Very Good Reading For All.

[Shaddex]

Not sure this has been posted as I couldnt find it in the forums.

Take a read.

http/www.bioconlabs.com/nitribactfacts.html

 

[daizeUK]

Some good information there, thanks for posting.
 

Each molecule of chloramine that is reduced will produce one molecule of ammonia. If the chloramine concentration is 2 ppm then your aquarium or system will start out with 2 ppm of ammonia. Chlorine Remover will reduce up to 2 ppm of chlorine at recommended dosages. During the warmer months chlorine levels may exceed 2 ppm. A double dose would be required to effectively eliminate the excess chlorine. 

 
This always confuses me.  That's the third time I've seen a 1:1 conversion ratio of chloramine to ammonia quoted by knowledgeable sources, yet the molecular weights of these two substances would suggest a 3:1 conversion depending on pH (this has been discussed before).  Can anyone clear up why 2ppm of chloramine produces 2ppm of ammonia?

 

[TwoTankAmin]

Having read that a few years ago I can tell you it has a few glaring holes. The biggest is that Nitrobacter are not the ones that oxidize nitrites, its Nitrospira and Nitrosopira.. That piece is primarily a sales pitch for Fritz-zyme. Second, they refer to "scientific studies" but do not provide references. I have been searching for a few years now for published research dealing with how much ammonia the bacteria can convert and have had almost no luck. While this does not mean such research doesn't exist, I sure have not been able to find it. It is my belief that the bacteria can process more ammonia thab cab the archaea which are the current hot topic regarding ammonia oxidation.
 
Most of what I can find relating to the efficacy of Fritz-zyme is not the complete research study, but are sales pitch type summaries. What I would need to see for this product is the same sort of study Dr, Hovanec did to identify the tank nitrifyers. This not only looked a various bacteria strains present at the start up of the experimental tanks, but then they tested down the road once the tanks were cycled to determine what bacteria were present at that point. Other studies I have read take a similar approach.
 
There are a variety of bacteria that can oxidize ammonia and nitrite, but just because one can add them to a tank and see immediate results doesn't mean those bacteria will persist. from the little I can find regarding Fritz-zyme, most seems to relate to sw with not much on their fw product.

 

[daizeUK]

The biggest is that Nitrobacter are not the ones that oxidize nitrites, its Nitrospira and Nitrosopira

 
Now personally I get confused between Nitrosomonas, Nitrospira, Nitrobacter et al, I can never remember which ones were discredited and which ones are meant to be the current favourites.  So I did look it up on Wikipedia to remind myself for the purposes of verifying the article and Wikipedia seems to agree, in summary:
 
A-Bacs
Nitrosomonas - Soil, Sewage, freshwater, Marine
Nitrosococcus - Freshwater, Marine
Nitrosospira - Soil
Nitrosolobus - Soil
 
N-Bacs
Nitrobacter - Soil, Freshwater, Marine
Nitrospina - Marine
Nitrococcus - Marine
Nitrospira - Marine, Soil
 
According to this, Nitrospira are not freshwater bacteria and Nitrosopira are soil A-bacs, so I am surpised that Wiki is completely wrong and nobody has bothered to correct it - can you verify those are definitely our nitrifiers?

 

[daizeUK]

Okay this intrigued my curiosity so I decided to delve in deeper to get to the bottom of it.
 
First off, that Wiki table that I referenced seems to be misleading and incomplete or uninformed and I think it's probably best to ignore it.  It certainly confused me.  I thought it meant that Nitrosospira was only a soil-based bacteria, but I've since discovered that both Nitrospira and Nitrosospira can play a part in freshwater nitrification.
 
A wider search of the web quickly reveals that TwoTankAmin is quite right in saying that Nitrospira are responsible for converting nitrite to nitrate, not nitrobacter.  Nobody seems to dispute this (except Wikipedia, which I really thought should be updated by now )
 
The A-bacs are a bit more complicated and extremely interesting.  I've seen studies claiming that Nitrosospira are the primary A-bacs, but they seem to be contradicted by this study:
 
Identification of Bacteria Responsible for Ammonia Oxidation in Freshwater Aquaria 2001
http/www.ncbi.nlm.nih.gov/pmc/articles/PMC93373/
 
I found it a bit heavy going but it seems to say that there are four different species of freshwater A-bacs, including Nitrosomonas and Nitrosospira, which operate most efficiently at different ammonia concentrations.  The study concludes that the specific species Nitrosomonas marina is the most efficient converter of ammonia to nitrite and is most commonly found at low ammonia concentrations, such as those found in an established tank.
 

 When ammonia concentrations were varied, AOB population shifts did occur, thereby altering the presence and activity of important AOB. Low-ammonia environments will likely produce Nitrosomonas marina-like AOB, while as the ammonia concentration increases, Nitrosospira tenuis-like and Nitrosomonas europaea-like AOB will become important until at the highest ammonia concentration Nitrosococcus mobilis-like AOB may be predominant. Our results suggest that the AOB found in fish culture environments, such as public aquaria, aquaculture facilities, and home aquaria, where the ambient ammonia concentration rarely exceeds 5 mg of N per liter, are different from the traditional Nitrosomonas europaea-Nitrosococcus mobilis cluster type AOB, which are prevalent in the high-ammonia concentrations typically found in environment such as wastewater and sewage treatment facilities. This, and our results with enrichments of the various strains of AOB in newly set-up aquaria, strongly suggest that start-up inocula for the establishment of nitrification in aquatic culture systems should optimally consist of Nitrosomonas marina-like AOB rather than Nitrosomonas europaea-Nitrosococcus mobilis cluster AOB.

 
TwoTankAmin have you seen this study?  What do you think of it?  The other studies I've seen talking about Nitrosospira don't seem to mention Nitrosomonas marina, only Nitrosomonas europaea.  Do you know of some other evidence to support Nitrosospira?

 

[TwoTankAmin]

Yes- if you look at who the authors of that study are you will discover Dr. Hovanec is one. That study was the 3rd in a series that began with a paper published in 1996 in which they discovered that the bacteria traditionally believed to be the ones to handle cycling in tanks were not the correct ones. The second paper published in 1998 he and his co-researchers discovered that it is was nitrospira and not nitrobacter that did the nitrite oxidizing. It took another 3 years to nail down the ammonia oxidizers in fresh water tanks in a study published in 2001 from which you quoted above.
 
And all that researching led first to Bio-Spira and then to DrTim's One and Only and Tetra's Safe Start. When Marineland was aquired by a pet congomerate that shut their facility in California and rolled it into Tetra and moved it to Germany with US operations in Virginia (I am quoting this from memory so I may be off a bit). Dr Hovanec took over the California facillity and started his own firm. He holds patents on both some of the techniques for identifying the bacteria and for the bacteria itself. Because of his relationship with the companies involved, Tetra's product contains the same bacteria to the best of my knowledge.
 
Now comes the part that tends to drive me crazy on this site at times. And that is folks who state none of Dr. H's work is any good nor that anything he says about the bacteria can be trusted because he sells products based on his research. But the fact is those studies are cited often over the years by many other reseachers and that his is not the only name on any of the studies.
 
Now if you really want to drive yourself nuts, start looking into ammonia oxidizing archaea. Since about 2005 this has been a hot topic in the field of nitrification by micro-organisms. I have spent a fair amount of time reseaching these guys as well as the bacteria. So far my conclusion is that while they may be relevant in nature, in fw tanks they are less so and I am not sure what their role may be in sw tanks. I have seen too much research which suggests that in many applications the bacteria carry the real load not the archaea. The problem with many of the studies in this area is they tend to rely on counting of amo genes for archaea vs bacteria. Because the former are always present in greater number the general conclusion was they must be carrying more of the load. Further research calls that into question.
 
I have actually had an exchange with another microiologist about this some time back. Then he was a proponent of the archaea theories and I was arguing the evidence was not really there and that there were too many unanswered questions. Since then I have found lots of research that says the same thing I felt to be the case or which tend to refute the role of archaea in many situations. I have also come across studies which support the idea that archaea are major ammonia oxidizers. An interesting thing about the archaea is they have yet to discover any that oxidize nitrite, only ammonia. They also have the strongest affinity for ammonia which allows them to function and reproduce at the lowest concentrations. Concentrations that are insufficient for the bacteria. They also seem to rely on copper rather than iron (which the bacteria use) in the oxidation process.
 
As an aside, I have posted on this site in the past on many of these things. Take a look at this thread http/www.fishforums.net/index.php?/topic/394320-an-open-challenge-to-ianho/
 
I became interested in the whole topic of the nitrifying bacteria in aquariums a couple of years back. Because I have the time to do so, I have spent many many hours researching all these things. I have read 100s of abstracts because I could not get free access to the full studies. I have read dozens of those full studies that are available as open source. Unfortunately, studies like those by Dr. Hovanec et. el. which are specifically about aqauriums are few and far between. Most of the studies relate to waste water or drinking water treatment, to aquaculture or to the bacteria in nature.
 
As best as I can tell the bacteria are highly adaptable which is why you see a lot of research which say the bacteria is close related to or seems to be a strain of. The biggest clues one can pick up are that in a lab setting bacteria behave differently than they do in nature, which complicates everything. For example, youregularly see posted on fish sites that nitrification stops at lower pH, even Dr. Hovanec will say that most of the time. However, this is not correct, and he also knows this. What he will tell you happens is that bacteria can adapt and function at acid pHs. However for most fish keepers this is not relevant as they normally do not keep tanks with a pH below about 6.5.
 
However, if one keeps fish like altum angels you need to have them in very acid water. Altums are a pretty sensitive fish, especially when freshly imported. Many folks will keep them long term in a tank with a pH under 5.0. It would be almost impossible if there was no cycle established. How one gets the bacteria to establish at a pH of 4.2 is a long process. But the fact that nitrification happens at those pH levels is in the research. If you are interested, have a read here, its a full study, http/aem.asm.org/content/72/6/4283.full The paper is titled "Nitrification in a Biofilm at Low pH Values: Role of In Situ Microenvironments and Acid Tolerance" and you will see this:
 

Instead, we found a strongly acidic microenvironment, evidence for a clear adaptation to the low pH in situ, and the presence of nitrifying populations related to subgroups with low Kms for ammonia (Nitrosopira spp., Nitrosomonas oligotropha, and Nitrospira spp.).

 
And here we are back at Nitrosospira, Nitrosomonas and Nitrospira. I am reminded of the saying: "What ever goes around, comes around."

 

[daizeUK]

Aha!  I should have noticed Dr Tim's name on that study.
 

The problem with many of the studies in this area is they tend to rely on counting of amo genes for archaea vs bacteria. Because the former are always present in greater number the general conclusion was they must be carrying more of the load. Further research calls that into question.

I see, that ties in with similar stories I've heard about heterotrophic bacteria etc. which can all process ammonia, but nowhere near as efficiently as a comparatively tiny population of the 'right' kind of nitrifying bacteria which actually does most of the work.
 
In the beginning, I guess the only thing we really care about is establishing a population of micro-organisms that are capable of processing ammonia and nitrite quickly in order to make the tank habitable.  As long as it can accomplish this then the tank will eventually mature and settle down and may end up with a completely different set of organisms depending on the conditions, it will find its own equilibrium over time.  The important thing is to get it up and running with something that works!
 

Instead, we found a strongly acidic microenvironment, evidence for a clear adaptation to the low pH in situ, and the presence of nitrifying populations related to subgroups with low Kms for ammonia (Nitrosopira spp., Nitrosomonas oligotropha, and Nitrospira spp.).

 
And here we are back at Nitrosospira, Nitrosomonas and Nitrospira. I am reminded of the saying: "What ever goes around, comes around."

 
I immediately notice that it's a different species of Nitrosomonas however.  It strikes me that the individual species of bacteria is crucially important as they all fulfill seperate niches.  Some operate at higher ammonia concentrations, other will thrive in low pH conditions.  It is starting to dawn on me that just saying 'Nitrosomonas' without specifying a species is perhaps too vague.
 
 
You've given me a lot to read through, I will work through it with interest.  (By the way, I'm not ignoring the other thread either, just slowly catching up on my reading )

 

[daizeUK]

Now comes the part that tends to drive me crazy on this site at times. And that is folks who state none of Dr. H's work is any good nor that anything he says about the bacteria can be trusted because he sells products based on his research. But the fact is those studies are cited often over the years by many other reseachers and that his is not the only name on any of the studies.

 
TTA, I've had a good read through of your old thread and associated posts where you discussed this in depth wth Ian and OldMan.  It seems to me that after you presented your evidence there was no further argument to the idea that Dr Tim's/SafeStart contains the right strain of nitrifiers and hardly any interest in opposing the idea that those bacteria can survive dormant in a bottle.
 
You effectively shot down the argument that his research is biased by commercial interests because of the timeline of the research, Dr Hovanec's employment status at the time of the research, the contribution of other neutral researchers, subsequent peer review and lack of contradictory research since.
 
It seems like pretty compelling evidence to me.
 
The weak argument that "Product X doesn't work, therefore all bacteria-in-a-bottle products don't work" doesn't wash, given that most Product X products won't even publish the contents of the bottle.
 
The anecdotal argument that "Dr Tim's didn't work for 50% of forum users who tried it" is also inconclusive since mostly we don't know if the product was used correctly in most of those cases.  However I have seen reports from people who swear blind they used it properly and it still didn't work, so let's assume for a moment that the product does fail for a certain percentage of cases through no fault of the user.  I'm personally coming to the conclusion that the properties of local tapwater and other ambient conditions beyond our control can play a huge part in fishless cycling.  To illustrate with examples, there's a post on the forum right now from someone who is almost fully cycled after two weeks with almost no effort, meanwhile others take several weeks just to see a drop in ammonia.  I can easily believe that these ambient conditions can also affect the effectiveness of bacterial additives, so not everyone should expect the same results.  That doesn't mean that the product is worthless.
 
So, after all the discussion and evidence, is anyone really still arguing that Dr Hovanec's research cannot be trusted?
 
If not then surely this information should be wrapped up into a newbie-friendly format (such as part of a beginner's guide to fishless cycling) and made more readily available for everyone to benefit from.  I'm finding it odd as a beginner myself that I have to deep-delve into complex scientific discussions to get to the bottom of it all.
 
Unless there are legal reasons why the forum can't endorse a particular product (or provide advice that would effectively amount to free advertising)?
 
I do wish something as important as this would be formally agreed and acknowledged in a permanent resource.  If nothing else, it must be as frustrating for you to keep arguing the same thing over and over again as it is for a beginner to have no other option than to read through the entire history from scratch.

 

[TwoTankAmin]

There is one good reason that there are some failures with the bottle bacteria. It gets exposed to fatal temperatures by the shipper or vendor. The stuff is pretty hardy as long as it isn't allowed to freeze or to get too hot. Either of these conditions will kill the bacteria. While the makers try to prevent this, they have no control. And how many of the failed users did not take care and caused this? You buy a bottle, its summer and you are running errand. You leave the stuff in your locked car. We all know how hot it can get or its winter and etc etc.
 
Also, you will see a lot of posts by people using it who are told to do something contrary to the directions, They listen and then things go wrong and they claim the product is no good. I have used Dr Tim's bacteria several times over the past two years. I got some directly from his site and some from a big online vendor- both worked as advertised. I have used his ammonium chloride too. But my saying it works has about the same weight as those who claim it doesn't. Neither is based on properly conducted research, only on anecdotal reports. When we go back and forth about the potential harm from various levels of ammonia exposure or the conditions involved we looked to the available research. We did not use anecdotal evidence, we tried to rely on the science.
 
But like you said the average fish keeping newbie is not looking to learn, they want to be told what to do. But when that results in suggestions which run counter to the science I think somebody needs to respond. It is difficult to make an intelligent decision when you do not have the correct facts. The problem is that the correct facts are no usually that simple nor easy to explain.
 
I got tired of reading posts where folks blindly repeated the same things as if they really knew rather than had seriously investigated. So one day i decided to check things out for myself, and when I started searching I discovered the research and also how misinformed many folks are due to the urban myths.
 
Daize- there is a wonderful thread on the angel site I use. Unfortunately, it is a membership required to view site (the only one I have ever joined). It was started by one of the admins and is about how to cycle a tank for a pH under 5. Part of the thread involved contacting Dr. Hovanec on this topic and posting both the email sent and then Dr. H's reply. In essence it boils down the the great adaptability of the bacteria to survive their specific situation. If you pour a bottle of his stuff, or try to seed by using media drop a cycled tank and you plop it into acid water it will pretty much be killed. But if you cycle a tank at a pH of 7 and then gradually lower the pH in small steps over an extended period something interesting happens. As the pH is lower many of the bacterium die off from it, but some will survive. And the survivors able to work at that pH will then multiply and resume fully oxidizing in a week or two. And then your repeat the incremental pH drop and then let the survivors multiply again. Done properly you end up with a tank cycled at a really low pH. But you also basically have developed you own special acid pH resistant nitrifiers.
 
So what is the right thing to be telling people? Do you tell them the cycle stops if the pH drops to low or do you tell them that while cycling can take place at a low pH, it is not the same thing as the normal cycle which will appear to halt for their purposes if the pH drops too low and under normal circumstances the pH needs to be kept above 6.5 or so? And now you can start to apply this to many of the so called facts repeated from site to site for year after year. Where is the proper middle ground?
 
What I do know is that the articles here on cycling need to be redone, they are flat out wrong and incomplete. Oh- And I bet i could help you to get your tank cycled a lot faster than you might believe- but the problem is I would tell you that I had one condition- you listen to what I suggest only, you follow what I suggest. If nothing else this would result in one of two things- either would would succeed and cycle faster because of my suggestions or you would fail because of them. I have always told folks looking for help that it is asking for trouble to listen to more than one voice. Its kind of like that old saying about too many cooks.
 
And I am not saying I am the only person to whom one should listen, far from it. What I am saying is it is best to pick one adviser and just follow them. Do not let other voices distract you. Better to fail because you followed the wrong advice from one source and to learn from that than it is to fail because too many voices confused you and you have no clue what things went wrong. And that also means, over time, hopefully one learns where to find reliable advice. I know it is an ongoing process for me. I am still learning more and more all the time. In fact, I can tell you what sites to read posts from years past which show me saying many of the things today I no longer believe and which I try to refute.
 
And I did offer to rewrite the articles on cycling here right after your post in that thread by wills in the beginner resource section. My preference now on this site is to try to keep most of my posting in the scientific section. It got really hard to keep slogging when some of the staff or well respected long standing members are saying one thing and I am saying another. That is a big reason why I quote and link so much. I am basically saying don't take my word for it, read what somebody who has the credentials is saying about these topics.

 

[daizeUK]

Totally agree. 
 
When I was looking for information about fishless cycling I looked all over the net for information, every site has a slightly different way of doing it but it quickly became clear that the pinned thread on this particular site is in need of some TLC.  I support them being re-written but I do believe it needs to be kept simple for newbies and not over-encumbered with scientific details.
 
As a complete beginner my ideal resource would be one that explains exactly what I need to do, step by step, without any scientific jargon or complexity, but which also gives me a basic understanding of why things should be done that way, with links to more in-depth explanations if I should wish to learn more.
 

And I bet i could help you to get your tank cycled a lot faster than you might believe- but the problem is I would tell you that I had one condition- you listen to what I suggest only, you follow what I suggest.

 
I will take you up on that offer!   I want to make sure that I understand the instructions for Dr Tim's products correctly, so I will read up on them before they arrive and post what I think I need to do and I would appreciate if you could check and make sure that I'm doing it right.

 

[Geoff-]

As a complete beginner my ideal resource would be one that explains exactly what I need to do, step by step, without any scientific jargon or complexity, but which also gives me a basic understanding of why things should be done that way, with links to more in-depth explanations if I should wish to learn more.

 
I think if someone was going to re-write the guides then it needs to be split into two parts.
 
Part one is "here is a list of steps to achieve a cycled tank as quickly as possible"
 
Part two is "this is a detailed discussion of filter bacteria and the nitrogen cycle"
 
Part one should touch on the nitrogen cycle but only in as much as saying there are different bacteria that process ammonia->nitrite, and nitrite->nitrate.  Ammonia is harmful to fish and nitrate is fine as long as it doesn't build up.  It explains why we cycle tanks without getting into the nitty gritty of how it all works, and should only be a couple of lines or a short paragraph.
 
Part 2 is where you get into an in-depth discussion of the role of pH in the ammonia/ammonium balance and toxicity, the ratio of ammonia->nitrite->nitrate conversions, and the different types of bacteria that may dominate depending on the tank's pH.
 
Most people don't care how it all works they just want to cycle their tank.  Others will want to know the "how" part and will delve into part 2.