Can the size of your nitrifying bacteria colony be measured?

[KimG]

Brilliant topic

#brandon429
How do you measure surface are based on a picture? Or did I miss understood?
Surface area is tridimensional. The internal structure of the media (rock) will play a vital role on how much is usable, as you said yourself (w example). The roughness of the surface area is another place where a picture isn't going to tell you much.

It definitely possible to have ramp up periods if the load is increased high enough and fast enough or the media reduced enough. What I believe is that we never do that in our reef tanks. However, its pretty common place in my field of work (aquaculture), where we are close to the edge often.

I think part of the miss understanding is just how little surface area you actually need to achieve ammonia conversion. Typical rule of thumb is 100m2 per kg of dried aquaculture feed. 100 m2 isn't that much. I know bioballs are out of favor this days, but to get 100m2 you would only need about 133l of media (assuming 750m2/m3). Assuming a 50% fill (and no safety margin), you could get a 260l barrel (approx 70g), fill it with media and aeration and have a biofilter capable of filtering 1kg of dried feed a day.
Almost no one as an aquarium that consumes 1kg of pellets a day. So most of our filtration is over dimensioned.

#Aqua Man You could start both tanks the same, and they would still not end up in the exact same amounts. (I have plenty of data from recirc systems to back this up). Its biology as its simplest. Its likely that the exact bacterial communities will be slightly different as well.


How much practical application does this topic have? Probably not massive, but very interesting anyway.

As for the OP. I don't think you could measure the exact numbers for the reasons stated above. You could in the water phase (and you would have to assume the water is completely mixed). You could also take samples from rock, but to have a exact number, that I don't think is possible.

 

[KimG]

Aquabiomics can tell you the diversity and relative abundance of each species of bacteria in the tank.

As stated above "total number" is not actually a useful measurement as each species does things at different rates and different effeciencies.

They can do that for the water phase.
However, not sure if it would be very accurate at representing the surface bound bacteria. It will very much depend on sampling methods.
Still, its great to see new technics applied to our hobby.
Unfortunately, money for peer review science in aquariums is difficult to get.

 

[Salemsoul]

As I mentioned earlier, I understood that the Nitrifying Bacteria Colony in a tank is proportional to the bio load.

More bio load, more bacteria required to process the load. Less load, less bacteria required to process.

I wanted to know if there was a way to test for nitrifying bacteria so that I could compare the results to the bio load in the tank.

The "more bio load, more bacteria" is complicated; some microbes repopulate equal to the amount of die off so they are constant, others can live a longer period of time during a lag phase and then continue to increase their population without the increased bio load or environmental changes.

There is a way to test the bacterium population in a controlled environment and see if they are NOB, AOA, AOB. So identifying your bacteria diversity. This is not hobbyist level information, you'd need a lab. We as reefers have know real way to quantify our bacteria population or identify the families of bacteria ourselves. This info was provided above so just reiterating some of it.

 

[taricha]

Aquabiomics is doing just this (quantifying microbes - nitrifiers and other) and interestingly, finds that nitrifier amounts vary a LOT in systems they test. Speculation that some systems may be mostly bypassing nitrifiers with ammonia uptake by algae, heterotrophic bacteria etc. Here's Eli discussing this point in an article on BattleCorals system.

EM: One of the things that really stood out about your tank for me is the high levels of nutrient-processing microbes. Ammonia-oxidizing microbes made up almost 8% of your sample, which is higher than about 85% of aquariums I’ve tested, about twice as high as the average sample. Your sample also had high levels of nitrite-oxidizing bacteria (0.9%), which is among the highest of any tanks tested (higher than 96% of samples), and over 3-times higher than the average sample.

This may not come as a surprise, since we expect to find these in a tank with a functional biofilter. But in fact, many established tanks have very low levels of these microbes. In some cases, nitrite-oxidizing bacteria aren’t even detected (although they’re likely still present at low levels).

As I review these surveys from different tanks, lately I’ve been thinking about competition between microbes and other organisms for ammonia. I’m considering the hypothesis that some tanks process most of the ammonia through nitrification, some through assimilation by invertebrates or heterotrophic bacteria, and some through assimilation by algae. In this framework, your tank appears to process most of its ammonia through nitrification, the classic pathway we all learn about when cycling a new tank.
...

more good discussion I left out of the quote. click through for the rest.

 

[Dom]

I was trying to explain that "More bioload = more bacteria" is not necessarily true. It is not axiomatic that more ammonia or nitrite means more bacteria.

Yes there are ways to measure the number of nitrifiers but you need specialized equipment.

Regards

Yes, I get that now. I also understand that generally speaking, it can be measured, but not at the hobbyist level.

Thank you.

 

[Dom]

The "more bio load, more bacteria" is complicated; some microbes repopulate equal to the amount of die off so they are constant, others can live a longer period of time during a lag phase and then continue to increase their population without the increased bio load or environmental changes.

There is a way to test the bacterium population in a controlled environment and see if they are NOB, AOA, AOB. So identifying your bacteria diversity. This is not hobbyist level information, you'd need a lab. We as reefers have know real way to quantify our bacteria population or identify the families of bacteria ourselves. This info was provided above so just reiterating some of it.

Yes. I do believe this is what Dr.Tim was saying too.

 

[Timfish]

Lets not forget corals are pulling out urea and ammonia to feed their zooxantheallea. They also have N2 fixing simbionts making nitrates for their use. Any variable that influences changes in the coral holobiont is going to influence other microbial processes in the rest of the system.

 

[Dom]

Brilliant topic

#brandon429
How do you measure surface are based on a picture? Or did I miss understood?
Surface area is tridimensional. The internal structure of the media (rock) will play a vital role on how much is usable, as you said yourself (w example). The roughness of the surface area is another place where a picture isn't going to tell you much.

It definitely possible to have ramp up periods if the load is increased high enough and fast enough or the media reduced enough. What I believe is that we never do that in our reef tanks. However, its pretty common place in my field of work (aquaculture), where we are close to the edge often.

I think part of the miss understanding is just how little surface area you actually need to achieve ammonia conversion. Typical rule of thumb is 100m2 per kg of dried aquaculture feed. 100 m2 isn't that much. I know bioballs are out of favor this days, but to get 100m2 you would only need about 133l of media (assuming 750m2/m3). Assuming a 50% fill (and no safety margin), you could get a 260l barrel (approx 70g), fill it with media and aeration and have a biofilter capable of filtering 1kg of dried feed a day.
Almost no one as an aquarium that consumes 1kg of pellets a day. So most of our filtration is over dimensioned.

#Aqua Man You could start both tanks the same, and they would still not end up in the exact same amounts. (I have plenty of data from recirc systems to back this up). Its biology as its simplest. Its likely that the exact bacterial communities will be slightly different as well.


How much practical application does this topic have? Probably not massive, but very interesting anyway.

As for the OP. I don't think you could measure the exact numbers for the reasons stated above. You could in the water phase (and you would have to assume the water is completely mixed). You could also take samples from rock, but to have a exact number, that I don't think is possible.

I'm beginning to see that my OP may have been a bit unclear. I didn't mean an actual tally of the number of bacteria, just if it could be measured in some way. It was for my own education, sort of like a home experiment to test for myself if the two are proportional.

 

[brandon429]

This thread uncovered details of existing bac that work harder to make up for varying bioload, didn’t know that one, and it mentions different clades sharing nitrification duties that’s really good info. Those details line up with work thread measures using our best ammonia readers I really like that part. -> though species might alternate roles and colony counts the net biofiltration is consistent among tanks, even ones that undergo marked changes in surface area

no ten reefs post the same bacterial makeup % on aquabiomics reports, but they all post the same ammonia conversion rates on a working calibrated seneye post-cycle, fascinating.

Those are direct explanations for a mechanism where live rock instantly handles more wastewater than it did before sandbed removal. Glad for the thread.

 

[AquaBiomics]

As the title says....

Hi Dom,

I'm late to the party because I've been busy (processing aquarium samples for bacterial analysis among other things), but here are my thoughts.

Using high-throughput DNA sequencing, we can absolutely measure the relative abundance of nitrifying microbes. (I emphasize microbes here since in many if not most tanks, the primary ammonia oxidizers are actually Archaea rather than Bacteria. But anyway)

We can also measure the types of nitrifying microbes. I see variation between tanks at the family and genus levels, and also at low levels (e.g. different genotypes within the same species).

I have a lot of data collected on this and have been meaning to write up an article on the diversity of nitrifying microbes in home aquariums. This thread is good motivation to get back to that project.

Now to read the rest of the thread! Thanks @taricha for bringing it to my attention.

-Eli

 

[homer1475]

Was just coming to this thread to tag @AquaBiomics.

 

[AquaBiomics]

They can do that for the water phase.
However, not sure if it would be very accurate at representing the surface bound bacteria. It will very much depend on sampling methods.
Still, its great to see new technics applied to our hobby.
Unfortunately, money for peer review science in aquariums is difficult to get.

Important to clarify this point, thanks for bringing it up. My beta test samples only included water samples, but since launching the service commercially I've also included a biofilm sample. This was important because water samples often lacked evidence of nitrifying microbes, and these are obviously really important to measure. So my database is primarily based on combined analysis of water + biofilm.

To further complicate matters (or simplify them, depending on your perspective), it turns out that
a) there are actually some free-living nitrifying microbes, including the ammonia-oxidizing Archaea [1,2] and
b) in aquariums, the surface-associated microbes are constantly washed off into the recirculating water. A large fraction (the majority, in many tanks) of the microbes detected in water samples are known to be surface-associated types.

So overall, while I think the method of sampling has a huge impact on the microbes we can detect, and there are some parts of the tank (e.g. internal pores of rocks) we are surely not sampling well, we can sample both the water and the surface biofilm.

[1] https://www.pnas.org/content/107/19/8818
[2] https://www.annualreviews.org/doi/full/10.1146/annurev-micro-092611-150128#_i3

 

[AquaBiomics]

The thread has spawned a bunch of interesting questions but it seems to me the central question was this -- is the population size of nitrifying microbes determined by available surface area or ammonia input?

IMO the first part of the answer is: I'm not aware of experimental data that can definitively answer this for an aquarium environment. I would love to be pointed to any if it exists.

That said, I expect based on my understanding of microbial population growth that
a) the available surface area limits the maximum population size for surface-associated types (but not free-living types), and
b) the amount of ammonia input (fish pee) promotes growth of AOM (ammonia-oxidizing microbes) and indirectly, growth of NOB (nitrite-oxidizing bacteria).

So I expect that both surface area and bioload contribute, but it different ways... adding surface area should increase the maximum capacity of the aquarium to support additional nitrifying microbes. Adding bioload should increase the population size until it becomes limited by either (a) some other nutrient, or (b) surface area.

What really throws a wrinkle in this is competition for ammonia. Nitrifying microbes compete with photoautotrophic assimilation (i.e., uptake of ammonia by algae) and heterotrophic assimilation (e.g. heterotrophic Bacteria and some symbiotic invertebrates). I often see low nitrifying signals in systems with productive algal refugia, and I suspect there is a connection. Its experimentally testable... someday!

 

[Dom]

Hi Dom,

I'm late to the party because I've been busy (processing aquarium samples for bacterial analysis among other things), but here are my thoughts.

Using high-throughput DNA sequencing, we can absolutely measure the relative abundance of nitrifying microbes. (I emphasize microbes here since in many if not most tanks, the primary ammonia oxidizers are actually Archaea rather than Bacteria. But anyway)

We can also measure the types of nitrifying microbes. I see variation between tanks at the family and genus levels, and also at low levels (e.g. different genotypes within the same species).

I have a lot of data collected on this and have been meaning to write up an article on the diversity of nitrifying microbes in home aquariums. This thread is good motivation to get back to that project.

Now to read the rest of the thread! Thanks @taricha for bringing it to my attention.

-Eli

Only fashionably late.

I'm surprised at how this thread has taken off...
What I have learned is that, yes, it is possible. But not at the hobbyist level. And I've also learned that while the load to colony relationship can be proportional, this isn't always the case.

Thank you for the reply!
Dom

 

[brandon429]

work threads match the suspended biofiltration component mentioned by AB, in the thread 'connecting established reef to new tank' our member Tuffloud directly cycles an all dry rock system in about 25 days (matches online cycling charts) by only plumbing it to a running reef. he then unplumbs and the new tank can move ammonia down in 24 hours/common outcome for the wait.

by water association only

He did not feed extra, that specifically addresses some of the applications behind Dom's question as I interpret it-how did double the filtration mass form when the bioloading constant stayed the same other than contaminations and seeding that naturally formed in the new plumbed tank? Going from current forum views, we'd have to feed more to earn that new bacteria biomass in the new tank, all dry substrate.

enough bacteria to cover every surface generated in the new tank using the feed constants from the main tank, that directly involves the concepts in Dom's post subject in my opinion.


no extra bottle bac was dosed into his setup, it was producing all new biomass off same feed, only changing water volume and new surface area.




I liked how Dr T mentioned simply working harder, helps fill in the gaps on that mechanism for how rocks pick up the work so fast after sandbed removals.

 

[brandon429]

taking science and applying it to challenge posts should be an outcome of our discussions on bacteria, population shifting and surface area.

Nano Tank - Sudden Ammonia Spike

Hello, My tank was cycled using Dr Tim’s one and only and ammonia 3 weeks ago. It was completely cycled about a week and a half ago, tested by adding ammonia drops and next day reading 0. I waited another week before adding my clownfish and he’s been doing fine. I got a few frags 6 plugs and...

www.reef2reef.com

in this tank, a person with a recent cycle completion is reporting the classic 'stuck cycle' condition, and Dom's thread is 100% why opinions vary on whether or not that poster's new tank is really truly failing to control free ammonia. Once our rules for cycling and surface area mechanics are all in line, like chemistry rules, then responses to his condition will streamline.

his entire post is about the variability and reliability of biofilters, and its specifically a hint of concern about ramp up*can his bacteria handle the addition of a fish, though it did not cycle that way.


*should he buy more bottle bac due to that test reading?

*should he do nothing and trust surface area mechanics to run his tank and ignore the test?


*should be buy a new test (which implies cycles are not consistent tank to tank at all)

Dom's thread shows how gaps in cycling science allows for guess purchasing, and for sure these gaps dont make cyclers confident, the gaps make them hesitant and ready to purchase some peace of mind. he's already bought bottle bac, and measured cycle completion...given the tank has typical rocks and sand, at what point can reefers simply trust what bacteria are doing??

*edit, see outcome of his thread.

 

[Big G]

a) the available surface area limits the maximum population size for surface-associated types (but not free-living types), and

This makes me think of how efficient chaeto is for bio load. Am I correct in thinking that macro algaes, like chaeto, provide the highest surface areas for "surface-associated" types or is it the environment created by the chaeto where the "free-living" types thrive between the algae's many and dense branches?

 

[brandon429]

wanted to make another report on thread patterning to be measured over the years against updated bacterial id/quantification etc.

We dont have to factor nitrite readings in reefing for display tanks.

people aren't dumping wildly varying amounts of ammonia, they're dumping what it takes to make api say 2 ppm and though that ranges like horseshoes its still not enough to affect ability to control a safe start with a supported bioload, even with nitrite not under control yet.


low surface area systems like qt tanks, or hospital tanks might be measured differently to assess medication impacts, but display tanks fit a recurring pattern in cycle start threads, am reporting that.

100% without variation we dont need to know nitrite to be able to cycle new tanks here and do live rock transfer skip cycles, its a pure data set. no outliers.

we don't care if its low. we don't care if it reads nine, not factored with zero consequence

as testing unfolds nitrite oxidizers will be measured and quantified and we will have a strong picture of their role overall; it will be neat to compare that with a fully shifted hobby that does not even measure for them in huge numbers.