Tank Cycling Article-Borrowed

RyanG

Reef enthusiast
Here is an article that I borrowed with permission.

Lately I have seen many questions on setting up/cycling a new reef tank. this is usually followed by "why and how to fix it threads" issues on algae out of control, phos levels crazy, not being able to rid the tank of nitrates, ph going crazy, ammonia spikes ect... its become some what of a pet peeve to see, hummm how to say, micro management
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IMO, its more important to know whats going on and why your doing this or that and how that relates to the big picture. Not, I waited two weeks and my tank has finish cycling
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its ready to become a reef what can I add or its safe to add this or that right??. So because I have nothing better to do I wrote this big phat thingy
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There are so many misunderstanding about establishing a new reef system. In part because there are so many ways to setup a reef system. Most of this will be based on the most common tank setups; sand beds with live rock and skimming. Will not get into sulfur systems or scrubbers or anything like that, only common basic setups. Like building anything its all about the prep work. Much like if your painting a wall, didn’t use primer first or didn't sand it smooth, or maybe started the second coat to soon peeling and chipping results, the finish product will be flawed. Same thinking should go into building a reef system. So an understanding of what the long term goals are and short term goals is very much needed. The first part of this may be repetitive as most have heard about “cycling” So lets start;

Ok the long term goal is to set up and establish a stable balanced reef ecosystem that will support our creatures using a bio filtration system via bacteria. The problem is this takes some time, a lot of time, and our systems have limits and need help to keep thing balanced. Good thing is you can enjoy watching things come together along the way. That does not mean after you “primer the wall” its ok to hang a couple pictures before you start panting. So some do’s and dont’s to consider is needed, there are many posts and articles on how to do this with some explanations. Like cycling the tank, but only a small part is usually explained and the goals for the next steps are often ignored as well as little mention how the dynamic involved. Its understanding the current goal and prep need for next goal that seems to be missing and in the end causes the most issues. Confused, hope not after this;

Like I said before, there are many ways to setup an ecosystem; here I am basing it on sand beds and LR, the nitrogen cycle. So before you read on, read this, the whole thing and understand it, even if you are familiar with it…Nitrogen Cycle

The first goal to establish a bio filtration system. This is where cycling (nitrogen) comes into play (well, really everything is just a cycle-we are just getting the ball rolling). The word cycling might not be the best usage of words here. Instead lets talk about what we are doing, growing/culturing bacteria. This takes time and must be done in stages. What we need to reach this goal;

Stage #1-growing aerobic bacteria. Water prep is just keeping temp, ph and salinity right. No need to skim or use lights. Best not to hook up either for now. Base rock is fine to use and perhaps much easier, less issues, than uncured or cured rock that really is not so cured, most LFS rock. Choosing rock is another thread, just want to note the die off and pollutants that can come from LR, in these cases using the skimmer right away adding carbon, getting a refugium going with macros and lots of water changes will be needed. An additional curing process maybe warranted as well. I hope by the end of this you will know why I say these things about LR and curing and die off.

1. Provide a surface area, a place for bacteria to attach and grow "spread”. The outer layers of live rock and/or upper layers of sand beds (top 2”) are the most common substrates used for this.

2. Provide O2. Aerobic bacteria use O2 for energy. O2 is provided by water currents and air currents via gas exchange at the surface. Limited to what is in the atmosphere and the % of water surface area coming in contact with air. (even a small sump increases this % big time, thus big time increase in gas exchange, just FYI) The more flow the more O2 will be carried to the bacteria. Keep in mind though the amount of gas exchange (CO2 for O2) at the surface is dependant on the amount of air flow and water flow coming in contact at the water surface. So a rippling of the water surface together with air flow at the water surface and good flow throughout the tank is needed, esp. if the tank is in a smaller closed room or if you like to keep the windows closed with the heater on. Pumps and fans will do, as seen in reading the link above increased gas exchange is needed at this time because of the rapid aerobic bacteria growth rates consuming up much of the O2. Extra power heads and bigger/more fans is a good idea right now, reduce it later after things start to balance themselves. If you don’t provide a good supply of O2 you will get overgrowths of unwanted bacteria like cyanobacteria. No lighting and good gas exchange really helps reduce this complication.

3. Provide food- more specific nitrogen via decomposition explained in the link above—ammonification and nitrification. From that you can see this can be provided from just the atmosphere. But that would take a real long time to establish a system that will support a fish. So we need to provide the best conditions for growth of certain bacteria. Don’t think about supporting fish at this time, focus on the prep work, the goal here is to grow bacteria and that’s it. Some use fish to provide a nitrogen source, but this is not only hard on the fish and is likely to kill it, it may actually overload the growing bacteria making it take even longer to balance things, remember we only want to encourage certain types of bacteria to grow here, those that convert ammonia. So the use of a deli (dead) shrimp is often used, which works fine. IMO, though it is best to use a few pieces of fresh/raw live rock and lots of base rock for this, with some feedings of flake foods or other type foods here and there. Whatever you use the thing is to understand what the goal is here (growing aerobic bacteria) and how it fits in with the long term goal, a balanced ecosystem.

4. Now sit back and test until NH3 and NH2 are at 0.0 and you see NO3 levels steadily rising. All this takes anywhere from 1 week to a couple months. It depends on the environment provided. If all the live rock was fresh/raw it will take some time, up to many months with heavy skimming, heavy flow, good air circulating and many water changes along the way to prevent unwanted things from overgrowing(cyano, sulfur pocket ect..) If not enough food was provided you end up getting a spike every time you add the smallest something. At this point, stage one is complete,
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Now don’t go off and start hanging pictures on the wall yet, this is only the primer coat
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Stage #2-growing anaerobic bacteria. Many issues get rooted in during this stage. The goal is two fold. Growing anaerobic bac and preventing excessive algae growths. Here is where your tank starts to balance things out. The issues are whether or not it will reach a wanted balance or an unwanted balance. Maintain ph, temp and salinity levels. Its gets a little weird here so hang on. Whats needed and going on;

1. Provide a surface area. The inner layers of live rock and/or deeper layers of sand beds does the job. Anaerobic bac grow in areas where low to no O2 is available. Through many mechanisms anaerobic bacteria do indeed use O2 as an energy source. They just can not uptake it directly. They must first steal it from NO3. As they grow close to aerobic bacteria, that produce NO3, they break it up and steal the O2 before the NO3 gets into the water Colum, in short that is. The link above should have given you a good idea of how it works here. By having to steal the O2 they grow a lot slower then aerobic bacterium. Major patients is very needed during this time.

2. Provide a steady food source for continual growth of aerobic bacteria which in turn will feed the anaerobic bacterium. The catch here is there are faster growing things like algae that feed on NO3 also, but they are able to directly uptake NO3 and use other means to obtain their energy like photosynthesis, thus algae competes with anaerobic bac for NO3. Futhermore, algae increase O2 levels fueling aerobic bac. consequently, we many not see NO3 but do see algae growth so we add more fish or add a fish too early, leading to the use of algae, instead of the intended goal of bacteria as the main bio filter. The aerobic and anaerobic bac may never balance themselves if the algae is allowed to out compete the bacteria. (not going into algae scrubbers here, common system basics only) Adding part of your cleaning crew is perfect for this job. Don’t wait till NO3 levels are at 50 or something before adding some of the cleaning crew. Around 20 would be max I would do. Its not a good thing to let NO3 levels rise and fall back to zero before starting to control it with water changes or what not. Once/if you see a diatom bloom or other bloom you know its time to work on the NO3 till your anaerobic bac take over, not algae. NO3 levels of lower than 5 or 0.0 dose not mean there is not enough for anaerobic bacterial growth, remember anaerobic bac removes the NO3 before it gets into the water column, the NO3 in the water column is what algae feed on not bacteria. Once NH3 and NO2 hit zero don’t let NO3 levels go to high, below 10 is a good target. you may need to do a water change or two to bring down the NO3 and keep levels under 20 at all times, the lower the better. After some of the cleaners have been in there about a week or so and start eating and producing some waste a hardy fish can be added. Do think about how with each addition you are providing a continued food source for aerobic bacteria, which grows many times faster than anaerobic bacteria, may end up feeding unwanted algae. To much continual food supply to early and the aerobic bacteria overgrows which results in prolonged balancing between aerobic and anaerobic bacteria or even worse algae balancing, will go into that next.
*note; even though NO3 are 0.0 your anaerobic bacteria levels are still growing but not yet fully established, why frequent water changes and testing is needed in the beginning to prevent NO3 form feeding algae but at the same time building the anaerobic bac. go slow-and keep the NO3 levels down till you can add a fish and see no rise in NO3 levels.

3. preventing excessive algae growths. Just prior to adding some of the clean up crew hook up the skimmer and skim wet, its time to slow the aerobic bacteria growth rates some and allow the anaerobic bacteria to catch up, which includes preventing excessive algae growths. The goal here is to provide the best environment for anaerobic bacteria growth. The addition of carbon and phosban will go a long way in preventing algae growths as well. If you got it, light up the refugium and add macros to combat micro algae growths. You still don’t need lighting in the main tank, but if you have a fish or just want to see things keep the lighting down to minimum so as not to encourage algae growth. Here is the deal. After your tank, what is commonly known and mistakenly so called “cycles” (stage one) it can support fish sure, but remember this for a reef tank not a fish tank. Reaching a balance with the aid of algae is fine in FO tank but with a reef tank we want to keep it to a minimum. We want algae but for different reasons and not now (again, not going into scrubbers here, basics only) Because the anaerobic bacteria have not grown/established themselves in numbers high enough to balance with the aerobic bacteria already established, the tank will use other means to balance out the nitrates. The fact that algae can uptake NO3 directly and combine that with the decomposition process and aerobic bacterial consumption of O2 the resulting elevated CO2 concentrations provides a great environment for algae growth. Why min lighting, we don’t want to make it the perfect environment for algae we are shooting for an environment perfect for anaerobic bacteria. Algae is just the fastest and easiest compensating mech our tanks have, to reduce nitrates. (for those in the know we are not going into other cycles like the sulfur cycle and photosynthesis effects on ph type stuff). Many see algae blooms as a good sign in a new tank, it is kinda, its exporting nutrients, aiding with ph regulations, many other things and more importantly marks the establishment of aerobic bacteria in a new system. Like said earlier though, algae is wanted just not yet. Instead, at this time, the bloom is only a indication of whats going on. Understanding that seeing the first algae bloom in your new tank is just a compensating mechanism. The tank is using algae to uptake the NO3 in a effort to make up for the lack of anaerobic bacterial activity. Simply put blooms are due impart to a lack of anaerobic bacterial growth. What little anaerobic bacterial growths are present can not handle the NO3 that is being produced by the aerobic bacteria. The anaerobic bac are slow growers and are just getting overwhelmed. So, in a new tank, if you see a algae bloom and your NO3 levels are 0.0 that does not mean your tank is ready to add another fish, no no, it means its time to start providing an environment which encourages anaerobic bac growth(which may include adding a fish), while keeping algae growths in check, unless you like lots of algae growths that is.

4. Cycling the lighting in (while keeping nutrient levels down-phosphates, silicates, nitrate ect..while not allowing algae to get a foot hold), getting the chemistry set and playing with your water flow and stuff is whats next on the agenda. depending on the environment maintained the rock used and all that stuff it could take anywhere form 6-18months for the tank to fully mature. depending on how things go the time of adding things speeds up as you go. one fish every 30-45days for the first few months-the time between additions decrease as you go, its up to the tank on when/how long to add or wait. no worries, relax it does go pretty quick after things get going. its those first few months you really got to watch out for
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5. chemisrty, flow patterns, turnover rates, respirations ect. ect... are topics to be mastered as your tank matures, basically too much to go into here
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Well hope this helps someone understand whats going on while setting up a new reef. This was not/is not intended to be a how to. Its just a little more of holistic view on the goals and some of the major dynamics involved. Maybe just maybe this will help someone follow some of the good advice given around here instead of just doing what was said but not exactly, if you know what I mean.


Note; bio balls and sponge filters are used for fish only tanks, as most fish are not so sensitive to nitrates, bio balls only provide a surface area to support aerobic bacterial growths and end up collecting decaying matter. So for a reef you can see why they are not the greatest thing to use. Your providing a greater surface area for aerobic bacteria (our tanks are already lacking in anaerobic surface area, unless you keep a 12”+ sand bed and the tank is extra long and wide increasing the sand beds area or something crazy like that). Crushed coral beds filter socks also have the same issues as bio balls.

Note; we all end up overstocking our reefs and our tanks use other mech to keep things balanced. We help with skimmers and water changes ect…,algae is one mech and many that have issues with algae in tanks is a result of not putting the “prep” work in. Understanding some of the dynamics well really help you enjoy your creation and avoid some future head aches. i hope it has become apparent why everyone is always stressing on stocking slow and limiting additions.

Note; algae is a great thing. It provides foods keeps ph steady absorbs excess nutrients removes CO2 and adds O2 + much more. it can cause some ph swinging issues too (will not go into that here). however, if you put the prep work in algae can be a tank savor. Yes is can handle the CO2 from the Ca+ reactor and act as a buffer for the system. It can consume that skimmate if the skimmer overflows. if the bacteria’s are balanced and you over feed or something die, no worries algae will help take care of it without blooming too much, but if its already being used just to keep NO3 balanced then huge blooms can result from just the slightest over feedings or a even a couple snails dyeing off will cause a bloom or worse. anything could result in a chronic problems, as one of the main compensating mech is already being taxed.

Thanks Prow at RS for letting me borrow this article, hopefully everyone finds it as useful as I did.
 
Good show Ryan. Lots of good solid information that normally would have come from a dozen write ups instead of just one. The person putting it together definately did some reading and studying to put it all together. Then there is the experience it takes to even know what to put in or leave out of such an article. Good find. See if we can post it in the LR Articles section or at least post a url for it there.
I do think the O2 section is a little dated. Most skimmers and sumps/refugiums (especially with macro algae) are making a bigger contribution to dissolved oxygen levels than the tanks surface, even with good circulation. The circualtoon is important for keeping the water and therefore the O2 iand nutrients in motion, but that is not so very dependant on most reef tank surface waters due to the wide usage of skimmers and sumps/refugiums.
Of course I am a pretty critical, judgemental sort of guy.
 
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Thank you, Ryan, that helps me to understand the process a little more in depth. Does this suggest that having a closed top can hinder the process of nitrates turning into nitrogen gas and expelling into the atmosphere?
 
Thank you, Ryan, that helps me to understand the process a little more in depth. Does this suggest that having a closed top can hinder the process of nitrates turning into nitrogen gas and expelling into the atmosphere?
If there are any gaps at all, and there are, unless you silicone your glass cover on. Then the nitrous gas will find its way out just fine. There is never enough gas being produced to see the gas bubble(s) migration to the top. :bounce:
 
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