An Open Challenge To Ianho -

[OldMan47]

Sorry shrimply. I must agree with TTA here. There is nothing that you present that conflicts with the statements that TTA has made. Scientific papers are all that we can really care about unless one of us has independent evidence that the science presented itself is wrong. I appreciate your desire to help me but I cannot, in good conscience, depend on what you are speculating.

TTA: some piece of work? Let's get this straight. I have no interest in the outcome besides getting things right. If you feel challenged by that, I am sorry about that. I am not on a crusade and hold absolutely no desire to predetermine the outcome of this supposed discussion. If my presentation of information strikes you that way, maybe you need to re-examine your own attitudes. I want to know the real answer, not the results of some wild eyed prejudice.

 

[shrimply]

My Paper was purely to add to the discussion, I am on no ones side....
I accept it might not be perfect ( everyone knows scientists need to get work published, there is always some element of making "discoveries" more important than they are)

However, in slagging off the paper you made a few points I would argue with.

The next thing to look at is their information regarding the 35 tanks they used in their study. A number of the fw and sw tanks sampled came from the same two retail fish store's display tanks. Exactly how hard is it to imagine the potential for cross contamination between them? This is far from a controlled scientific source. And this brings me to another issue. You can see the parameters and other related data in Figure 1. It shows tank by tank information for gene copies for bacteria (none of which is ever identified by name anywhere in the study), Archaea and for the amo for each. it also lists info on tank parameters etc. They used sophisticated equipment to test for ammonia and for pH, but they state they performed the tests for nitrite, nitrate, hardness and alkalinity using Jungle Test Strips. Hmmmm.

They are scientists, I very much doubt they went round and emptied the filters into the same bucket, and if the retail tanks were connected to the same filter I doubt they'd count it as an independent unit. Of course there in no guarantee but I think its unfair to presume anything other than these being independent measures. If you mean that there may be cross contamination from cleaning etc then its possible, but not necessarily important. Which leads onto my next point, how many of us are interested in the situation in a "controlled scientific source"?. You can bang on about laboratory based experimental studies all you want, but you need to show their relevance in "the field". The data is only significant if you can relate it to the situation it is being used in, and without studies looking at home aquaria then you have no idea how significant it is.

Also take a look at the level of detail this study provides on its methods vs those in any of the 3 Hovanec studies. This one seems to be fairly short on information by comparison.

Scientist are under increasing pressure from journals to make papers as short as possible, therefore detail has to be dropped. I again don't think this is really a valid argument.

However, what I will say is that providing the data is correct, it doesn't argue your point. It occurs to me that there is very much likely to be some sort of succession going on here, with bacteria as the colonisers and archea coming in afterwards. Maybe this is known, or wrong I have not read as many papers as you on the subject clearly.

 

[TwoTankAmin]

Shrimply-

They are scientists, I very much doubt they went round and emptied the filters into the same bucket,

Did I say that? I indicated cross contamination, So you are saying the authors know for a fact that no nets were used in common, no hand/arms that went into one tank never went into another without a thorough washing first. You know decor, fish etc were never moved. Would it surprise you to learn that Archaea have been found inside NASA clean rooms? Google it. Contamination in the world of microorganisms such as bacteria and Archaea is a well known fact. And I guess you agree that Jungle test strips constitute scientific measurements. What did you say they never identify the bactreria they did find in the study? You refuted none of my comments above, sorry.

But aside form all that you have not done any checking up on either that studies, authors, its lone citation despite Archaea being the hottest topic for some time in microbiology circles involved with such things. And finally you have no idea howe Plos One works or the controvercies surrounding it. I do not trust what I find there without independent confirmation from more reputable and rigorous sources. I never link to studies on Plos One as I have checked them out and if you want to spend a few hours doing the same, here is a good start:
40 odd page article in pdf form PLoS ONE, Open Access, and the Future of Scholarly Publishing
These are shorter but much less comprehensive:
Is PLoS ONE Slowing Down?
Peer review lite at Plos One
The Problems With Calling Comments "Post-Publication Peer-Review"

And if you are really ambitious, you can locate the guidelines for peer review on both the site for the peer reviewed journal which published the studies by Hovanec et al and the ones from Plos one.

As to the statement about papers shrinking:
Hovanec et al. 1996 8.50 pages
Hovanec et al. 1998 7.00 pages
Hovanec et al. 2001 9.25 pages

And now back to the topic at hand. Ianho you have done a great job of evading the issue. 21 days and you have not responded by finding fault in the two studies. You did manage to misquote/distort what I said twice though and then failed to give readers links to the posts you chopped stuff out of to spin things. You have a good future in politics I think. But stay away form the world of science.

The stuff about bacteria surviving harsh conditions does not belong in this thread, the stuff about Archaea does not belong in this thread. So if you can not critique the science, may I assume it is a tacit admission that is it good science and that the bacteria identified are correct? That way we can move onto the next relevant topic, can bacteria, especially non-sporulating, autotrophic nitrifying bacteria survive the sort of conditions which would be present if they are put into a bottle for sale and be able to last in there be effective nitrifyers if put into a tank some months later. At least 6 months at room temps and as much as double that if refrigerated.

While I would like to move on with this discussion to the next phase. I still invite folks to post here any solid, peer reviewed, evidence that Hovanec et al. were wrong in their identification of the bacteria involved. Nothing to date supports the Archaea argument of ammonia oxidation relative to aquariums, especially fw tanks. In fact the literature on Archaea seems to suggest the opposite. And if somebody wants to start a thread in this section on this subject, I would be happy to participate. I have already begun bookmarking research studies on this topic in preparation. There are tons of them.

 

[ian]

thats because i'm waiting for the evidence you said you'd give me but quite clearly haven't! lol I'm not going to comment on stuff that i'm not overly interested in.


i'm waiting for the hard and fast evidence on the products we put in our tanks, specific to what we put in our tanks. I could go as far to say you're skirting around the subject.

I want a article with the title...''Does the One and Only really work?''


you have yet to provide me with it. You have provided info that states we 'might' be able to keep bacteria alive in bottles. You have provided evidence that Dr Tim has discovered various bacs...still waiting.


now climb from that soap box and find me some quick, i'm starting to get very bored of this thread.

 

[TwoTankAmin]

Lets try this from another angle then.

Ianho, I have just purchased a bottle of Dr Tim's and I have just purchased a bottle of Tetra Safe Start. Please tell me what is in each bottle.

 

[ian]

nooooo, please tell me if they work...

 

[TwoTankAmin]

I just realized something I should have spotted the first time I read this study last year. I should have spotted when shrimply's post made me reread it. It is about as close as you are going to get to the scientific proof you want.

I would ask you to take a look at the AOA article referenced by shrimply earlier in the thread http/www.plosone.o...al.pone.0023281 Ignore the fact that I do not believe the study reached reliable conclusions. If you believe their genetic testing methods for the presence of ammonia oxidizing archaea and bacteria and their amoA genes as well are correct and done properly, then this is scientific proof that two bacterial products contain, at the very least, ammonia oxidizing bacteria. You can read the following in that study:

Bacterial supplements (typically bottled liquid suspensions) are intended to aid in populating newly established aquaria with active nitrifying bacteria, to help ensure that ammonia and nitrite concentrations remain below toxic levels during the initial 1–2 months of aquarium filter colonization. The aquarium supplements included were Cycle (SP1; Rolf C. Hagen Inc., Montreal, Canada), and Bio-Support (SP2; Big Al's Distribution Centre, Niagara Falls, NY).

And later in the DNA extraction section

For supplements, aliquots (15 mL) of liquid aquarium supplements were pelleted by centrifugation at 7,000×g for 30 min, then suspended in lysis buffer for extraction. A beadbeating extraction was performed according to the published protocol with minor modifications.

So they did genetic tests on the bottle contents. Now go to Table S1. Details of aquaria and associated quantitative real-time PCR data. Go down to the bottom two lines for Bio-Support and for Cycle. All the measurements for both are n/a except those for amoA gene copies for AOA and AOB as well as those for Archaeal and Bacterial 16S rRNA gene copies. Both products show AOA gene and AOA amoA gene copies as being BDL (Below Detection Limits) and both bacterial amoA and 16S rRna gene copies were abundant. There were way more AOB amoA genes present in both supplements than in any of the 35 tanks in the study. BigAls bacterial 16S rRna counts were higher than any of the 35 tanks but Cycles's counts were on the lower end of the 35 tank range.

But, there is scientific proof that there must be some bacteria in at least those two products. And neither Hagen nor BigAls have any connection to that study.

 

[OldMan47]

We do not exercise MOD rights to simply shut off discussion Noahs ark96. I will not tolerate Ianho doing it and I would bet real money that he would not tolerate me doing it. Contrary to what some people here might think, I really look forward to learning something more in this thread. A proper discussion and even a confrontation based on facts is exactly what I would love to see. The whole concept of a "Conflict of Interests" must be considered in any discussion where a manufacturer is the only sponsor of basic research. As Ianho has already said, the examples where it happens are just too common to ignore, including the one he cited.

Bae1994, it simply will never happen dude. Both Ianho and I work here at the consent of the rest of the MOD group. There is no such thing as a rogue MOD for very long at all. We each place our own reputations on each other's actions and that makes a big difference in what we tolerate from each other among the MOD group. That does not mean that we never disagree on a subject, but it means that we hold each other to very high standards of conduct.

 

[bae1994]

Yeah I wasn't saying it happens nor would it happen

But I was saying it would be funny if it did

Bae

 

[Dieses Madchen]

I haven't read the papers posted nor have I done a lot of research regarding the whole bacteria in a bottle thing....

Whst I can tell you is this. I am a lab tech with access to all sorts of fun stuff. I did take the time to culture a bottle of bacteria and it actually did grow a nitrifying bacteria. Whether or not it is the same as what would naturally grow in the tank, I am not sure. I left my old job before i had a chance to culture my filter.....

So if there is a question as to whether or not there is living bacteria in these bottles....yes there is. Do they work? Still unknown

I will post pictures of the plates after work..

 

[TwoTankAmin]

Happy to see that the mods with whom I may disagree on this topic both have the integrity to keep the thread open for obvious reasons. While I may come off a little rough around the edges, my goal is to get to the bottom of the facts, as is their's.

While waiting for Ianho to comment on my post regarding there being proof that at least two products do contain bacteria, and that most of the rest do as well (as far as I am concerned), I would like to correct a wrong impression one gets from accepting what OldMan posted earlier:

I can agree with your anecdotal evidence that the additives used by the commercial aquaria were effective to some degree, what in the world does that have to do with 8 oz samples found on the shelf of my local fish shop? These people order directly from large corporations and can expect far superior responses than you or I would get buying the stuff after it had been on the LFS shelf for 6 months. I am afraid that we are comparing apples and oranges./quote]

This in fact is not the case. Unlike most big corporations, Dr. Hovanec actually works with the the very folks Oldman feels he would/does not. There are a least two forums of which I am aware (I am a long time member at one) where Dr. Hovanev is a member and where he does post. He will try to help out folks with cycling issues or questions. This includes trying to help folks use his bacterial starter properly so they achieve the sort of results the product is designed to produce. I have seen threads where he has replaced the product for users who bought a small bottle and had problems, including those most likely due to user failure and not to product failure.

I have seen him offer to send some free bottles to forum members to try and then followed their responses when they tried them. So while many people or companies may focus solely on the big buyers and let the small guys dangle in the wind, Dr. Hovanec does not behave this way. I would link to these sites and threads so anybody interested could see all of this, but it would violate this site's policies against posting links to competing forums. The most interesting thing about how silly this rule is - on the one general fish site larger than this one I recently made a post which has a link to one of my posts here. I was too lazy to rewrite it so I did a copy paste from here, and I always reference quotes (even if they are mine), so the post includes a link to here.

Moreover, I have now corresponded with Dr. Hovanec on four separate occasions and every time I got an answer back very quickly. I have never met Dr. H. he doesn't know me from a hole in the ground. Yet his responses have been timely.

And I also am somewhat familiar with his background. He has been keeping fish for more years than many of the members here have been alive. He is a past president and the current treasurer of one of the worlds largest and most prestigious cichlid organizations. And he still keeps his own personal tanks. And for anybody who is planning to attend the InterZoo 2012 in Germany this month, he will be there and you can talk to him yourself.
http/www.interzoo.com/en/

As an aside to this. I was checking out places to buy the product online in the states. Because DrTims is in the states, anyone can order directly from there. So, at least in this country one can get it from the source. I do not know how the product is produced and sold into the market in European countries etc. I know it is distributed in the UK by Midlands Reef and they show a lot of places that retail their products. So the stuff appears to be easy to get in the UK. After all the London Aquarium used it. So I wonder why Ianho has never bothered to test out a bottle of the stuff himself. I know he has never done a fishless cycle, but it isn't all that hard. At least that way when he makes the claims he does, it would have been based on some level of personal experience. I can't say whether I have seen posts by OldMan indicating he had personally tried it.

And now back to the topics at hand. I will wait for Ianho and/or OldMan to comment on my last post showing two bacterial products do contain bacteria as well as DM's post above which is more anecdotal than scientific but implied the use of science.

If these two gentlemen are willing to agree that DrTim's One and Only does, at least initially, contain live nitrifying bacteria. We could move onto the next phase We could discuss whether the bacteria can survive in a bottle and still be useful for cyling a tank 6-12 months after it was bottled. We can determine whether, if it is not mishandled and is used within the date limitations, it is still likely live bacteria. We could even try to determine if it works, as DrTim's sites claims, for folks who are not huge public aquariums. I have a reasonable way to do a home based experiment, not truly lab grade standards, but which I think would be acceptable to most. It would only take about a week once everything required is assembled.

 

[atlas101]

I think Oldman was talking about the 'response' of the product not the person behind it, as in a large quantity batch, made fresh to order and immediatley shipped may well have very different results to a bottle left on a shops shelf for six months.

Also just to add on abit of a side tangent, I came across 2 papers on google scholar with regards to nitrospira bacteria being present in soil, if that is the case could throwing a few handfulls of soil into a tank during an initial fishless cycle introduce nitrospira and help reduce cycle time?

 

[ian]

I actually read your post TTA on the last page and it was the first post that didn't come across condescending and patronising, it was actually the first post which also has pricked my ears. I also wasn't aware of the midlands reef being able to get hold of the Dr Tim stuff. Yes, i would try it and i am about to rescape my nano shortly, it may be an option not to plant it from the beginning and actually try it. There's a couple of my aquascaping friends going to Interzoo also...

I must also admit that there MAY be something in this product (swallows pride lol), but i would like to try it myself. I would also like a few others to give it a bash. I wonder whether we could get 3 or 4 people doing the same thing. It would have to be that stringent as we are hobbyists and not scientists, and i think it may be a better measure of things doing it that way.

 

[Livewire88]

I have an empty 100litre tank and a brand new filter in my garage, I dont mind setting it up and am happy to follow instructions to test weather this sort of product works.

Just an offer

 

[TwoTankAmin]

The bacteria are in continuous production, they are not just whipped up. They are grown under controlled conditions. I have read descriptions of how it is done and what parameters are maintained.

I folks in general were a bit more open minded about Dr. Hovanec's background and what he does beyond this one product, they would find there is a wealth of information available from him. You can learn about the biofilms in which the bacteria live, why bio-wheels are good hosts for them. You can learn things about cycling and bacteria that have nothing at all to do with bottled bacteria. It is a mistake to merely dismiss any information that he provides in this area simply because he happens to sell a product.

The fact that the bacteria live in a biofilm has nothing to do with a product, the fact that elevated ammonia and/or nitrite levels inhibit nitrifying or kill bacteria has nothing to do with bottled bacteria. The fact that nitrifying bacteria do have strategies for surviving times of little or no food or oxygen exists independently of the existence of bacteria in a bottle products, though it does explain why they can last in a bottle.

One can do a Google Scholar search for Nitrospira and get back some 3600+ studies and books. You will read lines like this:

Nitrospira are barely studied and mostly uncultured nitrite-oxidizing bacteria, which are, according to molecular data, among the most diverse and widespread nitrifiers in natural ecosystems and biological wastewater treatment.

From A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria (incidentally this 2010 study is edited by one of the et als. of the Hovanec et als. I often mention.)
or

Chemolithoautotrophic nitrite oxidizers of the genus Nitrospira are a monophyletic but diverse group of organisms, are widely distributed in many natural habitats, and play a key role in nitrogen elimination during biological wastewater treatment. Phylogenetic analyses of cloned 16S rRNA genes and fluorescence in situ hybridization with newly developed rRNA-targeted oligonucleotide probes revealed coexistence of uncultured members of sublineages I and II of the genus Nitrospira in biofilm and activated sludge samples taken from nitrifying wastewater treatment plants.

From Nitrite concentration influences the population structure of Nitrospira-like bacteria

So atlas101 you don't need dirt- you can use waste water sludge. But I think you would much prefer to have the bacteria without all the other stuff.