.

Interpret your result.


5.3          Define the Q10 relationship. Use your textbook or an online resource to find it.

By definition, Q10 means that Δt=10.

Cite your source for global soil respiration and what it would be in a world warmer by 3oC.

Chapter 6 Problems [page 231, Due 11.16.2015]:

Undergraduate Students: Problems 6.1, 6.2 & 6.3

Graduate Students: All problems [6.1-6.5]


Chapter 6 Problem Hints

6.1 Use the information from Table 6.2 related to the meq of NH4+ and NO3- uptake. Use a linear equation to estimate, x, the proportion of NH4+ taken up from the soil.

6.2 None needed

6.3 You can make the simplifying assumption that animal tissue is composed solely of protein.

6.4. Assume all N taken up begins in the form of NH4+; Nitrification reactions are given in Equations 2.17 and 2.18 (p. 37); compare to global cycle (Figure 11.9)

6.5 Recall:  δ15N = 1000 *  [(Rsample – Rstd)/Rstd]



This semester the recitation section will be held Tuesday evenings from 5-6pm. We will begin by reading The Alchemy of Air by Thomas Hager. (C) 2008. Broadway Books, New York NY. You can order the book here.

For 9.29.2015 Please read Chapters 1 – 8.

For 10.13.2015 Please read Chapters 9 – 16


In-Class Discussions

I. Poschl et al. 2010  Science DOI:10.1126/science.1191056 & Vocabulary List

II. Morford et al 2011 Nature DOI: 10.1038/nature10415

III. Averill et al 2014 Nature DOI:10.1038/nature12901

IV. Wang et al 2014 Biogeosciences DOI:10.5194/bg-11-1817-2014

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