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

[lexinverts]

Bumping this thread to get more of the members aware and more eyes on it!

I just gave Eli four more samples on Friday. Can't wait to see the results!

P.S. Word on the street is that Eli may be interviewed by some of the R2R folks soon....and some other exciting things are on the horizon for his lab.

 

[Flippers4pups]

I just gave Eli four more samples on Friday. Can't wait to see the results!

P.S. Word on the street is that Eli may be interviewed by some of the R2R folks soon....and some other exciting things are on the horizon for his lab.

Lol can't confirm or deny that! Lol

Yes it will be cool to see!

 

[Bills beginning]

That would be AWESOME. Thinking this approach would help in avoiding new tank start ups and avoid the ugly stages imo GHA, cyano and dino to establish the right bacterium to achieve the right balance to establish an ecosystem that is balanced instead of reacting to imbalance.

 

[Gareth elliott]

@AquaBiomics
I admittedly have not scoured your website. But when someone turns in a sample are their any survey questions answered on the tank itself and its current situation? Mainly wondering on outbreak situations like dinoflagellates, cyanobacteria, presence of bacteria infection in live stock. Might be interesting to see the correlations.

And back to dinoflagellates, any interest in using your dna system perhaps as a diagnostic tool for species?

 

[reefwiser]

Will be having a video on this soon.

 

[Matt Carden]

@AquaBiomics
I admittedly have not scoured your website. But when someone turns in a sample are their any survey questions answered on the tank itself and its current situation? Mainly wondering on outbreak situations like dinoflagellates, cyanobacteria, presence of bacteria infection in live stock. Might be interesting to see the correlations.

And back to dinoflagellates, any interest in using your dna system perhaps as a diagnostic tool for species?

All of this has been discussed. The answer to all your questions is yes eventually

 

[AquaBiomics]

@AquaBiomics
I admittedly have not scoured your website. But when someone turns in a sample are their any survey questions answered on the tank itself and its current situation? Mainly wondering on outbreak situations like dinoflagellates, cyanobacteria, presence of bacteria infection in live stock. Might be interesting to see the correlations.

And back to dinoflagellates, any interest in using your dna system perhaps as a diagnostic tool for species?

Hi Gareth,
The short answer is yes, when clients send in a sample, they are asked to record info about their tanks (some required, some optional). See this post for more details.

I appreciate any feedback especially on this questionnaire. Theres a fine balance between not enough detail to be useful, and so much detail few people will fill it out. And I am constantly getting good suggestions about important things I've failed to include, so please let me know if you see anything missing.

--

As for Dinos. The microbiome tests use a marker that is "universal" among prokaryotes (bacteria + archae). This same technology (amplicon sequencing) is very easy to change to a different target, and similar markers and databases are already available for eukaryotic (everything but bacteria & archae) profiling. There are several different markers available for identifying marine plankton.

I'd like to add this service, and am running some test samples in the next sequencing run. While I'm optimistic since its a pretty straightforward extension, I'm sure it will take longer than I want to bring that service online!

 

[AquaBiomics]

Hi all,

Hot off the presses. So I've mentioned how little we know about coral pathogens. The research required to identify coral pathogens is not easy, and takes time.

Well, a new parasitic bacterium causes reduced growth in corals has recently been identified. Thanks @reefwiser for bringing this article to my attention!

Phylogenetic, genomic, and biogeographic characterization of a novel and ubiquitous marine invertebrate-associated Rickettsiales parasite, Candidatus Aquarickettsia rohweri, gen. nov., sp. nov - The ISME Journal

Bacterial symbionts are integral to the health and homeostasis of invertebrate hosts. Notably, members of the Rickettsiales genus Wolbachia influence several aspects of the fitness and evolution of their terrestrial hosts, but few analogous partnerships have been found in marine systems. We...

www.nature.com

I looked in our data... lo and behold, there it is. Two out of the twenty tanks sampled for this initial study have Candidatus Aquarickettsia rohweri. Which has been very recently shown to cause reduced growth rates in corals. I will notify the owner(s) of those tanks personally for further discussion...

But I figured I'd bring it up here. I think this is a great example of the value of this kind of data. We didnt know the name of that bacterium, or its parasitic nature, when people sampled their tanks. But its easy to add the newly discovered parasite to the list and update the clients with new info. The more we learn, the more valuable these data are. And this can move fast!

-Eli

 

[reefwiser]

Eli great that you where able find this in the samples. I am always reading up on this type of issues.

 

[Flippers4pups]

Great find everyone!

 

[taricha]

I think this is a great example of the value of this kind of data. We didnt know the name of that bacterium, or its parasitic nature, when people sampled their tanks. But its easy to add the newly discovered parasite to the list and update the clients with new info.

Wow. I hadn't realized how powerful this setup is, that you can match new info back to previous collected samples. Eye-opening.

On another topic - it's been discussed that there's no measurement of bacterial counts or amount of DNA being done here. Yet when discussing group C&D deviations from standard, expectations about total abundance are that they'll be similar.

In both groups, the increased relative abundance of Flavobacteriaceae & Pelagibacteraceae is accompanied by corresponding reductions in the relative abundance of other core families. The simplest interpretation of this pattern is that Flavobacteriaceae & Pelagibacteraceae are truly present at higher levels, pushing the relative abundance of all other families lower without any real changes in their absolute abundances.

I totally agree with that interpretation: one huge increased family and a background mostly unchanged is more likely than one family unchanged and everything else decreased dramatically and pretty evenly.
But....
In the Feldman article on bacterial counts in reef aquaria, they found a difference of an order of magnitude between reef tanks, and in natural waters a difference of two orders of magnitude.
Since we do things like carbon dose and run uv and ozone, etc. Could some measurement of relative abundance be possible, even if it's not direct cell counts? Like total amount of sequences detected or something?

 

[AquaBiomics]

Wow. I hadn't realized how powerful this setup is, that you can match new info back to previous collected samples. Eye-opening.

On another topic - it's been discussed that there's no measurement of bacterial counts or amount of DNA being done here. Yet when discussing group C&D deviations from standard, expectations about total abundance are that they'll be similar.


I totally agree with that interpretation: one huge increased family and a background mostly unchanged is more likely than one family unchanged and everything else decreased dramatically and pretty evenly.
But....
In the Feldman article on bacterial counts in reef aquaria, they found a difference of an order of magnitude between reef tanks, and in natural waters a difference of two orders of magnitude.
Since we do things like carbon dose and run uv and ozone, etc. Could some measurement of relative abundance be possible, even if it's not direct cell counts? Like total amount of sequences detected or something?

This is a great question. You're right, sequencing alone does not provide information on total abundance.

You correctly anticipate the way to do it - quantify the target (16S) DNA in the sample, then based on the volume sampled we can convert this into copies per ml.

There are equipment (=money) intensive ways and labor intensive ways to do this... this is high on my list for additions to the lab and service. For now I am sticking with relative abundance, the same kind of data that has supported so many discoveries in the earth and human microbiome projects. But we all agree and recognize that additional data on total abundance is really useful when we can get it.

(The following goes into the weeds a little, sorry )

With that said, I can say that based on the behavior of these samples during PCR, I can see variation in target DNA levels that is consistent with the direct cell count data you describe. Probably an order of magnitude variation among samples, roughly, based on the minimum number of cycles required to produce detectable PCR product. (The logic of this analysis is the same as qPCR, just much less precise).

--

About the looking back aspect of this. That is something I *love* about sequence-based analyses versus of the older methods.

Every time we learn something new about marine microbes, existing clients can learn something new about their tanks.

Its so direct. The paper that describes the new parasite gave an ID number for the GreenGenes database, a collection of known microbial DNA sequences that have been classified and named. So this sequence was already present in our data as "Unclassified (Rickettsiales)". All I had to do was look it up, manually examine some BLAST reports to confirm it was a real match, then ask which tank had the parasites.

What is enormously fun for me is that now I have a database of who has what bacteria in their tanks. So when I find a new bug I want to study, I know who to get in touch with! In this case, since its a coral parasite, I hope to take some coral samples and get this bug into an experimental tank for further work.

---

After digesting that new parasite paper a bit more, here is what I'm wondering about.

The parasite is apparently widespread in wild corals. Many have noted that tank-grown corals are faster growing and more robust than wild corals. I wonder if this parasite contributes to the relatively picky behavior of newly imported wild corals in captivity?

 

[taricha]

Every time we learn something new about marine microbes, existing clients can learn something new about their tanks.

Wow. Again, way more powerful analysis than I realized.

There are equipment (=money) intensive ways and labor intensive ways to do this... this is high on my list for additions to the lab and service.

Excellent. Was hoping you'd say that (except the part that there's no easy, cheap way to do it).

I can see variation in target DNA levels that is consistent with the direct cell count data you describe. Probably an order of magnitude variation among samples, roughly, based on the minimum number of cycles required to produce detectable PCR product.

Thanks for sharing this observation. Even this tentative confirmation is really interesting.

 

[Flippers4pups]

Eli, thank you for the quick delivery!

Kit looks comprehensive and well thought out!

I've got the rest of the week off work and will be definitely sending the sample soon!

 

[LARedstickreefer]

Gonna start dumping frag water from successful growers into my tank from now on.

 

[Flippers4pups]

Gonna start dumping frag water from successful growers into my tank from now on.

You never know, just might help!

 

[LARedstickreefer]

You never know, just might help!

Jason Fox gonna start selling his tank water now.

 

[AquaBiomics]

That idea has come up a couple times - along with stories about how reefers in the old days used to mix and swap sand.

For my money, I think solid substrates like sand or live rock rubble would be the way to go. We sample the water (and pipe biofilm) because its possible to do so in a consistent way across tanks. And the biofilm bugs do show up in the water. But theyre much more abundant in substrate.

I've set up experimental tanks where the only difference is dry rock or different sources of live rock. And they have very different microbiomes (article coming soon). So its clear that adding live rock affects the microbiome.

I think the right analogy here is fecal transplant therapy, which appears to be the most effective therapy emerging from human microbiome studies. (Few "probiotics" or related products sold for human health have any evidence supporting them. But poop transplants appear to work well.) Great thing is, we get to handle rock or sand instead of poop!

 

[pdxmonkeyboy]

I really can't over emphasize how excited I am about this! In all honesty, this is a view into the very very complex invisible world in our tanks. I have long thought, that it is the microrobial population that is responsible for "stable tanks" and not much else. Ask anyone.. when should I add SPS to my tank.. and everyone gives the same answer "when its stable"
So what causes initial instability? One of the principle tenants in ecology is that species multiply when food is available and decline when it is absent. My theory is that initial instability is a result of these boom and bust cycles in microbial populations. Ammonia...microbial explosion (I mean if you add to much vodka the bacteria will multiply so fast they strip the water of oxygen) then food is exhausted too quickly... then bacteria crashes..ammonia levels start to rise.. etc etc. This cycle continues but each successive growth and decline becomes less and less as microbial levels stabilize. Of course, this is highly highly complicated given inter and intra-species competition between bacteria and other variables that affect the biome...like temperature, but now we have a method to test these variables.

People that think this is some kind of snake oil sale or want to focus on the "well, what do i do now that I have this bacteria" and insinuate that the diagnosis is not valuable without a cure, you are missing the point to some extent. This work has the possibility of statistically establishing what a "healthy" and resistant biome is and more importantly, given a more detailed glimpse into the old worn out phrase "every tank is different".

Why do many tanks respond well to vibrant and some crash?
Why does Mr. Smiths tank look great with 0.20 phosphate and mine would die at that level?
Why do I have an breakout of cyano?
Why does vibrant cause dino outbreaks in some tanks and not others?

Microbial species and abundance data may very well reveal the answers.
It will take time and a large data set to reveal patterns, but this is how science works. If this leads to the sale of the perfect "biology in bottle or clump of sand sale" then sign me up!!!

Anyways.. just my 2 cents, but I feel this is really really really exciting stuff for the hobby. More exciting to me than a radion gen 5 or trident. Kudos for having the skills and drive to put this into action!!

 

[Scott Campbell]

"I really can't over emphasize how excited I am about this! In all honesty, this is a view into the very very complex invisible world in our tanks. I have long thought, that it is the microrobial population that is responsible for "stable tanks" and not much else. Ask anyone.. when should I add SPS to my tank.. and everyone gives the same answer "when its stable"
So what causes initial instability? One of the principle tenants in ecology is that species multiply when food is available and decline when it is absent. My theory is that initial instability is a result of these boom and bust cycles in microbial populations. Ammonia...microbial explosion (I mean if you add to much vodka the bacteria will multiply so fast they strip the water of oxygen) then food is exhausted too quickly... then bacteria crashes..ammonia levels start to rise.. etc etc. This cycle continues but each successive growth and decline becomes less and less as microbial levels stabilize. Of course, this is highly highly complicated given inter and intra-species competition between bacteria and other variables that affect the biome...like temperature, but now we have a method to test these variables."

All of this!! I mailed my samples back this morning. My wife has been laughing at me because I am so excited. I will probably be less excited once I discover my tank has multiple strains of syphilis, plague, tuberculosis, leprosy, tetanus, cholera and so on. But for the moment I am jazzed about discovering what bacterial strains live in my tank.