Bacteria in a bottle, Myth or Fact

[Belgian Anthias]

In general, I agree.

But if you have a pest like cyano, and add a different species that may consume some of the same resources (organics, or example) then you might get less cyano. In a way, its like probiotics to keep desirable bacteria in the human GI tract if it becomes colonized with undesirable species.

And which species would that be? A species that is not already present?
In a running aquarium all bacteria needed are present, I always thought. It should be. What would be the benefice of adding more as probably not enough nutrients and building materials are available to sustain the growth of what is already present. Cyano's will win the battle for nutrients and building materials in nutrient limited conditions.

 

[Randy Holmes-Farley]

And which species would that be? A species that is not already present?
In a running aquarium all bacteria needed are present, I always thought. It should be. What would be the benefice of adding more as probably not enough nutrients and building materials are available to sustain the growth of what is already present. Cyano's will win the battle for nutrients and building materials in nutrient limited conditions.

My post does not relate to nitrifying bacteria. It relates to shifting the balance, at least temporarily, from a problem bacteria (cyano) to a less problematic one.

It was answering a different question, which is would adding other types of heterotrophs ever be useful? In that scenario, it may be useful to add heterotrophs that compete with cyano for nutrients. I do not know or care what the species might be, if it seems to help. A product like MB-7:

http://brightwellaquatics.com/products/microbacter7t.php

"Complex system of non-pathogenic aerobic and anaerobic microbes,"

 

[MnFish1]

It is impossible to accelerate the autotropic nitrification capacity of a new system as the time needed to install an autotropic nitrifying capacity will not change much, even when the system is seeded. Nitrifying bacteria from a bottle.? it will probably be heterotrophs. Even fresh cultures will not change a thing. They will not grow faster because they come from a bottle; if this would be possible.
Autotropic nitrifiers do not form spores and they can not survive in a closed bottle while in log phase. The same fore heterotrophs. They will not survive in log phase longer than a few hours !
Heterotropic Bacteria which have formed endospores ( not all in aquaria living strains of heterotrops can form endospores) may survive but they need time to wake up. When the nutrients are present to wake them up I think the present active bacteria will already have started up there log phase and outcompete and outperform any added bacteria. So, why adding them?

There is no evidence that adding bacteria for nitrification to an aquarium changes a thing. A fact is that living cultures of nitrifiers in log phase can not survive in a closed bottle for a period of time. Not the period needed to commercialize it . When nutrients and building materials are added, who will tell it are the bacteria already present which are winning the battle or the once which are added?
These products have no added value for a new system and there is no necessity for these products at all. What will they be able to add what is not already there by introducing rock, sand . etc Putting new made water into a plastic bucket will develop a thriving bacteria community.

One is able to add heterotrops which are able to maintain the carrying capacity but these bacteria are already present the moment water is put in the plastic bucket which will provide organic carbohydrates. To maintain a heterotrophic carrying capacity only enough organics are needed.

Even when everything what is promised is in the bottle it is very unlikely those bacteria can compete with the active bacteria already present. The only thing one has to do to install the proper carrying capacity is adding the nutrients and building materials needed. These building materials may come from phytho- and zoo-plankton cultures. Seeding the new aquarium with fresh media from a biofilter will certainly help introducing diversity but it will not accelerate things in a remarkable way.

What is in the bottle? Take it to a lab and let it be examined for types and living strains of bacteria . Discussion closed. The rest is based on sensory experience or believe (empirical evidence), it is difficult to prove. There is nothing wrong by adding these bacterial supplements if it is known what is in it. One does support the business which in this case may be the most important issue.

I happen to think you’re wrong. For any number of reasons. Firstly i have never had a problem are starting a new tank when using these products as directed. Don’t even own an ammonia test kit. There just is no problem even when starting a bare bottom tank with no rock with just a filter and a large population of fish and no daily water changes. Secondly unless you have taken the bottle to a lab and tested it all of your comments are conjecture so I don’t think you can claim the discussion is “closed “. Why dont you provide the evidence?

 

[Porpoise Hork]

From my own experience as of the last 10 days. I started with dosing with Dr. Tim's and after 5-6 days of no results I dosed with Bio-Spira.

Water temp 77.5F
PH 8.2
Alk 9.5
Cal 400
Mg 1300


I dosed my 75G with Dr. Tim's on 6/10 and then dosed with Ammonium Chloride to raise Ammonia to 2.0. Checked the tank at 48 hours in and no change in Ammonia levels. On day 5 I checked it again and the Ammonia rose to 4.0. This is with Reef Saver rock and rinsed crushed substrate with little to no organics. Nitrite and nitrates remained at 0 the entire time.

On day 6 I dosed with Bio-Spira and checked the levels at 24 hours. Ammonia had already started to fall to 3.0-4.0 and nitrites were now at a solid 2 still no showing of nitrates. 48 hours after dosing Bio-Spira Ammonia is nearly undetectable. Nitrites now a solid 4.0 and nitrates just starting to register. By day 5 after dosing Bio Ammonia is now at 0. Nirites at 1.5-2 and nitrates at 20-30.

After a week Dr. Tim's did nothing. No reduction of ammonia or hint that the cycle had started. I verified that it was not past the expiration date as well.

However within 24 hours of dosing Bio-Spira I saw clear evidence that the cycle is well under way.

 

[CherBear811]

Just a few comments:

1) fish 'pee' ammonia (not urea) and they pee ammonia via their gills by passive diffusion,
2) the bacteria will not starve and die in any short period of time (days or weeks)
3) nitrifying bacteria do not colonize 'poop', heterotrophic bacteria do and since they multiple in 20 to 30 minutes (versus 20 to 30 hours for nitrifiers) they are mineralizing the poop into ammonia which the nitrifiers can then use.
4) using ammonia rather then fish is fine for cycling, there is not difference in ammonia you add via ammonium chloride or ammonia produced by mineralization of fish poop - ammonia is ammonia

Cheers

Dr Tim, thanks for the response, much appreciated! Question.... do you recommend re-dosing ammonia then or just the first initial dose? I have only ever done it with bacteria and usually live rock or a fish or two, depending on the tank size. I bought ammonia to do it that way the last time I cycled with bacteria but my coral arrived before I could do that so everything went in the fist night. Cured rock, sand, bacteria and coral. No losses. (Nooo, I do not recommend that to newbies, but I felt I have enough experience to be able to do it without harming anything)

 

[DrTim]

Hello - this is much that is incorrect with this, I will point out the major a parts

Most of the nitrification and denitrification takes place in a biofilm which is a complex comunity, a mix of all kinds of bacteria and archaea which must work together. To build up this community time is needed minimum +- 20 days. Ammonia oxidizing bacteria are slow growers and Archaea need even a lot more time. Only +- 30% of a nitrifying biofilm growing on calcium carbonate is occupied performing nitrification and denitrification. Normally bacteria and archaea are introduced growing on and in everything what is introduced into the aquarium.
Do mixed bacteria in bottles contain Archaea?
Do these bottles contain all needed bacteria? Because they are all needed to form a balanced biofilm which is able to perform nitrification and denitrification continuously! Cells must be renewed and recycled. The nitrifying biofilm will not survive without sulphur bacteria present.

Never said that the bottled bacteria contain all the bacteria needed to an aquarium and it takes a lot more than 20 days to achieve a balance - it ever. Denitrification in most aquariums is a very minor process which is why nitrite build-up. While people like to think the inside of some special medium is full of denitrifying bacteria that is not the case. I gave those results years ago at a MACNA. Most 'denitrification' in aquarium is assimilation not denitrification.

Have no idea why your wrote The nitrifying biofilm will not survive without sulphur bacteria present - there is no evidence of this and I have been growing nitrifies for over 20 years.

Favouring some trains of bacteria may prevent others to grow out normally as they are competitors for the same nutrients and building materials.

We kid ourselves to think we can favor some strains of bacteria - not all bacteria can live in the aquarium environment. The system will always go where it wants and we have little control except to the extend that we add organics and use skimmer, UV and other devices to kill most pelagic bacteria to the benefit of surface bacteria.

How autotropic nitrifiers survive in a bottle? They do not form spores. Most heterotropic nitrifiers which are active in the water column and are r-strategists do form spores. +- 1 million cells are needed to obtain the same nitrification capacity of one autotrophic nitrifier. And they need organics to grow.
Installing the necessary carrying capacity which is based on the capacity to reduce ammonia, on a balance between foto-autotrophic, autotrophic and heterotrophic ammonia reduction, needs time , time and patience which can not be provided in a bottle.

Why can't they survive in a bottle? What is to prevent them. I already detailed this. Autotrophic nitrifies do well in the bottle. The question is are the ones in the bottle the ones that can survive and grow in the aquarium. All nitrifiers are not equal - some only grow in high ammonia/nitrite environments while others will only grow in low ammonia/nitrite environments. This is well know by researcher and I showed this in one of my publications. The confounding problem with much past research is that the ammonia concentration used by researchers favored Nitrosomonas europaea over all other strains of AOB. Basically, the researcher was unknowingly selecting for N. europaea even though it was not the dominant AOB in the environment being studied but was selected for by the culture-dependent methods used in the testing. Again I (and others) showed this is published research.

Of coarse one can add heterotrops from a bottle which are able to maintain the carrying capacity mainly by assimilation and continue to do so as long they are able to grow and are supplied organics. Such aquaria can support a certain bioload after a few days. As this would prevent nitrifying biofilms to develop, no autotrophic carying capacity will be installed. What if heterotropic growth is interrupted for some reason? This is not the way I would manage an aquarium system but it is certainly possible to maintain a VLNS or LNS this way.

Just because you grow heterotrophs does not mean you can grow autotrophs. Heterotrophic bacteria cannot manage the ammonia and nitrite in an aquarium - there is no evidence of this and much evidence to the contrary.

 

[Belgian Anthias]

Seeding an aquarium and its filters is as old as the hobby. With the right stuff!!


What I am saying is that adding more bacteria will not speed up conditioning a new aquarium. Starting with one biofilm or starting with 100 biofilms, it will take about the same time to make them ready for business. of coarse when all building materials are provided.

As most autotropic nitrification takes place in a biofilm the growth of the biofilm is crucial, not only the growth of the nitrifiers. Growth means dead. The nitrifying capacity depends also of the rate this dead material is recycled and removed as this influences the growth of the nitrifiers as does a lot of other parameters. Adding a lot of nitrifiers does not change a thing as long as al the other bacteria needed to build the biofilm are not present in adequate numbers. The bacteria go in a lag phase while building the film and while building up the communication channels, The community grows very slowly. if enough nutrients are present more biofilms will be produced, increasing the carrying capacity, but it will not go faster as every connection needs time. The AOB must hide from light to function, so they have to wait to be overgrown by an outer layer of bacteria .
Do these bottles contain all types sulpur bacteria? Do we have to wait until they happen to land in the water from the air! Without these bacteria no nitrifying biofilm.

More capcity? of coarce! if it is all in the bottle. Faster? To condition a new aquarium and for installing an autotropic carrying capacity? I do not think so.

When speaking about heterotropic nitrification one may double the nitrification rate of the heterotrops very fast but the nitrification rate will stay very low compared to autotropic nitrification as +- 1000000 cells are needed to replace 1 autotropic nitrifier



When seeding a new biofilter from an established biofilter it will be faster full of all types bacteria but this does not mean the biofilter will be conditioned faster as all the connections for building a film must be made from zero. But the filter will have maximum capacity when conditioned which may not be the case when not seeded. The biofilms must be build up. Starting with 1 ore 100 biofilms at the same time? The time needed to build one functioning film may not change much but it will probably take longer for 100 biofilms when only the nitrifiers for 100 films are provided.

My Conclusion: Seeding an aquarium with only a few species of nitrifiers will not change much in building up the nitrifying biofilm and will not speed up installing an autotropic carrying capacity.

 

[DrTim]

How bacteria from a bottle will be able to do that? Nitrifying heterotrophs have a very low nitrifying capacity and most ammonia reduction will be due to assimilation, not by nitrification, if organics are available.
Are autotropic AOB , AOA and NOB able to survive in a bottle? And even if they can they will need weeks to grow. How those bacteria, which must be in there lag phase to have a chance to survive, will be able to compete with the active bacteria already present in the system? Autotropic nitrifiers and denitrifiers in lag phase may need a week to start up the log phase.

The answer is simple - numbers. You present no evidence that AOB, NOB and AOA cannot survive in a bottle. Why would they not survive. If you have sufficient numbers in the bottle they will out compete the meager number of bacteria in the newly set-up system. Assimilation will only work if you have a lot of organisms that can assimilate which is usually not the case. Bacteria do not have to be in lag phase to survive.

 

[DrTim]

This is off topic here but would like your OP.
We all want to increase bacteria levels for all kinds of reasons. For out competing algae etc. I need to do this in my "existing tanks."
I'm about to pick up a bottle Seachem Stability . Sound like a good choice?
I would think the bacteria we use for cycling a tank would have different bacteria in them, focusing more nitrtfication. )

Using bacteria to outcompete cyanobacteria is a good idea - I have been promoting it for years. But nitrifiers are the wrong type of bacteria because that grow so slow. So using our One & Only or BioSpira or Stability is not the way to go. You need to use heterotrophic bacteria or what are commonly called sludge busters (our Waste-Away). Then put your skimmer to work for you instead of against you. Sanjay published a study years ago showing how your skimmer dramatically reduces the bacteria in the water column. But it does not touch nitrate or phosphate. So those nutrients are available to cyanobacteria which is why the old tale of getting a bigger skimmer to take care of cyano is wrong. You need to skim less and let the bacteria in the water assimilate the nitrate and phosphate and then turn your skimmer on to remove those bacteria.

 

[Brew12]

All nitrifiers are not equal - some only grow in high ammonia/nitrite environments while others will only grow in low ammonia/nitrite environments. This is well know by researcher and I showed this in one of my publications

Dr Tim, I've read your research on this. I have assumed that this is why some systems will show rapid processing of ammonia from 5ppm down to 1ppm but then takes much longer to go from 1ppm down to 0ppm.

Could you confirm or correct that assumption?

 

[DrTim]

There is even more wrong in this post than the earlier one.
You know there are published peer-reviews paper on this - I wrote a lot of them!

It is impossible to accelerate the autotropic nitrification capacity of a new system as the time needed to install an autotropic nitrifying capacity will not change much, even when the system is seeded. Nitrifying bacteria from a bottle.? it will probably be heterotrophs. Even fresh cultures will not change a thing. They will not grow faster because they come from a bottle; if this would be possible.
Autotropic nitrifiers do not form spores and they can not survive in a closed bottle while in log phase. The same fore heterotrophs. They will not survive in log phase longer than a few hours !

This is all 100% wrong. As I wrote in my first post - the bacteria are not growing because there is not ammonia or nitrite for this to grow. Further, just because a bacterium is not grow does not mean it is dead. It is very possible to accelerate autotrophic nitrification from a bottle - it's my business and I work with largest labs, public aquariums, and thousands of hobbyist. Is it successful 100% of the time - no, nothing is. The reason is seldom due to the bacteria.

Do you have any real evidence to back-up any of your claims - I didn't think so.

There is no evidence that adding bacteria for nitrification to an aquarium changes a thing. A fact is that living cultures of nitrifiers in log phase can not survive in a closed bottle for a period of time. Not the period needed to commercialize it . When nutrients and building materials are added, who will tell it are the bacteria already present which are winning the battle or the once which are added?
These products have no added value for a new system and there is no necessity for these products at all. What will they be able to add what is not already there by introducing rock, sand . etc Putting new made water into a plastic bucket will develop a thriving bacteria community.

Just plain wrong and you are ignoring all the science and practical results from hobbyist for years.

What is in the bottle? Take it to a lab and let it be examined for types and living strains of bacteria . Discussion closed. The rest is based on sensory experience or believe (empirical evidence), it is difficult to prove. There is nothing wrong by adding these bacterial supplements if it is known what is in it. One does support the business which in this case may be the most important issue.

Discussion is not closed - for some reason you are ignoring the facts, the science and the reality.

 

[Belgian Anthias]

I doubt you have ever used biospira or dr. Tims then, because if you had, you'd know they can work very quickly and well. Ime 2ppm ammonia converted in 24hrs 75% of the time out of the 15-20 times I've used it. Certainly there isn't a necessity but there definitely is value (especially in a pinch for qt or hospital). You can cycle a tank much faster.

To do this I only have to provide enough organic carbon.
When installing a heterotrophic carrying capacity the tank may cycle within a week I do not need any bacterial supplement for this.

And no, I never used these products. Do they say on the bottle what is in it exactly? I use bio filters and have no need for this. I have plenty of the real stuff.

 

[crashegordon]

I personally have used Dr Tim's and it worked great. I started my 180 with dry rock, dry sand, two bottles of Dr Tim's, two clowns, a blue hippo and a yellow tang. They all lived and did amazing. No major cycling and still have all four fish two years later.

 

[Belgian Anthias]

There is even more wrong in this post than the earlier one.
You know there are published peer-reviews paper on this - I wrote a lot of them!



This is all 100% wrong. As I wrote in my first post - the bacteria are not growing because there is not ammonia or nitrite for this to grow. Further, just because a bacterium is not grow does not mean it is dead. It is very possible to accelerate autotrophic nitrification from a bottle - it's my business and I work with largest labs, public aquariums, and thousands of hobbyist. Is it successful 100% of the time - no, nothing is. The reason is seldom due to the bacteria.

Do you have any real evidence to back-up any of your claims - I didn't think so.






Just plain wrong and you are ignoring all the science and practical results from hobbyist for years.



Discussion is not closed - for some reason you are ignoring the facts, the science and the reality.

I do know what I am talking about and I do have research and references to prove what I am saying. if you want I can publish the articles containing the references. if you claim I am 100% wrong you must have prove for it and I will gladly consult your references.
How long bacteria in log phase will survive in a bottle? I published this before: "Bacteria in a bottle" by Physics Professor Al Bartlett, U. Colorado.
http://www.cryerfamily.eclipse.co.uk/BacteriaBottleParable.htm

I have studied the working of biofilters for many years and documented myself about the functioning of nitrifying biofilms especially of those growing on a substrate of calcium carbonate and or sulphur, just for trying to understand how it works and how we can use this knowledge to manage a closed marine aquaculture system.
This includes the study of bacteria involved. There metabolism, live cycle and so on. I think I am aware of some basics.

It is always interesting to learn more, about AOB and NOB stored in a bottle without nutrients; What pathways may they follow to survive. And for how long.
I must have papers in my database with the answers. I will look it up.

 

[gcarroll]

My head is spinning. Do we really have a physics professor and a biologists debating if bacteria can live in a bottle? If so, Dr Tim can you help me with my calculations on how much thrust I need to launch my VW into orbit? JK!

Glad to see so much good information regarding bacteria and how it all relates.

BTW, I cycled my current 25g with dry rock and sand using Dr Tim’s method. I was fully cycled in 4.5 days. I have had no issues since.

 

[DrTim]

Dr Tim, thanks for the response, much appreciated! Question.... do you recommend re-dosing ammonia then or just the first initial dose? I have only ever done it with bacteria and usually live rock or a fish or two, depending on the tank size. I bought ammonia to do it that way the last time I cycled with bacteria but my coral arrived before I could do that so everything went in the fist night. Cured rock, sand, bacteria and coral. No losses. (Nooo, I do not recommend that to newbies, but I felt I have enough experience to be able to do it without harming anything)

We recommend three dosing of ammonia which generally takes about 10 days to complete. Many people are under the mistaken impression that fishless cycling is faster but that is not true. When fishless cycling you are adding a lot of ammonia, compared to a tank with a few fish, so it will take longer for the system to cycle.

 

[DrTim]

I do know what I am talking about and I do have research and references to prove what I am saying. if you want I can publish the articles containing the references. if you claim I am 100% wrong you must have prove for it and I will gladly consult your references.
How long bacteria in log phase will survive in a bottle? I published this before: "Bacteria in a bottle" by Physics Professor Al Bartlett, U. Colorado.
http://www.cryerfamily.eclipse.co.uk/BacteriaBottleParable.htm.

This does not apply because they are not in log phase growth. As I wrote at the beginning we don't add ammonia so they have no substrate to consume so they are not growing. I have lots of reference - my own published work. I was the first researcher to show Nitrospira in the nitrite-oxidizer in aquatic system not Nitrobacteria. That work was confirmed by 3 other labs around the World 20 years ago.

I have studied the working of biofilters for many years and documented myself about the functioning of nitrifying biofilms especially of those growing on a substrate of calcium carbonate and or sulphur, just for trying to understand how it works and how we can use this knowledge to manage a closed marine aquaculture system.
This includes the study of bacteria involved. There metabolism, live cycle and so on. I think I am aware of some basics.

The basics fine but have you designed and used RNA/DNA probes to determine the species - I have. Have you used clone libraries to determine the species - I have. Have you used DGGE to determine the make-up of the consortium - I have. If you have please provide a list of your publications would be interested in reading them

It is always interesting to learn more, about AOB and NOB stored in a bottle without nutrients; What pathways may they follow to survive. And for how long.
I must have papers in my database with the answers. I will look it up.

I'll help you - start here. From Geets et al 2006. Fellow Belgians!
"Nitrosomonas europaea cells starved for weeks, months or even almost a year of ammonium were able to regain their ammonia-oxidizing activity within minutes in batch and retentostat experiments (Wilhelm et al., 1998; Tappe et al., 1999; Laanbroek & Ba ̈r-Gilissen, 2002)."

I do not understand your standpoint when there is just so much research and practical results on this. You will find a lot looking on google scholar in 10 minutes.

 

[DrTim]

My head is spinning. Do we really have a physics professor and a biologists debating if bacteria can live in a bottle? If so, Dr Tim can you help me with my calculations on how much thrust I need to launch my VW into orbit? JK!

Glad to see so much good information regarding bacteria and how it all relates.

BTW, I cycled my current 25g with dry rock and sand using Dr Tim’s method. I was fully cycled in 4.5 days. I have had no issues since.

Hey Greg no problem! We can do it at RAP this weekend but bad news - Elon's Tesla has a big head start - don't think you can catch-up!

 

[DrTim]

Dr Tim, I've read your research on this. I have assumed that this is why some systems will show rapid processing of ammonia from 5ppm down to 1ppm but then takes much longer to go from 1ppm down to 0ppm.

Could you confirm or correct that assumption?

You are correct and much depends on the initial nitrifying bacteria if you use a supplement. Bottles of bacteria that claim to accelerate the establishment of nitrification fall into 3 general groups: 1) those that do not contain any nitrifying bacteria; 2) those that contain nitrifying bacteria that are grown in, and survive only in, high ammonia concentrations; and 3) those that contain nitrifying bacteria that live and thrive in low ammonia concentrations.

What is low versus high ammonia - the dividing line is around 5 to 10 mg/L ammonia-nitrogen. How do I know this - I published a peer-reviewed study on this.

This is why I say to not allow the ammonia during cycling to get above 5 mg/L ammonia-nitrogen.

So in the case you describe - you may have used a culture from group 2 above. They do in the beginning but once the ammonia get low the do not work very well. Many times you will see a secondary ammonia spike a few week later as the AOB switch from the high concentration bugs to the low concentration bugs.

Not all ammonia-oxidizing bacteria are equal!

 

[Sallstrom]

Just talked a bit with my colleugues about the experiment setup.

One option to get replicates is to do one treatment in each tank(you had 4 right?). So you do this one round. Then you do it again at least 2 more times but ramdomly select what tank is for what treatment the next rounds. That way you get a better result and you get 3 replicates.

Another way to do it and get more replicates and get a better results is to use smaller buckets and just an airline for bubbles. Easy to do a lot of replicates at once.

Good luck!

/ David