Since 2003, the J. Craig Venter Institute has conducted a study of marine microbial communities using shotgun sequencing.  Samples have been collect from every ocean, several major inland seas, lakes, and the Amazon River. I will present two studies emerging from this dataset.  The first examines the results of a collaborative survey with the Scripps Institution of Oceangraphy in the eastern subtropical Pacific.  Here, metagenomics and metatranscriptomics were used to examine marine microbes across gradients in light and primary productivity.  The results highlight a discordance between genomic abundance and transcriptional activity, and suggests that relatively rare, but fast growing bacteria contribute disproportionately to biogeochemical processes.  The results also suggest that a previously overlooked  class of algae, the Pelagophyceae, contribute disproportionately to nitrate reduction.  Second, I will present  a  metagenomic assembly generated from 227 surface ocean metagenome.  This assembly, 3Gbp in total including over 9000 contigs greater than 30kbp in length, provides core and pan genomes for roughly 85% of the taxa found in the ocean, the vast majority of which are still uncultivated.  Multivariate analyses identify the environmental variables, specifically temperature and chlorophyll a, that drive differentiation within these uncultivated lineages and between communities.  Finally, select metabolic insights into what was previously biological dark matter will be presented.