The topic of microorganisms in a tank or in nature is quite complex. The real key to a lot of it is in the biofilms. These holed a myriad of varying bacteria. There is ample research on the make of of such biofilms. Science know how the various microorganism inside the biofim are layer. They actually work in concert.
When it comes to which bacteria thrive in a given system, it is very much ammonia dependent. That is why there are different bacteria dominant in and aquarium vs a waste water treatment plant. You will find that aquariums have much more in common with drinking water plants and aquaculture.
What is at issue here is which types/strains of nitrifiers do most of the nitrification in tanks. As Byron pointed out, the ammonia oxidizers in fw and sw are not the same. Recent research (since 1005) has discovered that another group or microorganisms called Archaea also appear to do ammonia oxidation. They are clearly doing this in salt water and they are found in most soil and freshwater habitats as well. However, there is still more research needed in terms of their potential role in fw tanks and other fw environs. Some believe they are key players here while others still are unconvinced. I am in the camp of the unconvinced. the one thing that is know about these Archaea, they have the lowest affinity for ammonia which means they do best at the lowest levels. As levels rise they are usually by bacteria.
Moreover, no matter which strains dominate in an given system, there are normally some amount of other strains present. These few seem to hang around because nothing is stable and when things change, i.e. ammonia levels drop or spike up, the bacterial mix will change in response.
There is an amazing amount of research out there on these topics. Most of it is over my head in many of the specifics, but I do get the gist of these things. So when a paper talks about the specific gene testing protocols, I am lost until they get to the line that states as a reult of doing them they found X to be the case. I understand the X.
My reason for posting this thread was due to a long discussion/argument on this site that went on for quite some time on the consept of bottled bacteria. I argued that it was viable, did work but was dependent on the strain of bacteria involved, how it was grown and packaged. the other side, with a a number of folks arguing for it claimed this was hokum and that Dr. Hovanec's research was not valid because it ended up years later with his selling bottled bacteria based on it. It took me months of quoting research studies etc. before some folks finally saw the light. But this whi refused to accept the science always came back with the argument that it was not showing research done using specific products. And when I did find a study all could read w/o institutional access, this was it and here I posted it.
There is actually a lot of research on this topic out there. For example, while it is true that the normal bacteria we have in or tanks will stop processing ammonia when the pH drops below about 6.0, the reason for this is at those pH levels the ammonia all exists in the for of NH4 (ammonium) and none in the toxic NH3 form (ammoia gas). So when the NH3 vanishes, the NH3 using bacteria don't function. But there are other bacteria that do. The have receptors for NH4 and can and do use it, They process less effectivly than those found in the higher pH levels, but nitrification continues.
Nitrification in a Biofilm at Low pH Values: Role of In Situ Microenvironments and Acid Tolerance
http
/aem.asm.org/content/72/6/4283.full.pdf+html
Changes in ammonia oxidiser population during transition to low pH in a biofilm reactor starting with Nitrosomonas europaea
http/gwri-ic.technion.ac.il/pdf/Professors/Michal_Green/11.pdf
And I can confirm that there is nitrification in acid waters. I brought a number of wild caught altum angels into and uncycled tank at pH 4.2. I have a second tank i was working to have the media cycled using fishless methods to produce cycled media at 6.0. The plan was to raise the tanks to 6.0 gradually and when it reached that level the bacteria being developed in the biofarm tank would be ready and functioning at 6.0. But something went wrong with that plant. The angel tank cycled itself during that time and there was no need for the cycled filters. trace ammonia levels between .25 and .5 ppm which had been in the angel tank early on (but not harmful at the pH) completely vanished and there was never an issue. So I know, anecdotally, from my own experience that nitrification takes place at well under 6.0.
I have been reading on these subject for a few years now. Unfortunately, I lack a lot of the background needed to understand the nuts and bolt part of the research, but I do understand the basic processes at work and generally what makes them tick. My current interest is with the process of denitrification which I am still learning about.
There are a few doctorate level practicing microbiologists in this hobby and I have learned a lot by paying attention to them. I have been fortunate enough to correspond with one and to meet and chat with the other. And I am nutty enough to have a running disagreement with the latter on the role of archaea vs bacteria in fw aquariums and fw in general. We have reached a point where he is willing to concede that the archaea might not be there in any numbers at the start, especially when one has to cycle using fish or ammonia dosing rather than lots of plants, but would appear and then dominate later once a tank is cycled. His belief is the Archaea come to dominate after this period when ammonia levels are lower. I have come to accept that archaea may be present, but do not agree they would necessarily dominate. The science in general says more research is needed here to be more certain about what is going on in fw.
A lot of the problems with research is it is rarely aquarium specific. Most of it looks at more commercial considerations- waste water, drinking water, aquaculture and natural environments such as oceans, lakes, rivers soils etc. etc. Given the cost of such research, there are very few who will underwrite these costs when the research specifically involves our hobby.
I would suggest this, however. One might think that if you asked the two lifelong fish keeping practicing microbiologists mentioned above about how they filter their tanks, we might learn some interesting things. I am in the process of replacing a bunch of my filters with this approach as a result:
http/www.swisstropicals.com/library/mattenfilter/ I just inserted the second one recently and have the first tank almost totally relying on one. It takes about 6-10 week to make the switchover gradually. So far so good.
As for nitrate, there is research, but a lot of it is not hugely helpful. It is almost universally related to natural environments which have a host of things living in it from crustaceans to fish and everything in between. What levels are safe for 100% of these is not representive of what night be safe for most fish we keep in tanks. I can find you research on channel catfish which shows they can be Ok in nitrate levels that would make us freak ou if we saw them in a tank. but how many of us keep daphnia or channel cats in out tanks? There is also research on farmed fish to some extend and for the salmonids- another thing we never keep in tanks. I have seen a bit of research on a few fish.
Recirculating systems for zebrafish
It is important to test total ammonia (NH4) and nitrite (NO2-), about once a week using a water quality test kit. The water sample should be taken from the wastewater sump tank, before the water has been processed by the biofilter.
Ammonia and nitrite levels should be below 0.3 ppm. Nitrate (NO3-) is relatively harmless to aquatic animals in low levels. There is no data that indicates any water quality problems with nitrate levels < 200 ppm. Weekly testing of nitrates is suggested, to maintain levels < 150 ppm. If ammonia, nitrites or nitrates reach the upper limits, a water exchange of 10% of the water volume at a time is recommended.
from
http/integrated-aqua.com/wordpress/wp-content/uploads/2011/04/Lab-Animal-Zfish_scourtland.pdf
I can show you a paper where they looked at sw/brackish Juvenile turbot. The used 3 levels of nitrate and a control over a 42 days. They considerd low level nitrate to be "125 mg/L NO3–N (low nitrate LN)." because they measured the nitrat as nitrogen ions as opposed to the total ions or hobby kits measure, the number on our kits would have been 550 ppm. Now when we talk about nirtrate levels in tanks we consider 80-100 to be pretty high. the high level in that study was 500 mg/L NO3–N (2,200 ppm on an API kit). So rather that state it as Byron has done, I would say that above specified levels, nitrate can become toxic to fish. But for even the most sensitive of species i have never seen anything to support the idea that 0 is the required level as it usually is with ammonia or nitrite. For even the most sensitive of species i have never seen it suggested that nitrate needs to be below about 8.8 ppm NO3 (aka 2 mg/L-N).
Nitrate toxicity to aquatic animals: a review with new data for freshwater invertebrates
from
http/www.researchgate.net/profile/Alvaro_Alonso3/publication/8063535_Nitrate_toxicity_to_aquatic_animals_a_review_with_new_data_for_freshwater_invertebrates/links/543f9e150cf2f3e82851e42d.pdf
What is clear from the few studies i have been able to find is that is is not possible to use any single number for nitrate which would apply to everything. Different fish do have different tolerances. But this is the case for ammonia and nitrite as well. What we can conclude here is that for ammonia and nitrite undetectible is the only acceptable number and, with nitrate, that lower is always better but that undetectible is not necessary.
Once last comment. I do not consider that plants and bacteria compete for ammonia. The plants can not use NH3 only NH4. The bacteria need NH3. So the amount of bacteria in any tank will be what is required to handle the available NH3. When plants are included, that level stays lower. But here is what ZI see as the main difference between plants and bacteria in relation to total ammonia. No matter how many plants are in a tank, there is always some amount of NH3 and hence some bacteria present even if it is not all that much. It is especially present in the planted tank substrate. In fact, the plants have nitrifying bacteria living on them and their roots. Plants host bacteria but no bacteria hosts plants . So it is really not possible to find an established tank, no matter how well planted, without some level of nitrifying bacteria. On the other hand, it is commonplace to have tanks with no plants at all that rely 100% on bacteria (and archaea?) to remove 100% of the NH3/NH4.
I see the role of the bacteria/archaea as being one of clearing the ammonia as NH3 that may be available in any aquatic system. It doesn't matter if that is a very low or a higher level, they size in number to meet that need. While the plants may reduce the need, they are not really in direct competition with the bacteria. No matter how fast or how much plants can take up ammonium, they can never do so rapidly enough to eliminate any NH3 from being present even if its only there long enough to support a small colony of microorganisms.
