Visitors since

Research Projects

1. Quantifying and Understanding Interannual Variability of Carbon, Water and Energy Exchange of an Oak Savanna and an Annual Grassland Ecosystem AmeriFlux Site

 D. Baldocchi, PI, John Battles, co-I, USDOE, Terrestrial Carbon Project, Sept 15, 2009-Sept 14, 2013

Project Summary

To develop a mechanistic understanding on the biophysical controls on ecosystem carbon budget and to develop the next generation of coupled climate-carbon cycle models, we need to understand how trends and inter-annual variations in climate affect carbon and water exchange between terrestrial ecosystems and the atmosphere on a decadal time scale. We propose a study that will investigate and quantify the dynamics of net carbon dioxide exchange between the biosphere and atmosphere, which are triggered by such critical features as switches, pulses, lags, and acclimation. The study will be conducted over two ecosystems that are representative of the Mediterranean climate zone and are model systems for studying how ecosystems respond to environmental perturbations. One site is an oak savanna woodland and the other is an annual grassland. They are separated by 2 km, are exposed to identical weather. We will investigate the biotic and abiotic factors contributing to interannual variability in CO 2 exchange by extending a data set we are collecting to nine years. The interpretation of these data and their dynamics will involve a comprehensive suite of biophysical, ecophysiological and ecological measurements. Net canopy-atmosphere carbon fluxes will be measured with the eddy covariance method and these fluxes will be partitioned into their constituent components, canopy photosynthesis and ecosystem respiration. This will be accomplished by making overstory and understory eddy covariance measurements and by measuring soil respiration with a flux-gradient system, developed by this team. Interpretation of the temporal variations of these fluxes will be based on the CANOAK and MAESTRO models and measurements of meteorological conditions (solar radiation, wind, temperature, rain, humidity), soil microenvironment (CO 2, moisture and temperature), soil physical and chemical properties (bulk density, texture, hydraulic conductivity, C and N), plant functional (photosynthetic capacity, stomatal and mesophyll conductance, transpiration) and structural (canopy height, leaf area index, diameter of breast height and three dimensional crown tructure) characteristics. We will upscale the fluxes in space and time with remote sensing and regional weather data. Upscaling will be accomplished in the following manner. First, periodic measurements of high resolution spectral reflectance will be made with a spectral radiometer and continuous measurements of vegetation indices (NDVI and PRI) will be made with an LED spectrometer developed in our lab. Second, relationships between vegetation indices and carbon fluxes will be derived from the field observations. And third, we will apply these algorithms to vegetation indices obtained from MODIS and produce ecosystem-scale estimates of carbon assimilation. We will add a new component to our project that will compare long term eddy flux measurements against changes in stand biomass and soil carbon. These will be based on a sequence of LIDAR measurements and biometry field sampling.

Our research site meets the criteria to be designated as an AmeriFlux super-site. First, we are making measurements that represent components of a larger landscape and region that is an appreciable carbon sink. Second, we are ranked as a Tier 1 AmeriFlux site, based on the breadth of measurements, the type of instrumentation, compliance with calibration procedures, the regular submission, quality and documentation of data, and length of data record. And third, our site is in a climate zone and ecosystem that is among the most under represented in the AmeriFlux network, according to the bioclimate zone analysis of Hargrove (2003) .

2. Assessing Greenhouse Gas Budgets of Representative Land Use Classes in the Sacramento-San Joaquin River Delta

California Department of Water Resources

Project Summary

The Sacramento-San Joaquin Delta region is ¾ of a million acres in size and is a complex patchwork of wetlands and agricultural peatlands. Over the past 150 years, the Delta region has undergone considerable land use change.   The peat soil within the region formed during the Holocene epoch as sea levels slowly rose with the melting glaciers, creating an extensive network of wetlands at the confluence of the Sacramento and San Joaquin Rivers.   After the Gold Rush(circa 1849), much of this region was reclaimed and drained for agriculture by building a network of ‘islands’ surrounded by levees to maintain an artificially low water table.  The exposure of organic peat soil to air has caused extensive oxidation, resulting in extreme rates of soil subsidence.   Today, a combination of oxidation, erosion, and compaction has caused the surface of Delta ‘islands’ to subside up to 10 m below sea level.

From scientific, ecological, and societal viewpoints, the Sacramento-San Joaquin Delta is vulnerable to additional degradation and eventual collapse.  The continuing oxidation and subsidence of the Delta peatlands threatens long-term agricultural use of these lands by pushing the soil level further and further below sea-level.  Delta levees are especially vulnerable to breaching by a major earthquake, winter storms, high tides, natural seepage, invasion by burrowing animals and rising sea-level.    Any flooding of the Delta islands will cause an intrusion of salt water from the San Francisco Bay estuary, which will have a dire impact on over 20 million Californians, who rely on high quality water flowing through the Delta for irrigation, commerce and drinking. 

While the future of Delta is very uncertain and a subject to great debate, it is clear that current land use practices in the Delta are not sustainable.  Fortunately, ecological solutions to the problem of subsidence are possible.  High rates of carbon sequestration and net primary productivity are expected from marshes in the Sacramento-San Joaquin River Delta because the region experiences a long and warm growing season with ample sunlight and water.  On the other hand, high CH4 effluxesmay occur because the flooded landscape overlays carbon-rich and anaerobic soils.   

Efforts are underway to restore these drained peatlands to flooded ecosystems with the reintroduction of wetland vegetation and maintenance of a higher water table.  While pilot studies show that ecological restoration is successful in sequestering carbon and building peat soils, it also produces methane at enhanced rates.  Hence, baseline information on methane fluxes from drained peatlands is needed to advise how methane fluxes may change if peatland pastures and farmland are restored to native vegetation and wetlands.

A number of local and state governmental institutions (e.g. Department of Water Resources, California Climate Action Registry, California Air Resources Board) are interested in reducing, capturing or offsetting carbon emissions to meet the guidelines legislated by AB 32 to reduce the state’s 1990 carbon emissions by 80% by 2050.  One potential, but relatively unexplored option, is to restore or create wetlands, with the intent of sequestering carbon and building up the soils.  

At present, the amount of scientific information available to guide such restoration decisions and assess the impact of these actions is sparse.  Critical questions to guide proper environmental management include: 1) knowing how fast soils may rebuild?; 2) how management may accelerate carbon sequestration?; 3) what are the optimal ecological design criteria for reconstructed wetlands?; and 4) what may be the environmental trade-offs of such land conversion?.  Once the wetlands are established, research is needed to ask and answer such the critical questions as:

Under current agricultural practices, what are the net greenhouse trace gas (methane, carbon dioxide, water vapor) fluxes to and from drained Delta peatlands?

How will changes in land-use, by restoring native tule/cattail wetlands, alter carbon sequestration and methane production of the Delta peatlands, compared to current baseline conditions?

 How do fluxes of methane, carbon dioxide and water vapor vary and co-vary seasonally, annually and inter-annually over peatlands pastures, crops and wetlands?

What are the effects of weather, water table, salinity and vegetation function on net greenhouse gas fluxes, on short and long time scales?

How do greenhouse gas fluxes of newly created wetlands change with time as soil carbon pools build and the density of vegetation increases?

Can we upscale carbon dioxide and methane fluxes and produce greenhouse accounting protocols using proxies that will be of value to State Agencies for assessing carbon offsets and planning additional wetland restoration projects?

To address these questions, we propose installing and operating a small regional network of eddy covariance towers to measure a suite of greenhouse gas fluxes across a representative spectrum of land-use classes in the Delta.  To develop net greenhouse gas sequestration protocols, we propose conducting this suite of greenhouse gas flux measurements for a 5 year period as disturbed soils and vegetation reach a new equilibrium.


 The eddy covariance method is suitable for this task as it measures greenhouse gas fluxes directly and on a quasi-continuous basis.  Moreover, recent developments in commercially-available, affordable, and stable tunable diode laser spectrometers and open-path sensors allow investigators to establish sites off the power grid make flux measurements at locations that are scientifically interesting, as power-hungry pumps are not needed.     

3.Climate change Mitigation and Adaptation in Rice Production in California’s San Joaquin – Sacramento Delta

USDA/AFRI, co-I with Will Horwath, UC Davis

We propose measuring budgets of water, energy, carbon dioxide and methane over a rice paddy for 5 years, using the eddy covariance method on hourly, daily, seasonal and yearly time scales.     This project builds on our current expertise on measuring water, energy, carbon dioxide and methane fluxes over a peatland pasture on Sherman Island


The eddy covariance measurements, proposed here, will complement budget measurements that will be made with various techniques on this project, like chamber measurements of carbon dioxide and methane and water budgets of the paddies.  For example, the eddy covariance method has numerous attributes for measuring fluxes of trace gases between vegetation and the atmosphere (Baldocchi 2003).  The method measure fluxes directly, in situ and without artifacts.  It can be applied quasi-continuously and measures fluxes that integrate a flux footprint, consisting of hundreds of square meters and it has proved to be successful producing carbon and water budgets over years to decades.   Applying the eddy covariance method in this study gives us the ability to measure field scale trace gas fluxes, which are not possible with small manually-deployed chambers that are operated periodically.   On the other hand, the eddy covariance method is not adept at measuring greenhouse gas fluxes on small treatment plots, where chambers are superior.  But together, use of the eddy covariance and chamber methods, in tandem, give us unprecedented ability to measure trace gas fluxes across a spectrum of time and space and to deduce the climatic, microbial and agronomic factors that may modulate those fluxes.


An overarching goal of our work is to study and examine unanticipated consequences of using agriculture for climate mitigation.  It is a given that ‘business as usual’ cannot continue in the Delta.  Land has subsided by over 10 m since these Delta islands were drained over 100 years ago for intensive farming of grains.  Strong pressure heads on weak levees between the river and drains make these islands vulnerable to collapse.  Key and immediate actions include stemming continued subsidence and accreting carbon in the soil.  Cultivation of rice has the potential to succeed with the former, and specific management actions may lead us to succeed with the later goal too.

In reality, carbon sequestration and accretion is not the only climate related action that may accompany rice cultivation.   Rice cultivation has the potential to be a large user of water and it may stimulate the emission of highly effective greenhouse gases like methane.  Hence, through an integrated set of flux measurements of coupled greenhouse gases (CO2, water vapor, and methane), we aim to study how rice cultivation in the Delta affects greenhouse gas fluxes.

We have one year of data from a prior project  and aim to acquire a multi-year record of trace gas exchange to better understand how management decisions and climate alter the greenhouse gas fluxes of the site.    Our first year of measurements detected relatively small effluxes of methane compared to methane emissions studies on rice that has been cultivated for many years.  We hypothesize that the pool of carbon substrate, prior to rice cultivation, is small and may have contributed to low methane emissions.  One hypothesis is that methane emissions will increase gradually time as the soil C pool increases.  Another hypothesis is that rates of methane emission, during the growing season, scale with recent photosynthesis, which can exude carbohydrates in the rhizosphere and stimulate methane production

Another plausible hypothesis relates to aeration of the water column.  Pumps continuously recalculate water in the paddy and winds in the Delta tend to be robust.  Vigorous mixing of the water column may oxidize methane diffusing through the water column and reduce efflux losses

Other hypotheses relate to the management of the rice.  Cultivation only occurs through a relatively short window, between April and September.  The rest of the year the field is fallow, and how that fallow field is managed will further affect the greenhouse gas budget of the site.    Flooding of the field during the fall is common to attract wildlife, which assist in the incorporation of straw into the soil.  Flooding the field should reduce decomposition during the winter and cool temperature should reduce methane emissions.  The field is drained prior to cultivation and planting.  In the bare aerated state, the field can become a strong source of carbon dioxide.  We hypothesize that the relative duration of flood to drained states will have a major impact on the annual budgets of carbon dioxide, water and methane.

On multi-years, we intend to develop a database than can evaluate interannual variability of net carbon exchange and methane production.  We are developing an interesting catalogue of conditions. This past year the rice was planted late, so its effective growing season has been compressed.  Another year, weeds dominated the field after the winter flooding and spring-plowing and planting. This gave the system an opportunity for carbon uptake.  And a third year, mold-board plowing buried straw and recalcitrant carbon deep. How would this affect net carbon and methane fluxes?

The climate of the Delta is sunny and warm, with a long growing season.  The potential evaporation for the region is over 1400 mm per year.   Flooded rice loses water at the potential evaporation rate, so expanding rice cultivation into the Delta may lead to high evaporation from a region that is rain starved and where water is a precious and conflicted resource, among agricultural, urban, environmental and fishery stakeholders.   With our direct flux measurements we intend to answer how much water is evaporated from a rice cultivation system, and if there are cultivation practices that may assist in reducing the amount of water consumed by the crop.

Finally, as we develop a large database of methane and carbon dioxide fluxes from rice, we have started correspondence with colleagues in Italy (Cescatti), Brazil (Roberti) and Japan (Miyata) who have been making eddy covariance flux measurements of methane and carbon dioxide fluxes over rice. We intend to work together and produce a paper synthesizing results from different climates and cultural practices.

4. Fluxnet, A global network of carbon, water, and energy flux measurement sites.

D. Baldocchi, PI, co-Is, Beverly Law, Robert Cook, Niall Hanan, Alex Knohl, Ray Leuning, Hank Margolis, Yoshikazu Otahni, GuiRu Yu, Ricarrdo Valentini. ILEAPS Project.

Project Summary

FLUXNET is a new ILEAPS project that constitutes a global network of carbon dioxide, water vapor and energy flux measurement sites. In this global configuration it expands the diversity of biomes, climate regions, disturbance and land use treatment that are associated with its constituent regional networks. Specific aims of FLUXNET are to quantify spatial/temporal variations of the physical and biological processes controlling carbon dioxide, water vapor and energy exchange between terrestrial ecosystems and the atmosphere. As a global network, the project will be responsible for recruiting, sharing and exchanging of newly acquired and extant data among collaborators and with the scientific community, in associated fields like atmospheric chemistry, remote sensing, biogeography, ecohydrology, ecosystem ecology and biogeochemistry. The scientific team will collaborate with the FLUXNET Data Information System (DIS) at Oak Ridge National Lab, and provide scientific guidance and computational software to produce value-added data products, like gap-filled datasets and daily and annual integrated fluxes. We will also provide software and guidance to FLUXNET DIS to create new and expanded datasets that partition net ecosystem carbon fluxes into photosynthetic and respiratory components. The FLUXNET will serve its constituent community, scientifically, by catalyzing, leading and conducting network-scale data synthesis analyzes. Examples include: 1) assessing the biophysical factors causing interannual variability of net carbon dioxide exchange for a selection of major biomes and climate zones; 2) examining the roles of disturbance, climate and plant functional type on carbon and water fluxes; 3) examining the biophysical controls of carbon fluxes from the expanded cohort of FLUXNET sites; 4) performing geostatistical analyzes across a regional array of study sites to quantify scales of coherent spatial patterns in carbon, water and energy fluxes; and 5) quantifying micrometeorological and turbulence characteristics across a spectrum of canopy structure, land surface complexity and atmospheric stability. This project will serve the international community by convening international workshops, hosting visiting scientists, and supporting a project scientist. Finally, FLUXNET aims to be instrumental in training the next generation of biogeoscientists from developed and under-developed countries by hosting a young scientist forum.

Last Updated: 2013-08-26

    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.