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Jul

2019

Remote sensing of terrestrial vegetation

By Leslie Willoughby

High Sierra near Mammoth Lakes, CA shows vegetated and nonvegetated surfaces.

A novel approach developed by the Berry Lab is opening a new window for remote sensing of terrestrial vegetation on incompletely vegetated surfaces across the planet. For decades scientists have been ...

Feb

2019

Predicting how forests in the western United States will respond to changing climate

By Carnegie HQ

Washington, DC— On the mountain slopes of the western United States, climate can play a major role in determining which tree communities will thrive in the harshest conditions, according to new work ...

Lab PI

Joe Berry

Acting Director & Senior Staff Scientist

Global Ecology

Carnegie Institution for Science

jberry@carnegiescience.edu
650-799-2678
Office:
260 Panama Street
Stanford, CA 94305, US

Profile

Bio

Joe Berry’s work is focused on photosynthesis and associated processes (exchange of gases, fluorescence, remote sensing, ecophysiology) at a hierarchy of scales from the chloroplasts to the planet. His goal is to distill this information into equations that can be used in models to represent these processes in the complex webs of interacting processes that comprise the Biosphere of planet Earth. The focus is on understanding and representing the fundamental mechanisms so that our models give the right behavior and also help us understand why. Dr. Berry had been a faculty member at the Carnegie Institution since 1972 and is a member by Courtesy of the Department of Biological Sciences at Stanford. He obtained his Ph.D. in 1970 at the University of British Columbia in Botany. He obtained a B.Sc. in Chemistry and a M.Sc. in Soil Science from the University of California at Davis. He is a Fellow of the American Geophysical Union and a member of the National Academy of Sciences.

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Berry Lab

Joseph A. Berry
Carnegie Instition for Science, Dept of Global Ecology

Current Position
Acting Director

Research Area: Plant Eco-physiology, Geochemistry, Biospheric Sciences

Education
Ph.D. Botany Univ of British Columbia, 1970
MSc. Soil Science, UC Davis, 1964
BSc. Chemistry, UC Davis, 1963

Relevant Experience
1970 -- 1972 Post Doctoral Fellow, Carnegie Institiution of Washington
1972 -- 2016 Staff Scientist, Carnegie Institution of Washington and
Professor (by courtesy) Dept. of Bio. Sci., Stanford University

Professional History
My interest is in understanding biological processes at the organismal, global and regional scales. The physiological parameterizations for gross primary production, respiration and stomatal conductance used in many land surface and carbon cycle models are based on equations originally developed and tested in my laboratory My publication record can be examined at: http://scholar.google.com/citations?user=JMHXmgwAAAAJ&hl=en

Honors and Awards
Fellow: American Geophysical Union
Member: National Academy of Sciences (USA)

Related Publications:

Berry, J., & Raison, J. (1981). Responses of macrophytes to temperature. In O. Lange, P. Nobel, C. Osmond, & H. Ziegler (Eds.), Encyclopedia of Plant Physiology (pp. 278–338). Encyclopedia of plant physiology.

Berry, J., & Bjorkman, O. (1980). Photosynthetic response and adaptation to temperature in higher plants. Annual Review of Plant Physiology, 31(1), 491–543.

Schreiber, U., & Berry, J. A. (1977). Heat-induced changes of chlorophyll fluorescence in intact leaves correlated with damage of the photosynthetic apparatus. Planta, 136(3), 233–238. http://doi.org/10.1007/BF00385990.

Berry, J. A. (1975). Adaptation of photosynthetic processes to stress. Science,, 188(4188), 644–650.

Farquhar, G. D., S. V. Caemmerer, et al. (1980). "A Biochemical-Model of Photosynthetic CO2 Assimilation in Leaves of C-3 Species." Planta 149(1): 78-90.

Ball, T. J., I. E. Woodrow, et al. (1987). A model predicting stomatal conductance and its contribution to the control of photosynthesis under different environmental conditions. Progress in Photosynthesis Research, Vol. III. e. Biggins. The Netherlands, Martinus Nijhoff: 221-224.

Weis, E., and Berry, J. (1987). Quantum efficiency of Photosystem II in relation to “energy-”dependent quenching of chlorophyll fluorescence. Biochimica et Biophysica Acta (BBA)-Bioenergetics, 894(2), 198–208.

Collatz, CJ, JT Ball, C Grivet and JA Berry 1991. Physiological and environmental regulation of stomatal conductance, photosynthesis and transpiration: A model that includes the boundary layer. Ag. and Forest Meteorol., 54:107-136.

Collatz, G. J., Ribas-Carbo, M., & Berry, J. A. (1992). Coupled photosynthesis-stomatal conductance model for leaves of C4 plants. Australian Journal of Plant Physiology, 19(5), 519–538.

Berry, J., Wolf, A., Campbell, J. E., Baker, I., Blake, N., Blake, D., et al. (2013). A coupled model of the global cycles of carbonyl sulfide and CO 2: A possible new window on the carbon cycle. Journal of Geophysical Research-Biogeosciences, n/a–n/a. http://doi.org/10.1002/jgrg.20068.

Van der Tol, C., Berry, J. A., Campbell, P. K. E., Campbell, P., & Rascher, U. (2014). Models of fluorescence and photosynthesis for interpreting measurements of solar‐induced chlorophyll fluorescence. Journal of Geophysical Research-Biogeosciences, 119(12), 2312–2327. http://doi.org/10.1002/2014JG002713.

Maseyk, K., Berry, J. A., Billesbach, D., Campbell, J. E., Torn, M. S., Zahniser, M., & Seibt, U. (2014). Sources and sinks of carbonyl sulfide in an agricultural field in the Southern Great Plains. Proceedings of the National Academy of Sciences. http://doi.org/10.1073/pnas.1319132111.

Guanter, L., Zhang, Y., Jung, M., Joiner, J., Voigt, M., Berry, J. A., et al. (2014). Global and time-resolved monitoring of crop photosynthesis with chlorophyll fluorescence. Proceedings of the National Academy of Sciences of the United States of America, 111(14), E1327–E1333. http://doi.org/10.1073/pnas.1320008111

Schlau-Cohen, G. S., & Berry, J. (2015). Photosynthetic fluorescence, from molecule to planet. Physics Today, 68(9), 66–67. http://doi.org/10.1063/PT.3.2924

Guan, K., Berry, J. A., Zhang, Y., Joiner, J., Guanter, L., Badgley, G., & Lobell, D. B. (2015). Improving the monitoring of crop productivity using spaceborne solar-induced fluorescence. Global Change Biology, 132-136. http://doi.org/10.1111/gcb.13136

Badgley, G., Field, C. B., & Berry, J. A. (2017). Canopy near-infrared reflectance and terrestrial photosynthesis. Science Advances, 3(3), e1602244. http://doi.org/10.1126/sciadv.1602244
Joseph A. Berry
Carnegie Instition for Science, Dept of Global Ecology

Current Position
Acting Director

Research Area: Plant Eco-physiology, Geochemistry, Biospheric Sciences

Education
Ph.D. Botany Univ of British Columbia, 1970
MSc. Soil Science, UC Davis, 1964
BSc. Chemistry, UC Davis, 1963

Honors and Awards
Fellow: American Geophysical Union
Member: National Academy of Sciences (USA)

Related Publications:

Berry, J., & Bjorkman, O. (1980). Photosynthetic response and adaptation to temperature in higher plants. Annual Review of Plant Physiology, 31(1), 491–543.

Berry, J. A. (1975). Adaptation of photosynthetic processes to stress. Science,, 188(4188), 644–650.

Farquhar, G. D., S. V. Caemmerer, et al. (1980). "A Biochemical-Model of Photosynthetic CO2 Assimilation in Leaves of C-3 Species." Planta 149(1): 78-90.

Collatz, G. J., Ribas-Carbo, M., & Berry, J. A. (1992). Coupled photosynthesis-stomatal conductance model for leaves of C4 plants. Australian Journal of Plant Physiology, 19(5), 519–538.

Schlau-Cohen, G. S., & Berry, J. (2015). Photosynthetic fluorescence, from molecule to planet. Physics Today, 68(9), 66–67. http://doi.org/10.1063/PT.3.2924

Badgley, G., Field, C. B., & Berry, J. A. (2017). Canopy near-infrared reflectance and terrestrial photosynthesis. Science Advances, 3(3), e1602244. http://doi.org/10.1126/sciadv.1602244

Schedule

Scientific Interests

Atmosphere

Biogeochemistry

Biosphere

Carbon dioxide

Remote sensing

Photosynthesis

Websites

Publications

Google Scholar

People

Lee Anderegg (Visiting Investigator)
Leander studies the biogeographic, demographic and biogeochemical implications of tree responses to climate change. He combines methods from community ecology, dendrochronology, plant ecophysiology, and stable isotope biogeochemistry to understand the sensitivity of forests in the western U.S.A. and Australia to various global change drivers.

A Colorado native, Leander received a PhD in Biology from the University of Washington in 2017 (working with Janneke Hille Ris Lambers), and started an NSF and NOAA-funded Postdoctoral Fellowship with Joe Berry (Carnegie Institution for Science, Dept. of Global Ecology) and Todd Dawson (UC Berkeley) in Aug. 2017.

Leander's research focuses on four themes:
1. Predicting plant and ecosystem responses to rising CO2. Human CO2 emissions have shifted the global water-carbon market place in plants favor, yet the observed ‘CO2 fertilization’ effect has proven extremely variable. Using historical plant specimens, modern comparison samples, and mechanistic physiological models, Leander is reconstructing how plants altered their physiology, morphology and growth in response to a century of rising CO2. The goal of this work is to understand how environmental context (e.g. amount of water stress) and plant traits (e.g. water use strategies) determine plant responses to CO2.
2. Determining where tree ranges are limited by climate vs. biotic interactions. This distinction is critical for anticipating range shifts, and Leander uses a variety of methods, particularly dendrochronology, to differentiate the drivers of tree range boundaries.
3. Exploring intraspecific trait variation in stress tolerance traits. Functional traits are a critical ecological tool, yet we know surprisingly little about trait variation within individual species. Leander uses geographic trait variation within species to explore the mechanisms that constraint species distributions as well as the physiological and evolutionary trade-offs that drive the integration of multiple traits into a whole organism.
4. Understanding climate-induced forest mortality and the ecological impacts of extreme drought. Leander studies the ecohydrology and ecophysiology behind climate-induced tree die-off, as well as the consequences of canopy tree mortality for plant communities.
Min Chen (Visiting Scholar)
Jennifer Johnson (Research Associate)
Jen Johnson is a Research Associate in the Department of Global Ecology at the Carnegie Institution for Science. Her research focuses on understanding the processes that control the exchange of energy, water, and carbon dioxide between the terrestrial biosphere and the atmosphere. She is currently developing new strategies for measuring trace gas concentrations and isotope ratios in complex environmental samples, and for modeling photosynthetic gas exchange and fluorescence at leaf to global scales.
Ari Kornfeld (Software Maintenance Assistant)
Ari Kornfeld, a member of the Berry Lab, works at the intersection of plant physiological ecology, instrumentation, and software design. His current research focuses primarily on optical remote sensing of photosynthesis through the measurement and analysis of solar-induced chlorophyll fluorescence.
Karine Prado (Postdoctoral Fellow)
Karine Prado studied Biology Science at the University of Montpellier 2 (France) where she obtained an MRes in Plant Functional Biology then a prestigious doctoral fellowship from INRA in 2010 (Contrat Jeune Scientifique). Prado's Ph.D. was carried out at INRA of Montpellier under the supervision of Dr Christophe Maurel and was aimed to determine the molecular and cellular mechanisms controlling the hydraulic properties of the Arabidopsis thaliana rosette, focusing on the role of water channel proteins in response to environmental stresses.
She pursued her CJS contract coupled to an AgreenSkills Fellowship (Marie-Curie FP7 Cofund People programme) in joining the lab of Professor Andrew Millar at the University of Edinburgh (UK) as a postdoctoral research associate. She studied the contribution of non-transcriptional mechanisms to biological timekeeping of the pico-alga Ostreococcus tauri that has become a new relevant model for plant Systems Biology then she studied how light and thermo-sensitive phytochrome photoreceptors regulate chloroplast RNA processing and photosynthesis in the lab of Professor Karen Halliday.
Now she studies mechanisms of thermoadaptation of a desert extremophile C4 plant at the Carnegie Institution for Science under the supervision of Dr. Joe Berry and Dr. Sue Rhee. This project is promising not only in term of translation of fundamental research into biotechnology applications for crop improvement and food security, but also to address relevant challenges faced by developing countries in response to worldwide climate changes.
Mary Whelan (Visiting Investigator)
The goal of my work is to use innovative tools to quantify important fluxes in the carbon cycle that we cannot measure directly. To do this, I combine soil science, atmospheric chemistry, and a little bit of plant physiology. My most promising tracer at the moment is a gas called carbonyl sulfide. It looks very similar to carbon dioxide and can interact with the same enzymes in plant leaves. By understanding the exchange of carbonyl sulfide with components of ecosystems (e.g. plants and soils), we can estimate photosynthetic carbon uptake by measuring the drawdown of carbonyl sulfide over ecosystems. I wrote an introduction to the many uses of carbonyl sulfide observations at cosanova.org. My latest paper on this subject came out recently in Biogeosciences: https://www.biogeosciences-discuss.net/bg-2017-427/.
Yelu Zeng (Postdoctoral Fellow)
Since July 2017, I have been as a postdoctoral research fellow in Joe Berry lab working on the radiative transfer of solar induced fluorescence from leaf to canopy scale. My research mainly focuses on the 3D radiative transfer modeling in canopies of natural and agricultural ecosystems. I'm also interested in the extraction of vegetation biophysical parameters (e.g., leaf area index ), the validation of remotely sensed LAI products, spatial sampling for up-scaling over heterogeneous land surfaces, and vegetation phenology.

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Acting Director & Senior Staff Scientist

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