Metagenomics, broadly speaking, is the study of pooled genetic material taken directly from environmental samples. This allows for the simultaneous characterization of a community of organisms present in a sample and can provide inference as to their metabolic capabilities as well. The current range of methods used for metagenomic analysis includes: clone library creation; DNA or RNA microarrays, such as the Phylochip or Geochip, which include probes for most previously known genetic information; and whole environmental sequencing of either entire genomes or certain subsets, such as functional genes or conserved 16S regions through high-throughput techniques such as 454 pyrosequencing. This session aims to bring together researchers using the methods described above to study the microbiomes (including one or all of bacteria, archaea and fungi) of all types of systems, and to provide a synthesis of how ecologists are using these tools to increase their understanding of the structure and functioning of ecosystems. Confirmed speakers will present research on techniques including GeoChip, PhyloChip, barcoded pyrosequencing, clone library construction and shotgun sequencing to study systems ranging from the human microbiome to hot springs and the soil under our feet. The scale of observation in these systems varies between thousands of kilometers in an open landscape to millimeters in the human mouth. Using these innovative technologies, the research presented in this session furthers our understanding about the ecological interactions between organisms, between organisms and their environment, and about the intersection of biodiversity and ecosystem function on multiple scales and in vastly different ecosystems.