Problems Due to Bacterial Imbalances? AquaBiomics Test Results.

[brandon429]

Connecting Established Reef To New Tank

EDIT: In conclusion, if using the method I did - connecting an established reef to a new system with dry rock (clean), I recommend the following: 1. Dose your new tank prior to connecting to your old tank with NO3 and PO4 enough to raise to your established tank levels. 2. Take your skimmer...

www.reef2reef.com

shows a high degree of transmissible ammonia oxidizing bacteria from any reef tank solely from the water. It’s the only study I know where the keeper cycles a fully dry system within cycle chart times only by water sharing. When Dr Tim said water didn’t have many nitrifiers, I guess other clades aren’t included that do the same job


Most aquarists don’t care which clade is present, or how they shift over time, only that nh3 is controlled

bottle bac cycles a reef tank for nh3 control within ten days, most brands, per Dr Reefs study. Reef tank water takes only ~20 days to cycle a new reef, rather potent and free. Even though pelagic water testing in this thread shows variable degrees of bacteria in water, this worked above first go because any matured reef tank can pull off the connected cycle test. They’re all transmitting lots of cycling bacteria via currents and sloughing etc

whether it’s dedicated nitrifers or heterotrophs pulling off the nh3 control doesn’t seem to matter very much, benefits seem the same

 

[SDK]

I'm late to the party, but nitrifying bacteria are not in the water. They form biofilms on the rockwork. You'd need to resuspend those before taking your sample to see high abundance. Most likely you will only get a little bit in the water itself.

Not sure why you quoted me here, but I would recommend reading the thread and attached articles more closely. The point that there is less bacterial density in the water column has been pointed out several times, and some of the testing involved taking swabs. The methodology used was able to find significant differences in bacterial population ratios in tanks started different ways.

So, extremely interesting and potentially useful information....

 

[MnFish1]

I'm late to the party, but nitrifying bacteria are not in the water. They form biofilms on the rockwork. You'd need to resuspend those before taking your sample to see high abundance. Most likely you will only get a little bit in the water itself.

You actually take 2 samples - one from the water column - and one from a specific area (where biofilm should be - using a q-tip type collector. Then you get a report that contains the values from both places (in one report)

 

[MnFish1]

\

Great! Thanks, this has been really interesting exploring unknown samples. Now you've got me all curious again about these, I will have to move this analysis back to the front burner.

Hi - any word on the samples yet (the liquid vs. swab)?

 

[Cv111]

Not sure why you quoted me here, but I would recommend reading the thread and attached articles more closely. The point that there is less bacterial density in the water column has been pointed out several times, and some of the testing involved taking swabs. The methodology used was able to find significant differences in bacterial population ratios in tanks started different ways.

So, extremely interesting and potentially useful information....

So i've done this kind of collection before and published an aquatic metagenomics paper..Depending on how the swab was done, it's very possible you'd still miss it. The rock would need to be placed in air for it to work accurately. A q tip swab in liquid media is a pretty poor way to collect a biofilm. I'm also not sure that the overall abundance of these bacteria needs to be high for them to do their job. I haven't purchased services from aquabiomics, so I don't know what form of results they give you. I'd be curious if there a no reads at all or just a low abundance. The process is not as simple and straightforward as you would assume. The other thing is that abundance doesn't indicate importance. It can suggest it, but a huge pitfall of metagenomics is misunderstanding how to read the data.

 

[MnFish1]

So i've done this kind of collection before and published an aquatic metagenomics paper..Depending on how the swab was done, it's very possible you'd still miss it. The rock would need to be placed in air for it to work accurately. A q tip swab in liquid media is a pretty poor way to collect a biofilm. I'm also not sure that the overall abundance of these bacteria needs to be high for them to do their job. I haven't purchased services from aquabiomics, so I don't know what form of results they give you. I'd be curious if there a no reads at all or just a low abundance. The process is not as simple and straightforward as you would assume. The other thing is that abundance doesn't indicate importance. It can suggest it, but a huge pitfall of metagenomics is misunderstanding how to read the data.

I think this is right. But - there are now numerous articles out there suggesting that the bacteria we 'think' are taking care of the nitrogen cycle - are actually not the main ones. Hopefully @AquaBiomics will respond

 

[Cv111]

I think this is right. But - there are now numerous articles out there suggesting that the bacteria we 'think' are taking care of the nitrogen cycle - are actually not the main ones. Hopefully @AquaBiomics will respond

There's algae and stuff that can use ammonia too so it is very plausible I won't deny that.

 

[flampton]

I think this is right. But - there are now numerous articles out there suggesting that the bacteria we 'think' are taking care of the nitrogen cycle - are actually not the main ones. Hopefully @AquaBiomics will respond

There's algae and stuff that can use ammonia too so it is very plausible I won't deny that.

Yup so what you're describing is the importation of ammonia for protein production. Not part of nitrogen cycle since there is no change in oxidation state. Lots of things in the tank can do this. You'll either skim the organism off to remove the nitrogen in the tank or it will be imported by an animal you care about e.g. coral.

Depending on how you care for your tank will adjust who are the members utilizing the most ammonia. For the heterotrophic bacteria in your tank carbon is the limiting factor. So the more carbon you dose the more you'll shift towards ammonia being utilized for bacterial growth. When people think about lowering nitrates with carbon dosing I think a number of people will be shocked how it truly does it. It takes the ammonia before the nitrifiers get it and short circuits the cycle. Thus less nitrate is produced. Then since there's less nitrate production the many organisms that utilize that substrate can bring down the levels.

Low carbon and you have to rely on the autotrophic nitrifiers. They don't require carbon because they fix it themselves.

 

[BZOFIQ]

This makes me think of old days when I used to go around asking people for muck from their fuge. Is this still something people do? I brought some muck from a local beach which you bet I put into the LR section of the sump, believe @Paul B does similar treatments. It's all about bacteria in the system.

 

[GlassMunky]

I think this is right. But - there are now numerous articles out there suggesting that the bacteria we 'think' are taking care of the nitrogen cycle - are actually not the main ones. Hopefully @AquaBiomics will respond

Good luck with that... I haven’t gotten a response from them either here on the forums or through email the last 3 months of testing from them.
And then this month we got a long winded email about how they are loosing money on the business and need even more than a month now to process things.
I’m not sure they will stay in business over the next year.
it’s a shame because I’ve been trying to do monthly AB testing along with ICP testing to follow and see trends but it’s useless when you can’t get an answer back on how to interpret the info.

The other thing is that abundance doesn't indicate importance. It can suggest it, but a huge pitfall of metagenomics is misunderstanding how to read the data.

This is by far the biggest issue. Understanding the info is almost impossible to scientists, let alone a layman at home with no biology degree.

 

[Cv111]

Good luck with that... I haven’t gotten a response from them either here on the forums or through email the last 3 months of testing from them.
And then this month we got a long winded email about how they are loosing money on the business and need even more than a month now to process things.
I’m not sure they will stay in business over the next year.
it’s a shame because I’ve been trying to do monthly AB testing along with ICP testing to follow and see trends but it’s useless when you can’t get an answer back on how to interpret the info.


This is by far the biggest issue. Understanding the info is almost impossible to scientists, let alone a layman at home with no biology degree.

In theory in a closed system like an aquarium you could try to get at the answers in a better way, but metagenomic datasets definitely have an issue with hypothesis testing. They can be great for forming a hypothesis, but trying to "test" one using that specific type of dataset is difficult without controlled comparisons.

Even measuring something like change over time or by location can be difficult for these type of environmental microbiomes in my experience, let alone trying to infer biochemical activity from it. That said, I do think there is probably something to be said about the diversity of species represented in the water column in general corresponding well with the stability of a system. In health models we sometimes have an organism (i.e. germ free mice vs pet store mice, etc.) that we can use to interrogate the functional relationships and roles of specific species, groups of species, or strains. For environmental samples you can't really do this...but I suppose with a fish tank you actually could... but good luck finding somebody willing to shell out the cash to do it properly.

 

[MnFish1]

Yup so what you're describing is the importation of ammonia for protein production. Not part of nitrogen cycle since there is no change in oxidation state. Lots of things in the tank can do this. You'll either skim the organism off to remove the nitrogen in the tank or it will be imported by an animal you care about e.g. coral.

Depending on how you care for your tank will adjust who are the members utilizing the most ammonia. For the heterotrophic bacteria in your tank carbon is the limiting factor. So the more carbon you dose the more you'll shift towards ammonia being utilized for bacterial growth. When people think about lowering nitrates with carbon dosing I think a number of people will be shocked how it truly does it. It takes the ammonia before the nitrifiers get it and short circuits the cycle. Thus less nitrate is produced. Then since there's less nitrate production the many organisms that utilize that substrate can bring down the levels.

Low carbon and you have to rely on the autotrophic nitrifiers. They don't require carbon because they fix it themselves.

No sorry to be unclear- what I was describing is newer discovered forms of bacteria - such as -

A New Perspective on Microbes Formerly Known as Nitrite-Oxidizing Bacteria - PMC

Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification, nitrite oxidation to nitrate, which is an important process of the biogeochemical nitrogen cycle. NOB were traditionally perceived as physiologically restricted organisms ...

www.ncbi.nlm.nih.gov

 

[Mark Gray]

I received results from AquaBiomics showing bacteria populations in my reef tank. As it turned out, this test shows my tank has bacteria indicative of a mature reef - a total of 442 bacteria types were found with a diversity score of .92 (on a scale of 0 to 1.0.) Interestingly, nitrifying bacteria are practically non-existent. Coral and fish pathogens were not found as well.
I tend to think using Florida live rock is at least partially responsible for the diversity score. Has anyone had this test done where only dry rock was used?

I will do it my tank is 100% dry rock I will look up their site tomorrow. It will be interesting.

 

[MnFish1]

I received results from AquaBiomics showing bacteria populations in my reef tank. As it turned out, this test shows my tank has bacteria indicative of a mature reef - a total of 442 bacteria types were found with a diversity score of .92 (on a scale of 0 to 1.0.) Interestingly, nitrifying bacteria are practically non-existent. Coral and fish pathogens were not found as well.
I tend to think using Florida live rock is at least partially responsible for the diversity score. Has anyone had this test done where only dry rock was used?

I used dry rock - and my score was .81 in one section of the tank - and .43 in another (I sent samples from multiple areas in the tank - to see if there was a difference (as kind of an experiment)