With the help of a really long stick or pole. Attach the jar to one end and then slowly scoop up a bit of sediment.
https://en.wikipedia.org/wiki/Plankton_net
They are special nets designed to catch microorganisms. Slowly move it through the water for a while (if you’re too fast, you’re just pushing the water and nothing will get in) and the microorganisms start accumulating in the small collection jar at the tip of the net. I saw one on amazon, but idk how good it is. They’re not very cheap unfortunately, but not super expensive either.