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

[flagg37]

This is great and exciting news. Are there any plans to test various locations around the world (Hawaii, Fiji,....) for comparison? Also will you be making public the data from all your customer’s tanks? It would be great to see a searchable database.

 

[lexinverts]

This is great and exciting news. Are there any plans to test various locations around the world (Hawaii, Fiji,....) for comparison? Also will you be making public the data from all your customer’s tanks? It would be great to see a searchable database.

That's already being done. See http://ocean-microbiome.embl.de/companion.html

AquaBiomics is doing the TARA Oceans Microbiome for reef tanks.

 

[taricha]

For those mulling the question - how much difference can there be in the immense bacterial community our tanks, this article from the @AquaBiomics is great.
https://aquabiomics.com/articles/how-aquarium-microbiomes-differ

It's pretty dramatic that the two overall most-represented families (flavo... and pelagi...) are almost entirely absent from one group of tanks. I need more read-throughs, but it's great.

Love this bit.

The microbiomes of tanks in group (d) differed from all other groups in having a higher relative abundance of microbes from the family Cryomorphaceae than other groups. This family of surface-associated Bacteria contributes to biofilm communities, and their growth is supported by amino acids or complex nutrient mixtures such yeast extract. The consistent observation of this same pattern only in all five independent systems maintained by a single operator suggests that some systematic difference in feeding, dosing, or maintenance is responsible, although we’ve failed to identify the cause so far.

but I think I disagree with this....

The specificity of these requirements suggests the hypothesis that variation in unmeasured dissolved nutrients drives the majority of variation in aquarium microbiomes. Specifically, reduced sulfur compounds (e.g. DMSP), carbon sources (e.g. polysaccharides and simple sugars), and nitrogen sources including methylamines, proteins, and amino acids are important for the growth of these groups. However, few if any aquarists measure or dose these compounds. The existing variation probably results from variation in the production of these nutrients through natural biological processes in each aquarium (e.g, DMSP production by algae).

If you look at the "coral food" section of any place like

Coral Foods

Bulk Reef Supply - Saltwater Aquarium Supplies for Reef Tanks

www.marinedepot.com

you'll find dozens of things people use that have at least one of those ingredients (as I understand it).

 

[lexinverts]

Nice tease! Would love to see that if it can be shared.

Briefly, here is part of my reports for two tanks; one doing well, and the other that was dealing with frequent dinoflagellate outbreaks.

First, here is the key that is provided by AquaBiomics to help you interpret your scores:

Here are the scores for one of my tanks that was doing well.

Here are the scores for the tank with dino outbreaks

The diversity score is in the red, and my microbial richness is in the yellow. Per the recommendations from this report, I added some live rock from the tank that was doing well. The dinoflagellate problems have subsided since. Soon, I will have a follow up report to see how the microbiome has changed, if at all, since the first snapshot.

 

[EMeyer]

For those mulling the question - how much difference can there be in the immense bacterial community our tanks, this article from the @AquaBiomics is great.
https://aquabiomics.com/articles/how-aquarium-microbiomes-differ

It's pretty dramatic that the two overall most-represented families (flavo... and pelagi...) are almost entirely absent from one group of tanks. I need more read-throughs, but it's great.

Love this bit.


but I think I disagree with this....

If you look at the "coral food" section of any place like

Coral Foods

Bulk Reef Supply - Saltwater Aquarium Supplies for Reef Tanks

www.marinedepot.com

you'll find dozens of things people use that have at least one of those ingredients (as I understand it).

Thanks, this is a good point. You are absolutely correct that many of the foods people add to their tanks (either for fish or corals) contain many of the compounds that affect the growth of specific bacteria.

I should amend my statement to say "few hobbyists deliberately dose these compounds, although some are contained in common foods".

I agree entirely that the foods we add to our tanks are likely to affect microbial communities... it is definitely on the list of experiments to try!
[edit - boy, I am really bad at this "two accounts thing". I will try to do better ]

 

[rkpetersen]

(the way the ICP testing outfits are not sharing that kind of info makes it very hard for me to have faith in their results).

And the fact that you can send identical samples simultaneously to several ICPOES labs and get back significantly different results for some parameters doesn't create a lot of confidence either. ;Shifty

 

[rkpetersen]

For those mulling the question - how much difference can there be in the immense bacterial community our tanks, this article from the @AquaBiomics is great.
https://aquabiomics.com/articles/how-aquarium-microbiomes-differ

It's pretty dramatic that the two overall most-represented families (flavo... and pelagi...) are almost entirely absent from one group of tanks. I need more read-throughs, but it's great.

Love this bit.


but I think I disagree with this....

If you look at the "coral food" section of any place like

Coral Foods

Bulk Reef Supply - Saltwater Aquarium Supplies for Reef Tanks

www.marinedepot.com

you'll find dozens of things people use that have at least one of those ingredients (as I understand it).

Thanks for the link.
Interesting that a few people actually had potentially infectious Legionella in their tanks.
That's no joke; wouldn't want to see that aerosolized in an enclosed space like a living room or basement.
Especially if L. pneumophilia is included in the mix of species.

 

[hart24601]

I used to do this professionally at DuPont, it's neat they can offer it to consumers as the price keeps dropping but I question the value to us in the hobby. It will be interesting to see the variation with tanks, but without testing the substrate and those biofilms I don't know how much we will gain from this information. Even different strains in the same species of bacteria can have drastically varying impacts due to the unique compounds they can produce. Even for pathogens it will be hard to judge the number in the water column vs what happens when infected, at that point you can see there is a problem, and I don't think even if a new bacterial population showed up in the water column you could conclusively ID the infection from that.

I wrote the above before seeing some of the same questions in the thread. It will be interesting to see if we learn any actionable items from this testing. What is "good", how can that be achieved if results are "not good" and the such.

When I did these we would also RNAseq to get expression profiles, is the limitation there still cost for something like this to the hobbyists (and cost with RNA preservation)? We found much more impactful data analyzing expression changes vs solely population changes.

 

[stacksoner]

If this is what it looks like, I think it represents a huge step forward for struggling hobbyists whose systems are plagued by a world of biological imbalances that we previously were unable to test for. I believe that this will help explain the vast array of differences between reefer's systems and help everyone become more successful in the long run.

For those who are tired of being asked "What's your alk, ca, p04, etc" when you know that's not the issue....this new offering sheds a glimmer of hope for those who are still chasing the dream.

 

[Reefahholic]

Be interesting to see if there’s a trend of decreasing bacteria after the initial start up if bottled bacteria is not adding back into the system. I believe it is likely skimmed out over time. Not all, but I feel the numbers decrease. Or is it the reverse. Do the numbers increase over time w/o adding back bacteria?

For example...does Paul B’s 40 year old tank have the most bacterial count/colonization or does the guy who’s dumping bacteria into the tank monthly with a 3 year old tank have higher numbers?? This is a tough one if you really think about it. It can almost go both ways depending on how the tank is maintained or ran.

 

[Scubabum]

Sent my test out last Friday on my 26 year old reef tank. Very interested to see the results...

 

[taricha]

Be interesting to see if there’s a trend of decreasing bacteria after the initial start up if bottled bacteria is not adding back into the system.

This was the other testable question that popped into my head today.
all other things being equal, does bacterial diversity trend up or down in a system over time?
Conventional hobby wisdom says down, but never seen evidence either way.

 

[AquaBiomics]

This is great and exciting news. Are there any plans to test various locations around the world (Hawaii, Fiji,....) for comparison? Also will you be making public the data from all your customer’s tanks? It would be great to see a searchable database.

As Andy mentioned, data from natural marine environments are available. I plan to write up a comparison at some point.

I want to touch briefly on the idea of making data public and searchable.

I see huge value in this idea and I am a big proponent of open sharing of raw data and methods. At the same time, as a service provider, I want to be conscious of clients' privacy. It seems appropriate that the client owns their data and determines whether it becomes public or not. Balancing these goals is not insurmountable but it's not trivial to do it right.

So at the beginning the policy is only the client can view their data but they are free to do whatever they want with it including sharing it online like ICP results to compare with others.

On the to-do list, I definitely would like to add a list of reference samples the client could compare their samples to. This would achieve a lot of the same goals without privacy concerns. But the to-do list is long

 

[AquaBiomics]

And the fact that you can send identical samples simultaneously to several ICPOES labs and get back significantly different results for some parameters doesn't create a lot of confidence either. ;Shifty

I havent done this comparison yet between different ICP service providers but I'd be curious to read the comparisons others have done. I'd expect disagreement on the very low abundance elements but if there is a lot of disagreement on the more abundant components that'd be more worrying!

Reproducibility is crucial for any quantitative analysis. I havent had a chance to compare with other labs yet, but within my own lab at least I should be able to get the same answer twice!

This was one of the first things I looked at and I was reasonably happy with the results. Here is a figure that shows microbial communities sampled twice from the same tank (A1 and A2) and from the tank right next to it (B). All three samples were processed together with all the others in that batch.

The figure shows that quantifying the microbial community of an aquarium from deep sequencing (10k DNA sequences per sample) provides a reproducible description of the community in that tank.

And it shows that the small difference between replicate samples are dwarfed by the differences between tanks. In this case, tanks that are half an inch apart.

(Please note that these are some of my experimental tanks and neither one has a typical microbial community!)

 

[rushbattle]

I havent done this comparison yet between different ICP service providers but I'd be curious to read the comparisons others have done. I'd expect disagreement on the very low abundance elements but if there is a lot of disagreement on the more abundant components that'd be more worrying!

Reproducibility is crucial for any quantitative analysis. I havent had a chance to compare with other labs yet, but within my own lab at least I should be able to get the same answer twice!

This was one of the first things I looked at and I was reasonably happy with the results. Here is a figure that shows microbial communities sampled twice from the same tank (A1 and A2) and from the tank right next to it (B). All three samples were processed together with all the others in that batch.

The figure shows that quantifying the microbial community of an aquarium from deep sequencing (10k DNA sequences per sample) provides a reproducible description of the community in that tank.

And it shows that the small difference between replicate samples are dwarfed by the differences between tanks. In this case, tanks that are half an inch apart.

(Please note that these are some of my experimental tanks and neither one has a typical microbial community!)

Here is a good study on ICP testing as done by Triton.

Skeptical Reefkeeping 12: Triton Lab ICP-OES Testing of a Certified Artificial Saltwater Standard

From ReefsMagazine By Rich Ross and Dr. Chris Maupin At MACNA 25 in Denver, the potential for the new ICP-OES aquarium water testing by Triton Lab in Germany made many saltwater hobbyists swoon. Th…

packedhead.net

 

[AquaBiomics]

This was the other testable question that popped into my head today.
all other things being equal, does bacterial diversity trend up or down in a system over time?
Conventional hobby wisdom says down, but never seen evidence either way.

This is one of many great questions people have asked in the thread that have me nodding my head going "I want to know that too!"

There are so many unanswered practical questions in this area.
How does the carbon source affect microbial communities in carbon dosed tanks?
How does the macroalgal community affect the microbiome?
and does the microbiome get more or less diverse over time?

In my new lab I started up many independent tanks using different approaches... this is one of many datasets I am still analyzing but I can say that within the short term we see the increase in diversity I think we would all expect. Long term experiments take a long time... but I have added "tank age" to my sample registration form so we can start to address that question using the database of client tanks.

But I am one guy, with one lab, and there are only so many experiments I can run. My vision is that all of you run the many excellent experiments you are already running on these questions, and I provide data on the microbial communities that result from your experiments.

 

[rkpetersen]

Received my kits very quickly (from just down the coast in Oregon) and sent them out this morning.
It will be interesting to see how my 3 current tanks compare, at 2.5, 1.5, and 0.5 years since startup.

 

[rkpetersen]

I havent done this comparison yet between different ICP service providers but I'd be curious to read the comparisons others have done. I'd expect disagreement on the very low abundance elements but if there is a lot of disagreement on the more abundant components that'd be more worrying!

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.

 

[rushbattle]

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.

Careful, Ehsan might come in here and threaten you with threatening his family angrily!

 

[lexinverts]

Coral-Bacteria Communities are WAY More Important than Anyone Thought

Reading through different coral scientific publication, we came across one, that could be quite relevant for us reef aquarist. In this publication published in Nature, scientist from the Red Sea Research center, from the King Abdullah University of Science and Technology (KAUST) in Saudia Arabia...

www.reef2reef.com