...When you say, "filamentous algae sequesters nutrients," are the "nutrients" phytoplankton? Are phytoplankton required to produce zooplankton?
Some of the limiting factors for plant growth, such as phosphorous and nitrogen are taken up by the filamentous algae, which makes them unavailable for other plants, such as single cell algae (which give the water a greener tint). Phytoplankton are microscopic plants, most of which are too small to be seen with the unaided eye. They use these nutrients to complete their life processes, and in turn are utilized by many types of zooplankton for nourishment. Zooplankton are microscopic animals which are then in turn eaten by other zooplankton and small fishes.
Also, should the presence of that zooplankton in the jar tell me anything definitive about the bottom on the food chain?
Yes, it tells you that the bottom of the food chain is indeed present, and judging by the activity in your jar it appears that it is thriving. This is a great sign. Now you need to learn to manipulate the fish community so that it doesn't overharvest this valuable resource.
