Abstract
Microorganisms can have a profound and varying effect on the chemical character of environments and, thereby, ecological health. Their capacity to consume or transform contaminants leads to contrasting outcomes, such as the dissipation of nutrient pollution via denitrification, the breakdown of spilled oil, or eutrophication via primary producer overgrowth. Recovering the genomes of organisms directly from the environment is useful to gain insights into resource usage, interspecies collaborations (producers and consumers), and trait acquisition. Microbial data can also be considered alongside the broader biological character of an environment through the co-recovery of eukaryotic DNA. The contributions of individual microorganisms (bacteria, archaea, and protists) to snapshots of ecosystem processes can be determined by integrating genomics with functional methods. This combined approach enables a detailed understanding of how microbial communities drive biogeochemical cycles, and although currently limited by scale, key attributes can be effectively extrapolated with lower-resolution methods to determine wider ecological relevance.