HL and WP, as you both state there are a number of right ways to do things. In no way am I trying to start a war but I would really appreciate to know why each of you feel the way you do about initial algae growth. HL, you stated that during the cycling of my tank I should see brown, then green and if I'm lucky some red algae. I already have the brown algae on my live rock and substrate. WP, you state that although I can deal with the algae growth problem later, I should make an attempt now not to start an algae growth. I respect and appreciate both of your comments but you can see that I'm confused! Am I misunderstanding either one of you?

It is my strong belief that there is little you can do about the algae blooms in the beginning.  It's my opinion that it is best to let nature take its course.  The more we start messing with our habitats, the more problems we may introduce - simpler is better.  In time all these algae blooms will go away (the green and brown are not harmful), they are feeding mainly on the phosphates and nitrates present in your water.  I don't know if this has already been covered, but watch for the "red algae". You want crusty looking red algae (usually more pinkish unless its Carib.). If it's slimy looking it's cyanobacteria (not harmful unless it starts to cover corals, polyps, etc.), which can be a pain.  With a good skimmer and careful feeding these will disappear.

During the cycling, most of the organisms on the live rock will die in the first few weeks, especially when the ammonia and the nitrite reach a very high level before the Nitrobacter and Nitrospira bacteria start to work.  The decomposition of these organisms will release lots of nitrate and phosphate into the water.  Therefore, you will notice a bloom of various micro-algae.  This situation will further be stimulated if you give a sufficient lighting period each day. Your question is really up to you because if you plan to keep some herbivorous animals like Yellow Tang, Hermit Crab, or Asteria Snails, etc, then your micro-algae is definitely a good source of foodstuff for them.  However, if your micro-algae or nuisance algae have already covered the living corals or other inverts, then these micro-algae will do more harms than any good at all.  Besides, these micro-algae will consume oxygen at night-time, just like other fishes.  So, you have to be aware about your oxygen content.  My friend had a very bad experience with all the brown algae covering the whole tank, not only the sandbed, live rock and even the glass.  Next morning, he found all the fishes were death.  Then, I did the water tests for him and I found that the oxygen content was very low and the fishes had probably died of suffocation.  Even though I had no absolute answer for the death of his fishes, I would like to draw your attention to this.

Maybe I should also share this experience with others in this forum and listen to others' opinion.  I have one of the books written by Horst E. Kipper (he was the founder of Dupla). In his book, he recommended not to give any light at the first two weeks of the cycling.  He tried to avoid the algae bloom as well.  Therefore, it's really up to you to use the herbivorous animals to deal with the algae or other ways.

The way I see it, algae are inevitable, but they're not all bad. What do I consider good and bad? It is bad when algae cover your corals or other livestock, and "smother" them to death. It is also bad when ugly slimy algae cover a nice looking piece of rock. It is good when algae grow in your tank and absorb excess nutrients, such as nitrate and/or phosphate, which, in excess could be detrimental to your fish, corals or other inverts. Algae are also a main food source for many marine fish, and for a host of small inverts as well. Thus, some algae in a tank make it more natural, IMO.

Algae, both "macro" and "nuisance" types, also produces oxygen and carbon dioxide (day and night time), and the latter has an effect on the pH, and alkalinity of the water, which could be good or bad....

The first alga growth in a newly set up tank is usually a golden-brown type, covering just about everything in the tank. In a well set-up tank this outbreak does not last very long, as they use up their particular nutrients quite quickly. The most common nuisance algae "problem" is with green "hair" algae. They tend to grow in areas of higher water flow, and with high light intensity. And they don't just go away....   The only way to keep green hair algae in check is to reduce their food (i.e. nitrate and phosphate), to reduce the light intensity, or to physically remove (or eat) them. Now, in a reef set-up one needs all the light one can get, so that leaves us with reducing the "food", or eating them. This can be done by filtration, or by having macro algae or a dedicated patch of hair algae or red algae competing for food. If you also have herbivores eating the algae, you are feeding your fish and restricting the growth of the "problem" algae at the same time.  The red "hair" or bushy type algae looks quite nice to me, and as they are quite slow growing they are a welcome addition to my tank. They make excellent hideouts for small inverts, remove nutrients and look good - what more could one ask for....

Macro algae also come in green (Caulerpa and Halimeda species are the best known), brown (Dictyopteris and Sargassum species, amongst others), red, even purple colours. The "Fan" and "Bubble" Caulerpa are probably the best "beginner" types to keep, though if you're lucky (and don't have herbivorous animals) you may find other species growing from your live rock.   Coralline algae come in colours ranging from light pink to deep purple. They will eventually cover the back and sides of your aquarium glass if you have enough water movement and a high enough calcium level in the water. They are good to have, and a sign of a healthy tank.

What to do with your new tank:   Don't try to suppress any algae growth during the first 6 months. If the green hair algae threaten to overrun the tank you should remove as much of it as possible by hand. After about 2 months you can also use some "reef janitors" i.e. snails and hermit crabs, to reduce the algae growth.   Restrict nutrient input into the tank, and ensure that you have decent filtration   Limit the introduction of nutrients via water changes, by using RO/DI water.

You may want to check your water supply (as HL mentioned) for phosphates and silicon...  I am still having problems with Diatoms (the brown algae) and finally found a silicon test kit.  It turned out that my local water supply is NOT good for aquariums, despite the reassurances of my old LFS.  If you live in a place with hard water, you may have similar problems.  Even after 6 months, I have well over 3 ppm (the highest reading on the test kit) SiO2 in my main tank, which is probably the main reason I still have the brown stuff all over the place.  I now purchase RO water from my new LFS, which is really economical at only 35 cents a gallon.  Certainly easier and cheaper in the short run than buying a RO filter myself.  Hopefully that will eliminate (or at least drastically reduce) the supply of silicon and subsequently eliminate the diatoms.

HL - what do you know about this diatom stuff?  I want to add some live rock to the tank, but I would like to wait until the diatom issue is done with.  I don't want my LR to end up with brown gunk all over it.  Do you think that is a good idea?  (The tank is a 50 gal. FO, very lightly stocked with 1 Damsel, 1 Percula Clown, 1 cleaner shrimp that shed for the first time yesterday, 3 hermits and 3 snails).  For what it's worth, the snails and hermits don't seem to do anything at all to the brown algae on the rocks or tank walls.

Q2- I purchased a quart of phosphate remover that is supposed to remove phosphates (have 0.5 ppm) and will remove silicon dioxide after all the phosphates are gone.  Anybody have any words of wisdom before I stick that in the tank?

Yes, RO water should reduce the Si level, which should help to get those Diatoms under control.   IMO, you should add at least the base rock at this time. It will assist with filtration, and will have some invert hitchhikers in/on it who will also probably be beneficial. It will not be serious if the base rock gets covered with Diatoms - this will only be temporary, until the Diatoms are either eaten by some of your creatures, or have reached equilibrium in your tank, having exhausted the excess nutrients. One or two Featherduster worms will also not be out of place (obviously only if you do not have anything which will eat them...) - they eat micro-organisms, and I think that they will help to control the Diatoms (just a guess, mind you).