Abundance measurements with bright background light sources, such as quasars and GRBs, probe the large-scale distribution and physical state of evolving, coupled gas-star-dark matter structures in the Universe. Not all baryons inferred from BBN and the CMB are accounted for in the local Universe; a significant fraction resides in warm-hot tenuous gas filaments tracing the large-scale distribution of dark matter. Understanding the chemo-dynamics of these structures can be advanced with sensitive X-ray studies of emission from diffuse baryons in the warm-hot medium residing in clusters and the filamentary cosmic web, and in absorption with bright, distant sources, in particular GRBs. Supernovae and galaxies are bright enough to be traced to high redshifts, but the diffuse gas in their vicinity is not luminous enough to be detectable in emission at such distances. This diffuse component can be probed with absorption spectroscopy of bright background sources. GRBs, associated with massive stars, provide beacons that may trace star formation to the first generations. Their large brightness allows abundances to be measured in early, small proto-galaxies, and to trace them to the era of re-ionization, at z > 6.