San Francisco Bay has been contaminated historically by mercury from mine tailings as well as contemporary industrial sources. Native Spartina foliosa and non-native S. alterniflora-hybrid cordgrasses are dominant florae within the SF Bay estuary environment. Understanding mercury uptake and transformations in these plants will help to characterize the significance of their roles in mercury biogeochemical cycling in the estuarine environment. Methylated mercury can be biomagnified up the food web, resulting in levels in sport fish up to one million times greater than in surrounding waters and resulting in advisories to limit fish intake. Understanding the uptake and methylation of mercury in the plant rhizosphere can yield insight into ways to manage mercury contamination. The transmission x-ray microscope on beamline 6-2 at the Stanford Synchrotron Radiation Lightsource (SSRL) was used to obtain absorption contrast images and 3D tomography of Spartina foliosa roots that were exposed to 1 ppm Hg (as HgCl2) hydroponically for one week. Absorption contrast images of micron-sized roots from S. foliosa revealed dark particles, and dark channels within the root, due to Hg absorption. 3D tomography showed that the particles are on the root surface, and slices from the tomographic reconstruction revealed that the particles are hollow, consistent with microorganisms with a thin layer of Hg on the surface. Hg L3 XANES of ground-up plant roots and Hg L3 micro-XANES from microprobe analysis of micron-sized roots (60–120 microns in size) revealed three main types of speciation in both Spartina species: Hg-S ligation in a form similar to Hg(II) cysteine, Hg-S bonding as in cinnabar and metacinnabar, and methylmercury-carboxyl bonding in a form similar to methylmercury acetate. These results are interpreted within the context of obtaining a “snapshot” of mercury methylation in progress.

The old saying that seeing is believing has particular resonance for studying biological cells and tissues. Since 1677, when Anton van Leeuwenhoek used a simple light microscope to discover single cell organisms, scientists have relied on structural information obtained from microscopes with improving capabilities to advance the understanding of how biological systems work. Optical and electron microscopes are essential for many of these important discoveries and have been widely employed in biomedical research laboratories. However, various limitations exist in these microscopy techniques. We describe below how the new xray imaging facility at the Stanford Synchrotron Radiation Laboratory (SSRL), based on an Xradia nano-XCT full-field transmission x-ray microscope (TXM), can provide complementary and unique capabilities to the current microscopy methods for studying complex biological systems.The TXM, developed at the 54 pole wiggler beam line 6-2 (BL6-2) at SSRL, is based on zone plate optics using absorption contrast over a wide energy range from 5-14 keV and Zernike phase contrast at 8 keV [1]. The instrument offers complementary capabilities to many imaging tools that are widely deployed in biomedical research. For example, the capability of high NIH Public Access NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscript resolution imaging of thick biological specimens is of importance to the study of complex biological systems because the biology of higher living organisms relies on the cooperation of cells. This is evident in the study of development and differentiation and of intra-cellular communication, not only through synapses, but also via the interplay of cells organized into organs and the development of cancer. Even bacterial plaques, so resistant to medical intervention, involve cooperation on the multi-cell level. While these systems are routinely studied by visible light and electron microscopy, visible light microscopy is limited in resolution, and electron microscopy inevitably requires sectioning, thereby losing a great deal of information on the three dimensional architecture. The high-resolution "virtual sectioning" capability of this instrument enables imaging at 40 nm resolution of any number of pre-selected regions within a visible light microscope specimen or even a cylindrical specimen such as obtained with a needle biopsy.Overall, the instrument offers several unique and complementary capabilities that are expected to have a significant impact for biologists studying complex biological structures. These include:• High resolution of 40 nm (or better with newer zone plates)• Imaging of tissues without cross sectioning• High penetration (~1-20 μm) for nondestructive imaging of relatively thick biological specimens• High quality images using single exposure times of 0.5 seconds• Rich contrast mechanisms (Zernike phase contrast at 8 keV, and soon at 5 keV) for imaging biological and marker materials• Absorption contrast in the 5-14 keV range, and X-ray absorption near ed...