Macroalgae in a refugium

Photo from the Reef2Reef archives courtesy of AlexG, © 2018, All Rights Reserved

In the beginner section of our forum, there is a sticky on top, written by David Hammontree, that's very very good. The article is called, The Supreme Guide to Setting up a Saltwater Reef Aquarium.

If you're a beginner, you should read that whole article. Below is an excerpt from the article on cycling the aquarium. I think this particular part on cycling is important for all beginners to understand, and I haven't come across a better explanation anywhere than the one David wrote. In the article, David answers the questions that beginners don't even know enough to ask.

He describes in detail the different phases that a brand new saltwater reef aquarium goes through from the time it's filled with water and rock and sand until you're ready to add livestock. Every. Single. New. Reef. Aquarium. So, read it and enjoy.


Section 5: The Cycle


image via @rusticgirls

In a freshwater aquarium you can add some flake food, wait a couple weeks, and then you can add fish. In the ocean there is much more involved than mechanical filtration. In fact, 70% of your aquariums' filtration relies on the maturity of the live rock. A combination of bacteria, algae, and various invertebrates compose the “live” part of the rock. It takes quite a while to establish an ecosystem, even on a microscopic level. Without a proper understanding of the Marine Cycle, you will be in for a long term battle with parameters and algae. There are six main stages to a properly cycled tank. Follow this guide, and you cannot mess up. You will need your basic test kit to test the progress.

Stage 1: Ammonia Cycle

Ammonia is the first thing that forms when something rots. It is a waste product in nearly all creatures as well. Instead of using a fish to start the cycle just use some food. Anything that is all natural and uncooked works just fine. Table shrimp that is uncooked works great. Drop it on the sand so it is in view. The shrimp should begin to rot within a couple hours or more. Let this shrimp rot until it is completely gone. If you are curious what your ammonia levels are, go ahead and take some tests. Keep track of the results as the shrimp rots. The smaller the food gets the more ammonia should be present in your water column, and pretty soon it should be off the charts. This will stay high for a while, but then start to drop. As soon as the ammonia starts to drop you will see a rise in nitrite; you are now on to the next stage.

Stage 2: Nitrite Cycle

Ammonia when broken down by bacteria becomes nitrite, which is still a toxin. As your nitrites rise your ammonia will drop, drop, and keep dropping as long as you haven’t added any animals. Keep up with testing to observe your progress. Eventually your ammonia will be very low, and your nitrites will peak out until the nitrite starts feeding a different type of bacteria that turns it into nitrates. Once your first signs of nitrates are seen, you are on to the next stage.

Stage 3: Nitrate Cycle

Nitrates are removed within the live rock deep inside in all of the deep pores. This hidden bacteria consumes the nitrate and creates nitrogen gas as a byproduct. The nitrogen gas rises in the water column and escapes into the air. When one gas leaves, another enters. Oxygen is then infused into the water. After the Nitrates start to dissipate your oxygen will increase and you will be ready for the intermission.


You are not done yet! You may have cultivated a nice crop of groovy bacteria, and your water may be clean as can be. However, there are still 3 more stages to the cycle process before you can start your stocking. Take this time to recognize all of which you have already accomplished. The next 3 stages often put fear into the eyes of many newcomers. These stages are perfectly natural and are partially a representation of how the earth became an oxygen-rich planet. Before there were any oxygen-breathing organisms, there was the evolution of cyanobacteria. This is a photosynthetic bacteria that creates oxygen as a byproduct. There are several colors, but the commonality is that it is like a slime. The cyanobacteria spread over a vast area, and the atmosphere became oxygen rich like we breath today, without the smog. Cyanobacteria is responsible for life as we know it. The same applies to the reef. Now that your mind has been blown you may move on to the next stage of the cycle.

Pre-Algae Cycle:


If your lights have not been setup yet do so now. Set your timers as you would for a reef tank. Anywhere from 6-12 hours is a good amount of time. Set the photoperiod to be on during the hours you will be viewing the tank most. If you work 2nd shift it is OK to have the lights come on after you get home from work or when you wake up in the morning. As long as there is not a supply of sunlight near the tank you wont have a long term battle with algae.

Stage 4: Diatoms


diatom algae image via reef2reef member @Steven R

Diatoms are a brown dusty life form that consumes silicates. There is no avoiding diatoms during their initial bloom. Leave it be. Let it go crazy. Before you know it, the brown stuff will soon start to change colors. Generally red, this is the start of the next stage!

Stage 5: Cyanobacteria


cyanobacteria image via reef2reef member @Murfman

Cyanobacteria will now begin its course. Again you will let the slime just do its thing. This will be the nastiest of the stages. cyanobacteria can gross some people out, especially if they catch a whiff of it. It is best to leave it be. It will start to clear up eventually. The clearing of the slime makes way for yet another stage.

Stage 6: Green/Brown algae


hair algae image via reef2reef member @johnmaloney

If you have made it this far, give yourself a round of applause. This is the final “battle” of the cycle process. When the slime is gone you will see your first signs of plant life, algae! Green Hair algae is usually the type that you see, but some other types have been known to occur. This stuff will grow like mad. At this point you are ready to move on to the next phase.

The cycle is a long process in terms of hobbies. Find yourself a good rhythm for testing. Get yourself in the habit of staring for long periods of time. Practice observation by watching as life forms start taking foot in the aquarium. You will see things from dust sized particles to worms that reach a foot long. There really is no telling what could form in your tank. This is a great time to prepare for the animals you will get. Knowing how to describe things and being able to correctly test the water will help you get the information you need. Your parameters are perfect now. You are now ready to move on to the next section. You should actually study the next section during your cycle, since you will have quite a bit of time on your hands with all that waiting.

Cycles can be artificially induced, but it is always preferred to use as little foreign liquids as possible. Another thing you can do during the cycle is preparing your clean up crew and first fish, but be prepared to keep them quarantined for a prolonged time since the cycle is unpredictable.

Section 6: Live Stock


mixed reef image via reef2reef member @ReefMP
A few holidays have passed, you have gone through a few types of hairstyles, and the seasons have changed dramatically. Your aquarium has gone from an idea in your head to a flowing ecosystem of algae and rock. You need to get some critters in there! But where do you begin? There are more bad combinations of marine animals than flavors of ice cream. Luckily, there are compatibility charts that do the vague guessing for you. Locate these charts to help you get a picture of what does and does not mix. Some fish are obvious. Mixing a shark and a seahorse is not a good idea. When you get into the fish of the reef there are some unexpected no-no’s. A huge tang could fall victim to even a small blenny bullying or nipping at him. Stocking will be more research than anything. It is improbable the part time employee at your LFS has a mental encyclopedia of everything they sell. Always check for yourself anyways. If you plan on having predator fish you can skip the clean up crew and corals since they will either get eaten or destroyed. Every animal you buy WILL NEED QUARANTINED....