I had my water tested but need explanation

[AquaBiomics]

Well you biodiversity is a lot different than a typical mature reef. Maybe you should tell them your the gold standard mature reef tank.

In all seriousness I consider this possibility each time I find an extreme outlier. Some of them are beautiful, thriving tanks. Some are sub optimal in one way or another, like many of our tanks (certainly each of mine has something I wish was a little different... less hair algae, less cyano, less RTN, whatever).

Its likely, maybe inevitable, that there are multiple kinds of communities that can support a thriving aquarium ecosystem. It probably is no surprise that a tank that's survived for decades would have a different community than the mostly younger tanks I've surveyed. Perhaps the ones that look most different from his wouldnt last as long... maybe his is the community we should all strive for! I would not rule that out.

Its also possible that rather than one "typical" successful community there are multiple successful strategies. Many ways to skin the cat.

 

[Paul B]

Here is my sponge. If anyone wants some, feel free to come and get as much as you want.

I see a friend of mine, Bob Goemans wrote about it. I may call him if I can find his number.

Section: Sponges: Group: General Aquarium Sponges: Species: Collospongia auris (Blue Ear Sponge)

Marine Aquarium Library: General Aquarium Sponges, Family Thorectidae, Collospongia auris

www.saltcorner.com

 

[Dan_P]

I’ve had coffee twice over and enjoy reading the info for sure. I’m waiting for the clinch cause v effect takeaway from it all, what the grand scope can be used for in Paul's tank to improve it in some way. Being able to make sustained changes in the measures by some action would be a neat reveal, tying any actions to outcome

Regarding the method as a measure / view into specifics within our tank, amazing. It’s categorizing things people previously guessed about, it’s neat as a lens into differences among tanks. Over time patterns might emerge agreed it will be neat to see. Vs asking how the Tolstoy reference applies I’m just going to ponder it all day.

I think what is happening here is a crowd funded marketing study. I expect to see in 1-3 years “microbiome“ additives developed on the information gleaned from our test results. Think of it as a bio-TRITON franchise in the works. “Test your bacteria levels and fill in the levels that are low with AquaBiomics Juice A, B, C, or D.”

What I am particularly looking forwards to is the product that puts a “microbiome detector“ chip in a probe for continuous monitoring of a system‘s bacterial levels. Or maybe what comes to the market first is a Checker-like device to test a subset of your microbiome In real time. Oh the possibilities!

 

[lexinverts]

I think what is happening here is a crowd funded marketing study. I expect to see in 1-3 years “microbiome“ additives developed on the information gleaned from our test results. Think of it as a bio-TRITON franchise in the works. “Test your bacteria levels and fill in the levels that are low with AquaBiomics Juice A, B, C, or D.”

What I am particularly looking forwards to is the product that puts a “microbiome detector“ chip in a probe for continuous monitoring of a system‘s bacterial levels. Or maybe what comes to the market first is a Checker-like device to test a subset of your microbiome In real time. Oh the possibilities!

Well, that’s a cynical take on this effort. Do you think medical researchers study the human microbiome just to make money? Or do we do it in order to develop novel treatments for disease? Why do coral biology researchers study the microbiome of natural reefs? Is that about making money? Clearly not. It’s about learning how the microbiology of our reefs works.

 

[Pdash]

I might add the caveat that most would agree detection of known pathogens was undesirable. So far 1 in 8 tanks has a known fish pathogen, and while no client tanks in this round had a known coral pathogen, I've detected A. rohweri in one of my experimental tanks in two client tanks from the last batch, and more recently in one of my experimental tanks.

In terms of the overall community, these are such complex systems that even researchers in well studied fields like the human gut or (to a much lesser extent) the coral microbiome hesitate to label a community as good or bad. As a relative newcomer in the much less studied field of aquarium microbiology, I'm certainly not ready to use those labels.

Its more defensible to say it's similar to the typical community or that its different in a particular way. Only after much study can researchers say a particular state definitively causes or results from a particular symptom.

I like the paint analogy. I'll respond by borrowing one of my favorites from the coral microbiome world. Coral microbiologists Zaneveld and colleagues noted that healthy corals appeared to converge on similar communities, while unhealthy corals differed from the typical community in a variety of ways (Zaneveld et al., 2017). They proposed an "Anna Karenina principle" for animal microbiomes, named for the famous line from Anna Karenina,


Similarly, when I compared communities in my initial survey of hobbyist tanks, I found that half of them converged on a similar community, while the rest each deviated from the typical pattern in interesting and characteristic ways. See for example the following figure, where the positions of each symbol indicate similarity among their microbiomes.

So while I absolutely agree, and think most do even in better studied systems, that we arent able to label a particular level of diversity or of most microbes as good or bad. But I do think that examining deviations from the typical community will lead to insights into dysfunctions in some tanks, like they have in a variety of other systems ranging from corals to humans.

This is so cool. Do the different groupings have any additional variables in common, like average temperature of the aquarium, geographic location, average ph, filtering methodology, etc? What about relative success at keeping soft or stony corals?

 

[sixty_reefer]

I think what is happening here is a crowd funded marketing study. I expect to see in 1-3 years “microbiome“ additives developed on the information gleaned from our test results. Think of it as a bio-TRITON franchise in the works. “Test your bacteria levels and fill in the levels that are low with AquaBiomics Juice A, B, C, or D.”

What I am particularly looking forwards to is the product that puts a “microbiome detector“ chip in a probe for continuous monitoring of a system‘s bacterial levels. Or maybe what comes to the market first is a Checker-like device to test a subset of your microbiome In real time. Oh the possibilities!

That’s a lot of speculation there mate, can’t see we’re does it fit in the discussion.

 

[sixty_reefer]

Eli, I want to thank you so much for this analysis. I am not a biologist, Zoologist, Chemist, proctologist, or any other kind of "Ist" so it is fascinating to me and I thank you and the people on here that are contributing to the discussion.

Since I moved the tank to my new home about a year and a half ago I have used 100% NSW from the Atlantic.
I do have to diatom filter it first because I throw a bilge pump into the surf and I collect all sorts of sand and chopped up seaweed so the water is milky. The diatom makes it crystal clear.

I also didn't add hardly any mud this year like I like to do. My boat is on Peconic Bay here on Long Island which had the Atlantic Ocean on one end but the other end, closer to me is a fresh water river so the water is brackish and the bottom is sand as opposed to mud which I like to add.

I think I also used a diatom filter the day before I tested the water to remove some cyano which may have skewed the results from diversity, but I doubt it.
(I do run an algae scrubber)

Another question I have is that I have a huge amount of sponge growing and I have a lot more sponge than rock or corals. It just exploded since I moved here and started using all NSW. Will the sponge affect the results?

The vast majority of my tank years used mostly ASW.
That sponge filters massive amounts of water, probably all my water goes through that sponge a few times a day which may account for the lack of organisms.

As for bioload, I have about 20 fish averaging about 3". I feed only frozen food such as clams that I buy live and freeze myself and I also use LRS food every day. I also feed frozen mysis (for the pipefish) and a few times a week I add live whiteworms.

My reverse UG filter has only been running for the 18 months I have been living here. Of course when I moved the contents of the tank here I had to clean out the muck and mud from under the 40+ year old original RUGF as I didn't want to add all that gunk to my tank but a lot of it is in there from the rock which I did not clean.

I only rinsed most of my gravel in seawater when I moved it here so it was left full of whatever was in the original tank.

Some of the bacteria has been in the tank from 1971 because I don't think it was ever emptied and refilled with new water that I can remember.

This blue sponge is all over my tank.

That’s a beautiful sponge, the blue that they have is just out of this world. I’ve tried to keep it in the past but unfortunately my lights at the time weren’t strong enough to keep them alive.
I believe this species to be photosynthetic may not be affecting the microbe population. I may also be wrong as am no sponge expert to

 

[Dan_P]

Well, that’s a cynical take on this effort. Do you think medical researchers study the human microbiome just to make money? Or do we do it in order to develop novel treatments for disease? Why do coral biology researchers study the microbiome of natural reefs? Is that about making money? Clearly not. It’s about learning how the microbiology of our reefs works.

Please forgive me! I thought AquaBiomics was a business.

 

[AquaBiomics]

This is so cool. Do the different groupings have any additional variables in common, like average temperature of the aquarium, geographic location, average ph, filtering methodology, etc? What about relative success at keeping soft or stony corals?

These are great questions that we are setting up to answer, by surveying the owners of each tank about many details like this. I think I've added some questions since taking the screenshots, but they give you some idea of the kind of info we are trying to capture.

The main reason I don't have answers yet is because tanks differ in so many ways, it will take a large sample size to detect significant effects. I don't want to prematurely claim there's an effect until we have the sample size to provide a conclusion supported by statistical tests. The database grows monthly, but we need more samples to detect these effects with any confidence.

As time allows I will be exploring these questions, and when the sample size allows me to find anything significant I'll be reporting back to the reefing community.

 

[Dan_P]

That’s a lot of speculation there mate, can’t see we’re does it fit in the discussion.

Sorry about my confusing post.

 

[AquaBiomics]

Please forgive me! I thought AquaBiomics was a business.

You're correct, I'm offering microbiome testing, and am answering questions about that service. I view this as analogous to ICP testing: an aquarium water testing service that quantifies multiple components of the water. Since it is new, I think its to be expected that people have a range of different views on the value of these measurements.

Personally, if I speculate about where microbiome data will lead us in the future, I don't see any reason to assume this will lead to a need for new products. I find it just as likely that we'll discover that adding mud to your tank is beneficial. Or that feeding raw clams is beneficial. I don't know where it will lead, but if I have to guess, I'd guess it will lead to us putting fewer bottled products in our tanks rather than more, depending on whether the claims of those products are supported by data.

 

[lexinverts]

Please forgive me! I thought AquaBiomics was a business.

Medical research companies who offer services that are derived from microbiome research need to charge fees for those services. As someone who recently almost lost a family member from a C.diff infection, I am grateful for both the basic research (mostly government funded) and the biomedical companies that have made appropriate treatment possible! Do they charge too much? Well, that is a different discussion...

Aquabiomics is a DNA sequencing service for the reef hobby that obviously cannot be free of charge.

 

[User1]

You're correct, I'm offering microbiome testing, and am answering questions about that service. I view this as analogous to ICP testing: an aquarium water testing service that quantifies multiple components of the water. Since it is new, I think its to be expected that people have a range of different views on the value of these measurements.

Personally, if I speculate about where microbiome data will lead us in the future, I don't see any reason to assume this will lead to a need for new products. I find it just as likely that we'll discover that adding mud to your tank is beneficial. Or that feeding raw clams is beneficial. I don't know where it will lead, but if I have to guess, I'd guess it will lead to us putting fewer bottled products in our tanks rather than more, depending on whether the claims of those products are supported by data.

One of the areas of concern with regards to ICP testing is the standards and/or processes between each water sample test. For example when are the machines calibrated (start of day or shift) compared to before and after every test. How do you handle this in your testing to mitigate noise and/or contamination.

 

[chema]

I didn't know there was already a company doing this kind of analyses. This is a complete new level of knowledge about our aquaria.
As already stated, it is very difficult or imposible to determine the desired or optimum bacterial community but all the comparative analyses that are posible to develop now open an amazing number of possibilities. Of utmost importance, to compare bacterial communities in healthy coral populations with the ones in our tanks.
I am a molecular geneticist but have a lot of microbiologists among my colleagues. I tell them that thanks to the new DNA sequencing methodologies that do not require microbial cultures they have arrived to a new era comparable to the one that was posible thanks to synthetic culture media and Petri dishes.
By the way, is it posible to send tank samples overseas to get them analysed?

 

[Pdash]

These are great questions that we are setting up to answer, by surveying the owners of each tank about many details like this. I think I've added some questions since taking the screenshots, but they give you some idea of the kind of info we are trying to capture.

The main reason I don't have answers yet is because tanks differ in so many ways, it will take a large sample size to detect significant effects. I don't want to prematurely claim there's an effect until we have the sample size to provide a conclusion supported by statistical tests. The database grows monthly, but we need more samples to detect these effects with any confidence.

As time allows I will be exploring these questions, and when the sample size allows me to find anything significant I'll be reporting back to the reefing community.

Very good. I might buy a test just for the science. But, even if your sample is large enough, are you still concerned about how representative it will be?

 

[Dan_P]

You're correct, I'm offering microbiome testing, and am answering questions about that service. I view this as analogous to ICP testing: an aquarium water testing service that quantifies multiple components of the water. Since it is new, I think its to be expected that people have a range of different views on the value of these measurements.

Personally, if I speculate about where microbiome data will lead us in the future, I don't see any reason to assume this will lead to a need for new products. I find it just as likely that we'll discover that adding mud to your tank is beneficial. Or that feeding raw clams is beneficial. I don't know where it will lead, but if I have to guess, I'd guess it will lead to us putting fewer bottled products in our tanks rather than more, depending on whether the claims of those products are supported by data.

Thank you for your reply.

Is ”home testing” of the microbiome or a subset of it very far in the future?

 

[AquaBiomics]

Thank you for your reply.

Is ”home testing” of the microbiome or a subset of it very far in the future?

Well, I guess it depends on what you mean by that.

The process overall is:

1. Sampling
2. DNA extraction
3. PCR #1
4. Gel electrophoresis
5. PCR #2
6. Quantifying each sample
7. DNA sequencing
8. Bioinformatics (analysis of thousands of DNA sequences per sample, up to 1 million per batch)

Step 1 can be done in home with my custom kit, or a DIY minded person could put together their own kit at home.
Steps 2-6 require molecular biology laboratory equipment to do. A typical college Mol Bio lab could do it, I think it would be challenging for a home user to get all the equipment together, and would require formal training or really exceptional levels of DIY to know how to use it.
Step 7 requires a machine that even well-funded professional biology labs don't purchase. We all outsource our DNA sequencing.
Step 8 requires some background in computing, currently, but I could imagine bundling the tools into a web app that enabled home users to analyze their data at the end instead of having a service provider do it.

For comparison, when you read a genomics or microbiome study, the authors have typically outsourced some of the steps from 2-8, sometimes all of them, and almost always step 7. So if an NSF funded lab doesnt do the whole thing in house, the question in my mind is what part of the process does it make sense for an end user to do? And I concluded just sampling.

--

Alternatively, if you mean testing of other microbiomes aside from the aquarium microbiome, I know of companies offering this for dog stool and several that offer it for human stool. I think they all operate more or less in the same framework of "send in a sample to be tested".

 

[Paul B]

I don't need bottled additives. These mud snails make it for me for free. I like to use this mud in my tank, like a couple of tablespoons.
Here where I moved to I can't get this mud any longer as it is mostly sand here so I use that.

Now I use the sand/mud from here where the fiddler crabs "inoculate" it for me. I hardly collected any this year but next summer I will add a lot more, after I filter out the fiddler crabs. All that fiddling drives me crazy.

This is probably where that "poop" bacteria came from so maybe it's a good thing. Who knows?

 

[User1]

Well, I guess it depends on what you mean by that.

The process overall is:

1. Sampling
2. DNA extraction
3. PCR #1
4. Gel electrophoresis
5. PCR #2
6. Quantifying each sample
7. DNA sequencing
8. Bioinformatics (analysis of thousands of DNA sequences per sample, up to 1 million per batch)

Step 1 can be done in home with my custom kit, or a DIY minded person could put together their own kit at home.
Steps 2-6 require molecular biology laboratory equipment to do. A typical college Mol Bio lab could do it, I think it would be challenging for a home user to get all the equipment together, and would require formal training or really exceptional levels of DIY to know how to use it.
Step 7 requires a machine that even well-funded professional biology labs don't purchase. We all outsource our DNA sequencing.
Step 8 requires some background in computing, currently, but I could imagine bundling the tools into a web app that enabled home users to analyze their data at the end instead of having a service provider do it.

For comparison, when you read a genomics or microbiome study, the authors have typically outsourced some of the steps from 2-8, sometimes all of them, and almost always step 7. So if an NSF funded lab doesnt do the whole thing in house, the question in my mind is what part of the process does it make sense for an end user to do? And I concluded just sampling.

--

Alternatively, if you mean testing of other microbiomes aside from the aquarium microbiome, I know of companies offering this for dog stool and several that offer it for human stool. I think they all operate more or less in the same framework of "send in a sample to be tested".

I don't think you replied yet but what are the procedures or process for calibration and cross water / tank contamination? This is one of the areas of concern with regards to hobby grade tests and ICP testing.

 

[lexinverts]

I don't think you replied yet but what are the procedures or process for calibration and cross water / tank contamination? This is one of the areas of concern with regards to hobby grade tests and ICP testing.

Generally, for each of the PCRs, you would run "blanks" or negative controls. If they amplify DNA, then you know that there was cross-contamination in the DNA extraction or PCR prep. You wouldn't proceed to the DNA sequencing step if you had contamination.

As for step 7, the DNA sequencing, I'm not sure what they do at the facility. Since these facilities run 1,000s of samples daily for research labs around the country, any problems would be reported very quickly. Unlike the ICP labs that do water tests for hobbyists, labs that do DNA sequencing for researchers must be 100% transparent about their methods.