"For every fish in the lagoon, there are a billion microbes. Bacteria and archaea do the real biogeochemistry — they cycle the nitrogen, decompose the muck, and even make the oxygen crashes. The lagoon is, mostly, a microbial system."
The Unseen Majority: Microbes Run the Lagoon
Microbes — bacteria, archaea, and microbial eukaryotes — are the most abundant and metabolically diverse organisms in the estuary, and they drive nearly every biogeochemical process. Nitrification, denitrification, sulfate reduction, organic matter decomposition, and much of primary production (cyanobacteria) are microbial. Despite this, traditional monitoring measures the chemical products (nutrients, oxygen) but not the microbial communities that produce them. Environmental sequencing changed this: we can now characterize the microbiome — who is present and what they can do — directly from water and sediment samples. Understanding the lagoon's microbiome connects the chemistry we measure to the biology that creates it, reveals the early warning signs of dysfunction (e.g., a shift toward sulfide-producing or pathogenic communities), and opens the door to microbiome-informed restoration. The unseen majority is no longer unseen.
