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Our research aims to improve understanding of the mechanisms that underlie whole plant and ecosystem responses to global change, and to improve representation of these processes in Earth System Models. The computational and analytical techniques we use in the TEST group are focused on quantifying model sensitivity, and measuring and scaling key whole plant and ecosystem processes.

Plant Physiology

The TEST physiology lab is well equipped to measure leaf area using the LI-3100C, or flatbed scanners. In canopies we use the LI-2200C to measure LAI and for leaf level gas exchange we have five LI-6400XT systems with both the 6400-02B LED light source and 6400-40 Leaf Chamber Fluorometer.


Biochemistry

The analytical focus of the TEST biochemistry lab is understanding the interactions of photosynthesis and respiration with carbon and nitrogen metabolism that underlie many of the commonly observed long term responses of plants and ecosystems to global change. For sample shipping and storage we have cryogenic shippers and two -80°C freezers with emergency power back up and dial out alarms. For sample preparation we have two grinders capable of high throughput and cryogenic sample preparation. To keep track of our samples we have a barcode maker and scanner.

Our wet lab has all the usual equipment you’d expect to find including a pH meter, top pan balances, drying ovens, bench top centrifuges and a wide range of pipetting tools. To enable high throughput processing most of our analysis is done on a 96-well-plate format using our two liquid handling robots that are equipped with automated incubators, shakers and tip washers. Downstream of the robots we have four plate readers to measure the changes in absorbance and fluorescence associated with all our assays. We also have an HPLC system dedicated to measuring amino acids and CHN elemental analyzer.


Spectroscopy

All materials interact with light energy in different and characteristic ways. Spectroscopic remote sensing methods utilize spectroradiometers - which are sensitive to wavelengths between 300-2500 nm - to measure the intensity of light reflected from or transmitted through leaves and plant canopies. In regards to terrestrial ecosystems, the capacity to monitor plant traits with spectroscopic data is based on the physical principle that plant physiological properties, which are fundamentally tied to the biochemical composition (chemical bonds and energy state of constituents), structure and distribution of foliage within canopies, are reflected in the optical characteristics of leaves within a canopy that can be observed using remote-sensing instrumentation.

Within terrestrial ecosystem science, spectroscopic remote sensing methods offer the capacity to advance the fields of agriculture, forestry, plant physiology and ecology by enabling the rapid, accurate, and non-destructive estimation of key plant photosynthetic, biochemical, and morphological traits, as well as detect stress and overall plant health over broad spatial regions and efficiently through time. Traditional destructive or direct methods can be very labor intensive, time consuming, expensive, and often require harvesting of plant material for later analyses. Spectroscopic methods, on the other hand, can yield rapid insights into ecological functioning at a range of scales, from the leaf to the landscape, and can provide repeat monitoring of ecosystems without the need for additional in-situ measurements.

The TEST group at Brookhaven National Laboratory has developed a modern, high-end facility for collecting, processing, and analyzing spectral observations from the leaf to larger scales. Our spectroscopy lab maintains various spectroradiometers that measure wavelengths in the visible (400-700 nm), near-infrared (NIR, 700-1300 nm), and shortwave infrared (SWIR, 1300-2500 nm). These include a PP Systems UniSpec dual channel (simultaneous measurement of downwelling and upwelling radiation) spectroradiometer and a Spectra Vista HR-1024i full spectrum (i.e. 300-2500 nm) instrument. We also have a range of accessories needed for analyzing plant spectral optical properties from leaves to canopies, including leaf-clip and plant probes, dry spectral sampling, integrating sphere, multiple fore optics for measuring canopy spectra, tripods and other field equipment, precision lamps and mounting equipment for measuring spectra indoors or in glasshouses, as well as a range of calibration equipment and standards. We also maintain custom software packages for processing spectral observations as well as for scaling key plant traits. Together with our laboratory, biochemical, and physiological expertise we are exploring novel ways to link plant physiology and biochemistry to spectral observations to examine a range of ecological research questions, often involving other relevant measurements (e.g. thermal infrared measurements, LiDAR, leaf photosynthesis).


Computation

The fields of ecology, remote sensing, and plant physiology are becoming increasingly data rich and computationally demanding requiring new analytical, statistical, and data-mining approaches as well as computational infrastructures that can be leveraged in order to manage the vast amounts of information and complex linkages between data that allow for broad sweeping and integrative research questions. In addition, computational and terrestrial ecosystem modeling architectures are becoming increasingly complex requiring new bioinformatics tools and computational horsepower to manage the streams of data coming into and out of models. These new tools are needed for efficient model parameterization, benchmarking, and quantifying uncertainties in model projections (i.e. uncertainty quantification and variance decomposition), as well as to diagnose and synthesize the projections of ecosystem responses to global changes.

The TEST group maintains a high-end server infrastructure and database system for managing datasets from our experiments and close collaborators, developing high-performance model code and analysis tools, running software and remote sensing image processing tools, ecosystem modeling and uncertainty quantification (modex.bnl.gov). This site also maintains the BNL instance of the Predictive Ecosystem Analyzer (PEcAn, pecanproject.org) scientific workflow system for model uncertainty quantification and data assimilation.  In addition, we maintain a radiative transfer model (RTM) code farm for analyzing spectral data and test parameter retrieval techniques. We also hook into the Brookhaven Linux Cluster (BLC) when running jobs that require a large number of processing cores.