This is what I've dreamed of for so long! Testing for microbes in our tanks!

[AltitudeAquarium]

Hi everyone,

As the owner of the company I'd be happy to answer any questions. There have been a lot asked already in the thread so forgive me if I miss some. I'd like to start with a few of the more important points.

1. I promise: no snake oil. I'm selling a testing service; whoever compared it to ICP is exactly right.
You will notice my site is conspicuously absent of promises that "this bacterium is bad" or "this bacterium is good". We simply don't know enough yet to make those claims.

2. By building a large database of samples from hobbyist and aquaculture tanks, we will learn a lot. I already have some data in hand and am gathering more.

3. There is some skepticism about what this means. Skepticism is a wise default position, but please do note what my service claims or does not claim. I claim to be able to identify the microbes in your tank, and provide information about what those microbes do. I will stand by those claims, since they are the basis for most modern microbial ecology.

I do NOT claim that I can sell you a magic bottle that will make everything happy. Or even that we understand everything about the microbes we find. In the reports, I try hard to not overstate the conclusions.

I've spent the last 20 years in Academia, so I'm comfortable with disagreement and discussion. Don't be shy about disagreeing - my service is simply DNA sequencing, I'm not selling bacteria. So I won't be offended if someone has an argument why bacterial type X is unimportant. (If there is someone who thinks it doesn't matter what kind of microbes are in your tank, I would disagree, but I'm not sure anyone in the reefing world holds that opinion anyway! And it would be an interesting discussion in any case)

4. Finally (for this post), some have raised the question of planktonic versus surface associated bacteria. Its an important distinction. But please recognize that water is constantly circulating past the surfaces in our tanks -- the biofilm microbes show up in the water column too. Lots of evidence in hand now to show this.

With that said, our first round did show that for a more sensitive analysis of biofilm microbes, we should include a direct sample of the biofilm. This contains important ammonia-oxidizing and nitrate-oxidizing microbes. So current sampling kits include a biofilm sample too.

I'm gonna stop there for now, but I'll come back and answer questions. There is a link on the main page of the company website that describes a basic overview of the microbes that live in reef tanks. Soon I'll be adding my analysis of differences between tanks, and my cycling experiment studying the succession of microbes in new aquariums started various ways.

We have a lot to learn - but the way we learn is by collecting data. Thats what my service is for.

-Eli

I think maybe this information will support the idea that it is the ratio of bacterium and not the species that determines the healthy biome of our aquariums. Also, I would to compare the list more to different wild waters that support healthy coral growth and fish. I look forward to learning more. Thank you for taking this on.

 

[taricha]

@AquaBiomics in the article on differences between aquarium biome groups, group b, had a notable amount of what is just labeled as "mitochondria" as opposed to any bacterial family name.
Can you shed some light on what that means or if it is meaningful at all?

 

[AquaBiomics]

Yeah, interesting observation. Thanks for bringing this up.

Most of you are probably aware that the mitochondria (tiny structures inside our cells) are thought to have evolved from bacteria. As a result, the same methods used to detect bacteria also detect mitochondria. These were present in all tanks, but at different levels. In group b, they made up more than 1% of the total so they show up on the graph. I must confess, I do not know why some tanks show more mitochondria than others.

Since the mitochondrial DNA can be used to identify species, In principle I should be able to use those sequences to identify the animals or algae from which those mitochondria originated. I just havent explored this yet, since I think people already have a pretty good idea what animals live in their tanks

 

[taricha]

[Mitochondria] were present in all tanks, but at different levels. In group b, they made up more than 1% of the total so they show up on the graph. I must confess, I do not know why...

Would this be consistent with greater organisms destruction in some tanks than others, such as constant messy herbivores grazing algae? (Herbivores generally needing to consume more material per day than carnivores)

 

[MnFish1]

Its an interesting topic - I would be concerned about a couple things (my guess they have tested this) - a 'microbiome' may be different in a sump as compared to a corner of the tank which might have detritus piled up vs on a live rock with a large amount of oxygenated flow - vs free flowing water in the tank.

From what I've read - the biome in a tank develops according to the conditions in the tank -once this happens trying to 'change it' without changing conditions is very difficult. (for example -vibrant is bacteria - unless its marketing - why is it required to add it every week or so - its becasue the added bacteria 'does its job' but then cannot establish itself in the tank' because of the biome thats established.

This tests sounds like the new triton test thats compared to many aquariums to get the 'triton ratio'- and though interesting - I guess I dont see how it will improve our tanks - since there is no 'preferred' biome (and certainly no evidence to suggest one) - averaging a bunch of tanks does not mean much IMHO. Of course I could be incorrect.

 

[hart24601]

Its an interesting topic - I would be concerned about a couple things (my guess they have tested this) - a 'microbiome' may be different in a sump as compared to a corner of the tank which might have detritus piled up vs on a live rock with a large amount of oxygenated flow - vs free flowing water in the tank.

From what I've read - the biome in a tank develops according to the conditions in the tank -once this happens trying to 'change it' without changing conditions is very difficult. (for example -vibrant is bacteria - unless its marketing - why is it required to add it every week or so - its becasue the added bacteria 'does its job' but then cannot establish itself in the tank' because of the biome thats established.

This tests sounds like the new triton test thats compared to many aquariums to get the 'triton ratio'- and though interesting - I guess I dont see how it will improve our tanks - since there is no 'preferred' biome (and certainly no evidence to suggest one) - averaging a bunch of tanks does not mean much IMHO. Of course I could be incorrect.

I have always wondered if vibrant was truly a bacterial additive or if it's more along the lines of a bacterial fermentation product or other bacterial extract that contains a bacterial based algaecide and the bacteria left in the bottle are not really the driving force for that product.

Would be interesting if you do some flow cytometry to get the overall bacterial counts as well. There were some advanced aquarist articles on that years ago and they varied quite a lot. Carbon dosing impact, skimming impacts and the such. Be interesting to see how the community changed as well. Look at changes running UV as well. Ideally would be great to see counts, population, and expression - all which are possible but not cost effective yet.

I still don't know how for our captive systems we judge 'good', 'ok' and 'bad' and then how to correct it. And if these results correlate with the observed tank phenotype.

 

[Thales]

I have two tanks on my system, they are 40 feet apart. I would like to see how their biomes compare. Does that make sense with what you are testing?

 

[taricha]

There were some advanced aquarist articles on that years ago and they varied quite a lot. Carbon dosing impact, skimming impacts and the such.

This is the referenced article by Feldman.

Feature Article: Bacterial Counts in Reef Aquarium Water: Baseline Values and Modulation by Carbon Dosing, Protein Skimming, and Granular Activated Carbon Filtration

What are the bacteria populations in the water column of reef tanks, and how does that value compare with bacterial counts in authentic reef water? Does carbon dosing indeed increase water column bacteria populations (i.e., is growth carbon limited)? Does mechanical filtration (protein skimming...

www.advancedaquarist.com

Until this current project, that was the best info we had about aquarium bacteria.
The Feldman article tells us that our aquarium husbandry choices can make a big difference in the amount of bacteria in our water.
The current microbiome may be saying our husbandry techniques can also shift the families of bacteria too.

 

[hart24601]

This is the referenced article by Feldman.

Feature Article: Bacterial Counts in Reef Aquarium Water: Baseline Values and Modulation by Carbon Dosing, Protein Skimming, and Granular Activated Carbon Filtration

What are the bacteria populations in the water column of reef tanks, and how does that value compare with bacterial counts in authentic reef water? Does carbon dosing indeed increase water column bacteria populations (i.e., is growth carbon limited)? Does mechanical filtration (protein skimming...

www.advancedaquarist.com

Until this current project, that was the best info we had about aquarium bacteria.
The Feldman article tells us that our aquarium husbandry choices can make a big difference in the amount of bacteria in our water.
The current microbiome may be saying our husbandry techniques can also shift the families of bacteria too.

It was a very interesting and valuable testing to see what occurs in our tanks. But again, what does it mean when it comes to our tanks? What is good and bad? I think he stated that the acro tanks with large skimmers had 1/10th the bacterial counts of non skimmed soft coral tanks - very interesting and logical from a research perspective but he wasn’t selling a kit to reefers. My hang up again is do those numbers and populations really have an impact on our tanks, can and how can we change them if we want, what should we look for, aka positive results from the change. Or do you just look at the population sheet and think “neat”.

 

[chefjpaul]

It was a very interesting and valuable testing to see what occurs in our tanks. But again, what does it mean when it comes to our tanks? What is good and bad? I think he stated that the acro tanks with large skimmers had 1/10th the bacterial counts of non skimmed soft coral tanks - very interesting and logical from a research perspective but he wasn’t selling a kit to reefers. My hang up again is do those numbers and populations really have an impact on our tanks, can and how can we change them if we want, what should we look for, aka positive results from the change. Or do you just look at the population sheet and think “neat”.

I believe right now its "look at the population sheet and think neat"

Further development could have the possibility to "define" what is either good, bad, or neutral.

I'm interested to see the evolution of this, and have no issues with purchasing a test to further help research and analysis, if that's the reference.

 

[Breadman03]

You will notice my site is conspicuously absent of promises that "this bacterium is bad" or "this bacterium is good". We simply don't know enough yet to make those claims.

2. By building a large database of samples from hobbyist and aquaculture tanks, we will learn a lot. I already have some data in hand and am gathering more.

I can't justify getting a test at the moment, but it sounds like you have a plan for learning what is good and bad.

@TheHarold, I had them test all 4 of my systems. The one system that I was having trouble with dino, was, by far, the system that had the lowest microbial diversity.

FYI, Eli has some data that he collected experimentally that he will be sharing soon.

Interesting. I might just have to pick up a few bottles of bacteria and start pumping up my system diversity since I just rebooted it. I'm interested to see if this data service can develop a strong correlation between low diversity and dino. It would certainly back up the suspected cause of new system uglies.

 

[hart24601]

I believe right now its "look at the population sheet and think neat"

Further development could have the possibility to "define" what is either good, bad, or neutral.

I'm interested to see the evolution of this, and have no issues with purchasing a test to further help research and analysis, if that's the reference.

oh it’s very interesting and I hope it leads to a new way of evaluating our systems, I have concerns obviously, but I do hope amazing things come from these tests eventually.

Since the counts of bacteria can be 10x between tanks would be interesting to see the total counts as well to see if those tanks with more bacteria are less or more diverse. It may be that carbon dosing increases only few families, then when population tested the diversity isn’t represented well with the overwhelming number of ‘pro carbon’ species however it’s hard to directly compare to a tank that has 20x fewer bacteria but we don’t know those total counts.

 

[MnFish1]

I believe right now its "look at the population sheet and think neat"

Further development could have the possibility to "define" what is either good, bad, or neutral.

I'm interested to see the evolution of this, and have no issues with purchasing a test to further help research and analysis, if that's the reference.

Isn't it kind of like sending in a genetic test to ancestry.com - or 23 and me - you get a nice report - but there probably isnt much to do with/about it?

I'm (as I said before) - I wonder if they have sampled from multiple areas of the same tank / sump / reactors?

 

[tripdad]

I think that right now it's an unknown. In other words we have no idea what any of it means. But by collecting data sets and then looking for correlation, i.e. tanks with these populations grow acros well, we can then start making use of the information and eventually actually be able to say "We know" something.

 

[Reefs and Geeks]

After over doing carbon dosing and dropping nitrate and phosphate to 0 and getting a dino outbreak I can see how this type of information could be useful. After dinos, it seems like everyone's suggesting every bottle of bacteria under the sun to add to the tank to increase the biodiversity in the tank to out compete the undesirable dinos. Having a good baseline of a healthy tank would make this testing valuable in that you can see if you're close to a healthy tank, or if you're not properly supporting the various bacteria and verging on undesirable outbreaks.

For $100/test this does seem like a pretty spendy test at this point, but once enough is known about the effects of varying biodiversity, the information could become much more valuable. If the test comes back and is able to say "you're missing these valuable strains of bacteria in your tank and at risk of dinos/GHA/bryopsis...etc" then you can preemptively add what is missing to the tank to stay away from the potential issues before they happen. Nothing worse than watching your large coral colonies dieing or being smothered by algae while you try to figure out how to combat it.

I'll be following along as I think this could turn into a vary useful test to run periodically. I'll just wait untill it gets to that point.

Thanks to everyone who does run this test though to allow the development of a firm information base that will result in known actions to take based on test results!

 

[Matt Carden]

It is definitely concerning.
When I first started to use ICPOES, I'd send samples to 3 different labs.
Here are just a few examples of simultaneous values I've received from the 3 labs:

Magnesium - 1333, 1380, 1279
Silicon - 113, 140, 0
Phosphorus - 0, 10, 90
Iodine - 99, 94, 216
Selenium - 8, 15, 46

Now I only send to 2, after finding that the results from one lab would often vary considerably from the results from the other two.

Which one did you disclude?
If you don't want to name at least give us a hint!

 

[AquaBiomics]

Isn't it kind of like sending in a genetic test to ancestry.com - or 23 and me - you get a nice report - but there probably isnt much to do with/about it?

The comparison to 23andme is a good one, but I'd suggest a key difference... we can't do anything about our DNA, but we can do something about our tanks' microbiome. We just have a very imperfect knowledge of how to do so!

For example, the figure I showed earlier in this thread, with bars labeled A1/A2/B... those were identical tanks set up right next to each other, but with different microbes. So those differences resulted from my decisions in setting up the tanks.

I wonder if they have sampled from multiple areas of the same tank / sump / reactors?

Because we know each microhabitat is different, I've focused on identifying samples that can be sampled consistently and compared across tanks. Theres little value in a sand sample when so many people run bare bottom tanks. Or a live rock sample; the rock itself varies too much for any realistic standardized sampling method.

The water flows past everything, and all the nutrient processing microbes found in sand samples are also found in water samples... just at a lower level. And the water can be sampled in a consistent way across tanks. As can the inner surface of a pipe.

With that said, I do plan a detailed map of microbial communities throughout the aquarium. A Microbial Atlas of the Saltwater Aquarium. It will be interesting, when we see microbe X in the water, to know that it primarily lives on live rock, or sand beds, etc.

 

[MnFish1]

The comparison to 23andme is a good one, but I'd suggest a key difference... we can't do anything about our DNA, but we can do something about our tanks' microbiome. We just have a very imperfect knowledge of how to do so!

For example, the figure I showed earlier in this thread, with bars labeled A1/A2/B... those were identical tanks set up right next to each other, but with different microbes. So those differences resulted from my decisions in setting up the tanks.

Because we know each microhabitat is different, I've focused on identifying samples that can be sampled consistently and compared across tanks. Theres little value in a sand sample when so many people run bare bottom tanks. Or a live rock sample; the rock itself varies too much for any realistic standardized sampling method.

The water flows past everything, and all the nutrient processing microbes found in sand samples are also found in water samples... just at a lower level. And the water can be sampled in a consistent way across tanks. As can the inner surface of a pipe.

With that said, I do plan a detailed map of microbial communities throughout the aquarium. A Microbial Atlas of the Saltwater Aquarium. It will be interesting, when we see microbe X in the water, to know that it primarily lives on live rock, or sand beds, etc.

Thanks for the reply - it will be interesting. Especially to see if indeed the proportions in the water are the same, for example as on rock or in the sump vs the tank, etc. Because unless its very close - getting a sample from the water may not mean as much - but again - its fascinating idea - and I hope you're successful

 

[Reesj]

Which one did you disclude?
If you don't want to name at least give us a hint!

Obviously the 3rd set as I deduced from his post!

 

[Reesj]

Thanks for the reply - it will be interesting. Especially to see if indeed the proportions in the water are the same, for example as on rock or in the sump vs the tank, etc. Because unless its very close - getting a sample from the water may not mean as much - but again - its fascinating idea - and I hope you're successful

Sorry but you seems to have no idea about statistics or data analysis!