Remote Sensing of Salt Marshes in California The Influence of  Tidal Channels on the Distribution of Salt Marsh Plant Species in Petaluma March, CA, USA Tidal channels influence the distribution and composition of salt marsh vegetation in a San Francisco Bay salt marsh. Two channel networks in the Petaluma Marsh, Sonoma County, CA, were mapped and characterized using global positioning and geographic information systems. Plant species abundance was sampled on transects placed perpendicular to and extending away from the channel banks. The vegetation showed significant increases in species richness along channel banks and larger areas of effect which increased approximately linearly with channel size. Composition of species assemblages varies with distance from the channel bank and channel size. These results demonstrate that salt marsh plant assemblages, comprised of both major and minor species, are distributed with respect to the channel network in Petaluma Marsh. Sanderson, W.E., S.L. Ustin, and T.C . Foin, 2000, The Influence of Tidal Channels on the Distribution of Salt Marsh Plant Species in Petaluma Marsh, CA, USA, Plant Ecology 146(1):29-41.   Geostatistical Scaling of Canopy Water Content in a California Salt Marsh Remote sensing data are typically collected at a scale which is larger in both grain and extent than traditional ecological measurements. To compare with remotely sensed data on a one-to-one basis, field measurements frequently must be rescaled to match the grain of image data. Once a one-to-one correspondence is established, it may be possible to extrapolate site based relationships over a wider extent. This paper presents a methodology for rescaling the grain of ecological field data to match the grain of remotely sensed data and gives an example of the method in verification of remote sensing estimates of canopy water content in a tidal salt marsh. We measured canopy water content at 169 points on a semi-regular grid in the Petaluma Marsh, CA. A variogram describing the spatial correlation structure of the canopy water content was calculated and modeled. Ordinary kriging estimates of the canopy water content were calculated over blocks corresponding to image pixels acquired by the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS). A water content index was determined from the reflectance data by calculating the area of a water absorption feature at 970 nm. A regression developed between the blocks and the pixels at the site was extrapolated over the image to obtain an estimate of canopy water content for the entire marsh. The patterns of canopy water content at the site and landscape levels suggest that different processes are important for determining patterns of canopy water content at different spatial extents. The errors involved in the rescaling procedures and the remote sensing interpretation are discussed.  Sanderson, E.W., M. Zhang, S.L. Ustin, and E. Rejmankova.  (1997), Geostatistical scaling of canopy water content in a California salt marsh.  Landscape Ecology 13:79-92. Monitoring Pacific Coast Salt Marshes using Remote Sensing The rapid decline in the extent and health of coastal salt marshes has created a need for non-destructive methods for evaluating the condition of salt marsh ecosystems. This paper describes simultaneous uses of field sampling and remote sensing approaches to understand salt marsh ecosystem functions and species distributions and discusses the implications for salt marsh monitoring using remote sensing. Three sites along the Petaluma River near the entrance into San Pablo Bay, California, that represented a range of soil salinity, water content, and nutrients were studied.  Standing biomass was directly assessed by field sampling and indirectly estimated through canopy reflectance.  The sites were dominated by almost monotypic stands of Salicornia virginica, Spartina foliosa and Scirpus robustus.  Results indicate that both biomass production and canopy water content can be accurately determined from remotely sensed spectral measures.  Species specific differences in these characteristics may be used for monitoring species distribution and abundance from airborne or satellite images.  Zhang, M.,  S.L. Ustin, E. Rejmankova, and E.W.  Sanderson. (1996) Monitoring Pacific Coast Salt Marshes using Remote Sensing. Ecological Applications 7(3):1039-1053 Differentiating salt marsh species using foreground/background analysis Three of the dominant California salt marsh plant species, Salicornia virginica, Spartina foliosa and Scirpus robustus, have distinctive canopy architectures and leaf morphologies resulting in characteristic canopy reflectance signatures in the visible and near infrared regions. This paper presents a method to differentiate wetland species using a modified spectral mixture analysis termed hierarchical foreground and background analysis (HFBA) based on our analysis of salt marsh vegetation in the Petaluma River watershed, CA. Foreground and background analysis allows the user to direct the analysis along a specified axis of variance by identifying vectors through the n-dimensional spectral volume. The goal of FBA is to project spectral variation along the most relevant axis of variance that maximizes spectral differences between groups, while minimizing spectral variation within each group. For this work, we selected a training set of field-acquired spectra that allowed us to create HFBA vectors which efficiently discriminate species based on canopy spectral characteristics. The results indicated that the dominant species in these salt marshes could be clearly differentiated with greater than 90% certainty, from field collected canopy spectrometer data. Ninety nine percent of Spartina and 79% of Salicornia were correctly classified at the first level of classification. The accuracy of classification for Salicornia improved to 87% in the second level of classification. The unclassified spectral samples were related to extraordinary conditions within the wetlands such as extreme biomass, salinity and nitrogen conditions. The vectors derived from the field-acquired spectra were applied to pixel spectra acquired by the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) flown over the field sites in 1994. Classified patterns in the image showed distinct zonation corresponding to the distributions of these species in the marsh. The analysis of AVIRIS images were confirmed by field reconnaissance. Zhang, M., J.E. Pinzon, S.L. Ustin, and E. Rejmankova.  (1996) Differentiating salt marsh species using foreground/background analysis.  in ERIM  2nd Ann. Airborne Remote Sensing Conference.  June 24-28, 1996, San Francisco, CA. I: 83-92. Validating spatial structure in canopy water content using geostatistics Heterogeneity in ecological phenomena are scale dependent and affect the hierarchical structure of image data (cf. Levin, 1992).  AVIRIS pixels average reflectance produced by complex absorption and scattering interactions between biogeochemical composition, canopy architecture, view and illumination angles, species distributions, and plant cover as well as other factors.  These scales affect validation of pixel reflectance, typically performed by relating pixel spectra to ground measurements acquired at scales of 1m2 or less (e.g., field spectra, foliage and soil samples, etc.).  As image analysis becomes more sophisticated, such as those for detection of canopy chemistry, better validation becomes a critical problem.  This paper presents a methodology for bridging between point measurements and pixels using geostatistics.  The overall goal of our AVIRIS project is to develop strategies for monitoring salt marsh conditions (species distributions, biomass, leaf area, water content, etc.) and identifying spectral signatures that can be used as diagnostic indicators of wetland functioning (chlorophyll, nitrogen, carbon, evapotranspiration and photosynthetic rates, etc.).  The study site is located along the northern shore of San Pablo Bay, CA (northern extension of San Francisco Bay) and includes the Petaluma and Napa estuaries and the Mare Island Naval Base.  These systems experience large naturally occurring spatial and temporal gradients in salinity, nitrogen, redox potential and are subject ot regional pollution and point sources of soil and groundwater contamination (toxics, heavy metals, and others).  Mare Island, schedules for decommissioning and transfer to the University of California, Davis, has multiple contaminated sites. Sanderson, E.W., M.H. Zhang, S.L. Ustin, E. Rejmankova, and R.S. Haxo. (1995) Validating spatial structure in canopy water content using geostatistics.  In Summaries of the Fifth Annual JPL Airborne Earth Science Workshop.  Jet Propulsion Laboratory, Pasadena, CA.  January 23-26, 1995. Vol. 95-1, p. 141-144. Effects of Salinity on Growth and Photosynthesis of Three California Tidal Marsh Species The comparative responses of photosynthesis and growth to salinity were investigated for two C3 and one C4 species native to the tidal marshes of the San Francisco Bay-Sacramento River estuary of Northern California. At low salinities (0 or 150 meq 1-1), where photosynthetic rates were maximal for all species, the C4 grass Spartina foliosa maintained the highest photosynthetic capacity and the C3 stem-succulent shrub Salicornia virginica the lowest; photosynthetic rates of the C3 sedge Scirpus robustus were intermediate. Differences in photosynthetic responses to intercellular CO2 pressure and temperature were consistent with those generally observed between C3 and C4 plants. Pearcy, R., and S.L. Ustin. (1984) Effects of Salinity on Growth and Photosynthesis of Three California Tidal Marsh Species. Oecologia 62(1): 68-73.