ESSM 622

BIOGEOCHEMISTRY OF TERRESTRIAL ECOSYSTEMS

SPRING SEMESTER T-TH 8:00-9:15 AM

INSTRUCTOR: Dr. Thomas W. Boutton Department of Ecosystem Science and Management Office: Animal Industry Bldg., Room 419 Phone: 845-8027 Fax: 845-6430 E-mail: boutton@neo.tamu.edu Home Page: http://essm.tamu.edu/people/Boutton/ BACKGROUND AND PURPOSE: The biogeochemical cycles of carbon, nitrogen, sulfur, and phosphorus have tremendous contemporary significance due to their critical roles in determining the structure and function of ecosystems, and their influence on atmospheric chemistry and the climate system. Human impacts on these nutrient cycles are now responsible for a multitude of global changes that threaten the sustainability of ecosystem services essential to mankind. This course provides a framework for understanding biogeochemical cycles, their significance at both global and ecosystem levels of organization, and their contemporary relevance to ecosystem science and management. The cycles of carbon, nitrogen, sulfur, and phosphorus are emphasized due to their significance in the earth-atmosphere-biosphere system. Ecosystem-level processes are studied in forest, grassland, and agricultural ecosystems. Because many of our current environmental problems are manifestations of disturbed biogeochemical cycles, this course is fundamental to understanding environmental issues such as global climate change, changes in atmospheric composition, land cover/land use changes, carbon sequestration, nitrogen saturation, acid precipitation, nonpoint-source pollution, and water quality. This course is of interest to graduate students in ecology, soil science, geosciences, hydrology, atmospheric sciences, agricultural sciences, and environmental engineering. There are no prerequisites other than graduate standing in one of these disciplines.

OBJECTIVES:

1) Define the basic characteristics and properties shared by all biogeochemical cycles, and establish the relevance of energy flow and the hydrologic cycle to all other nutrient cycles.

2) Examine biogeochemical cycles of carbon, nitrogen, sulfur, and phosphorus

3) Investigate key biogeochemical processes at the ecosystem level of organization,

and evaluate the role of soil structure, biology, and biochemistry in those processes.

4) Consider biogeochemical cycling in relation to land uses in grassland, forest,

agricultural, and urban ecosystems.

5) Study the interactions between biogeochemical cycles and global changes. EVALUATION PROCEDURES: Two exams (100 points each) will be given during the course of the semester. In addition, each student will give approximately 7-10 brief (10-15 min) oral presentations (50 points each) that summarize and interpret an assigned reading Class participation in discussions of the assigned readings is expected of all students throughout the semester. COURSE MATERIALS: Assigned reading: available on Vista (http://elearning.tamu.edu) Class notes: available on Vista (http://elearning.tamu.edu) AMERICANS WITH DISABILITIES ACT (ADA) POLICY STATEMENT: The Americans with Disabilities Act (ADA) is a federal anti-discrimination statute that provides comprehensive civil rights protection for persons with disabilities. Among other things, this legislation requires that all students with disabilities be guaranteed a learning environment that provides for reasonable accommodation of their disabilities. If you believe you have a disability requiring an accommodation, please contact the Department of Student Life, Services for Students with Disabilities, in Room 126 of the Koldus Building or call 845-1637. ACADEMIC INTEGRITY STATEMENT: "An Aggie does not lie, cheat, or steal or tolerate those who do."

For more information see the Honor Council Rules and Procedures on the web at:

http://www.tamu.edu/aggiehonor

ESSM 622 – BIOGEOCHEMISTRY OF TERRESTRIAL ECOSYSTEMS Jan 19 Tue Course introduction A) The Major Biogeochemical Cycles Jan 21 Thu Energy flow and the hydrologic cycle in biogeochemistry Jan 26 Tue Carbon cycle Jan 28 Thu Nitrogen cycle Feb 2 Tue Sulfur cycle Feb 4 Thu Phosphorus cycle Feb 9 Tue To be determined Feb 11 Thu To be determined B) Key Biogeochemical Processes in Ecosystems Feb 16 Tue Soil respiration Feb 18 Thu Root turnover Feb 23 Tue Organic matter decay Feb 25 Thu Nitrogen fixation Mar 2 Tue Nitrogen transformations Mar 4 Thu Phosphorus loss and retention C) Soil Structure, Biology, and Biochemistry Mar 9 Tue Soil physical structure Mar 11 Thu Organic matter chemistry Mar 16 Tue Spring Break Mar 18 Thu Spring Break Mar 23 Tue Dissolved organic matter Mar 25 Thu Soil microbial diversity and function Mar 30 Tue Mycorrhizae Apr 1 Thu Soil enzymes Apr 6 Tue Soil animals D) Land Uses and Biogeochemistry Apr 8 Thu Plant species effects, invasive species, vegetation change Apr 13 Tue Agricultural lands – tillage and rotation effects Apr 15 Thu Rangelands – grazing effects Apr 20 Tue Forestlands – management effects E) Global Changes and Biogeochemistry Apr 22 Thu Elevated CO2 Apr 27 Tue Atmospheric deposition Apr 29 Thu Climate effects May 4 Tue Redefined as a Friday May 5-6 Reading Days May 10 Mon Final Exam, 1-3 PM

ESSM 622 – BIOGEOCHEMISTRY OF TERRESTRIAL ECOSYSTEMS

(A) THE MAJOR BIOGEOCHEMICAL CYCLES (1) Thur Jan 21 - Role of Energy Flow and Hydrologic Cycle in Biogeochemistry

(a) Foley JA, Costa MH, Delire C, Ramankutty N, Snyder P. 2003. Green surprise? How terrestrial ecosystems could affect earth’s climate. Frontiers in Ecology and the Environment 1(1): 38-44. (b) Meir P, Cox P, Grace J. 2006. The influence of terrestrial ecosystems on climate. Trends in Ecology and Evolution 21(5): 254-260. (c) National Research Council and National Academies. 2005. Understanding and responding to climate change. The National Academies Press, Washington DC.

(d) Oki T, Kanae S. 2006. Global hydrologic cycles and world water resources. Science 313: 1068-1072.

(2) Tue Jan 26 - Carbon Cycle

(a) Houghton RA. 2007. Balancing the global carbon budget. Annual Review of Earth and Planetary Sciences 35: 313-347.

(b) U.S. Climate Change Science Program. 2007. The first state of the carbon cycle report (SOCCR): The North American carbon budget and implications for the global carbon cycle. U.S. Climate Change Science Program, Synthesis and Assessment Product 2.2. NOAA, National Climatic Data Center, Asheville, NC.

(3) Thur Jan 28 - Nitrogen Cycle

(a) Jaffe DA. 2000. The nitrogen cycle. IN: Jacobson MC, Charlson RJ, Rodhe H, Orians GH (eds), Earth System Science, pp. 322-342. Elsevier/Academic Press, New York. (b) Robertson GP, Groffman PM. 2007. Nitrogen transformations: IN: Paul EA (ed), Soil Microbiology, Biochemistry, and Ecology, pp. 341-364. Springer, New York.

(c) National Atmospheric Deposition Program. 2001. Nitrogen in the Nation’s Rain. National Atmospheric Deposition Program, Champaign, IL.

(4) Tue Feb 2 - Sulfur Cycle

(a) Brimblecombe P. 2005. The global sulfur cycle. IN: Schlesinger WH (ed), Treatise on Geochemistry, Vol. 8 (Biogeochemistry), pp. 645-682. Elsevier Science, Amsterdam.

(b) Paul EA, Clark FE. 1996. Sulfur transformations in soil. IN: Soil Microbiology and Biochemistry (EA Paul and FE Clark), pp. 299-313. Academic Press, NY.

(5) Thur Feb 4 - Phosphorus Cycle

(a) Smil V. 2000. Phosphorus in the environment: Natural flows and human interferences. Annual Review of Energy and the Environment 25: 53-88. (b) Paul EA, Clark FE. 1996. Phosphorus transformations. IN: Soil Microbiology and Biochemistry (EA Paul and FE Clark), pp. 289-298. Academic Press, NY.

_________________________________________ Tue Feb 9 Test 1 Thur Feb 11 No class – work on presentations _________________________________________ (B) KEY BIOGEOCHEMICAL PROCESSES IN ECOSYTEMS (1) Tue Feb 16 - Soil Respiration

(a) Baldocchi D, Tang J, Xu L. 2006. How switches and lags in biophysical regulators affect spatial-temporal variation of soil respiration in an oak-grass savanna. Journal of Geophysical Research 111: G02008, doi:10.1029/ 2005JG000063, 2006

(b) Hogberg P, Read DJ. 2006. Towards a more plant physiological perspective on soil ecology. Trends in Ecology and Evolution

(2) Thur Feb 18 - Root Production and Turnover

(a) Rasse D, Rumpel C, Dignac MF. 2005. Is soil carbon mostly root carbon? Mechanisms for a specific stabilization. Plant and Soil 269: 341-356.

(b) Joslin JD, Gaudinski JB, Torn MS, Riley WJ, Hanson PJ. 2006. Fine-root turnover patterns and their relationship to root diameter and soil depth in a 14C-labeled hardwood forest. New Phytologist 172: 523-535.

(3) Tue Feb 23 - Organic Matter Stabilization and Decay

(a) Chapin FS, Matson PA, Mooney HA. 2002. Terrestrial decomposition. IN: Principles of Terrestrial Ecosystem Ecology (Chapin FS, Matson PA, Mooney HA), pp. 151-175. Springer-Verlag, Berlin. (b) Lutzow M, Kogel-Knabner I, Ekschmitt K, Matzner E, Guggengerger G, Marschner B, Flessa H. 2006. Stabilization of organic matter in temperate soils: Mechanisms and their relevance under different soil conditions – a review. European Journal of Soil Science 57: 426-445.

(4) Thur Feb 25 - Nitrogen Fixation

(a) Houlton BZ, Wang YP, Vitousek PM, Field CB. 2008. A unifying framework for dinitrogen fixation in the terrestrial biosphere. Nature 454: 327-330. (together with associated commentary) (b) Kreibich H, Kern J, Camargo P, Moreira M, Victoria R, Werner D. 2006. Estimation of symbiotic N2 fixation in an Amazon floodplain forest. Oecologia 147: 359-368.

(5) Tue Mar 2 - Nitrogen Transformations

(a) Schimel JP, Bennett J. 2004. Nitrogen mineralization: Challenges of a changing paradigm. Ecology 85(3): 591-602.

(b) Erickson H, Keller M, Davidson E. 2001. Nitrogen oxide fluxes and nitrogen cycling during postagricultural succession and forest fertilization in the humid tropics. Ecosystems 4: 67-84.

(6) Thur Mar 4 - Phosphorus Transformation and Retention

(a) Wood T, Bormann FH, Voigt GK. 1984. Phosphorus cycling in a northern hardwood forest: Biological and chemical control. Science 223: 391-393.

(b) Garcia-Montel DC, Neill C, Melillo J, Thomas S, Steudler P, Cerri CC. 2000. Soil phosphorus transformations following forest clearing for pasture in the Brazilian Amazon. Soil Science Society of America Journal 64: 1792-1804.

(C) SOIL STRUCTURE, BIOLOGY, AND BIOCHEMISTRY (1) Tue Mar 9 - Soil Physical Structure

(a) Jastrow JD, Miller RM. 1997. Soil aggregate stabilization and carbon sequestration: Feedbacks through organomineral associations. IN: Lal R, Kimble J, Follett R, Stewart B (eds), Soil Processes and the Carbon Cycle pp. 207-223. CRC Press, Boca Raton, FL.

(b) Liao JD, Boutton TW, Jastrow JD. 2006. Storage and dynamics of carbon and nitrogen in soil physical fractions following woody plant invasion of grassland. Soil Biology and Biochemistry 38: 3184-3196.

(2) Thur Mar 11 - Organic Matter Chemistry

(a) Poirier N, Sohi S, Gaunt J, Mahieu N, Randall E, Powlson D, Evershed R. 2005. The chemical composition of measurable soil organic matter pools. Organic Geochemistry 36: 1174-1189.

(b) Filley TR, Boutton TW, Liao JD, Jastrow JD, Gamblin DE. 2008. Chemical changes to nonaggregated particulate soil organic matter following grassland-to-woodland transition in a subtropical savanna. Journal of Geophysical Research 113: G03009, doi:10.1029/2007JG000564, 2008 ______________________________ Tue Mar 16 Spring Break

Thur Mar 18 Spring Break ______________________________

(3) Tue Mar 23 - Dissolved Organic Matter

(a) van Hees P, Jones DL, Finlay R, Godbold DL, Lundstrom US. 2005. The carbon we do not see – the impact of low molecular weight compounds on carbon dynamics and soil respiration in forest soils: a review. Soil Biology and Biochemistry 37: 1-13. (b) Giesler R, Hogberg M, Strobel B, Richter A, Nordgren A, Hogberg P. 2007. Production of dissolved organic carbon and low molecular weight organic acids in soil solution driven by recent tree photosynthate. Biogeochemistry 84: 1-12.

(4) Thur Mar 25 - Soil Microbial Diversity and Function

(a) Leckie S. 2005. Methods of microbial community profiling and their application to forest soils. Forest Ecology and Management 220: 88-106. (b) Kreuzer-Martin HW. 2007. Stable isotope probing: Linking functional activity to specific members of microbial communities. Soil Science Society of America Journal 71: 611-619.

(5) Tue Mar 30 - Mycorrhizae

(a) Leake J, Johnson D, Donnelly D, Muckle G, Boddy L, Read D. 2004. Networks of power and influence: The role of mycorrhizal mycelium in controlling plant communties and agroecosystem functioning. Canadian Journal of Botany 82: 1016-1045.

(b) Talbot JM, Allison SD, Treseder KK. 2008. Decomposers in disguise: Mycorrhizal fungi as regulators of soil C dynamics in ecosystems under global change. Functional Ecology 22: 955-963.

(6) Thur Apr 1 - Soil Enzymes

(a) Sinsabaugh RL, Antibus RK, Linkins AE, McClaugherty CA, Rayburn L, Repert D, Weiland T. 1993. Wood decomposition: Nitrogen and phosphorus dynamics in relation to extracellular enzyme activity. Ecology 74(5): 1586-1593. (b) Sinsabaugh RL, Lauber CL, Weintraub MN, Ahmed B, Allison SD, Crenshaw A, Contosta AR, et al. 2008. Stoichiometry of soil enzyme activity at global scale. Ecology Letters 11: 1252-1264.

(7) Tue Apr 6 - Soil Animals

(a) Bonkowski M. 2004. Protozoa and plant growth: The microbial loop in soil revisited. New Phytologist 162: 617-631.

(b) Filley TR, McCormick MK, Crow SE, Szlavecz K, Whigham DF, Johnston CT, van den Heuvel RN. 2008. Comparison of the chemical trajectory of Liriodendron tulipifera L. leaf litter among forests with different earthworm abundance. Journal of Geophysical Research 113: G01027, doi:10.1029/ 2007JG000542, 2008

(D) LAND USES AND BIOGEOCHEMISTRY (1) Thur Apr 8 - Plant Species Effects, Invasive Species, Vegetation Change

(a) Lata JC, DeGrange V, Raynaud X, Maron PA, Lensi R, Abbadie L. 2004. Grass populations control nitrification in savanna soils. Functional Ecology 18: 605-611.

(b) Bezemer TM, Lawson C, Hedlund K, Edwards A, Brook A, Igual J, Mortimer S, van der Putten WH. 2006. Plant species and functional group effects on abiotic and microbial soil properties and plant-soil feedback responses in two grasslands. Journal of Ecology 94: 893-904.

(2) Tue Apr 13 - Agricultural Lands: Tillage and Rotation Effects

(a) Haile-Mariam S, Collins HP, Wright S, Paul EA. 2008. Fractionation and long-term laboratory incubation to measure soil organic matter dynamics. Soil Science Society of America Journal 72: 370-378.

(b) White PM, Rice CW. 2009. Tillage effects on microbial and carbon dynamics during plant residue decomposition. Soil Science Society of America Journal 73: 138-145.

(3) Thur Apr 15 – Rangelands: Grazing Effects

(a) Patra AK, Abbadie L, Clays-Josserand A, Degrange V, Grayston SJ, Loiseau P, Louault F, Mahmood S, Nazaret S, Philippot L, Poly F, Prosser JI, Richaume A, LeRoux X. 2005. Effects of grazing on microbial functional groups involved in soil N dynamics. Ecological Monographs 75(1): 65-80. (b) Frank DA, Groffman PM. 1998. Ungulate vs. landscape control of soil C and N processes in grasslands of Yellowstone National Park. Ecology 79(7): 2229-2241.

(4) Tue Apr 20 – Forests and Forest Management

(a) Gough CM, Vogel CS, Schmid HP, Curtis PS. 2008. Controls on annual forest carbon storage: Lessons from the past and predictions for the future. BioScience 58: 609-622. (b) Diochon A, Kellman L, Beltrami H. 2009. Looking deeper: An investigation of soil carbon losses following harvesting from a managed northeastern red spruce (Picea rubens Sarg.) forest chronosequence. Forest Ecology and Management 257: 413-420.

(E) GLOBAL CHANGES AND BIOGEOCHEMISTRY (1) Thur Apr 22 - Elevated CO2

(a) Jastrow JD, Miller RM, Matamala R, Norby R, Boutton TW, Rice CW, Owensby CE. 2005. Elevated atmospheric carbon dioxide increases soil carbon. Global Change Biology 11: 2057-2064.

(b) Finzi A, Sinsabaugh R, Long T, Osgood M. 2006. Microbial community responses to atmospheric carbon dioxide enrichment in a warm-temperate forest. Ecosystems 9: 215-226.

(2) Tue Apr 27 - Atmospheric Deposition

(a) Magnani F, Mencuccini M, Borghetti M, Berbigier P, Berninger F, Delzon S, Grelle A, Hari P, Jarvis P, Kolari P, Kowalski A, Lankreijer H, Law B, Lindroth A, Loustau D, Manca G, Moncrieff J, Rayment M, Tedeschi V, Valentini R, Grace J. 2007. The human footprint in the carbon cycle of temperate and boreal forests. Nature 447: 848-852. (together with associated commentaries) (b) Zak DR, Holmes WE, Burton AJ, Pregitzer KS, Talhelm AF. 2008. Simulated atmospheric NO3

- deposition increases soil organic matter by slowing decomposition. Ecological Applications 18: 2016-2027.

(3) Thur Apr 29 - Climate Effects

(a) Luo Y. 2007. Terrestrial carbon-cycle feedback to climate warming. Annual Review of Ecology, Evolution, and Systematics 38: 683-712. (b) Sardans J, Penuelas J, Estiarte M, Prieto P. 2008. Warming and drought alter C and N concentration, allocation, and accumulation in a Mediterranean shrubland. Global Change Biology 14: 1-13.

MON MAY 10 FINAL EXAM (1-3 PM)