Let's talk DIATOMS! I so often get asked about the "brown stuff" in the water.
Typically, when setting up a new jar or tank, you will encounter biofilm within the first week or 2. That's the white flaky stuff swimming on the water surface. Then it turns brown and most newbies start to panic.
What's most important to know is that all of this is alive and very useful!
The brown phase usually peaks around weeks 2 to 4 of a new jar. It might look ugly, but it is actually producing oxygen and feeding your micro-fauna. Keep your jar in indirect sunlight, don't open it, and let nature do its thing!
Whenever a fresh surface (like glass, a rock, or new aquarium decorations) is placed in water, free-floating bacteria and organic molecules land on it almost immediately. They secrete a sticky, slimy matrix of sugars and proteins. This is the initial biofilm.
Freshwater diatoms happen when sunlight, dissolved silica, and nutrients like nitrates and phosphates come together in rivers, lakes, streams, or new jars and tanks.
Diatoms are a special type of single-celled algae. But unlike regular green algae, diatoms build a microscopic, hard shell around themselves made out of silica. They are naturally present in almost all bodies of water.
Once anchored, the diatoms begin using sunlight to photosynthesize, multiplying rapidly across that exact patch of slime.
Using sunlight and chlorophyll, they convert carbon dioxide into energy and oxygen just like plants do. When nutrient levels, especially nitrates, phosphates, or silica, rise or when light conditions become ideal (such as in spring or in a newly filled aquarium), they divide rapidly.
Here are the typical critters found in jars that munch on diatoms, and those that don't:
• Snails (Bladder, Ramshorn, Pond): The absolute kings of diatom control. They use a sand-paper-like tongue called a radula to literally scrape diatoms off the glass, shell and all.
• Ostracods (Seed Shrimp): Absolute powerhouses for diatoms. They continuously scurry along surfaces, using their appendages to scoop up and munch down diatoms and biofilm.
• Scuds (Amphipods): These are voracious shredders and scavengers. While they love decaying leaves, they will happily graze down the diatom/biofilm carpet covering substrate and plants.
• Mayfly Nymphs & some Caddisfly Larvae: If users catch these nymphs in their wild ecospheres, they are major "scrapers." Their mouthparts are built to shear diatoms cleanly off river rocks.
• Rotifers & Ciliates (like Stentors): The microscopic clean-up crew. Many benthic (surface-dwelling) rotifers and ciliates use hair-like cilia to create vortexes, sucking free-floating or loosely attached diatoms directly into their gullets.
• Copepods: Cyclopoid copepods mostly hunt smaller animals, but Harpacticoid copepods (the ones that crawl on the glass rather than jerky-swimming in open water) will graze on diatoms.
• Tubifex & Detritus Worms: These guys eat mud, decaying organic waste, and bacteria. Because diatoms die and sink into the substrate sludge, worms digest them along with the mud.
• Water Boatmen (Corixidae): Unlike most aquatic bugs, water boatmen are mostly vegetarian! They use their straw-like mouthparts to inject saliva into algae and suck out the juices, though they prefer soft green filamentous algae over hard diatoms.
• Chironomid Larva (Bloodworms): These midge fly larvae spin little tubes in the mud and use silk nets to trap organic debris, which inevitably includes a lot of tasty diatoms.
• Hydra: Pure carnivores with stinging tentacles. They only eat moving meat (like daphnia or copepods).
• Planarians: Predatory or scavengers of dead animal matter. They hunt small invertebrates by wrapping around them and secreting slime.
• Rhabdocoela flatworm: While they do occasionally eat tiny protozoans if they happen to run into them, their primary diet consists of bacteria, organic debris, and yes—diatoms! Because they have a simple, vacuum-like mouth on their underside, they glide right over surfaces and suck up microscopic particles.
• Asian Leeches & Snail Leeches: Snail leeches hunt snails; Asian leeches hunt worms. Zero interest in salad.
• Diving Beetles & Damselfly/Dragonfly Nymphs: Voracious apex predators of the jar. They want live, moving prey.
• Water Mites: Most water mites are parasitic on insects or hunt tiny micro-crustaceans.
Here is a jar I emptied after a couple of months, because the water wouldn't clear. Turns out it wasn't the water, it was the glass tinted by diatoms. I ran this jar 3 times through the dishwasher before I filmed this.
The reason why it didn't come off is that diatoms build their shells out of silica, which is the exact same material the glass jar is made of. The dishwasher soap cannot break down or dissolve silica without ruining the glass itself. The underlying biofilm creates a waterproof, chemical-resistant shield. The dishwasher detergent simply slides right over it without penetrating the core layer.
Video credit: Micronaut (https://www.youtube.com/watch?v=TS-EI\_3gvjw)