Planktonic "bloom" and bust

Everyone setting up an aquarium is familiar with the "cloudy water" syndrome, where the water takes on a whitish opalescence, in which light seems to be caught and scattered in the water column. If you think you might be confusing "cloudy water" with green water, fill a white coffee mug with some and decide.
 
There are three sources for cloudy water. When the tank is first filled, the least impatience or clumsiness in adding the water can stir up the finest particles from the substrate, "rock flour" and silt. Common practice is to overwash the substrate when you're first setting up. Bucking the general trend, the Skeptical Aquarist suggests that in fact you don't want to wash all these minute particles out of the substrate, because with a little time, bacterial coatings will control them and they'll give plant root hairs the purchase they need. But this initial cloudiness is one of those nagging problems that you have to deal with in setting up.
 
Then, when a new aquarium is a few days into its initial cycling, often comes a second cloudiness, caused by a bloom of bacteria. A "bloom" of any population betokens a system that is not in balance. (Human populations are not excluded.) Disturbance makes resources available to some rapidly reproducing organism for which there are no local competitors or predators. These parameters are characteristic of an aquarium in its early stages, where everything is still in upheaval. It's rare to find a "bacterial" bloom or green water in an established aquarium. And the "cure" for an initial bacterial bloom is patience.
 
Sure enough, the "bacterial" bloom in a newly-set up tank is usually quickly followed by yet a third bloom, caused by plankton. (Of course, the bacterial bloom and the planktonic bloom may seamlessly overlap.) The planktonic bloom is caused by multiplying populations of grazers, the free-swimming ciliates and rotifers that feed on bacteria and drifting algae and euglenids, organisms that old-time aquarists lumped together as "infusoria," when they fed them to the smallest fish fry. Within a few weeks, the grazing copepods that form the next trophic level will have reduced these primary grazers to a low and stable population, and the aquarium water will clear. Copepods themselves can even "bloom" enough to cloud the water temporarily with their nauplii, but soon, when the over-grazed populations of lesser plankton crash, the copepod boom crashes too, and the last cloudiness "dissipates."
 
Struggles. Now, you may sense that the fishkeepers who pull out all their rocks and ornaments for a periodic scrub and bleaching and ruthlessly vacuum deep into their substrate are striving fruitlessly to keep the natural plankton and biofilm from developing. The result of their efforts is more likely to be a bloom of just one kind of microorganism, and perhaps it will be an undesirable type, such as cyanobacteria. A population "bloom" is more typical of a disturbed system than a mature one, as when fireweed carpets a burnt-over forest. You may have noticed that a uniform sheet of one type of green algae re-covers the perpetually-cleaned front glass on your tank. By contrast, the back glass, which is untouched by you and continually grazed by your algae-eaters, develops a mottled pattern of dozens of kinds of algae and diatoms.
 
Windfall resources. Disturbance may release a "windfall" resource, which the few fastest-reproducing, most successful opportunists will "bloom" upon. An unseen dead fish may provide a rich resource, with cascading effects down and up the food web. Another example is the phosphate in the lower levels of your substrate. Hypoxic conditions down there have rendered some of that phosphate soluble; then, when you stir up the substrate with a gravel vacuum, the PO₄ gets stirred into the water column. A few days later, your water may become slightly cloudy with the temporary bloom of plankton, until the temporary phosphate resource is exhausted, and the water clears again.
 
Competitive exclusion. Sometimes in the first stages of an aquarium, wood that you've used in your aquascape will develop a white film of Saprolegnia "fungus." But you'll find that as the rich variety of biofilm develops, the opportunistic fungus is crowded away. It's still there of course, and its spores are everywhere, but it's taken its more natural role, as one kind of organism among many. A good term for this is "competitive exclusion." When I have a healthy "green water" culture going, I periodically innoculate my aquaria with half a cupful of it per ten gallons or so. The "green water" doesn't proliferate in the balanced planted aquarium, as you might fear, but the "foreign" strains of organisms keep populations of bacteria and protists diversified.
 
In my "plant nursery" (at times this has been no more elaborate than a large drum-shaped glass bowl full of clippings, at others a plastic sweater box with filters hanging on the rim), perhaps twice a year I gently stir the water and then pour out half. I want a water change, but I don't want to eliminate any of the plankton species. As Richard Dawkins points out, no matter which bucketful you draw from a well-churned river, it will be representative of the water of that river. So, though I may discard half the water or give it to houseplants, I'm likely to be keeping all the species of the plankton in the plant nursery.