{"id":145,"date":"2010-03-22T13:59:51","date_gmt":"2010-03-22T17:59:51","guid":{"rendered":"http:\/\/www.thepufferforum.com\/forum\/library\/water-filtration\/aquariummicrobespart1\/"},"modified":"2011-05-12T13:21:13","modified_gmt":"2011-05-12T17:21:13","slug":"aquariummicrobespart1","status":"publish","type":"post","link":"https:\/\/www.thepufferforum.com\/forum\/library\/water-filtration\/aquariummicrobespart1\/","title":{"rendered":"I. Aquarium Microbes, Part 1: Nitrification"},"content":{"rendered":"
\t
<\/title> \t<meta name=\"GENERATOR\" content=\"OpenOffice.org 3.1 (Unix)\" \/><\/p>\n<style type=\"text\/css\"> \t<!-- \t\t@page { margin: 0.79in } \t\tP { margin-bottom: 0.08in } \t\tA:link { so-language: zxx } \t--> \t<\/style>\n<p style=\"margin-bottom: 0.19in\"><font size=\"4\">Aquarium Microbes <\/font><\/p>\n<p style=\"margin-top: 0.19in; margin-bottom: 0.19in\"><font size=\"4\">Part 1:\u00a0 Nitrification<\/font><\/p>\n<p style=\"margin-top: 0.19in; margin-bottom: 0.19in\">What do you keep in your tanks?\u00a0 A big school of Tetras?\u00a0 A pair of Cichlids?\u00a0 A few billion bacteria?\u00a0 Don\u2019t gag.\u00a0 The \u201cbugs\u201d are the most numerous things in our tanks and are ultimately responsible for our success if we are to keep our fish alive and healthy.\u00a0 Every solid surface in our tanks has a biofilm on it, of bacteria, algae, etc., composed of whatever type(s) of microorganism that finds that surface and adjacent water conditions hospitable.\u00a0 These bugs are not the enemy or in any way unwelcome.\u00a0 They aid us in the upkeep and function of the micro-ecologies needed to make our tanks stable and safe for our wet pets.<\/p>\n<p><!--more--><\/p>\n<p style=\"margin-top: 0.19in; margin-bottom: 0.19in\">Hopefully, most of us are aware that most life forms are sensitive to their own waste products.\u00a0 Waste would not be waste if the critter could still use it, it is waste because they cannot, and most often because it is toxic if retained.\u00a0 Also we are aware that fish produce ammonia (NH3) as a primary nitrogenous (nitrogen-containing) waste product.\u00a0 We know that ammonia can kill fish at what seems to us to be fairly low concentrations.\u00a0 This pair of articles is aimed not at details of bacterial growth and metabolism, but at giving just a glimpse at the massive populations of bacteria and other microscopic life forms that are so very important to our aquarium systems.\u00a0 I hope that I can clarify the some of the roles these \u201cgood guys\u201d play in our tanks, and a few things that can go wrong when we intentionally or accidentally abuse our microscopic helpers.<\/p>\n<p style=\"margin-top: 0.19in; margin-bottom: 0.19in\">The most familiar groups of bacteria to tank keepers are the two types needed to process nitrogenous waste to relatively harmless forms.\u00a0 For years just about everybody has said these are Nitrosomas and Nitrobacter species, and most books will refer to these two forms.\u00a0 Now it appears that those bacteria may play a role in saltwater, but have little or no function in freshwater systems.\u00a0 Research from Dr. Tim Hovanec and others pointed to Nitrospira and Nitrosomonas (1) as the freshwater bacteria primary in oxidizing nitrogenous waste in captive FW systems.\u00a0 But in the end, we do not care as much about what their names might be as we do care about what they do in our tanks.\u00a0 I said before that ammonia (2) is a primary nitrogen waste product for fish, which happens to be excreted largely through the gills, but also in part in urine, less in solid waste although many ammonia precursors are available there.\u00a0 Ammonia has a great affinity for water, and diffuses readily and rapidly throughout any available volume of water.\u00a0 Land animals must arrange to get rid of nitrogen wastes from the blood through the kidneys as urea in urine.\u00a0 Fish can rid themselves of much ammonia just by the circulation of the blood through their gills, where it will readily and rapidly diffuse out into the surrounding water.\u00a0 This is great for the fish in the wild, less favorable within the limited confines of out tanks. We have limited water volume, so ammonia builds up quickly.\u00a0 Ammonia tests used in the hobby read in milligrams per liter (mg\/l), or as parts-per-million (PPM or ppm), 1 mg\/l = 1 ppm for our purposes.\u00a0 Ammonia is toxic as low as 0.25 ppm as other than very short-term exposures.\u00a0 Between 0.5 and 1.0 ppm there can be long term or permanent damage to the gills by chemical burning.\u00a0 At levels much higher than 1.5 ppm death may occur at any time.\u00a0 There is a significant difference in the range of resistance of any particular genus or species, and by the age of the particular fish, to ammonia damage, or in exact levels of damaging or fatal concentrations.\u00a0 Ammonia it is never healthy at levels detectable by standard aquarium test kits.\u00a0 Even the lowest detectable levels, maintained for any length of time, can have negative effects.\u00a0 Ammonia is also added to the tank water as metabolic waste from the microbes and infusoria in our tanks, and from their action on fish solid waste and uneaten food, decaying plants, etc.<\/p>\n<p style=\"margin-top: 0.19in; margin-bottom: 0.19in\">Mother Nature has provided bacteria that \u201ceat\u201d ammonia, oxidizing it to nitrite and gaining energy for use in their own metabolism.\u00a0 You can think of ammonia for these bugs as serving a similar role to carbohydrates for us.\u00a0 These ammonia-oxidizers will grow and multiply to populations sufficient to consume whatever levels of ammonia are present in their native water (our fish tank).\u00a0 Great, they have gotten rid of the toxic ammonia that would otherwise kill our fish, not as a public service, but by working for a living as we do.\u00a0 Wonderful, BUT their nitrogenous waste product is nitrite ion (the same nitrogen atom, oxidized by the addition of two oxygen atoms, NO2).\u00a0 Nitrite (3) is also highly toxic to fish. Again 0.25 ppm nitrite-N is not good other than very short term, above 0.5 ppm dangerous, and 1.0 ppm can be fatal.\u00a0 At nitrite-N concentrations, the numbers are even worse than for ammonia. If you wish to use true nitrite ion concentrations (the whole NO2 ion), the nitrite-N reading should be multiplied by 3.3 \u2013 on the boards you should specify which figure you are using.\u00a0 That is because 0.25 ppm of nitrite-nitrogen is >0.75 ppm of nitrite ion.<\/p>\n<p style=\"margin-top: 0.19in; margin-bottom: 0.19in\">Again Mother Nature has provided for our nitrite issue.\u00a0 A second type of bacteria uses nitrite just as the first group used ammonia, as an energy source.\u00a0 It “eats” nitrite and oxidizes it to nitrate (the same nitrogen atom, but now with a third oxygen atom attached, NO3, nitrate ion).\u00a0 Guess what?\u00a0 Nitrate is essentially non-toxic short term at these concentrations, more than two orders of magnitude less toxic than the preceding two metabolites, ammonia and nitrite.\u00a0 Long-term toxicities are a slightly different matter.\u00a0 High levels of nitrates, above 40-50 ppm, (along with other less testable pollutants) in the tank water can slow growth, suppress breeding, depress the immune system – making the fish more susceptible to disease, etc.\u00a0 Again there are apparently significant species variations in nitrate ion and other pollutant tolerance, and the whole area is poorly studied.\u00a0 Most laboratory studies use nitrate alone, the simplest case.\u00a0 That test platform does not, and cannot, reflect the real-world situation in out tanks.\u00a0 Nitrate to us is a symptom and indicator of general pollution.\u00a0 For general use, 20 ppm to maybe 40 or 50 ppm might be an acceptable range, but I try to keep my tanks at or below 10 ppm, or at least below 20 ppm, with 10 ppm as the post-partial water change goal.\u00a0 The \u201cacceptable level\u201d has to be set by each tank keeper, depending on their own level of comfort and their plans for the tank inhabitants by considering the importance of breeding, growth rates, and long life balanced against the upkeep required.\u00a0 Nitrate testing is for me a useful measure of the general pollution level in the tank.\u00a0 The other pollutants are much harder to measure, impractical at home, so nitrate serves as general pollution indicator in other than heavily planted tanks with light fish loads.<\/p>\n<p style=\"margin-top: 0.19in; margin-bottom: 0.19in\">The bacteria responsible for oxidizing ammonia to nitrite, and nitrite to nitrate are called lithotrophic bacteria, or lithotrophs.\u00a0 This name means \u201crock-lover\u201d or \u201crock-grower\u201d, because they are found firmly attached to solid, usually quite firm (to them if not necessarily so to us), substrates.\u00a0 To these bacteria, plastic foams (sponges) are hard, as are most synthetic fibers.\u00a0 These bacteria do not occur as functional metabolizing and multiplying forms in the water column, only when attached.\u00a0 They can and will occupy any solid surface in the tank \u2013 gravel, rocks, glass, filter sponges or floss of fiber mats, ceramic or glass beads, plastics, etc.\u00a0 They can occur any of these places, but the most favorable dwelling for them is in the filter.\u00a0 That is the case whether it is gravel for a UG or RFUG, sponges, floss, beads, spheres, or whatever, in canisters or HOT\/HOB power filters, or in fluidized bed filters.\u00a0 This is the most favorable location for them because the constant flow of water is providing the bugs with the two things they need most after an attachment site \u2013 oxygen and an energy source (ammonia or nitrite) along with an assortment of other nutrients. The bugs in such a home will have a competitive edge over bugs living dispersed on the glass or ornaments in the tank or even the gravel, which have to rely on diffusion or much lower water currents for their food and oxygen needs.\u00a0 Unfortunately, neither of the originally named two types, nor the most likely current candidates have a spore or other resting forms, so in practice both types must be obtained live and actively metabolizing.<\/p>\n<p style=\"margin-top: 0.19in; margin-bottom: 0.19in\">Where do we get these wonderful tank helpers?\u00a0 Well, it is possible to get them with fish. As fish nibble on their environment a lot in the search for food, they tend to have ingested a few good guy bacteria as they grazed, and when we bring them home, some of these bugs may survive the fish\u2019s gut to initiate a colony in our tanks.\u00a0 This is the old way to \u201ccycle\u201d a tank, using a few, hopefully relatively ammonia resistant, fish to start off.\u00a0 It does work, but it is anything from lightly to severely stressful for the fish (and keeper).\u00a0 It can lead to the development of numerous diseases in and on the fish (from the stress-reduced resistance of the fish).\u00a0 Thus we are multiplying the chances for fish death not just from direct toxicity of the metabolites, but by disease, and also from inappropriate treatment with shotgun medications (used in attempts to combat and control the stress-induced diseases).\u00a0 Those same medications may also directly suppress or kill the good guy bacteria we have been trying to cultivate, kicking us back to square one and starting the whole cycle over, but with weakened fish.\u00a0 If you have existing tanks, you can prepare for additions by getting your filters in advance and running them for 3-6 weeks (the longer the batter) on existing, healthy, balanced, mature tanks along with those tanks\u2019 regular filters. This will inoculate the new filter quite well.\u00a0 Then it can be moved to the new unit and it will be ready for at least starter fish.\u00a0 Mature colonies of these good-guy bacteria are not static – if they are eating well they multiply by division.\u00a0 Old biofilms (large or tiny sheets of attached bacteria, joined to one another and the surface they grow on) can shed or \u201cshale\u201d off.\u00a0 Some of these loose fragments of film or individual bacteria may be in the water column temporarily.\u00a0 But they cannot metabolize there.\u00a0 If they cannot attach to a vacant surface soon they will die.\u00a0 Or you can use Dr Chris Cow\u2019s fishless cycling techniques (3), which I strongly support.\u00a0 There have been many earlier attempts to cycle tanks without fish, and some even worked- but many required access to and experience in a laboratory, or were poor and uncontrolled processes.\u00a0 Dr Cow\u2019s technique is not cut-and-dried.\u00a0 It may need a bit of minor juggling depending on local conditions (<a href=\"http:\/\/www.thepufferforum.com\/forum\/library\/water-filtration\/fishless-cycling\/\"><u>Please See: Fishless Cycling<\/u><\/a>), but it is far better, safer, and surer than any other I have seen and tried.\u00a0 The most difficult part of the technique is learning patience while the process is establishing the needed bacteria in the tank.<\/p>\n<p style=\"margin-top: 0.19in; margin-bottom: 0.19in\">If you do use fish to cycle the tank, monitor the metabolites regularly, at least once a day – and twice is better.\u00a0 If or when they move to detectable levels, reduce your feeding markedly.\u00a0 It is hard to starve a fish (other than Loricariids, sucker-mouth catfish, or other specialized feeders, and even that is not short term).\u00a0 Drop back to every other day or even every third day feeding.\u00a0 This will reduce the waste load.\u00a0 I suggest water changes whenever the metabolites reach any potentially toxic levels, to bring the concentrations back down to merely undesirable ranges, or even better, to undetectable levels.\u00a0 The nitrifying bacteria seem to “saturate” (grow and divide at maximum rate) at ammonia or nitrite levels well below hobby test kit detection, so are growing at full speed before we can read their “food” by our kits.\u00a0 The filters should not be disturbed (unless they are clogged) with this water change, nor the gravel vacuumed (unless you have overfed and have visible decaying\/molding food on the substrate – then vacuum lightly \u2013 the lesser of two evils).\u00a0 The preferred site is the filter, but new colonies may appear anywhere.\u00a0 Over time the colonies in the filter will carry almost the whole load, but this cannot be guaranteed initially.\u00a0 Add stock to the tank very slowly.\u00a0 The water changes done to reduce the concentrations of toxic metabolites will <strong>not<\/strong> slow the development of the good-guy bacterial colonies.\u00a0 That is due to the already mentioned fact that these bacteria are growing and dividing as fast as they can <em>below<\/em> the lowest detectable level of our test kits.\u00a0 If we reduce the concentration of ammonia in the tank from say 1.0 ppm to 0.25 ppm or lower, we are reducing the damage to the fish markedly.\u00a0 We will be protecting the fish against damage or death, without slowing the development of the bacteria.<\/p>\n<p style=\"margin-top: 0.19in; margin-bottom: 0.19in\">So long as there is detectable or just undetectable ammonia (or nitrite) in the tank, the bacteria are multiplying as fast as they are can to meet the available food supply.\u00a0 These bacteria are not fast growing.\u00a0 Their division and multiplication is very slow in relation to most other bacteria.\u00a0 If you start cycling with no inoculum, or with a very small inoculum, the total cycle is going to be longer.\u00a0 Slow growth means a longer time spans to a mature colony.\u00a0 This is one advantage to fishless cycling. The higher levels or titers used there do not give faster growth, but do in the end give much larger colonies of each type of bacteria.\u00a0 When you measure ammonia or nitrite in a tank with fish, you are taking a snapshot of the ammonia present at that moment, not the rate of accumulation of one or several days, unless you have been testing and recording data in the past.\u00a0 Fishless cycling uses single daily doses of more ammonia as needed to maintain levels greater than the maximum produced in an overstocked tank in 24 hours.\u00a0 If that can be cleared within 24 hours, and the resulting nitrite cleared in the same 24 hours, then your filter will handle a full bioload from day one.\u00a0 With fish cycling, the colony will handle the daily production of the fish present now, period.\u00a0 Adding more fish means a mini-cycle that may or may not be detectable by standard hobby test kits, depending on the number of fish added in relation to the original stock.\u00a0 High titers cannot be allowed during fish cycling, it will injure and can kill the fish (both counter-productive and cruel).\u00a0 I hope that makes sense and is clear. The take-home lesson here is that the level or titer of ammonia or nitrite shown by hobby teat kits does not affect the growth rate for the bugs in the ranges we can detect, but does affect total colony population size.\u00a0 By the same token, excessive titers of either metabolite (ammonia or nitrite) can inhibit the bacteria we want to support.\u00a0 Some to enough food is good, too much can be a problem.<\/p>\n<p style=\"margin-top: 0.19in; margin-bottom: 0.19in\">One other point is that if the initial inoculation is small, as it is by adding fish, the ammonia-oxidizers will build numbers so slowly that the nitrite-oxidizers may starve before there is enough nitrite to “feed” them, so they may die off in part or completely.\u00a0 This can give an even longer nitrite “spike” (detectable accumulation of nitrite) than the ammonia spike was. This can be defeated by re-inoculation of the filter\/tank after any extended (10 days to 2 weeks or more) ammonia spike.<\/p>\n<p style=\"margin-top: 0.19in; margin-bottom: 0.19in\">By the way, the first time I used the term “cycle” above, I put it in quotation marks. This was intentional.\u00a0 The nitrogen cycle is well known and recognized in biology and ecology, and we borrow the term for the process of conditioning our tanks by development of the two needed bacterial types for the oxidation of ammonia through nitrite to nitrate.\u00a0 In reality, we do not have a complete nitrogen cycle in our systems.\u00a0 If we did, we would need to have cyanobacteria or other life forms capable of \u201cfixing\u201d atmospheric nitrogen (taking nitrogen gas from the air or dissolved in water and incorporating it into body mass).\u00a0 Then we would need the use of that fixed nitrogen by other creatures in the food chain until it got to the level of our fish and was used by them until excreted as ammonia waste, oxidized to nitrite and then nitrate. That nitrate would then need to be reduced (via anaerobic bacteria such as in a plenum or denitrator) to nitrogen gas, N2, and returned to the atmosphere to complete the loop of the cycle.\u00a0 So we really have only a very small slice of the nitrogen cycle in our tanks, but we use the broader term routinely.\u00a0 It is okay; it is that part of the full nitrogen cycle that we have in our tanks.\u00a0 We do lots of things that are worse.<\/p>\n<p style=\"margin-top: 0.19in; margin-bottom: 0.19in\">The next section of this article will talk about some of the other good guy bacteria and other life forms that inhabit our tanks, and which are needed to bring the tank to “maturity” (balance, with no upsets in nitrification or water clarity causing cloudiness) and keep it at that level indefinitely. Plus a few things that can go wrong, and some thing that can help the tank come into balance, or at least help us understand why and how it is out of balance.<\/p>\n<p style=\"margin-top: 0.19in; margin-bottom: 0.19in\">Footnotes:<\/p>\n<p style=\"margin-top: 0.19in; margin-bottom: 0.19in\">(1) <a href=\"http:\/\/en.wikipedia.org\/wiki\/Ammonia\/\/\"><u>http:\/\/en.wikipedia.org\/wiki\/Ammonia<\/u><\/a><\/p>\n<p style=\"margin-top: 0.19in; margin-bottom: 0.19in\">(2) Ammonia, NH3: A nitrogen atom with three hydrogen atoms attached, or in water, commonly with extra hydrogen to make the ammonium ion, NH4+.<\/p>\n<p style=\"margin-top: 0.19in; margin-bottom: 0.19in\">Note that while the dissolved gas ammonia is highly toxic, the ammonium ion is effectively non-toxic. In water there is a complex equilibrium between the two forms, which is determined by the temperature and the pH of the water. There is no simple cut-off, but a gradual curve of the shift in the balance between the two forms. For more detail, see:<\/p>\n<p style=\"margin-top: 0.19in; margin-bottom: 0.19in\"><a href=\"http:\/\/www.thekrib.com\/Chemistry\/ammonia-toxicity.html\/\/\"><u>http:\/\/www.thekrib.com\/Chemistry\/ammonia-toxicity.html<\/u><\/a><\/p>\n<p style=\"margin-top: 0.19in; margin-bottom: 0.19in\">(3) Some of the test kits that I use for measuring ammonia, nitrite, or nitrate measure nitrogen only \u2013 that is, it is measuring the nitrogen content only, not the whole ammonium, nitrite, or nitrate ion. So if you were discussing such test kit results on the boards, it would be better to specify the readings as \u201cnitrite-N\u201d or \u201cnitrite-nitrogen\u201d if using such a kit or just as “nitrite” if your test reads the whole ion, not just nitrite-nitrogen. In practice this is seldom done.\u00a0 Most kits seem to be becoming more consistent in specifying, but there will always be some confusion on this.\u00a0 By the way, these types of kits (nitrogen-only versus total ion) use the same chemistry; their reporting scales are just different.\u00a0 In chemistry and biology, there are advantages to tracking the nitrogen-only, as one ppm of total ammonia nitrogen gives one ppm of nitrite-nitrogen when first oxidized, and that in turn gives one ppm of nitrate-nitrogen when fully oxidized.\u00a0 Material balances are easy with those scales.\u00a0 With total ion measures, material balances are more complex.\u00a0 One ppm total ammonia-nitrogen (TAN) gives 3.3 ppm nitrite ion which in turn gives 4.4 ppm nitrate ion.\u00a0 That difference is due to the various total weights of the ions in the sequence of metabolites.<\/p>\n<p style=\"margin-top: 0.19in; margin-bottom: 0.19in\">(4) <a href=\"http:\/\/www.tropicalfishcentre.co.uk\/Fishlesscycle.htm\/\/\"><u>http:\/\/www.tropicalfishcentre.co.uk\/Fishlesscycle.htm<\/u><\/a><\/p>\n<p style=\"margin-top: 0.19in; margin-bottom: 0.19in\"><u><font face=\"Times New Roman, serif\">An earlier version of this article appeared originally in AquaSource magazine. It has been edited and updated for this site, March, 2010.<\/font><\/u><\/p>\n<p style=\"margin-top: 0.19in; margin-bottom: 0.19in\">Robert T. Ricketts, a.k.a. RTR<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Aquarium Microbes Part 1:\u00a0 Nitrification What do you keep in your tanks?\u00a0 A big school of Tetras?\u00a0 A pair of Cichlids?\u00a0 A few billion bacteria?\u00a0 Don\u2019t gag.\u00a0 The \u201cbugs\u201d are the most numerous things in our tanks and are ultimately responsible for our success if we are to keep our fish alive and healthy.\u00a0 Every … <a href=\"https:\/\/www.thepufferforum.com\/forum\/library\/water-filtration\/aquariummicrobespart1\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">I. Aquarium Microbes, Part 1: Nitrification<\/span><\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[6],"tags":[],"class_list":["post-145","post","type-post","status-publish","format-standard","hentry","category-water-filtration"],"amp_enabled":true,"_links":{"self":[{"href":"https:\/\/www.thepufferforum.com\/forum\/library\/wp-json\/wp\/v2\/posts\/145","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.thepufferforum.com\/forum\/library\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.thepufferforum.com\/forum\/library\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.thepufferforum.com\/forum\/library\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.thepufferforum.com\/forum\/library\/wp-json\/wp\/v2\/comments?post=145"}],"version-history":[{"count":0,"href":"https:\/\/www.thepufferforum.com\/forum\/library\/wp-json\/wp\/v2\/posts\/145\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.thepufferforum.com\/forum\/library\/wp-json\/wp\/v2\/media?parent=145"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.thepufferforum.com\/forum\/library\/wp-json\/wp\/v2\/categories?post=145"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.thepufferforum.com\/forum\/library\/wp-json\/wp\/v2\/tags?post=145"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}