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News 2013


AGU 2013 San Francisco

B12A-08. EFFECTS OF WINTER FLOODING PEAT SOILS ON GREENHOUSE GAS EMISSIONS IN THE SACRAMENTO-SAN JOAQUIN DELTA Frank E. Anderson; Brian A. Pellerin; Brian A. Bergamaschi; Cove S. Sturtevant; Joseph G. Verfaillie; Sara H. Knox; Dennis D. Baldocchi; Roger Fujii

B21A-0474Evaluating the value of enhanced atmospheric measurements and models to improve interpretation of flux data Jessica L. Osuna; Sonia Wharton; Matthias Falk; Rex D. Pyles; Siyan Ma; Dennis D. Baldocchi

B33A-0461. Greenhouse gas emissions from agricultural and restored Delta peatlands Sara H. Knox; Cove S. Sturtevant; Laura E. Koteen; Jaclyn H. Matthes; Joseph G. Verfaillie; Dennis D. Baldocchi

B21C-0499. Intercomparison of the AmeriFlux In Situ Measurements Across Multiple Biomes as an Alternative to Climatic Classification Boris Faybishenko; Deb Agarwal; Dennis D. Baldocchi; Catharine van Ingen; Sebastien Biraud; Gilberto Z. Pastorello; Dario Papale

 B33A-0462. Towards up-scaling restored wetland CO2 and CH4 exchange in the Sacramento - San Joaquin River Delta Cove S. Sturtevant; Sara H. Knox; Laura E. Koteen; Jaclyn H. Matthes; Joseph G. Verfaillie; Dennis D. Baldocchi

B33A-0465. Managing Restored Wetlands in the Sacramento-San Joaquin Delta to Reduce Methane Emissions and Increase Carbon Uptake Laura E. Koteen; Sara H. Knox; Cove S. Sturtevant; Joseph G. Verfaillie; Jaclyn H. Matthes; Dennis D. Baldocchi

 A31C-0097. Comparison of methane emissions from wetlands measured from aircraft and towers. Stephen A. Conley; Ian C. Faloona; Judith Z. Drexler; Frank E. Anderson; Dennis D. Baldocchi; Cove S. Sturtevant; Joseph G. Verfaillie; Sara H. Knox

 B51K-07. The role of hydrodynamic transport in greenhouse gas fluxes at a wetland with emergent vegetation Cristina Poindexter; Emily Gilson; Sara H. Knox; Jaclyn H. Matthes; Joseph G. Verfaillie; Dennis D. Baldocchi; Evan A. Variano

B54A-06. Surface Energy Balance: Lessons Learned from Modeling Simulations and Field Measurements at an Oak-grass Savanna in California
Siyan Ma; Dennis D. Baldocchi; Jordi Vila-Guerau Arellano; Jessica L. Osuna; Sonia Wharton

Other Meetings

Exploring methane and carbon dioxide exchange from agricultural and wetland land use classes in the Sacramento-San Joaquin Peatland Delta of California, Royal Society International Seminar on ‘Scaling methods for greenhouse gas fluxes in British lowland peatland’, Chicheley Hall, Dec 10-11, 2013



Jordi Vil`a-Guerau de Arellano, Huug G. Ouwersloot, Dennis Baldocchi and Cor Jacobs. Shallow cumulus rooted in photosynthesis. Geophysical Research Letters, submitted

Michael Toomey, Mark Friedl, Steven Frolking, Koen Hufkens, Stephen Klosterman, Oliver Sonnentag, Dennis D. Baldocchi, Carl J. Bernacchi, Gil Bohrer, Edward Brzostek, Sean P. Burns, Carole Coursolle, David Y. Hollinger, Hank A. Margolis, Harry McCaughey, Russell K. Monson, J. William Munger, Steven Pallardy, Richard P. Phillips, Margaret Torn, Sonia Wharton, Marcelo Zeri, Andrew D. Richardson. Greenness indices from digital cameras predict the timing and seasonal dynamics of canopy-scale photosynthesis. Ecological Applications. submitted

Staff News

Sara Knox won First Place for the Best Student Poster at the 11th Biennial State of the Estuary Conference!  Her poster was titled “Greenhouse Gas Emissions from Agricultural and Restored Delta Peatlands.

Sara Knox was a winner of the Outstanding Student Paper Awards in Biogeosciences at the 2013 American Geophysical Union Meeting

ddb was profiled in a 'Where they are Now?' series of the University of Nebraska, School of Natural Resources newsletter.



The Biomet Lab met for the annual AGU Lunch



Jean-Luc Widlowski visited the Biomet Lab and gave a seminar on Radiative transfer modeling and the RAMI project

Hideki Kobayshi from JAMSEC in Yokahama, Japan visited the Biomet Lab before AGU

Colin Prentice, and his student Shuangxi Zhou, visited to talk about global modeling and leaf photosynthesis under water stressed conditions


ddb gave a presentation on Shaking hands between eddy fluxes and Remote Sensing. COST Action ES0903 Eurospec final Conference, Trento, IT Nov. 6-8, 2013

At the meeting was my scientific granddaughter, Galam Lee, from Seoul National University in Korea



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New Flux Tower installed at the new wetland on Twitchell Island


ddb gave a seminar on 'What is Annual Ecosystem Photosynthesis?:An Exploration of Data and Models from Ecosystem to Globe' to the Berkeley Atmospheric Science Center

He attended the DOE BERAC (Biological and Environmental Research Advisory Committee) Meeting in Rockville, MD

Sara Knox presented a poster on Greenhouse Gas emission from Agricultural and restored peatlands at the State of the San Francisco Estuary Conference, 20/20 vision: Past Reflections, Future Directions, Oakland.

Cove Sturtevant presented a poster on Towards up-scaling restored wetland CO2 and CH4 exchange in the Delta at the State of the San Francisco Estuary Conference, 20/20 vision: Past Reflections, Future Directions, Oakland.



Béland, M., D. D. Baldocchi, J.-L. Widlowski, R. A. Fournier, and M. M. Verstraete (2014), On seeing the wood from the leaves and the role of voxel size in determining leaf area distribution of forests with terrestrial LiDAR, Agricultural and Forest Meteorology, 184(0), 82-97.

Staff News

Patty Oikawa joined the Biomet lab as a USDA/AFRI postdoctoral fellow. Her project is on 'Investigating changes in greenhouse gas emissions resulting from land-use conversion in the Sacramento-San Joaquin River Delta'


Sebastian Wolf is attending workshop on Greenhouse Gas Management in European Land Use Systems in Antwerp, Belgium and he gave a seminar at the University of Montreal


On Seeing the Wood from the Leaves and the Role of Voxel Size in Determining Leaf Area Distribution of Forests with Terrestrial LiDAR Agricultural and Forest Meteorology ; Martin Beland; Dennis D Baldocchi; Jean-Luc Widlowski; Richard A Fournier; Michel M Verstraete has been accepted by Agricultural and Forest Meteorology

Staff News

Two new undergraduates started working in the Biomet Lab. One is Samuel Pennypacker, who will evaluate FLUXNET data and extract information on canopy height from wind and turbulence

the other is Pascal Polonik. he will work on analyzing measurements from the Delta greenhouse gas study.

Yanel Saentz will also continue working with us over the fall semester


Joe Berry from the Carnegie Institute near Stanford visited to discuss collaboration on measuring and modeling photosynthesis with fluorescence.


Shiping Chen from the Botanical Institute of the Chinese Academy of Science started her one year visit in the Biomet lab.  Dr. Chen gave a lab seminar on her research that is focusing on Mongolian grasslands and how their carbon fluxes respond to rain pulses and grazing.


ddb attended the 16th International Conference on Photosynthesis in St Louis, Mo and gave a presentation on Assessing Photosynthesis from Canopy to Global Scales in the Symposium of Photosynthesis at Larger Scales


A new collaborative paper was submitted to Plant, Cell and Environment on "Drought effects on photosynthetic and water use dynamics in Blue oak (Quercus douglasii): integrating Eddy Covariance and carbon stable isotope methods" by Mambelli, Stefania; Tu, Kevin; Ma, Siyan; Knohl, Alexander; Baldocchi, Dennis; Dawson, Todd

Staff News

Martin Beland won an award for the Best Dissertation in Remote Sensing in Canada, 2012. Congratulations.


Eva Rubio from Spain is visiting the Biomet Lab for the next 3 months

Staff News

Biomet Lab at Picnic and Hike at Dillon Beach

We celebrated Bastille Day at the Beach with barbacue, games and hikes


biometlab dillon beach.JPG

Jordi Vila from Wageningen is visiting the Biomet lab for July.  He gave a seminar on the linkages between the land surface, growth of the planetary boundary and clouds using LES and bulk PBL models.

jordi vila.jpg

Dario Papale from the Universita' degli Studi della Tuscia is visiting the Biomet Lab for July and August. We are working together on FLUXNET.

dario papale and stomper.jpg

 Hideki Kobayashi, a former Biomet Postdoc, now at JAMSEC in Yokohama, Japan visited the Biomet Lab and gave a seminar on his advancements in modeling radiative transfer through 3 dimensional canopies. He is working with us to transform his FLIES model from a lollypop representation of trees to one using voxels based on the ground based LIDAR Martin Beland is collecting for Tonzi Ranch


Baldocchi, D.D. and Ma, S. 2013. How Will Land Use Affect Air Temperature in the Surface Boundary Layer?:  Lessons Learned from a Comparative Study on the Energy Balance of an Oak Savanna and an Annual Grassland in California, USA.. Tellus B, 65, 19994, http://dx.doi.org/10.3402/tellusb.v65i0.19994.

Staff News

Yanel Saenz joins the Biomet lab for the summer as part of the undergraduate Biological Scholar Program. She will work on the Delta project

Taichi Natake will work this summer in the Biomet lab on studying clumping in forest crowns. Taichi was an undergraduate at Cal and is now a graduate student at Duke in the environmental science Master's program.

Cove Sturtevant will join the Biomet lab as a postdoc working on the Delta projects


ddb was a Trainer: COST Action Training School on Flux Measurement Techniques of non-CO2 Greenhouse Gases. Mierzecin, Poland, May 7-12, 2013

ddb attended the DOE TES workshop in Potomac, MD

Staff News

Sara Knox passed her PhD Oral Exams and is now a PhD Candidate. Congratulations

Tom Shapland gave a lab seminar on his work on use of surface renewal method to evaluate heat transfer, and evaporation by residual, over grapes. Tom is a visiting postdoctoral scientist from the Viticulture program at UC Davis.


Sebastian Wolf attended the Open Conference on Climate Extremes and Biogeochemical Cycles
Date: 2 - 5 April 2013 Venue: Seefeld, Austria


Baldocchi, D., 2013: Ecosystem Services of Energy Exchange and Regulation. Climate Vulnerability: Understanding and Addressing Threats to Essential Resources. Elsevier Inc., Academic Press, 81–92 pp.

Kobayashi, H., Ryu, Y., Baldocchi, D.D., Welles, J.M., Norman, J.M., 2013. On the correct estimation of gap fraction: How to remove scattered radiation in gap fraction measurements? Agricultural and Forest Meteorology 174–175, 170-183.

Vargas, R., Sonnentag, O., Abramowitz, G., Carrara, A., Chen, J., Ciais, P., Correia, A., Keenan, T., Kobayashi, H., Ourcival, J.-M., Papale, D., Pearson, D., Pereira, J., Piao, S., Rambal, S., Baldocchi, D., 2013. Drought Influences the Accuracy of Simulated Ecosystem Fluxes: A Model-Data Meta-analysis for Mediterranean Oak Woodlands. Ecosystems, 1-16.

Staff News

Jaclyn Hatala is now Dr. Hatala. She just completed her dissertation entitled 'Spatio temporal dynamics of carbon dioxide and methane fluxes from agricultural and restored wetlands in the California Delta

She will get married next month, then take a postdoc in Mike Dietze lab at Boston University.


Suzanne Tringe and Susanna Theroux from the Joint Genome Institute visited to discuss sampling microbes at the wetlands and understand who is producing methane and where.

Frank Anderson of USGS visited and gave a presentation on his trace gas flux measurements on Staton Island. He measured fluxes over corn fields flooded for water fowl, and non flooded.


Sebastian Wolf and ddb attended the North American Carbon Project meeting in Albuquerque, New Mexico and gave a set of presentations

AmeriFlux, Yesterday, Today and Tomorrow    (Dennis Baldocchi, Margaret Torn, Deb Agarwal, Bev Law, Tom Boden)   [abstract]   [presentation]

and posters

Rice Culture in the Sacramento-San Joaquin Delta to Mitigate Past Agricultural Impacts, Improve Water Quality and Sequester Carbon  -- (Will Horwath, Dennis Baldocchi, Phil Bachand, Steve Deverel)
Session: Theme 2: Drivers of Anthropogenic Emissions

A Decade of Grass-Oak Savanna Measurements and Beyond  -- (Dennis Baldocchi, Siyan Ma, Joe Verfaillie)
Session: Theme 1: Diagnosis of the Atmospheric Carbon Cycle

Response of ecosystem carbon and water dynamics to spring drought in Switzerland  -- (Sebastian Wolf, Werner Eugster, Christof Amman, Matthias Häni, Sebastian Zielis, Rebecca Hiller, Jacqueline Stieger, Dennis Imer, Lutz Merbold, Nina Buchmann)

Other former biomet alumni at the meeting included Rodrigo Vargas, Naama Raz-Yaseef, Jessica Osuna, Lianhong Gu, Liukang Xu, Jianwu Tang, Matthias Falk, and Josh Fisher.

Jacyln Hatala interviewed at the University of Michigan and presented a seminar on her greenhouse gas research.

Jaclyn Hatala and Sara Knox represented the Biomet Lab at the Freedom High
School (Oakley) Science day. They demonstrated methane measurements to the students

DDB attended the February DOE BERAC meeting in Washington, DC


Reichstein, M., Baldocchi, D. Jung, M., Kattge, J., Musavi, T. 2013. Integrating plant and ecosystem functional biogeography within a data driven Earth System Science approach. Proceedings of the National Academy of Science. submitted

Peichl, M, Sonnentag, O., Wohlfahrt, G., Flanagan, L.B., Baldocchi, D.D., Kiely, G., Galvagno, M., Gianelle, D., Marcolla, B., Pio, C., Migliavacca, M., Jones, M.B. Saunders, M. Convergence of potential net ecosystem production among contrasting C3 grassland. Ecology Letters. doi: 10.1111/ele.12075.

Raz-Yaseef, N., Koteen, L., Baldocchi, D.D., 2013. Coarse root distribution of a semi-arid oak savanna estimated with ground penetrating radar. Journal of Geophysical Research: Biogeosciences, DOI: 10.1029/2012JG002160.

Staff News

Tom Shapland from UC Davis is resident in the lab.


Matteo Detto from Smithsonian visited and give a presentation on this spatial analysis of biodiversity of tropical trees in Panama

Josep Penuelas is visiting from Barcelona between Feb 12 and 26.

Susan Ustin from UC Davis visited to discuss upcoming collaborative research

Mark Friedl from Boston University visited and gave a presentation on his phenology research using LANDSAT and MODIS


ddb attended the Editors-in Chief meeting for the American Geophysical Union in Coral Gables, FL, Jan 29-30.


Koteen, L. and Baldocchi, D.D. A randomization method for efficiently and accurately processing fine roots, and separating them from debris, in the laboratory. Plant and Soil. 363:383–398.

Vargas, Rodrigo, Sonnentag, Oliver, Abramowitz, Gab, Carrara, Arnaud, Chen, Jing, Ciais, Philippe, Correia, Alexandra, Keenan, Trevor, Kobayashi, Hideki, Ourcival, Jean-Marc, Papale, Dario, Pearson, David, Pereira, Joao Santos, Piao, Shilong, Rambal, Serge, Baldocchi, Dennis. 2013. How drought conditions influence simulated ecosystem fluxes: a model-data meta-analysis. Ecosystems. accepted.

Raz-Yaseef, N., Koteen, L., Verfaillie, J., Baldocchi, D. Root system structure of a water limited oak savanna estimated with a ground penetrating radar. Journal of Geophysical Research, Biogeosciences. In press

  This material is based upon work supported by the National Science Foundation and US Department of Energy. Any opinions, findings, conclusions, or recommendations expressed in the material are those of the author(s) and do not necessarily reflect the views of the supporters.