Periphyton on your rocks


Active member
What is Periphyton?

Periphyton is what turns your rocks different colors. You know... the white rocks you started with in saltwater, or the grey rocks (or brown wood) you started with in freshwater. After several months or years, the rocks become a variety of different colors and textures. Why? Because the periphyton that has grown on it is a mix of different living things, with different colors, and thicknesses. And the important part is: It is LIVING. And the thicker it is, the more living material there is.

That's right: The colored stuff that has coated your rocks is all living organisms. Sponges, microbes, algae, cyano, biofilms, and of course coralline in saltwater. After all, "peri" means "around the outside", and "phyto" means "plant". Have you ever slipped while walking on rocks in a stream? That's the periphyton that made it slippery. It can be a very thin coating on the rocks, sometimes paper thin, but it covers the entire surface, especially across the top which gets more light.

There is a lot of photosynthetic organisms in periphyton, and this means that they need light; but they need nutrients too (ammonia, nitrate, phosphate). And as you might guess, the organisms will prefer the illuminated portions of the rocks, and will grow to intercept food particles in the water, based on the water flow. Just think about how sponges orient their openings for water flow; the micro sponges in periphyton do it too, but on a tiny scale.

What about in caves and holes? Well periphyton here don't get much light, so they are primarily filter feeders (non-photo). So they REALLY grow and position themselves to be able to intercept food particles in the flowing water.You'll sometimes see little tree-like arms or branches sticking out to get the particles; these are usually "forams", otherwise known as foraminifera. They require a lot of food particles in the water. Think of them as coral polyps without the coral.

Reef studies have shown that at certain depths, more of the filtering of the water comes from periphyton and benthic algae, than comes from the phytoplankton which filters the deeper water. And in streams, almost all the filtering is done by periphyton because the water is so shallow. So, what you have on rocks that are "mature" or "established" is a well-developed layer of periphyton (and all the good natural things that comes from it, like nutrient absorption and food generation). They have nice colors too.

This is why mandarin fish can eat directly off the rocks of an "established" tank (tons of pods grow in and consume the periphyton), but not on the rocks of a new tank. Or why some animals can lay their eggs on established rocks, but not new ones. Or why established tanks seem to "yo-yo" less than new ones (the periphyton is a giant, self-adjusting filter). Even tangs can eat periphyton directly when it's thick enough. Yes periphyton can also develop on the sand, but since the sand is moved around so much, the periphyton does not get visibly thick like it does on rocks. So thick periphyton on established rocks is your friend. And totally natural too. That's why there are no pure white rocks in natural reefs. Keep in mind though I'm not referring to nuisance algae on rocks; I'm only referring to the layer of coloring and textures that coats the rocks, and the little arm-like structures that stick out from under rocks.

But what happens when you "scrub all the stuff off your rocks"? Well, you remove some of the periphyton, which means you remove some of your natural filter and food producer. What if you take the rocks out of the water and scrub them? Well now you not only remove more of your natural filter and food producer, but the air is going to kill even more of the microscopic sponges. And what if you bleach the rocks? Well, goodbye all filtering and food producing for another year. It's an instant reduction of the natural filtering that the periphyton was providing. So it's best to not do these things at all.

However, what if you just re-arrange the rocks? Well, some of the periphyton that was in the light, now will be in the dark; so this part will die. And some of the periphyton that was in the dark will now be in the light, so it will not be able to out-compete some photosynthetic growth and thus will be grown over and will partially die too. And even if the light is the same in the new location, the direction and amount of water flow (and food particles) will change; forams and micro sponges that were oriented to get food particles from one direction will now starve. So, since the light and food supply is cut off in the new location, the filtering that the periphyton was providing stops almost immediately, due only to your re-arranging of the rocks.

Starvation takes a little longer. The periphyton organisms won't die immediately, since they have some energy saved up; but instead they will wither away over several weeks. So on top of the instant reduction in filtering that you get by just moving the rocks, you get a somewhat stretched-out period of nutrients going back into the water. And after all this, it takes another long period of time for the periphyton to build up to the levels it was at before: 1 to 2 years. Even changing the direction of a powerhead will affect the food particle supply in the area it used to be pointed at. This is why "mature tanks" take 1 or 2 years to develop.

So a good idea is to try to keep everything the same. Pick your lighting, flow, layout, and then try to never again change anything. In other words, treat your rocks just like the rocks on a reef. It's a different way of thinking, but you should have a stronger natural filter and food producer because of it.


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Premium Member
Lets not forget endoliths (from "endo" meaning inside and "lithos" meaning stone) that are burrowing and living in much of our aquascaping (including sand) and coral skeletons. Endoliths the discoloration that's still there after removing off the periphyton or epiliths and can contribute significant percentatges of the net photosynthesis (~30% - ~45%). :)

And I'm glad you brought up what's happening in cryptic areas, some real important biofiltration happening there. Look at what's happening just with sponges in cryptic areas, they're recycling DOC a whole lot faster than bacterioplankton.

Element cycling on tropical coral reefs.

This is Jasper de Geoij's ground breaking research on reef sponges. (The introduction is in Dutch but the content is in English.)

Sponge symbionts and the marine P cycle

Phosphorus sequestration in the form of polyphosphate by microbial symbionts in marine sponges

Differential recycling of coral and algal dissolved organic matter via the sponge loop.

Sponges treat DOC from algae differently than DOC from corals

Surviving in a Marine Desert The Sponge Loop Retains Resources Within Coral Reefs

Dissolved organic carbon and nitrogen are quickly processed by sponges and released back into the reef food web in hours as carbon and nitrogen rich detritus.

Natural Diet of Coral-Excavating Sponges Consists Mainly of Dissolved Organic Carbon (DOC)

The Role of Marine Sponges in Carbon and Nitrogen Cycles of COral Reefs and Nearshore Environments.