Over 30 years ago, it was learned that the so-called microbial loop in marine planktonic ecosystems is responsible for processing about half of the primary productivity. Since then, a series of discoveries have shown with increasing detail the processes that make up this loop and the organisms involved. Viruses went from being completely unknown and ignored to now known as the most abundant biological entities, with many ecological, biogeochemical, and evolutionary impacts. Results from cloning and sequencing 16S rRNA yielded the totally unexpected result that mesophilic archaea, previously unknown, are remarkably abundant in seawater, with metagenomics and then cultivation showing many are ammonia-oxidizing chemoautotrophs. Patterns in the distribution of microbes is now studied by high-throughput molecular methods. At our 13-year San Pedro Ocean Time Series, we have found repeating seasonal patterns in community composition near the sea surface, though much less in water slightly deeper at the chlorophyll-maximum depth. We developed tools to show Microbial Association Networks, and these are showing many potential interactions among bacteria, archaea, protists, and viruses, with interesting patterns like contrasting network connectivity in bacteria-protist vs bacteria-virus networks.